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Sun Z, Braga-Neto MB, Xiong Y, Bhagwate AV, Gibbons HR, Sagstetter MR, Hamdan FH, Baheti S, Friton J, Nair A, Ye Z, Faubion WA. Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease. J Crohns Colitis 2023; 17:1847-1857. [PMID: 37280154 PMCID: PMC10673812 DOI: 10.1093/ecco-jcc/jjad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/14/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND The development of Crohn's disease [CD] involves immune cell signalling pathways regulated by epigenetic modifications. Aberrant DNA methylation has been identified in peripheral blood and bulk intestinal tissue from CD patients. However, the DNA methylome of disease-associated intestinal CD4+ lymphocytes has not been evaluated. MATERIALS AND METHODS Genome-wide DNA methylation sequencing was performed from terminal ileum CD4+ cells from 21 CD patients and 12 age- and sex-matched controls. Data were analysed for differentially methylated CpGs [DMCs] and methylated regions [DMRs]. Integration was performed with RNA-sequencing data to evaluate the functional impact of DNA methylation changes on gene expression. DMRs were overlapped with regions of differentially open chromatin [by ATAC-seq] and CCCTC-binding factor [CTCF] binding sites [by ChIP-seq] between peripherally derived Th17 and Treg cells. RESULTS CD4+ cells in CD patients had significantly increased DNA methylation compared to those from the controls. A total of 119 051 DMCs and 8113 DMRs were detected. While hypermethylated genes were mostly related to cell metabolism and homeostasis, hypomethylated genes were significantly enriched within the Th17 signalling pathway. The differentially enriched ATAC regions in Th17 cells [compared to Tregs] were hypomethylated in CD patients, suggesting heightened Th17 activity. There was significant overlap between hypomethylated DNA regions and CTCF-associated binding sites. CONCLUSIONS The methylome of CD patients shows an overall dominant hypermethylation yet hypomethylation is more concentrated in proinflammatory pathways, including Th17 differentiation. Hypomethylation of Th17-related genes associated with areas of open chromatin and CTCF binding sites constitutes a hallmark of CD-associated intestinal CD4+ cells.
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Affiliation(s)
- Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Manuel B Braga-Neto
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Adytia V Bhagwate
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jessica Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Greehey Children’s Cancer Research Institute, UT Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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Jha D, Al-Taie Z, Krek A, Eshghi ST, Fantou A, Laurent T, Tankelevich M, Cao X, Meringer H, Livanos AE, Tokuyama M, Cossarini F, Bourreille A, Josien R, Hou R, Canales-Herrerias P, Ungaro RC, Kayal M, Marion J, Polydorides AD, Ko HM, D’souza D, Merand R, Kim-Schulze S, Hackney JA, Nguyen A, McBride JM, Yuan GC, Colombel JF, Martin JC, Argmann C, Suárez-Fariñas M, Petralia F, Mehandru S. Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.542863. [PMID: 37333091 PMCID: PMC10274630 DOI: 10.1101/2023.06.02.542863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ γδ+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.
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Affiliation(s)
- Divya Jha
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Shadi Toghi Eshghi
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Aurelie Fantou
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Thomas Laurent
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Michael Tankelevich
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuan Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Hadar Meringer
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra E Livanos
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arnaud Bourreille
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Regis Josien
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Pablo Canales-Herrerias
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan C. Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maia Kayal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Marion
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Huaibin M. Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center-New York Presbyterian Hospital, New York, New York
| | - Darwin D’souza
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphael Merand
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason A. Hackney
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Allen Nguyen
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Jacqueline M. McBride
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Jean Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome C. Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Carmen Argmann
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Saurabh Mehandru
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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