The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1⁺ mesothelial cells

Abstract

Intestinal fibroblasts (FB) play essential roles in intestinal homeostasis. Here we show that the small and large intestinal lamina propria (LP) contain similar FB subsets that locate in specific anatomical niches and express distinct arrays of epithelial support genes. However, there were tissue specific differences in the transcriptional profile of intestinal FB subsets in the two sites. All adult intestinal LP mesenchymal stromal cells (MSC), including FB, smooth muscle cells (SMC) and pericytes derive from Gli1-expressing embryonic precursors which we identify as mesothelial cells. Trajectory analysis suggested that adult SMC and FB derive from distinct embryonic intermediates, and that adult FB subsets develop in a linear trajectory from CD81+ FB. Finally, we show that colonic subepithelial PDGFRαhi FB comprise several functionally and anatomically distinct populations that originate from an Fgfr2-expressing FB intermediate. Collectively our results provide novel insights into MSC diversity, location, function and ontogeny, with implications for our understanding of intestinal development, homeostasis and disease.

Fibroblasts in intestinal homeostasis, damage, and repair

“…CD81 + fibroblasts ( 10 ), also called trophocytes ( 5 ), crypt-bottom fibroblasts (CBFs) ( 11 ), MAP3K2-regulated intestinal stromal cells (MRISCs) ( 17 ) or pi16 + fibroblasts ( 15 ). They are located within the submucosa, near vascular structures and below crypts, and are the primary cellular source of WNTs (e.g.…”

“…They are located within the submucosa, near vascular structures and below crypts, and are the primary cellular source of WNTs (e.g. Wnt2 and Wnt2b ), the BMP antagonist Gremlin 1, and R-spondins ( 8 – 10 , 15 , 17 ). They mainly function to maintain intestinal stem cell identity and proliferation.…”

“…They are characterized by expression of high levels of PDGFRα , BMPs, among which Bmp3 and Bmp7 are uniquely expressed, Wnt5a , F3 , Sox6, Foxl1 , and low levels of Acta2 ( 8 – 12 , 14 – 18 ). They are localized directly under the epithelial layer and are concentrated at the top of crypts and villi ( 8 , 10 , 11 , 13 , 15 , 25 ). They may also include subepithelial myofibroblasts, as they express αSMA ( 5 , 13 ).…”

“…PDGFRα lo CD81 - fibroblasts , which reside in the lamina propria, around crypts and inside the villous core ( 9 , 10 ). They can be further divided into at least two subsets that express Col15a1, Igfbp5/CD90 (small intestine/colon) and Fgfr2, Fbln, respectively ( 9 , 10 , 15 ). They secrete basement membrane proteins and contribute to ECM production and remodeling ( 15 ).…”

“…Varying levels of Acta2 , Myh11 and Des can help with the distinction between SMCs and myofibroblasts, but the two terms are sometimes used interchangeably in single cell RNA sequencing analyses ( 9 – 12 , 14 , 16 , 18 ). Notably, the small intestine and colon display similar mesenchymal subsets with location-specific differences in their transcriptional profiles ( 5 , 10 ).…”