Application Of DNA Microarray Technology Research Articles

L’analyse globale de l’expression circadienne des gènes

A major goal of chronobiology is to identify clock-controlled genes. The expression of thousands of genes can be monitored simultaneously using DNA microarrays. Application of DNA microarray technology to the field of circadian rhythm has already shown that a number of genes coding for proteins involved in very diverse functions are under the control of the circadian clock.

Clinical application of cDNA microarrays in oncology.

DNA microarrays represent an important new tool to analyze human tissues. The technology enables investigators to measure the expression of several thousand mRNA species simultaneously in a biological specimen. This process, called transcriptional profiling, represents a technological breakthrough in the analysis of biological specimens. It may be used to screen for individual genes that are differentially expressed between normal and diseased tissues in the hope of finding novel targets for drug development or finding new single-gene markers of clinical outcome. Microarrays are also applied to learn about the complex biology of cancer by simultaneously monitoring interactions between hundreds of genes during experimental conditions in vitro or during therapy in vivo. Analysis of gene expression patterns may also be used as a classification tool to sort cancer into various clinically relevant subgroups that is not currently possible with other methods. The first clinically important applications of this technology will likely be its use as a tool to refine diagnosis and improve the accuracy of predictions of prognosis and response to therapy. DNA microarrays in several "proof-of-principle" experiments have demonstrated that they can predict important clinical outcomes, including outcomes that cannot currently be predicted with other methods, but the true clinical utility and the limits of this exciting new technology are yet to be established. This paper reviews the current methodology and applications of this technique as they relate to clinical oncology.

DNA microarrays and development.

Gene expression is a central concept in molecular biology: its control, frequently exquisite in terms of cell specificity and timing, forms part of our explanation of most biological processes. The importance of the control of gene expression for developmental biologists is made obvious by just considering the nature of their discipline. Development is the term we use to describe the coordination in time and space of numerous cellular activities such as mitosis, migration, differentiation and apoptosis. Understanding the role of genes in these processes thus necessitates the use of methods to determine patterns of transcription during development with a high degree of sensitivity and specificity, conventionally by in situ hybridization. However, there is a widespread conviction amongst biologists that the description of gene expression patterns is of no immediate functional relevance: definitive functional data are the exclusive prerogative of biochemistry and genetics. In this review of recent applications of DNA microarray technology by developmental biologists, we suggest that genome-wide expression profiling has met with some resistance owing to such preconceived ideas about the status of gene expression pattern descriptions and, in particular, the format in which these are delivered by microarrays.

Looking Beyond Morphology: Cancer Gene Expression Profiling Using DNA Microarrays

Although molecular testing has been increasingly used in clinical practice, the precise diagnosis and prognosis of most human cancers still heavily rely on descriptive histopathological data. Identification of robust molecular markers associated with distinctive morphological parameters will assist in diagnostic and prognostic assessment. On the other hand, the diversity of morphologically identical/similar cancers can be manifested at multiple levels, most importantly at the level of clinical outcome. In the past several years, DNA microarray technology has been widely used in the context of cancer research, resulting in a deluge of new information that can be used to identify molecular alterations common to all tumors as well as signatory profiles unique to a subcategory of cancers. These new findings will very likely transform the clinical management of cancer patients in the near term. This article reviews recent advances in cancer gene expression-profiling results derived from the application of DNA microarray technology, with an emphasis on studies performed on human prostate cancer specimens. We discuss broad issues relevant to cancer expression profiling and attempt to illustrate the rapid pace of novel discoveries using prostate cancer as examples wherever appropriate.

DNA microarrays: implications for cardiovascular medicine.

Dramatic progress has been made in the technologies available to assess global alterations in mRNA levels in both clinical and research samples. Through commercial services and institutional core laboratories, these technologies are increasingly accessible to individual investigators. Although such transcript profiling can provide a powerful research tool, the broad range of options can be bewildering for the uninitiated and more often than not the limitations and pitfalls of this approach are not fully appreciated. Moreover, consensus standards for data collection, analysis, and validation have yet to emerge. It is important to recognize that the goals of transcript profiling experiments can be quite diverse. These goals range from hypothesis generation and identification of novel therapeutic targets to delineation of complex patterns of gene expression that provide a potentially pathognomonic molecular phenotype. We will first present a practical review of the commonly used approaches for data collection and analysis, and discuss possible standards for contextual validation. We will then examine the clinical and scientific applications of DNA microarray technology with an emphasis on important limitations and implications for cardiovascular medicine.

Application of DNA microarray technology to study genes controlled by progesterone in human endometrial stromal cells in vitro

Application of DNA microarray technology to study genes controlled by progesterone in human endometrial stromal cells in vitro

DNA Microarrays in Medicine: Can the Promises Be Kept?

DNA Microarrays in Medicine: Can the Promises Be Kept?

Molecular Heterogeneity of Diffuse Large B-cell Lymphoma: Implications for Disease Management and Prognosis

Diffuse large B-cell lymphoma (DLBCL) accounts for approximately 40% of all B-cell non-Hodgkin lymphomas of the Western world. According to the "WHO classification of tumours of the haematopoietic and lymphoid tissues", the term DLBCL is likely to include more than one disease entity, as suggested by the marked variability of the clinical presentation and response to treatment of this disease. Such heterogeneity may reflect the occurrence of distinct molecular subtypes of DLBCL as well as differences in the host's immune function. In immunocompetent hosts, approximately 50% DLBCL carry one of two primary molecular lesions defining two distinct genotypic subgroups, characterized by activation of either the BCL-6 or the BCL-2 proto-oncogene. Conversely, the remaining DLBCL of immunocompetent hosts display one of several molecular lesions, each associated with a small subset of cases and including activation of the proto-oncogenes REL, MUC-1, BCL-8 and c-MYC. The molecular pathogenesis of immunodeficiency-associated DLBCL differs substantially from that of DLBCL in immunocompetent hosts. In fact, EBV infection is present in a large fraction of immunodeficiency-associated DLBCL, whereas it is consistently negative in DLBCL of immunocompetent hosts, probably reflecting the critical role of disruption of the immune system in this disease. Finally, the application of DNA microarray technology to DLBCL has led to the distinction of two disease variants: a germinal center like DLBCL and an activated peripheral B-cell like DLBCL. Overall the molecular features of DLBCL may identify prognostic categories of the disease and may represent a powerful tool for therapeutic stratification.

Positional Cloning Utilizing Genomic DNA Microarrays: The Niemann–Pick Type C Gene as a Model System

A major obstacle in positional cloning is identifying the specific mutated gene from within a large physical contig. Here we describe the application of DNA microarray technology to a defined genomic region (physical map) to identify: (i) exons without a priori sequence data and (ii) the disease gene based on differential gene expression in a recessive disorder. The feasibility was tested using resources from the positional cloning of the Neimann–Pick Type C (NP-C) disease gene, NPC1. To identify NPC1 exons and optimize the technology, an array was generated from genomic fragments of the 110-kb bacterial artificial chromosome, 108N2, which encodes NPC1. First, as a test case for blindly identifying exons, fluorescently labeled NPC1 cDNA identified 108N2 fragments that contained NPC1 exons, many of which also contained intronic sequences and could be used to determine part of the NPC1 genomic structure. Second, to demonstrate that the NPC1 disease gene could be identified based upon differential gene expression, subarrays of 108N2 fragments were hybridized with fluorescently labeled cDNA probes generated from total RNA from hamster cell lines differentially expressing NPC1. A probe derived from the NP-C cell line CT60 did not detect NPC1 exons or other genomic fragments from 108N2. In contrast, several NPC1 exons were detected by a probe generated from the non-NP-C cell line 911D5A13, which was derived from CT60, and expressed NPC1 as a consequence of stable transduction with a YAC that contains NPC1 and encompasses 108N2. Thus, the array technology identified NPC1 as a candidate gene based on a physical contig and differential NPC1 expression between NP-C and non-NP-C cells. This technique should facilitate gene identification when a physical contig exists for a region of interest and mutations result in changes in the mRNA level of the disease gene or portions thereof.

Genome-wide mapping of meiosis-induced DNA double-strand breaks

The major applications of DNA microarray technology to date have been genome-wide analysis of gene expression and analysis of DNA variation. Our goal is to develop an approach using DNA microarray technology to quantitatively study the distribution of DNA-associated proteins at the whole-genome level. An initial approach will determine the genomic distribution of DNA double-strand breaks (DSBs) that initiate meiotic recombination in Saccharomyces cerevisiae. DSB formation involves an intermediate stage where DNA ends are covalently linked to Spo11p. In a rad50S mutant background these intermediates accumulate throughout meiosis. Our approach is to purify Spo11p::His6/DNA intermediates by immobilized metal-affinity chromatography. The DNA purified from these intermediates is then hybridized to DNA microarrays to map the distribution and frequency of Spo11p-linked double-strand breaks throughout the genome. With the addition of a formaldehyde cross-linking step, this approach could be used to map the distribution of any protein that interacts with the genome, either independently or as part of a protein complex. The affinity chromatography approach allows large amounts of material to be purified, and should enable the detection of minor or transient protein/DNA intermediates.