Early-life mucosal T cells direct intestinal stem cell fate via a coordinated developmental program 2305986

Abstract

Although early-life immunity was once considered immature, the human fetal immune system is dynamic and compartmentalized by the 2nd trimester. By the 21st gestational week, T lymphocytes dominate the fetal small intestine (SI), yet their mucosal functions prenatally are unclear. Because fetal T cell infiltration is concomitant with rapid intestinal epithelial growth and differentiation in utero, we hypothesized that early-life intestinal T cells support normal mucosal development and function. We generated an ex vivo co-culture model where SI T cells from fetal or adult donors are integrated with SI organoids, assessing organoid generation and differentiation by microscopy, single-cell RNA sequencing, and multiplexed cytokine assays. To complement our ex vivo approach, we also performed spatial transcriptomics on healthy and diseased SI tissue to investigate T cell-epithelial interactions throughout the human lifespan. Fetal SI T cells significantly promoted organoid generation and cell cycling gene programs, even in organoids derived from adults or diseased neonates, suggesting they can reprogram the epithelium towards a regenerative state. Uniquely, fetal SI T cells also directed intestinal stem cell (ISC) differentiation towards the secretory lineage. Yet, adult SI T cells did not support organoid growth or differentiation, highlighting specialized roles of fetal T cells. To test whether secreted factors direct ISC fate, we cultured organoids with T cell-derived conditioned media, which was insufficient to stimulate organoid generation. Additionally, fetal SI T cells were significantly more likely to localize near ISCs, supporting the need for physical interactions. Overall, we report a unique and coordinated developmental program where fetal SI T cells shape ISC programming by balancing growth and differentiation, offering a new therapeutic angle for intestinal diseases where these processes are disrupted. NIH AI171980, AI179570; NIH P30DK034854-36; YSM Science Fellows 2024 Program and Grant; Yale Department of Pediatrics Trainee Pilot Grant Mucosal and Regional Immunology (MUC)