Mapping gene regulatory networks of primary CD4⁺ T cells using single-cell genomics and genome engineering

Abstract

Gene regulatory programs controlling the activation and polarization of CD4⁺ T cells are incompletely mapped and the interindividual variability in these programs remain unknown. We sequenced the transcriptomes of ~160k CD4⁺ T cells from 9 donors following pooled CRISPR perturbation targeting 140 regulators. We identified 134 regulators that affect T cell functionalization, including IRF2 as a positive regulator of Th₂ polarization. Leveraging correlation patterns between cells, we mapped 194 pairs of interacting regulators, including known (e.g. BATF and JUN) and novel interactions (e.g. ETS1 and STAT6). Finally, we identified 80 natural genetic variants with effects on gene expression, 48 of which are modified by a perturbation. In CD4⁺ T cells, CRISPR perturbations can influence in vitro polarization and modify the effects of trans and cis regulatory elements on gene expression.