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Transcriptome analysis of DSS-treated DOK3-deficient and wildtype mouse colonic cells

ABSTRACT: Transcriptome analysis of DSS-treated DOK3-deficient and wildtype mouse colonic cells

PROVIDER: PRJNA774736 | ENA |

REPOSITORIES: ENA

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Transcriptome analysis of DSS-treated DOK3-deficient and wildtype mouse colonic cells

Project description:How pathogenesis of inflammatory bowel disease (IBD) depends on the complex interplay of host genetics, microbiome and the immune system is not fully understood. Here, we showed that Downstream of Kinase 3 (DOK3), an adaptor protein involved in immune signaling, confers protection of mice from dextran sodium sulfate (DSS)-induced colitis. DOK3-deficiency promotes gut microbial dysbiosis and enhanced colitis susceptibility, which can be reversed by the transfer of normal microbiota from wild-type mice. Mechanistically, DOK3 exerts its protective effect by suppressing JAK2/STAT3 signaling in colonic neutrophils to limit their S100a8/9 production, thereby maintaining gut microbial ecology and colon homeostasis. Hence, our findings reveal that the immune system and microbiome function in a feed-forward manner, whereby DOK3 maintains colonic neutrophils in a quiescent state to establish a gut microbiome essential for intestinal homeostasis and protection from IBD.

2021-11-10 | GSE186597 | GEO

H3K27ac profiling in control and DSS-treated colonic epithelium

Project description:We determined changes in enhancer chromatin that occur during colonic inflammation, found that dynamic chromatin regions are enriched for HNF4A binding motirfs, and then measured HNF4A binidng by ChIP-seq in each condition. Examination of H3K27ac histone modification in normal and DSS-treated colon, examination of HNF4A binding by ChIP-seq in normal and DSS-treated colon epithelium

2014-06-30 | E-GEOD-52426 | biostudies-arrayexpress

Gene expression analysis in Tyk2 deficient AOM/DSS colorectal tumors in mice

Project description:The goal of this study was to determine differences in gene expression profiles in colonic tumors of AOM/DSS treated mice with a total (Tyk2KO) or conditional deletion of Tyk2 in the intestinal epithelium (Tyk2DIEC).

2022-07-01 | GSE202954 | GEO

Transcriptomic anlaysis of the early response of the colonic epithelium to colitis induction by dextran sodium sulfate (DSS)

Project description:We compared the transcriptional signatures of the colonic mucosa from control mice (WT) versus mice deficient for the epithelial pantetheinase Vnn1 (Vnn1KO) or overexpressing Vnn1 specifically in intestinal epithelial cells (VIVA transgenic mice), during the development of DSS-induced colitis.

2022-11-24 | GSE174166 | GEO

Colonic gene expression data of acute and chronic dextran sodium sulphate (DSS) colitis mice

Project description:The lack of suitable animal models reflecting chronically relapsing inflammation and tissue remodeling have hindered fibrosis research in inflammatory bowel diseases (IBD). This study investigated changes in connective tissue in a chronic murine model using different cycles of dextran sodium sulphate (DSS) to mimic the relapsing nature of the disease. We used whole gene expression arrays to study differences in colonic gene expression levels between acute and more chronic DSS colitis, Acute and chronic relapsing colonic inflammation was induced in C57BL6 female mice using several cycles of exposure to DSS in drinking water, followed by recovery phases. Total RNA, extracted from snap frozen colon from five mice per condition was used to analyze mRNA expression via Affymetrix Mouse Gene 1.0 ST arrays.

2013-09-03 | E-GEOD-42768 | biostudies-arrayexpress

miRNome of colonic crypt stem cells from DSS-induced colitis mice

Project description:To identify potential unique miRs that contribute to shaping the intestinal stemness in colitis, we analyzed the miRNome of colonic crypt stem cells from DSS-induced colitis mice.

2019-09-24 | GSE137892 | GEO

Expression data from untreated and DSS-treated Adamts12 WT and KO mice

Project description:Adamts12-deficient mice undergo more severe colitis than WT mice after induction with DSS. We used microarrays to determine the gene expression differences between Adamts12-deficient and WT mice during ulcerative colitis induced with DSS (dextran sodium sulfate) Fragments of distal colon from DSS-treated (2% DSS during 7 days and 1 day of recovery) and untreated Adamts12-deficient and WT mice were obtained for RNA extraction and hybridiztion with Affymetrix microarrays

2012-09-01 | E-GEOD-40529 | biostudies-arrayexpress

Temporal transcriptional profiles of colonic tissue during DSS-induce colitis

Project description:Inflammation dramatically alters the gut microenvironment. To investigate the transcriptome changes the temporal profile of multiple signaling pathways throughout the progression of colitis, we collected the colonic tissue at a series of time points during DSS colitis for bulk RNA sequencing.

2022-09-06 | GSE210405 | GEO

Expression data from the isolated mouse colonic epithelial cells during colon inflammation induced by DSS

Project description:We used microarray to examine microRNA expression in the mouse colonic epithelial cells changed after DSS treatment

2016-01-23 | GSE77117 | GEO

Loss of colonic primary cilia promotes inflammation and carcinogenesis

Project description:Primary cilia (PC) are important signaling hubs in cells and we explored their role in colorectal cancer (CRC) and colitis. In the colon we found PC to be mostly present on different subtypes of fibroblasts and exposure of mice to either chemically induced colitis-associated colon carcinogenesis (CAC) or dextran sodium sulfate (DSS)-induced acute colitis decreased PC numbers. We employed conditional knock-out strains for the PC essential genes, Kif3A and Ift88, to generate mice with reduced numbers of PC on colonic fibroblasts. These mice showed an increased susceptibility in the CAC model as well as in DSS-induced colitis. Secretome and immunohistochemical analyses of DSS-treated mice displayed an elevated production of the pro-inflammatory cytokine IL-6 in PC-deficient colons. An inflammatory environment diminished PC presence in primary fibroblast cultures. This was triggered by IL-6 as identified by RNAseq analysis together with blocking experiments, suggesting an activation loop between IL-6 production and PC loss. Notably, an analysis of PC presence on biopsies of patients with ulcerative colitis as well as CRC patients revealed decreased numbers of PC on colonic fibroblasts in pathological versus surrounding normal tissue. Taken together, we provide evidence that a decrease in colonic PC numbers promotes colitis and CRC.

2022-11-29 | PXD033440 | Pride

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