Significant Gene Sets Research Articles

Functional Genomic Relationships in HIV‐1 Disease Revealed by Gene‐Expression Profiling of Primary Human Peripheral Blood Mononuclear Cells

An assessment of biomarkers from an analysis of human peripheral blood mononuclear cell gene-expression profiles was made, to acquire an understanding of transcriptional changes associated with human immunodeficiency virus type 1 (HIV-1) infection in vivo. Supervised learning algorithms were used to create signature gene sets that could be used to distinguish seropositive from seronegative samples and delineate changes in disease status during the early stages of infection. Bioinformatic tools were used to classify persons and to functionally characterize groups of differentially expressed genes, to elucidate the impact of viral infection on host cell gene-expression patterns. A 10-gene signature set that could be used to accurately determine the HIV-1 serostatus was identified. A 6-gene signature set was used to distinguish seropositive persons exhibiting differential changes in CD4(+) T cell counts, with 93% accuracy. Functional classification of differentially expressed genes in HIV-1 indicated a preponderance of down-regulated genes with functions related to the immune response and apoptosis. Hierarchical cluster analysis in persons whose CD4(+) T cell counts increased, compared with that in persons whose CD4(+) T cell counts decreased, was characterized by the down-regulation of genes associated with apoptosis, mitochondrial function, protein biosynthesis, and RNA binding. Gene-expression profile analysis of a complex infectious virus, such as HIV-1, may be useful to elucidate the functional genomic relationships associated with viral infection.

Gene expression signature predicts lymphatic metastasis in squamous cell carcinoma of the oral cavity

Metastasis via the lymphatics is a major risk factor in squamous cell carcinoma of the oral cavity (OSCC). We sought to determine whether the presence of metastasis in the regional lymph node could be predicted by a gene expression signature of the primary tumor. A total of 18 OSCCs were characterized for gene expression by hybridizing RNA to Affymetrix U133A gene chips. Genes with differential expression were identified using a permutation technique and verified by quantitative RT-PCR and immunohistochemistry. A predictive rule was built using a support vector machine, and the accuracy of the rule was evaluated using crossvalidation on the original data set and prediction of an independent set of four patients. Metastatic primary tumors could be differentiated from nonmetastatic primary tumors by a signature gene set of 116 genes. This signature gene set correctly predicted the four independent patients as well as associating five lymph node metastases from the original patient set with the metastatic primary tumor group. We concluded that lymph node metastasis could be predicted by gene expression profiles of primary oral cavity squamous cell carcinomas. The presence of a gene expression signature for lymph node metastasis indicates that clinical testing to assess risk for lymph node metastasis should be possible.

A gene expression signature for oxidant stress/reactive metabolites in rat liver

Formation of free radicals and other reactive molecules is responsible for the adverse effects produced by a number of hepatotoxic compounds. cDNA microarray technology was used to compare transcriptional profiles elicited by training and testing sets of 15 oxidant stressors/reactive metabolite treatments to those produced by approximately 85 other paradigm compounds (mostly hepatotoxicants) to determine a shared signature profile for oxidant stress-associated hepatotoxicity. Initially, 100 genes were chosen that responded significantly different to oxidant stressors/reactive metabolites (OS/RM) compared to other samples in the database, then a 25-gene subset was selected by multivariate analysis. Many of the selected genes (e.g., aflatoxin aldehyde reductase, diaphorase, epoxide hydrolase, heme oxgenase and several glutathione transferases) are well-characterized oxidant stress/Nrf-2-responsive genes. Less than 10 other compounds co-cluster with our training and testing set compounds and these are known to generate OS/RMs as part of their mechanisms of toxicity. Using OS/RM signature gene sets, compounds previously associated with macrophage activation formed a distinct cluster separate from OS/RM and other compounds. A 69-gene set was chosen to maximally separate compounds in control, macrophage activator, peroxisome proliferator and OS/RM classes. The ease with which these ‘oxidative stressor’ classes can be separated indicates a role for microarray technology in early prediction and classification of hepatotoxicants. The ability to rapidly screen the oxidant stress potential of compounds may aid in avoidance of some idiosyncratic drug reactions as well as overtly toxic compounds.

Global expression profiling identifies signatures of tumor virulence in MMTV-PyMT-transgenic mice: correlation to human disease.

FVB/N-Tg (MMTV-PyMT)(634Mul)-transgenic mice develop multifocal mammary tumors with a high incidence of pulmonary metastasis. We have demonstrated previously that mammary tumors derived from transgene-positive F1 progeny in particular inbred strains display altered latency, tumor growth rates, and metastatic rates when compared with the FVB/NJ homozygous parent. To identify genes with expression that might be critical in modifying the biological behavior of MMTV-PyMT tumors, we performed a detailed comparative analysis of expression profiles from mammary tumors arising in the parental FVB/NJ background and F1 progeny from crosses with I/LnJ, LP/J, MOLF/Ei, and NZB/B1NJ mice. Compared with normal mammary glands, gene expression profiles of tumors from all five strains exhibited up-regulation of genes involved in cell growth (e.g., Cks1 and CDC25C) and down-regulation of cell adhesion molecules, with many genes associated previously with human breast cancer such as STAT2, CD24 antigen, gelsolin, and lipocalin2. To identify genes with significant variation in expression between the five different genotypes, significance analysis of microarrays (SAM) and one-way ANOVA were used. Three definable groupings of tumors were identified: (a) tumors derived in the LP/J F1 and MOLF/Ei F1 strains in which tumor growth and dissemination are suppressed and latency prolonged; (b) the most aggressive tumors from the FVB/NJ parental strain and I/LnJ F1 genomic backgrounds; and (c) an intermediate virulence phenotype with tumors from NZB/B1NJ-F1 crosses. These array based assessments correlated well with a composite phenotype ranking using a "virulence" index. The gene expression signature that is associated with a high metastatic rate in the mouse contains the same 17 genes described recently as the signature gene set predictive of metastasis in human tumors (1) with 16 of the 17 genes exhibiting the same directional change in expression associated with human metastases. These results demonstrate that the genetic analysis of mouse models of tumorigenesis may be highly relevant to human cancer and that the metastatic phenotype of a tumor may be affected by the germline genetic configuration of the host.

Gene expression profile of Vitamin D3 treated HL60 cells shows an incomplete molecular phenotypic conversion to monocytes.

By high density oligonucleotide microarrays we have studied the expression profile of proliferating and VD treated HL60 cells and the molecular phenotype of VD monocytes and that of CD14+ peripheral monocytes has been compared. The results indicate that important changes in functional categories of the differentially expressed genes underlie the differentiation transition from myeloblasts to monocytes. This differential gene expression pattern leads to an increased expression of mRNAs involved in surface and external activities since many of the VD induced genes belong to ligand binding, receptors, cell surface antigens, defense/immunity and adhesion molecules functional categories. The results also indicate that the molecular phenotypes of monocytes and VD induced cells diverge for a small but significant set of defense related genes. Particularly, class II MHC genes are not expressed in these cells. Furthermore, the high levels of expression of these genes induced by serum treatment of monocytes are decreased by VD.

Gene induction/repression response profiling of hepatotoxic agents using cDNA microarrays

DNA microarray technology is a powerful technique that allows for the simultaneous expression analysis of thousands of genes. In the field of toxicology, microarray analysis can be used to identify individual genes or families of genes regulated during adverse drug reactions. Such information provides us with a more detailed understanding of the molecular mechanisms underlying toxic effects. Additionally, microarray technology can be used to identify gene expression profiles for new therapeutic compounds, thus providing an early screening method for potential toxic effects. An important step in using microarray analysis in toxicity screening is to construct a library of genes that are regulated positively or negatively during hepatotoxicity, as these genes may not be represented in libraries prepared from normal tissue. In order to facilitate this, we have treated rats with hepatotoxins representing diverse structural and therapeutic classes. These compounds induce a variety of hepatotoxic responses including peroxisomal proliferation, hepatic necrosis and apoptosis, cholestasis, DNA damage, protein synthesis inhibition, oxidative stress, mitochondrial damage, P-450 induction and phospholipidosis. The livers were harvested from the treated rats and mRNA was isolated. The mRNA was pooled and gene expression analysis of treated versus untreated rats was assayed using microarray analysis. The data gathered from microarray and sequence analysis allows us to identify signature sets of genes regulated during toxicity. These gene responses are then used to identify mechanisms of toxicity. Knowledge of specific toxicologic pathways can help determine potential human liabilities, and the identification of signature gene sets can be used to evaluate drug candidates for potential adverse effects. In a follow-up case study, using microarrays, we evaluated changes in gene expression in rat liver associated with hypertrophy, hyperplasia and single cell necrosis (apoptosis) following administration of a drug candidate.

Genetics of asthma and atopy

Asthma and airways hyperresponsiveness are the respiratory manifestations of sensitization to exogenous materials including protein allergens and chemical sensitizers that may trigger ongoing inflammation and respiratory symptomatology in those people who are predisposed to develop the asthmatic syndrome. That genetics plays a major role in this particular syndrome is without question, since twin studies have shown a greater prevalence of disease for monozygotic as opposed to dizygotic twins. There have been the beginnings of the development of an approach to a number of candidate genes for major genetic input in the asthmatic syndrome. However, unlike cystic fíbrosis or even other autoimmune and inflammatory diseases such as juvenile diabetes and/or multiple sclerosis, a single gene or a significant set of major genes may not be easily identified. Rather the small contribution of multiple genes and/or sets of genes may be summed together and added to environmental exposure in people who will develop asthmatic syndromes. The identification of a genetic component to asthma would be of great significance. Even without a major or predominant gene, identification of the minor sets of genes interacting to cause asthma would represent a great advance. Knowledge of those minor genetic alleles involved in asthma susceptibility would allow great latitude in offering diagnostic screening and new therapeutic interventions in asthma.