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Related Concept Videos

Inflammatory Bowel Disease III: Crohn's Disease01:25

Inflammatory Bowel Disease III: Crohn's Disease

Crohn’s disease is a chronic, relapsing form of inflammatory bowel disease characterized by segmental, transmural inflammation that can affect any part of the gastrointestinal tract. Its pathogenesis arises from a combination of genetic susceptibility, environmental exposures, epithelial barrier dysfunction, and immune dysregulation. Together, these factors lead to an exaggerated immune response against components of the gut microbiome.Genetic and Environmental InfluencesMultiple genetic...
Inflammatory Bowel Disease I: Ulcerative Colitis01:27

Inflammatory Bowel Disease I: Ulcerative Colitis

Introduction
Inflammatory bowel disease, or IBD, encompasses a group of disorders characterized by chronic inflammation or ulceration of the gastrointestinal tract.
Risk Factors
The exact cause of IBD remains unclear, although it is believed to be due to a mix of genetic, environmental, microbial, and immune factors. Genetic factors are significant in determining susceptibility to IBD, with family history being a critical risk factor. Individuals with a first-degree relative who has IBD are at...
Inflammatory Bowel Disease II: Ulcerative Colitis01:20

Inflammatory Bowel Disease II: Ulcerative Colitis

Ulcerative colitis is a chronic inflammatory disorder of the colon characterized by continuous mucosal inflammation that typically begins in the rectum and extends proximally in a uniform pattern. Its pathogenesis involves a complex interplay of genetic predisposition, immune dysregulation, and environmental influences. These factors converge to impair the colon’s epithelial defenses and promote an exaggerated inflammatory response against luminal contents.Breakdown of the Mucosal BarrierA...
Inflammatory Bowel Disease I: Introduction01:26

Inflammatory Bowel Disease I: Introduction

Inflammatory bowel disease is a group of chronic disorders marked by recurrent inflammation of the gastrointestinal tract due to an abnormal immune response against gut microflora. This leads to tissue damage. The two main forms are Crohn’s disease and ulcerative colitis.Crohn’s DiseaseCrohn’s disease is a relapsing inflammatory disorder that can affect any part of the GI tract, from the mouth to the anus. It involves all layers of the bowel wall (transmural) and shows “skip lesions” in which...
Inflammatory Bowel Disease II: Crohn's Disease01:30

Inflammatory Bowel Disease II: Crohn's Disease

Introduction
Inflammatory bowel disease, commonly known as IBD, refers to a collection of disorders that lead to persistent inflammation of the gastrointestinal tract. The two types of IBD are ulcerative colitis, which impacts the colon, and Crohn's disease, which can involve any part of the gastrointestinal segment.
Crohn's disease
Crohn's disease is a chronic, systemic inflammatory bowel disease (IBD) that predominantly affects the gastrointestinal tract. It is marked by transmural...
Inflammatory Bowel Disease IV: Clinical Manifestations01:20

Inflammatory Bowel Disease IV: Clinical Manifestations

Inflammatory bowel disease (IBD) encompasses two major chronic disorders—ulcerative colitis and Crohn’s disease—each characterized by relapsing episodes of gastrointestinal inflammation. Although they share certain clinical features, their patterns of involvement and manifestations differ in ways that aid diagnosis and guide management.Ulcerative ColitisUlcerative colitis is limited to the colon and rectum and involves continuous inflammation of the mucosal layer. The disease course is marked...

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Related Experiment Video

Updated: Jun 5, 2026

Chronic Salmonella Infection Induced Intestinal Fibrosis
08:40

Chronic Salmonella Infection Induced Intestinal Fibrosis

Published on: September 22, 2019

Cell-type-resolved genetic variation shapes inflammatory bowel disease risk.

Tobi Alegbe1,2,3, Bradley T Harris1, Laura Fachal1

  • 1Wellcome Sanger Institute, Hinxton, UK.

Nature
|June 3, 2026
PubMed
Summary

This study maps gene expression across millions of single cells to pinpoint genetic links to inflammatory bowel disease (IBD). It identifies specific genes and cell types involved in IBD, offering a new framework for understanding complex genetic diseases.

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Evaluating Therapeutic Interventions in the SHIP-deficient Mouse Model of Crohn Disease-like Ileitis and Fibrosis
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Evaluating Therapeutic Interventions in the SHIP-deficient Mouse Model of Crohn Disease-like Ileitis and Fibrosis
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Evaluating Therapeutic Interventions in the SHIP-deficient Mouse Model of Crohn Disease-like Ileitis and Fibrosis

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Area of Science:

  • Genomics
  • Immunology
  • Cell Biology

Background:

  • Genetic variants in non-coding regions complicate disease gene identification.
  • Understanding cell-type-specific gene regulation is crucial for complex diseases like inflammatory bowel disease (IBD).

Purpose of the Study:

  • To map cis-expression quantitative trait loci (eQTLs) across single cells to identify effector genes and cell types in IBD.
  • To provide a mechanistic link between genetic risk and specific genes/cell types in IBD.
  • To develop a framework for interpreting genome-wide association study (GWAS) loci using single-cell eQTL mapping.

Main Methods:

  • Single-cell RNA sequencing of intestinal biopsies and blood from 421 individuals (125 with IBD).
  • Mapping of cis-expression quantitative trait loci (eQTLs) at single-cell resolution.
  • Colocalization analysis of eQTLs with IBD genome-wide association study (GWAS) loci.

Main Results:

  • Cell-type-level eQTLs are more distal, enriched in enhancers, and show higher colocalization with IBD GWAS loci compared to tissue-level eQTLs.
  • Identified effector genes (e.g., MAML2, PSEN2, ZMIZ1) in myeloid cells, implicating Notch signaling in IBD.
  • Identified Wnt-regulated genes (e.g., MYC) in epithelial stem/progenitor cells, suggesting impaired renewal contributes to barrier dysfunction.

Conclusions:

  • Single-cell eQTL mapping provides a powerful approach to link genetic risk to specific genes and cell types in complex diseases.
  • This study nominates effector genes at over half of known IBD loci, advancing understanding of IBD pathogenesis.
  • The findings offer a generalized framework for interpreting GWAS loci in disease-relevant tissues.