Histone methylation mediates plasticity of human FOXP3+ regulatory T cells by modulating signature gene expressions

Summary CD 4 + FOXP 3 + regulatory T (Treg) cells constitute a heterogeneous and plastic T‐cell lineage that plays a pivotal role in maintaining immune homeostasis and immune tolerance. However, the fate of human Treg cells after loss of FOXP 3 expression and the epigenetic mechanisms contributing to such a phenotype switch remain to be fully elucidated. In the current study, we demonstrate that human CD 4 + CD 25 high CD 127 low/− Treg cells convert to two subpopulations with distinctive FOXP 3 + and FOXP 3 − phenotypes following in vitro culture with anti‐ CD 3/ CD 28 and interleukin‐2. Digital gene expression analysis showed that upon in vitro expansion, human Treg cells down‐regulated Treg cell signature genes, such as FOXP 3 , CTLA 4 , ICOS , IKZF 2 and LRRC 32 , but up‐regulated a set of T helper lineage‐associated genes, especially T helper type 2 (Th2)‐associated, such as GATA 3 , GFI 1 and IL 13 . Subsequent chromatin immunoprecipitation‐sequencing of these subpopulations yielded genome‐wide maps of their H3K4me3 and H3K27me3 profiles. Surprisingly, reprogramming of Treg cells was associated with differential histone modifications, as evidenced by decreased abundance of permissive H3K4me3 within the down‐regulated Treg cell signature genes, such as FOXP 3 , CTLA 4 and LRRC 32 loci, and increased abundance of H3K4me3 within the Th2‐associated genes, such as IL 4 and IL 5 ; however, the H3K27me3 modification profile was not significantly different between the two subpopulations. In conclusion, this study revealed that loss of FOXP 3 expression from human Treg cells during in vitro expansion can induce reprogramming to a T helper cell phenotype with a gene expression signature dominated by Th2 lineage‐associated genes, and that this cell type conversion may be mediated by histone methylation events.