Researchers from the Wellcome Sanger Institute, Cambridge University Hospitals NHS Foundation Trust (CUH), and Open Targets have created a detailed cellular study of Crohn’s disease (CD), mapping how gene activity changes across more than 50 cell types in the gut. (Founded in 2014, Open Targets is a pre-competitive, public-private partnership that uses human genetics and genomics data to systematically identify and prioritize drug targets.)
Co-led by Tim Raine, MD, PhD, consultant gastroenterologist at Cambridge University Hospitals NHS Foundation Trust, the team analyzed over a million gut cells from people with Crohn’s and from healthy controls, comparing changes in the gut lining and identifying immune cells that drive inflammation. The resulting single cell RNA-sequencing (sc-RNA-seq) resource, IBDverse, characterizes each cell type and those whose activity shifts in disease, uncovering new molecular and cellular signatures of immune activity in the gut lining.
Co-first author Monika Krzak, PhD, formerly at the Wellcome Sanger Institute and now based at the Institute of Metabolic Science, University of Cambridge, said, “Crohn’s disease is complex, variable and deeply personal to every individual living with it, which is why understanding it at the level of single cells is so important. By creating this unprecedented map of more than one million gut cells, we are giving researchers around the world a powerful new tool to uncover how inflammation begins, persists and may one day be stopped. This is the kind of open science that can accelerate discoveries and bring us closer to better treatments for patients.”
Raine added, “There is an urgent need for increased understanding of the biology of Crohn’s disease if we are to develop more effective and safe medications for people living with this condition. The patients who contributed to this research have helped us build insight into the different ways that gut function and immune function are disrupted in the disease, and with the insight comes immediate new avenues for drug development and targeted therapies.”
Reported in Nature Genetics (“Single-cell RNA sequencing of terminal ileal biopsies identifies signatures of Crohn’s disease pathogenesis,”) the research revealing the cell types and molecular changes involved in Crohn’s inflammation is one of two complementary studies—the other a paper recently published in Nature—built on IBDverse to investigate different aspects of the disease.
In their newly published report the team concluded, “These findings establish a comprehensive cellular and molecular framework for CD, offering insights into disease mechanisms and therapeutic opportunities.”
Inflammatory bowel disease (IBD) is an umbrella term used to describe disorders that cause chronic inflammation of the gastrointestinal tract. Over half a million people in the U.K. are estimated to be living with IBD, which includes Crohn’s disease and ulcerative colitis.
Crohn’s is a chronic condition that causes inflammation and ulcers in the digestive tract, from the mouth to the anus, often affecting the small intestine and colon. However, the authors noted, “Although inflammation is most commonly observed in the terminal ileum, CD exhibits substantial heterogeneity in disease location, severity and behavior, both between patients and within patients, over time.”
Although inflammation is most commonly observed in the terminal ileum—the final section of the small intestine—Crohn’s is found in many locations of the body and with variation in severity both between patients and within patients over time.
While therapies targeting immune cells have improved clinical outcomes for some patients, non-response to treatment remains high, with 15% of Crohn’s patients requiring surgery within five years of diagnosis. Consequently, there is an urgent need to better understand the etiology of CD in order to broaden therapeutic opportunities,” the investigators stated.
For their newly reported study the researchers took and analyzed biopsies from 111 patients with Crohn’s and a history of current or previous terminal ileitis—inflammation of the ileum—and 232 healthy volunteers. The team performed single-cell RNA sequencing to measure gene expression in individual cells. “Single-cell RNA sequencing (scRNA-seq) technologies provide a high-throughput means to dissect complex tissues at the resolution of single cells and cell types,” they noted.
By creating a comprehensive map of cellular and molecular differences in Crohn’s compared to healthy controls, the researchers established IBDverse as a result—an online data resource of over 1,185,000 cells isolated from small intestine samples. The large IBDverse dataset will serve as an open resource for future research.
Using the data, the scientists identified genes that are abnormally expressed in Crohn’s and those where expression is specific to given cell types and cellular processes.
One of the study’s most striking findings was a ‘molecular scar’ in the gut lining. Even after visible inflammation had healed, genes that help send messages to the immune system stayed switched on in the gut’s stem cells—the cells that constantly renew the lining. This suggests that an episode of inflammation leaves a lasting mark on these cells, which may shape how the gut responds to inflammation in future. In their paper the authors noted, “We uncovered epithelial changes marked by interferon-driven upregulation of major histocompatibility complex class I molecules that persisted in progenitor cells after macroscopic inflammation resolution.”
The researchers also identified a population of macrophages—immune cells that engulf and digest cellular debris—with high expression of the gene ITGA4. These cells were key drivers of inflammation through the JAK/STAT pathway, which carries signals from the cell surface to the nucleus to switch genes on and off. “ITGA4+ macrophages were identified as key inflammatory drivers, showing enriched JAK–STAT signaling and cytokine expression (interleukin-6 (IL-6), IL-12 and IL-23),” the investigators stated. Drugs that block this pathway, known as JAK inhibitors, are already used to treat IBD, which points to these macrophages as a likely target of therapies.
Co-first author Tobi Alegbe, PhD, at the Wellcome Sanger Institute and Open Targets, said “For inflammatory bowel diseases like Crohn’s and ulcerative colitis, it’s still unclear what is going wrong in the gut cells to cause inflammation. We have been able to compare gut cells of hundreds of people with and without IBD. This has given us new insight into the genes and cell types that are involved during active disease, and lays the groundwork for similar approaches to understand diseases of other major organs like eczema and asthma.”
Co-senior author Carl Anderson, PhD, at the Wellcome Sanger Institute, said “What makes this study different is that we designed replication in from the start and found that even with hundreds of patients and standardized protocols, fewer than half of the gene expression changes we detected in one cohort replicated in the other. That’s a sobering finding for the field. The biology that did replicate consistently points to the gut lining itself as a key player in Crohn’s with a molecular signature in epithelial cells that persists even after inflammation has resolved. We don’t yet know what that persistence means, but it likely influences how the gut responds to future inflammatory insults.”
