Gene Expression Microarray Studies Research Articles

Could 2′5′-oligoadenylate synthetase isoforms be biomarkers to differentiate between disease flare and infection in lupus patients? A pilot study

2'5'-Oligoadenylate synthetase (OAS) was shown to be related to systemic lupus erythematosus (SLE) 20 years ago, and was rediscovered to be involved in type I interferon pathway in SLE by several microarray gene expression studies recently. The goal of this study was to investigate OAS isoform expressions in lupus patients, to evaluate whether they could become biomarkers to differentiate between disease flare and infection. Fifty-four SLE patients presented with fever or systemic inflammatory syndrome, or both, were enrolled. Gene expressions of OAS1, OAS2, and OASL were studied by using real time PCR in active SLE (SLEDAI >or=9, n=29) and in those complicated with infections (n=25). The latter group was composed of 19 patients with invasive bacterial infections, and six patients with viral infections. C reactive protein (CRP) and other clinical parameters were also measured. Twenty-nine healthy individuals made up a normal control group. The mRNA expressions of OAS1, OAS2, and OASL were higher in patients with lupus flares than those with infections (p<0.03), or normal controls (p<0.001). SLE complicated with infections have higher OAS1 expression level (P=0.002), lower OASL (P=0.004), and equivalent OAS2 (P=0.135), when compared with those of normal controls. OASL expression level was negatively correlated with infection in lupus by logistic regression analysis (p=0.008). Area under the receiver operating characteristic curve for the prediction of infection was 0.92 (p<0.0001) for OASL, and 0.77 (p=0.007) for CRP. Therefore, our preliminary data suggest that the pattern of OAS isoform expressions, OASL in particular, may provide useful information in differentiating disease flares from certain infections in SLE.

Rosetta error model for gene expression analysis

In microarray gene expression studies, the number of replicated microarrays is usually small because of cost and sample availability, resulting in unreliable variance estimation and thus unreliable statistical hypothesis tests. The unreliable variance estimation is further complicated by the fact that the technology-specific variance is intrinsically intensity-dependent. The Rosetta error model captures the variance-intensity relationship for various types of microarray technologies, such as single-color arrays and two-color arrays. This error model conservatively estimates intensity error and uses this value to stabilize the variance estimation. We present two commonly used error models: the intensity error-model for single-color microarrays and the ratio error model for two-color microarrays or ratios built from two single-color arrays. We present examples to demonstrate the strength of our error models in improving statistical power of microarray data analysis, particularly, in increasing expression detection sensitivity and specificity when the number of replicates is limited.

The SERPINE2 Gene Is Associated with Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is a complex human disease likely influenced by multiple genes, cigarette smoking, and gene-by-smoking interactions, but only severe alpha 1-antitrypsin deficiency is a proven genetic risk factor for COPD. Prior linkage analyses in the Boston Early-Onset COPD Study have demonstrated significant linkage to a key intermediate phenotype of COPD on chromosome 2q. We integrated results from murine lung development and human COPD gene-expression microarray studies with human COPD linkage results on chromosome 2q to prioritize candidate-gene selection, thus identifying SERPINE2 as a positional candidate susceptibility gene for COPD. Immunohistochemistry demonstrated expression of serpine2 protein in mouse and human adult lung tissue. In family-based association testing of 127 severe, early-onset COPD pedigrees from the Boston Early-Onset COPD Study, we observed significant association with COPD phenotypes and 18 single-nucleotide polymorphisms (SNPs) in the SERPINE2 gene. Association of five of these SNPs with COPD was replicated in a case-control analysis, with cases from the National Emphysema Treatment Trial and controls from the Normative Aging Study. Family-based and case-control haplotype analyses supported similar regions of association within the SERPINE2 gene. When significantly associated SNPs in these haplotypic regions were included as covariates in linkage models, LOD score attenuation was observed most markedly in a smokers-only linkage model (LOD 4.41, attenuated to 1.74). After the integration of murine and human microarray data to inform candidate-gene selection, we observed significant family-based association and independent replication of association in a case-control study, suggesting that SERPINE2 is a COPD-susceptibility gene and is likely influenced by gene-by-smoking interaction.

Microarray studies of gene expression of endothelial cells in response to pulsatile vs. steady shear stress

Microarray studies of gene expression of endothelial cells in response to pulsatile vs. steady shear stress

Effect of simulated microgravity on oxidation-sensitive gene expression in PC12 cells

Oxygen utilization by and oxygen dependence of cellular processes may be different in biological systems that are exposed to microgravity (micro-g). A baseline in which cellular changes in oxygen sensitive molecular processes occur during micro-g conditions would be important to pursue this question. The objective of this research is to analyze oxidation-sensitive gene expression in a model cell line [rat pheochromocytoma (PC12)] under simulated micro-g conditions. The PC12 cell line is well characterized in its response to oxygen, and is widely recognized as a sensitive model for studying the responses of oxygen-sensitive molecular and cellular processes. This study uses the rotating wall vessel bioreactor (RWV) designed at NASA to simulate micro-g. Gene expression in PC12 cells in response to micro-g was analyzed by DNA microarray technology. The microarray analysis of PC12 cells cultured for 4 days under simulated micro-g under standardized oxygen environment conditions revealed more than 100 genes whose expression levels were changed at least twofold (up-regulation of 65 genes and down-regulation of 39 genes) compared with those from cells in the unit gravity (unit-g) control. This study observed that genes involved in the oxidoreductase activity category were most significantly differentially expressed under micro-g conditions. Also, known oxidation-sensitive transcription factors such as hypoxia-inducible factor-2α, c-myc, and the peroxisome proliferator-activated receptor-γ were changed significantly. Our initial results from the gene expression microarray studies may provide a context in which to evaluate the effect of varying oxygen environments on the background of differential gene regulation of biological processes under variable gravity conditions.

Novel susceptibility genes in inflammatory bowel disease

The inflammatory bowel disease, Crohn's disease and ulcerative colitis, are polygenic disorders with important environmental interactions. To date, the most widely adopted approach to identifying susceptibility genes in complex diseases has involved genome wide linkage studies followed by studies of positional candidate genes in loci of interest. This review encompasses data from studies into novel candidate genes implicated in the pathogenesis of inflammatory bowel disease. Novel techniques to identify candidate genes-genome wide association studies, yeast-two hybrid screening, microarray gene expression studies and proteomic profiling, are also reviewed and their potential role in unravelling the pathogenesis of inflammatory bowel disease are discussed.

A New Map for Navigating the Yeast Epigenome

The posttranslational modification of histones by acetylation or methylation regulates chromatin structure and can determine how a DNA sequence is interpreted by, for example, the transcriptional machinery. In this issue of Cell, Pokholok and colleagues (2005) describe a new and reliable genome-wide microarray study of histone modifications and gene expression in yeast. Their epigenetic map can be used to guide further research on the epigenome.

Polymorphisms of myelin-associated glycoprotein gene are associated with schizophrenia in the Chinese Han population

Results of gene expression microarray and quantitative PCR studies have suggested abnormalities in the expression of myelin-related genes including myelin-associated glycoprotein ( MAG) in schizophrenic patients. Research provides strong evidence for oligodendrocyte dysfunction in schizophrenics. In order to further assess the role of MAG in schizophrenia, we examined four single nucleotide polymorphisms (SNPs), namely rs2301600, rs3746248, rs720309 and rs720308, of this gene in Chinese schizophrenic patients ( n = 470) and healthy controls ( n = 470). The distribution of rs720309 T/A genotypes showed a strong association with schizophrenia ( χ 2 = 14.58, d.f. = 2, P = 0.0008). A haplotype constructed of rs720309–rs720308 also revealed a significant association with schizophrenia ( χ 2 = 11.914, d.f. = 3, P = 0.0084). Our findings of a significant associations between schizophrenia and the MAG gene suggest that this gene may be involved in susceptibility to schizophrenia in the Chinese Han population.

Osteopontin Expression Correlates with Melanoma Invasion

Osteopontin Expression Correlates with Melanoma Invasion

Reassessing design and analysis of two‐colour microarray experiments using mixed effects models

Gene expression microarray studies have led to interesting experimental design and statistical analysis challenges. The comparison of expression profiles across populations is one of the most common objectives of microarray experiments. In this manuscript we review some issues regarding design and statistical analysis for two-colour microarray platforms using mixed linear models, with special attention directed towards the different hierarchical levels of replication and the consequent effect on the use of appropriate error terms for comparing experimental groups. We examine the traditional analysis of variance (ANOVA) models proposed for microarray data and their extensions to hierarchically replicated experiments. In addition, we discuss a mixed model methodology for power and efficiency calculations of different microarray experimental designs.

A Time Course Microarray Study of Gene Expression in the Mouse Lacrimal Gland after Acute Corneal Trauma

To investigate the effect of corneal trauma on gene expression in the lacrimal gland and to assess how many genes and what specific genes are regulated in response to corneal trauma. A mouse model with acute corneal trauma was created with a chemical burn to the cornea with silver nitrate. Sixty-four female BALB/c mice at 12 weeks of age were randomly divided into eight groups, eight mice per group. The corneas of four mice in each group were bilaterally cauterized with silver nitrate, and another four time-matched mice were used as the control. The total RNA of the lacrimal gland was then extracted, at eight time points--0.5, 1, 3, 8, 24, 72, 120, and 360 hours--after the corneal burn, and gene expression was examined with using cDNA microarray technology. Evaluation of 15,065 genes with multiple array replications showed significantly altered expression in 3,799 genes at one or more of the eight time points. Of those, 1,528 were known genes and 2,271 were unknown. The analysis of known genes showed broad and long-lasting gene suppression in most functional gene groups, including housekeeping, energy metabolism, protein degradation, DNA and protein synthesis, and apoptosis-associated genes. Heat shock genes were upregulated beginning at the 8-hour time point, indicating a stress response. This study demonstrates that corneal trauma has profound effects on the regulation of gene expression in the lacrimal gland and may provide genetic evidence for a cornea-to-lacrimal gland feedback mechanism in dry eye.

Predicting the sites of metastases

Recent work has identified genes implicated in the tissue tropism of breast-cancer metastasis.

Sample Selection for Microarray Gene Expression Studies

Summary Objectives: The choice of biomedical samples for microarray gene expression studies is decisive for both validity and interpretability of results. We present a consistent, comprehensive framework to deal with the typical selection problems in microarray studies. Methods: Microarray studies are designed either as case-control studies or as comparisons of parallel groups from cohort studies, since high levels of random variation in the experimental approach thwart absolute measurements of gene expression levels. Validity and results of gene expression studies heavily rely on the appropriate choice of these study groups. Therefore, the so-called principles of comparability, which are well known from both clinical and epidemiological studies, need to be applied to microarray experiments. Results: The principles of comparability are the study-base principle, the principle of deconfounding and the principle of comparable accuracy in measurements. We explain each of these principles, show how they apply to microarray experiments, and illustrate them with examples. The examples are chosen as to represent typical stumbling blocks of microarray experimental design, and to exemplify the benefits of implementing the principles of comparability in the setting of micro-array experiments. Conclusions: Microarray studies are closely related to classical study designs and therefore have to obey the same principles of comparability as these. Their validity should not be compromised by selection, confounding or information bias. The so-called study-base principle, calling for comparability and thorough definition of the compared cell populations, is the key principle for the choice of biomedical samples and controls in microarray studies.

Adrenomedullin Is Highly Expressed in Blood Monocytes Associated with Acute Kawasaki Disease: A Microarray Gene Expression Study

Kawasaki disease (KD) is an acute inflammatory disorder of children frequently associated with the development of coronary artery abnormalities. Although a great deal is known about inflammatory and immune responses in acute KD, the mechanisms linking the immune response to vascular changes are not known. To gain further insight into this process, we performed a microarray gene expression analysis on RNA isolated from the peripheral blood mononuclear cells of four patients with KD during both their acute and convalescent phases. Forty-seven genes of 7129 genes examined showed an increased expression in three or all four patients in the acute compared with the convalescent phase of KD. Fourteen of these genes were significantly (p < 0.05) up-regulated, including several inflammatory response genes (e.g. S-100 A9 protein) and also anti-inflammatory genes (e.g. TSG-6). Of greatest interest, the adrenomedullin (ADM) gene, known to be associated with coronary artery vasodilation, was up-regulated in the acute phase of KD (p = 0.024). Up-regulation of ADM in the acute phase of KD was confirmed in peripheral blood mononuclear cells of 11 additional KD patients by reverse transcriptase-PCR (p < 0.01). Isolated blood monocytes but not lymphocytes were demonstrated by real-time PCR to have increased ADM mRNA (p = 0.01). Plasma ADM protein level in 32 additional KD patients was also confirmed to be higher in acute KD compared with convalescent KD (p < 0.032). It is interesting that from microarray results, other molecules known to be associated with coronary dilation, including nitric oxide, prostacyclin, acetylcholine, bradykinin, substance P, and serotonin, were not elevated in acute KD. Our current study suggests that ADM-expressing monocytes that infiltrate the coronary vascular wall may be the cause of coronary dilation in the acute phase of KD.

Prolonged Toll-Like Receptor Signaling byMycobacterium tuberculosisand Its 19-Kilodalton Lipoprotein Inhibits Gamma Interferon-Induced Regulation of Selected Genes in Macrophages

Infection of macrophages with Mycobacterium tuberculosis or exposure to M. tuberculosis 19-kDa lipoprotein for >16 h inhibits gamma interferon (IFN-gamma)-induced major histocompatibility complex class II (MHC-II) expression by a mechanism involving Toll-like receptors (TLRs). M. tuberculosis was found to inhibit murine macrophage MHC-II antigen (Ag) processing activity induced by IFN-gamma but not by interleukin-4 (IL-4), suggesting inhibition of IFN-gamma-induced gene regulation. We designed an approach to test the ability of M. tuberculosis-infected cells to respond to IFN-gamma. To model chronic infection with M. tuberculosis with accompanying prolonged TLR signaling, macrophages were infected with M. tuberculosis or incubated with M. tuberculosis 19-kDa lipoprotein for 24 h prior to the addition of IFN-gamma. Microarray gene expression studies were then used to determine whether prolonged TLR signaling by M. tuberculosis broadly inhibits IFN-gamma regulation of macrophage gene expression. Of 347 IFN-gamma-induced genes, M. tuberculosis and 19-kDa lipoprotein inhibited induction of 42 and 36%, respectively. Key genes or gene products were also examined by quantitative reverse transcription-PCR and flow cytometry, confirming and extending the results obtained by microarray studies. M. tuberculosis inhibited IFN-gamma induction of genes involved in MHC-II Ag processing, Ag presentation, and recruitment of T cells. These effects were largely dependent on myeloid differentiation factor 88, implying a role for TLRs. Thus, prolonged TLR signaling by M. tuberculosis inhibits certain macrophage responses to IFN-gamma, particularly those related to MHC-II Ag presentation. This inhibition may promote M. tuberculosis evasion of T-cell responses and persistence of infection in tuberculosis.

Thiamine Transporter Gene Expression and Exogenous Thiamine Modulate the Expression of Genes Involved in Drug and Prostaglandin Metabolism in Breast Cancer Cells

In previous studies, we have shown that RNA levels of the thiamine transporter THTR2 were down-regulated in breast cancer tumors in comparison with normal tissues and that THTR2-mediated increases in thiamine uptake activity contributed to increased apoptosis after exposure to ionizing radiation. To further understand the biological effects of the alteration of THTR2 expression, we conducted a DNA microarray study of gene expression in THTR2-transfected breast cancer cells and found that, in addition to increased expression of THTR2 attributable to the transgene, three other genes were up-regulated >2.5-fold in the transfected cells: cytochrome P450 isoform CYP4B1, 15-hydroxyprostaglandin dehydrogenase (15-PGDH), and transcription factor CRIP1. In addition, two genes were confirmed to be down-regulated in THTR2-transfected cells: trefoil factor 1 (TFF1) and Rho-GDP dissociation inhibitor (RGDI). Up-regulation of 15-PGDH and CYP4B1 expression was observed in other breast cancer cell lines transfected with THTR2, and down-regulation was observed after suppression of THTR2 with siRNA vectors. To determine the role of exogenous thiamine in the expression of these genes, we analyzed THTR2-transfected breast cancer cells grown in thiamine-depleted medium by quantitative reverse transcription-PCR and showed that three of these five genes showed evidence of regulation by exogenous thiamine in a manner concordant with the effects of THTR2 overexpression. One of the genes up-regulated by THTR2 transfection was down-regulated by thiamine depletion (CYP4B1), and two genes with decreased expression in THTR2-transfected breast cancer cells were up-regulated by thiamine depletion (TFF1 and RGDI). In summary, these studies show unexpected relationships between thiamine metabolism and genes that may be involved in the oncogenesis of breast and lung cancer.

Match/X, A Gene Expression Pattern Recognition Algorithm Used to Identify Genes Which May be Related to CDC2 Function and Cell Cycle Regulation

Large-scale microarray gene expression studies can provide insight into complex genetic networks and biological pathways. A comprehensive gene expression database was constructed using Affymetrix GeneChip microarrays and RNA isolated from more than 6,400 distinct normal and diseased human tissues. These individual patient samples were grouped into over 700 sample sets based on common tissue and disease morphologies, and each set contained averaged expression data for over 45,000 gene probe sets representing more than 33,000 known human genes. Sample sets were compared to each other in more than 750 normal vs. disease pairwise comparisons. Relative up or down-regulation patterns of genes across these pairwise comparisons provided unique expression fingerprints that could be compared and matched to a gene of interest using the Match/X algorithm. This algorithm uses the kappa statistic to compute correlations between genes and calculate a distance score between a gene of interest and all other genes in the database. Using cdc2 as a query gene, we identified several hundred genes that had similar expression patterns and highly correlated distance scores. Most of these genes were known components of the cell cycle involved in G2/M progression, spindle function or chromosome arrangement. Some of the identified genes had unknown biological functions but may be related to cdc2 mediated mechanism based on their closely correlated distance scores. This algorithm may provide novel insights into unknown gene function based on correlation to expression profiles of known genes and can identify elements of cellular pathways and gene interactions in a high throughput fashion.

ChromSorter PC: a database of chromosomal regions associated with human prostate cancer.

BackgroundOur increasing use of genetic and genomic strategies to understand human prostate cancer means that we need access to simplified and integrated information present in the associated biomedical literature. In particular, microarray gene expression studies and associated genetic mapping studies in prostate cancer would benefit from a generalized understanding of the prior work associated with this disease. This would allow us to focus subsequent laboratory studies to genomic regions already related to prostate cancer by other scientific methods. We have developed a database of prostate cancer related chromosomal information from the existing biomedical literature. The input material was based on a broad literature search with subsequent hand annotation of information relevant to prostate cancer.DescriptionThe database was then analyzed for identifiable trends in the whole scale literature. We have used this database, named ChromSorter PC, to present graphical summaries of chromosomal regions associated with prostate cancer broken down by age, ethnicity and experimental method. In addition we have placed the database information on the human genome using the Generic Genome Browser tool that allows the visualization of the data with respect to user generated datasets.ConclusionsWe have used this database as an additional dataset for the filtering of genes identified through genetics and genomics studies as warranting follow-up validation studies. We would like to make this dataset publicly available for use by other groups. Using the Genome Browser allows for the graphical analysis of the associated data . Additional material from the database can be obtained by contacting the authors (mdatta@mcw.edu).

Mouse striatal transcriptome analysis: effects of oral self-administration of alcohol

Results of recent studies support the notion that substance self-administration is partially a genetically controlled component of addiction tied to habit formation and cellular modification of the striatum. Aiming to define pathways among genomic, neural, and behavioral determinants of addiction, we investigated global striatal gene expression in a paradigm of oral self-administration of alcohol by using genomically very similar alcohol-nonpreferring B6.Cb 5i 7-α3/Vad (C5A3) and alcohol-preferring B6.Ib 5i 7-β25A/Vad (I5B25A) quasi-congenic mouse strains and their progenitors, C57BL/6By (B6By) and BALB/cJ. Expression of 12,488 genes and expressed sequence tags (ESTs) was studied by using 24 high-density oligonucleotide microarrays. Transcript signal intensity differences were analyzed with z test after iterative median normalization across groups and Hochberg step-down Bonferroni procedure. As expected, striatal transcriptome differences were far more extensive between the independently derived progenitor strains than between the quasi-congenic strains and their background partner, B6By. However, the genes, which were differentially expressed between the quasi-congenic strains and their background partner, were not subsets of the progenitorial differences and were not located on the chromosome segments introgressed into the quasi-congenic strains from the donor BALB/cJ strain that have been so far defined. Although 25 transcripts showed significantly different expression between the progenitor strains, only two transcripts, phosphatidylserine decarboxylase and a hypothetical 21.2-kDa protein, and one transcript, molybdenum co-factor synthesis 2, showed significantly different expression between C5A3 and I5B25A, and between B6By and I5B25A, respectively. The latter three transcripts are not located on previously identified chromosome segments introgressed from the donor BALB/cJ strain, supporting the suggestion of trans-acting regulatory variations among strains. Exposure to alcohol did not induce statistically significant striatal gene expression changes in any of the mouse strains. In conclusion, the results support the hypothesis that in functional genomic studies the chance of detecting function-relevant genes can be increased by the comparative analysis of quasi-congenic and background strains because the number of functionally irrelevant, differentially expressed genes between genomically similar strains is reduced. Lack of statistically significant alcohol-induced changes in transcript abundance indicated that oral self-administration had subtle effects on striatal gene expression and directed attention to important implications for the experimental design of future microarray gene expression studies on complex behaviors.

Laboratory scale structural genomics.

At Lawrence Livermore National Laboratory, the development of the TB structural genomics consortium crystallization facility has paralleled several local proteomics research efforts that have grown out of gene expression microarray and comparative genomics studies. Collective experience gathered from TB consortium labs and other centers involved in the NIH-NIGMS protein structure initiative allows us to explore the possibilities and challenges of pursuing structural genomics on an academic laboratory scale. We discuss our procedures and protocols for genomic targeting approaches, primer design, cloning, small scale expression screening, scale-up and purification, through to automated crystallization screening and data collection. The procedures are carried out by a small group using a combination of traditional approaches, innovative molecular biochemistry approaches, software automation, and a modest investment in robotic equipment.