Background: A single-cell map examining patient variation and reproducibility

A study of the terminal ileum in people with Crohn’s disease found antigen-presentation-related changes in some epithelial progenitor cells even in tissue without visible inflammation. In inflamed tissue, ITGA4⁺ macrophages were more abundant, and expression of genes linked to cytokine signaling was prominent. The researchers built IBDverse, a single-cell RNA map, from more than 1.1 million cells obtained from biopsies of 111 patients and 232 healthy controls. The study was published in Nature Genetics on June 15, 2026.

Crohn’s disease is a chronic inflammatory bowel disease whose location, severity, and response to treatment vary among patients. Earlier single-cell studies also revealed cell-level differences, but small samples made results difficult to reproduce amid disease heterogeneity and technical noise. This study increased the sample size and was designed to assess whether observed changes could also be confirmed in a separately allocated cohort.

Key findings: Epithelial MHC-I changes and ITGA4⁺ macrophages

Samples from all 343 participants were randomly assigned to discovery and replication cohorts. Patient biopsies were classified as inflamed (64 patients) or non-inflamed (47 patients) according to endoscopic inflammation scores for the terminal ileum. In a separate, randomly selected set of 70 samples, the researchers defined 57 cell clusters and used them to classify cells across the full dataset.

In inflamed patient tissue, expression of genes associated with interferon (IFN) responses and major histocompatibility complex class I (MHC-I) antigen presentation increased across the intestinal epithelium. MHC-I helps cells present antigen fragments to the immune system. MHC-I-related changes were also observed in some progenitor cells from patients without visible inflammation. The researchers interpreted these as a possible molecular trace left by inflammation. However, a comparison of biopsies alone did not establish how long the changes persist within the same patient.

Experiments treating intestinal organoids with interferon gamma (IFNγ) also showed increased expression of genes in the MHC-I antigen-processing pathway across several epithelial cell types. A comparison of unstimulated patient-derived organoids with organoids from healthy controls found weak enrichment in some MHC-I pathways as well, supporting the possibility that some changes persist outside an inflammatory environment.

Among immune cells, ITGA4⁺ macrophages made up an average of 16% of myeloid cells in the inflamed group, compared with 10% in healthy controls. Differential-expression and gene-set enrichment analyses highlighted Janus kinase–signal transducer and activator of transcription (JAK–STAT) signaling and pathways related to interleukin (IL)-6, IL-12, and IL-23. These are transcriptomic findings and should be distinguished from direct measurements of protein activity or drug response. In an analysis combining cell-specific gene expression with genetic association data for the disease, Crohn’s disease heritability was enriched in expression profiles from inflammatory monocytes and several macrophage populations, among others. This did not establish that variants in particular patients caused cell activation.

Meaning and outlook: A basis for target discovery, with interpretive limits

IBDverse brings together epithelial antigen-presentation changes and immune-cell signals in a resource that can help narrow candidates for follow-up functional studies. However, only 44% of differentially expressed genes in the discovery cohort showed significant differential expression in the same direction in the same cell type in the replication cohort. Inflammatory cells that are rare in healthy tissue were difficult to compare, and stromal cells were not captured adequately because of biopsy and cell-isolation methods. Participants were limited to people of European ancestry aged 18–70, so further validation is needed when applying the findings to other populations.

Processed data and analysis models have been made public, but access to raw biopsy sequencing data and clinical metadata requires approval to protect privacy. This study was not a clinical trial evaluating treatment efficacy, and cell signals alone do not yet enable patient-specific prescribing or prediction of relapse. The study design and results are available in the original Nature Genetics paper.