Ulcerative Colitis: Novel Epithelial Insights Provided by Single Cell RNA Sequencing

Abstract

Ulcerative Colitis (UC) is a chronic inflammatory disease of the intestinal tract for which a definitive etiology is yet unknown. Both genetic and environmental factors have been implicated in the development of UC. Recently, single cell RNA sequencing (scRNA-seq) technology revealed cell subpopulations contributing to the pathogenesis of UC and brought new insight into the pathways that connect genome to pathology. This review describes key scRNA-seq findings in two major studies by Broad Institute and University of Oxford, investigating the transcriptomic landscape of epithelial cells in UC. We focus on five major findings: (1) the identification of BEST4 + cells, (2) colonic microfold (M) cells, (3) detailed comparison of the transcriptomes of goblet cells, and (4) colonocytes and (5) stem cells in health and disease. In analyzing the two studies, we identify the commonalities and differences in methodologies, results, and conclusions, offering possible explanations, and validated several cell cluster markers. In systematizing the results, we hope to offer a framework that the broad scientific GI community and GI clinicians can use to replicate or corroborate the extensive new findings that RNA-seq offers.

Keywords: Ulcerative Colitis; colonic microfold cells; goblet cells; intestinal epithelium; single cell RNA sequencing; stem cells.

FIGURE 1

BEST4⁺ cell characteristic transcripts in health and UC inflammation. Heat maps of transcripts significantly elevated in BEST4⁺ cells in (A) both studies or (B) one of the studies in healthy epithelium presented as log₂[fold change (FC)]; (C) transcripts characteristic for BEST4⁺ cells in UC inflamed epithelia. Transcripts in orange are BEST4⁺ cell-specific in both studies and thus might serve as cluster markers in health or disease. Transcripts in blue are specific to healthy BEST4⁺ cells in Oxford study; transcripts in pink are specific to healthy BEST4⁺ cells in Broad study. * – transcripts are elevated in healthy BEST4 cells in both studies, but are downregulated in active UC in the Broad study.

FIGURE 2

Goblet cell characteristic transcripts in health and UC inflammation. Heap maps of transcripts characteristic for differentiated and undifferentiated goblet cells in healthy tissue [A,B; log₂(FC)]; transcripts characteristic for differentiated and undifferentiated goblet cells in UC (C) in both datasets. Transcripts in orange are common for healthy and UC-affected GCs. ITLN1 and CCL20 are GWAS genes.

FIGURE 3

Colonocyte characteristic transcripts in health and UC inflammation. Heat maps of transcripts characteristic for differentiated and undifferentiated colonocytes in healthy tissue [A,B; log₂(FC)]; colonocytes – characteristic transcripts in UC in both datasets (C,D).