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Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

ABSTRACT: Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

PROVIDER: PRJNA1054155 | ENA |

REPOSITORIES: ENA

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Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy CITE-seq]

Project description:Ulcerative colitis (UC) is a chronic inflammatory condition of the colon, driven by mucosal immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin monoclonal antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed a single-cell and spatial transcriptomic and proteomic analysis of peripheral blood and colonic biopsies in healthy controls (HC) and patients with UC on VDZ or other therapies. We identified significant effects of VDZ on mononuclear phagocyte (MNP) subsets, in addition to modest effects on lymphocyte populations. Spatial transcriptomics and proteomics of formalin-fixed, paraffin-embedded (FFPE) biopsies at single-cell resolution demonstrated trends towards increased abundance and proximity of activated MNP and fibroblast subsets in active colitis compared to HC, with inhibition by VDZ. Spatial transcriptomics of archived FFPE specimens pre-treatment identified epithelial-, MNP-, and fibroblast-enriched genes related to VDZ response versus non-response, and these were validated in an external, publicly accessible bulk transcriptomic dataset. Single cell and spatial multi-omics highlight important roles for myeloid, stromal, and epithelial subsets in UC.

2024-01-22 | GSE250490 | GEO

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [blood scRNA-seq]

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Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy scRNA-seq]

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Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy scRNA-seq]

Project description:Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy scRNA-seq]

| PRJNA1054148 | ENA

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [blood scRNA-seq]

Project description:Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [blood scRNA-seq]

| PRJNA1054167 | ENA

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy CITE-seq]

Project description:Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis [biopsy CITE-seq]

| PRJNA1054168 | ENA

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-01-22 | GSE250498 | GEO

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Project description:Ulcerative Colitis subjects

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Project description:Ulcerative colitis related gene expressions analysis in colonic biopsy samples from control and ulcerative colitis patients

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Project description:The series was designed to identify the different methylated single CpGs involved in the pathophysiology of ulcerative colitis. A cohort of n=20 monozygotic twins, discordant for ulcerative colitis was selected. Illumina and Nimblegen platforms were used.

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