Intestinal fibroblast heterogeneity: unifying RNA-seq studies and introducing consensus-driven nomenclature

Abstract Figure Graphical abstract In the colon, single-layered epithelium lines the crypts, which descend into the underlying mucosa. Colonic crypts are surrounded by a network of fibroblasts essential for various functions, including the production and remodeling of the extracellular matrix (ECM), supporting the epithelial stem cell niche, and promoting the differentiation of epithelial cells. Recent studies indicate that fibroblasts are not a homogeneous cell population. However, differences in nomenclature and a lack of exact markers hindered their classification and functional understanding. Here, we used single-cell RNA-sequencing (scRNA-seq) to identify six distinct fibroblast subpopulations in mouse colonic mucosa, each with unique molecular signatures and functional specialization. Our analysis reveals that some fibroblasts are primarily involved in ECM production and remodeling, while others exhibit high contractility. Additionally, a subset of fibroblasts produces cytokines that promote epithelial cell differentiation, whereas another group secrete cytokines essential for maintaining the epithelial stem cell niche. We also map the spatial distribution of these fibroblast subpopulations within the colonic mucosa. Differentiation trajectory analysis suggests distinct pathways for fibroblast differentiation, while cell cycle scoring reveals that fibroblasts do not proliferate under homeostatic conditions. Furthermore, we integrated our scRNA-seq data with previously published datasets to identify common fibroblast populations and propose a standardized nomenclature for intestinal fibroblasts. This unified framework aims to improve communication within the research community and enhance understanding of fibroblast roles in gut homeostasis and gastrointestinal diseases.