UCSF

T cell receptor (TCR) stimulation and cytokine cues drive the differentiation of CD4+ naïve T cells into effector T cell populations with distinct pro-inflammatory or regulatory functions. Unlike adult naïve T cells, human fetal naïve CD4+ T cells preferentially differentiate into FOXP3+ regulatory T (Treg) cells upon TCR activation independent of exogenous cytokine signalling. This cell-intrinsic predisposition for Treg differentiation is implicated in generating tolerance in utero; however, the underlying mechanisms remain largely unknown. Here, we reveal FOXP3-independent transcriptional and epigenetic programs shared between fetal naive T cells and committed adult Treg cells that are inactive in adult naive T cells. We further demonstrate that these transcriptional programs are retained upon Treg cell differentiation only in fetal-derived, but not adult-derived induced Treg (iTreg) cells. We identify a subset of Treg-specific enhancers that are already active in fetal naive T cells, including two active super-enhancers at Helios, a signature thymic Treg gene. Helios is expressed in fetal naive T cells, but not in adult naïve T cells, and only fetal iTreg cells maintain Helios expression. Fetal, but not adult iTreg cells, have suppressed IL-2 production, which is regulated by Helios in committed Treg cells. CRISPR-Cas9 ablation of Helios in fetal naive T cells thus resulted in increased IL-2 production by fetal iTreg cells. Critically, Helios knockout in fetal naïve T cells impaired their subsequent differentiation into Treg cells upon TCR stimulation, reduced the upregulation of immunosuppressive genes such as IL10 in fetal iTreg cells, and resulted in the increased upregulation of pro-inflammatory genes including IFNG. Subsequently, Helios knockout fetal iTreg cells produced less IL-10 and more IFNγ cytokines. Taken together, our results indicate a dual role for Helios in enhancing the cell-intrinsic predisposition of fetal naïve T cells for Treg differentiation and fine-tuning eventual fetal Treg function through transcriptional modulation. The Treg-biased transcriptional and epigenetic programs within fetal naive T cells identified here could thus be utilized to engineer enhanced iTreg populations from adult naïve T cells for adoptive cellular therapies.