Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn’s Disease
Up to 40% patients with Crohn's disease suffer from perianal disease, a debilitating complication with unclear etiology. This study identified unique pathophysiology which may help develop novel therapies.
Participants15
Samples21
Reuse6.6/10
Study facts
Organism
Homo sapiens
Platform
10X Visium
Age group
adult
Disease groups
Crohn's disease, Non-IBD controls
Anatomical sites
Perianal Fistula
Data availability
Raw counts
Processed matrix
Spatial coordinates
Single-cell single-molecule spatial transcriptomics using CosMx on colectomy specimens collected during Pouch surgery in IBD patients.
<h4>Background and aims</h4>Total abdominal colectomy (TAC) with a staged ileal pouch-anal anastomosis (IPAA) is a common surgical treatment for ulcerative colitis (UC). However, a significant percentage of patients experience pouch failure, leading to morbidity. This retrospect…
Participants8
Samples8
Reuse7.0/10
Study facts
Organism
Homo sapiens
Platform
—
Age group
adult
Disease groups
Ulcerative colitis
Anatomical sites
Left colon, failure, Left colon, non-failure
Data availability
Raw counts
Processed matrix
Analysis code
Granzyme K CD8⁺ T cells with tissue-resident features promote intestinal inflammation in patients with Crohn’s disease
The role of CD8<sup>+</sup> T cells in Crohn's disease (CD) pathogenesis remains incompletely understood. This study aimed to characterize CD8<sup>+</sup> T cells in CD and elucidate their potential contribution to intestinal inflammation. T cells from blood and intestinal tissu…
Participants2
Samples45
Reuse8.1/10
Study facts
Organism
Homo sapiens
Platform
10x Genomics Visium and 10x Genomics Xenium
Age group
—
Disease groups
Crohn's disease
Anatomical sites
Lamina propria of the uninflamed small intestine, Submucosa of the uninflamed small intestine, Blood, Inflamed small intestine, Uninflamed small intestine, 10 µm section Inflamed small intestine
Data availability
Raw counts
Processed matrix
Spatial coordinates
Histology images
Analysis code
Elucidating the fibrotic niche and cellular dynamics in crohn’s disease-associated fibrostenosis
<h4>Background & aims</h4>Fibrostenosis is a major complication of Crohn's disease (CD) characterized by intestinal remodeling and excessive extracellular matrix (ECM) deposition. A prominent feature is bowel wall muscularization, involving expansion of submucosal myoid cells an…
Participants2
Samples2
Reuse7.4/10
Study facts
Organism
Homo sapiens
Platform
10x Genomics Visium HD
Age group
—
Disease groups
Crohn's disease
Anatomical sites
The strictured and fibrotic ileum sample from Crohn's disease patient., The non-strictured and non-fibrotic ileum sample from Crohn's disease patient.
Data availability
Raw counts
Processed matrix
Spatial coordinates
Histology images
Analysis code
Genetic profiles of small intestinal and colonic metaplastic Paneth cells by spatial transcriptomics
Paneth cell metaplasia (PCM) is a phenomenon in which Paneth cells, typically found in the small intestine, appear in the colonic epithelium of patients with ulcerative colitis (UC). Our study demonstrates that the PCM occurrence correlates with disease duration and active infla…
Imaging-based, single-cell, spatial transcriptomics (iSCST) of FFPE tissue enables comprehensive analysis of archived specimens while preserving spatial context, critical to an understanding of ulcerative colitis (UC) pathology. Here, we deployed a robust framework for applying …
Participants—
Samples7
Reuse7.9/10
Study facts
Organism
Homo sapiens
Platform
Xenium
Age group
—
Disease groups
—
Anatomical sites
Non-IBD controls and patients with ulcerative colitis (UC), Non-IBD controls and patients with either ulcerative colitis (UC) or immune checkpoint inhibitor-induced colitis (ICI)
Data availability
Raw counts
Processed matrix
Spatial coordinates
Analysis code
IBD CosMx NanoString data from colonic mucosa
Ulcerative colitis and Crohn's disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to ex…
Imaging-based, single-cell, spatial transcriptomics (iSCST) of FFPE tissue enables comprehensive analysis of archived specimens while preserving spatial context, critical to an understanding of ulcerative colitis (UC) pathology. Here, we deployed a robust framework for applying …
Participants—
Samples1
Reuse6.4/10
Study facts
Organism
Homo sapiens
Platform
MERSCOPE
Age group
—
Disease groups
—
Anatomical sites
Non-IBD controls and patients with ulcerative colitis (UC)
Data availability
Raw counts
Processed matrix
Spatial coordinates
Analysis code
Spatial and single cell transcriptomics reveals cellular crosstalk changes in ileal Crohn’s disease during inflammation
Crohn's disease (CD) involves a complex intestinal microenvironment driven by chronic inflammation. While single-cell RNA sequencing has provided valuable insights into this biology, the spatial context is lost during single-cell preparation of mucosal biopsies. To deepen our un…
Participants—
Samples24
Reuse6.3/10
Study facts
Organism
Homo sapiens
Platform
10x Genomics Visium
Age group
mixed
Disease groups
—
Anatomical sites
Ileal mucosal cells, Ileal Surgical tissue
Data availability
Raw counts
Spatial coordinates
Histology images
Analysis code
Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - Spatial Transcriptomics
The success of checkpoint inhibitors (CPIs) for cancer has been tempered by immune-related adverse effects including colitis. CPI-induced colitis is hallmarked by expansion of resident mucosal IFNγ cytotoxic CD8<sup>+</sup> T cells, but how these arise is unclear. Here, we track…
