Project description:Here we focus on the function of BRG1 in colitis and colitis-associated-cancer, in the aim of finding the direct target genes of BRG1 which may response for the phenotype we observed in BRG1 conditional knock-out mice, ChIP-Seq assay is used. The cells used for ChIP-Seq is colon epithelial cells which isolated from DSS treated mice.
Project description:We demonstrate single-cell RNA sequencing with time course study on DSS-induced colitis mouse model to reveal the overall cellular status during colon inflammation. Based on single cell transcriptome analysis in inflamed colon, we showed that the stromal cell population of colon functions as a hub to coordinate dynamic change with other cell type. We also found the Serpina3n, a serine protease inhibitor is specific up-regulation in the stromal cells during the resolution phase of colon inflammation. Furthermore, we found that systemic administration of Serpina3n promoted the recovery of resolution phase and ameliorated colitis-related symptoms. This study provides a comprehensive understanding of cell-cell interactions during colorectal inflammation at the single-cell level and reveals a potential therapeutic target by hijacking the endogenous inflammation resolution mechanism.
Project description:The SWI/SNF complex remodels chromatin in an ATP-dependent manner through the ATPase subunits BRG1 and BRM. Chromatin remodeling alters nucleosome structure to change gene expression, however aberrant remodeling and gene expression can result in cancer. The function and localization on chromatin of the SWI/SNF complex depends on the protein makeup of the complex. Here we report the protein-protein interactions of wild-type BRG1 or mutant BRG1 in which the HSA domain has been deleted (BRG1-HSA). We demonstrate the interaction of BRG1 with most SWI/SNF complex members and a failure of a number of these members to interact with BRG1-HSA. These results demonstrate that the HSA domain of BRG1 is a critical interaction platform for the correct formation of SWI/SNF remodeling complexes.
Project description:Purpose: To validate the novel ColoType assay for computing consensus molecular subtypes of colon cancer tumor samples Method: Whole-genome RNA-sequencing of colon cancer samples from formalin-fixed paraffin-embedded (FFPE) provided data for consensus molecular subtyping samples using multiple independent methods, including the novel ColoType method. A custom Illumina AmpliSeq library was also used to implement ColoType on these samples by targeted RNA-sequencing. Results: Multiple independent methods for computing CMS subtypes for FFPE colon cancer samples have widespread agreement with ColoType assay.
Project description:To determine the molecular regulation of ILC3s by Brg1, small intestinal ILC3s (Lin-Thy1highCD45low) from Brg1-deficient and control ILC3s were subjected to assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq).
Project description:Here we show that epithelial BRG1, the catalytic subunit of SWI/SNF complex is critical for colitis and colitis-associated-cancer. Depletion of BRG1 in colonrectal epithelial cells make mice develop Spontaneous colitis. To dissect underlying mechanism, we conducted gene expression profile analysis (RNA-Seq) by using primary colonrectal epithelial cells isolated from BRG1CTRL and BRG1IEC-KO(Tamoxifen induced BRG1 knock-out) mice to gain molecular insights into the affected biological processes. To this end, colorectal epithelial cells were isolated after 14 days of tamoxifen treatment, on which day BRG1-depleted mice showed little morphological defects in colon in comparison with control littermates. IECs were isolated by EDTA isolation buffer. Each sample contains pooled mRNA from 3 mice, and was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
Project description:siRNA mediated knockdown of BRG1/SMARCA4 in scratch wounded cell culture PHEKs, used to identify specific BRG1/SMARCA4 dependent gene expression programs which are initiated during immediate and early (1h and 24h) epithelial wounding. 3 human donors.
Project description:Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in SCCOHT cell lines +/- BRG1 re-expression. BRG1 re-expression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant negative AP-1 cell line, we found that both AP-1 DNA binding activity and BRG1 re-expression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that BRG1 re-expression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon AP-1 activity.