Identification of gene expression signature of LILRA3 stimulation
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Hui Zhi Low
PROVIDER: E-GEOD-61356 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Inflammation is a hallmark of multiple disease processes, including inflammatory bowel disease (IBD). The transcription factor NF-kappaB plays a critical role in this response through its effects on pro-inflammatory gene expression. Consequently, homeostatic mechanisms that control NF-kappaB activity have been found to play important roles in controlling inflammatory responses in physiologic and pathologic states. Copper Metabolism Murr1 Domain containing 1 (COMMD1), a regulator of copper excretion and other transport pathways, has been shown to play a role in limiting NF-kappaB activation. However, it remains unclear if this factor plays a necessary role in the control of inflammation or in the pathogenesis of inflammatory disorders in vivo. Using a myeloid-cell specific model of Commd1 deficiency in mice we evaluated the contribution of this factor to inflammatory responses. We found that this gene plays an important role as a negative regulator of the LPS transcriptional response, and deficiency in this factor led to sensitization to in vivo models of sepsis. In addition, we identified single nucleotide variants located near COMMD1 that are associated with decreased expression of this gene in humans. Interestingly, these polymorphisms also show a suggestive association signal with ulcerative colitis risk. Consistent with the possibility that genetic variation in COMMD1 expression may predispose to colitis, we find that myeloid deletion of Commd1 leads to more severe colonic inflammation and cancer progression in experimental colitis models. Altogether, the data support the notion that COMMD1 expression in myeloid cells plays an important anti-inflammatory role in physiologic states and human disease. Bone marrow derived macrophages (BMDM) were isolated from two individual wildtype - and two Commd1 knockout mice. Cells from individual mice were splitted and were treated with LPS for 3h, 24h, or, were left untreated. The corresponding 12 cell samples were subjected to total RNA preparation and subsequently used for Single-Color-based Microarray Analysis (Agilent Technologies).
2014-05-19 | E-GEOD-53368 | biostudies-arrayexpress
Project description:The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of the TAK1-controlled NF-M-NM-:B subunit p65 in relation to active enhancers and promoters of transcribed genes by ChIP-seq experiments. Out of 35,000 active enhancer regions, 410 H3K4me1-positive enhancers show interleukin (IL)-1-induced H3K27ac and p65 binding. Inhibition of TAK1, IKK2 or depletion of p65 blocked inducible enhancer activation and gene expression. As exemplified by the CXC chemokine cluster located on chromosome 4, the TAK1-p65 pathway also regulates the recruitment kinetics of the histone acetyltransferase CBP, of NF-M-NM-:B p50 and of AP-1 transcription factors to both, promoters and enhancers. This study provides a high resolution view of epigenetic changes occurring during the IL-1 response and allows the first genome-wide identification of a novel class of inducible p65 NF-M-NM-:B-dependent enhancers in epithelial cells. Two sets of experiments were performed as biological replicate series (rep1 and rep2) each comprising of the following 4 conditions: Human epithelial KB cells were 1) left untreated or were 2) treated with Interleukin-1-alpha (10ng/M-BM-5l) for 1 hour, 3) treated for 1.5h with the TAK1 inhibitor 5Z-7-oxozeaenol (1M-BM-5M) or were 4) treated with 5Z-7-oxozeaenol for 30 minutes followed by Interleukin-1-alpha for 1 hour.
2014-12-17 | E-GEOD-64201 | biostudies-arrayexpress
Project description:Intestinal epithelial cells were isolated from total small intestine of each four 28-day old conventionally raised (conv) and germ-free (GF) bred C57BL/6 mice (protocol according to: Lotz et al., J. Exp Med. 2006). Total RNA was isolated by TriZol and ist purity was examined using a Bioanalyszer. We used microarrays to comparatively detail the global gene expression in primary total isolated intestinal epithelial cells. Four biological replicates from isolated intestinal epithelial cells obtained from each 4 germ-free bred and conventionally raised mice. Colour change.
2012-05-16 | E-GEOD-35597 | biostudies-arrayexpress
Project description:1-day-old C57BL/6 mice were left untreated (co) or orally infected with 10E2 CFU wildtype (wt) or delta invC SPI1 mutant Salmonella Typhimurium (ATCC14028). Four biological replicates obtained from individual animals were exmained; each group contained animals from at least 2 different litters. On day 4 p.i., animals were sacrificed and intestinal epithelial cells were isolated from total small intestine (protocol according to: Lotz et al., J. Exp. Med. 2006). Total RNA was isolated by TriZol and its purity was examined using a Bioanalyzer. We used microarrays to detail the global gene expression in primary total isolated intestinal epithelial cells. Four biological replicates of isolated intestinal epithelial cells obtained 4 daysp.i. from neonate mice infected at the age of 1 day (each group with animals from at least two litteres). Single color array.
2014-09-01 | E-GEOD-51160 | biostudies-arrayexpress
Project description:Intestinal epithelial cells of 28-day-old female mice were isolated according to a recently published protocol (Lotz et al., J Exp. Med. 2006). Isolated intestinal epithelial cells of four individual animals (four biological replicates) were examined. Single color array.
2014-08-23 | E-GEOD-51269 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-12-16 | E-GEOD-64224 | biostudies-arrayexpress
Project description:Chlamydomonas reinhardtii exposed to various concentrations of silver For this experiment,C. reinhardtii were exposed to (4) different concentrations of silver, as biological triplicates
2013-10-01 | E-GEOD-48677 | biostudies-arrayexpress
Project description:HTLV-1 preferentially infects CD4+ T cells and these cells play a central role in HTLV-1 infection. In this study, we investigated the global gene expression profile of circulating CD4+ T cells from distinct clinical status of HTLV-1-infected individuals in regard to Tax expression levels. CD4+ T cells were isolated from asymptomatic HTLV-1 carrier (HAC) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients, in order to identify genes involved in the HAM/TSP development. Hierarchical clustering analysis showed that healthy controls (CT) and HTLV-1-infected samples clustered separately. We also observed that HAC and HAM/TSP groups clustered separately regardless Tax expression. The gene expression profile of CD4+ T cells was compared among CT, HAC and HAM/TSP groups. The IL-27, PXN, CXCR4, GZMA, PRF1 and Foxp3 genes were differentially expressed between HAC and HAM/TSP groups and the frequency of CD4+Foxp3+ regulatory T cells (Treg) were higher in HTLV-1-infected individuals. These findings suggest that CD4+ T cells activity is distinct between HAC and HAM/TSP groups as expected. In order to study the transcriptional changes in CD4 T cell from HTLV-1-infected individuals, immunomagnetically purified CD4+ T-cells from the peripheral blood of 4 asymptomatic HTLV-1 carrier individuals (HAC) and 4 individuals with HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP), as well as from 4 healthy controls (CT) were isolated and processed the microarray assay according Agilent's protocol. The differential expressed genes, molecular characterization and networks analysis were evaluated using robust bioinformatic tools, then the real time PCR was done to validate the genes.
2013-06-01 | E-GEOD-38537 | biostudies-arrayexpress
Project description:Using whole-genome Affymetrix microarrays (HG-U133A), we characterized the transcriptome profile of cultured human macrophages stimulated for 4 h with interleukin 1 (IL-1) or interleukin 6 (IL-6). We found that, in distinction to liver cells, IL-1 is much more potent than IL-6 in modifying macrophage gene expression, although considerable heterogeneity in response of macrophages deriving from individual blood donors was observed. The obtained results permitted to identify a large number of cytokine-responsive genes. coding for proteins of unknown function that are now being studied in our laboratory. They may represent novel targets in the anti-inflammatory therapy. Experiment Overall Design: Analysis of the transcriptome of human monocyte-derived macrophages stimulated in vitro by low doses of IL-1 or IL-6.
2008-06-16 | E-GEOD-8515 | biostudies-arrayexpress
Project description:We applied a custom tiled microarray to examine murine gammaherpesvirus 68 (MHV68) polyadenylated transcript expression in a timecourse of de novo infection of fibroblast cells and following phorbol ester-mediated reactivation from a latently-infected B cell line. During de novo infection, all ORFs were transcribed and clustered into four major temporal groups that were overlapping, yet distinct from clusters based on the phorbol ester-stimulated B cell reactivation timecourse. High-density transcript analysis at two-hour intervals during de novo infection mapped gene boundaries with a 20-nt resolution, including a previously undefined ORF73 transcript and the MHV68 ORF63 homolog of KSHV vNLRP1. ORF6 transcript initiation was mapped by tiled array and confirmed by 5' RACE. The ~1.3 kb region upstream of ORF6 was responsive to lytic infection and MHV68 RTA, identifying a novel RTA-responsive promoter. Transcription in intergenic regions consistent with the previously defined expressed genomic regions was detected during both types of productive infection. We conclude that the MHV68 transcriptome during de novo fibroblast infection and upon phorbol ester-stimulated B cell reactivation is dynamic and distinct, highlighting the need to evaluate further transcript structure and the context-dependent molecular events that govern viral gene expression during chronic infection. This SuperSeries is composed of the following subset Series: GSE35863: Tiled Array Experiment of Murine Gammaherpesvirus 68 Transcripts In Newly Infected Fibroblasts GSE35865: Tiled Array Experiment of Murine Gammaherpesvirus 68 Transcripts Upon TPA-Stimulated Reactivation From Latency Refer to individual Series
2012-02-16 | E-GEOD-35866 | biostudies-arrayexpress