Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation

Intestinal stem cells (ISCs) are maintained by a niche mechanism, in which multiple ISCs undergo differential fates where a single ISC clone ultimately occupies the niche. Importantly, mutations continually accumulate within ISCs creating a potential competitive niche environment. Here we use single cell lineage tracing following stochastic transforming growth factor beta receptor 2 (Tgf beta R2) mutation to show cell autonomous effects of Tgf beta R2 loss on ISC clonal dynamics and differentiation. Specifically, Tgf beta R2 mutation in ISCs increased clone survival while lengthening times to monoclonality, suggesting that Tgf beta signaling controls both ISC clone extinction and expansion, independent of proliferation. In addition, Tgf beta R2 loss in vivo reduced crypt fission, irradiation-induced crypt regeneration, and differentiation toward Paneth cells. Finally, altered Tgf beta signaling in cultured mouse and human enteroids supports further the in vivo data and reveals a critical role for Tgf beta signaling in generating precursor secretory cells. Overall, our data reveal a key role for Tgf beta signaling in regulating ISCs clonal dynamics and differentiation, with implications for cancer, tissue regeneration, and inflammation.