Multimodal single-cell analyses reveal mechanisms of perianal fistula in diverse patients with Crohn's disease

Rachel M Levantovsky; Christopher Tastad; Jiayu Zhang; Kyle Gettler; Ksenija Sabic; Robert Werner; Colleen Chasteau; Ujunwa Korie; Diana Paguay; Michelle Bao; Huajun Han; Neha Maskey; Sayali Talware; Manishkumar Patel; Carmen Argmann; Mayte Suarez-Farinas; Noam Harpaz; Ling-Shiang Chuang; Judy H Cho

doi:10.1016/j.medj.2024.03.021

Multimodal single-cell analyses reveal mechanisms of perianal fistula in diverse patients with Crohn's disease

Med. 2024 Apr 18:S2666-6340(24)00133-8. doi: 10.1016/j.medj.2024.03.021. Online ahead of print.

Authors

Rachel M Levantovsky¹, Christopher Tastad², Jiayu Zhang², Kyle Gettler², Ksenija Sabic², Robert Werner², Colleen Chasteau², Ujunwa Korie², Diana Paguay², Michelle Bao³, Huajun Han², Neha Maskey⁴, Sayali Talware⁵, Manishkumar Patel⁶, Carmen Argmann⁷, Mayte Suarez-Farinas⁷, Noam Harpaz², Ling-Shiang Chuang², Judy H Cho⁸

Affiliations

¹ Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
² Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
³ Division of Pediatric Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁴ Hunter College, New York, NY 10065, USA.
⁵ Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁶ Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁷ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁸ Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: judy.cho@mssm.edu.

PMID: 38663404
DOI: 10.1016/j.medj.2024.03.021

Abstract

Background: Crohn's disease complicated by perianal fistulae is more prevalent and severe in patients of African ancestry.

Methods: We profiled single cells from diverse patients with Crohn's disease with perianal fistula from colorectal mucosa and fistulous tracts. Immunofluorescence was performed to validate predicted cell-cell interactions. Unstimulated monocytes were chronically cultured in diverse cohorts. A subset was analyzed by single-nucleus RNA + ATAC sequencing.

Findings: Fistulous tract cells from complete proctectomies demonstrated enrichment of myeloid cells compared to paired rectal tissues. Ligand-receptor analysis highlights myeloid-stromal cross-talk and cellular senescence, with cellular co-localization validated by immunofluorescence. Chitinase-3 like-protein-1 (CHI3L1) is a top upregulated gene in stromal cells from fistulae expressing both destructive and fibrotic gene signatures. Monocyte cultures from patients of African ancestry and controls demonstrated differences in CHI3L1 and oncostatin M (OSM) expression upon differentiation compared to individuals of European ancestry. Activating protein-1 footprints are present in ATAC-seq peaks in stress response genes, including CHI3L1 and OSM; genome-wide chromatin accessibility including JUN footprints was observed, consistent with reported mechanisms of inflammatory memory. Regulon analyses confirm known cell-specific transcription factor regulation and implicate novel ones in fibroblast subsets. All pseudo-bulked clusters demonstrate enrichment of genetic loci, establishing multicellular contributions. In the most significant African American Crohn's genetic locus, upstream of prostaglandin E receptor 4, lymphoid-predominant ATAC-seq peaks were observed, with predicted RORC footprints.

Conclusions: Population differences in myeloid-stromal cross-talk implicate fibrotic and destructive fibroblasts, senescence, epigenetic memory, and cell-specific enhancers in perianal fistula pathogenesis. The transcriptomic and epigenetic data provided here may guide optimization of promising mesenchymal stem cell therapies for perianal fistula.

Funding: This work was supported by grants U01DK062422, U24DK062429, and R01DK123758.

Keywords: AP-1; CHI3L1; Crohn's disease; PTGER4; Translation to patients; ancestry; myeloid; perianal fistula; senescence; single cell; stromal.