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PubMed2006

A generic concept for large-scale microarray analysis dedicated to medical diagnostics.

BACKGROUND: The development of diagnostic procedures based on microarray analysis confronts the bioinformatician and the biomedical researcher with a variety of challenges. Microarrays generate a huge amount of data. There are many, not yet clearly defined, data processing steps and many clinical response variables which may not match gene expression patterns. OBJECTIVES: To design a generic concept for largescale microarray experiments dedicated to medical diagnostics; to create a system capable of handling several 1000 microarrays per analysis and more than 100 clinical response variables; to design a standardized workflow for quality control, data calibration, identification of differentially expressed genes and estimation of classification accuracy; and to provide a user-friendly interface for clinical researchers with respect to biomedical interpretation. METHODS: We designed a database structure suitable for the storage of microarray data and analysis results. We applied statistical procedures to identify differential genes and developed a technique to estimate classification accuracy of gene patterns with confidence intervals. RESULTS: We implemented a Gene Analysis Management System (GAMS) based on this concept, using MySQL for data storage, R/Bioconductor for analysis and PHP for a web-based front-end for the exploration of microarray data and analysis results. This system was utilized with large data sets from several medical disciplines, mainly from oncology (approximately 2000 microarrays). CONCLUSIONS: A systematic approach is necessary for the analysis of microarray experiments in a medical diagnostics setting to get comprehensible results. Due to the complexity of the analysis, data processing (by bioinformaticians) and interactive exploration of results (by biomedical experts) should be separated.

Adult↗
PubMed2003

Microarray analysis in drug discovery: an uplifting view of depression.

Genomic profiling provides insights into drug evaluation for diseases without defined molecular mechanisms or cellular assays. Levy provides a brief background in the development of microarray analysis and discussion of the application of this technique to pharmacogenomics. Highlighted is the microarray analysis of primary human neurons treated with antidepressants, antipsychotics, or opioid receptor agonists, demonstrating that these classes of drugs can be properly categorized by using two different statistical analysis methods: classification tree and random forest. Not only is microarray analysis valuable for drug evaluation and leading candidate development, but the genes identified as markers for the various drug classifications point to new directions for research into the underlying pathways responsible for human diseases, such as depression and psychosis.

Animals↗
PubMed2001

cDNA microarray analysis of adapting bowel after intestinal resection.

BACKGROUND/PURPOSE: Studies of the genetic regulation of various physiologic processes have been hampered by methodologies that are limited to the analysis of individual genes. The advent of cDNA microarray technology has permitted the simultaneous screening of numerous genes for alterations in expression. In this study, cDNA microarrays were used to evaluate gene expression changes during the intestinal adaptive response to massive small bowel resection (SBR). METHODS: Male ICR mice (n = 20) underwent either a 50% SBR or sham operation and then were given either orogastric epidermal growth factor (EGF, 50 microg/kg/d) or saline. After 3 days, cDNA microarray analysis was performed on mRNA extracted from the remnant ileum. RESULTS: From over 8,700 different genes, the array identified 27 genes that were altered 2-fold or greater after SBR. Small proline-rich protein 2 (sprr2), the gene with the greatest expression change (4.9-fold), was further upregulated by EGF. This gene has never been characterized in the intestine or described in intestinal adaptation. CONCLUSIONS: cDNA microarray analysis showed enhanced expression of sprr2, a gene not previously known to be involved in the physiology of adaptation after SBR. This technology provides a more rapid and efficient means of dissecting the complex genetic regulation of gut adaptation.

Adaptation, Biological↗
PubMed2007

Novel insights into lung transplant rejection by microarray analysis.

Gene expression microarrays can estimate the prevalence of mRNA for thousands of genes in a small sample of cells or tissue. Organ transplant researchers are increasingly using microarrays to identify specific patterns of gene expression that predict and characterize acute and chronic rejection, and to improve our understanding of the mechanisms underlying organ allograft dysfunction. We used microarrays to assess gene expression in bronchoalveolar lavage cell samples from lung transplant recipients with and without acute rejection on simultaneous lung biopsies. These studies showed increased expression during acute rejection of genes involved in inflammation, apoptosis, and T-cell activation and proliferation. We also studied gene expression during the evolution of airway obliteration in a murine heterotopic tracheal transplant model of chronic rejection. These studies demonstrated specific patterns of gene expression at defined time points after transplantation in allografts, whereas gene expression in isografts reverted back to that of native tracheas within 2 wk after transplantation. These studies demonstrate the potential power of microarrays to identify biomarkers of acute and chronic lung rejection. The application of new genetic, genomic, and proteomic technologies is in its infancy, and the microarray-based studies described here are clearly only the beginning of their application to lung transplantation. The massive amount of data generated per tissue or cell sample has spawned an outpouring of invention in the bioinformatics field, which is developing methodologies to turn data into meaningful and reproducible clinical and mechanistic inferences.

Animals↗
PubMed2003

Microarray analysis reveals complex remodeling of cardiac ion channel expression with altered thyroid status: relation to cellular and integrated electrophysiology.

Although electrophysiological remodeling occurs in various myocardial diseases, the underlying molecular mechanisms are poorly understood. cDNA microarrays containing probes for a large population of mouse genes encoding ion channel subunits ("IonChips") were developed and exploited to investigate remodeling of ion channel transcripts associated with altered thyroid status in adult mouse ventricle. Functional consequences of hypo- and hyperthyroidism were evaluated with patch-clamp and ECG recordings. Hypothyroidism decreased heart rate and prolonged QTc duration. Opposite changes were observed in hyperthyroidism. Microarray analysis revealed that hypothyroidism induces significant reductions in KCNA5, KCNB1, KCND2, and KCNK2 transcripts, whereas KCNQ1 and KCNE1 expression is increased. In hyperthyroidism, in contrast, KCNA5 and KCNB1 expression is increased and KCNQ1 and KCNE1 expression is decreased. Real-time RT-PCR validated these results. Consistent with microarray analysis, Western blot experiments confirmed those modifications at the protein level. Patch-clamp recordings revealed significant reductions in I(to,f) and I(K,slow) densities, and increased I(Ks) density in hypothyroid myocytes. In addition to effects on K+ channel transcripts, transcripts for the pacemaker channel HCN2 were decreased and those encoding the alpha1C Ca2+ channel (CaCNA1C) were increased in hypothyroid animals. The expression of Na+, Cl-, and inwardly rectifying K+ channel subunits, in contrast, were unaffected by thyroid hormone status. Taken together, these data demonstrate that thyroid hormone levels selectively and differentially regulate transcript expression for at least nine ion channel alpha- and beta-subunits. Our results also document the potential of cDNA microarray analysis for the simultaneous examination of ion channel transcript expression levels in the diseased/remodeled myocardium.

Animals↗
PubMed2004

Morphological and microarray analysis of T-2 toxin-induced rat fetal brain lesion.

To examine morphological and gene expression changes induced by T-2 toxin in the fetal brain in detail, pregnant rats on day 13 of gestation were treated orally with a single dose of T-2 toxin (2 mg/kg) and sacrificed at 1, 3, 6, 9, 12 and 24 h after treatment (HAT). Histopathologically, the number of apoptotic neuroepithelial cells in the telencephalon increased from 1 HAT and peaked at 12 HAT. Based on the histopathological examinations, microarray analysis was performed at 6, 12 and 24 HAT. Microarray analysis showed that the expression of oxidative stress-related genes (heat shock protein 70 (HSP70) and heme oxygenase (HO)) was strongly induced by T-2 toxin at 12 HAT, the peak time point of apoptosis induction. The expression of mitogen-activated protein kinase (MAPK)-related genes (MEKK1 and c-jun) and other apoptosis-related genes (caspase-2 and insulin-like growth factor-binding protein-3 (IGF-BP3)) was also induced by the T-2 toxin treatment. The changes observed by microarray analysis were confirmed for four up-regulated genes (HSP70, HO, IGF-BP3 and VEGF-A) using real-time RT-PCR. Our results suggest that the T-2 toxin-induced apoptosis in the fetal brain is due to oxidative stress, and that the MAPK pathway may be involved in T-2 toxin-induced toxicity.

Administration, Oral↗
PubMed2005

Microarray analysis of gene expression in the liver during the urinary ethanol cycle in rats fed ethanol intragastrically at a constant rate.

The regulation of gene expression in the liver of ethanol fed rats was studied using microarray analysis. The changes in gene expression were compared between pair-fed controls and rats fed ethanol intragastrically at a constant rate for 1 month. The rats fed ethanol were sacrificed at low and high urinary ethanol levels (UAL) during the UAL cycle in order to compare the effects of high and low blood alcohol levels (BAL). The results of the microarray analysis indicated that the pattern of gene expression was very different when the controls, high UAL, and low UAL livers were compared. Many of the gene expression changes reflected nonparenchymal cell alterations such as neuroendocrine or muscle related gene expression. When the results of protein levels and gene expression were compared for individual genes, correlations were variable indicating that post-translational factors modified the effects of the changes in gene expression. This was further emphasized by the fact that activation of proteins by phosphorylation as the result of signaling kinase cascades, was not reflected in the microarray analysis results. For instance, the importance of blood alcohol levels at the time that the assays were performed, profoundly changed the gene expression, protein level, and protein phosphorylation level profiles.

Animals↗
PubMedDate not supplied

Microarray-analysis: a new approach to study the molecular mechanisms of thermo-chemotherapy.

BACKGROUND: Experimental studies for the treatment of relapsed neuroblastoma include the use of hyperthermia in combination with chemotherapeutic drugs. Cytotoxic effects of alkylants and platinum compounds on tumor cells can be enhanced by hyperthermia in various in vitro models. However, the underlying molecular mechanisms are still largely unknown. METHOD: In this study, we used microarray-analysis as a new biological approach to gain insight into the pharmacogenomics and possible target genes of thermochemotherapy. As a model, LAN 1 neuroblastoma cells were treated for 1 h with low doses of cisplatin alone, with simultaneous heating to 42 degrees C or with hyperthermia alone. Gene expression was analyzed at five time points 0 to 24 h after treatment using U95Av2 oligonucleotide arrays (Affymetrix Inc). Significant changes of gene expression levels were calculated by similarity metrices and Pearson correlation. RESULTS: Only a few genes (n = 23) demonstrated altered expression following treatment of LAN 1 cells with cisplatin alone. Hyperthermia alone resulted in significant expression changes of 136 genes in comparison to untreated control cells. Combination therapy of cisplatin and hyperthermia resulted in expression changes of 251 genes, interestingly including 131 genes with unchanged expression under treatment with either cisplatin or hyperthermia alone. Significant changes of expression levels could be annotated to genes involved in heat shock response, protein degradation and apoptosis. These results are now being validated on mRNA- and protein levels by RT-PCR and Western Blot analysis. CONCLUSION: Microarray-Analysis is a suitable new approach for the identification of target genes, which might play an important role for the synergistic effect of hyperthermia and chemotherapy in tumor cells.

Antineoplastic Agents↗
PubMed2006

Microarray analysis of thyroid nodule fine-needle aspirates accurately classifies benign and malignant lesions.

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.

Biopsy, Fine-Needle↗
PubMed2001

Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems.

It has recently been shown through DNA microarray analysis of Bacillus subtilis two-component regulatory systems (DegS-DegU, ComP-ComA, and PhoR-PhoP) that overproduction of a response regulator of the two-component systems in the background of a deficiency of its cognate sensor kinase affects the regulation of genes, including its target ones. The genome-wide effect on gene expression caused by the overproduction was revealed by DNA microarray analysis. In the present work, we newly analyzed 24 two-component systems by means of this strategy, leaving out 8 systems to which it was unlikely to be applicable. This analysis revealed various target gene candidates for these two-component systems. It is especially notable that interesting interactions appeared to take place between several two-component systems. Moreover, the probable functions of some unknown two-component systems were deduced from the list of their target gene candidates. This work is heuristic but provides valuable information for further study toward a comprehensive understanding of the B. subtilis two-component regulatory systems. The DNA microarray data obtained in this work are available at the KEGG Expression Database website (http://www.genome.ad.jp/kegg/expression).

Bacillus subtilis↗
PubMed2005

cDNA microarray analysis to compare HCV subgenomic replicon cells with their cured cells.

The hepatitis C virus (HCV) replicon system carrying autonomously replicating HCV subgenomic RNA in human hepatocyte cells is a potent tool for basic studies of HCV, such as viral replication and drug development. Recently, we developed two HCV subgenomic replicons (50-1 and 1B-2R1) derived from two HCV strains, 1B-1 and 1B-2, respectively. Since the expression of HCV proteins is thought to affect the host cells' gene expression profiles, we attempted to identify target genes of HCV proteins using microarray analysis (9970 genes) by comparing 50-1 and 1B-2R1 replicon cells with their "cured cells", from which the replicons had been eliminated by prolonged treatment with interferon-alpha. The results showed that HCV replicons could have a variety of expression profiles in human hepatocytes. The results also showed that 2 and 6 genes were commonly up-regulated (more than 2.0-fold) and down-regulated (less than 0.50-fold), respectively, in both 50-1 and 1B-2R1 replicon cells compared with their cured cells. The differential expression profiles of genes selected by the microarray analysis were confirmed with standard RT-PCR and real-time LightCycler PCR. It was noteworthy that the commonly down-regulated genes contained large multifunctional proteases 2 and 7, which are known as catalytic subunits of immunoproteasome, and serine proteinase inhibitor clade C. Our microarray analysis demonstrated that HCV subgenomic replicons can change the gene expression profiles of host cells, and it allowed us to compile the first list of genes that the replicons transcriptionally regulate.

Base Sequence↗
PubMed2004

DNA microarray analysis of chromosomal susceptibility regions to identify candidate genes for allergic disease: a pilot study.

OBJECTIVE: To examine whether DNA microarray analysis of chromosomal susceptibility regions for allergy can help to identify candidate genes. MATERIAL AND METHODS: Nasal biopsies were obtained from 23 patients with allergic rhinitis and 12 healthy controls. RNA was extracted from the biopsies and pooled into three patient and three control pools. These were then analysed in duplicate with DNA microarrays containing 12626 genes. Candidate genes were further examined in nasal biopsies (real-time polymerase chain reaction) and blood samples (single nucleotide polymorphisms) from other patients with allergic rhinitis and from controls. RESULTS: A total of 37 differentially expressed genes were identified according to criteria involving both the size and consistency of the gene expression levels. The chromosomal location of these genes was compared with the chromosomal susceptibility regions for allergic disease. Using a statistical method, five genes were identified in these regions, including serine protease inhibitor, Kazal type, 5 (SPINK5) and HLA-DRB2. The relevance of these genes was examined in other patients with allergic rhinitis and in controls; none of the genes were differentially expressed in nasal biopsies. Moreover, no association between allergic rhinitis and SPINK5 polymorphisms was found, at either the genotype or haplotype level. CONCLUSIONS: DNA microarray analysis of chromosomal susceptibility regions did not lead to identification of candidate genes that could be validated in a new material. However, because gene polymorphisms may cause differential gene expression, further studies, including validation data, are needed to examine this approach.

Adolescent↗
PubMed2003

Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis.

Conventional approaches to target labelling for expression microarray analysis typically require relatively large amounts of total RNA, a serious limitation when the sample available is small. Here we explore the cycle-dependent amplification characteristics of Template-Switching PCR and validate its use for microarray target labelling. TS-PCR identifies up to 80% of the differentially expressed genes identified by direct labelling using 30-fold less input RNA for the amplification, with the equivalent of 1000-fold less starting material being used for each hybridisation. Moreover, the sensitivity of microarray experiments is increased considerably, allowing the identification of differentially expressed transcripts below the level of detection using targets prepared by direct labelling. We have also validated the fidelity of amplification and show that the amplified material faithfully represents the starting mRNA population. This method outperforms conventional labelling strategies, not only in terms of sensitivity and the identification of differentially expressed genes, but it is also faster and less labour intensive than other amplification protocols.

DNA, Complementary↗
PubMed2004

Microarray analysis of differentially expressed genes associated with human ovarian cancer.

To define the molecular changes associated with ovarian cancer, DNA microarray analysis has been adapted to detect differentially expressed genes in human normal ovary tissue, borderline, and invasive epithelial ovarian tumors. The differential expression of genes in the tumor tissues and normal tissues was confirmed by Northern and/or semi-quantitative RT-PCR analysis. Analysis of the differential gene-expression profiles of the normal and neoplastic ovary allowed us to detect previously unidentified genes in ovarian tissues. We observed up-regulation of the following genes in ovarian cancer: catechol-O-methyltransferase (COMT), the autocrine motility factor neuroleukin (NLK), the transcription regulator high mobility group I proteins (HMGI), the tyrosine kinase receptor ErbB-3, S100-alpha protein and Acyl-CoA-binding protein (ACBP). The transcription factor, chicken ovalbumin up-stream promoter transcription factor II (COUP-TFII), was the only gene down-regulated in ovarian cancer. Comparable gene-expression profiles were previously reported in breast cancer, suggesting that similar molecular events also exist in ovarian cancer. Our microarray analysis showed that most differentially expressed genes in ovarian cancer are linked to glucose/insulin metabolism, providing a possible molecular link between the glucose/insulin signaling pathway and the neoplasms of ovarian cancer.

Biomarkers, Tumor↗
PubMedDate not supplied

Microarray analysis of differential gene expression in androgen independent prostate cancer using a metastatic human prostate cancer cell line model.

Progression to androgen independence (AI) leading to uncontrolled cell growth is the main cause of death in prostate cancer. While almost all patients with metastatic prostate cancer will initially respond to anti-androgen treatments, the majority will fail hormonal treatments in less than 2 yrs. Both genetic and epigenetic alterations in gene expression contribute significantly to the development of AI. To investigate this we have used an in vitro cell line model of AI prostate cancer from which we have identified a number of differentially expressed genes associated with progression to AI in prostate cancer. We used an in vitro cell line model of AI prostate cancer, to study differential gene expression using cDNA microarray analysis and corroborated the microarray results with Ribonuclease Protection Assay (RPA). Approximately 4480 out of 7075 (63.3%) cDNA cloned genes were differentially expressed, of which, 6 genes were differentially expressed by at least fivefold. RPA was used to corroborate the microarray results for the five most highly differentially expressed genes. Using an in vitro cell line model and microarray analysis we have identified a number of candidate genes for further investigation in AI prostate cancer.

Androgen Antagonists↗
PubMed2005

cDNA microarray analysis of isogenic paclitaxel- and doxorubicin-resistant breast tumor cell lines reveals distinct drug-specific genetic signatures of resistance.

cDNA microarray analysis is a highly useful tool for the classification of tumors and for prediction of patient prognosis to specific cancers based on this classification. However, to date, there is little evidence that microarray approaches can be used to reliably predict patient response to specific chemotherapy drugs or regimens. This is likely due to an inability to differentiate between genes affecting patient prognosis and genes that play a role in response to specific drugs. Thus, it would be highly useful to identify genes whose expression correlates with tumor cell sensitivity to specific chemotherapy agents in a drug-specific manner. Using cDNA microarray analysis of wildtype MCF-7 breast tumor cells and isogenic paclitaxel-resistant (MCF-7(TAX)) or doxorubicin-resistant (MCF-7(DOX)) derivative cell lines, we have uncovered drug-specific changes in gene expression that accompany the establishment of paclitaxel or doxorubicin resistance. These changes in gene expression were confirmed by quantitative reverse transcription polymerase chain reaction and immunoblotting experiments, with a confirmation rate of approximately 91-95%. The genes identified may prove highly useful for prediction of response to paclitaxel or doxorubicin in patients with breast cancer. To our knowledge this is the first report of drug-specific genetic signatures of resistance to paclitaxel or doxorubicin, based on a comparison of gene expression between isogenic wildtype and drug-resistant tumor cell lines. Moreover, this study provides significant insight into the wide variety of mechanisms through which resistance to these agents may be acquired in breast cancer.

Antibiotics, Antineoplastic↗
PubMed2004

Anti-invasive gene expression profile of curcumin in lung adenocarcinoma based on a high throughput microarray analysis.

Curcumin has been reported to exhibit anti-invasive and/or antimetastatic activities, but the mechanism remains unclear. In this study, microarray analysis of gene expression profiles were used to characterize the anti-invasive mechanisms of curcumin in highly invasive lung adenocarcinoma cells (CL1-5). Results showed that curcumin significantly reduces the invasive capacity of CL1-5 cells in a concentration range far below its levels of cytotoxicity (20 microM) and that this anti-invasive effect was concentration dependent (10.17 +/- 0.76 x 10(3) cells at 0 microM; 5.67 +/- 1.53 x 10(3) cells at 1 microM; 2.67 +/- 0.58 x 10(3) cells at 5 microM; 1.15 +/- 1.03 x 10(3) cells at 10 microM; P < 0.05) in the Transwell cell culture chamber assay. Using microarray analysis, 81 genes were down-regulated and 71 genes were up-regulated after curcumin treatment. Below sublethal concentrations of curcumin (10 microM), several invasion-related genes were suppressed, including matrix metalloproteinase 14 (MMP14; 0.65-fold), neuronal cell adhesion molecule (0.54-fold), and integrins alpha6 (0.67-fold) and beta4 (0.63-fold). In addition, several heat-shock proteins (Hsp) [Hsp27 (2.78-fold), Hsp70 (3.75-fold), and Hsp40-like protein (3.21-fold)] were induced by curcumin. Real-time quantitative reverse transcription-polymerase chain reaction, Western blotting, and immunohistochemistry confirmed these results in both RNA and protein levels. Curcumin (1 to 10 microM) reduced the MMP14 expression in both mRNA and protein levels and also inhibited the activity of MMP2, the down-stream gelatinase of MMP14, by gelatin zymographic analysis. Based on these data, it can be concluded that curcumin might be an effective antimetastatic agent with a mechanism of anti-invasion via the regulation of certain gene expressions.

Antineoplastic Agents↗
PubMed2026

Prenatal SNP-array chromosomal microarray analysis in 3,549 pregnancies: indication-specific yields and clinical implications.

BACKGROUND: SNP-based chromosomal microarray analysis (CMA) is widely used in invasive prenatal diagnosis, yet real-world performance across contemporary referral pathways, especially in the NIPT era, remains incompletely characterized. METHODS: We retrospectively analyzed 3,549 prenatal invasive samples tested by SNP array, and evaluated diagnostic yield overall and by referral indication and ultrasound phenotype. RESULTS: In total, we identified 398 pathogenic or likely pathogenic (P/LP) variants across 386 fetuses, resulting in an overall diagnostic yield of 10.9% (386/3,549). These findings comprised 223 aneuploidies and 175 pathogenic CNVs. In contrast, variants of uncertain significance (VOUS) were detected in 12.0% (426/3,549) of cases. Diagnostic yields were heavily stratified by indication: yields peaked in NIPT high-risk referrals (38.9%) and were intermediate in ultrasound-based cases (~&#x2009;11%), but dropped significantly in the advanced maternal age (AMA; 4.2%) and serum screening (~&#x2009;5-6%) groups. Conversely, VOUS rates remained remarkably stable across all referral categories. Sub-analysis of ultrasound abnormalities revealed that multisystem anomalies conferred the highest risk (27.3%), driven predominantly by aneuploidies; among soft markers, increased nuchal translucency (NT) emerged as the strongest predictor of chromosomal pathology. CONCLUSIONS: In our cohort, SNP-array identified clinically actionable findings in 10.9% of cases. NIPT enriched diagnostic yields, particularly for aneuploidies, and NT thickness was strongly associated with pathogenic findings. These results support an indication-based approach to genomic testing, with NIPT as a triage tool for aneuploidy and CMA for high-risk populations, while improving VOUS counseling.

Humans↗