Epigenetic changes induced by Bacteroides fragilis toxin (BFT) [ATAC-seq]
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ABSTRACT:
PROVIDER: PRJNA450440 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7012090_1.fastq.gz | Fastqsanger.gz | |||
| SRR7012090_2.fastq.gz | Fastqsanger.gz | |||
| SRR7012100_1.fastq.gz | Fastqsanger.gz | |||
| SRR7012100_2.fastq.gz | Fastqsanger.gz | |||
| SRR7012091_1.fastq.gz | Fastqsanger.gz |
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Project description:Epigenetic changes induced by Bacteroides fragilis toxin (BFT)
| PRJNA450439 | ENA
Project description:Epigenetic changes induced by Bacteroides fragilis toxin (BFT) [RNA-seq]
| PRJNA450654 | ENA
Project description:Aided by deep sequencing techniques, recent studies suggest the existence of distinct breast microbiota and a shift in microbial community composition in diseased breast compared to normal breast. However, their functional impact and underlying mechanisms are unknown. Present study examines the contribution of pro-carcinogenic bacteria in breast cancer initiation, growth and progression. Extensive data mining and metagenomic analyses of existing datasets revealed the presence of toxin producing Bacteriodes fragilis in malignant breast. B. fragilis is a pro-carcinogenic bacterium known for its potential to initiate and promote colon cancer; its pathogenicity has been attributed to its unique toxin ‘BFT’. About 35% of human population asymptomatically harbor ETBF colonization in the gut. Mice with enteric B fragilis infection exhibited a significant amount of circulating BFT and distinct morphological alterations in mammary gland similar to focal hyperplasia. Histological analysis revealed inflammation, fibrosis, breast duct thickening and hyperproliferation of breast epithelial cells. In vitro, upon treatment with BFT, prominent cytoskeletal reorganization, significant increase in migration and invasion potential and decreased adhesion of MCF10A and MCF7 cells were observed along with molecular markers of epithelial-to-mesenchymal transition. Decreased expression of epithelial marker, E-cadherin along with elevated levels of mesenchymal markers, N-cadherin and vimentin were observed. BFT also increased the expression of EMT-related transcription factors, Snail, Slug and Twist. BFT-treated cells attained stem cell-like phenotype exhibiting an increased ability to form secondary and tertiary mammospheres. Mechanistic studies showed that BFT induced expression and nuclear translocation of NICD and β-catenin resulting in activation of downstream targets. Inhibition of Notch1 and β-catenin using γ-secretase and β-catenin inhibitors successfully inhibited functional effects of BFT. Mammary gland implantation and in vivo limiting dilution assays were utilized to corroborate the in vitro findings. BFT-pretreated MCF7 cells exhibit increased tumor growth and form multifocal tumors in mice. In vivo limiting dilution assay using breast tumors from BFT-pretreated MCF7 cells exhibited a striking increase in tumor-initiating cells. Follow-up analyses of these tumors demonstrated increased migratory, invasive, and -mammospheres-forming behavior confirming that brief BFT exposure elicits long-term molecular changes. Altered expression of stemness markers was also confirmed by RNA sequencing.
2023-04-10 | GSE149241 | GEO
Project description:Purpose: The goal of this study is to determine how BFT2 alters chromatin accessibility at relatively early time points in colon epithelial cells, and to correlate the changes in chromatin accessibility with changes in gene expression, transcription factor binding sites, and the location of common single nucleotide variants (SNVs) and differentially methylated regions (DMRs) in colorectal cancer. Methods: HT29/C1 cells were plated at low density and allowed to grow for 4 days at 37C and 10% CO2. Afterwards, cells were either left untreated or treated with 100ng/mL BFT2 for 24 or 48 hours. After the specified time point, cells were counted and DNA was collected in order to prepare ATAC-seq libraries. ATAC-seq library was prepared as outlined by Buenrostro et al. (2013). The 4nM pooled ATAC-seq library was sequenced using the Illumina HiSeq. For each sample, three biological replicates were sequenced. After sequencing, the data was analyzed using the pipeline developed by the Kundaje lab, as outlined on ENCODE (Lee et al., 2016). Briefly, reads were trimmed, aligned and filtered using Bowtie2, and peaks were called using MACS2. The three replicate peak files were combined in order to create one consensus file for each treatment condition using an irreproducible discovery rate (IDR) threshold of 0.1. For all analyses, the “optimal set” consensus file was used. Results: Our data show that several genes are differentially expressed after BFT treatment and these changes correlate with changes in chromatin accessibility. This correlation is mediated by an increase in chromatin accessibility at particular transcription factor binding sites. Also, sites of increased chromatin accessibility are associated with a lower frequency of common single nucleotide variants (SNVs) in CRC and with a higher frequency of common differentially methylated regions (DMRs) in CRC. Conclusions: This study adds critical knowledge to our understanding of host-microbe interactions in the gut. While scientists have begun to analyze the effect of specific bacteria on the epigenome of colon epithelial cells, to date, no other studies have surveyed the effect of a specific bacterial toxin on chromatin accessibility in colon epithelial cells. We conclude that BFT2 alters chromatin accessibility in colon epithelial cells, and that these changes correlate with subsequent changes in gene expression. Also, sites of BFT2-induced increased chromatin accessibility are associated with a lower frequency of common single nucleotide variants (SNVs) in CRC and with a higher frequency of common differentially methylated regions (DMRs) in CRC.
2018-04-18 | GSE113219 | GEO
Project description:Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 double mutant compared to the wild-type strain. Keywords: expression analysis A six chip study using total RNA recovered from three separate wild-type cultures of Bacteroides fragilis NCTC 9343 and three separate cultures of a double mutant strain, Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2, in which ungD1 (BF1706) and ungD2 (BF2848) are deleted. Each chip measures the expression level of 4,302 genes from Bacteroides fragilis NCTC 9343 and the associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2010-04-15 | E-GEOD-7450 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp mutant strain and a Bacteroides fragilis NCTC 9343 delta-lfg mutant strain, each as compared to the wild-type strain. The mutations engineered into these strains interfere with B. fragilis protein glycosylation.
2010-08-06 | GSE12440 | GEO
Project description:Genome expression study of Bacteroides fragilis ATCC25285 strain containing the EcfO gene constitutively expressed from plasmid pFD340
2013-01-01 | GSE35536 | GEO
Project description:To elucidate whether Enterotoxigenic Bacteroides fragilis (ETBF) plays a role in colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of ETBF treated DLD-1 colorectal cancer cell lines.
2020-04-13 | GSE130152 | GEO
Project description:Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH triple mutant, compared to the wild-type strain. The mutations engineered into this strain render it acapsular. The mutants analyzed in this study are further described in Coyne, M. J., M. Chatzidaki-Livanis, L. C. Paoletti, and L. E. Comstock. 2008. Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis. PNAS 105(35):13098-13103 (PID 18723678). A six chip study using total RNA recovered from three separate wild-type cultures of Bacteroides fragilis NCTC 9343 and three separate cultures of a triple mutant strain, Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH, in which ungD1 (BF1706), ungD2 (BF2848), and six genes (BF3454 through BF3459) of the PSH capsular polysaccharide locus are truncated or deleted entirely. Each chip measures the expression level of 4,302 genes from Bacteroides fragilis NCTC 9343 and the associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2008-09-02 | E-GEOD-11268 | biostudies-arrayexpress
Project description:Genome expression study of Bacteroides fragilis strain 638R comparing a EcfO null mutant with an empty vector to a anti-EcfO null mutant containing the EcfO gene on a plasmid under the control of an IPTG inducible promoter.
2013-01-01 | GSE35537 | GEO