Multimodal Single-cell Analyses Reveal Mechanisms of Perianal Fistula in Diverse Patients with Crohn's Disease

Overview

Journal Med

Publisher Cell Press

Specialty General Medicine

Date 2024 Apr 25

PMID 38663404

Authors

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

Affiliations

Soon will be listed here.

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.

Citing Articles

Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn's Disease.

Cao S, Nguyen K, Ma K, Yao X, Liu T, Ayoub M bioRxiv. 2024; .

PMID: 39574705 PMC: 11581043. DOI: 10.1101/2024.11.08.620717.

Single-cell transcriptomics of rectal organoids from individuals with perianal fistulizing Crohn's disease reveals patient-specific signatures.

Murthy S, Anbazhagan M, Maddipatla S, Kolachala V, Dodd A, Pelia R Sci Rep. 2024; 14(1):26142.

PMID: 39477985 PMC: 11526126. DOI: 10.1038/s41598-024-75947-4.

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