Use Of Microarray Analysis Research Articles

Use of microarray analysis to study gene expression in the avian epiphyseal growth plate

Longitudinal bone growth depends upon the execution of an intricate series of cellular activities by epiphyseal growth plate chondrocytes. In order to better understand these coordinated events, microarray analysis was used to compare gene expression in chondrocytes isolated from the proliferative and hypertrophic zones of the avian growth plate. RT-PCR was used to confirm the identity of a select number of genes. The expression of 745 genes was found to differ 3-fold or greater at the 0.05 level of probability. Transferrin was the most highly up-regulated (321-fold) gene associated with chondrocyte hypertrophy. Immunohistochemistry localized this peptide adjacent to the penetrating blood vessels in the growth plate of 3-week-old chicks. Fibulin, OC-116, DMP-1 and PHEX were among the expanded number of genes associated with extracellular matrix metabolism. The presence of NELL2, ATOH8 and PLEXIN suggests a neuronal involvement in growth plate physiology. In addition, the expression of a large number of genes associated with angiogenesis and cellular stress was up-regulated. These processes are important to the physiology and survival of chondrocytes in the unique and stressful environment of the epiphyseal growth plate.

Assessing a Novel Room-Temperature RNA Storage Medium for Compatibility in Microarray Gene Expression Analysis

RNA integrity is a critical factor in obtaining meaningful gene expression data. Current methodologies rely on maintaining samples in cold environments during collection, transport, processing, and storage procedures, which are also extremely time-sensitive. Several RNA storage products are commercially available to help prevent degradation during the handling and storage steps; however, samples must be kept cold for optimal protection. We have evaluated a novel RNA storage medium based on anhydrobiosis for stabilizing and protecting samples from degradation at room temperature that are intended for use in microarray analysis. Samples were stored dry at room temperature for various time periods to assess any degradation or loss of activity as compared with frozen control samples. Recovered samples were used directly for analysis without further purification and exhibited no interference or inhibition in downstream applications. Comparison of gene expression profiles indicate no significant differences between freezer-stored control samples and those kept at room temperature protected in the RNA storage medium. The quality of recovered RNA was confirmed using spectrophotometry and Bioanalyzer analysis and was identical to control samples. The ability to stabilize RNA samples at ambient temperatures for extended time periods will have tremendous use, particularly for sample shipment to core facilities.

Use of microarray analysis of differentially expressed genes in luminal B subtype of breast cancers to evaluate NHERF1 as a marker of endocrine resistance

11015 Background: In vitro and in vivo data demonstrate that the expression of estrogen receptor (ER) in breast cancer is mainly associated with low proliferation. Gene expression profiling has recently been used to identify a group of high proliferating estrogen receptor positive breast cancers (the luminal B subtype), which are associated with a prognosis that is even worse than that of high proliferating estrogen receptor negative tumors. The analysis of those tumors might provide valuable information about breast cancer biology and could be helpful for adjuvant or neoadjuvant treatment decisions.Methods and Results: We analyzed microarray data from breast cancer specimens to gain insight into genes which play a role in estrogen receptor signalling. Genes were identified showing strong expression in high proliferating ER-positive tumors but no expression in either Ki67-/ER+ or Ki67+/ER- samples. Among these genes the Na+/H+ exchanger regulatory factor NHERF1 was found. We assessed the clinical relevance of NHERF1 transcript levels using a total of 2469 breast cancers. Analysis indicates that enhanced NHERF1 expression is associated with metastatic progression and poor prognosis of breast cancer patients. We found no correlation between NHERF1 and the nodal status as well as age, but positive correlations for tumor size (P<0.001), grade (P<0.001) and erbb2 (P=0.033). Weak NHERF1 expression correlated with longer disease free survival (DFS) in grade 1 and 2 tumors, but not in grade 3 breast cancers. Since NHERF1 expression is strongly linked to the presence of ER, the predictive value for endocrine treatment was analyzed. For samples with weak or none NHERF1 expression a treatment benefit was observed (P=0.007). While untreated patients display a 10 yr DFS rate of 67.2 ± 3.8%, endocrine treatment resulted in 80.1 ± 4.0%. In contrast no differences in disease free survival were found for corresponding NHERF1 expressing breast cancers. Conclusions: Our data indicate that expression of NHERF1 defines a state of differentiation, where breast cancer cells are refractory to endocrine treatment. No significant financial relationships to disclose.

Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics

In order to design a method for the accurate detection and identification of food-borne pathogens, we used comparative genomics to select 70-mer oligonucleotide probes specific for 11 major food-borne pathogens (10 overlapping probes per pathogen) for use in microarray analysis. We analyzed the hybridization pattern of this constructed microarray with the Cy3-labeled genomic DNA of various food-borne pathogens and other bacteria. Our microarray showed a highly specific hybridization pattern with the genomic DNA of each food-borne pathogen; little unexpected cross-hybridization was observed. Microarray data were analyzed and clustered using the GenePix Pro 6.0 and GeneSpring GX 7.3.1 programs. The analyzed dendrogram revealed the discriminating power of constructed microarray. Each food-borne pathogen clustered according to its hybridization specificity and non-pathogenic species were discriminated from pathogenic species. Our method can be applied to the rapid and accurate detection and identification of food-borne pathogens in the food industry. In addition, this study demonstrates that genome sequence comparison and DNA microarray analysis have a powerful application in epidemiologic and taxonomic studies, as well as in the food safety and biodefense fields.

Plasma Polymerization of Amines and Acetone: Functionalized Surfaces for Microarray Applications

AbstractPlasma polymerization (PP) afforded amine as well as carbonyl containing films which are suitable for use in microarray analysis. The polymerization process with acetone (AC), ethylenediamine (EDA) and diethylamine (DEA) has to be performed in the presence of argon as a carrier gas to be successful. Different activation steps of the polymer based support yield surfaces which differ significantly in their elemental composition after the PP step. Angle dependent XPS proves a take off angle dependence of the carbonyl PP film in contrast to a homogeneous PP film for amine functionalized PP layers while microarray experiments have been successful for both functional films.

Microarray analysis of exstrophic human bladder smooth muscle

To compare the genetic profiles of 'healthy' bladder smooth muscle cells (SMCs) and exstrophic SMCs (ESMCs) to identify genes that are over- and under-expressed in ESMCs, thus providing a molecular evaluation of the quality and therapeutic potential of ESMC tissue. Classical bladder exstrophy is a rare disorder, occurring in 1 in 30,000 live births. Studies have shown that exstrophic bladders are developmentally immature at birth. After surgical closure, the bladder typically undergoes abnormal remodelling (such as over-expression of collagen III) throughout early development. We hypothesized that the predominant genetic differences between normal SMCs and ESMCs are in the developmental genes. This hypothesis was tested by the use of microarray analysis. Bladder SM biopsies were taken from 'healthy' subjects undergoing bladder surgeries for other conditions (for example, urinary reflux) and patients with bladder exstrophy. Cells were expanded in vitro, and total RNA was isolated and hybridized to the Affymetrix U133A GeneChip (Affymetrix Inc., Santa Clara, CA, USA) by the Wake Forest University School of Medicine Affymetrix core facility, using standard protocols. We created a genetic signature consisting of 961 genes that are over-expressed and 432 genes that are under-expressed in ESMCs. Analysis of these signatures identified an over-expression of inflammatory genes and an under-expression of developmental genes. Our data is in concordance with previous studies and histological data showing that ESMCs are developmentally immature relative to healthy bladder SM. The clinical implication of the ESMC genetic signature is that it provides a list of targets that can be (i) manipulated ex vivo and/or in vivo to induce differentiation (the completion of development) and (ii) used as biomarkers to explain the variability of the clinical symptoms after surgical closure.

Homozygosity for a NovelABCA4Founder Splicing Mutation Is Associated with Progressive and Severe Stargardt-like Disease

To clinically characterize and genetically analyze members of six families who reside in the same village and manifest a rare form of retinal degeneration. Ophthalmic evaluation included a full clinical examination, perimetry, color vision testing, and electroretinography. Genomic DNA was screened for ABCA4 mutations with the use of microarray analysis and direct sequencing. RNA analysis was performed with RT-PCR and sequencing. The authors recruited 15 patients with a unique retinal disease who are members of six highly consanguineous Arab-Muslim families from a single village. During early stages of disease, funduscopic and angiographic findings as well as retinal function resemble those of Stargardt disease. However, later in life, severe, widespread cone-rod degeneration ensues. Marked progressive involvement of the retinal periphery distinguishes this phenotype from classic Stargardt disease. Genetic analysis of ABCA4 revealed two novel deletions, p.Cys1150del and c.4254-15del23. One patient, who was a compound heterozygote, manifested typical Stargardt disease. The remaining 14 patients were homozygote for the c.4254- 15del23 intronic deletion and had the progressive form of disease. We identified an identical ABCA4 haplotype in all alleles carrying this mutation, indicating a founder mutation. Detailed RT-PCR analysis in normal retina and lymphoblastoid cells revealed expression of the full-length ABCA4 transcript and three novel transcripts produced by alternative splicing. The full-length ABCA4 transcript, however, could not be detected in lymphoblastoid cells of affected homozygote patients. These results expand the genotype-phenotype correlation of ABCA4, showing that homozygosity for the novel c.4254-15del23 splicing mutation is associated with a severe progressive form of disease.

Possible utilization of in vitro synthesized mRNAs specifically expressed in certain tissues as standards for quantitative evaluation of the results of microarray analysis

To examine the possible usefulness of in vitro synthesized RNA as standards in microarray analysis, we prepared full-length mRNAs encoded by 3 rat metabolic genes for heart/muscle type carnitine palmitoyltransferase I (M-CPTI), uncoupling protein (UCP1), and heart/muscle type fatty acid-binding protein (H-FABP). Artificial RNA samples were prepared by adding known amounts of these synthetic mRNAs to total RNA from rat liver, and transcript levels of various genes were compared between the prepared artificial RNA samples and total RNA samples of rat liver by using an Agilent oligo microarray system. Upon the addition of these synthetic RNAs, signals from the DNA spots corresponding to these 3 genes were elevated, but those from the DNA spots representing other genes were not markedly influenced. Using the ratio of the increase in signal intensity of DNA spot to the amount of added RNA, we estimated the expression levels of several genes and compared them with the absolute expression levels determined by calibrated Northern analysis. As a result, the absolute transcript levels of 3 genes encoding acidic ribosomal phosphoprotein P0, type-1 voltage-dependent anion channel (VDAC1), and type-2 glucose transporter (GLUT2) were successfully estimated by this procedure. Furthermore, genes specifically expressed in certain tissues such as UCP1 were concluded to be good candidates as standards for use in microarray analysis.

Transcriptional Profiles of the Response to Ketoconazole and Amphotericin B in Trichophyton rubrum

Trichophyton rubrum is a pathogenic filamentous fungus of increasing medical concern. Two antifungal agents, ketoconazole (KTC) and amphotericin B (AMB), have specific activity against dermatophytes. To identify the mechanisms of action of KTC and AMB against T. rubrum, a cDNA microarray was constructed from the expressed sequence tags of the cDNA library from different developmental stages, and transcriptional profiles of the responses to KTC and AMB were determined. T. rubrum was exposed to subinhibitory concentrations of KTC and AMB for 12 h, and microarray analysis was used to examine gene transcription. KTC exposure induced transcription of genes involved in lipid, fatty acid, and sterol metabolism, including ERG11, ERG3, ERG25, ERG6, ERG26, ERG24, ERG4, CPO, INO1, DW700960, CPR, DW696584, DW406350, and ATG15. KTC also increased transcription of the multidrug resistance gene ABC1. AMB exposure increased transcription of genes involved in lipid, fatty acid, and sterol metabolism (DW696584, EB801458, IVD, DW694010, DW688343, DW684992), membrane transport (Git1, DW706156, DW684040, DMT, DW406136, CCH1, DW710650), and stress-related responses (HSP70, HSP104, GSS, AOX, EB801455, EB801702, TDH1, UBI4) but reduced transcription of genes involved in maintenance of cell wall integrity and signal transduction pathways (FKS1, SUN4, DW699324, GAS1, DW681613, SPS1, DW703091, STE7, DW703091, DW695308) and some ribosomal proteins. This is the first report of the use of microarray analysis to determine the effects of drug action in T. rubrum.

MCT-1 Protein Interacts with the Cap Complex and Modulates Messenger RNA Translational Profiles

MCT-1 is an oncogene that was initially identified in a human T cell lymphoma and has been shown to induce cell proliferation as well as activate survival-related pathways. MCT-1 contains the PUA domain, a recently described RNA-binding domain that is found in several tRNA and rRNA modification enzymes. Here, we established that MCT-1 protein interacts with the cap complex through its PUA domain and recruits the density-regulated protein (DENR/DRP), containing the SUI1 translation initiation domain. Through the use of microarray analysis on polysome-associated mRNAs, we showed that up-regulation of MCT-1 was able to modulate the translation profiles of BCL2L2, TFDP1, MRE11A, cyclin D1, and E2F1 mRNAs, despite equivalent levels of mRNAs in the cytoplasm. Our data establish a role for MCT-1 in translational regulation, and support a linkage between translational control and oncogenesis.

Noise and Bias in Microarray Analysis of Tumor Specimens

Microarray-based investigations can provide fundamental insights into cancer biology and have the potential to predict patient outcome and response to therapy. For microarray analysis to be informative, measured gene expression must accurately reflect tumor biology. Given the increasing use of microarray analysis in clinical oncology, it is imperative that investigators understand how to minimize expression noise and bias through effective trial design. Expression noise is inherent to microarray-based measurement of gene expression. Noise can be defined as gene expression variation that does not correlate with the biology or behavior being studied and is introduced both by unrelated biologic phenomena and during tissue processing for analysis. Expression noise can obscure informative patterns of gene expression (resulting in a false-negative finding, a beta error), and most computational approaches to microarray analysis are focused on finding true associations despite profound noise. Bias is not inherent to microarray-based analysis but is easily introduced by faulty experimental design. For this discussion, expression bias can be defined as expression variation that correlates with the hypothesis being tested but caused by experimental factors that are independent of the hypothesis. Bias confounds analysis and begets false associations (false-positive associations, alpha errors). Bias is not accounted for by most analytic methodologies, and investigators therefore need to minimize the potential for bias by implementing appropriate experimental design. In this issue of the Journal of Clinical Oncology, Lin et al detail gene expression changes in prostate tissue that occur during tissue processing by comparing prostate biopsies performed in situ during surgery with those performed ex vivo during gross pathologic assessment. The authors performed microarray analysis on paired samples from 12 patients and determined that 1.5% of the genes studied (n 62) have increased expression in the ex vivo biopsies. For this analysis, the authors used a false-discovery rate (FDR) threshold of 0.10 as an arbitrary statistical cutoff, which estimates that 10% of the genes identified are falsely associated with ischemia. No genes had significantly decreased expression using the same statistical cutoff. Quantitative polymerase chain reaction confirmed a representative subset of the genes identified. Pathway analysis using GenMAPP (http://www.genmapp.org/) determined that the observed gene expression was similar to that seen with stress responses caused by cytotoxic drugs, heat shock, and radiation. The trial design of Lin et al demonstrates how successful microarray investigations minimize noise and avoid bias through thoughtful experimental design and meticulous execution. Although their detailed methodology provides a solid roadmap for successful microarray analysis, there are several aspects of their methods that warrant specific comment. First, the authors minimized potential bias by taking biopsies from both the in situ and ex vivo prostates rather than comparing the in vivo biopsies to a section of tissue collected from the prostate during gross dissection. Second, the authors minimized noise by performing lasercapture microdissection (LCM). LCM allows the selective analysis of a specific cell population (eg, epithelial cells) and will minimize noise introduced by variation in tissue composition. Although LCM may not be appropriate for all tumor-based expression studies, its use by Lin et al minimized the effect of tissue heterogeneity on subsequent analysis. Finally, the use of FDR sufficiently accounts for multiple hypothesis testing and minimizes the chance of false positives caused solely by expression noise and FDR is becoming an accepted standard in microarray analysis. The genes with differential gene expression between in situ and ex vivo biopsies are characterized by the authors as being associated with cellular stress. This is supported by the presence of DUSP1 and JUN, which have previously been shown to have differential expression in response to cellular insults. Their ischemia-related genes also partially overlaps with a previous set of genes induced during warm ischemia (for example, JUNB and JUND). These genes likely contribute to noise in most tumorbased microarray studies as, even in the best of settings, the time between tissue devascularization during surgery and specimen freezing can vary significantly. Thus, this work further underscores the importance of standardized sample handling to minimize noise. However, the association between the genes induced by hypoxia with cellular stress also suggests that these changes can potentially act as confounding variables and introduce bias. As a quick survey to determine whether the 62 ischemic genes identified by Lin et al can introduce bias, we used gene set enrichment analysis (GSEA) to assess coordinate differential expression JOURNAL OF CLINICAL ONCOLOGY E D I T O R I A L VOLUME 24 NUMBER 23 AUGUST 1

Microarrays in Parkinson’s Disease: A Systematic Approach

Neurological disease (ND) is one of the greatest challenges facing our population, from medical, financial, and social perspectives. The application of new research approaches to understand the underlying pathogenesis of ND is critical. In this article, we review the use of microarray analysis in Parkinson's disease (PD). Microarrays have tremendous power, simultaneously querying the expression of tens of thousands of genes from a given biological sample. Coupled with impressive advances in statistical tools for analyzing large, complex data sets, well-designed microarray experiments are poised to make a big impact in the field of ND. Parkinson's disease is a devastating neurodegenerative disease well suited to a systems-based microarray analysis. Genetic and environmental rodent models of PD emulate many of the cardinal features of human PD, providing the unique opportunity to compare gene expression profiles from different etiologies of the same disease. The elucidation of important gene expression patterns during disease will make possible identification of genetic susceptibility markers, biomarkers of disease progression, and new therapeutic targets.

Gene expression profiles of normal proliferating and differentiating human intestinal epithelial cells: A comparison with the Caco-2 cell model

cDNA microarray technology enables detailed analysis of gene expression throughout complex processes such as differentiation. The aim of this study was to analyze the gene expression profile of normal human intestinal epithelial cells using cell models that recapitulate the crypt-villus axis of intestinal differentiation in comparison with the widely used Caco-2 cell model. cDNA microarrays (19,200 human genes) and a clustering algorithm were used to identify patterns of gene expression in the crypt-like proliferative HIEC and tsFHI cells, and villus epithelial cells as well as Caco-2/15 cells at two distinct stages of differentiation. Unsupervised hierarchical clustering analysis of global gene expression among the cell lines identified two branches: one for the HIEC cells versus a second comprised of two sub-groups: (a) the proliferative Caco-2 cells and (b) the differentiated Caco-2 cells and closely related villus epithelial cells. At the gene level, supervised hierarchical clustering with 272 differentially expressed genes revealed distinct expression patterns specific to each cell phenotype. We identified several upregulated genes that could lead to the identification of new regulatory pathways involved in cell differentiation and carcinogenesis. The combined use of microarray analysis and human intestinal cell models thus provides a powerful tool for establishing detailed gene expression profiles of proliferative to terminally differentiated intestinal cells. Furthermore, the molecular differences between the normal human intestinal cell models and Caco-2 cells clearly point out the strengths and limitations of this widely used experimental model for studying intestinal cell proliferation and differentiation.

Analysis of Breast Cell‐Lineage Response Differences to Taxol Using a Novel Co‐Culture System

We have established a new co-culture system in which normal human mammary epithelial cells (HMEC) and breast tumor cells (TC) were physically grown together. We hypothesized that cells in co-culture would generate gene expression profiles different from homogeneous cell populations. A second equally important question addressed was involved whether cell sensitivity to the antitumor agent Taxol (paclitaxel) differed in co-culture from conventional cultures. Preliminary data showed normal HMEC to be most sensitive to Taxol followed by estrogen receptor (ER) positive TC and ER negative TC, respectively. In this study, cells were transfected with green or red fluorescent proteins (FP) and co-cultured. Using deconvolution microscopy, co-cultured HMEC were observed to form focal, gland-like structures surrounded by TC derived from an invasive ductal carcinoma. Using a novel antibody-based, cell capture system coupled with differential trypsinization, we rapidly separated cell populations to perform RNA extractions (<2 h) in order to obtain expression profiles from still viable cells. Cell population purity was determined by telomerase activity. Microarray was utilized to analyze differential gene expression between parent cell lines and cells co-cultured, with or without Taxol at concentrations of 2.21 x 10−7 M. This study has significant relevance for breast cancer research on several levels. Our novel capture system allowed cells to be co-cultured and then quickly separated while maintaining ~90% viability. In addition, the use of microarray analysis allowed us to address the role co-culture may play in gene expression and responses by different breast cell populations to the antitumor agent Taxol.

Efficacy of the farnesyltransferase inhibitor R115777 in a rat mammary tumor model: role of Ha-ras mutations and use of microarray analysis in identifying potential targets

Rats treated with the alkylating agent methylnitrosourea (MNU) develop multiple, hormonally dependent mammary tumors. Roughly 50% of the tumors have Ha-ras mutation, whereas 50% do not. The MNU-induced rat mammary tumor model was employed to examine the therapeutic efficacy of the farnesyltransferase inhibitor (FTI), R115777, and to examine the use of genomics in identifying susceptible tumors as well as identifying genes whose expression are modulated by FTI treatment. In animals bearing palpable mammary tumors (< 7 mm diameter), we performed a surgical biopsy, and 3 days following the biopsy, rats were treated with R115777 (50 mg/kg body wt/day) by gavage. Tumors with Ha-ras mutations underwent profound regression, with nearly 90% showing complete regressions within 4 weeks. In contrast, the non-Ha-ras mutation-bearing tumors yielded a more variable response, although roughly half of the non-Ha-ras mutation tumors underwent significant regression. These results show that although all tumors appear to respond to the FTI inhibitor the tumors with Ha-ras mutations were exquisitely sensitive. We employed a microarray approach to define potential targets and the mechanism of action of R115777 in Ha-ras mutant or wildtype tumors following treatment with FTI. In addition, we determined whether gene expression prior to FTI treatment can be used to differentiate highly sensitive tumors (Ha-ras mutant) and tumors with variable sensitivity (Ha-ras wildtype). Untreated or FTI-treated (4 days at 50 mg/kg body wt) tumors (Ha-ras mutant or wildtype) were examined using oligonucleotide arrays. A significant number of genes were differentially expressed in control rat mammary tumors with or without an activated Ha-ras mutation, suggesting that a microarray analysis might differentiate highly sensitive and variably sensitive tumors. Most of the genes whose expressions were modulated by FTI in tumors were independent of Ha-ras status and were presumably modulated by effects on farnesylation of proteins other than Ha-ras. However, treatment of Ha-ras-mutated mammary tumors with R155777 results in preferential modulation of genes involved in ras-MAP kinase signal transduction pathway and in decreased expression of many genes involved with cell proliferation. In contrast, several classes of genes are altered in rat mammary tumors without a mutated Ha-ras, suggesting that non-ras targets are involved. Ras pathway related genes, p53, WT1 and PCNA, were preferentially modulated in Ha-ras-mutated tumors, whereas modulation of genes in the G-protein pathway, various cytochrome p450s and RB1 are involved in Ha-ras wildtype tumors. Elucidation of gene expression changes in FTI-treated or control rat mammary adenocarcinomas will help in identifying potential pharmacodynamic markers of FTI treatment as well as potential molecular targets of R115777 and other FTIs.

Comments on selected fundamental aspects of microarray analysis

Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.

Effect of Heptitis C Virus Core Protein on Cellular Gene Expression: Specific Inhibition of Cyclooxygenase 2

Hepatitis C virus (HCV) core protein plays a significant role in the alteration of cellular gene expression. We expressed HCV core protein using a tetracycline-inducible expression system in HeLa cell lines. Profiles of gene expression in cells expressing the HCV core protein were compared with those in control cells by use of microarray analysis. Cells expressing the HCV core protein showed 86 down-regulated and 41 up-regulated genes, compared with control cells. One gene affected was cyclooxygenase 2 (COX-2). Levels of both COX-2 RNA and the Cox-2 protein were significantly inhibited after the expression of HCV core protein in HeLa cells. Similar results were obtained in hepatoma cells and in a functional assay that measured the production of the Cox-2 protein in response to a mitogenic stimulus. The inhibition of the Cox-2 protein could serve as a means of muting the cellular inflammatory response during HCV infection. Correlation of these findings with analysis of clinical specimens from chronically infected patients should lend further significance to the down-regulation of the inflammatory response via Cox-2.

A3. The use of micro-array analyses in the adjuvant setting for breast cancer?

A3. The use of micro-array analyses in the adjuvant setting for breast cancer?

E15. Use of micro-array analysis to predict outcome and response in breast cancer patients

E15. Use of micro-array analysis to predict outcome and response in breast cancer patients

Microarray analysis of changes in renal phenotype in the ethylene glycol rat model of urolithiasis: potential and pitfalls.

To investigate, in an initial study, the use of microarray analysis (MA) to develop an information base for urolithiasis. MA enables the screening of thousands of genes simultaneously making it the technique of choice for situations where the results are known, but the underlying mechanisms are not. Little is known about the pathological changes occurring in the kidney during urolithiasis and this has severely hampered efforts to develop effective therapeutics. Male rats were treated with 0.75% ethylene glycol for 2, 4 or 8 weeks; after death the kidneys were processed for RNA isolation and MA, conducted using a rat-based chip (one kidney/chip) and the results confirmed by reverse transcription-polymerase chain reaction (RT-PCR, 21 probe sets; control, four rats; treated, five rats). Targets were defined as different by the software if the fold change (FC) was >or= 2, and sorted into functional categories using a data-mining tool. The repeatability of MA was investigated by subjecting the 4-week samples to MA in two independent runs. The results for targets with a FC of >or= 2 were plotted (y = 1.01x - 0.75; r(2) 0.84). Comparing the results obtained by RT-PCR and MA showed a good qualitative correlation for those targets having a FC of >or= 5 as determined by MA. Changes in the expression of genes associated with tubule function and regulation, oxidative damage, and inflammation were the most common in the functional categories. Changes in the expression of tubule-specific markers indicated that there was damage to the proximal (gamma-adducin, organic anion and cation transporters, sodium-hydrogen exchange protein-isoform 3) and distal tubules (gamma-adducin, kallikrein) at 2 and 4 weeks. Increased expression of mitochondrial uncoupling protein indicated that there were changes to the mitochondria and oxidative stress at 2 and 4 weeks. This study shows the power of MA as an exploratory technique, and changes in the expression of several physiologically important genes whose expression has not previously been reported to be affected by hyperoxaluria or calcium oxalate crystalluria.