scRNA-seq for thymocyte subsets from WT or SETDBf/fCD4-Cre mice

Suppressing immune response promotes allograft survival, but also favors tumor progression and recurrence. How to selectively suppress allograft rejection while maintaining or even enhancing antitumor immunity is challenging. Here, we found mice deficient in Setdb1, an H3K9 methyltransferase, retained allograft but enhanced antitumor immunity. To explore the underlying mechanism, RNA-Seq was applied to compare the transcriptome between CD4+ T cells from wildtype mice and Setdb1-deficient mice. The data show that Setdb1 deficiency did not affect T cell activation or cytokine production, but induced more regulatory T (Treg) cell-associated gene expression. Treg cell depletion impaired the graft acceptance in Setdb1-deficient mice, indicating that the Treg cell promoted allograft survival. Surprisingly, Treg cell-specific Setdb1 deficiency could not prolong allograft survival, suggesting Setdb1 might function before Foxp3 induction. By using single cell RNA sequencing, we found that Setdb1 deficiency induced a new Treg population in thymus. This subset of Treg cells expressed less IL-1R2 and IL-18R1. Mechanistically, during Treg cell induction, Setdb1 was recruited by transcription factor ATF and modified histone methylation. Our data define Setdb1 in T cells as a target to suppress allograft rejection but maintain the antitumor immunity. Overall design: Thymocytes from WT or SETDBf/fCD4-Cre mice were enriched by anti-CD25 beads