Functional CRISPR dissection of gene networks controlling human regulatory T cell identity.

Human regulatory T (T) cells are essential for immune homeostasis. The transcription factor FOXP3 maintains T cell identity, yet the complete set of key transcription factors that control T cell gene expression remains unknown. Here, we used pooled and arrayed Cas9 ribonucleoprotein screens to identify transcription factors that regulate critical proteins in primary human T cells under basal and proinflammatory conditions. We then generated 54,424 single-cell transcriptomes from T cells subjected to genetic perturbations and cytokine stimulation, which revealed distinct gene networks individually regulated by FOXP3 and PRDM1, in addition to a network coregulated by FOXO1 and IRF4. We also discovered that HIVEP2, to our knowledge not previously implicated in T cell function, coregulates another gene network with SATB1 and is important for T cell-mediated immunosuppression. By integrating CRISPR screens and single-cell RNA-sequencing profiling, we have uncovered transcriptional regulators and downstream gene networks in human T cells that could be targeted for immunotherapies.