CRISPRa Perturb-seq decodes stimulation responses in primary human T cells

Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. University of California San Francisco researchers report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin-2 (IL-2) and interferon-γ (IFN-γ) production. Arrayed CRISPRa confirmed key hits and enabled multiplexed secretome characterization, revealing reshaped cytokine responses. Coupling CRISPRa screening with single-cell RNA sequencing enabled deep molecular characterization of screen hits, revealing how perturbations tuned T cell activation and promoted cell states characterized by distinct cytokine expression profiles. These screens reveal genes that reprogram critical immune cell functions, which could inform the design of immunotherapies.

Genome-wide CRISPRa/i screens discover tunable regulators of stimulation-responsive cytokine production in primary human T cells. Genome-wide CRISPRa/i gain-of-function and loss-of-function screens in human T cells allowed for systematic identification of regulators of cytokine production. Follow-up on key CRISPRa screen hits with secretome and scRNA-seq analysis helped to decode how these regulators tune T cell activation and program cells into different stimulation-responsive states.