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Medina TS, Murison A, Smith M, Kinker GS, Chakravarthy A, Vitiello GAF, Turpin W, Shen SY, Yau HL, Sarmento OF, Faubion W, Lupien M, Silverberg MS, Arrowsmith CH, De Carvalho DD. The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population. Front Immunol 2023; 14:1161901. [PMID: 37600767 PMCID: PMC10436103 DOI: 10.3389/fimmu.2023.1161901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The imbalance between Th17 and regulatory T cells in inflammatory bowel diseases (IBD) promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate or repress gene expression. Methods Here, we characterized the chromatin landscape and heterogeneity of intestinal and peripheral CD4 T cellsfrom IBD patients using in house ATAC-Seq and single cell RNA-Seq libraries. Results We show that chromatin accessibility profiles of CD4 T cells from inflamed intestinal biopsies relate to genes associated with a network of inflammatory processes. After integrating the chromatin profiles of tissue-derived CD4 T cells and in-vitro polarized CD4 T cell subpopulations, we found that the chromatin accessibility changes of CD4 T cells were associated with a higher predominance of pathogenic Th17 cells (pTh17 cells) in inflamed biopsies. In addition, IBD risk loci in CD4 T cells were colocalized with accessible chromatin changes near pTh17-related genes, as shown in intronic STAT3 and IL23R regions enriched in areas of active intestinal inflammation. Moreover, single cell RNA-Seq analysis revealed a population of pTh17 cells that co-expresses Th1 and cytotoxic transcriptional programs associated with IBD severity. Discussion Altogether, we show that cytotoxic pTh17 cells were specifically associated with IBD genetic variants and linked to intestinal inflammation of IBD patients.
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Affiliation(s)
- Tiago S. Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle Smith
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Gabriela S. Kinker
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Williams Turpin
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen L. Yau
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Olga F. Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - William Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mark S. Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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