Single cell sequencing data identify distinct B cell and fibroblast populations in stricturing Crohn’s disease

Abstract

We used human full thickness Crohns disease (CD) small bowel resection specimens and single cell RNA sequencing to identify potential therapeutic targets for stricturing (S)CD. Using an unbiased approach, 16 cell lineages were assigned within 14,539 sequenced cells from patient-matched SCD and non-stricturing (NSCD) preparations. SCD and NSCD contained identical cell types. Amongst immune cells, B cells and plasma cells were selectively increased in SCD samples. B cell subsets suggested formation of tertiary lymphoid tissue in SCD and compared with NSCD there was an increase in IgG, and a decrease in IgA plasma cells, consistent with their potential role in CD fibrosis. Two Lumican-positive fibroblast subtypes were identified and subclassified based on expression of selectively enriched genes as fibroblast clusters (C)12 and C9. Cells within these clusters expressed the profibrotic genes Decorin (C12) and JUN (C9). C9 cells expressed ACTA2; ECM genes COL4A1, COL4A2, COL15A1, COL6A3, COL18A1 and ADAMDEC1; LAMB1 and GREM1. GO and KEGG Biological terms showed extracellular matrix, stricture organisation and regulation of WNT pathway genes are associated with the C12 and C9 gene sets. Trajectory and differential gene analysis of C12 and C9 identified four sub-clusters. Intra sub-cluster gene analysis detected co-regulated gene modules that aligned along predicted pseudotime trajectories and identified CXCL14 and ADAMDEC1 as key module markers. Our findings support further investigation of fibroblast heterogeneity and interactions with local and circulating immune cells at earlier time points in fibrosis progression. Breaking these interactions by targeting one or other population may improve therapeutic management for SCD.

Epigenetic and Metabolic Reprogramming of Fibroblasts in Crohn’s Disease Strictures Reveals Histone Deacetylases as Therapeutic Targets

“…Consequently, HDAC expression was assessed in our previously published scRNA-seq dataset [Array Express accession code: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11792 ] from primary fibroblasts isolated from full-thickness sections of SCD and NSCD ileum. 22 This revealed distinct profiles of HDAC expression associated with the four fibroblast clusters, notably for HDAC2 and HDAC7 [ Supplementary Figure S1A and B ], as categorized by differentiation trajectory analysis of the two Lumican-positive fibroblast subtypes identified from our scRNA-seq data reported previously. 22 These findings support the data given in Table 1 .…”

“… 22 This revealed distinct profiles of HDAC expression associated with the four fibroblast clusters, notably for HDAC2 and HDAC7 [ Supplementary Figure S1A and B ], as categorized by differentiation trajectory analysis of the two Lumican-positive fibroblast subtypes identified from our scRNA-seq data reported previously. 22 These findings support the data given in Table 1 . HDAC2 localization was documented using IHC in FFPE sections from SCD and NSCD intestine isolated from CD patient resection specimens [ Supplementary Table S2 ].…”