In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer

Improving effector activity of antigen-specific T cells is a major goal in cancer immunotherapy. Despite the identification of several effector T cell (TEFF)-driving transcription factors (TFs), the transcriptional coordination of TEFF biology remains poorly understood. We developed an in vivo T cell CRISPR screening platform and identified a key mechanism restraining TEFF biology through the ETS family TF, Fli1. Genetic deletion of Fli1 enhanced TEFF responses without compromising memory or exhaustion precursors. Fli1 restrained TEFF lineage differentiation by binding to cis-regulatory elements of effector-associated genes. Loss of Fli1 increased chromatin accessibility at ETS:RUNX motifs, allowing more efficient Runx3-driven TEFF biology. CD8+ T cells lacking Fli1 provided substantially better protection against multiple infections and tumors. These data indicate that Fli1 safeguards the developing CD8+ T cell transcriptional landscape from excessive ETS:RUNX-driven TEFF cell differentiation. Moreover, genetic deletion of Fli1 improves TEFF differentiation and protective immunity in infections and cancer. [Display omitted] •OpTICS In vivo CD8+ T cell CRISPR screening platform developed for focused gene discovery•OpTICS identifies genes involved in effector versus exhausted CD8+ T cells•The Fli1 transcription factor represses optimal effector CD8+ T cells during exhaustion•Fli1 antagonizes epigenetic accessibility at ETS-RUNX sites limiting Runx3 activity An in vivo T cell CRISPR screening platform identifies Fli1 as a factor modulating CD8+ T cell effector differentiation with limited effects on memory or exhaustion.