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Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients [scRNA-seq]

ABSTRACT: Total proctocolectomy with ileal pouch anal anastomosis (IPAA) is the standard treatment for patients with severe treatment resistant ulcerative colitis (UC). Despite significant improvements in patient outcomes, up to 50% of patients will develop inflammation of the pouch (pouchitis) within 1-2 years following surgery. The pathogenesis of pouchitis is not well understood. Functionalization of UC pouches is associated with histological changes, whether these reflect changes in cellular identity and metaplasia remains unclear. To address this question, we generated cellular atlases of single-cell transcriptomes and accessible chromatin to assess the cellular composition, transcriptomic and epigenetic profiles in UC pouches.

ORGANISM(S): Homo sapiens

PROVIDER: GSE242086 | GEO | 2023/11/15

REPOSITORIES: GEO

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Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients [scATAC-seq]

Project description:Total proctocolectomy with ileal pouch anal anastomosis (IPAA) is the standard treatment for patients with severe treatment resistant ulcerative colitis (UC). Despite significant improvements in patient outcomes, up to 50% of patients will develop inflammation of the pouch (pouchitis) within 1-2 years following surgery. The pathogenesis of pouchitis is not well understood. Functionalization of UC pouches is associated with histological changes, whether these reflect changes in cellular identity and metaplasia remains unclear. To address this question, we generated cellular atlases of single-cell transcriptomes and accessible chromatin to assess the cellular composition, transcriptomic and epigenetic profiles in UC pouches.

2023-11-15 | GSE242085 | GEO

Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets

Project description:The pathophysiology of Crohn’s-like disease of the pouch (CDP) that develops after restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) is unknown. We examined mucosal cells from patients with and without CDP using single cell analyses.

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Pouch transcriptional differences between UC and FAP indicate altered immune response.

Project description:A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and selected patients with ulcerative colitis (UC). However, this surgical treatment often associates with a long-term complication, pouchitis, which occurs mostly in UC patients. To better define the molecular background of pouchitis, the microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients operated for UC and FAP, respectively. A number of 4771 genes was significantly differentiating uninflamed from inflamed mucosal samples, and their functional features were represented mostly by alerted metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed probe sets between UC and FAP samples, irrespectively of mucosal inflammation status, revealed multiple pathways and terms which were linked to changes in immune response. Noteworthy, the comparison of uninflamed UC and FAP samples distinguished a set of 26 altered mRNAs including inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most discrete changes in gene expression profiles differentiating uninflamed UC and FAP mucosal samples were attributed to a Gene Ontology category innate immune response. Our study confirmed alterations of the immune responses as dominant in UC pouchitis which were earlier found in the studies using analyses of singular molecular elements. This observation may be important when managing IPAA patients. Each sample represents three biopsies taken from single patient, from the same areas of the lower part of the pouch mucosa (above the rectal cuff) during endoscopic examination. 28 patients underwent surgery for UC and 8 patients for FAP.

2014-05-01 | E-GEOD-50788 | biostudies-arrayexpress

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

2015-01-27 | GSE65270 | GEO

Pouch transcriptional differences between UC and FAP indicate altered immune response.

2014-05-01 | GSE50788 | GEO

Microarray analysis from paired biopsies from ileal pouch-anal anastomosis surgery patients with ulcerative colitis and familial adenomatous polyposis

Project description:Pouchitis is a common complication for ulcerative colitis (UC) patients with ileal pouch-anal anastomosis (IPAA) surgery. Similarly to IBD, both innate host factors such as genetics, and environmental stimuli including the tissue-associated microbiome have been implicated in the pathogenesis. In this study, we make use of the IPAA model of inflammatory bowel disease (IBD) to carry out a study associating mucosal host gene expression with the microbiome and corresponding clinical outcomes. In order to determine how host gene expression might influence, or be influenced by the tissue associated microbiome, we analyzed 205 IPAA patients with biopsies collected from the pouch and afferent limb for host transcriptomics and 16S rDNA gene sequencing. Metadata included antibiotic use, inflammation score, and clinical classification. To achieve power for a genome-wide microbiome-transcriptome association study, we used principal component analysis to reduce OTUs and host transcripts to eigengenes and eigenclades explaining 50% of observed variance. These were subsequently tested for significant covariation with one another and/or outcome using multivariate linear modeling.

2015-01-27 | E-GEOD-65270 | biostudies-arrayexpress

Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis

Project description:Restorative proctocolectomy with ileal pouch-anal anastomosis is a surgical procedure in patients with ulcerative colitis refractory to medical therapies. Pouchitis, the most common complication, is inflammation of the pouch of unknown etiology. To define how the intestinal immune system is distinctly organized in response to inflammation and to develop mechanistic hypotheses of pouchitis, we analyzed tissues from patients with and without pouchitis and from patients with ulcerative colitis using single-cell RNA sequencing. We examined pouch lamina propria CD45+ hematopoietic cells from intestinal tissues of ulcerative colitis patients with (n=15) and without an ileal pouch-anal anastomosis (n=11). Further in silico meta-analysis was performed to generate transcriptional interaction networks and identify drug targets for patients with inflamed pouches. We identified a population of IL1B+ antimicrobial macrophages and FOXP3+/BATF+ T cells that are expanded in inflamed tissues, which we further validated in other single cell RNA-seq datasets from IBD patients. Cell type specific markers obtained from single-cell RNA-sequencing was used to infer representation from bulk RNA sequencing datasets, which further implicated antimicrobial macrophages expressing IL1B with S100A8/A9 calprotectin as being associated with inflammation, and Bacteroidiales and Clostridiales bacterial taxa. We found that non-responsiveness to anti-integrin biologic therapies in ulcerative colitis patients was associated with the signature of this antimicrobial macrophage population in a subset of patients. This study identified conserved and distinct features of intestinal inflammation between parts of the small and large intestine undergoing similar inflammation conditions. Specifically, we relate inflammation of the pouch, a surgically constructed organ, to other inflammatory contexts throughout the gastrointestinal tract.

2020-12-01 | GSE162335 | GEO

Insights into ulcerative colitis and ileal pouchitis from a model of stasis-induced enteric dysbiosis and genetic susceptibility

Project description:Gut dysbiosis and host genetics are implicated as causative factors in inflammatory bowel disease, yet mechanistic insights are lacking. Longitudinal analysis of ulcerative colitis patients following total colectomy with ileal anal anastomosis (IPAA) where >50% develop pouchitis, offers a unique setting to examine cause vs. effect. To recapitulate human IPAA, we employed a mouse model of surgically-created blind self-filling (SFL) and self-emptying (SEL) ileal loops. SFL exhibit fecal stasis due to directional peristalsis motility oriented towards away from the loop end, whereas SEL remain empty. In wild type mice, SFL, but not SEL, develop pouch-like microbial communities without accompanying active inflammation. However, in genetically susceptible IL-10-/- deficient mice, SFL, but not SEL, exhibit severe inflammation and mucosal transcriptomes resembling human pouchitis. Germ-free IL10-/- mice conventionalized with wild type SFL, but not SEL, microbiota, develop severe colitis. These data demonstrate an essential role for fecal stasis, gut dysbiosis, and genetic susceptibility and offer insights into human pouchitis and ulcerative colitis.

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Ileal pouch transcriptomics reveal shared pathogenesis between pouchitis and ulcerative colitis

Project description:UC pouchitis is a potential model of UC. We prospectively examined the pouch transcriptomes of UC and familial adenomatous polyposis (FAP) IPAA patients to unveil molecular mechanisms of UC pouchitis susceptibility. Methods: Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7. RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit. Results: Unlike FAP patients, UC subjects exhibited a large set of differentially expressed genes (DEGs) between pouch and pre-pouch mucosa as early as 4 months after pouch functionalization. Functional pathway analysis of DEGs in UC pouch revealed: (1) Gain of colon-associated gene expressions and loss of ileum associated gene expressions, (2) enhanced state of immune/inflammatory response, and (3) suppressed xenobiotic, lipid, and bile acid metabolic pathways. These changes were corroborated upon reanalysis of a published larger cross-sectional study of UC and FAP patients. Moreover, >70% of DEGs mapped to published IBD and normal colonic microarray datasets displayed directional changes consistent with active UC, but not Crohn's disease. Conclusions: UC patients exhibit a unique transcriptomic response to ileal pouch creation that can be observed well before disease. The transcriptome alterations provide insights into pouchitis

2016-05-11 | GSE81266 | GEO

Pouch metabolome

Project description:The goal of the study was to compare the influence of Ileal pouch-anal anastomosis (IPAA) surgical treatment on patients with ulcerative colitis (UC) vs those with familial adenomatous polyposis (FAP). Stool samples were obtained at the time of clinic visit, immediately frozen and stored at -80oC until the assay. There were no exclusion criteria.

2014-09-10 | ST000277 | MetabolomicsWorkbench

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