The small and large intestine contain related mesenchymal subsets that derive from embryonic Gli1+ precursors

Abstract

The intestinal lamina propria contains a diverse network of fibroblasts that provide key support functions to cells within their local environment. Despite this, our understanding of the diversity, location and ontogeny of fibroblasts within and along the length of the intestine remains incomplete. Here we show that the small and large intestinal lamina propria contain similar fibroblast subsets that locate in specific anatomical niches. Nevertheless, we find that the transcriptional profile of similar fibroblast subsets differs markedly between the small intestine and colon suggesting region specific functions. We perform in vivo transplantation and lineage-tracing experiments to demonstrate that adult intestinal fibroblast subsets, smooth muscle cells and pericytes derive from Gli1-expressing precursors present in embryonic day 12.5 intestine. Trajectory analysis of single cell RNA-seq datasets of E12.5 and adult mesenchymal cells suggest that adult smooth muscle cells and fibroblasts derive from distinct embryonic intermediates and that adult fibroblast subsets develop in a linear trajectory from CD81+ fibroblasts. Finally, we provide evidence that colonic subepithelial PDGFRαhi fibroblasts comprise several functionally distinct populations that originate from an Fgfr2-expressing fibroblast intermediate. Our results provide insights into intestinal stromal cell diversity, location, function, and ontogeny, with implications for intestinal development and homeostasis.

Identification of a targetable ST2-expressing fibroblast subset driving Peutz-Jeghers syndrome polyposis

“…GI fibroblast heterogeneity has been under intensive investigation in recent years (Brügger et al, 2020;Deng et al, 2022;Jasso et al, 2022;Kinchen et al, 2018;Kraiczy et al, 2023;Manieri et al, 2023;McCarthy, Manieri, et al, 2020;Paerregaard et al, 2023) We found that antral fibroblasts clustered similarly to intestinal and colonic fibroblasts, including the formation of Wnt and Bmp gradients (Brügger et al, 2020;McCarthy, Manieri, et al, 2020) but with differences in specific marker expression: for example, in the gastric mucosa Cd81 was expressed across all fibroblast subsets, as opposed to intestinal and colonic fibroblasts where…”

“…GI fibroblast heterogeneity has been under intensive investigation in recent years (Kinchen et al 2018;Brügger et al 2020;Deng et al 2022;Jasso et al 2022;Paerregaard et al 2023;Kraiczy et al 2023) with little data on gastric fibroblasts (Kim et al 2020). We found that antral fibroblasts clustered similarly to intestinal and colonic fibroblasts, including the formation of Wnt and Bmp gradients (Brügger et al, 2020;McCarthy, Manieri, et al, 2020) but with differences in specific marker expression: for example, in the gastric mucosa…”

“…We identified five distinct fibroblast clusters positive for the pan-fibroblast markers Pdpn , Pdgfra, and Col6a1 (Figure 1B-C). We compared these with fibroblast populations characterized in the GI tract (Brügger et al, 2020; Brügger & Basler, 2023; Manieri et al, 2023; Pærregaard et al, 2023), consisting of: i) the Pdgfra -low, Cd34 + , Cd55 + crypt bottom fibroblasts (CBFs) forming the niche for the stem cells residing at the crypt bottom by secreting stemness-supporting factors such as R-Spondin 3 (encoded by Rspo3 ) as well as the Bmp inhibitor Gremlin 1 (encoded by Grem1 ); and ii) the Pdgfra -high, Cd34 - , Cd55 - crypt top fibroblasts (CTFs), promoting epithelial differentiation in the upper parts of the crypts by expressing e.g. BMP ligands.…”

“…GI fibroblast heterogeneity has been under intensive investigation in recent years (Kinchen et al 2018; McCarthy et al 2020; Brügger et al 2020; Deng et al 2022; Jasso et al 2022; Pærregaard et al 2023; Kraiczy et al 2023) with little data on gastric fibroblasts (Kim et al 2020). We found that antral fibroblasts clustered similarly to intestinal and colonic fibroblasts, including the formation of Wnt and Bmp gradients (Brügger et al, 2020; McCarthy, Manieri, et al, 2020) but with differences in specific marker expression: for example, in the gastric mucosa Cd81 was expressed across all fibroblast subsets, as opposed to intestinal and colonic fibroblasts where Cd81 specifically marks one of the fibroblast population providing the trophic support for stem cells (McCarthy et al 2020; Brügger et al 2020).…”

An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal and neural cells

“…Mesenchymal cells that were localized in the pores of the membrane, separating the top and bottom channel, were detected in all media conditions, demonstrating their capacity to migrate from the top to the bottom channel (Figure S3C). The localization of mesenchymal cells relative to intestinal epithelial cells may reflect their natural position in the human small intestine, where (myo)fibroblasts form a supportive layer directly under the intestinal epithelial barrier 22,23 . Mesenchymal cells were most prominent in the EM condition, whereas they were reduced and restricted to the bottom channel in the EM-DM condition and almost depleted in the DM condition (Figures 2A, S3A and S3D).…”