Crohn’s disease is a chronic inflammatory bowel disease that affects millions of people worldwide. Although researchers have identified many genetic and environmental factors associated with the disease, patients often experience very different symptoms and responses to treatment. Understanding the cellular and molecular differences that drive these variations remains a major challenge.

Researchers have now created one of the largest single-cell RNA sequencing resources ever assembled for Crohn’s disease. The work was led by researchers  from the Wellcome Sanger Institute and involved profiling more than 1.1 million cells collected from terminal ileal biopsies of 111 Crohn’s disease patients and 232 healthy individuals.

The resulting resource, called IBDverse, provides a detailed map of the cellular changes associated with Crohn’s disease at single-cell resolution. By examining individual cells rather than averaging signals across entire tissue samples, researchers were able to identify specific cell populations, genes, and biological pathways linked to disease development.

Single-cell expression atlas for the terminal ileum in healthy controls and patients with CD

a, Terminal ileum biopsies from 343 individuals were dissociated to single cells on ice in HBSS containing B. licheniformis protease. This was followed by a brief incubation in collagenase and then red blood cell (RBC) lysis buffer. Single-cell suspensions were then profiled using a Chromium 10x 3′ kit. Samples from the full cohort were assigned at random to either the discovery or replication cohort and all reported analyses are required to be statistically significant in both cohorts. b, Center, uniform manifold approximation and projection (UMAP) of ~216,000 cells from the atlas cohort that met quality control criteria, with eight colors representing the primary cell populations. Surrounding the central UMAP, these major populations are further subdivided into 57 distinct cell subtypes. c, Differential cell-type abundance between healthy controls and participants with CD for the full cohort. Values show the log[fold change] for CD versus healthy controls. Positive values indicate enrichment in CD and negative values indicate enrichment in healthy controls. Asterisks denote cell types significantly and reproducibly (same direction and FDR < 0.05 in both cohorts) enriched in either health or disease.

One of the most notable findings involved the intestinal epithelium, the layer of cells that lines the gut and acts as a barrier between the body and the intestinal environment. The researchers found evidence of increased interferon signaling that led to elevated expression of major histocompatibility complex class I (MHC-I) molecules. Surprisingly, these molecular changes persisted even after visible inflammation had resolved.

This suggests that some cellular abnormalities may remain active beneath the surface, potentially contributing to disease recurrence or ongoing immune dysfunction.

The analysis also identified a specific population of immune cells called ITGA4-positive macrophages as important drivers of inflammation. These cells displayed heightened activity of the JAK-STAT signaling pathway and produced inflammatory cytokines including IL-6, IL-12, and IL-23. All of these molecules are known to play important roles in immune regulation and inflammatory disease.

Macrophages are immune cells that help coordinate responses to infection and tissue damage. In Crohn’s disease, however, certain macrophage populations may become overly active and contribute to chronic inflammation.

The researchers further explored the genetic basis of Crohn’s disease by linking disease-associated genetic variants to specific immune cell populations. Their findings suggest that both resident immune cells already present in the intestine and newly recruited inflammatory immune cells contribute to disease susceptibility and progression.

One of the strengths of this work is the scale of the dataset. By integrating both discovery and replication cohorts, the researchers were able to validate their findings across large patient populations and improve confidence in the identified disease signatures.

The IBDverse resource provides an important framework for future Crohn’s disease research. By identifying specific cell types and pathways involved in disease progression, the findings may help guide the development of more targeted therapies and improve patient stratification for treatment selection.

As single-cell RNA sequencing continues to advance, large-scale cellular atlases such as IBDverse are helping researchers move beyond broad disease classifications and toward a more precise understanding of the cellular mechanisms that drive chronic inflammatory diseases.

Availability – all of the data exploration, version history and unrestricted file access  is available on the project website at https://www.ibdverse.info/.