Amplification of Minor Pathogenic Stem Cell Variants in Crohn's Disease

Crohn’s disease (CD) is a progressive inflammatory and fibrotic disorder of the intestinal tract thought to arise from defective interactions of immune cells, intestinal microbes, and intervening mucosal barriers. Here we perform novel clonogenic analyses of stem cells derived from the terminal ileum of pediatric and adult patients with CD. We show that CD stem cell libraries are dominated by two variants that display ingrained pro-inflammatory and pro-fibrotic signaling. Transplantation of these variants to immunodeficient mice triggers key features of CD including leukocyte infiltration and fibrosis. These variants, which exist at low levels in control and fetal terminal ileum, display an absolute commitment to gastric epithelial fates. Together, this work links CD to the amplification of minor stem cell variants whose conventional roles are in the response to ancient human pathogens and suggests mechanistic analogies to chronic obstructive pulmonary disease (COPD) and perhaps other chronic inflammatory conditions. If true, Crohn's disease can be mitigated by therapeutics that selectively target these variant stem cells allowing existing normal stem cells to compensate for the loss of those. We develop a high-throughput chemical screening platform to uncover small molecules that specifically target these variant stem cells. Furthermore, these small molecules, in a unique combination with promoters, protect and promote normal stem cells while eradicating variant stem cells. Lastly, the clonogenic mucosal stem cell variants tied to pathological features of the disease are selectively targeted by candidate small molecules in the xenograft model diminishing those features in parallel and leaving normal stem cells to repopulate and maintain homeostasis.