Mar 17, 2023 / Immunology

Single cell atlas maps individual differences in Crohn’s disease

Jeanene Swanson

March is National Autoimmune Disease Awareness Month, and, for millions of Americans living with these chronic and often debilitating conditions, it’s a chance to raise awareness. Though no autoimmune disease as yet has a cure, increased education and research could lead to improved treatments for type 1 diabetes, thyroid disorders, Crohn’s disease, and many more. In this blog, we highlight a publication that uses single cell analysis to create a transcriptomic map of changes occurring in the small intestine and colon during the course of Crohn’s disease. This foundational resource can be used to further understand disease progression and identify novel drug targets.

Sometimes the systems that our body has put into place to protect us against dangerous infections malfunction and attack healthy cells, tissues, and organs. When this happens, an autoimmune disease can develop. More than 24 million people in the United States are affected by one or more of at least 80 different autoimmune diseases (1). Ulcerative colitis and Crohn’s disease (CD), which are types of inflammatory bowel disease (IBD), are chronic conditions increasing in prevalence and in need of more research (2).

Crohn’s disease causes inflammation of the digestive tract and its key symptoms include pain, diarrhea, and weight loss. Unlike ulcerative colitis, CD can occur across both the small and large intestinal tract, primarily affecting the terminal ileum (TI) and colon (CO). Understanding similarities and differences in the cellular processes behind ileal and colonic inflammation in individual patients will go a long way toward improving treatment for what could potentially be separate conditions.

In a recent publication (3), The landscape of immune dysregulation in Crohn’s disease revealed through single cell transcriptomic profiling in the ileum and colon, scientists in the lab of Ramnik Xavier, MD, at the Broad Institute of MIT and Harvard created the largest single cell transcriptomic map to date to study CD. Led by first author Lingjia Kong, PhD, they took tissue from a total of 71 people, comparing healthy non-IBD controls to both inflamed and non-inflamed regions of the TI and CO from people with CD. Using Chromium Single Cell Gene Expression to perform single cell RNA sequencing (scRNA-seq) on a total of 720,633 ileal and colonic cells, they created a transcriptomic atlas that allowed them to determine the changes that happen during CD in different cell types and locations.

Complex changes in composition and gene expression across cell types and tissues

First, they clustered cells into three major cell-type compartments: epithelial cells, stromal cells, and immune cells. In analyzing the data, their results pointed to a complicated network of changes across different diseased tissue types. They saw broad changes in cell-type composition within the immune cell and stromal cell subsets, predominantly in CO T cells and TI myeloid cells. However, in terms of gene expression, they found more transcriptional changes across epithelial cells, which exhibited a broad increase in expression of MHC class II genes. Stromal cells showed both compositional and transcriptional changes, “perhaps reflecting a joint reprogramming and tissue remodeling,” the authors wrote.

Interestingly, transcriptional changes in all three cell types were similar between non-inflamed (inactive CD) and inflamed (active CD) disease samples, building off previous research showing that cell-type composition profiles aren’t reliable to tell whether CD is in a relapsed or remitting state (4). Therefore, it’s necessary to further understand pathways involved in transcriptional differences to discover key drug targets.

Their map also showed tissue-specific responses. Differential expression was more pronounced in the CO, where more inflammation-induced differentially expressed genes were detected compared to the TI. There were, however, several pathways that were enriched in the TI, including numerous disease-related pathways in three specific cell types: HHIP+ NPNT+ myofibroblasts, glial cells, and lymphatics.

A role for fibroblast transcription factors in CD

The researchers were particularly interested in the HHIP+ NPNT+ cells and wanted to dig in deeper. Collagen is essential to the wound healing process, but in CD, dysregulated collagen production can lead to fibrosis. Looking further at the HHIP+ NPNT+ myofibroblast cells in inflamed TI, they showed higher expression of collagen genes COL18A1 and COL23A1. To investigate pathways behind collagen expression in CD myofibroblasts, Dr. Kong used pseudotime trajectory analysis, starting from collagen-negative GREM1+ GREM2+ myofibroblasts to HHIP+ NPNT+ collagen-positive myofibroblasts, and uncovered a set of six transcription factors (TFs) and 10 other genes involved in the transition. Functional knockdown studies further pinpointed TFs CHMP1A, TBX3, and RNF168 as playing a part in regulating collagen production in these cells—leading the researchers to believe that these TFs could be novel targets for managing fibrosis in CD.

A resource for more translational studies of CD

Knowing more about the cell-type and tissue-specific changes that occur during CD will help in making more accurate diagnoses and discovering novel therapies. Dr. Kong and team are helping us on the way to this goal by providing the largest single cell map to date for studying CD. Additionally, others can mine their atlas data for future studies that attempt to assign function to risk genes and gene variants involved in the complex expression of inflammation along the intestinal tract in CD.

Learn how 10x Genomics multiomic single cell and spatial technologies are redefining immunology.


  2. Ng SC, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet 390: 2769–2778 (2017).
  3. Kong L, et al. The landscape of immune dysregulation in Crohn's disease revealed through single cell transcriptomic profiling in the ileum and colon. Immunity 56: 444–458.e5 (2023).
  4. Mitsialis V, et al. Single-cell analyses of colon and blood reveal distinct immune cell signatures of ulcerative colitis and Crohn’s disease. Gastroenterology 159: 591–608.e10 (2020).