Single-cell analyses of Crohn\u2019s disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions

Natalia Jaeger,Jorge L Schettini,Charles V Rosadini,Ekaterina Esaulova,Marco Colonna,Scott A Jelinsky,Thomas A Wynn,William Vermi,Mattia Bugatti,Blanda Di Luccia,Marina Cella,Shanrong Zhao,Ramya Gamini,Ramnik J Xavier,Maxim N Artyomov,Baylee Kinnett

doi:10.1038/s41467-021-22164-6

Abstract

Crohn’s disease (CD) is a chronic transmural inflammation of intestinal segments caused by dysregulated interaction between microbiome and gut immune system. Here, we profile, via multiple single-cell technologies, T cells purified from the intestinal epithelium and lamina propria (LP) from terminal ileum resections of adult severe CD cases. We find that intraepithelial lymphocytes (IEL) contain several unique T cell subsets, including NKp30+γδT cells expressing RORγt and producing IL-26 upon NKp30 engagement. Further analyses comparing tissues from non-inflamed and inflamed regions of patients with CD versus healthy controls show increased activated TH17 but decreased CD8+T, γδT, TFH and Treg cells in inflamed tissues. Similar analyses of LP find increased CD8+, as well as reduced CD4+T cells with an elevated TH17 over Treg/TFH ratio. Our analyses of CD tissues thus suggest a potential link, pending additional validations, between transmural inflammation, reduced IEL γδT cells and altered spatial distribution of IEL and LP T cell subsets.

Highlights

Crohn’s disease (CD) is a chronic transmural inflammation of intestinal segments caused by dysregulated interaction between microbiome and gut immune system
Comparing intraepithelial lymphocytes (IEL) T cell profiles with those of T cells purified from the lamina propria (LP), our data provide an unbiased view of T cell lineages diversity and functional states in the intestinal mucosa under both healthy and CD conditions, and identify an altered spatial distribution of T cell subsets between the IEL and the LP compartments that potentially correlates with transmural inflammation, this remains to be validated with larger patient cohorts
IEL were prepared from surgical resections of the terminal ileum of CD patients, which included both macroscopically inflamed tissue (II) and adjacent non-inflamed tissue (NI) (Supplementary Fig. 1a–c)

Summary

Introduction

Crohn’s disease (CD) is a chronic transmural inflammation of intestinal segments caused by dysregulated interaction between microbiome and gut immune system. High-dimensional single-cell profiling approaches, such as single-cell RNA sequencing (scRNA-seq) and mass cytometry, have been recently performed on intestinal specimens from patients with CD or UC and controls These studies provided unbiased analyses of cell lineages and their functional states in IBD, deconvoluted pathways underlying IBD pathogenesis and supplied biomarkers predicting the course of disease and the response to therapy[4,5,6,7,8,9,10]. While these studies have analyzed whole mucosal biopsies or the lamina propria (LP) selectively, few studies have analyzed intraepithelial lymphocytes (IEL) purified from CD specimens. Comparing IEL T cell profiles with those of T cells purified from the LP, our data provide an unbiased view of T cell lineages diversity and functional states in the intestinal mucosa under both healthy and CD conditions, and identify an altered spatial distribution of T cell subsets between the IEL and the LP compartments that potentially correlates with transmural inflammation, this remains to be validated with larger patient cohorts

Methods

Results

Conclusion