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1

NCI-Frederick PHL - Tissue Microarray  

Cancer.gov

Services Price List Courier Services & Shipment Procedures Scheduling Contact Information Related Links Establishing an Account PHL Forms PHL Portal Rodent Tissue Microarray Tissue microarays allow the possibility to represent a large number of tissue

2

An alternative high output tissue microarray technique  

PubMed Central

Background Tissue microarray (TMA) is a high throughput research tool, which has greatly facilitated and accelerated in situ tissue analyses. However, its productivity has been restricted due to the confined thickness of traditional donor block. Here, we introduce an improved high output TMA method that is applicable to a broader range of tissue samples. Methods In this method, a 3.6 cm long and 2.7 cm wide recipient block with 88 square lattices (3 mm in width) was first prepared using several commercial instruments. A 2 mm wide and 6 mm long tissue rod was then prepared using a self-made blade-shaped knife from each paraffin embedded donor block of gastrointestinal stromal tumors. These rods were manually arrayed one by one into the corresponding lattices of the 60°C pre-softened recipient block with the guide of holes drilled with a steel needle. A 70-rod TMA was made to testify this method. Results The prepared TMA had well defined array configurations, good tissue morphology and fully preserved proteins and DNA. A total of 500–1000 TMA sections could be easily obtained from a TMA block. Conclusion This low-cost and time-saving method provides an alternative sampling tool for high output TMA. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1979605867857990 PMID:23336116

2013-01-01

3

The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data  

PubMed Central

Background: Tissue microarrays (TMAs) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration. Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format. Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES) to OWL. Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts. PMID:20805954

Kang, Hyunseok P.; Borromeo, Charles D.; Berman, Jules J.; Becich, Michael J.

2010-01-01

4

Practical aspects of planning, building, and interpreting tissue microarrays: The Cooperative Prostate Cancer Tissue Resource experience  

Microsoft Academic Search

This is a review of several new approaches developed at or adopted by the Cooperative Prostate Cancer Tissue Resource (CPCTR)\\u000a to resolve issues involved in tissue microarray (TMA) construction and use. CPCTR developed the first needle biopsy TMA, allowing\\u000a researchers to obtain 200 or more consecutive cancer sections from a single biopsy core. Using radiographs of original paraffin\\u000a blocks to

A. Kajdacsy-Balla; J. M. Geynisman; V. Macias; S. Setty; N. M. Nanaji; J. J. Berman; K. Dobbin; J. Melamed; X. Kong; M. Bosland; J. Orenstein; J. Bayerl; M. J. Becich; R. Dhir; M. W. Datta

2007-01-01

5

TAMEE: data management and analysis for tissue microarrays  

PubMed Central

Background With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. Results TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator. Conclusion We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from . PMID:17343750

Thallinger, Gerhard G; Baumgartner, Kerstin; Pirklbauer, Martin; Uray, Martina; Pauritsch, Elke; Mehes, Gabor; Buck, Charles R; Zatloukal, Kurt; Trajanoski, Zlatko

2007-01-01

6

Microarrays  

ERIC Educational Resources Information Center

Microarrays are revolutionizing genetics by making it possible to genotype hundreds of thousands of DNA markers and to assess the expression (RNA transcripts) of all of the genes in the genome. Microarrays are slides the size of a postage stamp that contain millions of DNA sequences to which single-stranded DNA or RNA can hybridize. This…

Plomin, Robert; Schalkwyk, Leonard C.

2007-01-01

7

Guidelines and considerations for conducting experiments using tissue microarrays.  

PubMed

Tissue microarrays (TMAs) represent a powerful method for undertaking large-scale tissue-based biomarker studies. While TMAs offer several advantages, there are a number of issues specific to their use which need to be considered when employing this method. Given the investment in TMA-based research, guidance on design and execution of experiments will be of benefit and should help researchers new to TMA-based studies to avoid known pitfalls. Furthermore, a consensus on quality standards for TMA-based experiments should improve the robustness and reproducibility of studies, thereby increasing the likelihood of identifying clinically useful biomarkers. In order to address these issues, the National Cancer Research Institute Biomarker and Imaging Clinical Studies Group organized a 1-day TMA workshop held in Nottingham in May 2012. The document herein summarizes the conclusions from the workshop. It includes guidance and considerations on all aspects of TMA-based research, including the pre-analytical stages of experimental design, the analytical stages of data acquisition, and the postanalytical stages of data analysis. A checklist is presented which can be used both for planning a TMA experiment and interpreting the results of such an experiment. For studies of cancer biomarkers, this checklist could be used as a supplement to the REMARK guidelines. PMID:23672312

Ilyas, Mohammad; Grabsch, Heike; Ellis, Ian O; Womack, Chris; Brown, Robert; Berney, Dan; Fennell, Dean; Salto-Tellez, Manuel; Jenkins, Martin; Landberg, Goran; Byers, Richard; Treanor, Darren; Harrison, David; Green, Andrew R; Ball, Graham; Hamilton, Peter

2013-05-01

8

Identification of different subtypes of breast cancer using tissue microarray.  

PubMed

Breast cancer may be classified into luminal A, luminal B, HER2+/ER-, basal-like and normal-like subtypes based on gene expression profiling or immunohistochemical (IHC) characteristics. The main aim of the present study was to classify breast cancer into molecular subtypes based on immunohistochemistry findings and correlate the subtypes with clinicopathological factors. Two hundred and seventeen primary breast carcinomas tumor tissues were immunostained for ER, PR, HER2, CK5/6, EGFR, CK8/18, p53 and Ki67 using tissue microarray technique. All subtypes were significantly associated with Malay ethnic background (p=0.035) compared to other racial origins. The most common subtypes of breast cancers were luminal A and was significantly associated with low histological grade (p<0.000) and p53 negativity (p=0.003) compared to HER2+/ER-, basal-like and normal-like subtypes with high histological grade (p<0.000) and p53 positivity (p=0.003). Luminal B subtype had the smallest mean tumor size (p=0.009) and also the highest mean number of lymph nodes positive (p=0.032) compared to other subtypes. All markers except EGFR and Ki67 were significantly associated with the subtypes. The most common histological type was infiltrating ductal carcinoma, NOS. Majority of basal-like subtype showed comedo-type necrosis (68.8%) and infiltrative margin (81.3%). Our studies suggest that IHC can be used to identify the different subtypes of breast cancer and all subtypes were significantly associated with race, mean tumor size, mean number of lymph node positive, histological grade and all immunohistochemical markers except EGFR and Ki67. PMID:21655659

Munirah, M A; Siti-Aishah, M A; Reena, M Z; Sharifah, N A; Rohaizak, M; Norlia, A; Rafie, M K M; Asmiati, A; Hisham, A; Fuad, I; Shahrun, N S; Das, S

2011-01-01

9

Gene Discovery in Bladder Cancer Progression using cDNA Microarrays  

PubMed Central

To identify gene expression changes along progression of bladder cancer, we compared the expression profiles of early-stage and advanced bladder tumors using cDNA microarrays containing 17,842 known genes and expressed sequence tags. The application of bootstrapping techniques to hierarchical clustering segregated early-stage and invasive transitional carcinomas into two main clusters. Multidimensional analysis confirmed these clusters and more importantly, it separated carcinoma in situ from papillary superficial lesions and subgroups within early-stage and invasive tumors displaying different overall survival. Additionally, it recognized early-stage tumors showing gene profiles similar to invasive disease. Different techniques including standard t-test, single-gene logistic regression, and support vector machine algorithms were applied to identify relevant genes involved in bladder cancer progression. Cytokeratin 20, neuropilin-2, p21, and p33ING1 were selected among the top ranked molecular targets differentially expressed and validated by immunohistochemistry using tissue microarrays (n = 173). Their expression patterns were significantly associated with pathological stage, tumor grade, and altered retinoblastoma (RB) expression. Moreover, p33ING1 expression levels were significantly associated with overall survival. Analysis of the annotation of the most significant genes revealed the relevance of critical genes and pathways during bladder cancer progression, including the overexpression of oncogenic genes such as DEK in superficial tumors or immune response genes such as Cd86 antigen in invasive disease. Gene profiling successfully classified bladder tumors based on their progression and clinical outcome. The present study has identified molecular biomarkers of potential clinical significance and critical molecular targets associated with bladder cancer progression. PMID:12875971

Sanchez-Carbayo, Marta; Socci, Nicholas D.; Lozano, Juan Jose; Li, Wentian; Charytonowicz, Elizabeth; Belbin, Thomas J.; Prystowsky, Michael B.; Ortiz, Angel R.; Childs, Geoffrey; Cordon-Cardo, Carlos

2003-01-01

10

Technology Insight: identification of biomarkers with tissue microarray technology  

Microsoft Academic Search

High-throughput technologies have been developed in the hope of increasing the pace of biomedical research, and accelerating the rate of translation from bench to bedside. Using such technology in target discovery has resulted in the need for systematic validation of the targets in an equally rapid manner. For example, gene expression microarrays have highlighted many potential targets in cancer, and

Jena M Giltnane; David L Rimm

2004-01-01

11

The extrinsic apoptotic signaling pathway in gastric adenocarcinomas assessed by tissue microarray  

Microsoft Academic Search

The purpose of this investigation was to analyze the immunoexpression of FasL, Fas, FADD, cleaved caspase 8, and cleaved caspase 3 in gastric cancer. Formalin-fixed and paraffin-embedded gastric adenocarcinoma tissues from 87 patients, including adjacent normal tissues, were included on tissue microarray by immunohistochemistry. The tumor and the adjacent normal tissues were positive for FasL in 66.7% and 90.6%, for

Thiago S. Gomes; Celina T. F. Oshima; Helena R. C. Segreto; Luis M. Barrazueta; Henrique O. Costa; Flavio O. Lima; Nora M. Forones; Daniel A. Ribeiro

2011-01-01

12

The tissue microarray data exchange specification: A document type definition to validate and enhance XML data  

Microsoft Academic Search

BACKGROUND: The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such

David G Nohle; Leona W Ayers

2005-01-01

13

Support vector machine classification and validation of cancer tissue samples using microarray expression data  

Microsoft Academic Search

MOTIVATION: DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data using support vector machines (SVMs). This analysis consists of both classification of the tissue samples, and

Terrence S. Furey; Nello Cristianini; Nigel P. Duffy; David W. Bednarski; Michèl Schummer; David Haussler

2000-01-01

14

Differential expression of HSPA1 and HSPA2 proteins in human tissues; tissue microarray-based immunohistochemical study  

Microsoft Academic Search

In the present study we determined the expression pattern of HSPA1 and HSPA2 proteins in various normal human tissues by tissue-microarray based immunohistochemical analysis. Both proteins belong to the HSPA (HSP70) family of heat shock proteins. The\\u000a HSPA2 is encoded by the gene originally defined as testis-specific, while HSPA1 is encoded by the stress-inducible genes (HSPA1A and HSPA1B). Our study

Dorota Scieglinska; Wojciech Piglowski; Mykola Chekan; Agnieszka Mazurek; Zdzis?aw Krawczyk

2011-01-01

15

Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection.  

PubMed

Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. Although each of the three stages has well-known clinical, virologic, and immunologic characteristics, much less is known of the molecular mechanisms underlying each stage. In this study, we report lymphatic tissue microarray analyses, revealing for the first time stage-specific patterns of gene expression during HIV-1 infection. We show that although there is a common set of key genes with altered expression throughout all stages, each stage has a unique gene expression signature. The acute stage is most notably characterized by increased expression of hundreds of genes involved in immune activation, innate immune defenses (e.g., RIG-1, MDA-5, TLR7 and TLR8, PKR, APOBEC3B, 3F, 3G), adaptive immunity, and in the proapoptotic Fas-Fas ligand pathway. Yet, quite strikingly, the expression of nearly all acute stage genes return to baseline levels in the asymptomatic stage, accompanying partial control of infection. This transition from acute to asymptomatic stage is tied to increased expression of a diverse array of immunosuppressive genes (e.g., CLEC12B, ILT4, galectin-3, CD160, BCMA, FGL2, LAG3, GPNMB). In the AIDS stage, decreased expression of numerous genes involved in T cell signaling identifies genes contributing to T cell dysfunction. These common and stage-specific gene expression signatures identify potential molecular mechanisms underlying the host response and the slow, natural course of HIV-1 infection. PMID:19596987

Li, Qingsheng; Smith, Anthony J; Schacker, Timothy W; Carlis, John V; Duan, Lijie; Reilly, Cavan S; Haase, Ashley T

2009-08-01

16

Distribution of AQP2 and AQP3 water channels in human tissue microarrays  

Microsoft Academic Search

SummaryThe objective of this investigation was to use semi-quantitative immunohistochemistry to determine the distribution and expression levels of AQP2 and AQP3 proteins in normal human Tissue MicroArrays. Expression of the vasopressin regulated AQP2 was observed in a limited number of tissues. AQP2 was prominent in the apical and subapical plasma membranes of cortical and medullary renal collecting ducts. Surprisingly, weak

A. Mobasheri; S. Wray; D. Marples

2005-01-01

17

Automatic Handling of Tissue Microarray Cores in High-Dimensional Microscopy Images  

Microsoft Academic Search

\\u000a This paper describes a specific tool to automatically perform the segmentation and archiving of tissue microarray (TMA) cores\\u000a in microscopy images at different magnification, that is, 5x, 10x, 20x and 40x. TMA enables researchers to extract small cylinder\\u000a of single tissues (core sections) from histological sections and arrange them in an array on a paraffin block such that hundreds\\u000a can

G. Bueno; M. Fernández; O. Déniz; M. García-Rojo

18

Candidate genes for the progression of malignant gliomas identified by microarray analysis  

Microsoft Academic Search

Malignant astrocytomas of World Health Organization (WHO) grade III or IV have a reduced median survival time, and possible\\u000a pathways have been described for the progression of anaplastic astrocytomas and glioblastomas, but the molecular basis of\\u000a malignant astrocytoma progression is still poorly understood. Microarray analysis provides the chance to accelerate studies\\u000a by comparison of the expression of thousands of genes

Oliver Bozinov; Sylvia Köhler; Birgit Samans; Ludwig Benes; Dorothea Miller; Markus Ritter; Ulrich Sure; Helmut Bertalanffy

2008-01-01

19

Tissue microarray immunohistochemical detection of brachyury is not a prognostic indicator in chordoma.  

PubMed

Brachyury is a marker for notochord-derived tissues and neoplasms, such as chordoma. However, the prognostic relevance of brachyury expression in chordoma is still unknown. The improvement of tissue microarray technology has provided the opportunity to perform analyses of tumor tissues on a large scale in a uniform and consistent manner. This study was designed with the use of tissue microarray to determine the expression of brachyury. Brachyury expression in chordoma tissues from 78 chordoma patients was analyzed by immunohistochemical staining of tissue microarray. The clinicopathologic parameters, including gender, age, location of tumor and metastatic status were evaluated. Fifty-nine of 78 (75.64%) tumors showed nuclear staining for brachyury, and among them, 29 tumors (49.15%) showed 1+ (<30% positive cells) staining, 15 tumors (25.42%) had 2+ (31% to 60% positive cells) staining, and 15 tumors (25.42%) demonstrated 3+ (61% to 100% positive cells) staining. Brachyury nuclear staining was detected more frequently in sacral chordomas than in chordomas of the mobile spine. However, there was no significant relationship between brachyury expression and other clinical variables. By Kaplan-Meier analysis, brachyury expression failed to produce any significant relationship with the overall survival rate. In conclusion, brachyury expression is not a prognostic indicator in chordoma. PMID:24086644

Zhang, Linlin; Guo, Shang; Schwab, Joseph H; Nielsen, G Petur; Choy, Edwin; Ye, Shunan; Zhang, Zhan; Mankin, Henry; Hornicek, Francis J; Duan, Zhenfeng

2013-01-01

20

Tissue Microarray Immunohistochemical Detection of Brachyury Is Not a Prognostic Indicator in Chordoma  

PubMed Central

Brachyury is a marker for notochord-derived tissues and neoplasms, such as chordoma. However, the prognostic relevance of brachyury expression in chordoma is still unknown. The improvement of tissue microarray technology has provided the opportunity to perform analyses of tumor tissues on a large scale in a uniform and consistent manner. This study was designed with the use of tissue microarray to determine the expression of brachyury. Brachyury expression in chordoma tissues from 78 chordoma patients was analyzed by immunohistochemical staining of tissue microarray. The clinicopathologic parameters, including gender, age, location of tumor and metastatic status were evaluated. Fifty-nine of 78 (75.64%) tumors showed nuclear staining for brachyury, and among them, 29 tumors (49.15%) showed 1+ (<30% positive cells) staining, 15 tumors (25.42%) had 2+ (31% to 60% positive cells) staining, and 15 tumors (25.42%) demonstrated 3+ (61% to 100% positive cells) staining. Brachyury nuclear staining was detected more frequently in sacral chordomas than in chordomas of the mobile spine. However, there was no significant relationship between brachyury expression and other clinical variables. By Kaplan-Meier analysis, brachyury expression failed to produce any significant relationship with the overall survival rate. In conclusion, brachyury expression is not a prognostic indicator in chordoma. PMID:24086644

Schwab, Joseph H.; Nielsen, G. Petur; Choy, Edwin; Ye, Shunan; Zhang, Zhan; Mankin, Henry; Hornicek, Francis J.; Duan, Zhenfeng

2013-01-01

21

Cell and Tissue Microarray Technologies for Protein and Nucleic Acid Expression Profiling  

PubMed Central

Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform. PMID:23172795

Cardano, Marina; Diaferia, Giuseppe R.; Falavigna, Maurizio; Spinelli, Chiara C.; Sessa, Fausto; DeBlasio, Pasquale

2013-01-01

22

Cell and tissue microarray technologies for protein and nucleic acid expression profiling.  

PubMed

Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform. PMID:23172795

Cardano, Marina; Diaferia, Giuseppe R; Falavigna, Maurizio; Spinelli, Chiara C; Sessa, Fausto; DeBlasio, Pasquale; Biunno, Ida

2013-02-01

23

Phosphoprotein Stability in Clinical Tissue and Its Relevance for Reverse Phase Protein Microarray Technology  

PubMed Central

Phosphorylated proteins reflect the activity of specific cell signaling nodes in biological kinase protein networks. Cell signaling pathways can be either activated or deactivated depending on the phosphorylation state of the constituent proteins. The state of these kinase pathways reflects the in vivo activity of the cells and tissue at any given point in time. As such, cell signaling pathway information can be extrapolated to infer which phosphorylated proteins/pathways are driving an individual tumor’s growth. Reverse Phase Protein Microarrays (RPMA) are a sensitive and precise platform that can be applied to the quantitative measurement of hundreds of phosphorylated signal proteins from a small sample of tissue. Pre-analytical variability originating from tissue procurement and preservation may cause significant variability and bias in downstream molecular analysis. Depending on the ex vivo delay time in tissue processing, and the manner of tissue handling, protein biomarkers such as signal pathway phosphoproteins will be elevated or suppressed in a manner that does not represent the biomarker levels at the time of excision. Consequently, assessment of the state of these kinase networks requires stabilization, or preservation, of the phosphoproteins immediately post tissue procurement. We have employed reverse phase protein microarray analysis of phosphoproteins to study the factors influencing stability of phosphoproteins in tissue following procurement. Based on this analysis we have established tissue procurement guidelines for clinical research with an emphasis on quantifying phosphoproteins by RPMA. PMID:21901591

Espina, Virginia; Mueller, Claudius; Liotta, Lance A.

2013-01-01

24

Decentralized Data Sharing of Tissue Microarrays for Investigative Research in Oncology  

PubMed Central

Tissue microarray technology (TMA) is a relatively new approach for efficiently and economically assessing protein and gene expression across large ensembles of tissue specimens. Tissue microarray technology holds great potential for reducing the time and cost associated with conducting research in tissue banking, proteomics, and outcome studies. However, the sheer volume of images and other data generated from even limited studies involving tissue microarrays quickly approach the processing capacity and resources of a division or department. This challenge is compounded by the fact that large-scale projects in several areas of modern research rely upon multi-institutional efforts in which investigators and resources are spread out over multiple campuses, cities, and states. To address some of the data management issues several leading institutions have begun to develop their own “in-house” systems, independently, but such data will be only minimally useful if it isn’t accessible to others in the scientific community. Investigators at different institutions studying the same or related disorders might benefit from the synergy of sharing results. To facilitate sharing of TMA data across different database implementations, the Technical Standards Committee of the Association for Pathology Informatics organized workshops in efforts to establish a standardized TMA data exchange specification. The focus of our research does not relate to the establishment of standards for exchange, but rather builds on these efforts and concentrates on the design, development and deployment of a decentralized collaboratory for the unsupervised characterization, and seamless and secure discovery and sharing of TMA data. Specifically, we present a self-organizing, peer-to-peer indexing and discovery infrastructure for quantitatively assessing digitized TMA’s. The system utilizes a novel, optimized decentralized search engine that supports flexible querying, while guaranteeing that once information has been stored in the system, it will be found with bounded costs. PMID:19081778

Chen, Wenjin; Schmidt, Cristina; Parashar, Manish; Reiss, Michael; Foran, David J.

2007-01-01

25

Microarray analysis of the AHR system: Tissue-specific flexibility in signal and target genes  

SciTech Connect

Data mining published microarray experiments require that expression profiles are directly comparable. We performed linear global normalization on the data of 1967 Affymetrix U74av2 microarrays, i.e. the transcriptomes of > 100 murine tissues or cell types. The mathematical transformation effectively nullifies inter-experimental or inter-laboratory differences between microarrays. The correctness of expression values was validated by quantitative RT-PCR. Using the database we analyze components of the aryl hydrocarbon receptor (AHR) signaling pathway in various tissues. We identified lineage and differentiation specific variant expression of AHR, ARNT, and HIF1{alpha} in the T-cell lineage and high expression of CYP1A1 in immature B cells and dendritic cells. Performing co-expression analysis we found unorthodox expression of the AHR in the absence of ARNT, particularly in stem cell populations, and can reject the hypothesis that ARNT2 takes over and is highly expressed when ARNT expression is low or absent. Furthermore the AHR shows no co-expression with any other transcript present on the chip. Analysis of differential gene expression under 308 conditions revealed 53 conditions under which the AHR is regulated, numerous conditions under which an intrinsic AHR action is modified as well as conditions activating the AHR even in the absence of known AHR ligands. Thus meta-analysis of published expression profiles is a powerful tool to gain novel insights into known and unknown systems.

Frericks, Markus [Institut fuer Umweltmedizinische Forschung (IUF) at the Heinrich Heine-University of Duesseldorf, Auf'm Hennekamp 50, 40225 Duesseldorf (Germany); Meissner, Marc [Institut fuer Umweltmedizinische Forschung (IUF) at the Heinrich Heine-University of Duesseldorf, Auf'm Hennekamp 50, 40225 Duesseldorf (Germany); Esser, Charlotte [Institut fuer Umweltmedizinische Forschung (IUF) at the Heinrich Heine-University of Duesseldorf, Auf'm Hennekamp 50, 40225 Duesseldorf (Germany)]. E-mail: chesser@uni-duesseldorf.de

2007-05-01

26

Datamining approach for automation of diagnosis of breast cancer in immunohistochemically stained tissue microarray images.  

PubMed

Cancer of the breast is the second most common human neoplasm, accounting for approximately one quarter of all cancers in females after cervical carcinoma. Estrogen receptor (ER), Progesteron receptor and human epidermal growth factor receptor (HER-2/neu) expressions play an important role in diagnosis and prognosis of breast carcinoma. Tissue microarray (TMA) technique is a high throughput technique which provides a standardized set of images which are uniformly stained, facilitating effective automation of the evaluation of the specimen images. TMA technique is widely used to evaluate hormone expression for diagnosis of breast cancer. If one considers the time taken for each of the steps in the tissue microarray process workflow, it can be observed that the maximum amount of time is taken by the analysis step. Hence, automated analysis will significantly reduce the overall time required to complete the study. Many tools are available for automated digital acquisition of images of the spots from the microarray slide. Each of these images needs to be evaluated by a pathologist to assign a score based on the staining intensity to represent the hormone expression, to classify them into negative or positive cases. Our work aims to develop a system for automated evaluation of sets of images generated through tissue microarray technique, representing the ER expression images and HER-2/neu expression images. Our study is based on the Tissue Microarray Database portal of Stanford university at http://tma.stanford.edu/cgi-bin/cx?n=her1, which has made huge number of images available to researchers. We used 171 images corresponding to ER expression and 214 images corresponding to HER-2/neu expression of breast carcinoma. Out of the 171 images corresponding to ER expression, 104 were negative and 67 were representing positive cases. Out of the 214 images corresponding to HER-2/neu expression, 112 were negative and 102 were representing positive cases. Our method has 92.31% sensitivity and 93.18% specificity for ER expression image classification and 96.67% sensitivity and 88.24% specificity for HER-2/neu expression image classification. PMID:21589855

Prasad, Keerthana; Zimmermann, Bernhard; Prabhu, Gopalakrishna; Pai, Muktha

2010-01-01

27

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies.  

PubMed

Biomarker research relies on tissue microarrays (TMA). TMAs are produced by repeated transfer of small tissue cores from a 'donor' block into a 'recipient' block and then used for a variety of biomarker applications. The construction of conventional TMAs is labor intensive, imprecise, and time-consuming. Here, a protocol using next-generation Tissue Microarrays (ngTMA) is outlined. ngTMA is based on TMA planning and design, digital pathology, and automated tissue microarraying. The protocol is illustrated using an example of 134 metastatic colorectal cancer patients. Histological, statistical and logistical aspects are considered, such as the tissue type, specific histological regions, and cell types for inclusion in the TMA, the number of tissue spots, sample size, statistical analysis, and number of TMA copies. Histological slides for each patient are scanned and uploaded onto a web-based digital platform. There, they are viewed and annotated (marked) using a 0.6-2.0 mm diameter tool, multiple times using various colors to distinguish tissue areas. Donor blocks and 12 'recipient' blocks are loaded into the instrument. Digital slides are retrieved and matched to donor block images. Repeated arraying of annotated regions is automatically performed resulting in an ngTMA. In this example, six ngTMAs are planned containing six different tissue types/histological zones. Two copies of the ngTMAs are desired. Three to four slides for each patient are scanned; 3 scan runs are necessary and performed overnight. All slides are annotated; different colors are used to represent the different tissues/zones, namely tumor center, invasion front, tumor/stroma, lymph node metastases, liver metastases, and normal tissue. 17 annotations/case are made; time for annotation is 2-3 min/case. 12 ngTMAs are produced containing 4,556 spots. Arraying time is 15-20 hr. Due to its precision, flexibility and speed, ngTMA is a powerful tool to further improve the quality of TMAs used in clinical and translational research. PMID:25285857

Zlobec, Inti; Suter, Guido; Perren, Aurel; Lugli, Alessandro

2014-01-01

28

Cancer and Leukemia Group B Pathology Committee Guidelines for Tissue Microarray Construction Representing Multicenter Prospective Clinical Trial Tissues  

PubMed Central

Practice-changing evidence requires confirmation, preferably in multi-institutional clinical trials. The collection of tissue within such trials has enabled biomarker studies and evaluation of companion diagnostic tests. Tissue microarrays (TMAs) have become a standard approach in many cooperative oncology groups. A principal goal is to maximize the number of assays with this precious tissue. However, production strategies for these arrays have not been standardized, possibly decreasing the value of the study. In this article, members of the Cancer and Leukemia Group B Pathology Committee relay our experiences as array facility directors and propose guidelines regarding the production of high-quality TMAs for cooperative group studies. We also discuss statistical issues arising from having a proportion of patients available for TMAs and the possibility that patients with TMAs fail to represent the greater study population. PMID:21519016

Rimm, David L.; Nielsen, Torsten O.; Jewell, Scott D.; Rohrer, Daniel C.; Broadwater, Gloria; Waldman, Frederic; Mitchell, Kisha A.; Singh, Baljit; Tsongalis, Gregory J.; Frankel, Wendy L.; Magliocco, Anthony M.; Lara, Jonathan F.; Hsi, Eric D.; Bleiweiss, Ira J.; Badve, Sunil S.; Chen, Beiyun; Ravdin, Peter M.; Schilsky, Richard L.; Thor, Ann; Berry, Donald A.

2011-01-01

29

Biofunctionalization of surfaces by energetic ion implantation: Review of progress on applications in implantable biomedical devices and antibody microarrays  

NASA Astrophysics Data System (ADS)

Despite major research efforts in the field of biomaterials, rejection, severe immune responses, scar tissue and poor integration continue to seriously limit the performance of today's implantable biomedical devices. Implantable biomaterials that interact with their host via an interfacial layer of active biomolecules to direct a desired cellular response to the implant would represent a major and much sought after improvement. Another, perhaps equally revolutionary, development that is on the biomedical horizon is the introduction of cost-effective microarrays for fast, highly multiplexed screening for biomarkers on cell membranes and in a variety of analyte solutions. Both of these advances will rely on effective methods of functionalizing surfaces with bioactive molecules. After a brief introduction to other methods currently available, this review will describe recently developed approaches that use energetic ions extracted from plasma to facilitate simple, one-step covalent surface immobilization of bioactive molecules. A kinetic theory model of the immobilization process by reactions with long-lived, mobile, surface-embedded radicals will be presented. The roles of surface chemistry and microstructure of the ion treated layer will be discussed. Early progress on applications of this technology to create diagnostic microarrays and to engineer bioactive surfaces for implantable biomedical devices will be reviewed.

Bilek, Marcela M. M.

2014-08-01

30

Global analysis of hematopoietic and vascular endothelial gene expression by tissue specific microarray profiling in zebrafish  

PubMed Central

In this study we utilize fluorescent activated cell sorting (FACS) of cells from transgenic zebrafish coupled with microarray analysis to globally analyze expression of cell type specific genes. We find that it is possible to isolate cell populations from Tg(fli1:egfp)y1 zebrafish embryos that are enriched in vascular, hematopoietic and pharyngeal arch cell types. Microarray analysis of GFP+ versus GFP? cells isolated from Tg(fli1:egfp)y1 embryos identifies genes expressed in hematopoietic, vascular and pharyngeal arch tissue, consistent with the expression of the fli1:egfp transgene in these cell types. Comparison of expression profiles from GFP+ cells isolated from embryos at two different time points reveals that genes expressed in different fli1+ cell types display distinct temporal expression profiles. We also demonstrate the utility of this approach for gene discovery by identifying numerous previously uncharacterized genes that we find are expressed in fli1:egfp positive cells, including new markers of blood, endothelial and pharyngeal arch cell types. In parallel, we have developed a database to allow easy access to both our microarray and in situ results. Our results demonstrate that this is a robust approach for identification of cell type specific genes as well as for global analysis of cell type specific gene expression in zebrafish embryos. PMID:16999953

Covassin, Laurence; Amigo, Julio D.; Suzuki, Kana; Teplyuk, Viktor; Straubhaar, Juerg; Lawson, Nathan D.

2006-01-01

31

Multi-Tissue Microarray Analysis Identifies a Molecular Signature of Regeneration  

PubMed Central

The inability to functionally repair tissues that are lost as a consequence of disease or injury remains a significant challenge for regenerative medicine. The molecular and cellular processes involved in complete restoration of tissue architecture and function are expected to be complex and remain largely unknown. Unlike humans, certain salamanders can completely regenerate injured tissues and lost appendages without scar formation. A parsimonious hypothesis would predict that all of these regenerative activities are regulated, at least in part, by a common set of genes. To test this hypothesis and identify genes that might control conserved regenerative processes, we performed a comprehensive microarray analysis of the early regenerative response in five regeneration-competent tissues from the newt Notophthalmus viridescens. Consistent with this hypothesis, we established a molecular signature for regeneration that consists of common genes or gene family members that exhibit dynamic differential regulation during regeneration in multiple tissue types. These genes include members of the matrix metalloproteinase family and its regulators, extracellular matrix components, genes involved in controlling cytoskeleton dynamics, and a variety of immune response factors. Gene Ontology term enrichment analysis validated and supported their functional activities in conserved regenerative processes. Surprisingly, dendrogram clustering and RadViz classification also revealed that each regenerative tissue had its own unique temporal expression profile, pointing to an inherent tissue-specific regenerative gene program. These new findings demand a reconsideration of how we conceptualize regenerative processes and how we devise new strategies for regenerative medicine. PMID:23300656

Mercer, Sarah E.; Cheng, Chia-Ho; Atkinson, Donald L.; Krcmery, Jennifer; Guzman, Claudia E.; Kent, David T.; Zukor, Katherine; Marx, Kenneth A.; Odelberg, Shannon J.; Simon, Hans-Georg

2012-01-01

32

Differential expression of HSPA1 and HSPA2 proteins in human tissues; tissue microarray-based immunohistochemical study.  

PubMed

In the present study we determined the expression pattern of HSPA1 and HSPA2 proteins in various normal human tissues by tissue-microarray based immunohistochemical analysis. Both proteins belong to the HSPA (HSP70) family of heat shock proteins. The HSPA2 is encoded by the gene originally defined as testis-specific, while HSPA1 is encoded by the stress-inducible genes (HSPA1A and HSPA1B). Our study revealed that both proteins are expressed only in some tissues from the 24 ones examined. HSPA2 was detected in adrenal gland, bronchus, cerebellum, cerebrum, colon, esophagus, kidney, skin, small intestine, stomach and testis, but not in adipose tissue, bladder, breast, cardiac muscle, diaphragm, liver, lung, lymph node, pancreas, prostate, skeletal muscle, spleen, thyroid. Expression of HSPA1 was detected in adrenal gland, bladder, breast, bronchus, cardiac muscle, esophagus, kidney, prostate, skin, but not in other tissues examined. Moreover, HSPA2 and HSPA1 proteins were found to be expressed in a cell-type-specific manner. The most pronounced cell-type expression pattern was found for HSPA2 protein. In the case of stratified squamous epithelia of the skin and esophagus, as well as in ciliated pseudostratified columnar epithelium lining respiratory tract, the HSPA2 positive cells were located in the basal layer. In the colon, small intestine and bronchus epithelia HSPA2 was detected in goblet cells. In adrenal gland cortex HSPA2 expression was limited to cells of zona reticularis. The presented results clearly show that certain human tissues constitutively express varying levels of HSPA1 and HSPA2 proteins in a highly differentiated way. Thus, our study can help designing experimental models suitable for cell- and tissue-type-specific functional differences between HSPA2 and HSPA1 proteins in human tissues. PMID:21373891

Scieglinska, Dorota; Piglowski, Wojciech; Chekan, Mykola; Mazurek, Agnieszka; Krawczyk, Zdzis?aw

2011-04-01

33

Role of ?-catenin expression in paediatric mesenchymal lesions: a tissue microarray-based immunohistochemical study  

PubMed Central

Beta-catenin is a major protein in the Wnt signalling pathway. Although it has been studied in various types of carcinoma, little is known about its expression in mesenchymal tumours. In this study 41 specimens of a variety of mesenchymal childhood tumours were compared to 24 samples of the corresponding adult tumours to assess the diagnostic value of nuclear ?-catenin expression using tissue microarray-based immunohistochemistry. Similar to adult sarcoma and fibromatosis, ?-catenin was not expressed in the majority of childhood sarcomas, and its nuclear translocation was detected in paediatric fibromatosis; non-negligible levels of nuclear staining in other tumour types demonstrate Wnt pathway activation in mesenchymal neoplasms of childhood and adolescence. PMID:23027341

Santoro, A.; Pannone, G.; Errico, M.E.; Bifano, D.; Lastilla, G.; Bufo, P.; Loreto, C.; Donofrio, V.

2012-01-01

34

TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data  

PubMed Central

Tissue microarrays (TMAs) allow multiplexed analysis of tissue samples and are frequently used to estimate biomarker protein expression in tumour biopsies. TMA Navigator (www.tmanavigator.org) is an open access web application for analysis of TMA data and related information, accommodating categorical, semi-continuous and continuous expression scores. Non-biological variation, or batch effects, can hinder data analysis and may be mitigated using the ComBat algorithm, which is incorporated with enhancements for automated application to TMA data. Unsupervised grouping of samples (patients) is provided according to Gaussian mixture modelling of marker scores, with cardinality selected by Bayesian information criterion regularization. Kaplan–Meier survival analysis is available, including comparison of groups identified by mixture modelling using the Mantel-Cox log-rank test. TMA Navigator also supports network inference approaches useful for TMA datasets, which often constitute comparatively few markers. Tissue and cell-type specific networks derived from TMA expression data offer insights into the molecular logic underlying pathophenotypes, towards more effective and personalized medicine. Output is interactive, and results may be exported for use with external programs. Private anonymous access is available, and user accounts may be generated for easier data management. PMID:23761446

Lubbock, Alexander L. R.; Katz, Elad; Harrison, David J.; Overton, Ian M.

2013-01-01

35

Identification of Novel Tissue-Specific Genes by Analysis of Microarray Databases: A Human and Mouse Model  

PubMed Central

Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI?s Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved. PMID:23741331

Suh, Yeunsu; Davis, Michael E.; Lee, Kichoon

2013-01-01

36

Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression  

PubMed Central

Background Type 2 diabetes mellitus (T2DM) is a complex systemic disease, with significant disorders of metabolism. The liver, a central energy metabolic organ, plays a critical role in the development of diabetes. Although gene expression levels are able to be measured via microarray since 1996, it is difficult to evaluate the contributions of one altered gene expression to a specific disease. One of the reasons is that a whole network picture responsible for a specific phase of diabetes is missing, while a single gene has to be put into a network picture to evaluate its importance. In the aim of identifying significant transcriptional regulatory networks in the liver contributing to diabetes, we have performed comprehensive active regulatory network survey by network screening in 4 weeks (w), 8-12 w, and 18-20 w Goto-Kakizaki (GK) rat liver microarray data. Results We identify active regulatory networks in GK rat by network screening in the following procedure. First, the regulatory networks are compiled by using the known binary relationships between the transcriptional factors and their regulated genes and the biological classification scheme, and second, the consistency of each regulatory network with the microarray data measured in GK rat is estimated to detect the active networks under the corresponding conditions. The comprehensive survey of the consistency between the networks and the measured data by the network screening approach in the case of non-insulin dependent diabetes in the GK rat reveals: 1. More pathways are active during inter-middle stage diabetes; 2. Inflammation, hypoxia, increased apoptosis, decreased proliferation, and altered metabolism are characteristics and display as early as 4weeks in GK strain; 3. Diabetes progression accompanies insults and compensations; 4. Nuclear receptors work in concert to maintain normal glycemic robustness system. Conclusion Notably this is the first comprehensive network screening study of non-insulin dependent diabetes in the GK rat based on high throughput data of the liver. Several important pathways have been revealed playing critical roles in the diabetes progression. Our findings also implicate that network screening is able to help us understand complex disease such as diabetes, and demonstrate the power of network systems biology approach to elucidate the essential mechanisms which would escape conventional single gene-based analysis. PMID:21689475

2011-01-01

37

Validation of a Tissue Microarray to Study Differential Protein Expression in Inflammatory and Non-Inflammatory Breast Cancer  

Microsoft Academic Search

Aims. Inflammatory breast cancer (IBC) is an aggressive subtype of breast cancer with poor prognosis. The mechanisms responsible for the aggressive clinical evolution are incompletely understood. We constructed a tissue microarray (TMA) and validated its use in translational IBC research. Differential expression of proteins that might play a role in causing the IBC phenotype was studied.

G. G. Van den Eynden; I. Van der Auwera; S. Van Laere; C. G. Colpaert; P. van Dam; S. Merajver; C. G. Kleer; A. L. Harris; E. A. Van Marck; L. Y. Dirix; P. B. Vermeulen

2004-01-01

38

Tissue microarray analysis of eIF4E and its downstream effector proteins in human breast cancer  

PubMed Central

Correction to Kleiner HE, Krishnan P, Tubbs J, Smith M, Meschonat C, Shi R, Lowery-Nordberg M, Adegboyega P, Unger M, Cardelli J et al: Tissue microarray analysis of eIF4E and its downstream effector proteins in human breast cancer. J Exp Clin Cancer Res 2009, 28:5.

Kleiner, Heather E; Krishnan, Prasad; Tubbs, Jesse; Smith, Mark; Meschonat, Carol; Shi, Runhua; Lowery-Nordberg, Mary; Adegboyega, Patrick; Unger, Marcia; Cardelli, James; Chu, Quyen; Mathis, J Michael; Clifford, John; De Benedetti, Arrigo; Li, Benjamin DL

2009-01-01

39

The usefulness of immunohistochemistry in tissue microarrays of Human Papillomavirus negative adenocarcinoma of the uterine cervix  

PubMed Central

Background The origin of adenocarcinomas presenting on the cervix uteri may be doubtful, i.e. whether it is of cervical or endometrial origin, due to the overlapping morphological features. In HPV negative samples, further tests may be needed to ascertain the nature of the tumours. We aimed to explore the use of immunohistochemistry profiles in tissue microarrays in archived samples of adenocarcinoma (ADC) of the cervix from Uganda that tested negative for HPV DNA. Findings Five commercially available antibodies were tested in tissue array sections immunostained utilizing the avidin-biotin (AB) technique. In 26 ADC samples, HPV was detected in 13, p16 in 15 (8 in HPV positive and 7 in HPV negative), CEA in 12, vimentin in 6, ER in 0, and PR in 2. Among the 13/25 HPV negative ADC samples, five were positive for CEA suggesting endocervical origin, and three were vimentin positive (one had a mucinous endocervical histological pattern and two were ADC, not otherwise specified, most likely of endometrial origin). Conclusions The immunoprofiles of ADC with the antibodies studied are rather nonspecific. By using immunohistochemistry in 13 HPV negative ADC, endocervical tumour origin was suspected in five CEA positive cases while two out of three vimentin positive samples were probably of endometrial origin, suggesting that CEA and vimentin may be valuable in distinguishing HPV negative cervical adenocarcinomas from endometrial adenocarcinomas. PMID:20199664

2010-01-01

40

Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues  

PubMed Central

Background Rice is one of the major crop species in the world helping to sustain approximately half of the global population’s diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray® microarray platform which is suitable for two major rice subspecies, japonica and indica. Results The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI’s Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R?=?0.95, p?microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in rice tissues. The rice OneArray® microarray platform revealed high specificity and sensitivity. Additional information for the rice OneArray® microarray can be found at http://www.phalanx.com.tw/index.php. PMID:24398116

2014-01-01

41

Molecular and clinico-pathological markers in rectal cancer: a tissue micro-array study  

PubMed Central

Aims The aims of the study were to study the effect of pre-operative treatment on the expression of tumour-related proteins and to correlate the expression of these proteins with response and survival of patients with advanced rectal cancer. Materials and methods Tissue micro-arrays from pre- and post-treatment biopsies of 99 patients with rectal cancer treated with pre-operative (chemo)radiotherapy were stained for epidermal growth factor receptor (EGFR), carbonic anhydrase IX, Ki67, vascular endothelial growth factor, cyclo-oxygenase 2 (COX-2) and cleaved cytokeratin 18 (c-CK18). Also, fibro-inflammatory alterations after treatment were evaluated. Results Pre-operative (chemo)radiotherapy caused fibro-inflammatory changes, a downregulation of proliferation (Ki67) and EGFR and an upregulation of apoptosis (cleaved CK18). Patients with a good regression during pre-operative treatment showed less proliferating and apoptotic cells in the resection specimen. Multivariate analysis showed that T downstaging, fibro-inflammatory changes in the resection specimen and COX-2 expression in the biopsy correlated with overall survival. Conclusions Pre-operative treatment has an effect on proliferation, apoptosis, inflammation and EGFR expression. The classical clinical parameters as well as fibro-inflammatory changes and COX-2 expression seem most valuable as predictors for survival. PMID:19050903

Goethals, Laurence; Libbrecht, Louis; Perneel, Christiaan; Geboes, Karel; Ectors, Nadine; McBride, William H.; Haustermans, Karin

2009-01-01

42

Fabrication of a three-dimensional tissue model microarray using laser foaming of a gas-impregnated biodegradable polymer.  

PubMed

A microarray containing three-dimensional (3D) tissue models is a promising substitute for the two-dimensional (2D) cell-based microarrays currently available for high throughput, tissue-based biomedical assays. A cell culture microenvironment similar to in vivo conditions could be achieved with biodegradable porous scaffolds. In this study, a laser foaming technique is developed to create an array of micro-scale 3D porous scaffolds. The effects of major process parameters and the morphology of the resulting porous structure were investigated. For comparison, cell culture studies were conducted with both foamed and unfoamed samples using T98G cells. The results show that by laser foaming gas-impregnated polylactic acid it is possible to generate an array of inverse cone shaped wells with porous walls. The size of the foamed region can be controlled with laser power and exposure time, while the pore size of the scaffold can be manipulated with the saturation pressure. T98G cells grow well in the foamed scaffolds, forming clusters that have not been observed in 2D cell cultures. Cells are more viable in the 3D scaffolds than in the 2D cell culture cases. The 3D porous microarray could be used for parallel studies of drug toxicity, guided stem cell differentiation, and DNA binding profiles. PMID:24999514

Ock, JinGyu; Li, Wei

2014-06-01

43

Chromosomal instability in gastric mucosa-associated lymphoid tissue lymphomas: a fluorescent in situ hybridization study using a tissue microarray approach.  

PubMed

Extranodal marginal zone B-cell lymphomas (mucosa-associated lymphoid tissue [MALT] lymphomas) of the gastrointestinal tract have been known to have characteristic chromosomal aberrations including trisomies of chromosomes 3, 12, and 18. However, knowledge of the clinical significance of cytogenetic changes in MALT lymphomas is still limited. In the present study, the frequency of the numeric and structural aberrations of the chromosomes 1, 3, 12, 18 and X and of the MALT1 gene as well as their potential clinical significance were analyzed by using fluorescent in situ hybridization on a tissue microarray containing 257 tissue samples from 203 cases of surgically resected primary gastric lymphomas including 115 cases of MALT lymphomas, 88 cases of diffuse large B-cell lymphomas (DLBCLs, 75 with an associated MALT lymphoma, so-called ex-MALT DLBCL, and 13 de novo), and 54 controls cases of Helicobacter pylori-associated chronic gastritis. Clinical follow-up information was available in 137 cases. Trisomies 1, 3, 12, and 18 were detected in 3.3%, 44.4%, 12.3%, and 19.2% of MALT lymphomas and in 11.1%, 42.2%, 26.5%, and 22.0% of ex-MALT DLBCLs, respectively. In addition, we found gains of the X chromosome in 36.4% of MALT lymphomas, in 34.5% of ex-MALT DLBCLs, and in 36.4% of de novo DLBCLs. Structural and/or numeric abnormalities of the MALT1 gene were observed in 37.0% of MALT lymphomas and in 22.2% of ex-MALT DLBCLs. In de novo DLBCL, trisomies for chromosomes 3, 12, 18, and X were found in 42.9%, 10.0%, 11.1%, and 36.4%, respectively, whereas alterations of MALT1 (namely, translocations) were found in 20.0% of the cases. An unexpected high and previously unreported gain of chromosome X in gastric MALT lymphomas was found. This tumor appears, therefore, to be a genetically unstable neoplasia. Our results point out that t(11;18) and aneuploidy may be both involved in lymphomagenesis and that at least a subset of MALT lymphomas may progress toward high-grade neoplasia. PMID:18234275

Bernasconi, Barbara; Karamitopoulou-Diamantis, Eva; Karamitopolou-Diamantiis, Eva; Tornillo, Luigi; Lugli, Alessandro; Di Vizio, Dolores; Dirnhofer, Stephan; Wengmann, Stephan; Glatz-Krieger, Katharyna; Fend, Falko; Capella, Carlo; Insabato, Luigi; Terracciano, Luigi M

2008-04-01

44

Identification of Glycoprotein Markers for Pancreatic Cancer CD24+CD44+ Stem-like Cells Using nano LC-MS/MS and Tissue Microarray  

PubMed Central

Pancreatic adenocarcinoma is characterized by late diagnosis due to lack of early symptoms, extensive metastasis, and high resistance to chemo/radiation therapy. Recently, a subpopulation of cells within pancreatic cancers, termed cancer stem cells (CSCs), has been characterized and postulated to be the drivers for pancreatic cancer and responsible for metastatic spread. Further studies on pancreatic CSCs are therefore of particular importance to identify novel diagnosis markers and therapeutic targets for this dismal disease. Herein, the malignant phenotype of pancreatic cancer stem-like CD24+CD44+ cells was isolated from a human pancreatic carcinoma cell line (PANC-1), and demonstrated 4-fold increased invasion ability compared to CD24?CD44+ cells. Using lectin microarray and nano LC-MS/MS, we identified a differentially expressed set of glycoproteins between these two subpopulations. Lectin microarray analysis revealed that fucose- and galactose-specific lectins, UEA-1 and DBA respectively, exhibit distinctly strong binding to CD24+CD44+ cells. The glycoproteins extracted by multi-lectin affinity chromatography were consequently analyzed by LC-MS/MS. 17 differentially expressed glycoproteins were identified, including upregulated Cytokeratin 8/CK8, Integrin ?1/CD29, ICAM1/CD54 and Ribophorin 2/RPN2, and downregulated Aminopeptidase N/CD13. Immunohistochemical analysis of tissue microarrays showed that CD24 was significantly associated with late-stage pancreatic adenocarcinomas, and RPN2 was exclusively coexpressed with CD24 in a small population of CD24-positive cells. However, CD13 expression was dramatically decreased along with tumor progression, preferentially present on the apical membrane of ductal cells and vessels in early-stage tumors. Our findings suggest that these glycoproteins may provide potential therapeutic targets and promising prognostic markers for pancreatic cancer. PMID:22335271

Zhu, Jianhui; He, Jintang; Liu, Yashu; Simeone, Diane M.; Lubman, David M.

2012-01-01

45

A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs  

PubMed Central

Microarrays to examine the global expression levels of microRNAs (miRNAs) in a systematic in-parallel manner have become important tools to help unravel the functions of miRNAs and to understand their roles in RNA-based regulation and their implications in human diseases. We have established a novel miRNA-specific microarray platform that enables the simultaneous expression analysis of both known and predicted miRNAs obtained from human or mouse origin. Chemically modified 2?-O-(2-methoxyethyl)-(MOE) oligoribonucleotide probes were arrayed onto Evanescent Resonance (ER) microchips by robotic spotting. Supplementing the complementary probes against miRNAs with carefully designed mismatch controls allowed for accurate sequence-specific determination of miRNA expression profiles obtained from a panel of mouse tissues. This revealed new expression signatures of known miRNAs as well as of novel miRNAs previously predicted using bioinformatic methods. Systematic confirmation of the array data with northern blotting and, in particular, real-time PCR suggests that the described microarray platform is a powerful tool to analyze miRNA expression patterns with rapid throughput and high fidelity. PMID:17355992

Beuvink, Iwan; Kolb, Fabrice A.; Budach, Wolfgang; Garnier, Arlette; Lange, Joerg; Natt, Francois; Dengler, Uwe; Hall, Jonathan; Weiler, Jan

2007-01-01

46

Extraction and labeling methods for microarrays using small amounts of plant tissue.  

PubMed

Procedures were developed to maximize the yield of high-quality RNA from small amounts of plant biomass for microarrays. Two disruption techniques (bead milling and pestle and mortar) were compared for the yield and the quality of RNA extracted from 1-week-old Arabidopsis thaliana seedlings (approximately 0.5-30 mg total biomass). The pestle and mortar method of extraction showed enhanced RNA quality at the smaller biomass samples compared with the bead milling technique, although the quality in the bead milling could be improved with additional cooling steps. The RNA extracted from the pestle and mortar technique was further tested to determine if the small quantity of RNA (500 ng-7 microg) was appropriate for microarray analyses. A new method of low-quantity RNA labeling for microarrays (NuGEN Technologies, Inc.) was used on five 7-day-old seedlings (approximately 2.5 mg fresh weight total) of Arabidopsis that were grown in the dark and exposed to 1 h of red light or continued dark. Microarray analyses were performed on a small plant sample (five seedlings; approximately 2.5 mg) using these methods and compared with extractions performed with larger biomass samples (approximately 500 roots). Many well-known light-regulated genes between the small plant samples and the larger biomass samples overlapped in expression changes, and the relative expression levels of selected genes were confirmed with quantitative real-time polymerase chain reaction, suggesting that these methods can be used for plant experiments where the biomass is extremely limited (i.e. spaceflight studies). PMID:19140889

Stimpson, Alexander J; Pereira, Rhea S; Kiss, John Z; Correll, Melanie J

2009-03-01

47

Relation between human papillomavirus positivity and p16 expression in head and neck carcinomas--a tissue microarray study.  

PubMed

Overexpression of p16 has been demonstrated to be strongly related to the presence of HPV16, 18. Squamous cell carcinoma of the head and neck has been shown to be associated with human papillomavirus (HPV) infection. The main aim of this study was to investigate the relationship between HPV presence and p16 expression in a representative collection of 60 head and neck carcinomas by tissue microarrays. The presence of HPV (HPV6, 11-low risk, HPV16, 18-high risk) was detected by applying in situ hybridisation. P-16 protein expression was detected immunohistochemically. HPV6, 11 positivity was observed in 10 out of 60 carcinomas. HPV16, 18 presence was found in 30 out of 60 tumours. P-16 expression was detected in 35 out of 60 tumours. A statistically significant relationship was demonstrated between HPV16, 18 presence and increased expression of p16. Also the HPV6, 11 presence was significantly correlated with p16 immunoreactivity. Additionally, this study demonstrates that it is possible to analyse p16 expression and HPV presence by tissue microarrays. PMID:17352245

König, Frank; Krekeler, Gisbert; Hönig, Johannes F; Cordon-Cardo, Carlos; Fischer, Gösta; Korabiowska, Monika

2007-01-01

48

A Texture Based Pattern Recognition Approach to Distinguish Melanoma from Non-Melanoma Cells in Histopathological Tissue Microarray Sections  

PubMed Central

Aims Immunohistochemistry is a routine practice in clinical cancer diagnostics and also an established technology for tissue-based research regarding biomarker discovery efforts. Tedious manual assessment of immunohistochemically stained tissue needs to be fully automated to take full advantage of the potential for high throughput analyses enabled by tissue microarrays and digital pathology. Such automated tools also need to be reproducible for different experimental conditions and biomarker targets. In this study we present a novel supervised melanoma specific pattern recognition approach that is fully automated and quantitative. Methods and Results Melanoma samples were immunostained for the melanocyte specific target, Melan-A. Images representing immunostained melanoma tissue were then digitally processed to segment regions of interest, highlighting Melan-A positive and negative areas. Color deconvolution was applied to each region of interest to separate the channel containing the immunohistochemistry signal from the hematoxylin counterstaining channel. A support vector machine melanoma classification model was learned from a discovery melanoma patient cohort (n?=?264) and subsequently validated on an independent cohort of melanoma patient tissue sample images (n?=?157). Conclusion Here we propose a novel method that takes advantage of utilizing an immuhistochemical marker highlighting melanocytes to fully automate the learning of a general melanoma cell classification model. The presented method can be applied on any protein of interest and thus provides a tool for quantification of immunohistochemistry-based protein expression in melanoma. PMID:23690928

Rexhepaj, Elton; Agnarsdottir, Margret; Bergman, Julia; Edqvist, Per-Henrik; Bergqvist, Michael; Uhlen, Mathias; Gallagher, William M.; Lundberg, Emma; Ponten, Fredrik

2013-01-01

49

Selective evolutionary pressure from the tissue microenvironment drives tumor progression  

Microsoft Academic Search

Cells grow within defined environmental niches and are subject to microenvironmental control. Outside of their niche, the environment is hostile, the normal cells lack appropriate survival signals which leads to anoikis. During tumor development and progression, malignant cells must escape the local tissue control and resist anoikis. The inherent genetic instability of tumor cells makes their phenotype very plastic, which

Keiran S. M. Smalley; Patricia A. Brafford; Meenhard Herlyn

2005-01-01

50

Microarray gene expression profiles from mature gonad tissues of Atlantic bluefin tuna, Thunnus thynnus in the Gulf of Mexico  

PubMed Central

Background Bluefin tunas are highly prized pelagic fish species representing a significant economic resource to fisheries throughout the world. Atlantic bluefin tuna (Thunnus thynnus) populations have significantly declined due to overexploitation. As a consequence of their value and population decline, T. thynnus has been the focus of considerable research effort concerning many aspects of their life history. However, in-depth understanding of T. thynnus reproductive biology is still lacking. Knowledge of reproductive physiology is a very important tool for determining effective fisheries and aquaculture management. Transcriptome techniques are proving powerful and provide novel insights into physiological processes. Construction of a microarray from T. thynnus ESTs sourced from reproductive tissues has provided an ideal platform to study the reproductive physiology of bluefin tunas. The aim of this investigation was to compare transcription profiles from the ovaries and testes of mature T. thynnus to establish sex specific variations underlying their reproductive physiology. Results Male and females T. thynnus gonad tissues were collected from the wild and histologically staged. Sub-samples of sexually mature tissues were also measured for their mRNA differential expression among the sexes using the custom microarray design BFT 4X44K. A total of 7068 ESTs were assessed for differential expression of which 1273 ESTs were significantly different (p<0.05) with >2 fold change in expression according to sex. Differential expression for 13 of these ESTs was validated with quantitative PCR. These include genes involved in egg envelope formation, hydration, and lipid transport/accumulation more highly expressed in ovaries compared with testis, while genes involved in meiosis, sperm motility and lipid metabolism were more highly expressed in testis compared with ovaries. Conclusions This investigation has furthered our knowledge of bluefin tunas reproductive biology by using a contemporary transcriptome approach. Gene expression profiles in T. thynnus sexually mature testes and ovaries were characterized with reference to gametogenesis and potential alternative functions. This report is the first application of microarray technology for bluefin tunas and demonstrates the efficacy by which this technique may be used for further characterization of specific biological aspects for this valuable teleost fish. PMID:23036107

2012-01-01

51

Quality Control of RNA Preservation and Extraction from Paraffin-Embedded Tissue: Implications for RT-PCR and Microarray Analysis  

PubMed Central

Analysis of RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathological diagnostics. We have performed a comprehensive and systematic investigation of the impact of factors in the pre-analytical workflow, such as different fixatives, fixation time, RNA extraction method and storage of tissues in paraffin blocks, on several downstream reactions including complementary DNA (cDNA) synthesis, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and microarray hybridization. We compared the effects of routine formalin fixation with the non-crosslinking, alcohol-based Tissue Tek Xpress Molecular Fixative (TTXMF, Sakura Finetek), and cryopreservation as gold standard for molecular analyses. Formalin fixation introduced major changes into microarray gene expression data and led to marked gene-to-gene variations in delta-ct values of qRT-PCR. We found that qRT-PCR efficiency and gene-to-gene variations were mainly attributed to differences in the efficiency of cDNA synthesis as the most sensitive step. These differences could not be reliably detected by quality assessment of total RNA isolated from formalin-fixed tissues by electrophoresis or spectrophotometry. Although RNA from TTXMF fixed samples was as fragmented as RNA from formalin fixed samples, much higher cDNA yield and lower ct-values were obtained in qRT-PCR underlining the negative impact of crosslinking by formalin. In order to better estimate the impact of pre-analytical procedures such as fixation on the reliability of downstream analysis, we applied a qRT-PCR-based assay using amplicons of different length and an assay measuring the efficiency of cDNA generation. Together these two assays allowed better quality assessment of RNA extracted from fixed and paraffin-embedded tissues and should be used to supplement quality scores derived from automated electrophoresis. A better standardization of the pre-analytical workflow, application of additional quality controls and detailed sample information would markedly improve the comparability and reliability of molecular studies based on formalin-fixed and paraffin-embedded tissue samples. PMID:23936242

Pichler, Martin; Zatloukal, Kurt

2013-01-01

52

Assessment of epidermal growth factor receptor (EGFR) expression in primary colorectal carcinomas and their related metastases on tissue sections and tissue microarray  

PubMed Central

Metastatic colorectal carcinomas (CRC) resistant to chemotherapy may benefit from targeting monoclonal therapy cetuximab when they express the epidermal growth factor receptor (EGFR). Because of its clinical implications, we studied EGFR expression by immunohistochemistry on tissue sections of primary CRC (n=32) and their related metastases (n=53). A tissue microarray (TMA) was generated from the same paraffin blocks to determine whether this technique could be used for EGFR screening in CRC. On tissue sections, 84% of the primary CRC and 94% of the metastases were EGFR-positive. When matched, they showed a concordant EGFR-positive status in 78% of the cases. Moreover, staining intensity and extent of EGFR-positive cells in the primary CRC correlated with those observed in the synchronous metastases. On TMA, 65% of the primary CRC, 66% of the metastases, and 43% of the matched primary CRC metastases were EGFR-positive. There was no concordant EGFR status between the primary and the metastatic sites. A strong discrepancy of EGFR status was noted between TMA and tissue sections. In conclusion, EGFR expression measured in tissue sections from primary CRC and their related metastases was found to be similar and frequent, but it was significantly underestimated by the TMA technique. PMID:16865406

Boissiere-Michot, Florence; Sabourin, Jean-Christophe; Gourgou-Bourgade, Sophie; Radal, Michele; Penault-Llorca, Frederique; Rochaix, Philippe; Arnould, Laurent; Bralet, Marie-Pierre; Azria, David; Ychou, Marc

2006-01-01

53

High-Throughput Tissue Microarray Analysis of Cyclin E Gene Amplification and Overexpression in Urinary Bladder Cancer  

PubMed Central

Studies by comparative genomic hybridization revealed that the 19q13 chromosomal region is frequently amplified in bladder cancer. The cyclin E gene (CCNE), coding for a regulatory subunit of cyclin-dependent kinase 2, has been mapped to 19q13. To investigate the role of cyclin E alterations in bladder cancer, a tissue microarray of 2,317 specimens from 1,842 bladder cancer patients was constructed and analyzed for CCNE amplification by fluorescence in situ hybridization and for cyclin-E protein overexpression by immunohistochemistry. Fluorescence in situ hybridization analysis showed amplification in only 30 of the 1,561 evaluable tumors (1.9%). Amplification was significantly associated with stage and grade (P < 0.0005 each). Immunohistochemically detectable cyclin E expression was strong in 233 (12.4%), weak in 354 (18.9%), and negative in 1,286 of the 1,873 interpretable tumors. The majority (62.1%) of CCNE-amplified tumors were strongly immunohistochemistry-positive (P < 0.0001). The frequency of protein expression increased from stage pTa (22.2%) to pT1 (45.5%; P < 0.0001) but then decreased for stage pT2-4 (29.4%; P < 0.0001 for pT1 versus pT2-4). Low cyclin E expression was associated with poor overall survival in all patients (P < 0.0001), but had no prognostic impact independent of stage. It is concluded that cyclin E overexpression is characteristic to a subset of bladder carcinomas, especially at the stage of early invasion. This analysis of the prognostic impact of CCNE gene amplification and protein expression in >1,500 arrayed bladder cancers was accomplished in a period of 2 weeks, illustrating how the tissue microarray technology remarkably facilitates the evaluation of the clinical relevance of molecular alterations in cancer. PMID:10980118

Richter, Jan; Wagner, Urs; Kononen, Juha; Fijan, Andre; Bruderer, James; Schmid, Ulrico; Ackermann, Daniel; Maurer, Robert; Alund, Goran; Knonagel, Hartmut; Rist, Marcus; Wilber, Kim; Anabitarte, Manuel; Hering, Franz; Hardmeier, Thomas; Schonenberger, Andreas; Flury, Renata; Jager, Peter; Luc Fehr, Jean; Schraml, Peter; Moch, Holger; Mihatsch, Michael J.; Gasser, Thomas; Kallioniemi, Olli P.; Sauter, Guido

2000-01-01

54

Tissue oxygen saturation during hyperthermic progressive central hypovolemia.  

PubMed

During normothermia, a reduction in near-infrared spectroscopy (NIRS)-derived tissue oxygen saturation (So2) is an indicator of central hypovolemia. Hyperthermia increases skin blood flow and reduces tolerance to central hypovolemia, both of which may alter the interpretation of tissue So2 during central hypovolemia. This study tested the hypothesis that maximal reductions in tissue So2 would be similar throughout normothermic and hyperthermic central hypovolemia to presyncope. Ten healthy males (means ± SD; 32 ± 5 yr) underwent central hypovolemia via progressive lower-body negative pressure (LBNP) to presyncope during normothermia (skin temperature ?34°C) and hyperthermia (+1.2 ± 0.1°C increase in internal temperature via a water-perfused suit, skin temperature ?39°C). NIRS-derived forearm (flexor digitorum profundus) tissue So2 was measured throughout and analyzed as the absolute change from pre-LBNP. Hyperthermia reduced (P < 0.001) LBNP tolerance by 49 ± 33% (from 16.7 ± 7.9 to 7.2 ± 3.9 min). Pre-LBNP, tissue So2 was similar (P = 0.654) between normothermia (74 ± 5%) and hyperthermia (73 ± 7%). Tissue So2 decreased (P < 0.001) throughout LBNP, but the reduction from pre-LBNP to presyncope was greater during normothermia (-10 ± 6%) than during hyperthermia (-6 ± 5%; P = 0.041). Contrary to our hypothesis, these findings indicate that hyperthermia is associated with a smaller maximal reduction in tissue So2 during central hypovolemia to presyncope. PMID:25031230

Schlader, Zachary J; Rivas, Eric; Soller, Babs R; Convertino, Victor A; Crandall, Craig G

2014-09-15

55

[Developmental expression changes of specific genes in adipose tissue for different pig breeds by using pathway-focused microarray].  

PubMed

The expression changes of genes associated with adipose metabolism and regulation of cell growth in backfat tissue at five growth stages (1, 2, 3, 4 and 5 months) of Landrace (a leaner Western breed) and Taihu pigs (a fatty indigenous Chinese breed) were measured by using pathway-focused Oligo microarray. The comparative results between two pig breeds of change ratios showed that the fold changes of 10, 6, 11, 8 and 19 genes were over two times at same month from 1 to 5 months respectively. Variance analysis (ANOVA) revealed that 25 genes in Landrace pigs showed significantly altered in expression among five growth stages (P < 0.05). Principal components analysis (PCA) revealed that angiopoietin-like 4 (ANGPTL4), cathepsin K (CTSK), isocitrate dehydrogenase 2(NADP+) (IDH2), lipoprotein lipase (LPL), malic enzyme 1 (ME1), stearoyl-CoA desaturase (SCD) and uncoupling protein 2 (UCP2) displayed distinctive expression patterns from other genes, which suggested that these genes may be subject to special regulation during the period from 1 to 5 months. K-means clustering analysis revealed that genes in Landrace pigs which showed up-regulation were mainly related to the positive regulation of fatty acid metabolism and genes in Taihu pigs which showed slight fluctuation were mainly related to the regulation of cell growth. Quantitative real-time RT-PCR was used to verify the microarray data for five modulated genes, and a good positive correlation between the two measures of expression was observed for both two pig breeds at different growth stages. These results highlight some possible candidate genes for porcine carcass and meat quality traits, reveal the expressional disciplinarian of correlative genes and provide some data on which to base further study of the dynamic balance process for fatty acid biogynthesis and hydrolyzation. PMID:18616180

Li, Mingzhou; Li, Xuewei; Zhu, Li; Jiang, Yanzhi; Tang, Guoqing

2008-04-01

56

Identification of Genes Associated With Progression and Metastasis of Advanced Cervical Cancers After Radiotherapy by cDNA Microarray Analysis  

SciTech Connect

Purpose: To identify a set of genes related to the progression and metastasis of advanced cervical cancer after radiotherapy and to establish a predictive method. Methods and Materials: A total of 28 patients with cervical cancer (15 stage IIIB, 13 stage IVA patients) who underwent definitive radiotherapy between May 1995 and April 2001 were included in this study. All patients were positive for human papillomavirus infection and harbored the wild-type p53 gene. The expression profiles of 14 tumors with local failure and multiple distant metastasis and 14 tumors without metastasis (cancer free) obtained by punch biopsy were compared before treatment, using a cDNA microarray consisting of 23,040 human genes. Results: Sixty-three genes were selected on the basis of a clustering analysis, and the validity of these genes was confirmed using a cross-validation test. The most accurate prediction was achieved for 63 genes (sensitivity, 78.8%; specificity, 38.1%). Some of these genes were already known to be associated with metastasis via chromosomal instability (TTK, BUB1B), extracellular matrix components (matrix metalloproteinase 1 [MMP-1]), and carcinogenesis (protein phosphatase 1 regulatory subunit 7 [PPP1R7]). A 'predictive score' system was developed that could predict the probability for development of metastases using leave-one-out cross-validation methods. Conclusions: The present results may provide valuable information for identified predictive markers and novel therapeutic target molecules for progression and metastasis of advanced cervical cancer.

Harima, Yoko, E-mail: harima@takii.kmu.ac.j [Department of Radiology, Takii Hospital, Kansai Medical University, 10-15 Fumizono-cho, Moriguchi, Osaka 570-8507 (Japan); Ikeda, Koshi; Utsunomiya, Keita; Shiga, Toshiko; Komemushi, Atsushi [Department of Radiology, Takii Hospital, Kansai Medical University, 10-15 Fumizono-cho, Moriguchi, Osaka 570-8507 (Japan); Kojima, Hiroyuki; Nomura, Motoo; Kamata, Minoru; Sawada, Satoshi [Department of Radiology, Hirakata Hospital, Kansai Medical University, 2-3 Shinmachi, Hirakata, Osaka 573-1191 (Japan)

2009-11-15

57

Hippocampus neuronal metabolic gene expression outperforms whole tissue data in accurately predicting Alzheimer's disease progression.  

PubMed

Numerous metabolic alterations are associated with the impairment of brain cells in Alzheimer's disease (AD). Here we use gene expression microarrays of both whole hippocampus tissue and hippocampal neurons of AD patients to investigate the ability of metabolic gene expression to predict AD progression and its cognitive decline. We find that the prediction accuracy of different AD stages is markedly higher when using neuronal expression data (0.9) than when using whole tissue expression (0.76). Furthermore, the metabolic genes' expression is shown to be as effective in predicting AD severity as the entire gene list. Remarkably, a regression model from hippocampal metabolic gene expression leads to a marked correlation of 0.57 with the Mini-Mental State Examination cognitive score. Notably, the expression of top predictive neuronal genes in AD is significantly higher than that of other metabolic genes in the brains of healthy subjects. All together, the analyses point to a subset of metabolic genes that is strongly associated with normal brain functioning and whose disruption plays a major role in AD. PMID:22560482

Stempler, Shiri; Waldman, Yedael Y; Wolf, Lior; Ruppin, Eytan

2012-09-01

58

Pathways regulated by glucocorticoids in omental and subcutaneous human adipose tissues: a microarray study  

PubMed Central

Glucocorticoids (GC) are powerful regulators of adipocyte differentiation, metabolism, and endocrine function and promote the development of upper body obesity, especially visceral fat stores. To provide a comprehensive understanding of how GC affect adipose tissue and adipocyte function, we analyzed patterns of gene expression (HG U95 Affymetrix arrays) after culture of abdominal subcutaneous (Abd sc) and omental (Om) adipose tissues from severely obese subjects (3 F, 1 M) in the presence of insulin or insulin (7 nM) plus dexamethasone (Dex, 25 nM) for 7 days. About 20% (561 genes in Om and 569 genes in sc) of 2,803 adipose expressed genes were affected by long-term GC. While most of the genes (90%) were commonly regulated by Dex in both depots, 26 in Om and 34 in Abd sc were affected by Dex in only one depot. 60% of the commonly upregulated genes were involved in metabolic pathways and were expressed mainly in adipocytes. Dex suppressed genes in immune/inflammatory (IL-6, IL-8, and MCP-1, expressed in nonadipocytes) and proapoptotic pathways, yet induced genes related to the acute-phase response (SAA, factor D, haptoglobin, and RBP4, expressed in adipocytes) and stress/defense response. Functional classification analysis showed that Dex also induced expression levels of 22 transcription factors related to insulin action and lipogenesis (LXR?, STAT5?, SREBP1, and FoxO1) and immunity/adipogenesis (TSC22D3) while suppressing 17 transcription factors in both depots. Overall, these studies reveal the powerful effects of GC on gene networks that regulate many key functions in human adipose tissue. PMID:21189358

Gong, Da-Wei; Burkey, Bryan F.; Fried, Susan K.

2011-01-01

59

Epidermal Growth Factor Receptor Protein Expression and Gene Amplification in Normal, Hyperplastic, and Cancerous Glottic Tissue: Immunohistochemical and Fluorescent in Situ Hybridization Study on Tissue Microarrays  

PubMed Central

Aim To evaluate the importance of epidermal growth factor receptor (EGFR) protein overexpression and gene amplification in carcinogenesis of glottic cancer. Method In order to evaluate EGFR expression at protein and gene level, immunohistochemical (IHC) analysis and fluorescent in situ hybridization (FISH) were performed on tissue microarrays of laryngeal tissue (145 samples) – 38 samples of normal mucosa, 46 samples of hyperplastic lesions, and 61 samples of cancerous lesions. Results Membranous (mEGFR) and cytoplasmic (cEGFR) EGFR expression was significantly different between the analyzed groups. The differences were most striking in the suprabasal-transforming zone. IHC evaluation showed that high and low mEGFR staining contributed to the differentiation of dysplastic lesions, simple hyperplasia, and cancerous tissue, as well as between different degrees of atypia in hyperplastic lesions (P?tissue, EGFR gene amplification was found in 8/50 samples. EGFR gene amplification was found in preinvasive cancer in one patient. In invasive carcinomas, gene amplification was not associated with stage or grade. Carcinomas with gene amplification showed significantly higher cEGFR expression (basal layer P?=?0.003; suprabasal layer P?=?0.002). Conclusions This study confirmed an increase in EGFR protein expression and gene amplification with the increase in biological aggressiveness of glottic lesions. A correlation between EGFR gene amplification and protein expression was established. Gene amplification proved to be an early event in glottic carcinogenesis, indicating its importance for glottic cancer prevention, early detection, and protocol selection. PMID:19673037

Braut, Tamara; Krstulja, Mira; Kujundzic, Milodar; Manestar, Dubravko; Hadzisejdic, Ita; Jonjic, Nives; Grahovac, Blazenka; Manestar, Darko

2009-01-01

60

Expression of small breast epithelial mucin (SBEM) protein in tissue microarrays (TMAs) of primary invasive breast cancers  

PubMed Central

Aims Small breast epithelial mucin (SBEM) is a recently described gene product that shows promise as a new breast biomarker. The aim was to investigate for the first time SBEM protein expression in a large cohort (n = 300) of invasive breast cancers, its relationship to established clinical variables and its association with clinical outcome. Methods and results Immunohistochemical analysis was performed on tissue microarrays consisting of 149 oestrogen receptor (ER) ?? and 151 ER?+ breast cancers. Overall, 18% of tumours were SBEM+ (n = 53/300). However, SBEM protein was more frequently observed in ER? (22%) than in ER+ cancers (13%; P = 0.049). A significant association with psoriasin/S100A7 expression (P? 0.0001) was observed in the entire cohort. SBEM was also positively associated with HER-2 (P = 0.046) in ER? cancers, and increased levels of SBEM were strongly associated with higher tumour grade (P = 0.0015). Furthermore, SBEM expression showed a trend towards an association with reduced overall survival and relapse-free survival in the ER+ cohort (P = 0.063 and P = 0.072, respectively). Conclusions Our results suggest that SBEM may identify a unique subset of breast cancers with poor prognosis and may have future implications for therapeutic management of this disease. PMID:18269587

Skliris, G P; Hube, F; Gheorghiu, I; Mutawe, M M; Penner, C; Watson, P H; Murphy, L C; Leygue, E; Myal, Y

2008-01-01

61

Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue  

SciTech Connect

Acute progressive feed restriction (APFR) represents a specific form of caloric restriction in which feed availability is increasingly curtailed over a period of a few days to a few weeks. It is often used for control animals in toxicological and pharmacological studies on compounds causing body weight loss to equalize weight changes between experimental and control groups and thereby, intuitively, to also set their metabolic states to the same phase. However, scientific justification for this procedure is lacking. In the present study, we analyzed by microarrays the impact on hepatic gene expression in rats of two APFR regimens that caused identical diminution of body weight (19%) but differed slightly in duration (4 vs. 10 days). In addition, white adipose tissue (WAT) was also subjected to the transcriptomic analysis on day-4. The data revealed that the two regimens led to distinct patterns of differentially expressed genes in liver, albeit some major pathways of energy metabolism were similarly affected (particularly fatty acid and amino acid catabolism). The reason for the divergence appeared to be entrainment by the longer APFR protocol of peripheral oscillator genes, which resulted in derailment of circadian rhythms and consequent interaction of altered diurnal fluctuations with metabolic adjustments in gene expression activities. WAT proved to be highly unresponsive to the 4-day APFR as only 17 mRNA levels were influenced by the treatment. This study demonstrates that body weight is a poor proxy of metabolic state and that the customary protocols of feed restriction can lead to rhythm entrainment.

Pohjanvirta, Raimo [Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, P.O. Box 66, FI-00014, University of Helsinki (Finland); Finnish Food Safety Authority EVIRA, Research Unit of Kuopio, P.O. Box 92, FI-70701 Kuopio (Finland); National Public Health Institute, Laboratory of Toxicology, P.O. Box 95, FI-70701 Kuopio (Finland)], E-mail: raimo.pohjanvirta@helsinki.fi; Boutros, Paul C.; Moffat, Ivy D. [Department of Pharmacology, University of Toronto, MSB, Toronto, Ontario, M5S 1A8 (Canada); Linden, Jere; Wendelin, Dominique [Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, P.O. Box 66, FI-00014, University of Helsinki (Finland); Okey, Allan B. [Department of Pharmacology, University of Toronto, MSB, Toronto, Ontario, M5S 1A8 (Canada)

2008-07-01

62

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns  

PubMed Central

Background Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations. Results In this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster. Conclusions This study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis. PMID:21951653

2011-01-01

63

Progress on thermobrachytherapy surface applicator for superficial tissue disease  

NASA Astrophysics Data System (ADS)

This work reports the ongoing development of a combination applicator for simultaneous heating of superficial tissue disease using a 915 MHz DCC (dual concentric conductor) array and High Dose Rate (HDR) brachytherapy delivered via an integrated conformal catheter array. The progress includes engineering design changes in the waterbolus, DCC configurations and fabrication techniques of the conformal multilayer applicator. The dosimetric impact of the thin copper DCC array is also assessed. Steady state fluid dynamics of the new waterbolus bag indicates nearly uniform flow with less than 1°C variation across a large (19×32cm) bolus. Thermometry data of the torso phantom acquired with computer controlled movement of fiberoptic temperature probes inside thermal mapping catheters indicate feasibility of real time feedback control for the DCC array. MR (magnetic resonance) scans of a torso phantom indicate that the waterbolus thickness across the treatment area is controlled by the pressure applied by the surrounding inflatable airbladder and applicator securing straps. The attenuation coefficient of the DCC array was measured as 3+/- 0.001% and 2.95+/-0.03 % using an ion chamber and OneDose dosimeters respectively. The performance of the combination applicator on patient phantoms provides valuable feedback to optimize the applicator prior use in the patient clinic.

Arunachalam, Kavitha; Craciunescu, Oana I.; Maccarini, Paolo F.; Schlorff, Jaime L.; Markowitz, Edward; Stauffer, Paul R.

2009-02-01

64

Strategies for cell manipulation and skeletal tissue engineering using high-throughput polymer blend formulation and microarray techniques  

Microsoft Academic Search

A combination of high-throughput material formulation and microarray techniques were synergistically applied for the efficient analysis of the biological functionality of 135 binary polymer blends. This allowed the identification of cell-compatible biopolymers permissive for human skeletal stem cell growth in both in vitro and in vivo applications. The blended polymeric materials were developed from commercially available, inexpensive and well characterised

Ferdous Khan; Rahul S. Tare; Janos M. Kanczler; Richard O. C. Oreffo; Mark Bradley

2010-01-01

65

A gene expression profile for detection of sufficient tumour cells in breast tumour tissue: microarray diagnosis eligibility  

Microsoft Academic Search

BACKGROUND: Microarray diagnostics of tumour samples is based on measurement of prognostic and\\/or predictive gene expression profiles. Typically, diagnostic profiles have been developed using bulk tumour samples with a sufficient amount of tumour cells (usually >50%). Consequentially, a diagnostic results depends on the minimal percentage of tumour cells within a sample. Currently, tumour cell percentage is assessed by conventional histopathological

Paul Roepman; Arenda Schuurman; Leonie JMJ Delahaye; Anke T Witteveen; Arno N Floore; Annuska M Glas

2009-01-01

66

Single-step procedure for the isolation of proteins at near-native conditions from mammalian tissue for proteomic analysis on antibody microarrays.  

PubMed

The process of extracting comprehensive proteome representations is a crucial step for many proteomic studies. While antibody microarrays are an evolving and promising methodology in proteomics, the issue of protein extraction from tissues for this kind of analysis has never been addressed. Here, we describe a single-step extraction buffer for the isolation of proteins from mammalian tissues under native conditions in an effective and reproducible manner. Protein was extracted from cell lines BxPC-3 and SU.86.86, rat organs (pancreas, liver, heart and lung) and human pancreatic cancer tissues using several buffer systems that contained individual nonionic or zwitterionic detergents in comparison to commercial extraction buffers. Also, detergent combinations were used that included at least one polymeric phenylethylene glycol, a long-chain amidosulfobetaine, cholate and a zwitterionic detergent. Extracts were analyzed for protein quantity and quality. The detergent cocktails exhibited superior extraction capacity. Additionally, they demonstrated a substantially higher recovery of membrane and compartmental proteins as well as much better preservation of protein functionality. Also, they did not interfere with subsequent analysis steps such as labeling. In Western blot and antibody microarray assays, they outperformed the other buffer systems, indicating that they should also be useful for other types of proteomic studies. PMID:20047340

Alhamdani, Mohamed Saiel Saeed; Schröder, Christoph; Werner, Jens; Giese, Nathalia; Bauer, Andrea; Hoheisel, Jörg D

2010-02-01

67

DNA Microarrays  

NASA Astrophysics Data System (ADS)

Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

Nguyen, C.; Gidrol, X.

68

Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues  

PubMed Central

Background Large-scale gene expression analysis of post-mortem brain tissue offers unique opportunities for investigating genetic mechanisms of psychiatric and neurodegenerative disorders. On the other hand microarray data analysis associated with these studies is a challenging task. In this publication we address the issue of low RNA quality data and corresponding data analysis strategies. Results A detailed analysis of effects of post chip RNA quality on the measured abundance of transcripts is presented. Overall Affymetrix GeneChip data (HG-U133_AB and HG-U133_Plus_2.0) derived from ten different brain regions was investigated. Post chip RNA quality being assessed by 5'/3' ratio of housekeeping genes was found to introduce a well pronounced systematic noise into the measured transcript expression levels. According to this study RNA quality effects have: 1) a "random" component which is introduced by the technology and 2) a systematic component which depends on the features of the transcripts and probes. Random components mainly account for numerous negative correlations of low-abundant transcripts. These negative correlations are not reproducible and are mainly introduced by an increased relative level of noise. Three major contributors to the systematic noise component were identified: the first is the probe set distribution, the second is the length of mRNA species, and the third is the stability of mRNA species. Positive correlations reflect the 5'-end to 3'-end direction of mRNA degradation whereas negative correlations result from the compensatory increase in stable and 3'-end probed transcripts. Systematic components affect the expressed transcripts by introducing irrelevant gene correlations and can strongly influence the results of the main experiment. A linear model correcting the effect of RNA quality on measured intensities was introduced. In addition the contribution of a number of pre-mortem and post-mortem attributes to the overall detected RNA quality effect was investigated. Brain pH, duration of agonal stage, post-mortem interval before sampling and donor's age of death within considered limits were found to have no significant contribution. Conclusion Basic conclusions for data analysis in expression profiling study are as follows: 1) testing for RNA quality dependency should be included in the preprocessing of the data; 2) investigating inter-gene correlation without regard to RNA quality effects could be misleading; 3) data normalization procedures relying on housekeeping genes either do not influence the correlation structure (if 3'-end intensities are used) or increase it for negatively correlated transcripts (if 5'-end or median intensities are included in normalization procedure); 4) sample sets should be matched with regard to RNA quality; 5) RMA preprocessing is more sensitive to RNA quality effect, than MAS 5.0. PMID:18298816

Popova, Tatiana; Mennerich, Detlev; Weith, Andreas; Quast, Karsten

2008-01-01

69

Pulp and dentin tissue engineering and regeneration: current progress  

PubMed Central

Dental pulp tissue is vulnerable to infection. Entire pulp amputation followed by pulp-space disinfection and filling with an artificial rubber-like material is employed to treat the infection – commonly known as root-canal therapy. Regeneration of pulp tissue has been difficult as the tissue is encased in dentin without collateral blood supply except from the root apical end. However, with the advent of the concept of modern tissue engineering and the discovery of dental stem cells, regeneration of pulp and dentin has been tested. This article will review the early attempts to regenerate pulp tissue and the current endeavor of pulp and dentin tissue engineering, and regeneration. The prospective outcome of the current advancement in this line of research will be discussed. PMID:19761395

Huang, George TJ

2009-01-01

70

DNA microarray (spot) .  

E-print Network

1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

71

Recent progress in interfacial tissue engineering approaches for osteochondral defects.  

PubMed

This review provides a brief synopsis of the anatomy and physiology of the osteochondral interface, scaffold-based and non-scaffold based approaches for engineering both tissues independently as well as recent developments in the manufacture of gradient constructs. Novel manufacturing techniques and nanotechnology will be discussed with potential application in osteochondral interfacial tissue engineering. PMID:22677924

Castro, Nathan J; Hacking, S Adam; Zhang, Lijie Grace

2012-08-01

72

Fiber-based tissue engineering: Progress, challenges, and opportunities.  

PubMed

Tissue engineering aims to improve the function of diseased or damaged organs by creating biological substitutes. To fabricate a functional tissue, the engineered construct should mimic the physiological environment including its structural, topographical, and mechanical properties. Moreover, the construct should facilitate nutrients and oxygen diffusion as well as removal of metabolic waste during tissue regeneration. In the last decade, fiber-based techniques such as weaving, knitting, braiding, as well as electrospinning, and direct writing have emerged as promising platforms for making 3D tissue constructs that can address the abovementioned challenges. Here, we critically review the techniques used to form cell-free and cell-laden fibers and to assemble them into scaffolds. We compare their mechanical properties, morphological features and biological activity. We discuss current challenges and future opportunities of fiber-based tissue engineering (FBTE) for use in research and clinical practice. PMID:23195284

Tamayol, Ali; Akbari, Mohsen; Annabi, Nasim; Paul, Arghya; Khademhosseini, Ali; Juncker, David

2013-01-01

73

Molecular Profiling of Bladder Cancer Using cDNA Microarrays: Defining Histogenesis and Biological Phenotypes1  

Microsoft Academic Search

This study was designed to characterize the expression profiles of nine bladder cancer cell lines (T24, J82, 5637, HT1376, RT4, SCaBER, TCCSUP, UMUC-3, and HT1197) using cDNA microarrays (8976 genes and expressed sequence tags). Novel targets involved in bladder cancer progression of potential clinical relevance were validated by immunohis- tochemistry using tissue microarrays of primary bladder tumors (n 193 cases).

Marta Sanchez-Carbayo; Nicholas D. Socci; Elizabeth Charytonowicz; Minglan Lu; Michael Prystowsky; Geoffrey Childs; Carlos Cordon-Cardo

2002-01-01

74

[Recent research progress of decellularization of native tissues].  

PubMed

Biologic scaffold materials composed of extracellular matrix (ECM) are typically obtained in processes that involve decellularization of tissues or organs. Decellularized tissues and organs have been successfully used in a variety of tissue engineering/regenerative medicine applications. Preservation of the complex composition and three-dimensional ultrastructure of the ECM is highly desirable but it is recognized that all methods of decellularization result in disruption of the structure and potential loss of composition. The efficiency of cell removal from a tissue is dependent on the origin of the tissue and the physical, chemical, and enzymatic methods that are used. Each of these treatments affects the biochemical composition, tissue ultrastructure, and mechanical behavior of the remaining ECM scaffold, and all of the treatment methods affect the host response to the material as well. Tissue decellularization with preservation of ECM integrity and bioactivity can be optimized by making correct decisions regarding the agents and techniques utilized during processing. In this paper, the most commonly used decellularization methods are described, and consideration given to the effects of these methods upon the biologic scaffold material and recently described antigen removal strategy are presented. PMID:23198451

Dong, Jiaoming; Mo, Xiumei; Li, Yu; Chen, Dakai

2012-10-01

75

Progress and opportunities for tissue-engineered skin  

NASA Astrophysics Data System (ADS)

Tissue-engineered skin is now a reality. For patients with extensive full-thickness burns, laboratory expansion of skin cells to achieve barrier function can make the difference between life and death, and it was this acute need that drove the initiation of tissue engineering in the 1980s. A much larger group of patients have ulcers resistant to conventional healing, and treatments using cultured skin cells have been devised to restart the wound-healing process. In the laboratory, the use of tissue-engineered skin provides insight into the behaviour of skin cells in healthy skin and in diseases such as vitiligo, melanoma, psoriasis and blistering disorders.

MacNeil, Sheila

2007-02-01

76

Recent progress in the study of brown adipose tissue.  

PubMed

Brown adipose tissue in mammals plays a critical role in maintaining energy balance by thermogenesis, which means dissipating energy in the form of heat. It is held that in mammals, long-term surplus food intake results in energy storage in the form of triglyceride and may eventually lead to obesity. Stimulating energy-dissipating function of brown adipose tissue in human body may counteract fat accumulation. In order to utilize brown adipose tissue as a therapeutic target, the mechanisms underlying brown adipocyte differentiation and function should be better elucidated. Here we review the molecular mechanisms involved in brown adipose tissue development and thermogenesis, and share our thoughts on current challenges and possible future therapeutic approaches. PMID:22035495

Yao, Xuan; Shan, Shifang; Zhang, Ying; Ying, Hao

2011-01-01

77

Progress towards seamless tissue fusion for wound closure.  

PubMed

Tissue fusion shows great promise in creating the ideal wound closure;however devices and materials are still at an early stage of development.Energy-based closure methods, such as laser tissue welding, have proven that a thermal-mediated tissue fusion can result in a closure that is physiologically and mechanically seamless, and has sufficient tensile strength.However, the techniques are not easily reproducible and are not cost effective, and therefore they are not gaining wide acceptance. Nevertheless,the work of the scientists who have been exploring tissue welding has laid the foundation for more rapid development of new systems that can deliver energy more efficiently and with greater control. Some additional energy-based systems are available or are being developed that show great promise;however, clinical efficacy has yet to be demonstrated. PMID:15823594

Flock, Stephen T; Marchitto, Kevin S

2005-04-01

78

Progress and opportunities for tissue-engineered skin  

Microsoft Academic Search

Tissue-engineered skin is now a reality. For patients with extensive full-thickness burns, laboratory expansion of skin cells to achieve barrier function can make the difference between life and death, and it was this acute need that drove the initiation of tissue engineering in the 1980s. A much larger group of patients have ulcers resistant to conventional healing, and treatments using

Sheila MacNeil

2007-01-01

79

Tendon Tissue Engineering: Progress, Challenges, and Translation to the Clinic  

PubMed Central

The tissue engineering field has made great strides in understanding how different aspects of tissue engineered constructs (TECs) and the culture process affect final tendon repair. However, there remain significant challenges in developing strategies that will lead to a clinically effective and commercially successful product. In an effort to increase repair quality, a better understanding of normal development, and how it differs from adult tendon healing, may provide strategies to improve tissue engineering. As tendon tissue engineering continues to improve, the field needs to employ more clinically relevant models of tendon injury such as degenerative tendons. We need to translate successes to larger animal models to begin exploring the clinical implications of our treatments. By advancing the models used to validate our TECs, we can help convince our toughest customer, the surgeon, that our products will be clinically efficacious. As we address these challenges in musculoskeletal tissue engineering, the field still needs to address the commercialization of products developed in the laboratory. TEC commercialization faces numerous challenges because each injury and patient is unique. This review aims to provide tissue engineers with a summary of important issues related to engineering tendon repairs and potential strategies for producing clinically successful products. PMID:21625053

Shearn, Jason T.; Kinneberg, Kirsten R.C.; Dyment, Nathaniel A.; Galloway, Marc T.; Kenter, Keith; Wylie, Christopher; Butler, David L.

2013-01-01

80

Rat Mitochondrion-Neuron Focused Microarray (rMNChip) and Bioinformatics Tools for Rapid Identification of Differential Pathways in Brain Tissues  

PubMed Central

Mitochondrial function is of particular importance in brain because of its high demand for energy (ATP) and efficient removal of reactive oxygen species (ROS). We developed rat mitochondrion-neuron focused microarray (rMNChip) and integrated bioinformatics tools for rapid identification of differential pathways in brain tissues. rMNChip contains 1,500 genes involved in mitochondrial functions, stress response, circadian rhythms and signal transduction. The bioinformatics tool includes an algorithm for computing of differentially expressed genes, and a database for straightforward and intuitive interpretation for microarray results. Our application of these tools to RNA samples derived from rat frontal cortex (FC), hippocampus (HC) and hypothalamus (HT) led to the identification of differentially-expressed signal-transduction-bioenergenesis and neurotransmitter-synthesis pathways with a dominant number of genes (FC/HC = 55/6; FC/HT = 55/4) having significantly (p<0.05, FDR<10.70%) higher (?1.25 fold) RNA levels in the frontal cortex than the others, strongly suggesting active generation of ATP and neurotransmitters and efficient removal of ROS. Thus, these tools for rapid and efficient identification of differential pathways in brain regions will greatly facilitate our systems-biological study and understanding of molecular mechanisms underlying complex and multifactorial neurodegenerative diseases. PMID:21494430

Su, Yan A.; Zhang, Qiuyang; Su, David M.; Tang, Michael X.

2011-01-01

81

A progressive rupture model of soft tissue stress relaxation.  

PubMed

A striking feature of stress relaxation in biological soft tissue is that it frequently follows a power law in time with an exponent that is independent of strain even when the elastic properties of the tissue are highly nonlinear. This kind of behavior is an example of quasi-linear viscoelasticity, and is usually modeled in a purely empirical fashion. The goal of the present study was to account for quasi-linear viscoelasticity in mechanistic terms based on our previously developed hypothesis that it arises as a result of isolated micro-yield events occurring in sequence throughout the tissue, each event passing the stress it was sustaining on to other regions of the tissue until they themselves yield. We modeled stress relaxation computationally in a collection of stress-bearing elements. Each element experiences a stochastic sequence of either increases in elastic equilibrium length or decreases in stiffness according to the stress imposed upon it. This successfully predicts quasi-linear viscoelastic behavior, and in addition predicts power-law stress relaxation that proceeds at the same slow rate as observed in real biological soft tissue. PMID:23508634

Bates, Jason H T; Ma, Baoshun

2013-06-01

82

Microarrays for Undergraduate Classes  

ERIC Educational Resources Information Center

A microarray experiment is presented that, in six laboratory sessions, takes undergraduate students from the tissue sample right through to data analysis. The model chosen, the murine erythroleukemia cell line, can be easily cultured in sufficient quantities for class use. Large changes in gene expression can be induced in these cells by…

Hancock, Dale; Nguyen, Lisa L.; Denyer, Gareth S.; Johnston, Jill M.

2006-01-01

83

Tissue Engineering of Blood Vessels: Functional Requirements, Progress, and Future Challenges  

PubMed Central

Vascular disease results in the decreased utility and decreased availability of autologus vascular tissue for small diameter (< 6 mm) vessel replacements. While synthetic polymer alternatives to date have failed to meet the performance of autogenous conduits, tissue-engineered replacement vessels represent an ideal solution to this clinical problem. Ongoing progress requires combined approaches from biomaterials science, cell biology, and translational medicine to develop feasible solutions with the requisite mechanical support, a non-fouling surface for blood flow, and tissue regeneration. Over the past two decades interest in blood vessel tissue engineering has soared on a global scale, resulting in the first clinical implants of multiple technologies, steady progress with several other systems, and critical lessons-learned. This review will highlight the current inadequacies of autologus and synthetic grafts, the engineering requirements for implantation of tissue-engineered grafts, and the current status of tissue-engineered blood vessel research. PMID:23181145

Kumar, Vivek A.; Brewster, Luke P.; Caves, Jeffrey M.; Chaikof, Elliot L.

2012-01-01

84

Microarray-Based Capture of Novel Expressed Cell Type-Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster  

PubMed Central

Faithful annotation of tissue-specific transcript isoforms is important not only to understand how genes are organized and regulated but also to identify potential novel, unannotated exons of genes, which may be additional targets of mutation in disease states or while performing mutagenic screens. We have developed a microarray enrichment methodology followed by long-read, next-generation sequencing for identification of unannotated transcript isoforms expressed in two Drosophila tissues, the ovary and the testis. Even with limited sequencing, these studies have identified a large number of novel transcription units, including 5? exons and extensions, 3? exons and extensions, internal exons and exon extensions, gene fusions, and both germline-specific splicing events and promoters. Additionally, comparing our capture dataset with tiling array and traditional RNA-seq analysis, we demonstrate that our enrichment strategy is able to capture low-abundance transcripts that cannot readily be identified by the other strategies. Finally, we show that our methodology can help identify transcriptional signatures of minority cell types within the ovary that would otherwise be difficult to reveal without the CoNECT enrichment strategy. These studies introduce an efficient methodology for cataloging tissue-specific transcriptomes in which specific classes of genes or transcripts can be targeted for capture and sequence, thus reducing the significant sequencing depth normally required for accurate annotation. PMID:22908036

Hong, X.; Doddapaneni, H.; Comeron, J. M.; Rodesch, M. J.; Halvensleben, H. A.; Nien, C. Y.; Bolei, F.; Metpally, R.; Richmond, T. A.; Albert, T. J.; Manak, J. R.

2012-01-01

85

Numerical and Structural Genomic Aberrations Are Reliably Detectable in Tissue Microarrays of Formalin-Fixed Paraffin-Embedded Tumor Samples by Fluorescence In-Situ Hybridization  

PubMed Central

Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL) and six malignant mesothelioma (MM) samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches. PMID:24733537

Horn, Heike; Bausinger, Julia; Staiger, Annette M.; Sohn, Maximilian; Schmelter, Christopher; Gruber, Kim; Kalla, Claudia; Ott, M. Michaela; Rosenwald, Andreas; Ott, German

2014-01-01

86

Recent progresses in gene delivery-based bone tissue engineering.  

PubMed

Gene therapy has converged with bone engineering over the past decade, by which a variety of therapeutic genes have been delivered to stimulate bone repair. These genes can be administered via in vivo or ex vivo approach using either viral or nonviral vectors. This article reviews the fundamental aspects and recent progresses in the gene therapy-based bone engineering, with emphasis on the new genes, viral vectors and gene delivery approaches. PMID:23994567

Lu, Chia-Hsin; Chang, Yu-Han; Lin, Shih-Yeh; Li, Kuei-Chang; Hu, Yu-Chen

2013-12-01

87

Pathomechanisms: homeostatic chemokines in health, tissue regeneration, and progressive diseases.  

PubMed

Homeostatic chemokines control stem and progenitor cell migration and activation during vasculogenesis and organ development. They orchestrate hematopoietic stem cell (HSC) homing to their bone marrow niches and direct immature lymphocytes to a series of maturation sites within lymphoid organs. Along these lines, homeostatic chemokines regulate the niches of peripheral committed progenitor cell populations for tissue renewal. These biological functions support neovascularization and wound healing, including the recruitment of endothelial and other progenitor cells from the bone marrow. Here, we summarize the roles of homeostatic chemokines, their signaling receptors, and atypical decoy receptors during homeostasis and tissue regeneration in order to better understand their pathogenic roles in disease, for example, in diabetes complications, cancer, autoimmunity, epithelial hyperplasia, or hypertrophic scarring and fibrosis. PMID:24440002

Anders, Hans-Joachim; Romagnani, Paola; Mantovani, Alberto

2014-03-01

88

[Bone and soft tissue tumors--progress in this decade].  

PubMed

Conventional plain film roentgenography is the basic examination of bone tumors. Modern digital roentgenography offers technical innovations but no fundamental new diagnostic dimensions. Computerized and magnetic resonance-tomography allow a far better delineation of the tumor spread (staging). These new imaging methods together with ultrasound have revolutionized the diagnosis of soft tissue neoplasms, not visible on plain film roentgenograms except lipomas and calcifications. PMID:3431245

Wenz, W; Hofmann, E; Schmidt, W; Richter, G; Adler, C P

1987-01-01

89

Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis.  

PubMed

Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851. PMID:24687888

Kume, Hideaki; Muraoka, Satoshi; Kuga, Takahisa; Adachi, Jun; Narumi, Ryohei; Watanabe, Shio; Kuwano, Masayoshi; Kodera, Yoshio; Matsushita, Kazuyuki; Fukuoka, Junya; Masuda, Takeshi; Ishihama, Yasushi; Matsubara, Hisahiro; Nomura, Fumio; Tomonaga, Takeshi

2014-06-01

90

Pax-5 immunoexpression in various types of benign and malignant tumours: a high-throughput tissue microarray analysis  

PubMed Central

Background Pax?5 belongs to the Pax gene family transcription factors that play an important role in organogenesis and in B cell ontogeny. It is expressed in B cell non?Hodgkin's lymphoma (B?NHL), Hodgkin's lymphoma (HL) and neuroendocrine carcinomas. However, its expression in other tumour types is not fully explored. Aims and methods To determine Pax?5 expression in other tumour types, immunohistochemistry was performed on 3758 benign and malignant tumours using multiple tumour microarrays, as well as on whole sections. Results Pax?5 was expressed in 108/118 (91.5%) B?NHLs, in 60/70 (85.7%) HLs and in 0/7 T cell lymphomas. In addition, Pax?5 was seen in 24/34 (70.6%) Merkel cell carcinomas, 42/53 (79.2%) small cell carcinomas, 1/164 (0.6%) breast carcinomas, 2/204 (1%) endometrial adenocarcinomas and 1/452 (0.2%) urothelial carcinoma of the bladder. Conclusion Despite its expression in a small subset of malignancies of epithelial origin, Pax?5 is still a good and reliable immunomarker in diagnosing B?NHL, HL and neuroendocrine carcinomas. PMID:16837628

Mhawech-Fauceglia, Paulette; Saxena, Rhakee; Zhang, Shaozeng; Terracciano, Luigi; Sauter, Guido; Chadhuri, Arundhuti; Herrmann, Francois R; Penetrante, Remedios

2007-01-01

91

A decade of progress in adipose tissue macrophage biology.  

PubMed

One decade has passed since seminal publications described macrophage infiltration into adipose tissue (AT) as a key contributor to inflammation and obesity-related insulin resistance. Currently, a PubMed search for 'adipose tissue inflammation' reveals over 3500 entries since these original reports. We now know that resident macrophages in lean AT are alternatively activated, M2-like, and play a role in AT homeostasis. In contrast, the macrophages in obese AT are dramatically increased in number and are predominantly classically activated, M1-like, and promote inflammation and insulin resistance. Mediators of AT macrophage (ATM) phenotype include adipokines and fatty acids secreted from adipocytes as well as cytokines secreted from other immune cells in AT. There are several mechanisms that could explain the large increase in ATMs in obesity. These include recruitment-dependent mechanisms such as adipocyte death, chemokine release, and lipolysis of fatty acids. Newer evidence also points to recruitment-independent mechanisms such as impaired apoptosis, increased proliferation, and decreased egress. Although less is known about the homeostatic function of M2-like resident ATMs, recent evidence suggests roles in AT expansion, thermoregulation, antigen presentation, and iron homeostasis. The field of immunometabolism has come a long way in the past decade, and many exciting new discoveries are bound to be made in the coming years that will expand our understanding of how AT stands at the junction of immune and metabolic co-regulation. PMID:25319332

Hill, Andrea A; Reid Bolus, W; Hasty, Alyssa H

2014-11-01

92

Friend leukaemia integration-1 expression in malignant and benign tumours: a multiple tumour tissue microarray analysis using polyclonal antibody  

PubMed Central

Background Friend leukaemia integration?1 (FLI?1) antibody is a useful marker for Ewing's sarcoma/primitive neuroectodermal tumour (EWS/PNET) and vascular tumours. However, it is also expressed in subsets of lymphoblastic lymphoma, Merkel cell carcinoma (MCC) and desmoplastic small round cell tumour (DSRCT). Aim To determine expression of FLI?1 in various benign and malignant neoplasms, by immunohistochemical analysis on 4323 tumours using multiple tumour microarrays, as well as on whole sections. Results FLI?1 was expressed in 46/62 EWS/PNETs, 2/3 olfactory neuroblastomas, 7/102 small cell carcinomas of the lung, 10/34 MCCs, 1/14 rhabdomyosarcoma, 19/132 non?Hodgkin's lymphomas, 2/3 DSRCTs, and in 53/74 benign and malignant vascular tumours. In addition, 27/508 squamous cell carcinomas, 19/837 adenocarcinomas, 10/400 urothelial bladder cancers, 1/40 basal cell carcinomas, 3/29 liposarcomas, 1/40 glioblastoma multiforme and 9/29 medullar carcinomas of the breast expressed FLI?1. The sensitivity and specificity of FLI?1 to distinguish EWS/PNET from all types of malignancies were 74.2% and 96.0%, respectively. Finally, the sensitivity and specificity of FLI?1 to distinguish EWS/PNET from other small round cell tumours (SRCTs) were 74.2% and 91.6%, respectively. Conclusion This study was the first to show that FLI?1 can be seen in a variety of solid tumours, some of which had never been explored before. This finding should be kept in mind, especially when using FLI?1 as a marker for finding the primary origin of poorly differentiated metastatic tumour. Finally, despite the expression of FLI?1 in numerous malignancies, it is still considered to be highly sensitive and specific in distinguishing EWS/PNET from other tumour types in general and from other SRCTs in particular. PMID:16917000

Mhawech-Fauceglia, Paulette; Herrmann, Francois R; Bshara, Wiam; Odunsi, Kunle; Terracciano, Luigi; Sauter, Guido; Cheney, Richard T; Groth, Jeff

2007-01-01

93

Brachyury, SOX-9, and Podoplanin, New Markers in the Skull Base Chordoma Vs Chondrosarcoma Differential: A Tissue Microarray Based Comparative Analysis  

PubMed Central

The distinction between chondrosarcoma and chordoma of the skull base/head and neck is prognostically important; however, both have sufficient morphologic overlap to make distinction difficult. As a result of gene expression studies, additional candidate markers have been proposed to help in this distinction. Hence, we sought to evaluate the performance of new markers: brachyury, SOX-9, and podoplanin alongside the more traditional markers glial fibrillary acid protein, carcinoembryonic antigen, CD24 and epithelial membrane antigen. Paraffin blocks from 103 skull base/head and neck chondroid tumors from 70 patients were retrieved (1969-2007). Diagnoses were made based on morphology and/or whole section immunohistochemistry for cytokeratin and S100 protein yielding 79 chordomas (comprising 45 chondroid chordomas and 34 conventional chordomas), and 24 chondrosarcomas. A tissue microarray containing 0.6 mm cores of each tumor in triplicate was constructed using a manual array (MTA-1, Beecher Instruments). For visualization of staining, the ImmPRESS detection system (Vector Laboratories) with 2 - diaminobenzidine substrate was used. Sensitivities and specificities were calculated for each marker. Core loss from the microarray ranged from 25-29% yielding 66-78 viable cases per stain. The classic marker, cytokeratin, still has the best performance characteristics. When combined with brachyury, accuracy improves slightly (sensitivity and specificity for detection of chordoma 98% and 100%, respectively). Positivity for both epithelial membrane antigen and AE1/AE3 had a sensitivity of 90% and a specificity of 100% for detecting chordoma in this study. SOX-9 is apparently common to both notochordal and cartilaginous differentiation, and is not useful in the chordoma-chondrosarcoma differential diagnosis. Glial fibrillary acid protein, carcinoembryonic antigen, CD24, and epithelial membrane antigen did not outperform other markers, and are less useful in the diagnosis of chordoma versus chondrosarcoma. Podoplanin still remains the only positive marker for chondrosarcoma, though its accuracy is less than previously reported. PMID:18820665

Oakley, GJ; Fuhrer, K; Seethala, RR

2014-01-01

94

Towards high-throughput FLIM for protein-protein interaction screening of live cells and tissue microarrays  

Microsoft Academic Search

Studying cellular protein-protein interactions in situ requires a technique such as fluorescence resonance energy transfer (FRET) which is sensitive on the nanometer scale. Observing FRET is significantly simplified if the fluorescence lifetime of the donor can be monitored. Results from live cells and tissue micro arrays are presented from an automated microscope incorporating time-domain TCSPC fluorescence lifetime imaging (FLIM). Novel

Paul R. Barber; Glenn P. Pierce; Simon M. Ameer-beg; Dan R. Matthews; Leo M. Carlin; Melanie Keppler; Muireann Kelleher; Frederick Festy; Cheryll Gillett; Robert Springall; Tony C. Ng; Borivoj Vojnovic

2008-01-01

95

Evaluation of Ki67 Expression across Distinct Categories of Breast Cancer Specimens: A Population-Based Study of Matched Surgical Specimens, Core Needle Biopsies and Tissue Microarrays  

PubMed Central

Introduction Tumor cell proliferation in breast cancer is strongly prognostic and may also predict response to chemotherapy. However, there is no consensus on counting areas or cut-off values for patient stratification. Our aim was to assess the matched level of proliferation by Ki67 when using different tissue categories (whole sections, WS; core needle biopsies, CNB; tissue microarrays, TMA), and the corresponding prognostic value. Methods We examined a retrospective, population-based series of breast cancer (n?=?534) from the Norwegian Breast Cancer Screening Program. The percentage of Ki67 positive nuclei was evaluated by visual counting on WS (n?=?534), CNB (n?=?154) and TMA (n?=?459). Results The median percentage of Ki67 expression was 18% on WS (hot-spot areas), 13% on CNB, and 7% on TMA, and this difference was statistically significant in paired cases. Increased Ki67 expression by all evaluation methods was associated with aggressive tumor features (large tumor diameter, high histologic grade, ER negativity) and reduced patient survival. Conclusion There is a significant difference in tumor cell proliferation by Ki67 across different sample categories. Ki67 is prognostic over a wide range of cut-off points and for different sample types, although Ki67 results derived from TMA sections are lower compared with those obtained using specimens from a clinical setting. Our findings indicate that specimen specific cut-off values should be applied for practical use. PMID:25375149

Knutsvik, G?ril; Stefansson, Ingunn M.; Aziz, Sura; Arnes, Jarle; Eide, Johan; Collett, Karin; Akslen, Lars A.

2014-01-01

96

Different detectability of cyclooxygenase-2 (COX-2) protein in standard paraffin sections and tissue microarrays of human melanomas and naevi - Comparative study.  

PubMed

Cyclooxygenase-2 (COX-2), overexpressed in many types of human cancer, may be a valuable marker for human melanoma. However, there are discrepancies between expression levels detected by different groups. The majority of the studies were carried out using standard paraffin sections. Tissue microarrays (TMAs) might enable analysis of COX-2 expression in numerous lesions. Our study assesses to what extent reprocessing of tissue samples used for preparing TMAs may influence reproducibility of data obtained for standard sections. The study included TMAs and standard histopathologic sections. COX-2 was detected by immunohistochemistry with two primary antibodies targeting different epitopes. COX-2 expression levels detected with both antibodies in standard sections were similar as in our previous study. Surprisingly, results obtained in TMAs were significantly different. While one of the antibodies yielded for TMAs results similar to standard sections, COX-2 expression levels found with the second antibody were very low and expression patterns strikingly different from those observed for standard sections and for both TMAs studied with the first antibody. Good performance of the antibodies found in standard sections of human skin and melanocytic lesions does not guarantee similar results in TMAs. The finding discloses a new aspect of immunohistochemical assays involving TMAs. PMID:24878108

Ku?bicki, Lukasz; Urban, Justyna; Chwirot, Barbara W

2014-09-01

97

A microarray analysis of sexual dimorphism of adipose tissues in high-fat-diet-induced obese mice  

Microsoft Academic Search

Objective:A sexual dimorphism exists in body fat distribution; females deposit relatively more fat in subcutaneous\\/inguinal depots whereas males deposit more fat in the intra-abdominal\\/gonadal depot. Our objective was to systematically document depot- and sex-related differences in the accumulation of adipose tissue and gene expression, comparing differentially expressed genes in diet-induced obese mice with mice maintained on a chow diet.Research Design

K L Grove; S K Fried; A S Greenberg; X Q Xiao; D J Clegg

2010-01-01

98

Applications of condensed matter understanding to medical tissues and disease progression: Elemental analysis and structural integrity of tissue scaffolds  

NASA Astrophysics Data System (ADS)

The investigations reported herein link tissue structure and elemental presence with issues of environmental health and disease, exemplified by uptake and storage of potentially toxic elements in the body, the osteoarthritic condition and malignancy in the breast and other soft tissues. Focus is placed on application of state-of-the-art ionizing radiation techniques, including, micro-synchrotron X-ray fluorescence (?-SXRF) and particle-induced X-ray emission/Rutherford backscattering mapping (?-PIXE/RBS), coherent small-angle X-ray scattering (cSAXS) and X-ray phase-contrast imaging, providing information on elemental make-up, the large-scale organisation of collagen and anatomical features of moderate and low atomic number media. For the particular situations under investigation, use of such facilities is allowing information to be obtained at an unprecedented level of detail, yielding new understanding of the affected tissues and the progression of disease.

Bradley, D. A.; Farquharson, M. J.; Gundogdu, O.; Al-Ebraheem, Alia; Che Ismail, Elna; Kaabar, W.; Bunk, O.; Pfeiffer, F.; Falkenberg, G.; Bailey, M.

2010-02-01

99

Potential Upstream Regulators of Cannabinoid Receptor 1 Signaling in Prostate Cancer: A Bayesian Network Analysis of Data From a Tissue Microarray  

PubMed Central

BACKGROUND The endocannabinoid system regulates cancer cell proliferation, and in prostate cancer a high cannabinoid CB1 receptor expression is associated with a poor prognosis. Down-stream mediators of CB1 receptor signaling in prostate cancer are known, but information on potential upstream regulators is lacking. RESULTS Data from a well-characterized tumor tissue microarray were used for a Bayesian network analysis using the max-min hill-climbing method. In non-malignant tissue samples, a directionality of pEGFR (the phosphorylated form of the epidermal growth factor receptor) ? CB1 receptors were found regardless as to whether the endocannabinoid metabolizing enzyme fatty acid amide hydrolase (FAAH) was included as a parameter. A similar result was found in the tumor tissue, but only when FAAH was included in the analysis. A second regulatory pathway, from the growth factor receptor ErbB2 ? FAAH was also identified in the tumor samples. Transfection of AT1 prostate cancer cells with CB1 receptors induced a sensitivity to the growth-inhibiting effects of the CB receptor agonist CP55,940. The sensitivity was not dependent upon the level of receptor expression. Thus a high CB1 receptor expression alone does not drive the cells towards a survival phenotype in the presence of a CB receptor agonist. CONCLUSIONS The data identify two potential regulators of the endocannabinoid system in prostate cancer and allow the construction of a model of a dysregulated endocannabinoid signaling network in this tumor. Further studies should be designed to test the veracity of the predictions of the network analysis in prostate cancer and other solid tumors. Prostate 74:1107–1117, 2014. © 2014 The Authors. The Prostate published by Wiley Periodicals, Inc. PMID:24913716

Haggstrom, Jenny; Cipriano, Mariateresa; Forshell, Linus Plym; Persson, Emma; Hammarsten, Peter; Stella, Nephi; Fowler, Christopher J

2014-01-01

100

Distribution of p63, cytokeratins 5\\/6 and cytokeratin 14 in 51 normal and 400 neoplastic human tissue samples using TARP4 multi-tumor tissue microarray  

Microsoft Academic Search

p63, cytokeratin (CK) 5\\/6 and CK 14 have been employed in diagnostic pathology as markers of basal, squamous and myoepithelial differentiation in several types of human neoplasms; however, there is scant data on the concurrent expression of these markers in large series of human neoplasms. We analyzed the distribution of these three immunohistochemical markers in 51 normal human tissue samples,

Jorge S. Reis-Filho; Pete T. Simpson; Albino Martins; Ana Preto; Fátima Gärtner; Fernando C. Schmitt

2003-01-01

101

RUNX2 correlates with subtype-specific breast cancer in a human tissue microarray, and ectopic expression of Runx2 perturbs differentiation in the mouse mammary gland  

PubMed Central

RUNX2, a master regulator of osteogenesis, is oncogenic in the lymphoid lineage; however, little is known about its role in epithelial cancers. Upregulation of RUNX2 in cell lines correlates with increased invasiveness and the capacity to form osteolytic disease in models of breast and prostate cancer. However, most studies have analysed the effects of this gene in a limited number of cell lines and its role in primary breast cancer has not been resolved. Using a human tumour tissue microarray, we show that high RUNX2 expression is significantly associated with oestrogen receptor (ER)/progesterone receptor (PR)/HER2-negative breast cancers and that patients with high RUNX2 expression have a poorer survival rate than those with negative or low expression. We confirm RUNX2 as a gene that has a potentially important functional role in triple-negative breast cancer. To investigate the role of this gene in breast cancer, we made a transgenic model in which Runx2 is specifically expressed in murine mammary epithelium under the control of the mouse mammary tumour virus (MMTV) promoter. We show that ectopic Runx2 perturbs normal development in pubertal and lactating animals, delaying ductal elongation and inhibiting lobular alveolar differentiation. We also show that the Runx2 transgene elicits age-related, pre-neoplastic changes in the mammary epithelium of older transgenic animals, suggesting that elevated RUNX2 expression renders such tissue more susceptible to oncogenic changes and providing further evidence that this gene might have an important, context-dependent role in breast cancer. PMID:24626992

McDonald, Laura; Ferrari, Nicola; Terry, Anne; Bell, Margaret; Mohammed, Zahra M.; Orange, Clare; Jenkins, Alma; Muller, William J.; Gusterson, Barry A.; Neil, James C.; Edwards, Joanne; Morris, Joanna S.; Cameron, Ewan R.; Blyth, Karen

2014-01-01

102

Adipose tissue dysfunction tracks disease progression in two Huntington's disease mouse models  

PubMed Central

In addition to the hallmark neurological manifestations of Huntington's disease (HD), weight loss with metabolic dysfunction is often observed in the later stages of disease progression and is associated with poor prognosis. The mechanism for weight loss in HD is unknown. Using two mouse models of HD, the R6/2 transgenic and CAG140 knock-in mouse strains, we demonstrate that adipose tissue dysfunction is detectable at early ages and becomes more pronounced as the disease progresses. Adipocytes acquire a ‘de-differentiated’ phenotype characterized by impaired expression of fat storage genes. In addition, HD mice exhibit reduced levels of leptin and adiponectin, adipose tissue-derived hormones that regulate food intake and glucose metabolism. Importantly, some of these changes occur prior to weight loss and development of some of the characteristic neurological symptoms. We demonstrate that impaired gene expression and lipid accumulation in adipocytes can be recapitulated by expression of an inducible mutant huntingtin transgene in an adipocyte cell line and that mutant huntingtin inhibits transcriptional activity of the PGC-1? co-activator in adipocytes, which may contribute to aberrant gene expression. Thus, our findings indicate that mutant huntingtin has direct detrimental effects in cell types other than neurons. The results also indicate that circulating adipose-tissue-derived hormones may be accessible markers for HD prognosis and progression and suggest that adipose tissue may be a useful therapeutic target to improve standard of life for HD patients. PMID:19124532

Phan, Jack; Hickey, Miriam A.; Zhang, Peixiang; Chesselet, Marie-Francoise; Reue, Karen

2009-01-01

103

Clinical utility of microarrays: current status, existing challenges and future outlook.  

PubMed

Microarray-based clinical tests have become powerful tools in the diagnosis and treatment of diseases. In contrast to traditional DNA-based tests that largely focus on single genes associated with rare conditions, microarray-based tests are ideal for the study of diseases with underlying complex genetic causes. Several microarray based tests have been translated into clinical practice such as MammaPrint and AmpliChip CYP450. Additional cancer-related microarray-based tests are either in the process of FDA review or under active development, including Tissue of Tumor Origin and AmpliChip p53. All diagnostic microarray testing is ordered by physicians and tested by a Clinical Laboratories Improvement Amendment-certified (CLIA) reference laboratory. Recently, companies offering consumer based microarray testing have emerged. Individuals can order tests online and service providers deliver the results directly to the clients via a password-protected secure website. Navigenics, 23andMe and deCODE Genetics represent pioneering companies in this field. Although the progress of these microarray-based tests is extremely encouraging with the potential to revolutionize the recognition and treatment of common diseases, these tests are still in their infancy and face technical, clinical and marketing challenges. In this article, we review microarray-based tests which are currently approved or under review by the FDA, as well as the consumer-based testing. We also provide a summary of the challenges and strategic solutions in the development and clinical use of the microarray-based tests. Finally, we present a brief outlook for the future of microarray-based clinical applications. PMID:19506735

Li, Xinmin; Quigg, Richard J; Zhou, Jian; Gu, Weikuan; Nagesh Rao, P; Reed, Elaine F

2008-11-01

104

Recent Progress on Tissue-Resident Adult Stem Cell Biology and Their Therapeutic Implications  

PubMed Central

Recent progress in the field of the stem cell research has given new hopes to treat and even cure diverse degenerative disorders and incurable diseases in human. Particularly, the identification of a rare population of adult stem cells in the most tissues/organs in human has emerged as an attractive source of multipotent stem/progenitor cells for cell replacement-based therapies and tissue engineering in regenerative medicine. The tissue-resident adult stem/progenitor cells offer the possibility to stimulate their in vivo differentiation or to use their ex vivo expanded progenies for cell replacement-based therapies with multiple applications in human. Among the human diseases that could be treated by the stem cell-based therapies, there are hematopoietic and immune disorders, multiple degenerative disorders, such as Parkinson’s and Alzeimeher’s diseases, type 1 or 2 diabetes mellitus as well as eye, liver, lung, skin and cardiovascular disorders and aggressive and metastatic cancers. In addition, the genetically-modified adult stem/progenitor cells could also be used as delivery system for expressing the therapeutic molecules in specific damaged areas of different tissues. Recent advances in cancer stem/progenitor cell research also offer the possibility to targeting these undifferentiated and malignant cells that provide critical functions in cancer initiation and progression and disease relapse for treating the patients diagnosed with the advanced and metastatic cancers which remain incurable in the clinics with the current therapies. PMID:18288619

2013-01-01

105

Microarray analysis of thioacetamide-treated type 1 diabetic rats  

SciTech Connect

It is well known that diabetes imparts high sensitivity to numerous hepatotoxicants. Previously, we have shown that a normally non-lethal dose of thioacetamide (TA, 300 mg/kg) causes 90% mortality in type 1 diabetic (DB) rats due to inhibited tissue repair allowing progression of liver injury. On the other hand, DB rats exposed to 30 mg TA/kg exhibit delayed tissue repair and delayed recovery from injury. The objective of this study was to investigate the mechanism of impaired tissue repair and progression of liver injury in TA-treated DB rats by using cDNA microarray. Gene expression pattern was examined at 0, 6, and 12 h after TA challenge, and selected mechanistic leads from microarray experiments were confirmed by real-time RT-PCR and further investigated at protein level over the time course of 0 to 36 h after TA treatment. Diabetic condition itself increased gene expression of proteases and decreased gene expression of protease inhibitors. Administration of 300 mg TA/kg to DB rats further elevated gene expression of proteases and suppressed gene expression of protease inhibitors, explaining progression of liver injury in DB rats after TA treatment. Inhibited expression of genes involved in cell division cycle (cyclin D1, IGFBP-1, ras, E2F) was observed after exposure of DB rats to 300 mg TA/kg, explaining inhibited tissue repair in these rats. On the other hand, DB rats receiving 30 mg TA/kg exhibit delayed expression of genes involved in cell division cycle, explaining delayed tissue repair in these rats. In conclusion, impaired cyclin D1 signaling along with increased proteases and decreased protease inhibitors may explain impaired tissue repair that leads to progression of liver injury initiated by TA in DB rats.

Devi, Sachin S. [Department of Toxicology, College of Pharmacy, University of Louisiana at Monroe, 700 University Ave, Sugar Hall 306, Monroe, LA 71209-0470 (United States); Mehendale, Harihara M. [Department of Toxicology, College of Pharmacy, University of Louisiana at Monroe, 700 University Ave, Sugar Hall 306, Monroe, LA 71209-0470 (United States)]. E-mail: mehendale@ulm.edu

2006-04-01

106

Tissue Transglutaminase (TG2)-Induced Inflammation in Initiation, Progression, and Pathogenesis of Pancreatic Cancer  

PubMed Central

Pancreatic cancer (PC) is among the deadliest cancers, with a median survival of six months. It is generally believed that infiltrating PC arises through the progression of early grade pancreatic intraepithelial lesions (PanINs). In one model of the disease, the K-ras mutation is an early molecular event during progression of pancreatic cancer; it is followed by the accumulation of additional genetic abnormalities. This model has been supported by animal studies in which activated K-ras and p53 mutations produced metastatic pancreatic ductal adenocarcinoma in mice. According to this model, oncogenic K-ras induces PanIN formation but fails to promote the invasive stage. However, when these mice are subjected to caerulein treatment, which induces a chronic pancreatitis-like state and inflammatory response, PanINs rapidly progress to invasive carcinoma. These results are consistent with epidemiologic studies showing that patients with chronic pancreatitis have a much higher risk of developing PC. In line with these observations, recent studies have revealed elevated expression of the pro-inflammatory protein tissue transglutaminase (TG2) in early PanINs, and its expression increases even more as the disease progresses. In this review we discuss the implications of increased TG2 expression in initiation, progression, and pathogenesis of pancreatic cancer. PMID:24212645

Mehta, Kapil; Han, Amy

2011-01-01

107

Tissue mechanics modulate microRNA-dependent PTEN expression to regulate malignant progression  

PubMed Central

Tissue mechanics regulate development and homeostasis and are consistently modified in tumor progression. Nevertheless, the fundamental molecular mechanisms through which altered mechanics regulate tissue behavior and the clinical relevance of these changes remain unclear. We demonstrate that increased matrix stiffness modulates microRNA expression to drive tumor progression through integrin activation of ?-catenin and MYC. Specifically, in human and mouse tissue, increased matrix stiffness induced miR-18a to reduce levels of the tumor suppressor PTEN, both directly and indirectly by decreasing levels of HOXA9. Clinically, extracellular matrix stiffness correlated significantly with miR-18a in human breast tumor biopsies. miR-18a expression was highest in basal-like breast cancers in which PTEN and HOXA9 levels were lowest and predicted for poor prognosis in patients with luminal breast cancers. Our findings identify a mechanically-regulated microRNA circuit that can promote malignancy and suggest potential prognostic roles for HOXA9 and miR-18a levels in stratifying patients with luminal breast cancers. PMID:24633304

Mouw, Janna K; Yui, Yoshihiro; Damiano, Laura; Bainer, Russell O; Lakins, Johnathan N; Acerbi, Irene; Ou, Guanqing; Wijekoon, Amanda C; Levental, Kandice R; Gilbert, Penney M; Chen, Yunn-Yi; Weaver, Valerie M

2014-01-01

108

Role of deregulated microRNAs in breast cancer progression using FFPE tissue.  

PubMed

MicroRNAs (miRNAs) contribute to cancer initiation and progression by silencing the expression of their target genes, causing either mRNA molecule degradation or translational inhibition. Intraductal epithelial proliferations of the breast are histologically and clinically classified into normal, atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). To better understand the progression of ductal breast cancer development, we attempt to identify deregulated miRNAs in this process using Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from breast cancer patients. Following tissue microdissection, we obtained 8 normal, 4 ADH, 6 DCIS and 7 IDC samples, which were subject to RNA isolation and miRNA expression profiling analysis. We found that miR-21, miR-200b/c, miR-141, and miR-183 were consistently up-regulated in ADH, DCIS and IDC compared to normal, while miR-557 was uniquely down-regulated in DCIS. Interestingly, the most significant miRNA deregulations occurred during the transition from normal to ADH. However, the data did not reveal a step-wise miRNA alteration among discrete steps along tumor progression, which is in accordance with previous reports of mRNA profiling of different stages of breast cancer. Furthermore, the expression of MSH2 and SMAD7, two important molecules involving TGF-? pathway, was restored following miR-21 knockdown in both MCF-7 and Hs578T breast cancer cells. In this study, we have not only identified a number of potential candidate miRNAs for breast cancer, but also found that deregulation of miRNA expression during breast tumorigenesis might be an early event since it occurred significantly during normal to ADH transition. Consequently, we have demonstrated the feasibility of miRNA expression profiling analysis using archived FFPE tissues, typically with rich clinical information, as a means of miRNA biomarker discovery. PMID:23372687

Chen, Liang; Li, Youhuai; Fu, Yebo; Peng, Jin; Mo, Meng-Hsuan; Stamatakos, Michael; Teal, Christine B; Brem, Rachel F; Stojadinovic, Alexander; Grinkemeyer, Michael; McCaffrey, Timothy A; Man, Yan-gao; Fu, Sidney W

2013-01-01

109

Progress in the development of a corneal replacement: keratoprostheses and tissue-engineered corneas.  

PubMed

Rapid progress has been made in the past 5 years in the development of corneal replacements. Traditionally they are divided into two categories, keratoprostheses and tissue-engineered corneal equivalents, as replacement tissues are increasingly in demand worldwide. There are currently several different keratoprosthesis models in clinical use around the world. The most popular and most widely publicized is the AlphaCor model, which has enjoyed significant clinical success. However, improvements remain to be made, and the aim of most of the current research is to better understand the interactions between a synthetic material and the surrounding biology on a more fundamental level. This improved understanding will no doubt lead to improvements in current models and to the development of new models in the near future. While tissue-engineered corneal equivalents have been under investigation for considerably less time, there is growing evidence to suggest that a tissue-engineered corneal equivalent comprised of primarily natural materials will exist in the not too distant future. Research groups have reported strong in vitro and in vivo results. The strength of the collagen matrix and its ability to support cell infiltration have been the primary avenues of research. Various collagen crosslinking techniques have been used. Infiltration of three major cells of the cornea has been observed. Most importantly, the ability of these materials to support nerve ingrowth has been demonstrated. While challenges remain with both types of corneal replacements, the considerable progress in the recent past suggests that reliable implants for the treatment of a variety of corneal diseases will be available. This review will provide an overview of recent results, and will provide insight into the future of research on corneal replacements. PMID:16359253

Duan, Derek; Klenkler, Bettina J; Sheardown, Heather

2006-01-01

110

A new paradigm in the periodontal disease progression: Gingival connective tissue remodeling with simultaneous collagen degradation and fibers thickening  

Microsoft Academic Search

Bacterial dental plaque is considered to be the main cause of periodontal diseases, but progression of the disease is also related to the host inflammatory response. The earliest affected tissue is the gingiva, but the specific mechanisms involved in the onset of this condition remain unclear. Frequently, collagen degradation is pointed as the main marker of periodontal disease progression, but

M. Lorencini; J. A. F. Silva; C. A. Almeida; A. Bruni-Cardoso; H. F. Carvalho; D. R. Stach-Machado

2009-01-01

111

Microarrays: Molecular allergology and nanotechnology for personalised medicine (II)  

Microsoft Academic Search

Progress in nanotechnology and DNA recombination techniques have produced tools for the diagnosis and investigation of allergy at molecular level. The most advanced examples of such progress are the microarray techniques, which have been expanded not only in research in the field of proteomics but also in application to the clinical setting.Microarrays of allergic components offer results relating to hundreds

J. M. Lucas

2010-01-01

112

MICROARRAY DATABASE RESOURCE FOR DESIGNING CUSTOM MICROARRAYS  

E-print Network

MICROARRAY DATABASE RESOURCE FOR DESIGNING CUSTOM MICROARRAYS By Ravi Shrikanth Gundlapalli M;#12;#12;DEDICATION This thesis is dedicated to my parents Mr. Subbarayudu Gundlapalli and Ms.Vijaya Kumari Gundlapalli whose love and support made this possible for me. iii #12;ACKNOWLEDGEMENTS I owe this work to many

Rouchka, Eric

113

Cellular origin of bladder neoplasia and tissue dynamics of its progression to invasive carcinoma.  

PubMed

Understanding how malignancies arise within normal tissues requires identification of the cancer cell of origin and knowledge of the cellular and tissue dynamics of tumour progression. Here we examine bladder cancer in a chemical carcinogenesis model that mimics muscle-invasive human bladder cancer. With no prior bias regarding genetic pathways or cell types, we prospectively mark or ablate cells to show that muscle-invasive bladder carcinomas arise exclusively from Sonic hedgehog (Shh)-expressing stem cells in basal urothelium. These carcinomas arise clonally from a single cell whose progeny aggressively colonize a major portion of the urothelium to generate a lesion with histological features identical to human carcinoma in situ. Shh-expressing basal cells within this precursor lesion become tumour-initiating cells, although Shh expression is lost in subsequent carcinomas. We thus find that invasive carcinoma is initiated from basal urothelial stem cells but that tumour cell phenotype can diverge significantly from that of the cancer cell of origin. PMID:24747439

Shin, Kunyoo; Lim, Agnes; Odegaard, Justin I; Honeycutt, Jared D; Kawano, Sally; Hsieh, Michael H; Beachy, Philip A

2014-05-01

114

Macro-Microarray  

NSDL National Science Digital Library

In this activity, learners explore the "nuts and bolts" of gene chips. Learners construct a simple model of a DNA microarray (also known as gene chips) and learn how microarrays can be used to identify and treat disease--including cancer. This resource includes references and an explanation of microarrays.

Yu, Julie

2007-01-01

115

Spectral Analysis of Normal and Malignant Microarray Tissue Sections Using a Novel Micro-optoelectricalmechanical System (Mod Pathol 2004; 17 Suppl 1: 358A)  

Microsoft Academic Search

Background: With light sources of increasingly broader ranges, spectral analysis of tissue sections has evolved from 2 wavelength image subtraction techniques to Raman near infra- red micro-spectroscopic mapping permitting discrimination of cell types & tissue patterns. We have developed & use a unique tuned light source based on micro-optoelectromechanical systems (MOEMS) with new algorithms for spectral microscopic analysis of normal

M Maggioni; G L Davis; F J Warner; F B Geshwind; A C Coppi; RA DeVerse

116

Tissue microarray detection of matrix metalloproteinases, in diseased tricuspid and bicuspid aortic valves with or without pathology of the ascending aorta  

Microsoft Academic Search

Objective: The degeneration of bicuspid aortic valve and its frequent association with ascending aortic pathology, point to a still unidentified genetic tissue defect with unknown mediators. Metalloproteinases (MMPs) are lytic enzymes that have been strongly implicated in aneurysm formation. The purpose of this study was to detect the presence of these enzymes in aortic valvular tissue in healthy and diseased

George J. Koullias; Dimitris P. Korkolis; Pars Ravichandran; Amanda Psyrri; Ioannis Hatzaras; John A. Elefteriades

2004-01-01

117

Transcriptional assessment by microarray analysis and large-scale meta-analysis of the metabolic capacity of cardiac and skeletal muscle tissues to cope with reduced nutrient availability in Gilthead Sea Bream (Sparus aurata L.).  

PubMed

The effects of nutrient availability on the transcriptome of cardiac and skeletal muscle tissues were assessed in juvenile gilthead sea bream fed with a standard diet at two feeding levels: (1) full ration size and (2) 70 % satiation followed by a finishing phase at the maintenance ration. Microarray analysis evidenced a characteristic transcriptomic profile for each muscle tissue following changes in oxidative capacity (heart?>?red skeletal muscle?>?white skeletal muscle). The transcriptome of heart and secondly that of red skeletal muscle were highly responsive to nutritional changes, whereas that of glycolytic white skeletal muscle showed less ability to respond. The highly expressed and nutritionally regulated genes of heart were mainly related to signal transduction and transcriptional regulation. In contrast, those of white muscle were enriched in gene ontology (GO) terms related to proteolysis and protein ubiquitination. Microarray meta-analysis using the bioinformatic tool Fish and Chips ( http://fishandchips.genouest.org/index.php ) showed the close association of a representative cluster of white skeletal muscle with some of cardiac and red skeletal muscle, and many GO terms related to mitochondrial function appeared to be common links between them. A second round of cluster comparisons revealed that mitochondria-related GOs also linked differentially expressed genes of heart with those of liver from cortisol-treated gilthead sea bream. These results show that mitochondria are among the first responders to environmental and nutritional stress stimuli in gilthead sea bream, and functional phenotyping of this cellular organelle is highly promising to obtain reliable markers of growth performance and well-being in this fish species. PMID:24626932

Calduch-Giner, Josep A; Echasseriau, Yann; Crespo, Diego; Baron, Daniel; Planas, Josep V; Prunet, Patrick; Pérez-Sánchez, Jaume

2014-08-01

118

Annotating nonspecific SAGE tags with microarray data.  

PubMed

SAGE (serial analysis of gene expression) detects transcripts by extracting short tags from the transcripts. Because of the limited length, many SAGE tags are shared by transcripts from different genes. Relying on sequence information in the general gene expression database has limited power to solve this problem due to the highly heterogeneous nature of the deposited sequences. Considering that the complexity of gene expression at a single tissue level should be much simpler than that in the general expression database, we reasoned that by restricting gene expression to tissue level, the accuracy of gene annotation for the nonspecific SAGE tags should be significantly improved. To test the idea, we developed a tissue-specific SAGE annotation database based on microarray data (). This database contains microarray expression information represented as UniGene clusters for 73 normal human tissues and 18 cancer tissues and cell lines. The nonspecific SAGE tag is first matched to the database by the same tissue type used by both SAGE and microarray analysis; then the multiple UniGene clusters assigned to the nonspecific SAGE tag are searched in the database under the matched tissue type. The UniGene cluster presented solely or at higher expression levels in the database is annotated to represent the specific gene for the nonspecific SAGE tags. The accuracy of gene annotation by this database was largely confirmed by experimental data. Our study shows that microarray data provide a useful source for annotating the nonspecific SAGE tags. PMID:16314072

Ge, Xijin; Jung, Yong-Chul; Wu, Qingfa; Kibbe, Warren A; Wang, San Ming

2006-01-01

119

Progress on ThermoBrachytherapy Surface Applicator for Superficial Tissue Diseases  

PubMed Central

This work reports the ongoing development of a combination applicator for simultaneous heating of superficial tissue disease using a 915 MHz DCC (dual concentric conductor) array and High Dose Rate (HDR) brachytherapy delivered via an integrated conformal catheter array. The progress includes engineering design changes in the waterbolus, DCC configurations and fabrication techniques of the conformal multilayer applicator. The dosimetric impact of the thin copper DCC array is also assessed. Steady state fluid dynamics of the new waterbolus bag indicates nearly uniform flow with less than 1°C variation across a large (19×32cm) bolus. Thermometry data of the torso phantom acquired with computer controlled movement of fiberoptic temperature probes inside thermal mapping catheters indicate feasibility of real time feedback control for the DCC array. MR (magnetic resonance) scans of a torso phantom indicate that the waterbolus thickness across the treatment area is controlled by the pressure applied by the surrounding inflatable airbladder and applicator securing straps. The attenuation coefficient of the DCC array was measured as 3± 0.001% and 2.95±0.03 % using an ion chamber and OneDose™ dosimeters respectively. The performance of the combination applicator on patient phantoms provides valuable feedback to optimize the applicator prior use in the patient clinic. PMID:24392196

Arunachalam, Kavitha; Craciunescu, Oana I.; Maccarini, Paolo F.; Schlorff, Jaime L.; Markowitz, Edward; Stauffer, Paul R.

2013-01-01

120

Helicobacter pylori and gastric mucosa-associated lymphoid tissue lymphoma: Recent progress in pathogenesis and management  

PubMed Central

Recent progress in the research regarding the molecular pathogenesis and management of gastric mucosa-associated lymphoid tissue (MALT) lymphoma is reviewed. In approximately 90% of cases, Helicobacter pylori (H. pylori) infection plays the causative role in the pathogenesis, and H. pylori eradication is nowadays the first-line treatment for this disease, which leads to complete disease remission in 50%-90% of cases. In H. pylori-dependent cases, microbe-generated immune responses, including interaction between B and T cells involving CD40 and CD40L co-stimulatory molecules, are considered to induce the development of MALT lymphoma. In H. pylori-independent cases, activation of the nuclear factor-?B pathway by oncogenic products of specific chromosomal translocations such as t(11;18)/API2-MALT1, or inactivation of tumor necrosis factor alpha-induced protein 3 (A20) are considered to contribute to the lymphomagenesis. Recently, a large-scale Japanese multicenter study confirmed that the long-term clinical outcome of gastric MALT lymphoma after H. pylori eradication is excellent. Treatment modalities for patients not responding to H. pylori eradication include a “watch and wait” strategy, radiotherapy, chemotherapy, rituximab immunotherapy, and a combination of these. Because of the indolent behavior of MALT lymphoma, second-line treatment should be tailored in consideration of the clinical stage and extent of the disease in each patient. PMID:24363507

Nakamura, Shotaro; Matsumoto, Takayuki

2013-01-01

121

Tissue microarray detection of matrix metalloproteinases in diseased tricuspid and bicuspid aortic valves with or without pathology of the ascending aorta  

Microsoft Academic Search

Abstract Objective: The degeneration of bicuspid aortic valve and its frequent association with ascending aortic pathology, point to a still unidentified genetic tissue defect with unknown,mediators. Metalloproteinases (MMPs) are lytic enzymes,that have been strongly implicated in aneurysm,formation. The purpose of this study was to detect the presence of these enzymes,in aortic valvular tissue in healthy and diseased aortic valves with

George J. Koullias; Dimitris P. KorkolisSUPaS; Pars Ravichandran; Amanda Psyrri; Ioannis Hatzaras; John A. Elefteriades

2010-01-01

122

DNA Microarray Fabrication  

NSDL National Science Digital Library

In this YouTube video, created by Southwest Center for Microsystems Education (SCME), viewers are introduced to the concept of DNA microarray fabrication. Specific topics include: non-contact printing process, photolithography process and maskless photolithography process. This is the third in a series of presentations on DNA microarrays. Supporting materials can be downloaded from the SCME website.

2014-07-03

123

Microarray Spot Synthesizer  

NSDL National Science Digital Library

The Microarray Spot Synthesizer, developed at Davidson College, is an electronic resource that permits faculty to generate simulated DNA microarray data for use in their teaching. The Spot Synthesizer is not intended to produce real data; its purpose is to enable teachers to help students improve their ability to work efficiently with experimental data by giving them practice with known outcomes.

A. Malcolm Campbell (Davidson College;Martin Genomics Program- Biology); William T. Hatfield (Davidson College;Biology Department); Laurie J. Heyer (Davidson College;Mathematics); Verna Miller Case (University of Miami ;)

2010-05-28

124

Microarray profiling of skeletal muscle tissues from equally obese, non-diabetic insulin-sensitive and insulin-resistant Pima Indians  

Microsoft Academic Search

  Abstract\\u000a \\u000a \\u000a Aims\\/hypothesis. We carried out global transcript profiling to identify differentially expressed skeletal muscle genes in insulin resistance,\\u000a a major risk factor for Type II (non-insulin-dependent) diabetes mellitus. This approach also complemented the ongoing genomic\\u000a linkage analyses to identify genes linked to insulin resistance and diabetes in Pima Indians.\\u000a \\u000a \\u000a \\u000a \\u000a Methods. We compared gene expression profiles of skeletal muscle tissues from

X. Yang; R. E. Pratley; S. Tokraks; C. Bogardus; P. A. Permana

2002-01-01

125

Microarray Technology: A Promising Tool in Nutrigenomics  

Microsoft Academic Search

Microarray technology is a powerful tool for the global evaluation of gene expression profiles in tissues and for understanding many of the factors controlling the regulation of gene transcription. This technique not only provides a considerable amount of information on markers and predictive factors that may potentially characterize a specific clinical picture, but also promises new applications for therapy. One

Andrea Masotti; Letizia Da Sacco; Gian Franco Bottazzo; Anna Alisi

2010-01-01

126

Factorial microarray analysis of zebrafish retinal development  

E-print Network

retina-specific Brg1- regulated genes that control cellular differentiation, we conducted a factorial microarray analysis. Gene expression profiles were compared from wild-type and yng retinas and stage, and begin synaptogenesis. The final product of retinal development is a complex neural tissue that conveys

Ma, Ping

127

DNA Microarrays An R Tutorial  

E-print Network

DNA Microarrays An R Tutorial Gene Expression Analysis & R Tutorial Weigang Qiu Department Expression Analysis & R Tutorial #12;DNA Microarrays An R Tutorial Outline 1 DNA Microarrays 2 An R Tutorial Weigang Qiu Gene Expression Analysis & R Tutorial #12;DNA Microarrays An R Tutorial Functional Genomics

Qiu, Weigang

128

Hidden Treasures in "Ancient" Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue  

PubMed Central

Objective: Novel statistical methods and increasingly more accurate gene annotations can transform “old” biological data into a renewed source of knowledge with potential clinical relevance. Here, we provide an in silico proof-of-concept by extracting novel information from a high-quality mRNA expression dataset, originally published in 2001, using state-of-the-art bioinformatics approaches. Methods: The dataset consists of histologically defined cases of lung adenocarcinoma (AD), squamous (SQ) cell carcinoma, small-cell lung cancer, carcinoid, metastasis (breast and colon AD), and normal lung specimens (203 samples in total). A battery of statistical tests was used for identifying differential gene expressions, diagnostic and prognostic genes, enriched gene ontologies, and signaling pathways. Results: Our results showed that gene expressions faithfully recapitulate immunohistochemical subtype markers, as chromogranin A in carcinoids, cytokeratin 5, p63 in SQ, and TTF1 in non-squamous types. Moreover, biological information with putative clinical relevance was revealed as potentially novel diagnostic genes for each subtype with specificity 93–100% (AUC?=?0.93–1.00). Cancer subtypes were characterized by (a) differential expression of treatment target genes as TYMS, HER2, and HER3 and (b) overrepresentation of treatment-related pathways like cell cycle, DNA repair, and ERBB pathways. The vascular smooth muscle contraction, leukocyte trans-endothelial migration, and actin cytoskeleton pathways were overexpressed in normal tissue. Conclusion: Reanalysis of this public dataset displayed the known biological features of lung cancer subtypes and revealed novel pathways of potentially clinical importance. The findings also support our hypothesis that even old omics data of high quality can be a source of significant biological information when appropriate bioinformatics methods are used. PMID:25325012

Kerkentzes, Konstantinos; Lagani, Vincenzo; Tsamardinos, Ioannis; Vyberg, Mogens; R?e, Oluf Dimitri

2014-01-01

129

Chromosomal Microarray versus Karyotyping for Prenatal Diagnosis  

PubMed Central

Background Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. Methods Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. Results We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down’s syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. Conclusions In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.) PMID:23215555

Wapner, Ronald J.; Martin, Christa Lese; Levy, Brynn; Ballif, Blake C.; Eng, Christine M.; Zachary, Julia M.; Savage, Melissa; Platt, Lawrence D.; Saltzman, Daniel; Grobman, William A.; Klugman, Susan; Scholl, Thomas; Simpson, Joe Leigh; McCall, Kimberly; Aggarwal, Vimla S.; Bunke, Brian; Nahum, Odelia; Patel, Ankita; Lamb, Allen N.; Thom, Elizabeth A.; Beaudet, Arthur L.; Ledbetter, David H.; Shaffer, Lisa G.; Jackson, Laird

2013-01-01

130

Applications of Functional Protein Microarrays in Basic and Clinical Research  

PubMed Central

The protein microarray technology provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. It is viewed as a new tool that overcomes the limitation of DNA microarrays. On the basis of its application, protein microarrays fall into two major classes: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be directly spotted on a slide to form the so-called “reverse-phase” protein microarray. In the last decade, applications of functional protein microarrays in particular have flourished in studying protein function and construction of networks and pathways. In this chapter, we will review the recent advancements in the protein microarray technology, followed by presenting a series of examples to illustrate the power and versatility of protein microarrays in both basic and clinical research. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade. PMID:22989767

Zhu, Heng; Qian, Jiang

2013-01-01

131

Progress in tissue engineering to repair joint damage in osteoarthritis A/P Cao Tong Medical scientists now have "clear" evidence that the damaged cartilage tissue in osteoarthritis and  

E-print Network

joint disorders can be encouraged to regrow and regenerate, and are developing tissue engineering, white, rubbery tissue that covers and cushions the ends of bones in joints -- is one of the most increase in obesity, which increases wear on joint cartilage. To assess progress toward medical use

Chaudhuri, Sanjay

132

Rapid protein display profiling of cancer progression directly from human tissue using a protein biochip  

Microsoft Academic Search

The complicated, changing pattern of protein expression should contain important infor- mation about the pathologic process taking place in the cells of actual tissue. Utilization of this information for the selection of druggable targets could be possible if a means existed to rapidly analyze and display changes in protein expression in defined microscopic cellular subpopulations. As a demonstration of feasi-

Cloud P. Paweletz; John W. Gillespie; David K. Ornstein; Nicole L. Simone; Monica R. Brown; Kristina A. Cole; Quan-Hong Wang; Jing Huang; Nan Hu; Tai-Tung Yip; William E. Rich; Elise C. Kohn; W. Marston Linehan; Thomas Weber; Phil Taylor; Mike R. Emmert-Buck; Lance A. Liotta; Emanuel F. Petricoin III

2000-01-01

133

Review paper: Progress in the Field of Conducting Polymers for Tissue Engineering Applications  

Microsoft Academic Search

This review focuses on one of the most exciting applications area of conjugated conducting polymers, which is tissue engineering. Strategies used for the biocompatibility improvement of this class of polymers (including biomolecules’ entrapment or covalent grafting) and also the integrated novel technologies for smart scaffolds generation such as micropatterning, electrospinning, self-assembling are emphasized. These processing alternatives afford the electroconducting polymers

Anca-Dana Bendrea; Luminita Cianga; Ioan Cianga

2011-01-01

134

A Cell-Regulatory Mechanism Involving Feedback between Contraction and Tissue Formation Guides Wound Healing Progression  

PubMed Central

Wound healing is a process driven by cells. The ability of cells to sense mechanical stimuli from the extracellular matrix that surrounds them is used to regulate the forces that cells exert on the tissue. Stresses exerted by cells play a central role in wound contraction and have been broadly modelled. Traditionally, these stresses are assumed to be dependent on variables such as the extracellular matrix and cell or collagen densities. However, we postulate that cells are able to regulate the healing process through a mechanosensing mechanism regulated by the contraction that they exert. We propose that cells adjust the contraction level to determine the tissue functions regulating all main activities, such as proliferation, differentiation and matrix production. Hence, a closed-regulatory feedback loop is proposed between contraction and tissue formation. The model consists of a system of partial differential equations that simulates the evolution of fibroblasts, myofibroblasts, collagen and a generic growth factor, as well as the deformation of the extracellular matrix. This model is able to predict the wound healing outcome without requiring the addition of phenomenological laws to describe the time-dependent contraction evolution. We have reproduced two in vivo experiments to evaluate the predictive capacity of the model, and we conclude that there is feedback between the level of cell contraction and the tissue regenerated in the wound. PMID:24681636

Valero, Clara; Javierre, Etelvina; Garcia-Aznar, Jose Manuel; Gomez-Benito, Maria Jose

2014-01-01

135

Differential cellular expression of FXYD1 (phospholemman) and FXYD2 (gamma subunit of Na, K-ATPase) in normal human tissues: A study using high density human tissue microarrays  

Microsoft Academic Search

FXYD proteins have been proposed to function as regulators of Na, K-ATPase function by lowering affinities of the system for potassium and sodium. However, their distribution in normal human tissues has not been studied. We have therefore used immunohistochemistry and semi-quantitative histomorphometric analysis to determine the relative expression at the protein level and distribution of FXYD1 (phospholemman) and FXYD2 (?

Rachel V. Floyd; Susan Wray; Pablo Martín-Vasallo; Ali Mobasheri

2010-01-01

136

LDRD Progress Report: Radioimmunotherapy using oxide nanoparticles: Radionuclide contaiment and mitigation of normal tissue toxicity.  

SciTech Connect

Radionuclides with specific emission properties can be incorporated into metal-chalcogenide and metal-oxide nanoparticles. Coupled to antibodies, these conjugates could be injected into the bloodstream to target and destroy non-solid tumors or target organs for radioimaging. In the first year of this project, two types of radioactive nanoparticles, CdTe: {sup 125m}Te and Y{sub 2}O{sub 3}: {sup 170}Tm were synthesized and coupled to antibodies specific to murine epithelial lung tissue. The nanoparticles successfully target the lung tissue in vivo. Some leaching of the radioisotope was observed. The coming year will explore other types of nanoparticles (other crystal chemistries) in order to minimize leaching.

Rondinone, Adam Justin [ORNL; Dai, Sheng [ORNL; Mirzadeh, Saed [ORNL; Kennel, Steve J [ORNL

2005-10-01

137

Evaluating the progress of restored cordgrass ( Spartina foliosa ) marshes: Belowground biomass and tissue nitrogen  

Microsoft Academic Search

We report the first data on belowground tissue mass and nitrogen (N) concentration forSpartina foliosa in southern California, assessing one natural and two constructed marshes on San Diego Bay. Biomass at the natural marsh\\u000a was low compared to that of otherSpartina spp., but higher than values reported forS. foliosa in northern California. In sandy constructed marshes planted 5 and 10

Katharyn E. Boyer; John C. Callaway; Joy B. Zedler

2000-01-01

138

Review paper: progress in the field of conducting polymers for tissue engineering applications.  

PubMed

This review focuses on one of the most exciting applications area of conjugated conducting polymers, which is tissue engineering. Strategies used for the biocompatibility improvement of this class of polymers (including biomolecules' entrapment or covalent grafting) and also the integrated novel technologies for smart scaffolds generation such as micropatterning, electrospinning, self-assembling are emphasized. These processing alternatives afford the electroconducting polymers nanostructures, the most appropriate forms of the materials that closely mimic the critical features of the natural extracellular matrix. Due to their capability to electronically control a range of physical and chemical properties, conducting polymers such as polyaniline, polypyrrole, and polythiophene and/or their derivatives and composites provide compatible substrates which promote cell growth, adhesion, and proliferation at the polymer-tissue interface through electrical stimulation. The activities of different types of cells on these materials are also presented in detail. Specific cell responses depend on polymers surface characteristics like roughness, surface free energy, topography, chemistry, charge, and other properties as electrical conductivity or mechanical actuation, which depend on the employed synthesis conditions. The biological functions of cells can be dramatically enhanced by biomaterials with controlled organizations at the nanometer scale and in the case of conducting polymers, by the electrical stimulation. The advantages of using biocompatible nanostructures of conducting polymers (nanofibers, nanotubes, nanoparticles, and nanofilaments) in tissue engineering are also highlighted. PMID:21680608

Bendrea, Anca-Dana; Cianga, Luminita; Cianga, Ioan

2011-07-01

139

Magnetic Analysis of Post-mortem Hippocampal Tissue from Alzheimer's Patients: Changes with Progression of the Disease.  

NASA Astrophysics Data System (ADS)

Increases of iron in the human brain with age have been observed and may be accompanied by the development of neurodegenerative diseases, such as Alzheimer's. We have measured the magnetic characteristics of several sets of slides of hippocampal tissue from deceased Alzheimer patients. The slides were made available by the Harvard Brain Bank. The pathology of the tissue was classified in the Braak stages I to VI used to describe the progression of the disease. In general, the slides from patients with higher Braak stages and development of fibrillary tangles and plaques had greater magnetic moments than did those with Braak stage II. However, the peak values were at stage IV and V. To mitigate errors due to the inevitable differences in masses of the tissue on individual slides and their precise location in the hippocampus, ratios of magnetic properties were also observed. Ratios of Anhysteretic Remanent Magnetizaton (ARM) to Isothermal Remanent Magnetization (IRM) were obtained and showed a decrease from Stage II to the more advanced stages, with the minimum values at stages IV and V. The acquisition and demagnetization of IRM are consistent with the presence of magnetite, but also indicate a magnetically harder phase.

Fuller, M.; Zinin, P.; Favia, J.; Tatsumi, L.; Kletetschka, G.; Adachi, T.

2007-12-01

140

Evaluating Erythropoietin-Associated Tumor Progression Using Archival Tissues from a Phase III Clinical Trial  

PubMed Central

Despite the prevalence of anemia in cancer, recombinant erythropoietin (Epo) has declined in use because of recent Phase III trials showing more rapid cancer progression and reduced survival in subjects randomized to Epo. Since Epo receptor (EpoR), Jak2, and Hsp70 are well-characterized mediators of Epo signaling in erythroid cells, we hypothesized that Epo might be especially harmful in patients whose tumors express high levels of these effectors. Because of the insensitivity of immunohistochemistry for detecting low level EpoR protein, we developed assays to measure levels of EpoR, Jak2 and Hsp70 mRNA in formalin-fixed paraffin-embedded (FFPE) tumors. We tested 23 archival breast tumors as well as 136 archival head and neck cancers from ENHANCE, a Phase III trial of 351 patients randomized to Epo versus placebo concomitant with radio-therapy following complete resection, partial resection, or no resection of tumor. EpoR, Jak2, and Hsp70 mRNA levels varied >30-fold, >12-fold, and >13-fold across the breast cancers, and >30-fold, >40-fold, and >30-fold across the head and neck cancers, respectively. Locoregional progression-free survival (LPFS) did not differ among patients whose head and neck cancers expressed above- versus below-median levels of EpoR, Jak2 or Hsp70, except in the subgroup of patients with unresected tumors (n = 28), where above-median EpoR, above-median Jak2, and below-median Hsp70 mRNA levels were all associated with significantly poorer LPFS. Our results provide a framework for exploring the relationship between Epo, cancer progression, and survival using archival tumors from other Phase III clinical trials. PMID:19544471

Miller, Chris P.; Lowe, Kimberly A.; Valliant-Saunders, Karine; Kaiser, Joringel F.; Mattern, Dominik; Urban, Nicole; Henke, Michael; Blau, C. Anthony

2010-01-01

141

Identification of degradome components associated with prostate cancer progression by expression analysis of human prostatic tissues  

PubMed Central

Extracellular proteases of the matrix metalloproteinase (MMP) and serine protease families participate in many aspects of tumour growth and metastasis. Using quantitative real-time RT–PCR analysis, we have undertaken a comprehensive survey of the expression of these enzymes and of their natural inhibitors in 44 cases of human prostate cancer and 23 benign prostate specimens. We found increased expression of MMP10, 15, 24, 25 and 26, urokinase plasminogen activator-receptor (uPAR) and plasminogen activator inhibitor-1 (PAI1), and the newly characterised serine proteases hepsin and matriptase-1 (MTSP1) in malignant tissue compared to benign prostate tissue. In contrast, there was significantly decreased expression of MMP2 and MMP23, maspin, and the protease inhibitors tissue inhibitor of metalloproteinase 3 (TIMP3), TIMP4 and RECK (reversion-inducing cysteine-rich protein with Kazal motifs) in the cancer specimens. The expression of MMP15 and MMP26 correlated positively with Gleason score, whereas TIMP3, TIMP4 and RECK expression correlated negatively with Gleason score. The cellular localisation of the expression of the deregulated genes was evaluated using primary malignant epithelial and stromal cell cultures derived from radical prostatectomy specimens. MMP10 and 25, hepsin, MTSP1 and maspin showed predominantly epithelial expression, whereas TIMP 3 and 4, RECK, MMP2 and 23, uPAR and PAI1 were produced primarily by stromal cells. These data provide the first comprehensive and quantitative analysis of the expression and localisation of MMPs and their inhibitors in human prostate cancer, leading to the identification of several genes involved in proteolysis as potential prognostic indicators, in particular hepsin, MTSP1, MMP26, PAI1, uPAR, MMP15, TIMP3, TIMP4, maspin and RECK. PMID:15928670

Riddick, A C P; Shukla, C J; Pennington, C J; Bass, R; Nuttall, R K; Hogan, A; Sethia, K K; Ellis, V; Collins, A T; Maitland, N J; Ball, R Y; Edwards, D R

2005-01-01

142

Progress in the tissue engineering and stem cell industry "are we there yet?".  

PubMed

This report presents a detailed update to our 2008 publication on the tissue engineering (TE) and stem cell industry. Data are reported through mid 2011 showing an almost three-fold growth in commercial sales over the past 4 years. In addition, the number of companies selling products or offering services has increased over two-fold to 106, and they are generating a remarkable $3.5 billion in sales. Overall, the TE and stem cell sector is spending $3.6 billion and employing almost 14,000 employees. These data suggest the TE and stem cell industry has stabilized and is on a path pointing toward continued success. PMID:22220809

Jaklenec, Ana; Stamp, Andrea; Deweerd, Elizabeth; Sherwin, Angela; Langer, Robert

2012-06-01

143

Microarray Applications in Cancer Research  

PubMed Central

DNA microarray technology permits simultaneous analysis of thousands of DNA sequences for genomic research and diagnostics applications. Microarray technology represents the most recent and exciting advance in the application of hybridization-based technology for biological sciences analysis. This review focuses on the classification (oligonucleotide vs. cDNA) and application (mutation-genotyping vs. gene expression) of microarrays. Oligonucleotide microarrays can be used both in mutation-genotyping and gene expression analysis, while cDNA microarrays can only be used in gene expression analysis. We review microarray mutation analysis, including examining the use of three oligonucleotide microarrays developed in our laboratory to determine mutations in RET, ?-catenin and K-ras genes. We also discuss the use of the Affymetrix GeneChip in mutation analysis. We review microarray gene expression analysis, including the classifying of such studies into four categories: class comparison, class prediction, class discovery and identification of biomarkers. PMID:20368836

Kim, Il-Jin; Kang, Hio Chung

2004-01-01

144

Macromodel of Microarray  

NSDL National Science Digital Library

This is an educator-led demonstration of microarray technology using a model created from a pizza box and ping-pong balls. This âmacroarrayâ model demonstrates how single-stranded DNA segments affixed to a solid support are used to separate and identify DNA segments in a solution.

Malone, Molly; Semadeni, Andrew; Freudenrich, Craig C.; Starr, Harmony

2004-01-01

145

Microarrays Genomische Datenanalyse  

E-print Network

, Diagnose aus der Vogelperspektive Wir messen nicht die Genexpression von einen oder zwei Genen, sondern von Microarray Expressionsprofil: Der diagnostische Befund Eine Liste von 30.000 Genen und ihren anderes als die Diagnose mit zwei Genen? Oder müssen wir nur die Methoden von 2 auf 30.000 Dimensionen

Spang, Rainer

146

Protein biomarkers in cancer: Natural glycoprotein microarray approaches  

PubMed Central

Protein glycosylation is the most versatile and common protein modification and plays important roles in various biological processes and disease progression. In this review, the development of microarray technology for protein glycosylation analysis is described. Three types are discussed: carbohydrate, lectin and natural glycoprotein microarrays. The advantages of microarray technology to study protein glycosylation are high-volume throughput coupled with a highly miniaturized platform. These techniques show great promise for detecting interactions that involve carbohydrates and as a screening tool to detect glycan patterns important for the early diagnosis of disease. PMID:19051138

Zhao, Jia; Patwa, Tasneem H; Lubman, David M

2010-01-01

147

Deficiency of DNA Repair Nuclease ERCC1-XPF Promotes Prostate Cancer Progression in a Tissue Recombination Model  

PubMed Central

Background The excision repair cross complementing (ERCC1) gene product plays a vital role in the nucleotide excision repair and DNA interstrand crosslink repair pathways, which protect the genome from mutations and chromosomal aberrations, respectively. Genetic deletion of Ercc1 in the mouse causes dramatically accelerated aging. We examined the effect of Ercc1 deletion in the development of prostate cancer in a prostate recapitulation model as Ercc1 deficient mice die within four weeks of birth. Methods Prostate tissues from Ercc1?/? mice or wild-type littermates were combined with embryonic rat urogenital mesenchyme and grown as renal grafts for a total of 8, 16 and 24 weeks before histological, expression and proliferative evaluation. Results Invasive adenocarcinoma was observed in Ercc1?/? tissue recombinants but not wild-type as early as 8 weeks post-grafting. PIN-like lesions in Ercc1?/? tissue recombinants had more cytologic and architectural atypia than wild-type (p=0.02, p=0.0065 and p=0.0003 at the 8, 16 and 24 weeks respectively), as well as more proliferative cells (p=0.022 and p=0.033 at 8 and 16 weeks respectively). With serial grafting, Ercc1?/? tissue recombinants progressed to a more severe histopathological phenotype more rapidly than wild-type (p=0.011). Conclusions Results show that ERCC1 and by implication the nucleotide excision repair and/or interstrand crosslink repair mechanisms protect against prostate carcinogenesis and mutations or polymorphisms affecting these DNA repair pathways may predispose prostate epithelial cells to transformation. PMID:22212909

Matoka, Derek John; Yao, Veronica; Harya, Diana Sisca; Gregg, Jennifer Lien; Robinson, Andria Rasile; Niedernhofer, Laura Jane; Parwani, Anil; Maier, Christoph; Bacich, Dean John

2012-01-01

148

Membrane connectivity estimated by digital image analysis of HER2 immunohistochemistry is concordant with visual scoring and fluorescence in situ hybridization results: algorithm evaluation on breast cancer tissue microarrays  

PubMed Central

Introduction The human epidermal growth factor receptor 2 (HER2) is an established biomarker for management of patients with breast cancer. While conventional testing of HER2 protein expression is based on semi-quantitative visual scoring of the immunohistochemistry (IHC) result, efforts to reduce inter-observer variation and to produce continuous estimates of the IHC data are potentiated by digital image analysis technologies. Methods HER2 IHC was performed on the tissue microarrays (TMAs) of 195 patients with an early ductal carcinoma of the breast. Digital images of the IHC slides were obtained by Aperio ScanScope GL Slide Scanner. Membrane connectivity algorithm (HER2-CONNECT™, Visiopharm) was used for digital image analysis (DA). A pathologist evaluated the images on the screen twice (visual evaluations: VE1 and VE2). HER2 fluorescence in situ hybridization (FISH) was performed on the corresponding sections of the TMAs. The agreement between the IHC HER2 scores, obtained by VE1, VE2, and DA was tested for individual TMA spots and patient's maximum TMA spot values (VE1max, VE2max, DAmax). The latter were compared with the FISH data. Correlation of the continuous variable of the membrane connectivity estimate with the FISH data was tested. Results The pathologist intra-observer agreement (VE1 and VE2) on HER2 IHC score was almost perfect: kappa 0.91 (by spot) and 0.88 (by patient). The agreement between visual evaluation and digital image analysis was almost perfect at the spot level (kappa 0.86 and 0.87, with VE1 and VE2 respectively) and at the patient level (kappa 0.80 and 0.86, with VE1max and VE2max, respectively). The DA was more accurate than VE in detection of FISH-positive patients by recruiting 3 or 2 additional FISH-positive patients to the IHC score 2+ category from the IHC 0/1+ category by VE1max or VE2max, respectively. The DA continuous variable of the membrane connectivity correlated with the FISH data (HER2 and CEP17 copy numbers, and HER2/CEP17 ratio). Conclusion HER2 IHC digital image analysis based on membrane connectivity estimate was in almost perfect agreement with the visual evaluation of the pathologist and more accurate in detection of HER2 FISH-positive patients. Most immediate benefit of integrating the DA algorithm into the routine pathology HER2 testing may be obtained by alerting/reassuring pathologists of potentially misinterpreted IHC 0/1+ versus 2+ cases. PMID:21943197

2011-01-01

149

In vivo monitoring of Yersinia ruckeri in fish tissues: progression and virulence gene expression.  

PubMed

In this study, the utilization of bioluminescence imaging (BLI) allowed us to define the progression of Yersinia ruckeri during the infection of rainbow trout. A luminescent Y.?ruckeri 150 strain was engineered using the pCS26-Pac plasmid containing the lux operon from Photorhabdus luminescens. Two different models of infection of rainbow trout were defined depending on the route in which bacteria were administered, being the gut the major organ affected following bath immersion. This indicates that this organ is important for bacterial dissemination inside the fish and the establishment of the infection. Moreover, the expression of three previously selected operons by in vivo expression technology (IVET) was analysed, the yhlBA involved in the production of a haemolysin, the cdsAB related to the uptake of cysteine and the yctCBA implicated in citrate uptake. Apart from these factors, the expression of yrp1 encoding a serralysin metalloprotease involved in pathogenesis was also analysed. The results indicated that all of the assayed promoters were expressed during infection of rainbow trout. In addition to these findings, the methodology described in this work constitutes a useful model for studying the infection process in other fish pathogenic bacteria. PMID:23757147

Méndez, J; Guijarro, J A

2013-02-01

150

Peptide-Based Microarray  

Microsoft Academic Search

\\u000a The peptide array has come into focus as an emerging screening platform for large-scale protein detection and activity studies.\\u000a The materials presented in this chapter examine the recent developments in the field of peptide microarrays with special emphasis\\u000a on the generation and applications of high-density arrays of peptides on glass slides.

Resmi C. Panicker; Hongyan Sun; Grace Y. J. Chen; Shao Q. Yao

151

Pancreatic Tissue Microarray (TMA) - SEER Residual Tissue Repository Program  

Cancer.gov

SEER is an authoritative source of information on cancer incidence and survival in the United States. SEER currently collects and publishes cancer incidence and survival data from population-based cancer registries covering approximately 28 percent of the U.S. population.

152

Lymph node tissue kallikrein-related peptidase 6 mRNA: a progression marker for colorectal cancer  

PubMed Central

Background: A most important characteristic feature for poor prognosis in colorectal cancer (CRC) is the presence of lymph node metastasis. Determination of carcinoembryonic antigen (CEA) mRNA levels in lymph nodes has proven powerful for quantification of disseminated tumour cells. Here, we investigate the utility of human tissue kallikrein-related peptidase 6 (KLK6) mRNA as a progression biomarker to complement CEA mRNA, for improved selection of patients in need of adjuvant therapy and intensified follow-up after surgery. Methods: Lymph nodes of pTNM stage I-IV CRC- (166 patients/503 lymph nodes) and control (23/108) patients were collected at surgery and analysed by quantitative RT–PCR. Results: Lymph node KLK6 positivity was an indicator of poor outcome (hazard ratio 3.7). Risk of recurrence and cancer death increased with KLK6 lymph node levels. Patients with KLK6 lymph node levels above the 90th percentile had a hazard ratio of 6.5 and 76 months shorter average survival time compared to patients with KLK6 negative nodes. The KLK6 positivity in lymph nodes with few tumour cells, that is, low CEA mRNA levels, also indicated poor prognosis (hazard ratio 2.8). Conclusion: In CRC patients, lymph node KLK6 positivity indicated presence of aggressive tumour cells associated with poor prognosis and high risk of tumour recurrence. PMID:22699826

Ohlsson, L; Lindmark, G; Israelsson, A; Palmqvist, R; Oberg, A; Hammarstrom, M-L; Hammarstrom, S

2012-01-01

153

Molecular profiling of bladder cancer using cDNA microarrays: defining histogenesis and biological phenotypes.  

PubMed

This study was designed to characterize the expression profiles of nine bladder cancer cell lines (T24, J82, 5637, HT1376, RT4, SCaBER, TCCSUP, UMUC-3, and HT1197) using cDNA microarrays (8976 genes and expressed sequence tags). Novel targets involved in bladder cancer progression of potential clinical relevance were validated by immunohistochemistry using tissue microarrays of primary bladder tumors (n = 193 cases). Hierarchical clustering classified uroepithelial cells based on their histopathogenesis and cell cycle alterations. Keratin 10 and caveolin-1 transcripts were more abundant in tumor cells from squamous and invasive origin. Their combined expression was shown to stratify bladder tumors and define squamous differentiation. To assess the robustness of the clustering analysis, a bootstrap resampling technique was used. This grouped tumor cell lines based on their biological properties, including cell cycle and cell adhesion features. E-cadherin, zyxin, and moesin were identified as genes differentially expressed in these clusters and related to the p53, RB, and INK4A status of the cell lines. Loss of these adhesion molecules was associated with stage and grade in primary tumors (P < 0.05), and moesin expression was also associated with survival (P = 0.01). Deregulation of cell cycle and apoptotic pathways, such as mutations or altered expression of p53, pRB, and INK4A (p16), is necessary for uroepithelial transformation. However, it appears that deregulation of cell adhesion is a common event associated with tumor progression in uroepithelial neoplasms. PMID:12460915

Sanchez-Carbayo, Marta; Socci, Nicholas D; Charytonowicz, Elizabeth; Lu, Minglan; Prystowsky, Michael; Childs, Geoffrey; Cordon-Cardo, Carlos

2002-12-01

154

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data  

Microsoft Academic Search

Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and funda- mental questions asked of microarray data is whe- ther individual genes are significantly activated or repressed by a particular stimulus. We have previ- ously presented two Bayesian statistical methods for this level of analysis, collectively known as variance-modeled

Albert Hsiao; Trey Ideker; Jerrold M. Olefsky; Shankar Subramaniam

2005-01-01

155

DNA self-polymers as microarray probes improve assay sensitivity  

Microsoft Academic Search

DNA microarrays provide a method for determining the expression levels of thousands of genes simultaneously. However, the phenotypic complexity of brain tissue and cross-dilution of transcripts from different sources make it difficult to detect many of the low abundance RNA species. Furthermore, these experiments require significant amounts of starting material, which must often be amplified by one or two rounds

Deborah Hollingshead; Željka Korade; David A. Lewis; Pat Levitt; Károly Mirnics

2006-01-01

156

GENERATING ENCODED COMPOUND LIBRARIES FOR FABRICATING MICROARRAYS AS A  

E-print Network

, Taiwan 2 Department of Optical Science and Engineering, Fudan University, Shanghai, China 3 Key, China 4 Department of Pharmacology, Upstate Cancer Research Institute, State University of New York microarray technique (tissue[11] =cellular,[12] DNA,[13,14] protein,[15,16] peptide, and small molecules[17

Zhu, Xiangdong

157

Protein microarray: sensitive and effective immunodetection for drug residues  

PubMed Central

Background Veterinary drugs such as clenbuterol (CL) and sulfamethazine (SM2) are low molecular weight (<1000 Da) compounds, or haptens, that are difficult to develop immunoassays due to their low immunogenicity. In this study, we conjugated the drugs to ovalbumin to increase their immunogenicity for antiserum production in rabbits and developed a protein microarray immunoassay for detection of clenbuterol and sulfamethazine. The sensitivity of this approach was then compared to traditional ELISA technique. Results The artificial antigens were spotted on microarray slides. Standard concentrations of the compounds were added to compete with the spotted antigens for binding to the antisera to determine the IC50. Our microarray assay showed the IC50 were 39.6 ng/ml for CL and 48.8 ng/ml for SM2, while the traditional competitive indirect-ELISA (ci-ELISA) showed the IC50 were 190.7 ng/ml for CL and 156.7 ng/ml for SM2. We further validated the two methods with CL fortified chicken muscle tissues, and the protein microarray assay showed 90% recovery while the ci-ELISA had 76% recovery rate. When tested with CL-fed chicken muscle tissues, the protein microarray assay had higher sensitivity (0.9 ng/g) than the ci-ELISA (0.1 ng/g) for detection of CL residues. Conclusions The protein microarrays showed 4.5 and 3.5 times lower IC50 than the ci-ELISA detection for CL and SM2, respectively, suggesting that immunodetection of small molecules with protein microarray is a better approach than the traditional ELISA technique. PMID:20158905

2010-01-01

158

Microarray platform for omics analysis  

NASA Astrophysics Data System (ADS)

Microarray technology has revolutionized genetic analysis. However, limitations in genome analysis has lead to renewed interest in establishing 'omic' strategies. As we enter the post-genomic era, new microarray technologies are needed to address these new classes of 'omic' targets, such as proteins, as well as lipids and carbohydrates. We have developed a microarray platform that combines self- assembling monolayers with the biotin-streptavidin system to provide a robust, versatile immobilization scheme. A hydrophobic film is patterned on the surface creating an array of tension wells that eliminates evaporation effects thereby reducing the shear stress to which biomolecules are exposed to during immobilization. The streptavidin linker layer makes it possible to adapt and/or develop microarray based assays using virtually any class of biomolecules including: carbohydrates, peptides, antibodies, receptors, as well as them ore traditional DNA based arrays. Our microarray technology is designed to furnish seamless compatibility across the various 'omic' platforms by providing a common blueprint for fabricating and analyzing arrays. The prototype microarray uses a microscope slide footprint patterned with 2 by 96 flat wells. Data on the microarray platform will be presented.

Mecklenburg, Michael; Xie, Bin

2001-09-01

159

Progress in developing a living human tissue-engineered tri-leaflet heart valve assembled from tissue produced by the self-assembly approach.  

PubMed

The aortic heart valve is constantly subjected to pulsatile flow and pressure gradients which, associated with cardiovascular risk factors and abnormal hemodynamics (i.e. altered wall shear stress), can cause stenosis and calcification of the leaflets and result in valve malfunction and impaired circulation. Available options for valve replacement include homograft, allogenic or xenogenic graft as well as the implantation of a mechanical valve. A tissue-engineered heart valve containing living autologous cells would represent an alternative option, particularly for pediatric patients, but still needs to be developed. The present study was designed to demonstrate the feasibility of using a living tissue sheet produced by the self-assembly method, to replace the bovine pericardium currently used for the reconstruction of a stented human heart valve. In this study, human fibroblasts were cultured in the presence of sodium ascorbate to produce tissue sheets. These sheets were superimposed to create a thick construct. Tissue pieces were cut from these constructs and assembled together on a stent, based on techniques used for commercially available replacement valves. Histology and transmission electron microscopy analysis showed that the fibroblasts were embedded in a dense extracellular matrix produced in vitro. The mechanical properties measured were consistent with the fact that the engineered tissue was resistant and could be cut, sutured and assembled on a wire frame typically used in bioprosthetic valve assembly. After a culture period in vitro, the construct was cohesive and did not disrupt or disassemble. The tissue engineered heart valve was stimulated in a pulsatile flow bioreactor and was able to sustain multiple duty cycles. This prototype of a tissue-engineered heart valve containing cells embedded in their own extracellular matrix and sewn on a wire frame has the potential to be strong enough to support physiological stress. The next step will be to test this valve extensively in a bioreactor and at a later date, in a large animal model in order to assess in vivo patency of the graft. PMID:24813743

Dubé, Jean; Bourget, Jean-Michel; Gauvin, Robert; Lafrance, Hugues; Roberge, Charles J; Auger, François A; Germain, Lucie

2014-08-01

160

Differentiated miRNA expression and validation of signaling pathways in apoE gene knockout mice by cross-verification microarray platform  

PubMed Central

The microRNA (miRNA) regulation mechanisms associated with atherosclerosis are largely undocumented. Specific selection and efficient validation of miRNA regulation pathways involved in atherosclerosis development may be better assessed by contemporary microarray platforms applying cross-verification methodology. A screening platform was established using both miRNA and genomic microarrays. Microarray analysis was then simultaneously performed on pooled atherosclerotic aortic tissues from 10 Apolipoprotein E (apoE) knockout mice (apoE?/?) and 10 healthy C57BL/6 (B6) mice. Differentiated miRNAs were screened and cross-verified against an mRNA screen database to explore integrative mRNA–miRNA regulation. Gene set enrichment analysis was conducted to describe the potential pathways regulated by these mRNA–miRNA interactions. High-throughput data analysis of miRNA and genomic microarrays of knockout and healthy control mice revealed 75 differentially expressed miRNAs in apoE?/? mice at a threshold value of 2. The six miRNAs with the greatest differentiation expression were confirmed by real-time quantitative reverse-transcription PCR (qRT–PCR) in atherosclerotic tissues. Significantly enriched pathways, such as the type 2 diabetes mellitus pathway, were observed by a gene-set enrichment analysis. The enriched molecular pathways were confirmed through qRT–PCR evaluation by observing the presence of suppressor of cytokine signaling 3 (SOCS3) and SOCS3-related miRNAs, miR-30a, miR-30e and miR-19b. Cross-verified high-throughput microarrays are optimally accurate and effective screening methods for miRNA regulation profiles associated with atherosclerosis. The identified SOCS3 pathway is a potentially valuable target for future development of targeted miRNA therapies to control atherosclerosis development and progression. PMID:23470715

Han, Hui; Wang, Yu-Hong; Qu, Guang-Jin; Sun, Ting-Ting; Li, Feng-Qing; Jiang, Wei; Luo, Shan-Shun

2013-01-01

161

Microarray methods for protein biomarker detection  

PubMed Central

The application of protein biomarkers as an aid for the detection and treatment of diseases has been subject to intensified interest in recent years. The quantitative assaying of protein biomarkers in easily obtainable biological fluids such as serum and urine offers the opportunity to improve patient care via earlier and more accurate diagnoses in a convenient, non-invasive manner as well as providing a potential route towards more individually targeted treatment. Essential to achieving progress in biomarker technology is the ability to screen large numbers of proteins simultaneously in a single experiment with high sensitivity and selectivity. In this article, we highlight recent progress in the use of microarrays for high-throughput biomarker profiling and discuss some of the challenges associated with these efforts. PMID:18645635

Lee, Hye Jin; Wark, Alastair W.; Corn, Robert M.

2009-01-01

162

The bioinformatics of microarrays to study cancer: Advantages and disadvantages  

NASA Astrophysics Data System (ADS)

Microarrays are devices designed to analyze simultaneous expression of thousands of genes. However, the process will adds noise into the information at each stage of the study. To analyze these thousands of data is necessary to use bioinformatics tools. The traditional analysis begins by normalizing data, but the obtained results are highly dependent on how it is conducted the study. It is shown the need to develop new strategies to analyze microarray. Liver tissue taken from an animal model in which is chemically induced cancer is used as an example.

Rodríguez-Segura, M. A.; Godina-Nava, J. J.; Villa-Treviño, S.

2012-10-01

163

Quantitative analysis of tumor mitochondrial RNA using microarray  

PubMed Central

AIM: To design a novel method to rapidly detect the quantitative alteration of mtRNA in patients with tumors. METHODS: Oligo 6.22 and Primer Premier 5.0 bio-soft were used to design 15 pairs of primers of mtRNA cDNA probes in light of the functional and structural property of mtDNA, and then RT-PCR amplification was used to produce 15 probes of mtRNA from one normal gastric mucosal tissue. Total RNA extracted from 9 gastric cancers and corresponding normal gastric mucosal tissues was reverse transcribed into cDNA labeled with fluorescein. The spotted mtDNA microarrays were made and hybridized. Finally, the microarrays were scanned with a GeneTACTM laser scanner to get the hybridized results. Northern blot was used to confirm the microarray results. RESULTS: The hybridized spots were distinct with clear and consistent backgrounds. After data was standardized according to the housekeeping genes, the results showed that the expression levels of some mitochondrial genes in gastric carcinoma were different from those in the corresponding non-cancerous regions. CONCLUSION: The mtDNA expression microarray can rapidly, massively and exactly detect the quantity of mtRNA in tissues and cells. In addition, the whole expressive information of mtRNA from a tumor patient on just one slide can be obtained using this method, providing an effective method to investigate the relationship between mtDNA expression and tumorigenesis. PMID:15609393

Han, Cheng-Bo; Mao, Xiao-Yun; Xin, Yan; Wang, Shao-Cheng; Ma, Jia-Ming; Zhao, Yu-Jie

2005-01-01

164

Microarray analysis in clinical oncology: pre-clinical optimization using needle core biopsies from xenograft tumors  

Microsoft Academic Search

BACKGROUND: DNA microarray profiling performed on clinical tissue specimens can potentially provide significant information regarding human cancer biology. Biopsy cores, the typical source of human tumor tissue, however, generally provide very small amounts of RNA (0.3–15 ?g). RNA amplification is a common method used to increase the amount of material available for hybridization experiments. Using human xenograft tissue, we sought

Elizabeth M Goley; Soni J Anderson; Cynthia Ménard; Eric Chuang; Xing Lü; Philip J Tofilon; Kevin Camphausen

2004-01-01

165

Physicochemically modified silicon as a substrate for protein microarrays.  

PubMed

Reverse phase protein microarrays (RPMA) enable high throughput screening of posttranslational modifications of important signaling proteins within diseased cells. One limitation of protein-based molecular profiling is the lack of a PCR-like intrinsic amplification system for proteins. Enhancement of protein microarray sensitivities is an important goal, especially because many molecular targets within patient tissues are of low abundance. The ideal array substrate will have a high protein-binding affinity and low intrinsic signal. To date, nitrocellulose-coated glass has provided an effective substrate for protein binding in the microarray format when using chromogenic detection systems. As fluorescent systems, such as quantum dots, are explored as potential reporter agents, the intrinsic fluorescent properties of nitrocellulose-coated glass slides limit the ability to image microarrays for extended periods of time where increases in net sensitivity can be attained. Silicon, with low intrinsic autofluorescence, is being explored as a potential microarray surface. Native silicon has low binding potential. Through titrated reactive ion etching (RIE), varying surface areas have been created on silicon in order to enhance protein binding. Further, via chemical modification, reactive groups have been added to the surfaces for comparison of relative protein binding. Using this combinatorial method of surface roughening and surface coating, 3-aminopropyltriethoxysilane (APTES) and mercaptopropyltrimethoxysilane (MPTMS) treatments were shown to transform native silicon into a protein-binding substrate comparable to nitrocellulose. PMID:16987550

Nijdam, A Jasper; Ming-Cheng Cheng, Mark; Geho, David H; Fedele, Roberta; Herrmann, Paul; Killian, Keith; Espina, Virginia; Petricoin, Emanuel F; Liotta, Lance A; Ferrari, Mauro

2007-01-01

166

Engraftment of human lymphocytes and thyroid tissue into scid and rag2-deficient mice: absent progression of lymphocytic infiltration  

Microsoft Academic Search

To study human autoimmune thyroid disease in an animal model we have investigated the in vivo survival of human thyroid tissues and functionality of human lymphocytes in severe combined immunodeficient (scid) mice and recombination-activating gene (rag2) knockout mice. We found successful engraftment of human thyroid tissues in both scid and rag2-deficient mice. However, when peripheral blood mononuclear cells were transplanted

A. Martin; M Valentine; P Unger; S W Yeung; L D Shultz; T F Davies

1994-01-01

167

Comparing Bacterial DNA Microarray Fingerprints  

SciTech Connect

Detecting subtle genetic differences between microorganisms is an important problem in molecular epidemiology and microbial forensics. In a typical investigation, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial strains, where the patterns of DNA fragment sizes are proxies for a microbe's genotype. The limited genomic sample captured on a gel is often insufficient to discriminate nearly identical strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if the number of probes on the microarray is sufficiently large, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate the statistical fingerprinting problem for 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

Willse, Alan R.; Chandler, Darrell P.; White, Amanda M.; Protic, Miroslava; Daly, Don S.; Wunschel, Sharon C.

2005-08-15

168

DNA microarrays: Types, Applications and their future  

PubMed Central

This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000’s of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies. PMID:23288464

Bumgarner, Roger

2014-01-01

169

Does regular consumption of green tea influence expression of vascular endothelial growth factor and its receptor in aged rat erectile tissue? Possible implications for vasculogenic erectile dysfunction progression  

PubMed Central

Erectile dysfunction (ED) is a highly prevalent disease affecting millions of men worldwide with a tendency for widespread increase. ED is now considered an early manifestation of atherosclerosis and, consequently, a precursor of systemic vascular disease. Atherosclerosis and ED share potentially modifiable risk factors, as smoking or high-fat food intake, but it is unclear how regular consumption of anti-oxidant rich drinks, which exhibit recognised anti-atherosclerotic features, affects ED progression. The objective of this study was to evaluate the modulating effects of chronic consumption of catechin-rich beverages on the vascular structure of the rat corpus cavernosum, and how this could contribute to delay or prevention of the onset of ED. Male Wistar rats aged 12 months were treated with green tea (GT) or a green tea extract solution (GTE) as the only liquid source for 6 months. Consumption of GT and GTE led to decreased plasma androgen levels without any significant change in plasma lipid levels. A reduction in corpus cavernosum intracellular storage of lipids, associated with decreased expression of vascular endothelial growth factor (VEGF) and its receptor VEGFR2 in endothelial cells, was observed. Taken together, these results suggest diminished atherosclerotic progression in cavernous tissue. However, functional studies will be necessary to elucidate if catechin-rich beverages are useful compounds in the prevention of deleterious vascular events associated with ED. It was also demonstrated that regular consumption of catechins reduces atherosclerotic progression and mortality due to cardiovascular disease. The results reported here suggest diminished atherosclerotic progression in cavernous tissue in aged rats following chronic ingestion of catechin-rich beverages. PMID:19424845

Assuncao, M.; Marques, F.; Andrade, J. P.; Almeida, H.

2008-01-01

170

Imaging the morphological change of tissue structure during the early phase of esophageal tumor progression using multiphoton microscopy  

NASA Astrophysics Data System (ADS)

Esophageal cancer is a common malignancy with a very poor prognosis. Successful strategies for primary prevention and early detection are critically needed to control this disease. Multiphoton microscopy (MPM) is becoming a novel optical tool of choice for imaging tissue architecture and cellular morphology by two-photon excited fluorescence. In this study, we used MPM to image microstructure of human normal esophagus, carcinoma in situ (CIS), and early invasive carcinoma in order to establish the morphological features to differentiate these tissues. The diagnostic features such as the appearance of cancerous cells, the significant loss of stroma, the absence of the basement membrane were extracted to distinguish between normal and cancerous esophagus tissue. These results correlated well with the paired histological findings. With the advancement of clinically miniaturized MPM and the multi-photon probe, combining MPM with standard endoscopy will therefore allow us to make a real-time in vivo diagnosis of early esophageal cancer at the cellular level.

Xu, Jian; Kang, Deyong; Xu, Meifang; Zhu, Xiaoqin; Zhuo, Shuangmu; Chen, Jianxin

2012-12-01

171

Application of physicochemically modified silicon substrates as reverse-phase protein microarrays.  

PubMed

Physicochemically modified silicon substrates can provide a high quality alternative to nitrocellulose-coated glass slides for use in reverse-phase protein microarrays. Enhancement of protein microarray sensitivities is an important goal, especially because molecular targets within patient tissues exist in low abundance. The ideal array substrate has a high protein binding affinity and low intrinsic background signal. Silicon, which has low intrinsic autofluorescence, is being explored as a potential microarray surface. In a previous paper ( Nijdam , A. J. ; Cheng , M. M.-C. ; Fedele , R. ; Geho , D. H. ; Herrmann , P. ; Killian , K. ; Espina , V. ; Petricoin , E. F. ; Liotta , L. A. ; Ferrari , M. Physicochemically Modified Silicon as Substrate for Protein Microarrays . Biomaterials 2007 , 28 , 550 - 558 ), it is shown that physicochemical modification of silicon substrates increases the binding of protein to silicon to a level comparable with that of nitrocellulose. Here, we apply such substrates in a reverse-phase protein microarray setting in two model systems. PMID:19170514

Nijdam, A Jasper; Zianni, Michael R; Herderick, Edward E; Cheng, Mark M-C; Prosperi, Jenifer R; Robertson, Fredika A; Petricoin, Emanuel F; Liotta, Lance A; Ferrari, Mauro

2009-03-01

172

Rapid Spoligotyping of Mycobacterium tuberculosis Complex Bacteria by Use of a Microarray System with Automatic Data Processing and Assignment  

PubMed Central

Membrane-based spoligotyping has been converted to DNA microarray format to qualify it for high-throughput testing. We have shown the assay's validity and suitability for direct typing from tissue and detecting new spoligotypes. Advantages of the microarray methodology include rapidity, ease of operation, automatic data processing, and affordability. PMID:22553239

Ruettger, Anke; Nieter, Johanna; Skrypnyk, Artem; Engelmann, Ines; Ziegler, Albrecht; Moser, Irmgard; Monecke, Stefan; Ehricht, Ralf

2012-01-01

173

Microarrays & Expression Matthias E. Futschik  

E-print Network

1 Microarrays & Expression profiling Matthias E. Futschik Institute for Theoretical Biology. Gattica becomes alive: Classification and Disease Profiling 7. The whole picture: An integrative approach to calculates summary indices exist (e.g. MAS,dchip, RMA...) #12;6 From Images to Numbers Impurities,Impurities

Futschik, Matthias E.

174

DNA Microarray Methodology - Flash Animation  

NSDL National Science Digital Library

This animation demonstrates how DNA microarray experiments are performed. DNA chips are used to determine which genes are activated and which genes are repressed when two populations are compared. In this case, the comparison is between yeast cells grown under either aerobic or anaerobic conditions. This animation is very effective for many different education levels. Teachers and students love this one.

Campbell, A. M.

2012-04-12

175

Medical image computing and computer-aided medical interventions applied to soft tissues. Work in progress in urology  

E-print Network

Until recently, Computer-Aided Medical Interventions (CAMI) and Medical Robotics have focused on rigid and non deformable anatomical structures. Nowadays, special attention is paid to soft tissues, raising complex issues due to their mobility and deformation. Mini-invasive digestive surgery was probably one of the first fields where soft tissues were handled through the development of simulators, tracking of anatomical structures and specific assistance robots. However, other clinical domains, for instance urology, are concerned. Indeed, laparoscopic surgery, new tumour destruction techniques (e.g. HIFU, radiofrequency, or cryoablation), increasingly early detection of cancer, and use of interventional and diagnostic imaging modalities, recently opened new challenges to the urologist and scientists involved in CAMI. This resulted in the last five years in a very significant increase of research and developments of computer-aided urology systems. In this paper, we propose a description of the main problems rel...

Troccaz, Jocelyne; Berkelman, Peter; Cinquin, Philippe; Daanen, Vincent; Leroy, Antoine; Marchal, Maud; Payan, Yohan; Promayon, Emmanuel; Voros, Sandrine; Bart, Stéphane; Bolla, Michel; Chartier-Kastler, Emmanuel; Descotes, Jean-Luc; Dusserre, Andrée; Giraud, Jean-Yves; Long, Jean-Alexandre; Moalic, Ronan; Mozer, Pierre

2006-01-01

176

Noninvasive near-infrared fluorescent protein-based imaging of tumor progression and metastases in deep organs and intraosseous tissues  

NASA Astrophysics Data System (ADS)

Whole-body imaging of experimental tumor growth is more feasible within the near-infrared (NIR) optical window because of the highest transparency of mammalian tissues within this wavelength spectrum, mainly due to improved tissue penetration and lower autofluorescence. We took advantage from the recently cloned infrared fluorescent protein (iRFP) together with a human immunodeficiency virus (HIV)-based lentiviral vector to produce virally transduced tumor cells that permanently express this protein. We then noninvasively explored metastatic spread as well as primary tumor growth in deep organs and behind bone barriers. Intrabone tumor growth was investigated through intracranial and intratibial injections of glioblastoma and osteosarcoma cells, respectively, and metastasis was assessed by tail vein injection of melanoma cells. We found that the emitted fluorescence is captured as sharp images regardless of the organ or tissue considered. Furthermore, by overlaying fluorescence spots with the white light, it was possible to afford whole-body images yet never observed before. This approach allowed us to continuously monitor the growth and dissemination of tumor cells with a small number of animals, minimal animal handling, and without the need for any additive. This iRFP-based system provides high-resolution readouts of tumorigenesis that should greatly facilitate preclinical trials with anticancer therapeutic molecules.

Jiguet-Jiglaire, Carine; Cayol, Mylène; Mathieu, Sylvie; Jeanneau, Charlotte; Bouvier-Labit, Corinne; Ouafik, L.'houcine; El-Battari, Assou

2014-01-01

177

Direct calibration of PICKY-designed microarrays  

PubMed Central

Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration. PMID:19849862

Chou, Hui-Hsien; Trisiriroj, Arunee; Park, Sunyoung; Hsing, Yue-Ie C; Ronald, Pamela C; Schnable, Patrick S

2009-01-01

178

Approximating Border Length for DNA Microarray Synthesis  

E-print Network

Approximating Border Length for DNA Microarray Synthesis Cindy Y. Li1 Prudence W.H. Wong1 Qin Xin2. The borders between the masked and unmasked regions are represented by bold lines. DNA microarray synthesis arises in microarray synthesis to place and embed probes in the array. The synthesis is based on a light

Wong, Prudence W.H.

179

The Microarray Revolution: Perspectives from Educators  

ERIC Educational Resources Information Center

In recent years, microarray analysis has become a key experimental tool, enabling the analysis of genome-wide patterns of gene expression. This review approaches the microarray revolution with a focus upon four topics: 1) the early development of this technology and its application to cancer diagnostics; 2) a primer of microarray research,…

Brewster, Jay L.; Beason, K. Beth; Eckdahl, Todd T.; Evans, Irene M.

2004-01-01

180

Engraftment of human lymphocytes and thyroid tissue into scid and rag2-deficient mice: absent progression of lymphocytic infiltration.  

PubMed

To study human autoimmune thyroid disease in an animal model we have investigated the in vivo survival of human thyroid tissues and functionality of human lymphocytes in severe combined immunodeficient (scid) mice and recombination-activating gene (rag2) knockout mice. We found successful engraftment of human thyroid tissues in both scid and rag2-deficient mice. However, when peripheral blood mononuclear cells were transplanted ip, human immunoglobulin production was poor in rag2-deficient mice compared to that in scid mice (mean human immunoglobulin G levels at 6 weeks, 0.2 +/- 0.2 microgram/mL in two of eight rag2-deficient mice compared to 20.8 +/- 7.0 micrograms/mL in seven of nine scid mice; P < 0.05). We, therefore, only pursued the further use of scid mice and transplanted them with thyroid tissue from patients with either Graves' disease (four patients) or Hashimoto's thyroiditis (one patient). At the functional level, we observed transiently increased thyroid hormone levels (T4 peaking at 5.4 +/- 0.2 microgram/dL compared to a normal level of 2.6 +/- 0.2 microgram/dL); human autoantibodies to human thyroglobulin, human thyroid peroxidase, and the human TSH receptor were also detected in thyroid-transplanted mice. In contrast to recent reports, histological examination of the thyroid explants showed no increase in the lymphocytic infiltrate compared to the original donor tissue, nor was there any thyroid follicular destruction observed. In fact, many of the transplants demonstrated a marked diminution in the infiltrates over time, with an absence of HLA-DR antigen expression by both T-cells and thyrocytes. Cotransplanted allogeneic thyroid tissues were unremarkable in terms of lymphocytic infiltrates and showed intact morphology. Taken together, these data point to a relative degree of T-cell inactivity within the thyroid explants from the scid mouse. Hence, a factor(s) present in the patient with autoimmune thyroid disease that activates their thyroid-specific T-cells may be absent in this murine model as presently constructed. PMID:8077352

Martin, A; Valentine, M; Unger, P; Yeung, S W; Shultz, L D; Davies, T F

1994-09-01

181

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs  

Microsoft Academic Search

Recent mammalian microarray experiments detected widespread transcription and indicated that there may be many undiscovered multiple-exon protein-coding genes. To explore this possibility, we labeled cDNA from unamplified, polyadenylation-selected RNA samples from 37 mouse tissues to microarrays encompassing 1.14 million exon probes. We analyzed these data using GenRate, a Bayesian algorithm that uses a genome-wide scoring function in a factor graph

Brendan J Frey; Naveed Mohammad; Quaid D Morris; Wen Zhang; Mark D Robinson; Sanie Mnaimneh; Richard Chang; Qun Pan; Eric Sat; Janet Rossant; Benoit G Bruneau; Jane E Aubin; Benjamin J Blencowe; Timothy R Hughes

2005-01-01

182

Raman microprobe investigation of molecular structure and organization in the native state of woody tissue. Progress report, April 1, 1987--July 31, 1989  

SciTech Connect

Although the primary emphasis of our program has remained with the application of Raman spectroscopy to the study of native tissue, the scope of the work has been expanded to include a number of complementary approaches. These have included Solid State 13C NMR, autoradiography of radiolabeled woody tissue sections, and the generation of biomimetic tertiary aggregates which simulate states of aggregation characteristic of cell walls. Our Raman spectroscopic studies have resulted in progress in the areas of interpretation of the spectral features, and confirmation of the variability of the patterns of orientation of lignin reported earlier. We have assembled and made operational our new microprobe and spectrometer systems acquired under the DOE-URIP program. We have also demonstrated that, operating with gated detection and pulsed laser excitation, we can discriminate against the laser-excited fluorescence characteristic of most woody tissue. Our studies of celluloses, which combine Raman spectroscopy and 13C NMR have shown that all native celluloses are composites of two forms which have the same secondary structure but different tertiary structures.

Atalla, R.H.

1989-08-01

183

Extracellular Matrix, Nuclear and Chromatin Structure and GeneExpression in Normal Tissues and Malignant Tumors: A Work inProgress  

SciTech Connect

Almost three decades ago, we presented a model where theextracellular matrix (ECM) was postulated to influence gene expressionand tissue-specificity through the action of ECM receptors and thecytoskeleton. This hypothesis implied that ECM molecules could signal tothe nucleus and that the unit of function in higher organisms was not thecell alone, but the cell plus its microenvironment. We now know that ECMinvokes changes in tissue and organ architecture and that tissue, cell,nuclear, and chromatin structure are changed profoundly as a result ofand during malignant progression. Whereas some evidence has beengenerated for a link between ECM-induced alterations in tissuearchitecture and changes in both nuclear and chromatin organization, themanner by which these changes actively induce or repress gene expressionin normal and malignant cells is a topic in need of further attention.Here, we will discuss some key findings that may provide insights intomechanisms through which ECM could influence gene transcription and howtumor cells acquire the ability to overcome these levels ofcontrol.

Spencer, Virginia A.; Xu, Ren; Bissell, Mina J.

2006-08-01

184

Fusion Transcript Discovery in Formalin-Fixed Paraffin-Embedded Human Breast Cancer Tissues Reveals a Link to Tumor Progression  

PubMed Central

The identification of gene fusions promises to play an important role in personalized cancer treatment decisions. Many rare gene fusion events have been identified in fresh frozen solid tumors from common cancers employing next-generation sequencing technology. However the ability to detect transcripts from gene fusions in RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissues, which exist in very large sample repositories for which disease outcome is known, is still limited due to the low complexity of FFPE libraries and the lack of appropriate bioinformatics methods. We sought to develop a bioinformatics method, named gFuse, to detect fusion transcripts in FFPE tumor tissues. An integrated, cohort based strategy has been used in gFuse to examine single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76 patients. In total, 118 fusion events were detected transcriptome-wide at base-pair resolution across the 212 samples. We selected 77 candidate fusions based on their biological relevance to cancer and supported 61% of these using TaqMan assays. Direct sequencing of 19 of the fusion sequences identified by TaqMan confirmed them. Three unique fused gene pairs were recurrent across the 212 patients with 6, 3, 2 individuals harboring these fusions respectively. We show here that a high frequency of fusion transcripts detected at the whole transcriptome level correlates with poor outcome (P<0.0005) in human breast cancer patients. This study demonstrates the ability to detect fusion transcripts as biomarkers from archival FFPE tissues, and the potential prognostic value of the fusion transcripts detected. PMID:24727804

Ma, Yan; Ambannavar, Ranjana; Stephans, James; Jeong, Jennie; Dei Rossi, Andrew; Liu, Mei-Lan; Friedman, Adam J.; Londry, Jason J.; Abramson, Richard; Beasley, Ellen M.; Baker, Joffre; Levy, Samuel; Qu, Kunbin

2014-01-01

185

Tissue injury and hypoxia promote malignant progression of prostate cancer by inducing CXCL13 expression in tumor myofibroblasts.  

PubMed

Prostate cancer (PC) is a slowly progressing malignancy that often responds to androgen ablation or chemotherapy by becoming more aggressive, acquiring a neuroendocrine phenotype, and undergoing metastatic spread. We found that B lymphocytes recruited into regressing androgen-deprived tumors by C-X-C motif chemokine 13 (CXCL13), a chemokine whose expression correlates with clinical severity, play an important role in malignant progression and metastatic dissemination of PC. We now describe how androgen ablation induces CXCL13 expression. In both allografted and spontaneous mouse PC, CXCL13 is expressed by tumor-associated myofibroblasts that are activated on androgen ablation through a hypoxia-dependent mechanism. The same cells produce CXCL13 after chemotherapy. Myofibroblast activation and CXCL13 expression also occur in the normal prostate after androgen deprivation, and CXCL13 is expressed by myofibroblasts in human PC. Hypoxia activates hypoxia-inducible factor 1 (HIF-1) and induces autocrine TGF-? signaling that promotes myofibroblast activation and CXCL13 induction. In addition to TGF-? receptor kinase inhibitors, myofibroblast activation and CXCL13 induction are blocked by phosphodiesterase 5 (PDE5) inhibitors. Both inhibitor types and myofibroblast immunodepletion block the emergence of castration-resistant PC in the transgenic adenocarcinoma of the mouse prostate (TRAMP) model of spontaneous metastatic PC with neuroendocrine differentiation. PMID:25267627

Ammirante, Massimo; Shalapour, Shabnam; Kang, Youngjin; Jamieson, Christina A M; Karin, Michael

2014-10-14

186

The Current Status of DNA Microarrays  

NASA Astrophysics Data System (ADS)

DNA microarray technology that allows simultaneous assay of thousands of genes in a single experiment has steadily advanced to become a mainstream method used in research, and has reached a stage that envisions its use in medical applications and personalized medicine. Many different strategies have been developed for manufacturing DNA microarrays. In this chapter, we discuss the manu facturing characteristics of seven microarray platforms that were used in a recently completed large study by the MicroArray Quality Control (MAQC) consortium, which evaluated the concordance of results across these platforms. The platforms can be grouped into three categories: (1) in situ synthesis of oligonucleotide probes on microarrays (Affymetrix GeneChip® arrays based on photolithography synthesis and Agilent's arrays based on inkjet synthesis); (2) spotting of presynthe-sized oligonucleotide probes on microarrays (GE Healthcare's CodeLink system, Applied Biosystems' Genome Survey Microarrays, and the custom microarrays printed with Operon's oligonucleotide set); and (3) deposition of presynthesized oligonucleotide probes on bead-based microarrays (Illumina's BeadChip microar-rays). We conclude this chapter with our views on the challenges and opportunities toward acceptance of DNA microarray data in clinical and regulatory settings.

Shi, Leming; Perkins, Roger G.; Tong, Weida

187

The Current Status of DNA Microarrays  

NASA Astrophysics Data System (ADS)

DNA microarray technology that allows simultaneous assay of thousands of genes in a single experiment has steadily advanced to become a mainstream method used in research, and has reached a stage that envisions its use in medical applications and personalized medicine. Many different strategies have been developed for manufacturing DNA microarrays. In this chapter, we discuss the manufacturing characteristics of seven microarray platforms that were used in a recently completed large study by the MicroArray Quality Control (MAQC) consortium, which evaluated the concordance of results across these platforms. The platforms can be grouped into three categories: (1) in situ synthesis of oligonucleotide probes on microarrays (Affymetrix GeneChip® arrays based on photolithography synthesis and Agilent's arrays based on inkjet synthesis); (2) spotting of presynthesized oligonucleotide probes on microarrays (GE Healthcare's CodeLink system, Applied Biosystems' Genome Survey Microarrays, and the custom microarrays printed with Operon's oligonucleotide set); and (3) deposition of presynthesized oligonucleotide probes on bead-based microarrays (Illumina's BeadChip microarrays). We conclude this chapter with our views on the challenges and opportunities toward acceptance of DNA microarray data in clinical and regulatory settings.

Shi, Leming; Perkins, Roger G.; Tong, Weida

188

Progression from High Insulin Resistance to Type 2 Diabetes Does Not Entail Additional Visceral Adipose Tissue Inflammation  

PubMed Central

Obesity is associated with a low-grade chronic inflammation state. As a consequence, adipose tissue expresses pro-inflammatory cytokines that propagate inflammatory responses systemically elsewhere, promoting whole-body insulin resistance and consequential islet ?-cell exhaustation. Thus, insulin resistance is considered the early stage of type 2 diabetes. However, there is evidence of obese individuals that never develop diabetes indicating that the mechanisms governing the association between the increase of inflammatory factors and type 2 diabetes are much more complex and deserve further investigation. We studied for the first time the differences in insulin signalling and inflammatory pathways in blood and visceral adipose tissue (VAT) of 20 lean healthy donors and 40 equal morbidly obese (MO) patients classified in high insulin resistance (high IR) degree and diabetes state. We studied the changes in proinflammatory markers and lipid content from serum; macrophage infiltration, mRNA expression of inflammatory cytokines and transcription factors, activation of kinases involved in inflammation and expression of insulin signalling molecules in VAT. VAT comparison of these experimental groups revealed that type 2 diabetic-MO subjects exhibit the same pro-inflammatory profile than the high IR-MO patients, characterized by elevated levels of IL-1?, IL-6, TNF?, JNK1/2, ERK1/2, STAT3 and NF?B. Our work rules out the assumption that the inflammation should be increased in obese people with type 2 diabetes compared to high IR obese. These findings indicate that some mechanisms, other than systemic and VAT inflammation must be involved in the development of type 2 diabetes in obesity. PMID:23110196

Barbarroja, Nuria; Lopez-Pedrera, Chary; Garrido-Sanchez, Lourdes; Mayas, Maria Dolores; Oliva-Olivera, Wilfredo; Bernal-Lopez, Maria Rosa; El Bekay, Rajaa; Tinahones, Francisco Jose

2012-01-01

189

DNA Microarrays for Identifying Fishes  

Microsoft Academic Search

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological\\u000a characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study,\\u000a a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species\\u000a from European seas based on

M. Kochzius; M. Nölte; H. Weber; N. Silkenbeumer; S. Hjörleifsdottir; G. O. Hreggvidsson; V. Marteinsson; K. Kappel; S. Planes; F. Tinti; A. Magoulas; E. Garcia Vazquez; C. Turan; C. Hervet; D. Campo Falgueras; A. Antoniou; M. Landi; D. Blohm

2008-01-01

190

JC Papovavirus Large Tumor (T)-Antigen Expression in Brain Tissue of Acquired Immune Deficiency Syndrome (AIDS) and Non-AIDS Patients with Progressive Multifocal Leukoencephalopathy  

NASA Astrophysics Data System (ADS)

Progressive multifocal leukoencephalopathy (PML) is a JC papovavirus infection of the central nervous system in immunocompromised patients. It is well established that demyelination in PML is caused by JC virus infection of oligodendroglia, but whether the nonstructural regulatory protein, large tumor (T) antigen, is detectable in infected human tissue was not known. Using a modification of the peroxidase-antiperoxidase technique, we found T antigen expressed in the nuclei of cells in virus-infected sites in five cases of PML studied, including two with acquired immune deficiency syndrome (AIDS). PML occurs in AIDS at a much higher frequency than in other immunosuppressive disorders, and PML in AIDS may represent a more severe form of JC virus infection of the central nervous system.

Stoner, Gerald L.; Ryschkewitsch, Caroline F.; Walker, Duard L.; Webster, Henry De F.

1986-04-01

191

JC papovavirus large tumor (T)-antigen expression in brain tissue of acquired immune deficiency syndrome (AIDS) and non-AIDS patients with progressive multifocal leukoencephalopathy.  

PubMed Central

Progressive multifocal leukoencephalopathy (PML) is a JC papovavirus infection of the central nervous system in immunocompromised patients. It is well established that demyelination in PML is caused by JC virus infection of oligodendroglia, but whether the nonstructural regulatory protein, large tumor (T) antigen, is detectable in infected human tissue was not known. Using a modification of the peroxidase-antiperoxidase technique, we found T antigen expressed in the nuclei of cells in virus-infected sites in five cases of PML studied, including two with acquired immune deficiency syndrome (AIDS). PML occurs in AIDS at a much higher frequency than in other immunosuppressive disorders, and PML in AIDS may represent a more severe form of JC virus infection of the central nervous system. Images PMID:3008157

Stoner, G L; Ryschkewitsch, C F; Walker, D L; Webster, H D

1986-01-01

192

Functions of Normal and Malignant Prostatic Stem/Progenitor Cells in Tissue Regeneration and Cancer Progression and Novel Targeting Therapies  

PubMed Central

This review summarizes the recent advancements that have improved our understanding of the functions of prostatic stem/progenitor cells in maintaining homeostasis of the prostate gland. We also describe the oncogenic events that may contribute to their malignant transformation into prostatic cancer stem/progenitor cells during cancer initiation and progression to metastatic disease stages. The molecular mechanisms that may contribute to the intrinsic or the acquisition of a resistant phenotype by the prostatic cancer stem/progenitor cells and their differentiated progenies with a luminal phenotype to the current therapies and disease relapse are also reviewed. The emphasis is on the critical functions of distinct tumorigenic signaling cascades induced through the epidermal growth factor system, hedgehog, Wnt/?-catenin, and/or stromal cell-derived factor-1/CXC chemokine receptor-4 pathways as well as the deregulated apoptotic signaling elements and ATP-binding cassette multidrug transporter. Of particular therapeutic interest, we also discuss the potential beneficial effects associated with the targeting of these signaling elements to overcome the resistance to current treatments and prostate cancer recurrence. The combined targeted strategies toward distinct oncogenic signaling cascades in prostatic cancer stem/progenitor cells and their progenies as well as their local microenvironment, which could improve the efficacy of current clinical chemotherapeutic treatments against incurable, androgen-independent, and metastatic prostate cancers, are also described. PMID:18292464

Mimeault, Murielle; Mehta, Parmender P.; Hauke, Ralph; Batra, Surinder K.

2008-01-01

193

Traumatic brain injury in young rats leads to progressive behavioral deficits coincident with altered tissue properties in adulthood.  

PubMed

Traumatic brain injury (TBI) affects many infants and children, and results in enduring motor and cognitive impairments with accompanying changes in white matter tracts, yet few experimental studies in rodent juvenile models of TBI (jTBI) have examined the timeline and nature of these deficits, histologically and functionally. We used a single controlled cortical impact (CCI) injury to the parietal cortex of rats at post-natal day (P) 17 to evaluate behavioral alterations, injury volume, and morphological and molecular changes in gray and white matter, with accompanying measures of electrophysiological function. At 60 days post-injury (dpi), we found that jTBI animals displayed behavioral deficits in foot-fault and rotarod tests, along with a left turn bias throughout their early developmental stages and into adulthood. In addition, anxiety-like behaviors on the zero maze emerged in jTBI animals at 60?dpi. The final lesion constituted only ?3% of brain volume, and morphological tissue changes were evaluated using MRI, as well as immunohistochemistry for neuronal nuclei (NeuN), myelin basic protein (MBP), neurofilament-200 (NF200), and oligodendrocytes (CNPase). White matter morphological changes were associated with a global increase in MBP immunostaining and reduced compound action potential amplitudes at 60?dpi. These results suggest that brain injury early in life can induce long-term white matter dysfunction, occurring in parallel with the delayed development and persistence of behavioral deficits, thus modeling clinical and longitudinal TBI observations. PMID:22697253

Ajao, David O; Pop, Viorela; Kamper, Joel E; Adami, Arash; Rudobeck, Emil; Huang, Lei; Vlkolinsky, Roman; Hartman, Richard E; Ashwal, Stephen; Obenaus, André; Badaut, Jérôme

2012-07-20

194

Development and function of membrane systems in plant tissue. Annual technical progress report, 15 September 1981-15 August 1982  

SciTech Connect

Over the past 11 months we have continued investigation of ion transport mechanisms in corn roots and mitochondria. In mitochondria we find that only citrate and isocitrate are transported by the H/sup +//citrate symporter. However, the in vivo function of this carrier remains in doubt because citrate does not appear to be an effective substrate for corn mitochondria. Studies with roots have been directed to why various types of injury or shock all result in temporary blockage of the H/sup +/-efflux pump in the plasmamembrane. It appears this may be due to an injury-mediated Ca/sup 2 +/ influx into the tissue, which by raising free Ca/sup 2 +/ in the cytosal activates calmodulin (CaM). In turn, the Ca.CaM complex appears to activate protein kinase, phosphorylating membrane proteins. It is possible that one of these phosphorylated proteins is responsible for inactivation of the H/sup +/-ATPase. Future work is planned around the consequences of Ca/sup 2 +/ influx into the root cell subsequent to injury, investigating the recovery of the H/sup +/-ATPase and the initiation of the biosyntheses which lead to augmented ion transport.

Hanson, J B

1982-01-01

195

Differential infection patterns of CD4+ T cells and lymphoid tissue viral burden distinguish progressive and nonprogressive lentiviral infections  

PubMed Central

Nonhuman primate natural hosts for simian immunodeficiency viruses (SIV) develop a nonresolving chronic infection but do not develop AIDS. Mechanisms to explain the nonprogressive nature of SIV infection in natural hosts that underlie maintained high levels of plasma viremia without apparent loss of target cells remain unclear. Here we used comprehensive approaches (ie, FACS sorting, quantitative RT-PCR, immunohistochemistry, and in situ hybridization) to study viral infection within subsets of peripheral blood and lymphoid tissue (LT) CD4+ T cells in cohorts of chronically SIV-infected rhesus macaques (RMs), HIV-infected humans, and SIVsmm-infected sooty mangabeys (SMs). We find: (1) infection frequencies among CD4+ T cells in chronically SIV-infected RMs are significantly higher than those in SIVsmm-infected SMs; (2) infected cells are found in distinct anatomic LT niches and different CD4+ T-cell subsets in SIV-infected RMs and SMs, with infection patterns of RMs reflecting HIV infection in humans; (3) TFH cells are infected at higher frequencies in RMs and humans than in SMs; and (4) LT viral burden, including follicular dendritic cell deposition of virus, is increased in RMs and humans compared with SMs. These data provide insights into how natural hosts are able to maintain high levels of plasma viremia while avoiding development of immunodeficiency. PMID:22990012

Vinton, Carol; Tabb, Brian; Hao, Xing Pei; Connick, Elizabeth; Paiardini, Mirko; Lifson, Jeffrey D.; Silvestri, Guido

2012-01-01

196

Traumatic Brain Injury in Young Rats Leads to Progressive Behavioral Deficits Coincident with Altered Tissue Properties in Adulthood  

PubMed Central

Abstract Traumatic brain injury (TBI) affects many infants and children, and results in enduring motor and cognitive impairments with accompanying changes in white matter tracts, yet few experimental studies in rodent juvenile models of TBI (jTBI) have examined the timeline and nature of these deficits, histologically and functionally. We used a single controlled cortical impact (CCI) injury to the parietal cortex of rats at post-natal day (P) 17 to evaluate behavioral alterations, injury volume, and morphological and molecular changes in gray and white matter, with accompanying measures of electrophysiological function. At 60 days post-injury (dpi), we found that jTBI animals displayed behavioral deficits in foot-fault and rotarod tests, along with a left turn bias throughout their early developmental stages and into adulthood. In addition, anxiety-like behaviors on the zero maze emerged in jTBI animals at 60?dpi. The final lesion constituted only ?3% of brain volume, and morphological tissue changes were evaluated using MRI, as well as immunohistochemistry for neuronal nuclei (NeuN), myelin basic protein (MBP), neurofilament-200 (NF200), and oligodendrocytes (CNPase). White matter morphological changes were associated with a global increase in MBP immunostaining and reduced compound action potential amplitudes at 60?dpi. These results suggest that brain injury early in life can induce long-term white matter dysfunction, occurring in parallel with the delayed development and persistence of behavioral deficits, thus modeling clinical and longitudinal TBI observations. PMID:22697253

Ajao, David O.; Pop, Viorela; Kamper, Joel E.; Adami, Arash; Rudobeck, Emil; Huang, Lei; Vlkolinsky, Roman; Hartman, Richard E.; Ashwal, Stephen; Obenaus, Andre

2012-01-01

197

On the classification of microarray gene-expression data.  

PubMed

We consider the classification of microarray gene-expression data. First, attention is given to the supervised case, where the tissue samples are classified with respect to a number of predefined classes and the intent is to assign a new unclassified tissue to one of these classes. The problems of forming a classifier and estimating its error rate are addressed in the context of there being a relatively small number of observations (tissue samples) compared to the number of variables (that is, the genes, which can number in the tens of thousands). We then proceed to the unsupervised case and consider the clustering of the tissue samples and also the clustering of the gene profiles. Both problems can be viewed as being non-standard ones in statistics and we address some of the key issues involved. The focus is on the use of mixture models to effect the clustering for both problems. PMID:22988257

Basford, Kaye E; McLachlan, Geoffrey J; Rathnayake, Suren I

2013-07-01

198

Analysis of protein glycosylation and phosphorylation using liquid phase separation, protein microarray technology, and mass spectrometry.  

PubMed

Protein glycosylation and phosphorylation are very common posttranslational modifications. The alteration of these modifications in cancer cells is closely related to the onset and progression of cancer and other disease states. In this protocol, strategies for monitoring the changes in protein glycosylation and phosphorylation in serum or tissue cells on a global scale and specifically characterizing these alterations are included. The technique is based on lectin affinity enrichment for glycoproteins, all liquid-phase two-dimensional fractionation, protein microarray, and mass spectrometry technology. Proteins are separated based on pI in the first dimension using chromatofocusing (CF) or liquid isoelectric focusing (IEF) followed by the second-dimension separation using nonporous silica RP-HPLC. Five lectins with different binding specificities to glycan structures are used for screening glycosylation patterns in human serum through a biotin streptavidin system. Fluorescent phosphodyes and phosphospecific antibodies are employed to detect specific phosphorylated proteins in cell lines or human tissues. The purified proteins of interest are identified by peptide sequencing. Their modifications including glycosylation and phosphorylation could be further characterized by mass-spectrometry-based approaches. These strategies can be used in biological samples for large-scale glycoproteome/phosphoproteome screening as well as for individual protein modification analysis. PMID:19241043

Zhao, Jia; Patwa, Tasneem H; Pal, Manoj; Qiu, Weilian; Lubman, David M

2009-01-01

199

Analysis of Protein Glycosylation and Phosphorylation Using Liquid Phase Separation, Protein Microarray Technology, and Mass Spectrometry  

PubMed Central

Summary Protein glycosylation and phosphorylation are very common posttranslational modifications. The alteration of these modifications in cancer cells is closely related to the onset and progression of cancer and other disease states. In this protocol, strategies for monitoring the changes in protein glycosylation and phosphorylation in serum or tissue cells on a global scale and specifically characterizing these alterations are included. The technique is based on lectin affinity enrichment for glycoproteins, all liquid-phase two-dimensional fractionation, protein microarray, and mass spectrometry technology. Proteins are separated based on pI in the first dimension using chromatofocusing (CF) or liquid isoelectric focusing (IEF) followed by the second-dimension separation using nonporous silica RP-HPLC. Five lectins with different binding specificities to glycan structures are used for screening glycosylation patterns in human serum through a biotin–streptavidin system. Fluorescent phosphodyes and phosphospecific antibodies are employed to detect specific phosphorylated proteins in cell lines or human tissues. The purified proteins of interest are identified by peptide sequencing. Their modifications including glycosylation and phosphorylation could be further characterized by mass-spectrometry-based approaches. These strategies can be used in biological samples for large-scale glycoproteome/phosphoproteome screening as well as for individual protein modification analysis. PMID:19241043

Zhao, Jia; Patwa, Tasneem H.; Pal, Manoj; Qiu, Weilian; Lubman, David M.

2010-01-01

200

Reverse phase protein microarrays advance to use in clinical trials  

PubMed Central

Individualizing cancer therapy for molecular targeted inhibitors requires a new class of molecular profiling technology that can map the functional state of the cancer cell signal pathways containing the drug targets. Reverse phase protein microarrays (RPMA) are a technology platform designed for quantitative, multiplexed analysis of specific phosphorylated, cleaved, or total (phosphorylated and non-phosphorylated) forms of cellular proteins from a limited amount of sample. This class of microarray can be used to interrogate tissue samples, cells, serum, or body fluids. RPMA were previously a research tool; now this technology has graduated to use in research clinical trials with clinical grade sensitivity and precision. In this review we describe the application of RPMA for multiplexed signal pathway analysis in therapeutic monitoring, biomarker discovery, and evaluation of pharmaceutical targets, and conclude with a summary of the technical aspects of RPMA construction and analysis. PMID:20974554

Mueller, Claudius; Liotta, Lance A.; Espina, Virginia

2010-01-01

201

Collagenase and tissue plasminogen activator production in developing rat calvariae: normal progression despite fetal exposure to microgravity  

NASA Technical Reports Server (NTRS)

Exposure to zero gravity has been shown to cause a decrease in bone formation. This implicates osteoblasts as the gravity-sensing cell in bone. Osteoblasts also are known to produce neutral proteinases, including collagenase and tissue plasminogen activator (tPA), which are thought to be important in bone development and remodeling. The present study investigated the effects of zero gravity on development of calvariae and their expression of collagenase and tPA. After in utero exposure to zero gravity for 9 days on the NASA STS-70 space shuttle mission, the calvariae of rat pups were examined by immunohistochemistry for the presence and location of these two proteinases. The ages of the pups were from gestational day 20 (G20) to postnatal (PN) day 35. Both collagenase and tPA were found to be present at all ages examined, with the greatest amount of both proteinases present in the PN14 rats. At later ages, high amounts were maintained for tPA but collagenase decreased substantially between ages PN21 to PN35. The location of collagenase was found to be associated with bone-lining cells, osteoblasts, osteocytes, and in the matrix along cement lines. In contrast, tPA was associated with endothelial cells lining the blood vessels entering bone. The presence and developmental expression of these two proteinases appeared to be unaffected by the exposure to zero gravity. The calvarial thickness of the pups was also examined; again the exposure to zero gravity showed little to no effect on the growth of the calvariae. Notably, from G20 to PN14, calvarial thickness increased dramatically, reaching a plateau after this age. It was apparent that elevated collagenase expression correlated with rapid bone growth in the period from G20 to PN14. To conclude, collagenase and tPA are present during the development of rat calvariae. Despite being produced by the same cell in vitro, i.e., the osteoblast, they are located in distinctly different places in bone in vivo. Their presence, developmental expression, and quantity do not seem to be affected by a brief exposure to zero gravity in utero.

Davis, B. A.; Sipe, B.; Gershan, L. A.; Fiacco, G. J.; Lorenz, T. C.; Jeffrey, J. J.; Partridge, N. C.

1998-01-01

202

A computational framework for optimal masking in the synthesis of oligonucleotide microarrays.  

PubMed

High-throughput genomic technologies are revolutionizing modern biology. In particular, DNA microarrays have become one of the most powerful tools for profiling global mRNA expression in different tissues and environmental conditions, and for detecting single nucleotide polymorphisms. The broad applicability of gene expression profiling to the biological and medical realms has generated expanding demand for mass production of microarrays, which in turn has created considerable interest in improving the cost effectiveness of microarray fabrication techniques. We have developed the computational framework for an optimal synthesis strategy for oligonucleotide microarrays. The problem was introduced by Hubbell et al. Here, we formalize the problem, obtain precise bounds on its complexity and devise several computational solutions. PMID:12384608

Kasif, Simon; Weng, Zhiping; Derti, Adnan; Beigel, Richard; DeLisi, Charles

2002-10-15

203

THE ABRF MARG MICROARRAY SURVEY 2005: TAKING THE PULSE ON THE MICROARRAY FIELD  

EPA Science Inventory

Over the past several years microarray technology has evolved into a critical component of any discovery based program. Since 1999, the Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) has conducted biennial surveys designed to generate a pr...

204

Spotting effect in microarray experiments  

PubMed Central

Background Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio) and intensity across the array. Results Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure. Conclusions The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis. PMID:15151695

Mary-Huard, Tristan; Daudin, Jean-Jacques; Robin, Stephane; Bitton, Frederique; Cabannes, Eric; Hilson, Pierre

2004-01-01

205

Protein Microarrays and Biomarkers of Infectious Disease  

PubMed Central

Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. Depending on the application, design issues should be considered, such as the need for multiplexing and label or label free detection methods. New developments, challenges, and future demands in infectious disease research will impact the application of protein microarrays for discovery and validation of biomarkers. PMID:21614200

Natesan, Mohan; Ulrich, Robert G.

2010-01-01

206

Minimum information about a microarray experiment (MIAME)—toward standards for microarray data  

Microsoft Academic Search

Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum

Paul Spellman; Chris Stoeckert; John Aach; Wilhelm Ansorge; Catherine A. Ball; Helen C. Causton; Terry Gaasterland; Patrick Glenisson; Frank C. P. Holstege; Irene F. Kim; Victor Markowitz; John C. Matese; Helen Parkinson; Alan Robinson; Ugis Sarkans; Steffen Schulze-Kremer; Jason Stewart; Ronald Taylor; Jaak Vilo; Martin Vingron; Alvis Brazma; John Quackenbush

2001-01-01

207

THE ABRF-MARG MICROARRAY SURVEY 2004: TAKING THE PULSE OF THE MICROARRAY FIELD  

EPA Science Inventory

Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. The goal of the surve...

208

Microarray blood testing: Pros & cons.  

PubMed

Blood donation screening represents rather a unique set of blood grouping-related and pathogen detection assays. We are confronted with continuously growing numbers of testing targets. Ideally, the spectrum of clinically significant blood group antigens and alloantibodies would be wider than allowed by current routine tests. At the same time, we are witnessing an increase in emerging and re-emerging human pathogens due to urbanisation, increased international travel and trade, climate change and other factors. The spectrum of blood-borne infectious agents requiring donation screening is expected to grow correspondingly. Dengue and chikungunya viruses, variant CJD and hepatitis E virus represent just some of the candidate infectious agents for future donation screening. Multiplexing techniques, such as microarrays are well suited to address the growing number of targets, pending the increase in sensitivity of some of the microarrays assays. There are several possible scenarios for future testing algorithms, combining new multiplexing techniques with the existing blood testing assays. New generation testing platforms capable of microbiology screening, blood grouping and potential additional types of targets, are also being developed. PMID:20079661

Petrik, Juraj

2010-01-01

209

Carbohydrate microarrays by microcontact printing.  

PubMed

This Article describes the preparation of carbohydrate microarrays by the immobilization of carbohydrates via microcontact printing (microCP) on glass and silicon substrates. To this end, diene-modified carbohydrates (galactose, glucose, mannose, lactose, and maltose) were printed on maleimide-terminated self-assembled monolayers (SAMs). A Diels-Alder reaction occurred exclusively in the contact area between stamp and substrate and resulted in a carbohydrate pattern on the substrate. It was found that cyclopentadiene-functionalized carbohydrates could be printed within minutes at room temperature, whereas furan-functionalized carbohydrates required long printing times and high temperatures. By successive printing, microstructured arrays of up to three different carbohydrates could be produced. Immobilization and patterning of the carbohydrates on the surfaces was investigated with contact angle measurements, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and fluorescence microscopy. Furthermore, the lectins concanavalin A (ConA) and peanut agglutinin (PNA) bind to the microarrays, and the printed carbohydrates retain their characteristic selectivity toward these proteins. PMID:20092308

Wendeln, Christian; Heile, Andreas; Arlinghaus, Heinrich F; Ravoo, Bart Jan

2010-04-01

210

Photoelectrochemical synthesis of DNA microarrays  

PubMed Central

Optical addressing of semiconductor electrodes represents a powerful technology that enables the independent and parallel control of a very large number of electrical phenomena at the solid-electrolyte interface. To date, it has been used in a wide range of applications including electrophoretic manipulation, biomolecule sensing, and stimulating networks of neurons. Here, we have adapted this approach for the parallel addressing of redox reactions, and report the construction of a DNA microarray synthesis platform based on semiconductor photoelectrochemistry (PEC). An amorphous silicon photoconductor is activated by an optical projection system to create virtual electrodes capable of electrochemically generating protons; these PEC-generated protons then cleave the acid-labile dimethoxytrityl protecting groups of DNA phosphoramidite synthesis reagents with the requisite spatial selectivity to generate DNA microarrays. Furthermore, a thin-film porous glass dramatically increases the amount of DNA synthesized per chip by over an order of magnitude versus uncoated glass. This platform demonstrates that PEC can be used toward combinatorial bio-polymer and small molecule synthesis. PMID:19706433

Chow, Brian Y.; Emig, Christopher J.; Jacobson, Joseph M.

2009-01-01

211

Integrated imaging instrument for self-calibrated fluorescence protein microarrays  

PubMed Central

Protein microarrays, or multiplexed and high-throughput assays, monitor multiple protein binding events to facilitate the understanding of disease progression and cell physiology. Fluorescence imaging is a popular method to detect proteins captured by immobilized probes with high sensitivity and specificity. Reliability of fluorescence assays depends on achieving minimal inter- and intra-assay probe immobilization variation, an ongoing challenge for protein microarrays. Therefore, it is desirable to establish a label-free method to quantify the probe density prior to target incubation to calibrate the fluorescence readout. Previously, a silicon oxide on silicon chip design was introduced to enhance the fluorescence signal and enable interferometric imaging to self-calibrate the signal with the immobilized probe density. In this paper, an integrated interferometric reflectance imaging sensor and wide-field fluorescence instrument is introduced for sensitive and calibrated microarray measurements. This platform is able to analyze a 2.5 mm × 3.4 mm area, or 200 spots (100 ?m diameter with 200 ?m pitch), in a single field-of-view. PMID:24182114

Reddington, A. P.; Monroe, M. R.; Unlu, M. S.

2013-01-01

212

Paraffin-Embedded Cell Line Microarray (PECLIMA): Development and Validation of a High-Throughput Method for Antigen Profiling of Cell Lines  

Microsoft Academic Search

The introduction of high-throughput techniques is increasingly providing abundant information on molecular alterations requiring validation at the posttranscriptional level. Protein expression is now efficiently evaluated in large series of tumors included in tissue microarrays. We propose, describe and validate a technique to elaborate paraffin-embedded cell line microarrays (PECLIMA) from fixed cell cultures, which can be processed like standard surgical pathology

Berta Ferrer; Raquel Bermudo; Timothy Thomson; Iracema Nayach; Marta Soler; Montserrat Sánchez; Mireia Castillo; Julia Calvo; Elias Campo; Pedro L. Fernández

2005-01-01

213

PRINCIPAL COMPONENTS ANALYSIS TO SUMMARIZE MICROARRAY EXPERIMENTS  

E-print Network

.stanford.edu A series of microarray experiments produces observations of differential expression for thousands of genes that application of PCA to expression data (where the experimental conditions are the variables, and the gene Introduction The study of gene expression has been greatly facilitated by DNA microarray technology (Schena et

Stuart, Josh

214

Hybridization thermodynamics of NimbleGen Microarrays  

Microsoft Academic Search

BACKGROUND: While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets. RESULTS: We demonstrate the benefits of an improved model for microarray hybridization and assess

Ulrike Mueckstein; Germán G. Leparc; Alexandra Posekany; Ivo L. Hofacker; David P. Kreil

2010-01-01

215

Transformation and Normalization of Oligonucleotide Microarray Data  

E-print Network

of the transformation, producing a data set without chip or slide effects but with constant variance and with symmetTransformation and Normalization of Oligonucleotide Microarray Data Sue C. Geller Department microarray data or doing power calculations have an underlying assumption of constant variance across all

Rocke, David M.

216

Between-group analysis of microarray data  

Microsoft Academic Search

Motivation: Most supervised classification methods are limited by the requirement for more cases than variables. In microarray data the number of variables (genes) far exceeds the number of cases (arrays), and thus filtering and pre-selection of genes is required. We describe the application of Between Group Analysis (BGA) to the analysis of microarray data. A feature of BGA is that

Aedín C. Culhane; Guy Perrière; Elizabeth C. Considine; Thomas G. Cotter; Desmond G. Higgins

2002-01-01

217

Pro-oncogene Pokemon promotes breast cancer progression by upregulating survivin expression  

PubMed Central

Introduction Pokemon is an oncogenic transcription factor involved in cell growth, differentiation and oncogenesis, but little is known about its role in human breast cancer. In this study, we aimed to reveal the role of Pokemon in breast cancer progression and patient survival and to understand its underlying mechanisms. Methods Tissue microarray analysis of breast cancer tissues from patients with complete clinicopathological data and more than 20 years of follow-up were used to evaluate Pokemon expression and its correlation with the progression and prognosis of the disease. DNA microarray analysis of MCF-7 cells that overexpress Pokemon was used to identify Pokemon target genes. Chromatin immunoprecipitation (ChIP) and site-directed mutagenesis were utilized to determine how Pokemon regulates survivin expression, a target gene. Results Pokemon was found to be overexpressed in 158 (86.8%) of 182 breast cancer tissues, and its expression was correlated with tumor size (P = 0.0148) and lymph node metastasis (P = 0.0014). Pokemon expression led to worse overall (n = 175, P = 0.01) and disease-related (n = 79, P = 0.0134) patient survival. DNA microarray analyses revealed that in MCF-7 breast cancer cells, Pokemon regulates the expression of at least 121 genes involved in several signaling and metabolic pathways, including anti-apoptotic survivin. In clinical specimens, Pokemon and survivin expression were highly correlated (n = 49, r = 0.6799, P < 0.0001). ChIP and site-directed mutagenesis indicated that Pokemon induces survivin expression by binding to the GT boxes in its promoter. Conclusions Pokemon promotes breast cancer progression by upregulating survivin expression and thus may be a potential target for the treatment of this malignancy. PMID:21392388

2011-01-01

218

Glycoprotein Analysis Using Protein Microarrays and Mass Spectrometry  

PubMed Central

Protein glycosylation plays an important role in a multitude of biological processes such as cell-cell recognition, growth, differentiation, and cell death. It has been shown that specific glycosylation changes are key in disease progression, and can have diagnostic value for a variety of disease types such as cancer and inflammation. The complexity of carbohydrate structures and their derivatives makes their study a real challenge. Improving the isolation, separation, and characterization of carbohydrates and their glycoproteins is a subject of increasing scientific interest. With development of new stationary phases and molecules that have affinity properties for glycoproteins, the isolation and separation of these compounds have advanced significantly. In addition to detection with mass spectrometry, the microarray platform has become an essential tool to characterize glycan structure and to study glycosylation-related biological interactions, by using probes as a means to interrogate the spotted or captured glycosylated molecules on the arrays. Furthermore, the high-throughput and reproducible nature of microarray platforms have been highlighted by its extensive applications in the field of biomarker validation, where a large number of samples must be analyzed multiple times. This review covers a brief survey of the other experimental methodologies that are currently being developed and used to study glycosylation, and emphasizes methodologies that involve the use of microarray platforms. This review describes recent advances in several options of microarray platforms used in glycoprotein analysis, including glycoprotein arrays, glycan arrays, lectin arrays, and antibody/lectin arrays. The translational use of these arrays in applications related to characterization of cells and biomarker discovery is also included. PMID:20077480

Patwa, Tasneem; Li, Chen; Simeone, Diane M.; Lubman, David M.

2009-01-01

219

Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics  

Microsoft Academic Search

Novel and powerful technologies such as DNA microarrays and proteomics have made possible the analysis of the expression levels of multiple genes simultaneously both in health and disease. In combination, these technologies promise to revolutionize biology, in particular in the area of molecular medicine as they are expected to reveal gene regulation events involved in disease progression as well as

Julio E Celis; Mogens Kruhøffer; Irina Gromova; Casper Frederiksen; Morten Østergaard; Thomas Thykjaer; Pavel Gromov; Jinsheng Yu; Hildur Pálsdóttir; Nils Magnusson; Torben F Ørntoft

2000-01-01

220

DNA Microarrays for Identifying Fishes  

PubMed Central

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products. PMID:18270778

Nolte, M.; Weber, H.; Silkenbeumer, N.; Hjorleifsdottir, S.; Hreggvidsson, G. O.; Marteinsson, V.; Kappel, K.; Planes, S.; Tinti, F.; Magoulas, A.; Garcia Vazquez, E.; Turan, C.; Hervet, C.; Campo Falgueras, D.; Antoniou, A.; Landi, M.; Blohm, D.

2008-01-01

221

Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach  

PubMed Central

Background The main limitation in performing genome-wide gene-expression profiling is the assay of low-expression genes. Approaches with high throughput and high sensitivity for assaying low-expression transcripts are urgently needed for functional genomic studies. Combination of the suppressive subtractive hybridization (SSH) and cDNA microarray techniques using the subtracted cDNA clones as probes printed on chips has greatly improved the efficiency for fishing out the differentially expressed clones and has been used before. However, it remains tedious and inefficient sequencing works for identifying genes including the great number of redundancy in the subtracted amplicons, and sacrifices the original advantages of high sensitivity of SSH in profiling low-expression transcriptomes. Results We modified the previous combination of SSH and microarray methods by directly using the subtracted amplicons as targets to hybridize the pre-made cDNA microarrays (named as "SSH/microarray"). mRNA prepared from three pairs of hepatoma and non-hepatoma liver tissues was subjected to the SSH/microarray assays, as well as directly to regular cDNA microarray assays for comparison. As compared to the original SSH and microarray combination assays, the modified SSH/microarray assays allowed for much easier inspection of the subtraction efficiency and identification of genes in the subtracted amplicons without tedious and inefficient sequencing work. On the other hand, 5015 of the 9376 genes originally filtered out by the regular cDNA microarray assays because of low expression became analyzable by the SSH/microarray assays. Moreover, the SSH/microarray assays detected about ten times more (701 vs. 69) HCC differentially expressed genes (at least a two-fold difference and P < 0.01), particularly for those with rare transcripts, than did the regular cDNA microarray assays. The differential expression was validated in 9 randomly selected genes in 18 pairs of hepatoma/non-hepatoma liver tissues using quantitative RT-PCR. The SSH/microarray approaches resulted in identifying many differentially expressed genes implicated in the regulation of cell cycle, cell death, signal transduction and cell morphogenesis, suggesting the involvement of multi-biological processes in hepato-carcinogenesis. Conclusion The modified SSH/microarray approach is a simple but high-sensitive and high-efficient tool for differentially profiling the low-expression transcriptomes. It is most adequate for applying to functional genomic studies. PMID:16737534

Pan, Yi-Shin; Lee, Yun-Shien; Lee, Yung-Lin; Lee, Wei-Chen; Hsieh, Sen-Yung

2006-01-01

222

Systematic review of accuracy of prenatal diagnosis for abnormal chromosome diseases by microarray technology.  

PubMed

The accuracy of prenatal diagnosis for abnormal chromosome diseases by chromosome microarray technology and karyotyping were compared. A literature search was carried out in the MEDLINE database with the keywords "chromosome" and "karyotype" and "genetic testing" and "prenatal diagnosis" and "oligonucleotide array sequence". The studies obtained were filtered by using the QUADAS tool, and studies conforming to the quality standard were fully analyzed. There was one paper conforming to the QUADAS standards including 4406 gravidas with adaptability syndromes of prenatal diagnosis including elderly parturient women, abnormal structure by type-B ultrasound, and other abnormalities. Microarray technology yielded successful diagnoses in 4340 cases (98.8%), and there was no need for tissue culture in 87.9% of the samples. All aneuploids and non-parallel translocations in 4282 cases of non-chimera identified by karyotyping could be detected using microarray analysis technology, whereas parallel translocations and fetal triploids could not be detected by microarray analysis technology. In the samples with normal karyotyping results, type-B ultrasound showed that 6% of chromosomal deficiencies or chromosome duplications could be detected by microarray technology, and the same abnormal chromosomes were detected in 1.7% of elderly parturient women and samples with positive serology screening results. In the prenatal diagnosis test, compared with karyotyping, microarray technology could identify the extra cell genetic information with clinical significance, aneuploids, and non-parallel translocations; however, its disadvantage is that it could not identify parallel translocations and triploids. PMID:25366803

Xu, H B; Yang, H; Liu, G; Chen, H

2014-01-01

223

Analysis of protein tyrosine phosphatase interactions with microarrayed phosphopeptide substrates using imaging mass spectrometry  

PubMed Central

Microarrays of peptide and recombinant protein libraries are routinely used for high-throughput studies of protein-protein interactions and enzymatic activities. Imaging mass spectrometry (IMS) is currently applied as a method to localize analytes on thin tissue sections and other surfaces. Here, we have applied IMS as a label-free means to analyze protein-peptide interactions in a microarray-based phosphatase assay. This IMS strategy visualizes the entire microarray in one composite image by collecting a pre-defined raster of MALDI-TOF MS spectra over the surface of the chip. Examining the bacterial tyrosine phosphatase YopH, we used IMS as a label-free means to visualize enzyme binding and activity with a microarrayed phosphopeptide library printed on chips coated with either gold or indium-tin oxide. Further, we demonstrate that microarray-based IMS can be coupled with surface plasmon resonance imaging to add kinetic analyses to measured binding interactions. The method described here is within the capabilities of many modern MALDI-TOF instruments and has general utility for the label-free analysis of microarray assays. PMID:23906642

McKee, Christopher J.; Hines, Harry B.; Ulrich, Robert G.

2013-01-01

224

Seasonal dynamics of harmful algae in outer Oslofjorden monitored by microarray, qPCR, and microscopy.  

PubMed

Monitoring of marine microalgae is important to predict and manage harmful algal blooms. Microarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a multi-species microarray as a tool to aid monitoring agencies. We tested the suitability of different prototype versions of the MIDTAL microarray for the monthly monitoring of a sampling station in outer Oslofjorden during a 1-year period. Microarray data from two different versions of the MIDTAL chip were compared to results from cell counts (several species) and quantitative real-time PCR (qPCR; only Pseudochattonella spp.). While results from generation 2.5 microarrays exhibited a high number of false positive signals, generation 3.3 microarray data generally correlated with microscopy and qPCR data, with three important limitations: (1) Pseudo-nitzschia cells were not reliably detected, possibly because cells were not sufficiently retained during filtration or lysed during the extraction, and because of low sensitivity of the probes; (2) in the case of samples with high concentrations of non-target species, the sensitivity of the arrays was decreased; (3) one occurrence of Alexandrium pseudogonyaulax was not detected due to a 1-bp mismatch with the genus probe represented on the microarray. In spite of these shortcomings our data demonstrate the overall progress made and the potential of the MIDTAL array. The case of Pseudochattonella - where two morphologically similar species impossible to separate by light microscopy were distinguished - in particular, underlines the added value of molecular methods such as microarrays in routine phytoplankton monitoring. PMID:23325054

Dittami, Simon M; Hostyeva, Vladyslava; Egge, Elianne Sirnæs; Kegel, Jessica U; Eikrem, Wenche; Edvardsen, Bente

2013-10-01

225

MARS: Microarray analysis, retrieval, and storage system  

PubMed Central

Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at . PMID:15836795

Maurer, Michael; Molidor, Robert; Sturn, Alexander; Hartler, Juergen; Hackl, Hubert; Stocker, Gernot; Prokesch, Andreas; Scheideler, Marcel; Trajanoski, Zlatko

2005-01-01

226

DNA Microarrays in Herbal Drug Research  

PubMed Central

Natural products are gaining increased applications in drug discovery and development. Being chemically diverse they are able to modulate several targets simultaneously in a complex system. Analysis of gene expression becomes necessary for better understanding of molecular mechanisms. Conventional strategies for expression profiling are optimized for single gene analysis. DNA microarrays serve as suitable high throughput tool for simultaneous analysis of multiple genes. Major practical applicability of DNA microarrays remains in DNA mutation and polymorphism analysis. This review highlights applications of DNA microarrays in pharmacodynamics, pharmacogenomics, toxicogenomics and quality control of herbal drugs and extracts. PMID:17173108

Chavan, Preeti; Joshi, Kalpana; Patwardhan, Bhushan

2006-01-01

227

Differentially expressed proteins and associated histological and disease progression changes in cotyledon tissue of a resistant and susceptible genotype of brassica napus infected with Sclerotinia sclerotiorum.  

PubMed

Sclerotinia rot caused by Sclerotinia sclerotiorum is one of the most serious diseases of oilseed rape. To understand the resistance mechanisms in the Brassica napus to S. sclerotiorum, comparative disease progression, histological and proteomic studies were conducted of two B. napus genotypes (resistant cv. Charlton, susceptible cv. RQ001-02M2). At 72 and 96 h post inoculation (hpi), lesion size on cotyledons was significantly (P?0.001) smaller in the resistant Charlton. Anatomical investigations revealed impeded fungal growth (at 24 hpi and onwards) and hyphal disintegration only on resistant Charlton. Temporal changes (12, 24, 48 and 72 hpi) in protein profile showed certain enzymes up-regulated only in resistant Charlton, such as those related to primary metabolic pathways, antioxidant defence, ethylene biosynthesis, pathogenesis related proteins, protein synthesis and protein folding, play a role in mediating defence responses against S. sclerotiorum. Similarly a eukaryotic translation initiation factor 5A enzyme with increased abundance in susceptible RQ001-02M2 and decreased levels in resistant Charlton has a role in increased susceptibility to this pathogen. This is the first time that the expression of these enzymes has been shown to be associated with mediating the defence response against S. sclerotinia in cotyledon tissue of a resistant cultivar of B. napus at a proteomics level. This study not only provides important new insights into the resistance mechanisms within B. napus against S. sclerotiorum, but opens the way for novel engineering of new B. napus varieties that over-express these key enzymes as a strategy to enhance resistance and better manage this devastating pathogen. PMID:23776450

Garg, Harsh; Li, Hua; Sivasithamparam, Krishnapillai; Barbetti, Martin J

2013-01-01

228

Integrated Genomic Analysis of Nodular Tissue in Macronodular Adrenocortical Hyperplasia: Progression of Tumorigenesis in a Disorder Associated with Multiple Benign Lesions  

PubMed Central

Context: Massive macronodular adrenocortical disease or ACTH-independent macronodular adrenal hyperplasia (AIMAH) is a clinically and genetically heterogeneous disorder. Objective and Design: Whole-genome expression profiling and oligonucleotide array comparative genomic hybridization changes were analyzed in samples of different nodules from the same patients with AIMAH. Quantitative RT-PCR and staining were employed to validate the mRNA array data. Results: Chromosomal gains were more frequent in larger nodules when compared with smaller nodules from the same patients. Among the 50 most overexpressed genes, 50% had a chromosomal locus that was amplified in the comparative genomic hybridization data. Although the list of most over- and underexpressed genes was similar between the nodules of different size, the gene set enrichment analysis identified different pathways associated with AIMAH that corresponded to the size; the smaller nodules were mainly enriched for metabolic pathways, whereas p53 signaling and cancer genes were enriched in larger nodules. Confirmatory studies demonstrated that BCL2, E2F1, EGF, c-KIT, MYB, PRKCA, and CTNNB1 were overexpressed in the larger nodules at messenger and/or protein levels. Chromosomal enrichment analysis showed that chromosomes 20q13 and 14q23 might be involved in progression of AIMAH from smaller to larger tumors. Conclusion: Integrated transcriptomic and genomic data for AIMAH provides supporting evidence to the hypothesis that larger adrenal lesions, in the context of this chronic, polyclonal hyperplasia, accumulate an increased number of genomic and, subsequently, transcript abnormalities. The latter shows that the disease appears to start with mainly tissue metabolic derangements, as suggested by the study of the smaller nodules, but larger lesions showed aberrant expression of oncogenic pathways. PMID:21252250

Almeida, Madson Q.; Harran, Michelle; Bimpaki, Eirini I.; Hsiao, Hui-Pin; Horvath, Anelia; Cheadle, Chris; Watkins, Tonya; Nesterova, Maria

2011-01-01

229

Differentially Expressed Proteins and Associated Histological and Disease Progression Changes in Cotyledon Tissue of a Resistant and Susceptible Genotype of Brassica napus Infected with Sclerotinia sclerotiorum  

PubMed Central

Sclerotinia rot caused by Sclerotinia sclerotiorum is one of the most serious diseases of oilseed rape. To understand the resistance mechanisms in the Brassica napus to S. sclerotiorum, comparative disease progression, histological and proteomic studies were conducted of two B. napus genotypes (resistant cv. Charlton, susceptible cv. RQ001-02M2). At 72 and 96 h post inoculation (hpi), lesion size on cotyledons was significantly (P?0.001) smaller in the resistant Charlton. Anatomical investigations revealed impeded fungal growth (at 24 hpi and onwards) and hyphal disintegration only on resistant Charlton. Temporal changes (12, 24, 48 and 72 hpi) in protein profile showed certain enzymes up-regulated only in resistant Charlton, such as those related to primary metabolic pathways, antioxidant defence, ethylene biosynthesis, pathogenesis related proteins, protein synthesis and protein folding, play a role in mediating defence responses against S. sclerotiorum. Similarly a eukaryotic translation initiation factor 5A enzyme with increased abundance in susceptible RQ001-02M2 and decreased levels in resistant Charlton has a role in increased susceptibility to this pathogen. This is the first time that the expression of these enzymes has been shown to be associated with mediating the defence response against S. sclerotinia in cotyledon tissue of a resistant cultivar of B. napus at a proteomics level. This study not only provides important new insights into the resistance mechanisms within B. napus against S. sclerotiorum, but opens the way for novel engineering of new B. napus varieties that over-express these key enzymes as a strategy to enhance resistance and better manage this devastating pathogen. PMID:23776450

Garg, Harsh; Li, Hua; Sivasithamparam, Krishnapillai; Barbetti, Martin J.

2013-01-01

230

A novel surface modification approach for protein and cell microarrays  

NASA Astrophysics Data System (ADS)

Tissue engineering and stem cell technologies have led to a rapidly increasing interest in the control of the behavior of mammalian cells growing on tissue culture substrates. Multifunctional polymer coatings can assist research in this area in many ways, for example, by providing low non-specific protein adsorption properties and reactive functional groups at the surface. The latter can be used for immobilization of specific biological factors that influence cell behavior. In this study, glass slides were coated with copolymers of glycidyl methacrylate (GMA) and poly(ethylene glycol) methacrylate (PEGMA). The coatings were prepared by three different methods based on dip and spin coating as well as polymer grafting procedures. Coatings were characterized by X-ray photoelectron spectroscopy, surface sensitive infrared spectroscopy, ellipsometry and contact angle measurements. A fluorescently labelled protein was deposited onto reactive coatings using a contact microarrayer. Printing of a model protein (fluorescein labeled bovine serum albumin) was performed at different protein concentrations, pH, temperature, humidity and using different micropins. The arraying of proteins was studied with a microarray scanner. Arrays printed at a protein concentration above 50 μg/mL prepared in pH 5 phosphate buffer at 10°C and 65% relative humidity gave the most favourable results in terms of the homogeneity of the printed spots and the fluorescence intensity.

Kurkuri, Mahaveer D.; Driever, Chantelle; Thissen, Helmut W.; Voelcker, Nicholas H.

2007-01-01

231

The Stanford Microarray Database accommodates additional microarray platforms and data formats  

Microsoft Academic Search

The Stanford Microarray Database (SMD) (http:\\/\\/ smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. Inaddition,SMDfunctionsasaresourcefortheentire biological research community by providing unrest- ricted access to microarray data published by SMD users and by disseminating its source code. In addi- tion to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the

Catherine A. Ball; Ihab A. B. Awad; Janos Demeter; Jeremy Gollub; Joan M. Hebert; Tina Hernandez-boussard; Heng Jin; John C. Matese; Michael Nitzberg; Farrell Wymore; Zachariah K. Zachariah; Patrick O. Brown; Gavin Sherlock

2005-01-01

232

NCI Assists Establishment of DNA Microarray Facilities  

Cancer.gov

The National Cancer Institute (NCI) announced today that it will spend $4.1 million to help 24 cancer research centers throughout the country purchase equipment needed to launch DNA microarray facilities.

233

Based Adaptive Wavelet Hidden Markov Tree for Microarray Image Enhancement  

Microsoft Academic Search

The accuracy of the gene expression depends on microarray image processing technology. However, eliminating the noise from different sources inherented in the DNA microarray still a challenging problem, which mainly contribute to the diversity and complexity of the noise of microarray image. Traditionally, statistical methods are used to estimate the noises of the microarray images. In this paper, we construct

Li Ying; Cui Li

2008-01-01

234

An Overview of DNA Microarray Image Requirements for Automated Processing  

Microsoft Academic Search

We present an overview of DNA microarray image requirements for automated processing and information extraction from spotted glass slides. Motivation of our review comes from the need to automate high-throughput microarray data processing due to exponentially growing amounts of microarray data. In order to automate microarray image processing and draw biologically meaningful conclusions from experiments, one has to understand the

Peter Bajcsy

2005-01-01

235

Contributions to Statistical Problems Related to Microarray Data  

ERIC Educational Resources Information Center

Microarray is a high throughput technology to measure the gene expression. Analysis of microarray data brings many interesting and challenging problems. This thesis consists three studies related to microarray data. First, we propose a Bayesian model for microarray data and use Bayes Factors to identify differentially expressed genes. Second, we…

Hong, Feng

2009-01-01

236

Tertiary lymphoid tissue  

PubMed Central

Tumor-infiltrating lymphocytes influence colorectal cancer progression. We have recently documented that tertiary lymphoid tissue in the colorectal cancer microenvironment orchestrates lymphocyte infiltration and that tertiary lymphoid tissue and lymphocytes cooperate in a coordinated antitumor immune response to improve patient outcome. Thus, tertiary lymphoid tissue represents a potential target in the design of tailored immune-based therapeutic approaches. PMID:25083321

Di Caro, Giuseppe; Marchesi, Federica

2014-01-01

237

Computational Intelligence Algorithms and DNA Microarrays  

Microsoft Academic Search

In this chapter, we present Computational Intelligence algorithms, such as Neural Network algorithms, Evolutionary Algorithms,\\u000a and clustering algorithms and their application to DNA microarray experimental data analysis. Additionally, dimension reduction\\u000a techniques are evaluated. Our aim is to study and compare various Computational Intelligence approaches and demonstrate their\\u000a applicability as well as their weaknesses and shortcomings to efficient DNA microarray data

Dimitris K. Tasoulis; Vassilis P. Plagianakos; Michael N. Vrahatis

2008-01-01

238

Protein Microarrays: Novel Developments and Applications  

Microsoft Academic Search

Protein microarray technology possesses some of the greatest potential for providing direct information on protein function\\u000a and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological\\u000a pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical\\u000a pathways and have been used for

Luis Berrade; Angie E. Garcia; Julio A. Camarero

2011-01-01

239

Expression profiling using cDNA microarrays  

Microsoft Academic Search

cDNA microarrays are capable of profiling gene expression patterns of tens of thousands of genes in a single experiment. DNA targets, in the form of 3´ expressed sequence tags (ESTs), are arrayed onto glass slides (or membranes) and probed with fluorescent– or radioactively–labelled cDNAs. Here, we review technical aspects of cDNA microarrays, including the general principles, fabrication of the arrays,

David J Duggan; Michael Bittner; Yidong Chen; Paul Meltzer; Jeffrey M. Trent

1999-01-01

240

Inferring Species Phylogenies: A Microarray Approach  

Microsoft Academic Search

\\u000a The incongruence between the gene trees and species remains a challenge in molecular phylogenetics. In this work, we propose\\u000a a novel microarray approach to resolve this problem based on our previously proposed phylogenomic mining method. In our microarray\\u000a approach, we first selected 28 genes from a set of statistically significant housekeeping genes from the S. cerevisiae cell cycle time series

Xiaoxu Han

2006-01-01

241

How the RNA isolation method can affect microRNA microarray results.  

PubMed

The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods. PMID:22146134

Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas; Fredholm, Merete; Cirera, Susanna

2011-01-01

242

Using microarrays to study the microenvironment in tumor biology: The crucial role of statistics  

PubMed Central

Microarrays represent a potentially powerful tool for better understanding the role of the microenvironment on tumor biology. To make the best use of microarray data and avoid incorrect or unsubstantiated conclusions, care must be taken in the statistical analysis. To illustrate the statistical issues involved we discuss three microarray studies related to the microenvironment and tumor biology involving: (i) prostatic stroma cells in cancer and non-cancer tissues; (ii) breast stroma and epithelial cells in breast cancer patients and non-cancer patients; and (iii) serum associated with wound response and stroma in cancer patients. Using these examples we critically discuss three types of analyses: differential gene expression, cluster analysis, and class prediction. We also discuss design issues. PMID:18455427

Baker, Stuart G.; Kramer, Barnett S.

2008-01-01

243

Identification of Novel Cholesteatoma-Related Gene Expression Signatures Using Full-Genome Microarrays  

PubMed Central

Background Cholesteatoma is a gradually expanding destructive epithelial lesion within the middle ear. It can cause extensive local tissue destruction in the temporal bone and can initially lead to the development of conductive hearing loss via ossicular erosion. As the disease progresses, sensorineural hearing loss, vertigo or facial palsy may occur. Cholesteatoma may promote the spread of infection through the tegmen of the middle ear and cause meningitis or intracranial infections with abscess formation. It must, therefore, be considered as a potentially life-threatening middle ear disease. Methods and Findings In this study, we investigated differentially expressed genes in human cholesteatomas in comparison to regular auditory canal skin using Whole Human Genome Microarrays containing 19,596 human genes. In addition to already described up-regulated mRNAs in cholesteatoma, such as MMP9, DEFB2 and KRT19, we identified 3558 new cholesteatoma-related transcripts. 811 genes appear to be significantly differentially up-regulated in cholesteatoma. 334 genes were down-regulated more than 2-fold. Significantly regulated genes with protein metabolism activity include matrix metalloproteinases as well as PI3, SERPINB3 and SERPINB4. Genes like SPP1, KRT6B, PRPH, SPRR1B and LAMC2 are known as genes with cell growth and/or maintenance activity. Transport activity genes and signal transduction genes are LCN2, GJB2 and CEACAM6. Three cell communication genes were identified; one CDH19 and two from the S100 family. Conclusions This study demonstrates that the expression profile of cholesteatoma is similar to a metastatic tumour and chronically inflamed tissue. Based on the investigated profiles we present novel protein-protein interaction and signal transduction networks, which include cholesteatoma-regulated transcripts and may be of great value for drug targeting and therapy development. PMID:23285167

Klenke, Christin; Janowski, Sebastian; Borck, Daniela; Widera, Darius; Ebmeyer, Jorg; Kalinowski, Jorn; Leichtle, Anke; Hofestadt, Ralf; Upile, Tahwinder; Kaltschmidt, Christian; Kaltschmidt, Barbara; Sudhoff, Holger

2012-01-01

244

Use of lectin microarray to differentiate gastric cancer from gastric ulcer  

PubMed Central

AIM: To investigate the feasibility of lectin microarray for differentiating gastric cancer from gastric ulcer. METHODS: Twenty cases of human gastric cancer tissue and 20 cases of human gastric ulcer tissue were collected and processed. Protein was extracted from the frozen tissues and stored. The lectins were dissolved in buffer, and the sugar-binding specificities of lectins and the layout of the lectin microarray were summarized. The median of the effective data points for each lectin was globally normalized to the sum of medians of all effective data points for each lectin in one block. Formalin-fixed paraffin-embedded gastric cancer tissues and their corresponding gastric ulcer tissues were subjected to Ag retrieval. Biotinylated lectin was used as the primary antibody and HRP-streptavidin as the secondary antibody. The glycopatterns of glycoprotein in gastric cancer and gastric ulcer specimens were determined by lectin microarray, and then validated by lectin histochemistry. Data are presented as mean ± SD for the indicated number of independent experiments. RESULTS: The glycosylation level of gastric cancer was significantly higher than that in ulcer. In gastric cancer, most of the lectin binders showed positive signals and the intensity of the signals was stronger, whereas the opposite was the case for ulcers. Significant differences in the pathological score of the two lectins were apparent between ulcer and gastric cancer tissues using the same lectin. For MPL and VVA, all types of gastric cancer detected showed stronger staining and a higher positive rate in comparison with ulcer, especially in the case of signet ring cell carcinoma and intra-mucosal carcinoma. GalNAc bound to MPL showed a significant increase. A statistically significant association between MPL and gastric cancer was observed. As with MPL, there were significant differences in VVA staining between gastric cancer and ulcer. CONCLUSION: Lectin microarray can differentiate the different glycopatterns in gastric cancer and gastric ulcer, and the lectins MPL and VVA can be used as biomarkers. PMID:24833877

Huang, Wei-Li; Li, Yang-Guang; Lv, Yong-Chen; Guan, Xiao-Hui; Ji, Hui-Fan; Chi, Bao-Rong

2014-01-01

245

Application of physicochemically modified silicon substrates as reverse phase protein microarrays  

PubMed Central

Physicochemically modified silicon substrates can provide a high quality alternative to nitrocellulose-coated glass slides for use in reverse-phase protein microarrays. Enhancement of protein microarray sensitivities is an important goal, especially because molecular targets within patient tissues exist in low abundance. The ideal array substrate has a high protein binding affinity and low intrinsic background signal. Silicon, which has low intrinsic autofluorescence, is being explored as a potential microarray surface. In a previous paper (Nijdam, A.J., Cheng, M.M.C., Fedele, R., Geho, D.H., Herrmann, P., Killian, K., Espina, V., Petricoin, E.F., Liotta, L.A., Ferrari, M. (2007) Physicochemically Modified Silicon As Substrate For Protein Microarrays Biomater, 28, 550-558), it is shown that physicochemical modification of silicon substrates increases the binding of protein to silicon to a level comparable with that of nitrocellulose. Here, we apply such substrates in a reverse-phase protein microarray setting in two model systems. PMID:19170514

Jasper Nijdam, A.; Zianni, Michael R.; Herderick, Edward E.; Cheng, Mark M-C; Prosperi, Jenifer R.; Robertson, Fredika A.; Petricoin, Emanuel F.; Liotta, Lance A.; Ferrari, Mauro

2009-01-01

246

Transcriptional Profiling of Endocrine Cerebro-Osteodysplasia Using Microarray and Next-Generation Sequencing  

PubMed Central

Background Transcriptome profiling of patterns of RNA expression is a powerful approach to identify networks of genes that play a role in disease. To date, most mRNA profiling of tissues has been accomplished using microarrays, but next-generation sequencing can offer a richer and more comprehensive picture. Methodology/Principal Findings ECO is a rare multi-system developmental disorder caused by a homozygous mutation in ICK encoding intestinal cell kinase. We performed gene expression profiling using both cDNA microarrays and next-generation mRNA sequencing (mRNA-seq) of skin fibroblasts from ECO-affected subjects. We then validated a subset of differentially expressed transcripts identified by each method using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Finally, we used gene ontology (GO) to identify critical pathways and processes that were abnormal according to each technical platform. Methodologically, mRNA-seq identifies a much larger number of differentially expressed genes with much better correlation to qRT-PCR results than the microarray (r2?=?0.794 and 0.137, respectively). Biologically, cDNA microarray identified functional pathways focused on anatomical structure and development, while the mRNA-seq platform identified a higher proportion of genes involved in cell division and DNA replication pathways. Conclusions/Significance Transcriptome profiling with mRNA-seq had greater sensitivity, range and accuracy than the microarray. The two platforms generated different but complementary hypotheses for further evaluation. PMID:21980446

Lahiry, Piya; Lee, Leo J.; Frey, Brendan J.; Rupar, C. Anthony; Siu, Victoria M.; Blencowe, Benjamin J.; Hegele, Robert A.

2011-01-01

247

Identifying pathogenic processes by integrating microarray data with prior knowledge  

PubMed Central

Background It is of great importance to identify molecular processes and pathways that are involved in disease etiology. Although there has been an extensive use of various high-throughput methods for this task, pathogenic pathways are still not completely understood. Often the set of genes or proteins identified as altered in genome-wide screens show a poor overlap with canonical disease pathways. These findings are difficult to interpret, yet crucial in order to improve the understanding of the molecular processes underlying the disease progression. We present a novel method for identifying groups of connected molecules from a set of differentially expressed genes. These groups represent functional modules sharing common cellular function and involve signaling and regulatory events. Specifically, our method makes use of Bayesian statistics to identify groups of co-regulated genes based on the microarray data, where external information about molecular interactions and connections are used as priors in the group assignments. Markov chain Monte Carlo sampling is used to search for the most reliable grouping. Results Simulation results showed that the method improved the ability of identifying correct groups compared to traditional clustering, especially for small sample sizes. Applied to a microarray heart failure dataset the method found one large cluster with several genes important for the structure of the extracellular matrix and a smaller group with many genes involved in carbohydrate metabolism. The method was also applied to a microarray dataset on melanoma cancer patients with or without metastasis, where the main cluster was dominated by genes related to keratinocyte differentiation. Conclusion Our method found clusters overlapping with known pathogenic processes, but also pointed to new connections extending beyond the classical pathways. PMID:24758699

2014-01-01

248

Nanotechnology: moving from microarrays toward nanoarrays.  

PubMed

Microarrays are important tools for high-throughput analysis of biomolecules. The use of microarrays for parallel screening of nucleic acid and protein profiles has become an industry standard. A few limitations of microarrays are the requirement for relatively large sample volumes and elongated incubation time, as well as the limit of detection. In addition, traditional microarrays make use of bulky instrumentation for the detection, and sample amplification and labeling are quite laborious, which increase analysis cost and delays the time for obtaining results. These problems limit microarray techniques from point-of-care and field applications. One strategy for overcoming these problems is to develop nanoarrays, particularly electronics-based nanoarrays. With further miniaturization, higher sensitivity, and simplified sample preparation, nanoarrays could potentially be employed for biomolecular analysis in personal healthcare and monitoring of trace pathogens. In this chapter, it is intended to introduce the concept and advantage of nanotechnology and then describe current methods and protocols for novel nanoarrays in three aspects: (1) label-free nucleic acids analysis using nanoarrays, (2) nanoarrays for protein detection by conventional optical fluorescence microscopy as well as by novel label-free methods such as atomic force microscopy, and (3) nanoarray for enzymatic-based assay. These nanoarrays will have significant applications in drug discovery, medical diagnosis, genetic testing, environmental monitoring, and food safety inspection. PMID:17984533

Chen, Hua; Li, Jun

2007-01-01

249

Genome-Wide Microarray Expression and Genomic Alterations by Array-CGH Analysis in Neuroblastoma Stem-Like Cells  

PubMed Central

Neuroblastoma has a very diverse clinical behaviour: from spontaneous regression to a very aggressive malignant progression and resistance to chemotherapy. This heterogeneous clinical behaviour might be due to the existence of Cancer Stem Cells (CSC), a subpopulation within the tumor with stem-like cell properties: a significant proliferation capacity, a unique self-renewal capacity, and therefore, a higher ability to form new tumors. We enriched the CSC-like cell population content of two commercial neuroblastoma cell lines by the use of conditioned cell culture media for neurospheres, and compared genomic gains and losses and genome expression by array-CGH and microarray analysis, respectively (in CSC-like versus standard tumor cells culture). Despite the array-CGH did not show significant differences between standard and CSC-like in both analyzed cell lines, the microarray expression analysis highlighted some of the most relevant biological processes and molecular functions that might be responsible for the CSC-like phenotype. Some signalling pathways detected seem to be involved in self-renewal of normal tissues (Wnt, Notch, Hh and TGF-?) and contribute to CSC phenotype. We focused on the aberrant activation of TGF-? and Hh signalling pathways, confirming the inhibition of repressors of TGF-? pathway, as SMAD6 and SMAD7 by RT-qPCR. The analysis of the Sonic Hedgehog pathway showed overexpression of PTCH1, GLI1 and SMO. We found overexpression of CD133 and CD15 in SIMA neurospheres, confirming that this cell line was particularly enriched in stem-like cells. This work shows a cross-talk among different pathways in neuroblastoma and its importance in CSC-like cells. PMID:25392930

Martínez-Soto, Soledad; Legarra, Sheila; Pata-Merci, Noémie; Guegan, Justine; Danglot, Giselle; Bernheim, Alain; Meléndez, Bárbara; Rey, Juan A.; Castresana, Javier S.

2014-01-01

250

Genome-Wide Microarray Expression and Genomic Alterations by Array-CGH Analysis in Neuroblastoma Stem-Like Cells.  

PubMed

Neuroblastoma has a very diverse clinical behaviour: from spontaneous regression to a very aggressive malignant progression and resistance to chemotherapy. This heterogeneous clinical behaviour might be due to the existence of Cancer Stem Cells (CSC), a subpopulation within the tumor with stem-like cell properties: a significant proliferation capacity, a unique self-renewal capacity, and therefore, a higher ability to form new tumors. We enriched the CSC-like cell population content of two commercial neuroblastoma cell lines by the use of conditioned cell culture media for neurospheres, and compared genomic gains and losses and genome expression by array-CGH and microarray analysis, respectively (in CSC-like versus standard tumor cells culture). Despite the array-CGH did not show significant differences between standard and CSC-like in both analyzed cell lines, the microarray expression analysis highlighted some of the most relevant biological processes and molecular functions that might be responsible for the CSC-like phenotype. Some signalling pathways detected seem to be involved in self-renewal of normal tissues (Wnt, Notch, Hh and TGF-?) and contribute to CSC phenotype. We focused on the aberrant activation of TGF-? and Hh signalling pathways, confirming the inhibition of repressors of TGF-? pathway, as SMAD6 and SMAD7 by RT-qPCR. The analysis of the Sonic Hedgehog pathway showed overexpression of PTCH1, GLI1 and SMO. We found overexpression of CD133 and CD15 in SIMA neurospheres, confirming that this cell line was particularly enriched in stem-like cells. This work shows a cross-talk among different pathways in neuroblastoma and its importance in CSC-like cells. PMID:25392930

Ordóñez, Raquel; Gallo-Oller, Gabriel; Martínez-Soto, Soledad; Legarra, Sheila; Pata-Merci, Noémie; Guegan, Justine; Danglot, Giselle; Bernheim, Alain; Meléndez, Bárbara; Rey, Juan A; Castresana, Javier S

2014-01-01

251

The development of common data elements for a multi-institute prostate cancer tissue bank: The Cooperative Prostate Cancer Tissue Resource (CPCTR) experience  

PubMed Central

Background The Cooperative Prostate Cancer Tissue Resource (CPCTR) is a consortium of four geographically dispersed institutions that are funded by the U.S. National Cancer Institute (NCI) to provide clinically annotated prostate cancer tissue samples to researchers. To facilitate this effort, it was critical to arrive at agreed upon common data elements (CDEs) that could be used to collect demographic, pathologic, treatment and clinical outcome data. Methods The CPCTR investigators convened a CDE curation subcommittee to develop and implement CDEs for the annotation of collected prostate tissues. The draft CDEs were refined and progressively annotated to make them ISO 11179 compliant. The CDEs were implemented in the CPCTR database and tested using software query tools developed by the investigators. Results By collaborative consensus the CPCTR CDE subcommittee developed 145 data elements to annotate the tissue samples collected. These included for each case: 1) demographic data, 2) clinical history, 3) pathology specimen level elements to describe the staging, grading and other characteristics of individual surgical pathology cases, 4) tissue block level annotation critical to managing a virtual inventory of cases and facilitating case selection, and 5) clinical outcome data including treatment, recurrence and vital status. These elements have been used successfully to respond to over 60 requests by end-users for tissue, including paraffin blocks from cases with 5 to 10 years of follow up, tissue microarrays (TMAs), as well as frozen tissue collected prospectively for genomic profiling and genetic studies. The CPCTR CDEs have been fully implemented in two major tissue banks and have been shared with dozens of other tissue banking efforts. Conclusion The freely available CDEs developed by the CPCTR are robust, based on "best practices" for tissue resources, and are ISO 11179 compliant. The process for CDE development described in this manuscript provides a framework model for other organ sites and has been used as a model for breast and melanoma tissue banking efforts. PMID:16111498

Patel, Ashokkumar A; Kajdacsy-Balla, Andre; Berman, Jules J; Bosland, Maarten; Datta, Milton W; Dhir, Rajiv; Gilbertson, John; Melamed, Jonathan; Orenstein, Jan; Tai, Kuei-Fang; Becich, Michael J

2005-01-01

252

Pattern-driven neighborhood search for biclustering of microarray data  

PubMed Central

Background Biclustering aims at finding subgroups of genes that show highly correlated behaviors across a subgroup of conditions. Biclustering is a very useful tool for mining microarray data and has various practical applications. From a computational point of view, biclustering is a highly combinatorial search problem and can be solved with optimization methods. Results We describe a stochastic pattern-driven neighborhood search algorithm for the biclustering problem. Starting from an initial bicluster, the proposed method improves progressively the quality of the bicluster by adjusting some genes and conditions. The adjustments are based on the quality of each gene and condition with respect to the bicluster and the initial data matrix. The performance of the method was evaluated on two well-known microarray datasets (Yeast cell cycle and Saccharomyces cerevisiae), showing that it is able to obtain statistically and biologically significant biclusters. The proposed method was also compared with six reference methods from the literature. Conclusions The proposed method is computationally fast and can be applied to discover significant biclusters. It can also used to effectively improve the quality of existing biclusters provided by other biclustering methods. PMID:22594997

2012-01-01

253

Analysis of High-Throughput ELISA Microarray Data  

SciTech Connect

Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

White, Amanda M.; Daly, Don S.; Zangar, Richard C.

2011-02-23

254

The use of microarrays in microbial ecology  

SciTech Connect

Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer oligonucleotide probes and covers more than 10,000 gene sequences in 150 gene categories involved in carbon, nitrogen, sulfur, and phosphorus cycling, metal resistance and reduction, and organic contaminant degradation. GeoChip can be used as a generic tool for microbial community analysis, and also link microbial community structure to ecosystem functioning. Examples of the application of both arrays in different environmental samples will be described in the two subsequent sections.

Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

2009-09-15

255

A PNA microarray for tomato genotyping.  

PubMed

The design and development of a PNA microarray designed for the simultaneous identification of several SNPs characteristic of seven different tomato varieties is described. Highly selective arginine-based monomer containing PNAs (Arg-PNAs) have been used in order to obtain very selective probes. Seven modified PNA probes were synthesised and their binding properties in solution were studied. PNA-microarrays based on these probes were prepared and applied to SNP discrimination in model experiments using oligonucleotide mixtures simulating the different sequences of the seven tomato varieties. The strength and the limitations of such a system for SNP recognition are thoroughly discussed. PMID:21465054

Tedeschi, Tullia; Calabretta, Alessandro; Bencivenni, Mariangela; Manicardi, Alex; Corrado, Giandomenico; Caramante, Martina; Corradini, Roberto; Rao, Rosa; Sforza, Stefano; Marchelli, Rosangela

2011-06-01

256

Analyzing Schizophrenia by DNA Microarrays  

PubMed Central

To understand the pathological processes of schizophrenia we must embrace the analysis of the diseased human brain: we will never be able to recapitulate the pathology of uniquely human disorders in an animal model. Based on the outcome of the transcriptome profiling experiments performed to date it appears that schizophrenia is associated with a global gene expression disturbance across many cortical regions. In addition, transcriptome changes are present in multiple cell types, including specific subclasses of principal neurons, interneurons and oligodendrocytes. Furthermore, transcripts related to synaptic transmission, energy metabolism and inhibitory neurotransmission are routinely found underexpressed in the postmortem brain tissue of subjects with schizophrenia. To put these transcriptome data in biological context we must make our data publicly available and report our findings in a proper, expanded MIAME format. Cell type specific expression profiling and sequencing-based transcripts assessments should be expanded, with particular attention to understanding splice-variant changes in various mental disorders. Deciphering the pathophysiology of mental disorders depends on integrating data from across many research fields and techniques. Leads from postmortem transcriptome profiling will be essential to generate model animals, perform tissue culture experiments and develop or evaluate novel drugs to treat this devastating disorder. PMID:20801428

Horváth, Szatmár; Janka, Zoltán; Mirnics, Károly

2010-01-01

257

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.  

PubMed

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the ?-CS tool, extending the preprocessing to SNP arrays that were not allowed in ?-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site http://sourceforge.net/projects/microanalyzer/. PMID:23731720

Guzzi, Pietro Hiram; Cannataro, Mario

2013-08-01

258

Agilent Microarray Grant Program The Agilent Microarray Grant Program is designed to promote increased awareness of the Agilent Microarray  

E-print Network

Spring addresses the challenges in multi-omics data analysis by providing comprehensive analytical Facility and to help seed promising new integrated genomics projects. Use Agilent microarrays in your and the underlying biology of various disease states. Furthermore, Agilent advances Integrated Genomics research via

Richardson, David

259

Interactive exploration of microarray gene expression patterns in a reduced dimensional space.  

PubMed

The very high dimensional space of gene expression measurements obtained by DNA microarrays impedes the detection of underlying patterns in gene expression data and the identification of discriminatory genes. In this paper we show the use of projection methods such as principal components analysis (PCA) to obtain a direct link between patterns in the genes and patterns in samples. This feature is useful in the initial interactive pattern exploration of gene expression data and data-driven learning of the nature and types of samples. Using oligonucleotide microarray measurements of 40 samples from different normal human tissues, we show that distinct patterns are obtained when the genes are projected on a two-dimensional plane spanned by the loadings of the two major principal components. These patterns define the particular genes associated with a sample class (i.e., tissue). When used separately from the other genes, these class-specific (i.e., tissue-specific) genes in turn define distinct tissue patterns in the projection space spanned by the scores of the two major principal components. In this study, PCA projection facilitated discriminatory gene selection for different tissues and identified tissue-specific gene expression signatures for liver, skeletal muscle, and brain samples. Furthermore, it allowed the classification of nine new samples belonging to these three types using the linear combination of the expression levels of the tissue-specific genes determined from the first set of samples. The application of the technique to other published data sets is also discussed. PMID:12097349

Misra, Jatin; Schmitt, William; Hwang, Daehee; Hsiao, Li-Li; Gullans, Steve; Stephanopoulos, George; Stephanopoulos, Gregory

2002-07-01

260

Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray  

PubMed Central

Background Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Results Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties. Conclusion All results suggest that our high-density flax oligo-microarray platform can be used as a very sensitive tool for analyzing gene expression in a large variety of tissues as well as in different cultivars. Moreover, this highly reliable platform can also be used for the quantification of mRNA transcriptional profiling in different flax tissues. PMID:20964859

2010-01-01

261

Identification of embryonic pancreatic genes using Xenopus DNA microarrays  

PubMed Central

The pancreas is both an exocrine and endocrine endodermal organ involved in digestion and glucose homeostasis. During embryogenesis, the anlagen of the pancreas arise from dorsal and ventral evaginations of the foregut that later fuse to form a single organ. In order to better understand the molecular genetics of early pancreas development, we sought to isolate markers that are uniquely expressed in this tissue. Microarray analysis was performed comparing dissected pancreatic buds, liver buds, and the stomach region of tadpole stage Xenopus embryos. A total of 912 genes were found to be differentially expressed between these organs during early stages of organogenesis. K-means clustering analysis predicted 120 of these genes to be specifically enriched in the pancreas. Of these, we report on the novel expression patterns of 24 genes. Our analyses implicate the involvement of previously unsuspected signaling pathways during early pancreas development. PMID:19191222

Hayata, Tadayoshi; Blitz, Ira L.; Iwata, Nahoko; Cho, Ken W. Y.

2014-01-01

262

Tissues from the irradiated dog/mouse archive  

SciTech Connect

The purpose of this project is to organize the databases/information and organize and move the tissues from the long-term dog (4,000 dogs) and mouse (over 30,000 mice) radiation experiments done at Argonne National Laboratory during the 1970's and 80's to Northwestern University. These studies were done with the intention of understanding the effects of exposure to radiation at a variety of different doses, dose-rates, and radiation qualities on end-points such as life-shortening, carcinogenesis, cause of death, shifts in disease incidence and other biological parameters. Organ and tissue samples from these animals including cancers, metastases and other significant degenerative and inflammatory lesions and those in a regular protocol of normal tissues were preserved in paraffin blocks, tissue impressions and sections and represent a great resource for the radiation biology community. These collections are particularly significant since these experiments are not likely to be repeated because of the extreme cost of monies and time for such large-scale animal studies. The long-term goal is to make these tissues and databases available to the wider scientific community so that questions such as tissue sensitivity, early and late effects, low dose and protracted dose responses of normal and tumor tissues, etc. can be examined and defined. Recent advances in biology particularly at the subcellular and molecular level now permit microarray-based gene expression array analyses from paraffin-embedded tissues (where RNA samples are significantly degraded), synchrotron-based studies of metal and other elemental distribution patterns in tissues, PCR-based analyses for mutation detection, and other similar approaches that were not available when the long¬ term animal studies were designed and initiated. Understanding the basis and progression of radiation damage should also permit rational approaches to prevention and mitigation of those damages. Therefore, as stated earlier, these tissues and their related documentation, represent a significant resource for future studies. For this project, we propose to accomplish the following objectives: (1) inventory and organize the tissues, blood smears, wet-tissues and paper-¬based information that is available in the tissue bank at Argonne National Laboratory; (2) convert the existing Oracle database of the mouse studies to MS Access( the dog data is already in this format which is far more user friendly and widely used in business and research) , (3) move the remaining samples and documentation from dogs that had been transferred from ANL to New Mexico (in Dr. F. Hahn's care) to Northwestern University and add these to the inventory; (4) move the tissues and Access database at Argonne National Laboratory to Northwestern University.

Gayle Woloschak

2007-04-01

263

PRACTICAL STRATEGIES FOR PROCESSING AND ANALYZING SPOTTED OLIGONUCLEOTIDE MICROARRAY DATA  

EPA Science Inventory

Thoughtful data analysis is as important as experimental design, biological sample quality, and appropriate experimental procedures for making microarrays a useful supplement to traditional toxicology. In the present study, spotted oligonucleotide microarrays were used to profile...

264

Photoelectromechanical synthesis of low-cost DNA microarrays  

E-print Network

Recent advances in de novo gene synthesis, library construction, and genomic selection for target sequencing using DNA from custom microarrays have demonstrated that microarrays can effectively be used as the world's ...

Chow, Brian, 1978-

2008-01-01

265

A Biomimetic Algorithm for the Improved Detection of Microarray Features  

E-print Network

A Biomimetic Algorithm for the Improved Detection of Microarray Features Dan V. Nicolau, Jr1 , Dan, either based on direct mechanical contact (as in the initial microarray technology), or thorough more

Maini, Philip K.

266

Mixture Modeling and Outlier Detection in Microarray Data Analysis  

E-print Network

Microarray technology has become a dynamic tool in gene expression analysis because it allows for the simultaneous measurement of thousands of gene expressions. Uniqueness in experimental units and microarray data platforms, coupled with how gene...

George, Nysia I.

2010-01-16

267

Screening candidate genes associated with bladder cancer using DNA microarray.  

PubMed

The aim of the present study was to screen candidate genes that are closely associated with bladder cancer and to select the most distinct candidate target genes in order to provide theoretical evidence and direction for improved treatment of bladder cancer. The gene microarray dataset GSE45184 was downloaded from the Gene Expression Omnibus database. There were a total of six expression prolife microarrays from three pairs of freshly frozen bladder cancer tissues and corresponding normal adjacent tissues. Differentially expressed genes (DEGs) were identified using the limma package in R software and then subjected to further biological information analysis, including hierarchical clustering analysis and gene ontology enrichment analysis. Co?expression networks and functional interaction networks were established using the up? and downregulated genes. Pathway enrichment analysis was then performed for the genes in the functional interaction networks. A total of 522 DEGs were identified, including 223 upregulated and 299 downregulated genes. Functional enrichment analysis of the target genes indicated that downregulated genes were associated with the regulation of biological processes, while the upregulated genes participated in the processes involved in the cell cycle. The functional network of the upregulated genes comprised 1,518 connections and 92 gene nodes that were associated with 10 closely?related functions, while the network of the downregulated genes consisted of 129 connections and 24 gene nodes involving 11 significantly related functions. Pathway enrichment analysis revealed that the downregulated genes were mainly involved in the mitogen?activated protein kinase signaling pathway, while the upregulated genes were closely associated with the cell cycle. These DEGs and the relevant cell cycle pathways have the potential to be used as targets for the treatment of bladder cancer. PMID:25323786

Xu, Axiang; Wang, Chunyang; Sun, Shengkun

2014-12-01

268

Making sense of microarray data distributions  

Microsoft Academic Search

Motivation: Typical analysis of microarray data has focused on spot by spot comparisons within a single organism. Less analysis has been done on the compar- ison of the entire distribution of spot intensities between experiments and between organisms. Results: Here we show that mRNA transcription data from a wide range of organisms and measured with a range of experimental platforms

David C. Hoyle; Magnus Rattray; Ray Jupp; Andy Brass

2002-01-01

269

MICROARRAY DATA ANALYSIS USING MULTIPLE STATISTICAL MODELS  

EPA Science Inventory

Microarray Data Analysis Using Multiple Statistical Models Wenjun Bao1, Judith E. Schmid1, Amber K. Goetz1, Ming Ouyang2, William J. Welsh2,Andrew I. Brooks3,4, ChiYi Chu3,Mitsunori Ogihara3,4, Yinhe Cheng5, David J. Dix1. 1National Health and Environmental Effects Researc...

270

Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates  

SciTech Connect

A diagnostic, genome-independent microbial fingerprinting method using DNA oligonucleotide microarrays was used for high-resolution differentiation between closely related Bacillus strains, including two strains of Bacillus anthracis that are monomorphic (indistinguishable) via amplified fragment length polymorphism fingerprinting techniques. Replicated hybridizations on 391-probe nonamer arrays were used to construct a prototype fingerprint library for quantitative comparisons. Descriptive analysis of the fingerprints, including phylogenetic reconstruction, is consistent with previous taxonomic organization of the genus. Newly developed statistical analysis methods were used to quantitatively compare and objectively confirm apparent differences in microarray fingerprints with the statistical rigor required for microbial forensics and clinical diagnostics. These data suggest that a relatively simple fingerprinting microarray and statistical analysis method can differentiate between species in the Bacillus cereus complex, and between strains of B. anthracis. A synthetic DNA standard was used to understand underlying microarray and process-level variability, leading to specific recommendations for the development of a standard operating procedure and/or continued technology enhancements for microbial forensics and diagnostics.

Chandler, Darrell P.; Alferov, Oleg; Chernov, Boris; Daly, Don S.; Golova, Julia; Perov, Alexander N.; Protic, Miroslava; Robison, Richard; Shipma, Matthew; White, Amanda M.; Willse, Alan R.

2006-01-01

271

Missing value estimation methods for DNA microarrays  

Microsoft Academic Search

Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression val- ues. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical cluster- ing and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. Methods

Olga G. Troyanskaya; Michael Cantor; Gavin Sherlock; Patrick O. Brown; Trevor Hastie; Robert Tibshirani; David Botstein; Russ B. Altman

2001-01-01

272

Shrinkage covariance matrix approach for microarray data  

NASA Astrophysics Data System (ADS)

Microarray technology was developed for the purpose of monitoring the expression levels of thousands of genes. A microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints including the high cost of producing microarray chips. As a result, the widely used standard covariance estimator is not appropriate for this purpose. One such technique is the Hotelling's T2 statistic which is a multivariate test statistic for comparing means between two groups. It requires that the number of observations (n) exceeds the number of genes (p) in the set but in microarray studies it is common that n < p. This leads to a biased estimate of the covariance matrix. In this study, the Hotelling's T2 statistic with the shrinkage approach is proposed to estimate the covariance matrix for testing differential gene expression. The performance of this approach is then compared with other commonly used multivariate tests using a widely analysed diabetes data set as illustrations. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.

Karjanto, Suryaefiza; Aripin, Rasimah

2013-04-01

273

Microarray-based genomic selection for high-  

E-print Network

a general method, microarray-based genomic selection (MGS), capable of selecting and enriching targeted artificial chromosome (BAC)-based genomic selection. We demonstrate that large human genomic regions- investigator laboratories. Technological innovation in DNA sequencing offers the promise of a more

Cai, Long

274

Oligonucleotide Microarray Data Distribution And Normalization  

Microsoft Academic Search

Variations in oligonucleotide microarray probe signals that result from various factors, including differences in sample concentrations, can lead to major problems in the interpretation of data obtained from different experiments. Normalization of such signals is typically performed by procedures involving division by a constant approxi- mately determined by average signal intensities as, e.g., in the Affymetrix software. Here we show

I. A. Sidorov; D. Gee; D. S. Dimitrov; Douglas A. Hosack; J. Yang; Richard A. Lempicki; M. C. Cam

2002-01-01

275

Gene Expression Profiling: From Microarrays to Medicine  

Microsoft Academic Search

With the mapping of the human genome comes the ability to identify genes of interest in specific diseases and the pathways involved therein. Laboratory technology has evolved in parallel, providing us with the ability to assay thousands of these genes at once, a technique known as microarray analysis. The main #x003Fion that this type of technology raises is how we

Ashani T. Weeraratna; James E. Nagel; Valeria de Mello-Coelho; Dennis D. Taub

2004-01-01

276

Navigation through Structured Microarray Analysis towards  

E-print Network

Diagnosis 2. DOM4J z An XML Parser (www.dom4j.org) z JAVA-specific z easy, fast... ê Big XML files++ II;26/05/03 13/26Navigation through Structured Microarray Analysis towards Clarified Diagnosis 1. JAVA & Swing z

Spang, Rainer

277

Bayesian models for DNA microarray data analysis  

E-print Network

as to perform future predictions. The method is applied to cancer classi?cation via cDNA microarrays. In particular, the genes BRCA1 and BRCA2 are associated with a hereditary disposition to breast cancer, and the method is used to identify the set of signi...

Lee, Kyeong Eun

2005-08-29

278

Nerve growth factor promotes expression of novel genes in intervertebral disc cells that regulate tissue degradation.  

PubMed

Object Increased neurotrophin activity in degenerative intervertebral discs (IVDs) is one potential cause of chronic low-back pain (LBP). The aim of the study was to assess if nerve growth factor (NGF) might alter gene expression of IVD cells and contribute to disc degeneration by enhancing expression or activity of factors that cause breakdown of IVD matrix. Methods Rat-tail IVD cells were stimulated by NGF and subjected to microarray analysis. Real-time polymerase chain reaction, Western blotting, and immunocytochemistry of rat and human IVD cells and tissues treated with NGF in vitro in the absence or presence of the NGF inhibitor Ro 08-2750 were used to confirm findings of the microarray studies. Phosphorylation of mitogen-activated protein kinase (MAPK) was used to identify cell signaling pathways involved in NGF stimulation in the absence or presence of Ro 08-2750. Results Microarray analysis demonstrated increased expression of chitinase 3-like 1 (Chi3l1), lipocalin 2 (Lcn2), and matrix metalloproteinase-3 (Mmp3) following NGF stimulation of rat IVD cells in vitro. Increased gene expression was confirmed by real-time polymerase chain reaction with a relative increase in the Mmp/Timp ratio. Increased expression of Chi3l1, Lcn2, and Mmp3 following NGF stimulation was also demonstrated in rat cells and human tissue in vitro. Effects of NGF on protein expression were blocked by an NGF inhibitor and appear to function through the extracellular-regulation kinase 1/2 (ERK1/2) MAPK pathway. Conclusions Nerve growth factor has potential effects on matrix turnover activity and influences the catabolic/anabolic balance of IVD cells in an adverse way that may potentiate IVD degeneration. Anti-NGF treatment might be beneficial to ameliorate progressive tissue breakdown in IVD degeneration and may lead to pain relief. PMID:25062286

Kao, Ting-Hsien; Peng, Yi-Jen; Tsou, Hsi-Kai; Salter, Donald M; Lee, Herng-Sheng

2014-10-01

279

Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray.  

PubMed

Pan viral DNA microarrays, which can detect known, novel and multiple viral infections, are major laboratory assets contributing to the control of infectious diseases. The large quantity of ribosomal RNA (rRNA) found in tissue samples is thought to be a major factor contributing to the comparatively lower sensitivity of detecting RNA viruses, as a sequence-independent PCR is used to amplify unknown samples for microarray analysis. This study aimed to determine whether depletion or exclusion of rRNA can improve microarray detection and simplify its analysis. Therefore, two different rRNA depletion and exclusion protocols, RiboMinus™ technology and non-rRNA binding hexanucleotides, were applied to the microarray sample processing and the outcome was compared with those of the sequence-independent amplification protocol. This study concludes that the two procedures, described to deplete or exclude rRNA, have negligible effect on the microarrays detection and analysis and might only in combination with further techniques result in a significant enhancement of sensitivity. Currently, existing protocols of random amplification and background adjustment are pertinent for the purpose of sample processing for microarray analysis. PMID:25034125

McGowan, Sarah; Nunez-Garcia, Javier; Steinbach, Falko; La Rocca, Anna; Blake, Damer; Dastjerdi, Akbar

2014-10-01

280

Identifying Fishes through DNA Barcodes and Microarrays  

PubMed Central

Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products. PMID:20838643

Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjorleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nolte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N.; Weber, Hannes; Blohm, Dietmar

2010-01-01

281

Microarray analysis at single molecule resolution  

PubMed Central

Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state of the art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack in appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of two to 20 micrometers and quantifies the abundance of target molecules by determining average pixel intensities, a novel high resolution approach [1] directly visualizes individual bound molecules as diffraction limited peaks. The now possible quantification via counting is less susceptible to labeling artifacts and background noise. We have developed an approach for the analysis of high-resolution microarray images. It consists first of a single molecule detection step, based on undecimated wavelet transforms, and second, of a spot identification step via spatial statistics approach (corresponding to the segmentation step in the classical microarray analysis). The detection method was tested on simulated images with a concentration range of 0.001 to 0.5 molecules per square micron and signal-to-noise ratio (SNR) between 0.9 and 31.6. For SNR above 15 the false negatives relative error was below 15%. Separation of foreground/background proved reliable, in case foreground density exceeds background by a factor of 2. The method has also been applied to real data from high-resolution microarray measurements. PMID:20123580

Muresan, Leila; Jacak, Jaroslaw; Klement, Erich Peter; Hesse, Jan; Schutz, Gerhard J.

2010-01-01

282

RNA-seq as a powerful tool for penaeid shrimp genetic progress  

PubMed Central

The sequences of all different RNA transcripts present in a cell or tissue that are related to the gene expression and its functional control represent what it is called a transcriptome. The transcripts vary between cells, tissues, ontogenetic and environmental conditions, and the knowledge that can be gained through them is of a solid relevance for genetic applications in aquaculture. Some of the techniques used in transcriptome studies, such as microarrays, are being replaced for next-generation sequencing approaches. RNA-seq emerges as a new possibility for the transcriptome complexity analysis as well as for the candidate genes and polymorphisms identification of penaeid species. Thus, it may also help to understand the determination of complex traits mechanisms and genetic improvement of stocks. In this review, it is first introduced an overview of transcriptome analysis by RNA-seq, followed by a discussion of how this approach may be applied in genetic progress within penaeid stocks.

Santos, Camilla A.; Blanck, Danielly V.; de Freitas, Patricia D.

2014-01-01

283

RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays  

Microsoft Academic Search

High-density microarrays are useful tools to study gene expression for the purpose of characterizing functional tissue changes in response to the action of drugs and chemicals. To test whether high-density expression data can identify mechanisms of toxicity and to identify an unknown sample through its RNA expression pattern, groups of male Wistar rats were administered 6 hepatotoxicants. The compounds chosen

Steven J. Bulera; Susan M. Eddy; Erika Ferguson; Timothy A. Jatkoe; James F. Reindel; Michael R. Bleavins; Felix A. De La Iglesia

2001-01-01

284

Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies  

PubMed Central

Background The most important challenge of performing insitu transcriptional profiling of the human ocular surface epithelial regions is obtaining samples in sufficient amounts, without contamination from adjacent tissue, as the region of interest is microscopic and closely apposed to other tissues regions. We have effectively collected ocular surface (OS) epithelial tissue samples from the Limbal Epithelial Crypt (LEC), limbus, cornea and conjunctiva of post-mortem cadaver eyes with laser microdissection (LMD) technique for gene expression studies with spotted oligonucleotide microarrays and Gene 1.0 ST arrays. Methods Human donor eyes (4 pairs for spotted oligonucleotide microarrays, 3 pairs for Gene 1.0 ST arrays) consented for research were included in this study with due ethical approval of the Nottingham Research Ethics Committee. Eye retrieval was performed within 36 hours of post-mortem period. The dissected corneoscleral buttons were immersed in OCT media and frozen in liquid nitrogen and stored at ?80°C till further use. Microscopic tissue sections of interest were taken on PALM slides and stained with Toluidine Blue for laser microdissection with PALM microbeam systems. Optimisation of the laser microdissection technique was crucial for efficient and cost effective sample collection. Results The starting concentration of RNA as stipulated by the protocol of microarray platforms was taken as the cut-off concentration of RNA samples in our studies. The area of LMD tissue processed for spotted oligonucleotide microarray study ranged from 86,253 ?m2 in LEC to 392,887 ?m2 in LEC stroma. The RNA concentration of the LMD samples ranged from 22 to 92 pg/?l. The recommended starting concentration of the RNA samples used for Gene 1.0 ST arrays was 6 ng/5 ?l. To achieve the desired RNA concentration the area of ocular surface epithelial tissue sample processed for the Gene 1.0 ST array experiments was approximately 100,0000 ?m2 to 130,0000 ?m2. RNA concentration of these samples ranged from 10.88 ng/12 ?l to 25.8 ng/12 ?l, with the RNA integrity numbers (RIN) for these samples from 3.3 to 7.9. RNA samples with RIN values below 2, that had failed to amplify satisfactorily were discarded. Conclusions The optimised protocol for sample collection and laser microdissection improved the RNA yield of the insitu ocular surface epithelial regions for effective microarray studies on spotted oligonucleotide and affymetrix platforms. PMID:24160452

2013-01-01

285

Decreased nuclear expression and increased cytoplasmic expression of ING5 may be linked to tumorigenesis and progression in human head and neck squamous cell carcinoma  

Microsoft Academic Search

Purpose  This study aimed to assess the protein level of inhibitor of growth gene 5 (ING5) in head and neck squamous cell carcinoma (HNSCC) and to explore its roles in tumorigenesis and cancer progression.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  ING5 expression was assessed in 172 cases of HNSCC by immunohistochemistry using tissue microarray, and in 3 oral SCC cell\\u000a lines by immunohistochemistry and Western blot. Expression

Xiaohan Li; Takeshi Nishida; Akira Noguchi; Yang Zheng; Hiroyuki Takahashi; Xianghong Yang; Shinji Masuda; Yasuo Takano

2010-01-01

286

Evaluation of microarray surfaces and arraying parameters for autoantibody profiling  

PubMed Central

Autoantigen microarrays are being used increasingly to study autoimmunity. Significant variation has been observed when comparing microarray surfaces, printing methods, and probing conditions. In the present study, 24 surfaces and several arraying parameters were analyzed using >500 feature autoantigen microarrays printed with quill pins. A small subset of slides, including FAST®, PATH®, and SuperEpoxy2, performed well while maintaining the sensitivity and specificity of autoantigen microarrays previously demonstrated by our laboratory. By optimizing the major variables in our autoantigen microarray platform, subtle differences in serum samples can be identified that will shed light on disease pathogenesis. PMID:18752214

Balboni, Imelda; Limb, Cindy; Tenenbaum, Jessica D.; Utz, Paul J.

2012-01-01

287

Visual DNA microarray for detection of epidermal growth factor receptor (EGFR) gene mutations.  

PubMed

Abstract Objective. To develop a gold nanoparticle-based visual DNA microarray for simple and rapid screening of EGFR gene mutations. Methods. The DNA fragments contain epidermal growth factor receptor (EGFR) exons 18, 19, 20 and 21 were amplified by polymerase chain reaction (PCR) using biotin-modified primers. The amino-modified oligonucleotides were immobilized on glass surface, which were used as the capturing probes to bind the complement biotinylated target DNA. After the PCR product has been hybridized to the immobilized capture probe DNA on the glass slides, the Streptavidin-conjugated gold nanoparticles were introduced to the microarray via specific binding to 5'-end biotin of the PCR products. The hybridization signal on array spots was enhanced and visualized by silver amplification. The EGFR mutation in 286 clinical samples from cancer patients were tested using the gold nanoparticle-based microarray and verified with Sanger DNA sequencing method. Results. A novel visual DNA microarray has been developed to detect EGFR mutations in tumor tissue specimens rapidly; its limit of detection (LOD) is up to 10(-9) mol/L and distinguishes power to detect 5% gene mutation in the mixture samples. Conclusion. For its high specificity and sensitivity, simplicity, lower price and higher speed, the present visual mutation detecting technique has potential application in clinical fields. PMID:25223598

Xue, Li; Fei, Jing-Jing; Song, Yi; Xu, Rong-Hua; Bai, Yu-Jie

2014-11-01

288

Symptomatic and asymptomatic benign prostatic hyperplasia: Molecular differentiation by using microarrays  

NASA Astrophysics Data System (ADS)

Benign prostatic hyperplasia (BPH) is a disease of unknown etiology that significantly affects the quality of life in aging men. Histologic BPH may present itself either as symptomatic or asymptomatic in nature. To elucidate the molecular differences underlying BPH, gene expression profiles from the prostate transition zone tissue have been analyzed by using microarrays. A set of 511 differentially expressed genes distinguished symptomatic and asymptomatic BPH. This genetic signature separates BPH from normal tissue but does not seem to change with age. These data could provide novel approaches for alleviating symptoms and hyperplasia in BPH.

Prakash, Kulkarni; Pirozzi, Gregorio; Elashoff, Michael; Munger, William; Waga, Iwao; Dhir, Rajiv; Kakehi, Yoshiyuki; Getzenberg, Robert H.

2002-05-01

289

Testing an aflatoxin B1 gene signature in rat archival tissues.  

PubMed

Archival tissues from laboratory studies represent a unique opportunity to explore the relationship between genomic changes and agent-induced disease. In this study, we evaluated the applicability of qPCR for detecting genomic changes in formalin-fixed, paraffin-embedded (FFPE) tissues by determining if a subset of 14 genes from a 90-gene signature derived from microarray data and associated with eventual tumor development could be detected in archival liver, kidney, and lung of rats exposed to aflatoxin B1 (AFB1) for 90 days in feed at 1 ppm. These tissues originated from the same rats used in the microarray study. The 14 genes evaluated were Adam8, Cdh13, Ddit4l, Mybl2, Akr7a3, Akr7a2, Fhit, Wwox, Abcb1b, Abcc3, Cxcl1, Gsta5, Grin2c, and the C8orf46 homologue. The qPCR FFPE liver results were compared to the original liver microarray data and to qPCR results using RNA from fresh frozen liver. Archival liver paraffin blocks yielded 30 to 50 ?g of degraded RNA that ranged in size from 0.1 to 4 kB. qPCR results from FFPE and fresh frozen liver samples were positively correlated (p ? 0.05) by regression analysis and showed good agreement in direction and proportion of change with microarray data for 11 of 14 genes. All 14 transcripts could be amplified from FFPE kidney RNA except the glutamate receptor gene Grin2c; however, only Abcb1b was significantly upregulated from control. Abundant constitutive transcripts, S18 and ?-actin, could be amplified from lung FFPE samples, but the narrow RNA size range (25-500 bp length) prevented consistent detection of target transcripts. Overall, a discrete gene signature derived from prior transcript profiling and representing cell cycle progression, DNA damage response, and xenosensor and detoxication pathways was successfully applied to archival liver and kidney by qPCR and indicated that gene expression changes in response to subchronic AFB1 exposure occurred predominantly in the liver, the primary target for AFB1-induced tumors. We conclude that an evaluation of gene signatures in archival tissues can be an important toxicological tool for evaluating critical molecular events associated with chemical exposures. PMID:22545673

Merrick, B Alex; Auerbach, Scott S; Stockton, Patricia S; Foley, Julie F; Malarkey, David E; Sills, Robert C; Irwin, Richard D; Tice, Raymond R

2012-05-21

290

Functionalized glass substrate for microarray analysis  

Microsoft Academic Search

A series of glass treatments were investigated to develop a miniaturized enzyme-linked immunosorbent assay microarray sensor with covalently immobilized antibody. Two glass compositions were photo-hydrolytically treated and functionalized with an amino- or mercapto-silane. Surface characterization was done using contact angle, X-ray photoelectron spectroscopy and atomic force microscopy data. Antibody binding efficiency was statistically compared between treatments and glass compositions.Photo-hydrolytic treatment

Rebecca L. DeRosa; Jean A. Cardinale; Ashleigh Cooper

2007-01-01

291

Preprocessing differential methylation hybridization microarray data  

Microsoft Academic Search

Background  DNA methylation plays a very important role in the silencing of tumor suppressor genes in various tumor types. In order to\\u000a gain a genome-wide understanding of how changes in methylation affect tumor growth, the differential methylation hybridization\\u000a (DMH) protocol has been developed and large amounts of DMH microarray data have been generated. However, it is still unclear\\u000a how to preprocess

Shuying Sun; Yi-Wen Huang; Pearlly S Yan; Tim HM Huang; Shili Lin

2011-01-01

292

Development of DNA microarray for pathogen detection  

Microsoft Academic Search

Pathogens pose a significant threat to humans, animals, and plants. Consequently, a considerable effort has been devoted to\\u000a developing rapid, convenient, and accurate assays for the detection of these unfavorable organisms. Recently, DNA-microarray\\u000a based technology is receiving much attention as a powerful tool for pathogen detection. After the target gene is first selected\\u000a for the unique identification of microorganisms, species-specific

Seung Min Yoo; Ki Chang Keum; So Young Yoo; Jun Yong Choi; Kyung Hee Chang; Nae Choon Yoo; Won Min Yoo; June Myung Kim; Duke Lee; Sang Yup Lee

2004-01-01

293

Microarray analysis of gene expression in mouse (strain 129) embryonic stem cells after typical synthetic musk exposure.  

PubMed

Synthetic musks are widely used in personal-care products and can readily accumulate in the adipose tissue, breast milk, and blood of humans. In this study, the Affymetrix Mouse Genome GeneChip was used to identify alterations in gene expression of embryonic stem cells from the 129 strain of the laboratory mouse after treatment with the synthetic musk tonalide (AHTN). Among the 45,037 transcripts in the microarray, 2,879 genes were differentially expressed. According to the microarray analysis, the potential influence of AHTN on the development to embryo should be of concern, and the toxicological effects of it and related musk compounds should be studied further. PMID:23099888

Shi, Jiachen; Li, Ming; Jiao, Zhihao; Zhang, Jing; Feng, Yixing; Shao, Bing

2013-01-01

294

DNA microarray technology for neonatal screening.  

PubMed

Modern molecular biology, owing much to the Human Genome Initiative, has elucidated many of the genetic mechanisms underlying heritable metabolic disease. While the use of molecular methods has flourished in research laboratories, complexity and cost have limited their utility in newborn screening. Newborn blood cards provide high quality DNA samples able to provide reliable support to highly multiplexed polymerase chain reactions (PCR). New manufacturing processes have reduced the cost of DNA microarray technology to the point where it is a practical tool for population screening. In a single assay, a DNA microarray facilitates the co-detection of amplification products diagnostic for several genetic diseases. High throughput is achieved with automation at every step, from DNA extraction to detection of hybrids. We suggest that it is both feasible and practical to develop a first-tier newborn screening protocol based upon multiplex PCR and analysis of amplification products using DNA microarrays. Initial data utilizing the model systems of sickle cell disease, alpha-1-antitrypsin deficiency and Factor V Leiden will be reported. PMID:10626582

Dobrowolski, S F; Banas, R A; Naylor, E W; Powdrill, T; Thakkar, D

1999-12-01

295

Microarray analysis in gastric cancer: A review  

PubMed Central

Gastric cancer is one of the most common tumors worldwide. Although several treatment options have been developed, the mortality rate is increasing. Lymph node involvement is considered the most reliable prognostic indicator in gastric cancer. Early diagnosis improves the survival rate of patients and increases the likelihood of successful treatment. The most reliable diagnostic method is endoscopic examination, however, it is expensive and not feasible in poorer countries. Therefore, many innovative techniques have been studied to develop a new non-invasive screening test and to identify specific serum biomarkers. DNA microarray analysis is one of the new technologies able to measure the expression levels of a large number of genes simultaneously. It is possible to define the gene expression profile of the tumor and to correlate it with the prognosis and metastasis formation. Several studies in the literature have been published on the role of microarray analysis in gastric cancer and the mechanisms of proliferation and metastasis formation. The aim of this review is to analyze the importance of microarray analysis and its clinical applications to better define the genetic characteristics of gastric cancer and its possible implications in a more decisive treatment.

D'Angelo, Giovanna; Di Rienzo, Teresa; Ojetti, Veronica

2014-01-01

296

Loss of equilibrative nucleoside transporter 1 in mice leads to progressive ectopic mineralization of spinal tissues resembling diffuse idiopathic skeletal hyperostosis in humans.  

PubMed

Diffuse idiopathic skeletal hyperostosis (DISH) is a noninflammatory spondyloarthropathy, characterized by ectopic calcification of spinal tissues. Symptoms include spine pain and stiffness, and in severe cases dysphagia and spinal cord compression. The etiology of DISH is unknown and there are no specific treatments. Recent studies have suggested a role for purine metabolism in the regulation of biomineralization. Equilibrative nucleoside transporter 1 (ENT1) transfers hydrophilic nucleosides, such as adenosine, across the plasma membrane. In mice lacking ENT1, we observed the development of calcified lesions resembling DISH. By 12 months of age, ENT1(-/-) mice exhibited signs of spine stiffness, hind limb dysfunction, and paralysis. Micro-computed tomography (µCT) revealed ectopic mineralization of paraspinal tissues in the cervical-thoracic region at 2 months of age, which extended to the lumbar and caudal regions with advancing age. Energy-dispersive X-ray microanalysis of lesions revealed a high content of calcium and phosphorus with a ratio similar to that of cortical bone. At 12 months of age, histological examination of ENT1(-/-) mice revealed large, irregular accumulations of eosinophilic material in paraspinal ligaments and entheses, intervertebral discs, and sternocostal articulations. There was no evidence of mineralization in appendicular joints or blood vessels, indicating specificity for the axial skeleton. Plasma adenosine levels were significantly greater in ENT1(-/-) mice than in wild-type, consistent with loss of ENT1--a primary adenosine uptake pathway. There was a significant reduction in the expression of Enpp1, Ank, and Alpl in intervertebral discs from ENT1(-/-) mice compared to wild-type mice. Elevated plasma levels of inorganic pyrophosphate in ENT1(-/-) mice indicated generalized disruption of pyrophosphate homeostasis. This is the first report of a role for ENT1 in regulating the calcification of soft tissues. Moreover, ENT1(-/-) mice may be a useful model for investigating pathogenesis and evaluating therapeutics for the prevention of mineralization in DISH and related disorders. PMID:23184610

Warraich, Sumeeta; Bone, Derek B J; Quinonez, Diana; Ii, Hisataka; Choi, Doo-Sup; Holdsworth, David W; Drangova, Maria; Dixon, S Jeffrey; Séguin, Cheryle A; Hammond, James R

2013-05-01

297

Identification of differentially expressed genes involved in colorectal carcinogenesis using a cDNA microarray.  

PubMed

To identify candidate genes involved in human colorectal carcinogenesis, we constructed the gene expression profiles of 50 colorectal cancers (CRCs) and 12 normal colorectal epithelia using a cDNA microarray specially constructed for CRC. Hierarchical clustering analysis and principal component analysis could clearly distinguish the gene profiles of cancer tissues from those of normal tissues. Our results confirm there are indeed differences in gene expression between cancer and normal mucosa. Our cDNA microarray identified 22 up-regulated genes and 32 down-regulated genes in CRC. Many of these genes have been previously identified in relation to human carcinogenesis, 68% and 78%, respectively. Subsequent validation of selected genes by serial analysis of gene expression and reverse transcription polymerase chain reaction, demonstrated expression patterns that were almost identical to our microarray analysis. Using a four-fold larger sample relative to that used in our previous study, candidate genes involved in human colorectal carcinogenesis were reproducibly identified. Further studies of comprehensive gene expression using our technique may elucidate the mechanism of CRC tumorigenesis. PMID:15595645

Komori, T; Takemasa, I; Higuchi, H; Yamasaki, M; Ikeda, M; Yamamoto, H; Ohue, M; Nakamori, S; Sekimoto, M; Matsubara, K; Monden, M

2004-09-01

298

Rapid Characterization of Candidate Biomarkers for Pancreatic Cancer Using Cell Microarrays (CMAs)  

PubMed Central

Tissue microarrays have become a valuable tool for high-throughput analysis using immunohistochemical labeling. However, the large majority of biochemical studies are carried out in cell lines to further characterize candidate biomarkers or therapeutic targets with subsequent studies in animals or using primary tissues. Thus, cell line-based microarrays could be a useful screening tool in some situations. Here, we constructed a cell microarray (CMA) containing a panel of 40 pancreatic cancer cell lines available from American Type Culture Collection in addition to those locally available at Johns Hopkins. As proof of principle, we performed immunocytochemical labeling of an epithelial cell adhesion molecule (Ep-CAM), a molecule generally expressed in the epithelium, on this pancreatic cancer CMA. In addition, selected molecules that have been previously shown to be differentially expressed in pancreatic cancer in the literature were validated. For example, we observed strong labeling of CA19-9 antigen, a prognostic and predictive marker for pancreatic cancer. We also carried out a bioinformatics analysis of a literature curated catalog of pancreatic cancer biomarkers developed previously by our group and identified two candidate biomarkers, HLA class I and transmembrane protease, serine 4 (TMPRSS4), and examined their expression in the cell lines represented on the pancreatic cancer CMAs. Our results demonstrate the utility of CMAs as a useful resource for rapid screening of molecules of interest and suggest that CMAs can become a universal standard platform in cancer research. PMID:22985314

Kim, Min-Sik; Kuppireddy, Sarada V.; Sakamuri, Sruthi; Singal, Mukul; Getnet, Derese; Harsha, H. C.; Goel, Renu; Balakrishnan, Lavanya; Jacob, Harrys K. C.; Kashyap, Manoj K.; Tankala, Shantal G.; Maitra, Anirban; Iacobuzio-Donahue, Christine A.; Jaffee, Elizabeth; Goggins, Michael G.; Velculescu, Victor E.; Hruban, Ralph H.; Pandey, Akhilesh

2013-01-01

299

A high-throughput strategy for protein profiling in cell microarrays using automated image analysis.  

PubMed

Advances in antibody production render a growing supply of affinity reagents for immunohistochemistry (IHC), and tissue microarray (TMA) technologies facilitate simultaneous analysis of protein expression in a multitude of tissues. However, collecting validated IHC data remains a bottleneck problem, as the standard method is manual microscopical analysis. Here we present a high-throughput strategy combining IHC on a recently developed cell microarray with a novel, automated image-analysis application (TMAx). The software was evaluated on 200 digital images of IHC-stained cell spots, by comparing TMAx annotation with manual annotation performed by seven human experts. A high concordance between automated and manual annotation of staining intensity and fraction of IHC-positive cells was found. In a limited study, we also investigated the possibility to assess the correlation between mRNA and protein levels, by using TMAx output results for relative protein quantification and quantitative real-time PCR for the quantification of corresponding transcript levels. In conclusion, automated analysis of immunohistochemically stained in vitro-cultured cells in a microarray format can be used for high-throughput protein profiling, and extraction of RNA from the same cell lines provides a basis for comparing transcription and protein expression on a global scale. PMID:17549799

Strömberg, Sara; Björklund, Marcus Gry; Asplund, Caroline; Sköllermo, Anna; Persson, Anja; Wester, Kenneth; Kampf, Caroline; Nilsson, Peter; Andersson, Ann-Catrin; Uhlen, Mathias; Kononen, Juha; Ponten, Fredrik; Asplund, Anna

2007-06-01

300

Assessing statistical significance in microarray experiments using the distance between microarrays.  

PubMed

We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations. For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis. The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data. An R software package, permtest, implementing the method is freely available from the Comprehensive R Archive Network at http://cran.r-project.org. PMID:19529777

Hayden, Douglas; Lazar, Peter; Schoenfeld, David

2009-01-01

301

Accurate genome-scale percentage DNA methylation estimates from microarray data  

PubMed Central

DNA methylation is a key regulator of gene function in a multitude of both normal and abnormal biological processes, but tools to elucidate its roles on a genome-wide scale are still in their infancy. Methylation sensitive restriction enzymes and microarrays provide a potential high-throughput, low-cost platform to allow methylation profiling. However, accurate absolute methylation estimates have been elusive due to systematic errors and unwanted variability. Previous microarray preprocessing procedures, mostly developed for expression arrays, fail to adequately normalize methylation-related data since they rely on key assumptions that are violated in the case of DNA methylation. We develop a normalization strategy tailored to DNA methylation data and an empirical Bayes percentage methylation estimator that together yield accurate absolute methylation estimates that can be compared across samples. We illustrate the method on data generated to detect methylation differences between tissues and between normal and tumor colon samples. PMID:20858772

Aryee, Martin J.; Wu, Zhijin; Ladd-Acosta, Christine; Herb, Brian; Feinberg, Andrew P.; Yegnasubramanian, Srinivasan; Irizarry, Rafael A.

2011-01-01

302

Microarray discovery of new OGT substrates: the medulloblastoma oncogene OTX2 is O-GlcNAcylated.  

PubMed

O-GlcNAc transferase (OGT) is a serine/threonine glycosyltransferase that is essential for development and continues to be critically important throughout life. Understanding OGT's complex biology requires identifying its substrates. Here we demonstrate the utility of a microarray approach for discovering novel OGT substrates. We also report a rapid method to validate OGT substrates that combines in vitro transcription-translation with O-GlcNAc mass tagging. Among the validated new OGT targets is Orthodenticle homeobox 2 (OTX2), a transcription factor critical for brain development, which is primarily expressed only during early embryogenesis and in medulloblastomas, where it functions as an oncogene. We show that endogenous OTX2 from a medulloblastoma cell line is O-GlcNAcylated at several sites. Our results demonstrate that protein microarray technology, combined with the target validation strategy we report, is useful for identifying biologically important OGT substrates, including substrates not present in most tissue types or cell lines. PMID:24580054

Ortiz-Meoz, Rodrigo F; Merbl, Yifat; Kirschner, Marc W; Walker, Suzanne

2014-04-01

303

Stromal protein periostin identified as a progression associated and prognostic biomarker in glioma via inducing an invasive and proliferative phenotype.  

PubMed

To explore the expression pattern, prognostic value and functional role of stromal periostin (POSTN) in glioma patients, POSTN expression was measured using the Agilent Whole Human Genome Oligo Microarray in 220 frozen glioma tissues. We analyzed POSTN expression in 71 independent validated glioma samples using immuno-histochemistry. The expression levels of POSTN were relative to glioma grade progression and inversely correlated with overall survival in high-grade glioma patients (anaplastic gliomas and glioblastomas). Gene ontology (GO) analysis performed using DAVID showed that the gene sets related to cell migration and proliferation were significantly enriched in the cases with POSTN overexpression. Functional analyses in LN229 and U87 cells revealed that POSTN was involved in cell invasion and proliferation. MMP-9 was an effector of POSTN signaling in glioma cells. The expression of stromal protein POSTN is relative to glioma grade progression and confers a poor prognosis via promoting cellular invasion and proliferation in high-grade glioma patients. PMID:23467707

Wang, Hongjun; Wang, Yongzhi; Jiang, Chuanlu

2013-05-01

304

Optimization and clinical validation of a pathogen detection microarray  

PubMed Central

DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics. PMID:17531104

Wong, Christopher W; Heng, Charlie Lee Wah; Wan Yee, Leong; Soh, Shirlena WL; Kartasasmita, Cissy B; Simoes, Eric AF; Hibberd, Martin L; Sung, Wing-Kin; Miller, Lance D

2007-01-01

305

A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis  

PubMed Central

Background Several high-throughput technologies can measure in parallel the abundance of many mRNA transcripts within a sample. These include the widely-used microarray as well as the more recently developed methods based on sequence tag abundances such as the Massively Parallel Signature Sequencing (MPSS) technology. A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Results We compared transcript abundance (gene expression) measurement data obtained using Affymetrix and Agilent microarrays with MPSS data. All three technologies were used to analyze the same set of mRNA samples; these samples were extracted from various wild type Arabidopsis thaliana tissues and floral mutants. We calculated correlations and used clustering methodology to compare the normalized expression data and expression ratios across samples and technologies. Abundance expression measurements were more similar between different samples measured by the same technology than between the same sample measured by different technologies. However, when expression ratios were employed, samples measured by different technologies were found to cluster together more frequently than with abundance expression levels. Furthermore, the two microarray technologies were more consistent with each other than with MPSS. We also investigated probe-position effects on Affymetrix data and tag-position effects in MPSS. We found a similar impact on Affymetrix and MPSS measurements, which suggests that these effects were more likely a characteristic of the RNA sample rather than technology-specific biases. Conclusion Comparisons of transcript expression ratios showed greater consistency across platforms than measurements of transcript abundance. In addition, for measurements based on abundances, technology differences can mask the impact of biological differences between samples and tissues. PMID:17997849

Chen, Junfeng; Agrawal, Vikas; Rattray, Magnus; West, Marilyn AL; St Clair, Dina A; Michelmore, Richard W; Coughlan, Sean J; Meyers, Blake C

2007-01-01

306

Adipose Gene Expression Profiles Related to Metabolic Syndrome Using Microarray Analyses in Two Different Models  

PubMed Central

Background Peroxisome proliferator-activated receptor-? (PPAR-?) agonist has a wide-ranging influence on multiple components of metabolic syndrome. The Otsuka Long-Evans Tokushima Fatty (OLETF) rat is a useful animal model of metabolic syndrome. To determine genes related to metabolic syndrome, we examined overlapping genes that are simultaneously decreased by PPAR-? agonists and increased in OLETF rats using microarrays in two different models. Methods In the first microarray analysis, PPAR-? agonist-treated db/db mice were compared to standard diet-fed db/db mice. In the second microarray analysis, OLETF rats were compared to Long-Evans Tokushima Otsuka (LETO) rats (control of OLETF rats). Results Among the overlapping genes, in the present study, we validated that lipocalin-2 expression was significantly decreased in the visceral adipose tissue of PPAR-? agonist-treated db/db mice compared to standard diet-fed db/db mice and increased in OLETF rats compared to LETO rats using real time reverse transcription polymerase chain reaction. Furthermore, we showed for the first time that lipocalin-2 expression was significantly increased in the visceral adipose tissues of obese humans compared with nonobese humans. In addition, the expression level of lipocalin-2 in human visceral adipose tissue had a significant positive correlation with body mass index, serum interleukin-6, adipocyte fatty acid binding protein levels, and white blood cell count. Conclusion Lipocalin-2 was confirmed to be a significant adipokine affected by PPAR-? agonist and obesity in the present study. Also, for the first time in human visceral adipose tissue, it was determined that the expression of lipocalin-2 from obese humans was significantly increased and correlated with circulating inflammatory markers.

Yoo, Hye Jin; Hwang, Hwan-Jin; Jung, Tae Woo; Ryu, Ja Young; Hong, Ho Cheol; Choi, Hae Yoon; Baik, Sei Hyun

2014-01-01

307

Microarray analyses of shrimp immune responses.  

PubMed

Shrimp aquaculture is one of the major foodproducing industries in the world. However, it is being impacted by several problems including diseases, antibiotic use, and environmental factors. The extent of the effects of these problems in the immune system of the shrimp at the molecular level is just beginning to be understood. Here, we review the gene expression profile of shrimp in response to some of these problems using the high-throughput microarray analysis, including white spot syndrome virus, yellow head virus, Vibrio spp., peptidoglycan, oxytetracycline, oxolinic acid, salinity, and temperature. PMID:20393773

Aoki, Takashi; Wang, Han-Ching; Unajak, Sasimanas; Santos, Mudjekeewis D; Kondo, Hidehiro; Hirono, Ikuo

2011-08-01

308

Robust semiparametric microarray normalization and significance analysis.  

PubMed

Microarray technology allows the monitoring of expression levels of thousands of genes simultaneously. A semiparametric location and scale model is proposed to model gene expression levels for normalization and significance analysis purposes. Robust estimation based on weighted least absolute deviation regression and significance analysis based on the weighted bootstrap are investigated. The proposed approach naturally combines normalization and significance analysis, and incorporates the variations due to normalization into the significance analysis properly. A small simulation study is used to compare finite sample performance of the proposed approach with alternatives. We also demonstrate the proposed method with a real dataset. PMID:16918920

Ma, Shuangge; Kosorok, Michael R; Huang, Jian; Xie, Hehuang; Manzella, Liliana; Soares, Marcelo Bento

2006-06-01

309

Evaluating Microarray-based Classifiers: An Overview  

PubMed Central

For the last eight years, microarray-based class prediction has been the subject of numerous publications in medicine, bioinformatics and statistics journals. However, in many articles, the assessment of classification accuracy is carried out using suboptimal procedures and is not paid much attention. In this paper, we carefully review various statistical aspects of classifier evaluation and validation from a practical point of view. The main topics addressed are accuracy measures, error rate estimation procedures, variable selection, choice of classifiers and validation strategy. PMID:19259405

Boulesteix, A.-L.; Strobl, C.; Augustin, T.; Daumer, M.

2008-01-01

310

ProMAT: protein microarray analysis tool  

SciTech Connect

Summary: ProMAT is a software tool for statistically analyzing data from ELISA microarray experiments. The software estimates standard curves, sample protein concentrations and their uncertainties for multiple assays. ProMAT generates a set of comprehensive figures for assessing results and diagnosing process quality. The tool is available for Windows or Mac, and is distributed as open-source Java and R code. Availability: ProMAT is available at http://www.pnl.gov/statistics/ProMAT. ProMAT requires Java version 1.5.0 and R version 1.9.1 (or more recent versions) which are distributed with the tool.

White, Amanda M.; Daly, Don S.; Varnum, Susan M.; Anderson, Kevin K.; Bollinger, Nikki; Zangar, Richard C.

2006-04-04

311

DESIGNING COMPRESSIVE SENSING DNA MICROARRAYS Mona A. Sheikh,  

E-print Network

the CS theory and the biochemistry of probe-target DNA hybridiza- tion. We employ Belief Propagation-- Compressive Sensing, DNA Microarrays, Probe Design, Hybridization Affinity 1. INTRODUCTION Biosensing

312

Studying cellular processes and detecting disease with protein microarrays  

SciTech Connect

Protein microarrays are a rapidly developing analytic tool with diverse applications in biomedical research. These applications include profiling of disease markers or autoimmune responses, understanding molecular pathways, protein modifications and protein activities. One factor that is driving this expanding usage is the wide variety of experimental formats that protein microarrays can take. In this review, we provide a short, conceptual overview of the different approaches for protein microarray. We then examine some of the most significant applications of these microarrays to date, with an emphasis on how global protein analyses can be used to facilitate biomedical research.

Zangar, Richard C.; Varnum, Susan M.; Bollinger, Nikki

2005-10-31

313

Estimating relative noise to signal in DNA microarray data  

PubMed Central

A method was proposed for estimating noise relative to signal in microarray data. A signal to noise index, SNI, was defined and used to measure the level of signal compared to the noise contained in two microarray data sets. Simulations were conducted to generate the quantitative relationship between the SNI and its measurement of relative noise. The method was applied to two well known microarray data sets. Relative noise was estimated for both data sets, and the results were consistent with the observations in the original papers, demonstrating the proposed method is reliable for estimating relative noise in microarray data. PMID:24001721

Hong, Qilong; Liu, Jie; Tong, Weida; Shi, Leming

2014-01-01

314

Nestin(+) tissue-resident multipotent stem cells contribute to tumor progression by differentiating into pericytes and smooth muscle cells resulting in blood vessel remodeling.  

PubMed

Tumor vessels with resistance to anti-angiogenic therapy are characterized by the normalization of the vascular structures through integration of mature pericytes and smooth muscle cells (SMC) into the vessel wall, a process termed vessel stabilization. Unfortunately, stabilization-associated vascular remodeling can result in reduced sensitivity to subsequent anti-angiogenic therapy. We show here that blockade of VEGF by bevacizumab induces stabilization of angiogenic tumor blood vessels in human tumor specimen by recruiting Nestin-positive cells, whereas mature vessels down-regulated Nestin-expression. Using xenograft tumors growing on bone-marrow (BM) chimera of C57Bl/6 wildtype and Nestin-GFP transgenic mice, we show for first time that Nestin(+) cells inducing the maturation of tumor vessels do not originate from the BM but presumably reside within the adventitia of adult blood vessels. Complementary ex vivo experiments using explants of murine aortas revealed that Nestin(+) multipotent stem cells (MPSCs) are mobilized from their niche and differentiated into pericytes and SMC through the influence of tumor-cell-secreted factors. We conclude that tissue-resident Nestin(+) cells are more relevant than BM-derived cells for vessel stabilization and therefore have to be considered in future strategies for anti-angiogenic therapy. The identification of proteins mediating recruitment or differentiation of local Nestin(+) cells with potential stem cell character to angiogenic blood vessels may allow the definition of new therapeutic targets to reduce tumor resistance against anti-angiogenic drugs. PMID:25019063

Klein, Diana; Meissner, Nicole; Kleff, Veronika; Jastrow, Holger; Yamaguchi, Masahiro; Ergün, Süleyman; Jendrossek, Verena

2014-01-01

315

Adipose-specific knockout of SEIPIN/BSCL2 results in progressive lipodystrophy.  

PubMed

Berardinelli-Seip congenital lipodystrophy type 2 (BSCL2) is the most severe form of human lipodystrophy, characterized by an almost complete loss of adipose tissue and severe insulin resistance. BSCL2 is caused by loss-of-function mutations in the BSCL2/SEIPIN gene, which is upregulated during adipogenesis and abundantly expressed in the adipose tissue. The physiological function of SEIPIN in mature adipocytes, however, remains to be elucidated. Here, we generated adipose-specific Seipin knockout (ASKO) mice, which exhibit adipocyte hypertrophy with enlarged lipid droplets, reduced lipolysis, adipose tissue inflammation, progressive loss of white and brown adipose tissue, insulin resistance, and hepatic steatosis. Lipidomic and microarray analyses revealed accumulation/imbalance of lipid species, including ceramides, in ASKO adipose tissue as well as increased endoplasmic reticulum stress. Interestingly, the ASKO mice almost completely phenocopy the fat-specific peroxisome proliferator-activated receptor-? (Ppar?) knockout (FKO-?) mice. Rosiglitazone treatment significantly improved a number of metabolic parameters of the ASKO mice, including insulin sensitivity. Our results therefore demonstrate a critical role of SEIPIN in maintaining lipid homeostasis and function of adipocytes and reveal an intimate relationship between SEIPIN and PPAR-?. PMID:24622797

Liu, Lu; Jiang, Qingqing; Wang, Xuhong; Zhang, Yuxi; Lin, Ruby C Y; Lam, Sin Man; Shui, Guanghou; Zhou, Linkang; Li, Peng; Wang, Yuhui; Cui, Xin; Gao, Mingming; Zhang, Ling; Lv, Ying; Xu, Guoheng; Liu, George; Zhao, Dong; Yang, Hongyuan

2014-07-01

316

Laser direct writing of biomolecule microarrays  

NASA Astrophysics Data System (ADS)

Protein-based biosensors are highly efficient tools for protein detection and identification. The production of these devices requires the manipulation of tiny amounts of protein solutions in conditions preserving their biological properties. In this work, laser induced forward transfer (LIFT) was used for spotting an array of a purified bacterial antigen in order to check the viability of this technique for the production of protein microarrays. A pulsed Nd:YAG laser beam (355 nm wavelength, 10 ns pulse duration) was used to transfer droplets of a solution containing the Treponema pallidum 17 kDa protein antigen on a glass slide. Optical microscopy showed that a regular array of micrometric droplets could be precisely and uniformly spotted onto a solid substrate. Subsequently, it was proved that LIFT deposition of a T. pallidum 17 kDa antigen onto nylon-coated glass slides preserves its antigenic reactivity and diagnostic properties. These results support that LIFT is suitable for the production of protein microarrays and pave the way for future diagnostics applications.

Serra, P.; Fernández-Pradas, J. M.; Berthet, F. X.; Colina, M.; Elvira, J.; Morenza, J. L.

317

Stem Cells and Tissue Engineering: Prospects for Regenerating Tissues in Dental Practice  

Microsoft Academic Search

In general, human tissues have a very limited potential to regenerate. However, recent progress in stem cell research and in tissue engineering promises novel prospects for tissue regeneration in dental practice in the future. Stem cells have been discovered in many adult tissues, including teeth, and stem cells from embryos have the potential to form all adult tissues. Embryonic stem

Irma Thesleff; Mark Tummers

2003-01-01

318

Microarray analysis of Xenopus endoderm expressing Ptf1a  

PubMed Central

Pancreas specific transcription factor 1a (Ptf1a), a bHLH transcription factor, has two temporally distinct functions during pancreas development; initially it is required for early specification of the entire pancreas, while later it is required for proper differentiation and maintenance of only acinar cells. The importance of Ptf1a function was revealed by the fact that loss of Ptf1a leads to pancreas agenesis in humans. While Ptf1a is one of the most important pancreatic transcription factors, little is known about the differences between the regulatory networks it controls during initial specification of the pancreas as opposed to acinar cell development, and to date no comprehensive analysis of its downstream targets has been published. In this paper, we use Xenopus embryos to identify putative downstream targets of Ptf1a. We isolated anterior endoderm tissue overexpressing Ptf1a at two early stages, NF32 and NF36, and compared their gene expression profiles using microarrays. Our results revealed that Ptf1a regulates genes with a wide variety of functions, providing insight into the complexity of the regulatory network required for pancreas specification. PMID:22815262

Bilogan, Cassandra K.; Horb, Marko E.

2012-01-01

319

Sequential Design for Microarray Experiments Gilles DURRIEU, and Laurent BRIOLLAIS  

E-print Network

an accurate assessment of differential gene expression without compromising the cost and size of the study studies by improving the usual experimental designs and methods of analysis. KEY WORDS: Microarray Study. A critical aspect in the design of microarray studies is the determination of the sample size necessary

Brest, Université de

320

Detailed insights from microarray and crystallographic studies into carbohydrate  

E-print Network

Detailed insights from microarray and crystallographic studies into carbohydrate recognition of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of TgMIC1 to 2-3- and 2-6-linked sialyl carbohydrates. Interestingly, two novel synthetic fluorinated

Davis, Ben G.

321

Removal of hybridization and scanning noise from microarrays.  

PubMed

Microarray technology for measuring gene expression values has created significant opportunities for advances in disease diagnosis and individualized treatment planning. However, the random noise introduced by the sample preparation, hybridization, and scanning stages of microarray processing creates significant inaccuracies in the gene expression levels, and hence presents a major barrier in realizing the anticipated advances. Literature presents several methodologies for noise reduction, which can be broadly categorized as: 1) model based approaches for estimation and removal of hybridization noise; 2) approaches using commonly available image denoising tools; and 3) approaches involving the need for control sample(s). In this paper, we present a novel methodology for identifying and removing hybridization and scanning noise from microarray images, using a dual-tree-complex-wavelet-transform-based multiresolution analysis coupled with bivariate shrinkage thresholding. The key features of our methodology include consideration of inherent features and type of noise specific to microarray images, and the ability to work with a single microarray without needing a control. Our methodology is first benchmarked on a fabricated dataset that mimics a real microarray probe dataset. Thereafter, our methodology is tested on datasets obtained from a number of Affymetrix GeneChip human genome HG-U133 Plus 2.0 arrays, processed on HCT-116 cell line at the Microarray Core Facility of Moffitt Cancer Center and Research Institute. The results indicate an appreciable improvement in the quality of the microarray data. PMID:20051337

Gopalappa, Chaitra; Das, Tapas K; Enkemann, Steven; Eschrich, Steven

2009-09-01

322

Photonic crystal Microarray Nanoplatform for High Throughput Detection of Biomolecules  

E-print Network

Photonic crystal Microarray Nanoplatform for High Throughput Detection of Biomolecules Swapnajit and experimental results for creating a microarray nanoplatform based on two- dimensional photonic crystal devices in silicon. Multiple photonic crystal microcavities are coupled along the length of a single photonic crystal

Chen, Ray

323

Applications of microarray technology in breast cancer research  

PubMed Central

Microarrays provide a versatile platform for utilizing information from the Human Genome Project to benefit human health. This article reviews the ways in which microarray technology may be used in breast cancer research. Its diverse applications include monitoring chromosome gains and losses, tumour classification, drug discovery and development, DNA resequencing, mutation detection and investigating the mechanism of tumour development. PMID:11305951

Cooper, Colin S

2001-01-01

324

Significance analysis of microarrays applied to the ionizing radiation response  

Microsoft Academic Search

Microarrays can measure the expression of thousands of genes to identify changes in expression between different biological states. Methods are needed to determine the significance of these changes while accounting for the enormous number of genes.We describe a method, Significance Analysis of Microarrays (SAM), that assigns a score to each gene on the basis of change in gene expression relative

V. G. Tusher; Robert Tibshirani; Gilbert Chu

2001-01-01

325

Microarray data analysis Gold-mining in a minefield  

E-print Network

1 Microarray data analysis ­ Gold-mining in a minefield Matthias E. Futschik Institute Mathematics Institut, 15 November 2004 Outline The Gold-mine Stake out the claim Microarray Boom: 10 years-out, design and validation Minefield III: Not everything is gold that shines Error detection and correction

Futschik, Matthias E.

326

Letter to the Editor Make Microarray Data with Known Ratios  

E-print Network

teachers and students alike. We have developed an electronic resource (Spot Synthesizer; www.bio.davidson.edu/projects/GCAT/Spot_synthe- sizer/Spot_synthesizer.html) that permits faculty to gener- ate simulated DNA microarray data for useRisi et al. (1997), DNA microarrays have become an increasingly powerful and popular research tool

Campbell, A. Malcolm

327

Platform influence on DNA microarray data in postmortem brain research  

Microsoft Academic Search

In addition to the substantial biological diversity among humans, our limited ability to reliably measure expression changes of small magnitude significantly reduces our capacity to obtain convergent sets of transcriptome data in postmortem brain. In particular, differences in the structure and sensitivity\\/reproducibility of microarray platforms, and in the variety of tools used to analyze microarray data, strongly influence experimental outcome.

Deborah Hollingshead; David A. Lewis; Károly Mirnics

2005-01-01

328

Improving missing value estimation in microarray data with gene ontology  

Microsoft Academic Search

Motivation: Gene expression microarray experiments produce data sets with frequent missing expression values. Accurate estimation of missing values is an important prerequisite for efficient data analysis as many statistical and machine learning techniques either require a complete data set or their results are significantly dependent on the quality of such estimates. A limitation of the existing estimation methods for microarray

Johannes Tuikkala; Laura Elo; Olli Nevalainen; Tero Aittokallio

2006-01-01

329

Emerging use of gene expression microarrays in plant physiology  

Microsoft Academic Search

Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide high- throughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better

Stan D. Wullschleger; Stephen P. Difazio

2003-01-01

330

Microfluidic Device for Rapid (15 min) Automated Microarray Hybridization  

Microsoft Academic Search

Background: Current hybridization protocols on mi- croarrays are slow and need skilled personnel. Microflu- idics is an emerging science that enables the processing of minute volumes of liquids to perform chemical, biochemical, or enzymatic analyzes. The merging of microfluidics and microarray technologies constitutes an elegant solution that will automate and speed up microarray hybridization. Methods: We developed a microfluidic flow

Regis Peytavi; Frederic R. Raymond; Dominic Gagne; Francois J. Picard; Guangyao Jia; Jim Zoval; Marc Madou; Karel Boissinot; Maurice Boissinot; Luc Bissonnette; Marc Ouellette; Michel G. Bergeron

2005-01-01

331

Improved Sensitivity of DNA Microarrays Using Photonic Crystal Enhanced Fluorescence  

E-print Network

. This PC is inexpensively and uniformly fabricated using a nanoreplica molding tech- nique, with very- stratres to achieve increased intensity from common microarray dyes, with signal enhancements ranging from,6 or the deposition of nanoparticles fabricated by spray pyrolysis7 to produce optical resonances to which microarray

Cunningham, Brian

332

The Importance of Normalization on Large and Heterogeneous Microarray Datasets  

EPA Science Inventory

DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

333

Demonstrating a multi-drug resistant Mycobacterium tuberculosis amplification microarray.  

PubMed

Simplifying microarray workflow is a necessary first step for creating MDR-TB microarray-based diagnostics that can be routinely used in lower-resource environments. An amplification microarray combines asymmetric PCR amplification, target size selection, target labeling, and microarray hybridization within a single solution and into a single microfluidic chamber. A batch processing method is demonstrated with a 9-plex asymmetric master mix and low-density gel element microarray for genotyping multi-drug resistant Mycobacterium tuberculosis (MDR-TB). The protocol described here can be completed in 6 hr and provide correct genotyping with at least 1,000 cell equivalents of genomic DNA. Incorporating on-chip wash steps is feasible, which will result in an entirely closed amplicon method and system. The extent of multiplexing with an amplification microarray is ultimately constrained by the number of primer pairs that can be combined into a single master mix and still achieve desired sensitivity and specificity performance metrics, rather than the number of probes that are immobilized on the array. Likewise, the total analysis time can be shortened or lengthened depending on the specific intended use, research question, and desired limits of detection. Nevertheless, the general approach significantly streamlines microarray workflow for the end user by reducing the number of manually intensive and time-consuming processing steps, and provides a simplified biochemical and microfluidic path for translating microarray-based diagnostics into routine clinical practice. PMID:24796567

Linger, Yvonne; Kukhtin, Alexander; Golova, Julia; Perov, Alexander; Qu, Peter; Knickerbocker, Christopher; Cooney, Christopher G; Chandler, Darrell P

2014-01-01

334

A rapid and inexpensive labeling method for microarray gene expression analysis  

E-print Network

Global gene expression profiling by DNA microarrays is anBackground DNA microarrays allow global profiling of nucleicDNA microarrays have been devel- oped in the past decade [1,2], differential gene expression profiling

Ouellet, Mario

2012-01-01

335

Investigating the biochemical progression of liver disease through fibrosis, cirrhosis, dysplasia, and hepatocellular carcinoma using Fourier transform infrared spectroscopic imaging  

NASA Astrophysics Data System (ADS)

Hepatocellular carcinoma (HCC) is the most common form of primary hepatic carcinoma. HCC ranks the fourth most prevalent malignant tumor and the third leading cause of cancer related death in the world. Hepatocellular carcinoma develops in the context of chronic liver disease and its evolution is characterized by progression through intermediate stages to advanced disease and possibly even death. The primary sequence of hepatocarcinogenesis includes the development of cirrhosis, followed by dysplasia, and hepatocellular carcinoma.1 We addressed the utility of Fourier Transform Infrared (FT-IR) spectroscopic imaging, both as a diagnostic tool of the different stages of the disease and to gain insight into the biochemical process associated with disease progression. Tissue microarrays were obtained from the University of Illinois at Chicago tissue bank consisting of liver explants from 12 transplant patients. Tissue core biopsies were obtained from each explant targeting regions of normal, liver cell dysplasia including large cell change and small cell change, and hepatocellular carcinoma. We obtained FT-IR images of these tissues using a modified FT-IR system with high definition capabilities. Firstly, a supervised spectral classifier was built to discriminate between normal and cancerous hepatocytes. Secondly, an expanded classifier was built to discriminate small cell and large cell changes in liver disease. With the emerging advances in FT-IR instrumentation and computation there is a strong drive to develop this technology as a powerful adjunct to current histopathology approaches to improve disease diagnosis and prognosis.

Sreedhar, Hari; Pant, Mamta; Ronquillo, Nemencio R.; Davidson, Bennett; Nguyen, Peter; Chennuri, Rohini; Choi, Jacqueline; Herrera, Joaquin A.; Hinojosa, Ana C.; Jin, Ming; Kajdacsy-Balla, Andre; Guzman, Grace; Walsh, Michael J.

2014-03-01

336

Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data  

PubMed Central

Background Multicategory Support Vector Machines (MC-SVM) are powerful classification systems with excellent performance in a variety of data classification problems. Since the process of generating models in traditional multicategory support vector machines for large datasets is very computationally intensive, there is a need to improve the performance using high performance computing techniques. Results In this paper, Parallel Multicategory Support Vector Machines (PMC-SVM) have been developed based on the sequential minimum optimization-type decomposition method for support vector machines (SMO-SVM). It was implemented in parallel using MPI and C++ libraries and executed on both shared memory supercomputer and Linux cluster for multicategory classification of microarray data. PMC-SVM has been analyzed and evaluated using four microarray datasets with multiple diagnostic categories, such as different cancer types and normal tissue types. Conclusion The experiments show that the PMC-SVM can significantly improve the performance of classification of microarray data without loss of accuracy, compared with previous work. PMID:17217507

Zhang, Chaoyang; Li, Peng; Rajendran, Arun; Deng, Youping; Chen, Dequan

2006-01-01

337

cDNA Microarray Screening in Food Safety  

PubMed Central

The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and genetically modified foods. In order to bring the microarray technology to mainstream food safety, it is important to develop robust user-friendly tools that may be applied in a field setting. In addition, there needs to be a standardized process for regulatory agencies to interpret and act upon microarray-based data. The cDNA microarray approach is an emergent technology in diagnostics. Its values lie in being able to provide complimentary molecular insight when employed in addition to traditional tests for food safety, as part of a more comprehensive battery of tests. PMID:16466843

ROY, SASHWATI; SEN, CHANDAN K

2009-01-01

338

Disease signatures are robust across tissues and experiments.  

PubMed

Meta-analyses combining gene expression microarray experiments offer new insights into the molecular pathophysiology of disease not evident from individual experiments. Although the established technical reproducibility of microarrays serves as a basis for meta-analysis, pathophysiological reproducibility across experiments is not well established. In this study, we carried out a large-scale analysis of disease-associated experiments obtained from NCBI GEO, and evaluated their concordance across a broad range of diseases and tissue types. On evaluating 429 experiments, representing 238 diseases and 122 tissues from 8435 microarrays, we find evidence for a general, pathophysiological concordance between experiments measuring the same disease condition. Furthermore, we find that the molecular signature of disease across tissues is overall more prominent than the signature of tissue expression across diseases. The results offer new insight into the quality of public microarray data using pathophysiological metrics, and support new directions in meta-analysis that include characterization of the commonalities of disease irrespective of tissue, as well as the creation of multi-tissue systems models of disease pathology using public data. PMID:19756046

Dudley, Joel T; Tibshirani, Robert; Deshpande, Tarangini; Butte, Atul J

2009-01-01

339

Differential expression of extracellular matrix proteins in senescent and young human fibroblasts: A comparative proteomics and microarray study  

Microsoft Academic Search

The extracellular matrix (ECM) provides an essential structural framework for cell attachment, proliferation, and differentiation,\\u000a and undergoes progressive changes during senescence. To investigate changes in protein expression in the extracellular matrix\\u000a between young and senescent fibroblasts, we compared proteomic data (LTQ-FT) with cDNA microarray results. The peptide counts\\u000a from the proteomics analysis were used to evaluate the level of ECM

Kyeong Eun Yang; Joseph Kwon; Ji-Heon Rhim; Jong Soon Choi; Seung Il Kim; Seung-Hoon Lee; Ik-Soon Jang

340

On the Statics for Micro-Array Data Analysis  

NASA Astrophysics Data System (ADS)

Recently after human genome sequence has been determined almost perfectly, more and more researchers have been studying genes in detail. Therefore, we are sure that accumulated gene information for human will be getting more important in the near future to develop customized medicine and to make gene interactions clear. Among plenty of information, micro array might be one of the most important analysis method for genes because it is the technique that can get big amount of the gene expressions data from one time experiment and also can be used for DNA isolation. To get the novel knowledge from micro array data, we need to enrich statistical tools for its data analysis. So far, many mathematical theories and definition have been proposing. However, many of those proposals are tested with strict conditions or customized to data for specific species. In this paper, we reviewed existing typical statistical methods for micro array analysis and discussed the repeatability of the analysis, construction the guideline with more general procedure. First we analyzed the micro array data for TG rats, with statistical methods of family-wise error rate (FWER) control approach and False Discovery Rate (FDR) control approach. As existing report, no significantly different gene could be detected with FWER control approach. On the other hand, we could find several genes significantly with FDR control approach even q=0.5. To find out the reliability of FDR control approach with micro array conditions, we have analyzed 2 more pieces of data from Gene Expression Omnibus (GEO) public database on the web site with SAM in addition to FWER and FDR control approaches. We could find a certain number of significantly different genes with BH method and SAM in the case of q=0.05. However, we have to note that the number and kinds of detected genes are different when we compare our result with the one from the published paper. Even if the same approach is used to analyze the same micro array data, we might get a different result because the distinct definition for micro array data has not been set yet. It means that from the same data we will get different results depending on researchers. We are afraid that this problem will have a big effect on developing new medicines and to progress the next step, like a 2nd screening. So, we suggest that we should have certain guidelines to analyze Micro-Array data validly with statistic method and it will surely be helpful for Micro-Array analysis for medical studies in the future.

Urushibara, Tomoko; Akasaka, Shizu; Ito, Makiko; Suzuki, Tomonori; Miyazaki, Satoru

2010-01-01

341

Microarrays for Pathogen Detection and Analysis  

PubMed Central

DNA microarrays have emerged as a viable platform for detection of pathogenic organisms in clinical and environmental samples. These microbial detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies like high-throughput sequencing. While pathogen detection arrays have been used primarily in a research context, several groups are aggressively working to develop arrays for clinical diagnostics, food safety testing, environmental monitoring and biodefense. Statistical algorithms that can analyze data from microbial detection arrays and provide easily interpretable results are absolutely required in order for these efforts to succeed. In this article, we will review the most promising array designs and analysis algorithms that have been developed to date, comparing their strengths and weaknesses for pathogen detection and discovery. PMID:21930658

2011-01-01

342

Digital microarray analysis for digital artifact genomics  

NASA Astrophysics Data System (ADS)

We implement a Spatial Voting (SV) based analogy of microarray analysis for digital gene marker identification in malware code sections. We examine a famous set of malware formally analyzed by Mandiant and code named Advanced Persistent Threat (APT1). APT1 is a Chinese organization formed with specific intent to infiltrate and exploit US resources. Manidant provided a detailed behavior and sting analysis report for the 288 malware samples available. We performed an independent analysis using a new alternative to the traditional dynamic analysis and static analysis we call Spatial Analysis (SA). We perform unsupervised SA on the APT1 originating malware code sections and report our findings. We also show the results of SA performed on some members of the families associated by Manidant. We conclude that SV based SA is a practical fast alternative to dynamics analysis and static analysis.

Jaenisch, Holger; Handley, James; Williams, Deborah

2013-06-01

343

Engineering Cartilage Tissue  

PubMed Central

Cartilage tissue engineering is emerging as a technique for the regeneration of cartilage tissue damaged due to disease or trauma. Since cartilage lacks regenerative capabilities, it is essential to develop approaches that deliver the appropriate cells, biomaterials, and signaling factors to the defect site. The objective of this review is to discuss the approaches that have been taken in this area, with an emphasis on various cell sources, including chondrocytes, fibroblasts, and stem cells. Additionally, biomaterials and their interaction with cells and the importance of signaling factors on cellular behavior and cartilage formation will be addressed. Ultimately, the goal of investigators working on cartilage regeneration is to develop a system that promotes the production of cartilage tissue that mimics native tissue properties, accelerates restoration of tissue function, and is clinically translatable. Although this is an ambitious goal, significant progress and important advances have been made in recent years. PMID:17976858

Chung, Cindy; Burdick, Jason A.

2008-01-01

344

microarray, and microRNA analysis  

E-print Network

Background: SOX2 is a key gene implicated in maintaining the stemness of embryonic and adult stem cells. SOX2 appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed response program of SOX2 in GBM has not yet been defined. Results: We show that knockdown of the SOX2 gene in LN229 GBM cells reduces cell proliferation and colony formation. We then comprehensively characterize the SOX2 response program by an integrated analysis using several advanced genomic technologies including ChIP-seq, microarray profiling, and microRNA sequencing. Using ChIP-seq technology, we identified 4883 SOX2 binding regions in the GBM cancer genome. SOX2 binding regions contain the consensus sequence wwTGnwTw that occurred 3931 instances in 2312 SOX2 binding regions. Microarray analysis identified 489 genes whose expression altered in response to SOX2 knockdown. Interesting findings include that SOX2 regulates the expression of SOX family proteins SOX1 and SOX18, and that SOX2 down regulates BEX1 (brain expressed X-linked 1) and BEX2 (brain expressed X-linked 2), two genes with tumor suppressor activity in GBM. Using next generation sequencing, we identified 105 precursor microRNAs (corresponding to 95 mature miRNAs) regulated by SOX2, including down regulation of miR-143,-145,-253-5p and miR-452. We also show that miR-145 and SOX2 form a double negative feedback loop in GBM cells, potentially

Xuefeng Fang; Jae-geun Yoon; Lisha Li; Wei Yu; Jiaofang Shao; Dasong Hua; Shu Zheng; Leroy Hood; David R Goodlett; Gregory Foltz; Biaoyang Lin

345

LncRNAs expression signatures of hepatocellular carcinoma revealed by microarray  

PubMed Central

AIM: To analyze the expression profiles of long non-coding RNAs (lncRNAs) in hepatocellular carcinoma. METHODS: Hepatocellular carcinoma (HCC) tissues and matched adjacent non-tumor (NT) liver tissues were collected from 29 patients with HCC, immediately after liver resection, between March 2011 and July 2013. The diagnosis of HCC was made based on histological examination. Differentially expressed lncRNAs between HCC and NT tissues were revealed through microarray-based lncRNAs expression profiling. Further, quantification of selected lncRNAs was performed using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: Six hundred and fifty-nine lncRNAs were differentially expressed between HCC and NT tissues, of which five [TCONS_00018278, AK093543, D16366, ENST00000501583, NR_002819 (MALAT1)] were selected for validation. Four of them were significantly downregulated in HCC tissues compared with NT tissues (P = 0.012, 0.045, 0.000 and 0.000, respectively), and the expression level of MALAT1 showed no significant difference (P = 0.114). CONCLUSION: This study identified a set of lncRNAs differentially expressed in HCC tissues and provided useful information for exploring potential therapeutic targets and diagnostic biomarkers of this cancer. PMID:24876753

Liu, Wu-Tao; Lu, Xin; Tang, Guang-Hua; Ren, Jin-Jun; Liao, Wen-Jun; Ge, Peng-Lei; Huang, Jie-Fu

2014-01-01

346

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton  

PubMed Central

Background The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and should provide insights in identifying potential targets for drug discovery. Here we report the development of a dedicated microarray, the Actichip, containing 60-mer oligonucleotide probes for 327 genes selected for transcriptome analysis of the human actin cytoskeleton. Results Genomic data and sequence analysis features were retrieved from GenBank and stored in an integrative database called Actinome. From these data, probes were designed using a home-made program (CADO4MI) allowing sequence refinement and improved probe specificity by combining the complementary information recovered from the UniGene and RefSeq databases. Actichip performance was analysed by hybridisation with RNAs extracted from epithelial MCF-7 cells and human skeletal muscle. Using thoroughly standardised procedures, we obtained microarray images with excellent quality resulting in high data reproducibility. Actichip displayed a large dynamic range extending over three logs with a limit of sensitivity between one and ten copies of transcript per cell. The array allowed accurate detection of small changes in gene expression and reliable classification of samples based on the expression profiles of tissue-specific genes. When compared to two other oligonucleotide microarray platforms, Actichip showed similar sensitivity and concordant expression ratios. Moreover, Actichip was able to discriminate the highly similar actin isoforms whereas the two other platforms did not. Conclusion Our data demonstrate that Actichip is a powerful alternative to commercial high density microarrays for cytoskeleton gene profiling in normal or pathological samples. Actichip is available upon request. PMID:17727702

Muller, Jean; Mehlen, Andre; Vetter, Guillaume; Yatskou, Mikalai; Muller, Arnaud; Chalmel, Frederic; Poch, Olivier; Friederich, Evelyne; Vallar, Laurent

2007-01-01

347

A New Way to Introduce Microarray Technology in a Lecture/Laboratory Setting by Studying the Evolution of This Modern Technology  

ERIC Educational Resources Information Center

DNA microarray is an ordered grid containing known sequences of DNA, which represent many of the genes in a particular organism. Each DNA sequence is unique to a specific gene. This technology enables the researcher to screen many genes from cells or tissue grown in different conditions. We developed an undergraduate lecture and laboratory…

Rowland-Goldsmith, Melissa

2009-01-01

348

Real-time monitoring of aRNA production during T7 amplification to prevent the loss of sample representation during microarray hybridization sample preparation  

Microsoft Academic Search

Gene expression analysis performed through com- parative abundance of transcripts is facing a new challenge with the increasing need to compare samples of known cell number, such as early embryos or laser microbiopsies, where the RNA contents of identical cellular inputs can by nature be variable. When working with scarce tissues, the success of microarray profiling largely depends on the

Isabelle Gilbert; Sara Scantland; Isabelle Dufort; Olga Gordynska; Aurelie Labbe; M.-A. Sirard; C. Robert

2009-01-01

349

Gene expression microarray analysis in cancer biology, pharmacology, and drug development: progress and potential 2 2 Abbreviations: ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; Cy, Cyanine; DLCL, diffuse large cell lymphoma; dNTPs, deoxyribonucleotides; ESTs, expressed sequence tags; mRNA, messenger RNA; NHL, non-Hodgkin’s lymphoma; ORF, open reading frame; RT-PCR, reverse transcription-polymerase chain reaction; and 17AAG, 17-allylamino,17-demethoxygeldanamycin  

Microsoft Academic Search

With the imminent completion of the Human Genome Project, biomedical research is being revolutionised by the ability to carry out investigations on a genome wide scale. This is particularly important in cancer, a disease that is caused by accumulating abnormalities in the sequence and expression of a number of critical genes. Gene expression microarray technology is gaining increasingly widespread use

Paul A. Clarke; Robert te Poele; Richard Wooster; Paul Workman

2001-01-01

350

Rapid and quantitative quality control of microarrays using cationic nanoparticles.  

PubMed

The fabrication quality of microarrays significantly influences the accuracy and reproducibility of microarray experiments. In this report, we present a simple and fast quality control (QC) method for spotted oligonucleotide and cDNA microarrays. It employs a nonspecific electrostatic interaction of colloidal gold nanoparticles with the chemical groups of DNA molecules and other biomolecules immobilized on the microarray surface that bear positive or negative charges. An inexpensive flatbed scanner is used to visualize and quantify the binding of cationic gold particles to the anionic DNA probes on the microarray surface. An image analysis software was designed to assess the various parameters of the array spots including spot intensity, shape and array homogeneity, calculate the overall array quality score, and save the detailed array quality report in an Excel file. The gold staining technique is fast and sensitive. It can be completed in 10 min and detect less than 1% of the probe amount commonly recommended for microarrays. Compared to the current microarray QC method that utilizes the hybridization of probes with short random sequence oligonucleotides labeled with fluorophore, our gold staining method requires less time for the analysis, reduces the reagent cost, and eliminates the need for the expensive laser scanner. PMID:19031423

Sun, Ye; Fan, Wenhua; McCann, Michael P; Golovlev, Val

2009-02-15

351

COX-2 gene expression in colon cancer tissue related to regulating factors and promoter methylation status  

PubMed Central

Background Increased cyclooxygenase activity promotes progression of colorectal cancer, but the mechanisms behind COX-2 induction remain elusive. This study was therefore aimed to define external cell signaling and transcription factors relating to high COX-2 expression in colon cancer tissue. Method Tumor and normal colon tissue were collected at primary curative operation in 48 unselected patients. COX-2 expression in tumor and normal colon tissue was quantified including microarray analyses on tumor mRNA accounting for high and low tumor COX-2 expression. Cross hybridization was performed between tumor and normal colon tissue. Methylation status of up-stream COX-2 promoter region was evaluated. Results Tumors with high COX-2 expression displayed large differences in gene expression compared to normal colon. Numerous genes with altered expression appeared in tumors of high COX-2 expression compared to tumors of low COX-2. COX-2 expression in normal colon was increased in patients with tumors of high COX-2 compared to normal colon from patients with tumors of low COX-2. IL1?, IL6 and iNOS transcripts were up-regulated among external cell signaling factors; nine transcription factors (ATF3, C/EBP, c-Fos, Fos-B, JDP2, JunB, c-Maf, NF-?B, TCF4) showed increased expression and 5 (AP-2, CBP, Elk-1, p53, PEA3) were decreased in tumors with high COX-2. The promoter region of COX-2 gene did not show consistent methylation in tumor or normal colon tissue. Conclusions Transcription and external cell signaling factors are altered as covariates to COX-2 expression in colon cancer tissue, but DNA methylation of the COX-2 promoter region was not a significant factor behind COX-2 expression in tumor and normal colon tissue. PMID:21668942

2011-01-01

352

A microarray analysis of gene expression patterns during early phases of newt lens regeneration  

PubMed Central

Purpose Notophthalmus viridescens, the red-spotted newt, possesses tremendous regenerative capabilities. Among the tissues and organs newts can regenerate, the lens is regenerated via transdifferentiation of the pigment epithelial cells of the dorsal iris, following complete removal (lentectomy). Under normal conditions, the same cells from the ventral iris are not capable of regenerating. This study aims to further understand the initial signals of lens regeneration. Methods We performed microarray analysis using RNA from a dorsal or ventral iris isolated 1, 3, and 5 days after lentectomy and compared to RNA isolated from an intact iris. This analysis was supported with quantitative real-time polymerase chain reaction (qRT-PCR) of selected genes. Results Microarrays showed 804 spots were differentially regulated 1, 3, and 5 days post-lentectomy in the dorsal and ventral iris. Functional annotation using Gene Ontology revealed interesting terms. Among them, factors related to cell cycle and DNA repair were mostly upregulated, in the microarray, 3 and 5 days post-lentectomy. qRT-PCR for rad1 and vascular endothelial growth factor receptor 1 showed upregulation for the dorsal iris 3 and 5 days post- lentectomy and for the ventral iris 5 days post-lentectomy. Rad1 was also upregulated twofold more in the dorsal iris than in the ventral iris 5 days post-lentectomy (p<0.001). Factors related to redox homeostasis were mostly upregulated in the microarray in all time points and samples. qRT-PCR for glutathione peroxidase 1 also showed upregulation in all time points for the ventral and dorsal iris. For the most part, mitochondrial enzymes were downregulated with the notable exception of cytochrome c–related oxidases that were mostly upregulated at all time points. qRT-PCR for cytochrome c oxidase subunit 2 showed upregulation especially 3 days post-lentectomy for the dorsal and ventral iris (p<0.001). Factors related to extracellular matrix and tissue remodeling showed mostly upregulation (except collagen I) for all time points and samples. qRT-PCR for stromelysin 1/2 alpha and avidin showed upregulation in all the time points for the dorsal and ventral iris. Conclusions The results show that the dorsal iris and the ventral iris follow the same general pattern with some distinct differences especially 5 days after lentectomy. In addition, while the expression of genes involved in DNA repair, redox homeostasis, and tissue remodeling in preparation for proliferation and transdifferentiation is altered in the entire iris, the response is more prominent in the dorsal iris following lentectomy. PMID:23378727

Sousounis, Konstantinos; Michel, Christian S.; Bruckskotten, Marc; Maki, Nobuyasu; Borchardt, Thilo; Braun, Thomas; Tsonis, Panagiotis A.

2013-01-01

353

Cancer Classification in Microarray Data using a Hybrid Selective Independent Component Analysis and ?-Support Vector Machine Algorithm  

PubMed Central

Microarray data have an important role in identification and classification of the cancer tissues. Having a few samples of microarrays in cancer researches is always one of the most concerns which lead to some problems in designing the classifiers. For this matter, preprocessing gene selection techniques should be utilized before classification to remove the noninformative genes from the microarray data. An appropriate gene selection method can significantly improve the performance of cancer classification. In this paper, we use selective independent component analysis (SICA) for decreasing the dimension of microarray data. Using this selective algorithm, we can solve the instability problem occurred in the case of employing conventional independent component analysis (ICA) methods. First, the reconstruction error and selective set are analyzed as independent components of each gene, which have a small part in making error in order to reconstruct new sample. Then, some of the modified support vector machine (?-SVM) algorithm sub-classifiers are trained, simultaneously. Eventually, the best sub-classifier with the highest recognition rate is selected. The proposed algorithm is applied on three cancer datasets (leukemia, breast cancer and lung cancer datasets), and its results are compared with other existing methods. The results illustrate that the proposed algorithm (SICA + ?-SVM) has higher accuracy and validity in order to increase the classification accuracy. Such that, our proposed algorithm exhibits relative improvements of 3.3% in correctness rate over ICA + SVM and SVM algorithms in lung cancer dataset.

Saberkari, Hamidreza; Shamsi, Mousa; Joroughi, Mahsa; Golabi, Faegheh; Sedaaghi, Mohammad Hossein

2014-01-01

354

Microarray analysis of genes differentially expressed in HepG2 cells cultured in simulated microgravity: preliminary report  

NASA Technical Reports Server (NTRS)

Developed at NASA, the rotary cell culture system (RCCS) allows the creation of unique microgravity environment of low shear force, high-mass transfer, and enables three-dimensional (3D) cell culture of dissimilar cell types. Recently we demonstrated that a simulated microgravity is conducive for maintaining long-term cultures of functional hepatocytes and promote 3D cell assembly. Using deoxyribonucleic acid (DNA) microarray technology, it is now possible to measure the levels of thousands of different messenger ribonucleic acids (mRNAs) in a single hybridization step. This technique is particularly powerful for comparing gene expression in the same tissue under different environmental conditions. The aim of this research was to analyze gene expression of hepatoblastoma cell line (HepG2) during early stage of 3D-cell assembly in simulated microgravity. For this, mRNA from HepG2 cultured in the RCCS was analyzed by deoxyribonucleic acid microarray. Analyses of HepG2 mRNA by using 6K glass DNA microarray revealed changes in expression of 95 genes (overexpression of 85 genes and downregulation of 10 genes). Our preliminary results indicated that simulated microgravity modifies the expression of several genes and that microarray technology may provide new understanding of the fundamental biological questions of how gravity affects the development and function of individual cells.

Khaoustov, V. I.; Risin, D.; Pellis, N. R.; Yoffe, B.; McIntire, L. V. (Principal Investigator)

2001-01-01

355

Tissue-Specific Differences in Human Transfer RNA Expression  

PubMed Central

Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge. We have developed a microarray method to quantify tRNAs based on a fluorescent dye-labeling technique. The first-generation tRNA microarray consists of 42 probes for nuclear encoded tRNAs and 21 probes for mitochondrial encoded tRNAs. These probes cover tRNAs for all 20 amino acids and 11 isoacceptor families. Using this array, we report that the amounts of tRNA within the total cellular RNA vary widely among eight different human tissues. The brain expresses higher overall levels of nuclear encoded tRNAs than every tissue examined but one and higher levels of mitochondrial encoded tRNAs than every tissue examined. We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms. PMID:17194224

Dittmar, Kimberly A; Goodenbour, Jeffrey M; Pan, Tao

2006-01-01

356

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database  

SciTech Connect

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

2010-01-27

357

New technologies for fabricating biological microarrays  

NASA Astrophysics Data System (ADS)

This dissertation contains the description of two technologies that we have developed to reduce the cost and improve the quality of spotted biological microarrays. The first is a device, called a fluid microplotter, that uses ultrasonics to deposit spots with diameters of less than 5 microns. It consists of a dispenser, composed of a micropipette fastened to a piece of PZT piezoelectric, attached to a precision positioning system. A gentle pumping of fluid to the surface occurs when the micropipette is driven at specific frequencies. Spots or continuous lines can be deposited in this manner. The small fluid features conserve expensive and limited-quantity biological reagents. We characterize the performance of the microplotter in depositing fluid and examine the theoretical underpinnings of its operation. We present an analytical expression for the diameter of a deposited spot as a function of droplet volume and wettability of a surface and compare it with experimental results. We also examine the resonant properties of the piezoelectric element used to drive the dispenser and relate that to the frequencies at which pumping occurs. Finally, we propose a mechanism to explain the pumping behavior within the microplotter dispenser. The second technology we present is a process that uses a cold plasma and a subsequent in vacuo vapor-phase reaction to terminate a variety of oxide surfaces with epoxide chemical groups. These epoxide groups can react with amine-containing biomolecules to form strong covalent linkages between the biomolecules and the treated surface. The use of a plasma activation step followed by an in vacuo vapor-phase reaction allows for the precise control of surface functional groups, rather than the mixture of functionalities normally produced. This process modifies a range of different oxide surfaces, is fast, consumes a minimal amount of reagents, and produces attachment densities for bound biomolecules that are comparable to or better than commercially available substrates. We show applications of these two technologies in the fabrication of protein microarrays, enhancement of MALDI mass spectrometry, deposition of polymer electronics, directed growth of carbon nanotubes, and the chemical modification of carbon-containing materials.

Larson, Bradley James

358

Imaging combined autoimmune and infectious disease microarrays  

NASA Astrophysics Data System (ADS)

Bacterial and viral pathogens are implicated in many severe autoimmune diseases, acting through such mechanisms as molecular mimicry, and superantigen activation of T-cells. For example, Helicobacter pylori, well known cause of stomach ulcers and cancers, is also identified in ischaemic heart disease (mimicry of heat shock protein 65), autoimmune pancreatitis, systemic sclerosis, autoimmune thyroiditis (HLA DRB1*0301 allele susceptibility), and Crohn's disease. Successful antibiotic eradication of H.pylori often accompanies their remission. Yet current diagnostic devices, and test-limiting cost containment, impede recognition of the linkage, delaying both diagnosis and therapeutic intervention until the chronic debilitating stage. We designed a 15 minute low cost 39 antigen microarray assay, combining autoimmune, viral and bacterial antigens1. This enables point-of-care serodiagnosis and cost-effective narrowly targeted concurrent antibiotic and monoclonal anti-T-cell and anti-cytokine immunotherapy. Arrays of 26 pathogen and 13 autoimmune antigens with IgG and IgM dilution series were printed in triplicate on epoxysilane covalent binding slides with Teflon well masks. Sera diluted 1:20 were incubated 10 minutes, washed off, anti-IgG-Cy3 (green) and anti-IgM-Dy647 (red) were incubated for 5 minutes, washed off and the slide was read in an ArrayWoRx(e) scanning CCD imager (Applied Precision, Issaquah, WA). As a preliminary model for the combined infectious disease-autoimmune diagnostic microarray we surveyed 98 unidentified, outdated sera that were discarded after Hepatitis B antibody testing. In these, significant IgG or IgM autoantibody levels were found: dsDNA 5, ssDNA 11, Ro 2, RNP 7, SSB 4, gliadin 2, thyroglobulin 13 cases. Since control sera showed no autoantibodies, the high frequency of anti-DNA and anti-thyroglobulin antibodies found in infected sera lend increased support for linkage of infection to subsequent autoimmune disease. Expansion of the antigen set with synthetic peptide sequences should reveal the shared bacterial/human epitopes involved.

Ewart, Tom; Raha, Sandeep; Kus, Dorothy; Tarnopolsky, Mark

2006-09-01

359

Impact of microRNA Expression in Human Atrial Tissue in Patients with Atrial Fibrillation Undergoing Cardiac Surgery  

PubMed Central

Background Although microRNA (miRNA) regulates initiation and/or progression of atrial fibrillation (AF) in canine AF models, the underlying mechanism in humans remains unclear. We speculated that certain miRNAs in atrial tissue are related to AF, and evaluated the relationship of miRNA expression in human atrial tissue in cardiac surgery patients. Methods Right atrial tissues from 29 patients undergoing cardiovascular surgery were divided into 3 groups [A: chronic AF or unsuccessful maze, n=6; B: successful maze, n=10; C: sinus rhythm (SR) n=13]. miRNA expression was determined using high density microarrays and with Reverse transcriptase-polymerase chain reaction (RT-PCR). Fibrosis was examined using Masson trichrome staining. Results miRNA microarray analysis showed elevated miRNA-21, miRNA-23b, miRNA-199b, and miRNA-208b in AF as compared to SR groups. RT-PCR showed elevated miRNA-21 (1.9-fold) and miRNA-208b (4.2-fold) in AF as compared to the SR groups. miRNA-21 expression increased from Group C to A (A: 2.1-fold, B: 1.8-fold, C: 1.0-fold). Fibrosis increased from C to A (A: 43.0±12.9%, B: 21.3±6.1%, C: 11.9±3.1%). Percent fibrosis and miRNA-21 expression were correlated (r=0.508, p<0.05). The plasma levels of miRNA-21 in AF patients was significantly decreased as compared to the healthy volunteers (p<0.05). Conclusion The expression of miRNA-21 in human atrial tissue was found to be related to atrial fibrosis and might affect AF occurrence, indicating its usefulness as a biomarker for cardiac surgery management. PMID:24069193

Nishi, Hiroyuki; Sakaguchi, Taichi; Miyagawa, Shigeru; Yoshikawa, Yasushi; Fukushima, Satsuki; Saito, Shunsuke; Ueno, Takayoshi; Kuratani, Toru; Sawa, Yoshiki

2013-01-01

360

Gene Expression Profiling of Colorectal Tumors and Normal Mucosa by Microarrays Meta-Analysis Using Prediction Analysis of Microarray, Artificial Neural Network, Classification, and Regression Trees  

PubMed Central

Background. Microarray technology shows great potential but previous studies were limited by small number of samples in the colorectal cancer (CRC) research. The aims of this study are to investigate gene expression profile of CRCs by pooling cDNA microarrays using PAM, ANN, and decision trees (CART and C5.0). Methods. Pooled 16 datasets contained 88 normal mucosal tissues and 1186 CRCs. PAM was performed to identify significant expressed genes in CRCs and models of PAM, ANN, CART, and C5.0 were constructed for screening candidate genes via ranking gene order of significances. Results. The first screening identified 55 genes. The test accuracy of each model was over 0.97 averagely. Less than eight genes achieve excellent classification accuracy. Combining the results of four models, we found the top eight differential genes in CRCs; suppressor genes, CA7, SPIB, GUCA2B, AQP8, IL6R and CWH43; oncogenes, SPP1 and TCN1. Genes of higher significances showed lower variation in rank ordering by different methods. Conclusion. We adopted a two-tier genetic screen, which not only reduced the number of candidate genes but also yielded good accuracy (nearly 100%). This method can be applied to future studies. Among the top eight genes, CA7, TCN1, and CWH43 have not been reported to be related to CRC. PMID:24959000

Chu, Chi-Ming; Yao, Chung-Tay; Chang, Yu-Tien; Chou, Hsiu-Ling; Chou, Yu-Ching; Chen, Kang-Hua; Terng, Harn-Jing; Huang, Chi-Shuan; Lee, Chia-Cheng; Su, Sui-Lun; Liu, Yao-Chi; Lin, Fu-Gong; Wetter, Thomas; Chang, Chi-Wen

2014-01-01

361

Functional Genomics in Chickens: Development of Integrated-Systems Microarrays for Transcriptional Profiling and Discovery of Regulatory Pathways  

PubMed Central

The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken. PMID:18629153

Wang, X.; Carre, W.; Rejto, L.; Aggrey, S. E.; Duclos, M. J.; Simon, J.; Porter, T. E.

2004-01-01

362

Microarray Analysis of Thyroid Nodule Fine-Needle Aspirates Accurately Classifies Benign and Malignant Lesions  

PubMed Central

Current preoperative diagnostic procedures for thyroid nodules rely mainly on the cytological interpretation of fine-needle aspirates (FNAs). DNA microarray analysis has been shown to reliably distinguish benign and malignant thyroid nodules in surgically resected specimens, but its diagnostic potential in thyroid FNA has not been examined. In the present study, the expression profiles of 50 benign thyroid lesions and papillary thyroid carcinoma tissue samples were compared, generating a list of 25 differentially expressed genes from this training set. A test set of 22 FNA specimens was evaluated by unsupervised hierarchical cluster analysis using this gene list, and the results were compared to FNA cytology. FNA specimens were found to fall into three clusters: malignant (n = 10), benign (n = 7), and indeterminate (n = 5). The benign and malignant groups showed complete concordance with the final histological diagnosis except for one histologically benign lesion, which was rediagnosed as follicular variant of papillary thyroid carcinoma on histological review. Paired analysis between FNA and matched tissues samples illustrated adequate sampling with FNA. These results illustrate that microarray analysis of FNA is feasible and has the potential to improve the accuracy of FNA in categorizing benign from malignant lesions beyond routine cytological evaluation. PMID:16931590

Lubitz, Carrie C.; Ugras, Stacy K.; Kazam, J. Jacob; Zhu, Biaxin; Scognamiglio, Theresa; Chen, Yao-Tseng; Fahey, Thomas J.

2006-01-01

363

A combinatorial cell-laden gel microarray for inducing osteogenic differentiation of human mesenchymal stem cells  

PubMed Central

Development of three dimensional (3D) microenvironments that direct stem cell differentiation into functional cell types remains a major challenge in the field of regenerative medicine. Here, we describe a new platform to address this challenge by utilizing a robotic microarray spotter for testing stem cell fates inside various miniaturized cell-laden gels in a systematic manner. To demonstrate the feasibility of our platform, we evaluated the osteogenic differentiation of human mesenchymal stem cells (hMSCs) within combinatorial 3D niches. We were able to identify specific combinations, that enhanced the expression of osteogenic markers. Notably, these ‘hit' combinations directed hMSCs to form mineralized tissue when conditions were translated to 3D macroscale hydrogels, indicating that the miniaturization of the experimental system did not alter stem cell fate. Overall, our findings confirmed that the 3D cell-laden gel microarray can be used for screening of different conditions in a rapid, cost-effective, and multiplexed manner for a broad range of tissue engineering applications. PMID:24473466

Dolatshahi-Pirouz, Alireza; Nikkhah, Mehdi; Gaharwar, Akhilesh K.; Hashmi, Basma; Guermani, Enrico; Aliabadi, Hamed; Camci-Unal, Gulden; Ferrante, Thomas; Foss, Morten; Ingber, Donald E.; Khademhosseini, Ali

2014-01-01

364

Genome-wide microarray comparison reveals downstream genes of Pax6 in the developing mouse cerebellum  

PubMed Central

The Pax6 transcription factor is expressed in cerebellar granule cells and when mutated, as in the Sey/Sey mouse, produces granule cells with disturbed survival, migration, and defects in neurite extension. The impact of Pax6 on other genes in the context of cerebellar development has not been identified. In this study, we performed transcriptome comparisons between wildtype and Pax6-null whole cerebellar tissue at embryonic day (E) 13.5, 15.5 and 18.5 using Affymetrix arrays (U74Av2). Statistical analyses identified 136 differentially regulated transcripts (FDR 0.05, 1.2 fold change cut-off) over time in Pax6-null cerebellar tissue. In parallel we examined the Math1-null granuloprival cerebellum and identified 228 differentially regulated transcripts (FDR 0.05, 1.2 fold change cut-off). The intersection of these two microarray datasets produced a total of 21 differentially regulated transcripts. For a subset of the identified transcripts, we used qRT-PCR to validate the microarray data and demonstrated the expression in the rhombic lip lineage and differential expression in Pax6-null cerebellum with in situ hybridization analysis. The candidate genes identified in this way represent direct or indirect Pax6-downstream genes involved in cerebellar development. PMID:22817342

Ha, Thomas J.; Swanson, Douglas J.; Kirova, Roumyana; Yeung, Joanna; Choi, Kunho; Tong, Yiai; Chesler, Elissa J.; Goldowitz, Daniel

2013-01-01

365

A microarray based identification of osteoporosis-related genes in primary culture of human osteoblasts.  

PubMed

Genetic factors influencing the pathogenesis of osteoporosis are still largely unknown. We employed genome-wide gene expression approach in order to discover novel genes involved in the pathogenesis of osteoporosis. To this end, primary cultures of osteoblasts isolated from osteoporotic and non-osteoporotic human bone tissue samples were prepared. One thousand six hundred six genes were found to be differentially expressed, indicating increased demand for protein synthesis and decreased cell proliferation rate in osteoblasts from osteoporotic tissue as compared to osteoblasts from non-osteoporotic tissue. At first, top four genes, based on the microarray data and potential role in bone metabolism, were further studied in bone tissue samples of 55 patients. PTN and COL15A1 were both downregulated in osteoporotic bone tissue (6.2- and 3.4-fold, respectively, both p<0.05), while IBSP and CXCL2 were both upregulated (5.7-fold, p<0.05, and 2.1-fold, p>0.05). Further biostatistical analysis of the microarray data by gene set enrichment analysis suggested oxidative stress may have an important part in the pathogenesis of osteoporosis. Thus, secondly, we tested it by an in vitro assay on human osteosarcoma cell line cells treated with hydrogen peroxide. After 72 h of treatment with 500 microM hydrogen peroxide, the upregulation of the same genes involved in the response to oxidative stress as on the microarrays was observed: MT1G (metallothionein 1G, 22.1-fold, p<0.05), TXNRD1 (thioredoxin reductase 1, 3.7-fold, p<0.05), AOX1 (aldehyde oxidase 1, 24.5-fold, p<0.05) and GSR (glutathione reductase, 4.7-fold, p<0.05). Our results present a novel list of genes and metabolic pathways that may be associated with the pathogenesis of osteoporosis. PTN, CXCL2, COL15A1, IBSP, AOX1, MT1G, GSR and TXNRD1 are candidate genes for further studies in the assessment of the genetic susceptibility to osteoporosis. In addition, differences in protein synthesis, cell proliferation rate and response to oxidative stress may also be involved in the pathogenesis of osteoporosis. PMID:19781675

Trost, Zoran; Trebse, Rihard; Prezelj, Janez; Komadina, Radko; Logar, Darja Bitenc; Marc, Janja

2010-01-01

366

Bayesian Pathway Analysis of Cancer Microarray Data  

PubMed Central

High Throughput Biological Data (HTBD) requires detailed analysis methods and from a life science perspective, these analysis results make most sense when interpreted within the context of biological pathways. Bayesian Networks (BNs) capture both linear and nonlinear interactions and handle stochastic events in a probabilistic framework accounting for noise making them viable candidates for HTBD analysis. We have recently proposed an approach, called Bayesian Pathway Analysis (BPA), for analyzing HTBD using BNs in which known biological pathways are modeled as BNs and pathways that best explain the given HTBD are found. BPA uses the fold change information to obtain an input matrix to score each pathway modeled as a BN. Scoring is achieved using the Bayesian-Dirichlet Equivalent method and significance is assessed by randomization via bootstrapping of the columns of the input matrix. In this study, we improve on the BPA system by optimizing the steps involved in “Data Preprocessing and Discretization”, “Scoring”, “Significance Assessment”, and “Software and Web Application”. We tested the improved system on synthetic data sets and achieved over 98% accuracy in identifying the active pathways. The overall approach was applied on real cancer microarray data sets in order to investigate the pathways that are commonly active in different cancer types. We compared our findings on the real data sets with a relevant approach called the Signaling Pathway Impact Analysis (SPIA). PMID:25036210

Korucuoglu, Melike; Isci, Senol; Ozgur, Arzucan; Otu, Hasan H.

2014-01-01

367

Peptide Microarrays to Interrogate the "Histone Code"  

PubMed Central

Histone posttranslational modifications (PTMs) play a pivotal role in regulating the dynamics and function of chromatin. Supported by an increasing body of literature, histone PTMs such as methylation and acetylation function together in the context of a “histone code,” which is read, or interpreted, by effector proteins that then drive a functional output in chromatin (e.g., gene transcription). A growing number of domains that interact with histones and/or their PTMs have been identified. While significant advances have been made in our understanding of how these domains interact with histones, a wide number of putative histone-binding motifs have yet to be characterized, and undoubtedly, novel domains will continue to be discovered. In this chapter, we provide a detailed method for the construction of combinatorially modified histone peptides, microarray fabrication using these peptides, and methods to characterize the interaction of effector proteins, antibodies, and the substrate specificity of histone-modifying enzymes. We discuss these methods in the context of other available technologies and provide a user-friendly approach to enable the exploration of histone–protein–enzyme interactions and function. PMID:22910205

Rothbart, Scott B.; Krajewski, Krzysztof; Strahl, Brian D.; Fuchs, Stephen M.

2013-01-01

368

Microarray analysis of DNA replication timing.  

PubMed

Although all of the DNA in an eukaryotic cell replicates during the S-phase of cell cycle, there is a significant difference in the actual time in S-phase when a given chromosomal segment replicates. Methods are described here for generation of high-resolution temporal maps of DNA replication in synchronized human cells. This method does not require amplification of DNA before microarray hybridization and so avoids errors introduced during PCR. A major advantage of using this procedure is that it facilitates finer dissection of replication time in S-phase. Also, it helps delineate chromosomal regions that undergo biallelic or asynchronous replication, which otherwise are difficult to detect at a genome-wide scale by existing methods. The continuous TR50 (time of completion of 50% replication) maps of replication across chromosomal segments identify regions that undergo acute transitions in replication timing. These transition zones can play a significant role in identifying insulators that separate chromosomal domains with different chromatin modifications. PMID:19488880

Karnani, Neerja; Taylor, Christopher M; Dutta, Anindya

2009-01-01

369

Microarray Analysis of DNA Replication Timing  

PubMed Central

Although all of the DNA in an eukaryotic cell replicates during the S-phase of cell cycle, there is a significant difference in the actual time in S-phase when a given chromosomal segment replicates. Methods are described here for generation of high-resolution temporal maps of DNA replication in synchronized human cells. This method does not require amplification of DNA before microarray hybridization and so avoids errors introduced during PCR. A major advantage of using this procedure is that it facilitates finer dissection of replication time in S-phase. Also, it helps delineate chromosomal regions that undergo biallelic or asynchronous replication, which otherwise are difficult to detect at a genome-wide scale by existing methods. The continuous TR50 (time of completion of 50% replication) maps of replication across chromosomal segments identify regions that undergo acute transitions in replication timing. These transition zones can play a significant role in identifying insulators that separate chromosomal domains with different chromatin modifications. PMID:19488880

Karnani, Neerja; Taylor, Christopher M.; Dutta, Anindya

2014-01-01

370

Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostate Cancer  

E-print Network

Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostate Cancer Sunita R array data from localized and metastatic prostate cancer. Comparison of metastatic cancer and localized pathways that were significantly dysregulated (P prostate cancer metastasis. The pathway

Gerstein, Mark

371

IDENTIFYING AND MONITORING ENVIRONMENTAL TOXICITY USING CERIODAPHNIA MICROARRAYS - PHASE I  

EPA Science Inventory

The current U.S. Environmental Protection Agency (EPA) SBIR solicitation states that “technology is needed to better identify and monitor sources of pollution and protect water quality.” Microarrays may be particularly well suited to identifying environmental toxic...

372

Oligonucleotide Fingerprint Identification for Microarray-Based Pathogen Diagnostic Assays.  

National Technical Information Service (NTIS)

Advances in DNA microarray technology and computational methods have unlocked new opportunities to identify 'DNA fingerprints,' i.e., oligonucleotide sequences that uniquely identify a specific genome. We present an integrated approach for the computation...

C. Chase, E. Bode, J. Geyer, N. Zavaljevski, T. Waibhav

2006-01-01

373

MOPAC: motif finding by preprocessing and agglomerative clustering from microarrays  

E-print Network

We propose a novel strategy for discovering motifs from gene expression data. The gene expression data comes from DNA microarray analysis of the bacterium E. coli in response to recovery from nutrient starvation. We have annotated the data...

Rajagopalan, Ganesh

2012-06-07

374

NCI Releases Software Tool for Sharing Microarray Data  

Cancer.gov

The National Cancer Institute (NCI), part of the National Institutes of Health (NIH), has released a new software tool that will facilitate the sharing and analysis of microarray data by the medical research community.

375

B7-H3 associated with tumor progression and epigenetic regulatory activity in cutaneous melanoma.  

PubMed

B7-H3, a cell surface transmembrane glycoprotein, was assessed for its functional and prognostic role in cutaneous melanoma progression. B7-H3 expression in melanoma cells was shown to be related to specific downstream signal transduction events as well as associated with functional epigenetic activity. B7-H3 expression and prognostic utility were shown by reverse transcription and real-time PCR and immunohistochemistry analysis on individual melanoma specimens and then verified in clinically annotated melanoma stage III and stage IV metastasis tissue microarrays in a double-blind study. B7-H3 messenger RNA expression was shown to be significantly increased with stage of melanoma (P<0.0001) and significantly associated with melanoma-specific survival in both stage III (P<0.0001) and stage IV (P<0.012) melanoma patients. B7-H3 expression was related to migration and invasion; overexpression of B7-H3 increased migration and invasion, whereas knockdown of B7-H3 reduced cell migration and invasion. MiR-29c expression was shown to inversely regulate B7-H3 expression. Furthermore, we demonstrated that melanoma B7-H3 expression was correlated to phosphorylated signal transducer and activator of transcription-3 activity level in melanoma tissues and cell lines. These studies demonstrate that B7-H3 is a significant factor in melanoma progression and events of metastasis. PMID:23474948

Wang, Jinhua; Chong, Kelly K; Nakamura, Yoshitaka; Nguyen, Linhda; Huang, Sharon K; Kuo, Christine; Zhang, Wang; Yu, Hua; Morton, Donald L; Hoon, Dave S B

2013-08-01

376

Using microarrays and functional genomics to understand and target cancer  

Microsoft Academic Search

Conclusion  In our work microarrays are of importance for screening the whole genome to sort out important genes and also for constructing\\u000a pathways systems for the understanding of the links between genes.\\u000a \\u000a Our studies demonstrate the potential clinical usefulness of microarrays for the classification of patients and for understanding\\u000a cancer biology and identifying new drug targets.

Torben F. Ørntoft

2005-01-01

377

Profiling In Situ Microbial Community Structure with an Amplification Microarray  

PubMed Central

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3?) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

2013-01-01

378

Evaluation of gene expression measurements from commercial microarray platforms  

Microsoft Academic Search

Multiple commercial microarrays for measuring genome-wide gene expression levels are currently available, including oligonucleotide and cDNA, single- and two-channel formats. This study reports on the results of gene expression measurements generated from identical RNA preparations that were obtained using three commercially available microarray platforms. RNA was collected from PANC-1 cells grown in serum-rich medium and at 24 h following the

Paul K. Tan; Thomas J. Downey; Edward L. Spitznagel Jr; Pin Xu; Dadin Fu; Dimiter S. Dimitrov; Richard A. Lempicki; Bruce M. Raaka; Margaret C. Cam

2003-01-01

379

Addressable droplet microarrays for single cell protein analysis.  

PubMed

Addressable droplet microarrays are potentially attractive as a way to achieve miniaturised, reduced volume, high sensitivity analyses without the need to fabricate microfluidic devices or small volume chambers. We report a practical method for producing oil-encapsulated addressable droplet microarrays which can be used for such analyses. To demonstrate their utility, we undertake a series of single cell analyses, to determine the variation in copy number of p53 proteins in cells of a human cancer cell line. PMID:25262574

Salehi-Reyhani, Ali; Burgin, Edward; Ces, Oscar; Willison, Keith R; Klug, David R

2014-09-29

380

Genomic and microarray approaches to coral reef conservation biology  

Microsoft Academic Search

New technologies based on DNA microarrays and comparative genomics hold great promise for providing the background biological\\u000a information necessary for effective coral reef conservation and management. Microarray analysis has been used in a wide range\\u000a of applications across the biological sciences, most frequently to examine simultaneous changes in the expression of large\\u000a numbers of genes in response to experimental manipulation

S. Forêt; K. S. Kassahn; L. C. Grasso; D. C. Hayward; A. Iguchi; E. E. Ball; D. J. Miller

2007-01-01

381

The Perils of SNP Microarray Testing: Uncovering Unexpected Consanguinity  

PubMed Central

Background While single nucleotide polymorphism (SNP) chromosomal microarrays identify areas of small genetic deletions/duplications, they can also reveal regions of homozygosity indicative of consanguinity. As more non-geneticists order SNP microarrays, they must prepare for the potential ethical, legal and social issues that result from revelation of unanticipated consanguinity. Patient An infant with multiple congenital anomalies underwent SNP microarray testing. Results The results of the SNP microarray revealed several large regions of homozygosity that indicated identity by descent most consistent with a second or third degree relative mating (e.g., uncle/ niece, half brother/sister, first cousins). Mother was not aware of the test's potential to reveal consanguinity. When informed of the test results, she reluctantly admitted to being raped by her half-brother around the time of conception. Conclusions During the pre-testing consent process, providers should inform parents that SNP microarray testing could reveal consanguinity. Providers must also understand the psychological implications, as well as the legal and moral obligations, that accompany SNP microarray results that indicate consanguinity. PMID:23827427

Tarini, Beth A.; Konczal, Laura; Goldenberg, Aaron J.; Goldman, Edward B.; McCandless, Shawn E.

2013-01-01

382

Design and analysis of mismatch probes for long oligonucleotide microarrays  

SciTech Connect

Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

2008-08-15

383

Shrinkage regression-based methods for microarray missing value imputation  

PubMed Central

Background Missing values commonly occur in the microarray data, which usually contain more than 5% missing values with up to 90% of genes affected. Inaccurate missing value estimation results in reducing the power of downstream microarray data analyses. Many types of methods have been developed to estimate missing values. Among them, the regression-based methods are very popular and have been shown to perform better than the other types of methods in many testing microarray datasets. Results To further improve the performances of the regression-based methods, we propose shrinkage regression-based methods. Our methods take the advantage of the correlation structure in the microarray data and select similar genes for the target gene by Pearson correlation coefficients. Besides, our methods incorporate the least squares principle, utilize a shrinkage estimation approach to adjust the coefficients of the regression model, and then use the new coefficients to estimate missing values. Simulation results show that the proposed methods provide more accurate missing value estimation in six testing microarray datasets than the existing regression-based methods do. Conclusions Imputation of missing values is a very important aspect of microarray data analyses because most of the downstream analyses require a complete dataset. Therefore, exploring accurate and efficient methods for estimating missing values has become an essential issue. Since our proposed shrinkage regression-based methods can provide accurate missing value estimation, they are competitive alternatives to the existing regression-based methods. PMID:24565159

2013-01-01

384

A brief introduction to tiling microarrays: principles, concepts, and applications.  

PubMed

Technological achievements have always contributed to the advancement of biomedical research. It has never been more so than in recent times, when the development and application of innovative cutting-edge technologies have transformed biology into a data-rich quantitative science. This stunning revolution in biology primarily ensued from the emergence of microarrays over two decades ago. The completion of whole-genome sequencing projects and the advance in microarray manufacturing technologies enabled the development of tiling microarrays, which gave unprecedented genomic coverage. Since their first description, several types of application of tiling arrays have emerged, each aiming to tackle a different biological problem. Although numerous algorithms have already been developed to analyze microarray data, new method development is still needed not only for better performance but also for integration of available microarray data sets, which without doubt constitute one of the largest collections of biological data ever generated. In this chapter we first introduce the principles behind the emergence and the development of tiling microarrays, and then discuss with some examples how they are used to investigate different biological problems. PMID:23975782

Lemetre, Christophe; Zhang, Zhengdong D

2013-01-01

385

Obesity and polymorphisms in genes regulating human adipose tissue  

Microsoft Academic Search

Obesity is the result of an imbalance between food intake and energy expenditure resulting in the storing of energy as fat. Adipose tissue contains the largest store of energy in the body and plays important roles in regulating energy partitioning. Developments in genomics, in particular microarray-based expression profiling, have provided scientists with a number of new candidate genes whose expression

I Dahlman; P Arner

2007-01-01

386

Studies of patterned surfaces for biological microarrays  

NASA Astrophysics Data System (ADS)

Over the past 10 years, biological microarrays have developed into an invaluable tool for genetic and protein research. The task to draw meaningful conclusions between variations of genes and their expression requires millions of comparisons between standard and stressed samples, usually the cDNA, RNA, or proteins within cells. For such a project, high-information-density, highly pure arrays are required. In fabricating an array on a uniform or an unpatterned substrate, droplets of solution, if placed too closely, can bleed into each other and can cross-contaminate several array sites. Therefore, a uniform surface limits the density of droplets that can be placed to create an array. When the surface is patterned with a barrier between the droplets, then the density of array sites can be significantly larger (uniform surface, ˜200--500mum center-to-center; patterned surface, 100mum center-to-center and less with present loading technology). We have explored the patterning of surfaces to construct biological microarrays, via altering the surface chemically to create array sites with gold-thiol chemistry, and via a template placed on the surface to outline the elements. In the template strategy, we have investigated poly(dimethyl siloxane) (PDMS) films (5--10mum) with holes in a regular array. However, the hydrophobic PDMS repels water to such an extent that the droplets do not wet the template and cannot travel down the wall of the PDMS hole to interact with the surface. As a consequence, if not accurately placed in the array sites, they also do not load into the holes to form filled features. Our current studies focus on altering the surface of the PDMS to allow the droplets to fall into the PDMS holes. To alter the surface and not the bulk, we have experimented with plasma chemistry. To create a temporary contact angle change, oxygen plasma has been employed. However, the PDMS recovers and reverts to it characteristically hydrophobic surface. When we expose PDMS to oxygen and then to SiCl4 or to CCl4 plasma, the surface change becomes long-lasting. The new plasma treatments allows for increased control over wetting properties of the PDMS material, which is key to our investigations into biological applications of PDMS. In our characterization of the plasma treatments, we have found new insights into the role of low-molecular-weight-groups of PDMS in the recovery of the contact angle over time. Contact angle data show a Langmuir isotherm curve, and coupled with XPS, AFM and ATR-FTIR studies, we have characterized the plasma-treated PDMS samples and the wetting behavior evolution over time. Using the behavior of plasma-treated PDMS, we have created DNA features as small as ˜1.1mum.

Gillmor, Susan Dale

387

Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Gba1 Mutant Mouse Model Treated with Velaglucerase alfa or Imiglucerase  

PubMed Central

Gaucher disease type 1, an inherited lysosomal storage disorder, is caused by mutations in GBA1 leading to defective glucocerebrosidase (GCase) function and consequent excess accumulation of glucosylceramide/glucosylsphingosine in visceral organs. Enzyme replacement therapy (ERT) with the biosimilars, imiglucerase (imig) or velaglucerase alfa (vela) improves/reverses the visceral disease. Comparative transcriptomic effects (microarray and mRNA-Seq) of no ERT and ERT (imig or vela) were done with liver, lung, and spleen from mice having Gba1 mutant alleles, termed D409V/null. Disease-related molecular effects, dynamic ranges, and sensitivities were compared between mRNA-Seq and microarrays and their respective analytic tools, i.e. Mixed Model ANOVA (microarray), and DESeq and edgeR (mRNA-Seq). While similar gene expression patterns were observed with both platforms, mRNA-Seq identified more differentially expressed genes (DEGs) (?3-fold) than the microarrays. Among the three analytic tools, DESeq identified the maximum number of DEGs for all tissues and treatments. DESeq and edgeR comparisons revealed differences in DEGs identified. In 9V/null liver, spleen and lung, post-therapy transcriptomes approximated WT, were partially reverted, and had little change, respectively, and were concordant with the corresponding histological and biochemical findings. DEG overlaps were only 8–20% between mRNA-Seq and microarray, but the biological pathways were similar. Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were most altered with the Gaucher disease process. Imig and vela differentially affected specific disease pathways. Differential molecular responses were observed in direct transcriptome comparisons from imig- and vela-treated tissues. These results provide cross-validation for the mRNA-Seq and microarray platforms, and show differences between the molecular effects of two highly structurally similar ERT biopharmaceuticals. PMID:24124461

Oh, Sunghee; Sun, Ying; Jia, Li; Keddache, Mehdi; Grabowski, Gregory A

2013-01-01

388

A critical comparison of protein microarray fabrication technologies.  

PubMed

Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance. PMID:24479125

Romanov, Valentin; Davidoff, S Nikki; Miles, Adam R; Grainger, David W; Gale, Bruce K; Brooks, Benjamin D

2014-03-21

389

Expression profiling of cervical cancers in Indian women at different stages to identify gene signatures during progression of the disease  

PubMed Central

Cervical cancer is the second most common cancer among women worldwide, with developing countries accounting for >80% of the disease burden. Although in the West, active screening has been instrumental in reducing the incidence of cervical cancer, disease management is hampered due to lack of biomarkers for disease progression and defined therapeutic targets. Here we carried out gene expression profiling of 29 cervical cancer tissues from Indian women, spanning International Federation of Gynaecology and Obstetrics (FIGO) stages of the disease from early lesion (IA and IIA) to progressive stages (IIB and IIIA–B), and identified distinct gene expression signatures. Overall, metabolic pathways, pathways in cancer and signaling pathways were found to be significantly upregulated, while focal adhesion, cytokine–cytokine receptor interaction and WNT signaling were downregulated. Additionally, we identified candidate biomarkers of disease progression such as SPP1, proliferating cell nuclear antigen (PCNA), STK17A, and DUSP1 among others that were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in the samples used for microarray studies as well in an independent set of 34 additional samples. Integrative analysis of our results with other cervical cancer profiling studies could facilitate the development of multiplex diagnostic markers of cervical cancer progression. PMID:24403257

Thomas, Asha; Mahantshetty, Umesh; Kannan, Sadhana; Deodhar, Kedar; Shrivastava, Shyam K; Kumar-Sinha, Chandan; Mulherkar, Rita

2013-01-01

390

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution  

PubMed Central

Background DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have been developed for evaluating the significance of the observed differences in gene expression. However, until now little attention has been given to the characterization of dispersion of DNA microarray data. Results Here we examine the expression data obtained from 682 Affymetrix GeneChips® with 22 different types and we demonstrate that the Gaussian (normal) frequency distribution is characteristic for the variability of gene expression values. However, typically 5 to 15% of the samples deviate from normality. Furthermore, it is shown that the frequency distributions of the difference of expression in subsets of ordered, consecutive pairs of genes (consecutive samples) in pair-wise comparisons of replicate experiments are also normal. We describe a consecutive sampling method, which is employed to calculate the characteristic function approximating standard deviation and show that the standard deviation derived from the consecutive samples is equivalent to the standard deviation obtained from individual genes. Finally, we determine the boundaries of probability intervals and demonstrate that the coefficients defining the intervals are independent of sample characteristics, variability of data, laboratory conditions and type of chips. These coefficients are very closely correlated with Student's t-distribution. Conclusion In this study we ascertained that the non-systematic variations possess Gaussian distribution, determined the probability intervals and demonstrated that the K? coefficients defining these intervals are invariant; these coefficients offer a convenient universal measure of dispersion of data. The fact that the K? distributions are so close to t-distribution and independent of conditions and type of arrays suggests that the quantitative data provided by Affymetrix technology give "true" representation of physical processes, involved in measurement of RNA abundance. Reviewers This article was reviewed by Yoav Gilad (nominated by Doron Lancet), Sach Mukherjee (nominated by Sandrine Dudoit) and Amir Niknejad and Shmuel Friedland (nominated by Neil Smalheiser). PMID:16959036

Novak, Jaroslav P; Kim, Seon-Young; Xu, Jun; Modlich, Olga; Volsky, David J; Honys, David; Slonczewski, Joan L; Bell, Douglas A; Blattner, Fred R; Blumwald, Eduardo; Boerma, Marjan; Cosio, Manuel; Gatalica, Zoran; Hajduch, Marian; Hidalgo, Juan; McInnes, Roderick R; Miller III, Merrill C; Penkowa, Milena; Rolph, Michael S; Sottosanto, Jordan; St-Arnaud, Rene; Szego, Michael J; Twell, David; Wang, Charles

2006-01-01

391

Development of multilayer constructs for tissue engineering  

Microsoft Academic Search

The rapidly developing field of tissue engineering produces living substitutes that restore, maintain or improve the function of tissues or organs. In contrast to standard therapies, the engineered products become integrated within the patient, affording a potentially permanent and specific cure of the disease, injury or impairment. Despite the great progress in the field, development of clinically relevantly sized tissues

N. M. S. Bettahalli; N. Groen; H. Steg; H. V. Unadkat; Boer de J; Blitterswijk van C. A; M. Wessling; D. Stamatialis

2012-01-01

392

Gene Expression Profiling of Human Lung Tissue from Smokers with Severe Emphysema  

Microsoft Academic Search

The mechanism by which inhaled smoke causes the anatomic lesions and physiologic impairment of chronic obstructive pulmonary dis- ease remains unknown. We used high-density microarrays to mea- sure gene expression in severely emphysematous lung tissue re- moved from smokers at lung volume reduction surgery (LVRS) and normal or mildly emphysematous lung tissue from smokers under- going resection of pulmonary nodules.

Avrum Spira; Jennifer Beane; Victor Pinto-Plata; Aran Kadar; Gang Liu; Vishal Shah; Bartolome Celli; Jerome S. Brody

2004-01-01

393

Molecular insights into the progression of crystalline silica-induced pulmonary toxicity in rats.  

PubMed

Identification of molecular target(s) and mechanism(s) of silica-induced pulmonary toxicity is important for the intervention and/or prevention of diseases associated with exposure to silica. Rats were exposed to crystalline silica by inhalation (15 mg m(-3), 6 h per day, 5 days) and global gene expression profile was determined in the lungs by microarray analysis at 1, 2, 4, 8 and 16 weeks following termination of silica exposure. The number of significantly differentially expressed genes (>1.5-fold change and <0.01 false discovery rate P-value) detected in the lungs during the post-exposure time intervals analyzed exhibited a steady increase in parallel with the progression of silica-induced pulmonary toxicity noticed in the rats. Quantitative real-time PCR analysis of a representative set of 10 genes confirmed the microarray findings. The number of biological functions, canonical pathways and molecular networks significantly affected by silica exposure, as identified by the bioinformatics analysis of the significantly differentially expressed genes detected during the post-exposure time intervals, also exhibited a steady increase similar to the silica-induced pulmonary toxicity. Genes involved in oxidative stress, inflammation, respiratory diseases, cancer, and tissue remodeling and fibrosis were significantly differentially expressed in the rat lungs; however, unresolved inflammation was the single most significant biological response to pulmonary exposure to silica. Excessive mucus production, as implicated by significant overexpression of the pendrin coding gene, SLC26A4, was identified as a potential novel mechanism for silica-induced pulmonary toxicity. Collectively, the findings of our study provided insights into the molecular mechanisms underlying the progression of crystalline silica-induced pulmonary toxicity in the rat. Published 2012. This article is a US Government work and is in the public domain in the USA. PMID:22431001

Sellamuthu, Rajendran; Umbright, Christina; Roberts, Jenny R; Cumpston, Amy; McKinney, Walter; Chen, Bean T; Frazer, David; Li, Shengqiao; Kashon, Michael; Joseph, Pius

2013-04-01

394

Gene profiling of the rat medial collateral ligament during early healing using microarray analysis  

PubMed Central

Ligament heals in a synchronized and complex series of events. The remodeling process may las