Single-nucleus multi-omics analysis of mouse small-intestinal Lgr5+ cell populations reveals Foxa3-induced Paneth cell-lineage differentiation

Lgr5+ stem cells play crucial roles in maintaining intestinal epithelial cell homeostasis. However, the cellular heterogeneity and underlying regulatory programs of Lgr5+ small intestinal stem cells (ISCs) remain elusive. In this study, we profiled gene expression and chromatin accessibility of Lgr5+ ISCs at single-cell resolution to gain a deeper understanding of the lineage specification and early fate determining mechanisms. Our analysis identified a total of 6 subsets of Lgr5+ cell populations, which exhibited heterogeneity in gene expression and chromatin structure. We found that early fate-determining processes diverged the absorptive and secretory lineages within Lgr5+ cells. We further constructed gene regulatory networks controlling lineage determination and identified Foxa3 as a key transcription factor that regulates the differentiation of the intestinal secretory precursor. In vitro knockdown of Foxa3 disrupted the differentiation of Paneth cells by modulating Peroxisome-Proliferator-Activated Receptors (PPARs). Further Foxa3-targeted CUT&Tag sequencing analysis also verified that Foxa3 predominantly drives Paneth cell differentiation in the small intestine by regulating the expression of core genes in the PPAR signaling pathway. These results provide a comprehensive reference map for advancing our understanding of intestinal epithelial development and related diseases.