Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states

Abstract

SummaryCell atlas projects have nominated recurrent transcriptional states as drivers of biological processes and disease, but their origins, regulation, and properties remain unclear. To enable complementary functional studies, we developed a scalable approach for recapitulating cell statesin vitrousing CRISPR activation (CRISPRa) Perturb-seq. Aided by a novel multiplexing method, we activated 1,836 transcription factors in two cell types. Measuring 21,958 perturbations showed that CRISPRa activated targets within physiological ranges, that epigenetic features predicted activatable genes, and that the protospacer seed region drove an off-target effect. Perturbations recapitulatedin vivofibroblast states, including universal and inflammatory states, and identifiedKLF4andKLF5as key regulators of the universal state. Inducing the universal state suppressed disease-associated states, highlighting its therapeutic potential. Our findings cement CRISPRa as a tool for perturbing differentiated cells and indicate thatin vivostates can be elicited via perturbation, enabling studies of clinically relevant statesex vivo.