Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [scMultiomics]
Emerging evidence highlights regulatory T cell (Treg) heterogeneity in lymphoid and non-lymphoid tissues, but we have limited understanding of context-dependent functions and spatiotemporal regulators of heterogenous Treg states, especially during perinatal life when immune tolerance is established. Using single-cell transcriptomics profiling and experimental validations, we revealed that Vps34 is essential for orchestrating effector Treg (eTreg) transitional heterogeneity during perinatal life. We found that loss of Vps34 reduced terminal eTreg accumulation in lymphoid tissues, associated with decreased generation of Treg cells in non-lymphoid tissues and development of an early-onset autoimmune disease. After perinatal life, Vps34-deficient eTreg accumulation was further impaired due to reduced survival, highlighting temporal regulation of eTreg heterogeneity and maintenance by Vps34. Accordingly, inhibition of Vps34 in mature Treg cells also disrupted immune homeostasis but boosted anti-tumor immunity. Mechanistically, multiomics profiling approaches uncovered that Vps34-orchestrated transcriptional and epigenetic remodeling promotes terminal eTreg programming. Further, via genetic deletion of the Vps34-interacting proteins Atg14 or Uvrag in Treg cells, we established that autophagy (via Atg14) but not endocytosis (via Uvrag) was required for the overall survival, but not transitional heterogeneity, of eTreg cells. Accordingly, mice with Treg-specific deletion of Atg14, but not Uvrag, had moderately disrupted immune homeostasis and reduced tumor growth, with Vps34 and Atg14-dependent gene signatures also being elevated in intratumoral Treg cells from human cancer patients. Collectively, our study reveals distinct Vps34-orchestrated signaling events that temporally regulate eTreg heterogeneity and functional adaptation and the pathophysiological outcomes on autoimmunity versus anti-tumor immunity. Overall design: We used scMultiomics (snRNA+scATAC; 10X Genomics) to compare the transcriptome of spleen-derived control (Control; n = 1) and Vps34-deficient (Vps34 KO; n = 2)  CD4+Foxp3-YFP+ Treg cells, isolated from 12-day-old control (Foxp3CrePik3c3+/fl) or Foxp3CrePikc3cfl/fl mice.