Spatiotemporal and molecular factors determining T cell stemness and differentiation in autoimmune Type 1 Diabetes 2328677

Abstract

Type 1 diabetes (T1D) is a T cell—mediated autoimmune disease driven by β cell-specific CD8 T cells. How autoreactive T cells arise and sustain disease remains unclear. Using the non-obese diabetic mouse model of T1D, we previously identified a stem-like CD8 T cell population in the pancreatic lymph node (pLN) which initiates and sustains β cell destruction: stem T cells (TSC) self-renew and continuously give rise to differentiated progeny (TDIFF) that migrate to the pancreas and kill β cells. Spatial positioning of somatic stem cells is critical for their maintenance, and that niche restricted signals (i.e., WNT and NOTCH) regulate the balance between self-renewal and differentiation. However, if and how T cell stemness is associated with distinct intranodal positioning in pLN, and whether interference in migration disrupts differentiation, is unknown. We conducted (i) paired single-cell RNA- and ATAC-sequencing, (ii) adoptive T cell transfer studies, (iii) high-resolution imaging, (iv) CRISPR/Cas9 mediated gene editing of autoimmune T cells in pLN to identify the molecular and functional characteristics of TSC and TDIFF. We discovered unique transcription factors and epigenetic programs governing autoimmune T cell stemness and differentiation. TSC and TDIFF express distinct chemokine receptors and integrins, suggesting that T cell stemness and differentiation are driven by intranodal positioning. Strikingly, WNT and NOTCH signaling were enriched in TSC, driving the expression of critical stem genes, thereby connecting T cell stemness to somatic stem cell biology. Pharmacological blockade and CRISPR/Cas9-mediated deletion of integrins and cell-cell interactions prevented autoimmune T cell differentiation and disease. Our studies identify novel transcriptional regulators and niche-dependent signals that determine autoimmune T cell stemness and differentiation, opening novel therapeutic avenues for the prevention and treatment of T1D and other autoimmune diseases. NIH F31DK141119, NIH R01AI173249, Juvenile Diabetes Research Foundation JDRF SRA-2023-1410-S-B, MSKCC Basic Research Innovation Award (BRIA), Hearst Foundation Lymphocyte Differentiation and Peripheral Maintenance (LYM)