Intra- And Inter-cellular Rewiring of the Human Colon During Ulcerative Colitis

Cell. 2019 Jul 25;178(3):714-730.e22. doi: 10.1016/j.cell.2019.06.029.

Abstract

Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC). To understand their cell type specificities and pathways of action, we generate an atlas of 366,650 cells from the colon mucosa of 18 UC patients and 12 healthy individuals, revealing 51 epithelial, stromal, and immune cell subsets, including BEST4+ enterocytes, microfold-like cells, and IL13RA2+IL11+ inflammatory fibroblasts, which we associate with resistance to anti-TNF treatment. Inflammatory fibroblasts, inflammatory monocytes, microfold-like cells, and T cells that co-express CD8 and IL-17 expand with disease, forming intercellular interaction hubs. Many UC risk genes are cell type specific and co-regulated within relatively few gene modules, suggesting convergence onto limited sets of cell types and pathways. Using this observation, we nominate and infer functions for specific risk genes across GWAS loci. Our work provides a framework for interrogating complex human diseases and mapping risk variants to cell types and pathways.

Keywords: anti-TNF resistance; cell-cell interactions; colon; genome-wide association studies; inflammation; inflammatory bowel disease; large intestine; single-cell RNA-seq; single-cell genomics; ulcerative colitis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Antibodies, Monoclonal / therapeutic use
  • Bestrophins / metabolism
  • CD8 Antigens / metabolism
  • Case-Control Studies
  • Colitis, Ulcerative / drug therapy
  • Colitis, Ulcerative / metabolism
  • Colitis, Ulcerative / pathology*
  • Colon / metabolism*
  • Colon / pathology
  • Enterocytes / cytology
  • Enterocytes / metabolism
  • Female
  • Genetic Loci
  • Genome-Wide Association Study
  • Humans
  • Interleukin-17 / metabolism
  • Male
  • Middle Aged
  • Risk Factors
  • T-Lymphocytes / cytology
  • T-Lymphocytes / metabolism
  • Thrombospondins / metabolism
  • Tumor Necrosis Factor-alpha / immunology
  • Tumor Necrosis Factor-alpha / metabolism
  • Young Adult

Substances

  • Antibodies, Monoclonal
  • BEST4 protein, human
  • Bestrophins
  • CD8 Antigens
  • Interleukin-17
  • RSPO3 protein, human
  • Thrombospondins
  • Tumor Necrosis Factor-alpha