Mycobacterium tuberculosis microarray to screen anti-tuberculosis compounds
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ABSTRACT: Feature reduction of microarray data from mycobacteria treated with a variety of various clinical and investigational drugs We are using feature reduction to demonstrate that subsets of biomarker genes representative of the whole genome are sufficient for MOA classification and deconvolution in a medium-throughput microfluidic format ultimately leading to a cost effective and rapid tool for routine antibacterial drug-discovery programs.
Project description:To understand the mechanism of action of the RelE family of toxins on metabolism of Mycobacterium tuberculosis. To this effect, toxin expression was induced under control of a tetracycline regulatable promoter and transcriptional profiles compared during overexpression of the three RelE toxin family members. Profiles were also compared to previously published profiles of drugs of known mechanism of action against this organism. For the design, RNA isolated from cells where toxin expression was induced with anhydrotetracycline was converted to Cy5-labeled cDNA whereas RNA derived from cells in which toxin expression was not induced (treated with ethanol solvent only) was converted to Cy3-labeled cDNA. Time points were taken for each overexpression condition. Treatments were performed indepedently a minimum of two times to give independent biological replicates.
Project description:The genomic diversity of 38 Bartonella henselae isolates was studied by comparative genomic hybridizations. In addition, the effect of growth time (5 or 10 days) was studied for 5 strains.
Project description:The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma Keywords: lymphochip; MCL; untreated Tumor biopsies from 71 untreated patients with mantle cell lymphoma
Project description:Using microarray gene expression profiling of liver RNA samples rerived from IRF2+/+ and IRF2-/- mice treated with saline or LPS, we identified >40 genes that were significantly down-regulated in IRF2 -/- mice, including STAT3 which has been reported to regulate apoptosis. Keywords: compound treatment design We compared gene expression in IRF2+/+ and IRF2-/- mice treated with Saline or LPS for 3 or 6 hours. Two repeats were done for the LPS treatments. The total number of arrays is 6.
Project description:Activation of NFkB pathway by CARD11 Cy3-labelled untreated sample and Cy5-labelled treated sample were hybridized to a Lymphochip microarray.
Project description:Gene expression profiles reflect unique aspects of individual biologic phenotypes and may characterize the heterogeneity of solid tumors. Using previously-described methodologies that employ DNA microarray data, a 50-gene expression profile (metagene) that predicts risk of recurrence in early stage colon carcinoma was identified. This analysis used an initial discovery cohort of 52 patients. The performance of the 50-gene predictor was evaluated in an independent validation cohort of 73 patients. Using a connectivity map analysis of the 50-gene model, we identified candidate agents and then tested the in vitro efficacy of these compounds in colon cancer cell lines. 73 samples that had patient recurrence data with stage information were used in the analysis. Keywords: Disease state analysis A total of 73 samples were spotted on microarray slides. No replicates are included in the study.
Project description:The variability in the prognosis of hepatocellular carcinoma (HCC) patients suggests that HCC may comprise several distinctive biological phenotypes. These phenotypes may result from different neoplastic pathways during the tumorigenesis and/or from a different cell of origin. Here we address if the transcriptional characteristics of the HCC would provide insight into the cellular origin of the tumors. We integrated gene expression data from rat fetal hepatoblasts and adult hepatocytes, HCC from mouse models, and human HCC. The HCC patients who shared gene expression patterns with fetal hepatoblasts showed extremely poor prognosis when compared with those lacking the hepatoblast signature. The gene expression program that distinguishes this novel subtype from the rest of HCC includes well known markers of hepatic oval cells, suggesting that HCC in this subtype may arise from hepatic progenitor cells. Two independent gene network analyses of the gene expression signature characteristic for the tumors sharing the hepatoblast expression patterns revealed that activation of AP-1 transcription factors might play key roles in tumor development in the newly identified HCC subtype. In addition, by applying hepatoblast-specific and genome-wide global signatures, HCC patients were further stratified into three distinct subgroups with a significant association with overall survival and recurrence. Total RNAs from 19 normal livers were pooled and used as the reference for all microarray experiments. To obtain gene expression profile data from 49 human HCC, 20 µg of total RNAs from tissues were used to drive fluorescently (Cy-5 or Cy-3) labeled cDNA. At least two hybridizations were carried out for each tissue using a dye-swap strategy to eliminate dye labeling bias.
Project description:To identify the prognostic subtypes of hepatocellular carcinoma with potential progenitor cell origin. Keywords: disease state design We used our in-house oligonucleotide microarray data of 238 HBV-positive HCC cases.
Project description:The plasmacytoid dendritic cell (pDC) is vital to the coordinated action of innate and adaptive immunity. pDC development has not been unequivocally traced, nor has its transcriptional regulatory network been fully clarified. Here we confirm an essential requirement for the BCL11A transcription factor in fetal pDC development, and demonstrate this lineage-specific requirement in the adult organism. Furthermore, we identify BCL11A gene targets and provide a molecular mechanism for its action in pDC commitment. Embryonic germ-line deletion of Bcl11a revealed an absolute cellular, molecular, and functional absence of pDCs in fetal mice. In adults, deletion of Bcl11a in hematopoietic stem cells resulted in perturbed yet continued generation of progenitors, loss of downstream pDC and B-cell lineages, and persisting myeloid, conventional dendritic, and T-cell lineages. Challenge with virus resulted in a marked reduction of antiviral response in conditionally deleted adults. Genome-wide analyses of BCL11A DNA binding and expression revealed that BCL11A regulates transcription of E2-2 and other pDC differentiation modulators, including ID2 and MTG16. Our results identify BCL11A as an essential, lineage- specific factor that regulates pDC development, supporting a model wherein differentiation into pDCs represents a primed "default" pathway for common dendritic cell progenitors. Raji cells were infected with retroviruses containing pXY-PURO (negative control vector) or pXY-BCL11A-XS. BJAB cells were infected with retroviruses containing pXY-PURO (negative control vector) or pXY-BCL11A-XL. Two arrays measured Raji BCL11A-XS expression and two arrays measured BJAB BCL11A-XL expression.