A genome-wide CRISPR activation map of surface protein expression in human CD4 T cells

Abstract

Surface proteins define T cell identity and function, but the abundance of each protein is not determined by transcription alone. Existing genome-wide CRISPR screens in primary human T cells either profile the transcriptome or isolate cells based on a single functional or protein phenotype. Here we present SCITO-Perturb-seq, a novel platform that couples combinatorial-indexed single-cell cytometry sequencing with pooled CRISPR activation (CRISPRa) to map the causal regulation of 201 surface proteins across 3.6 million human CD4 T cells. We find that 16% of activated genes significantly alter the expression of at least one surface protein. By applying semi-nonnegative matrix factorization to the perturbation effect matrix, we identified five modules corresponding to known CD4 T cell states. Notably, these modules group surface proteins by their shared response to perturbation, revealing coordinated regulation of proteins that are not co-expressed in unperturbed cells. SCITO-Perturb-seq represents the first genome-wide CRISPRa screen paired with direct, high-dimensional surface protein profiling, providing a comprehensive regulatory map of the CD4 T cell surface proteome.