Modular Pooled Discovery of Synthetic Knockin Sequences to Program Durable Cell Therapies

Abstract

SUMMARYChronic stimulation can cause T cell dysfunction and limit efficacy of cellular immunotherapies. CRISPR screens have nominated gene targets for engineered T cells, but improved methods are required to compare large numbers of synthetic knockin sequences to reprogram cell functions. Here, we developed Modular Pooled Knockin Screening (ModPoKI), an adaptable platform for modular construction of DNA knockin libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors. Over 20 ModPoKI screens across human TCR and CAR T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct to enhance long-term T cell fitness and anti-cancer functionin vitroandin vivo. ModPoKI’s modularity allowed us to generate a ∼10,000-member library of TF combinations. Non-viral knockin of a combined BATF-TFAP4 polycistronic construct further enhanced functionin vivo. ModPoKI facilitates discovery of complex gene constructs to program cellular functions.HighlightsModular pooled knockins of hundreds of TF and surface receptor constructs combined with different antigen receptorsChronic stimulation screens discover programs to improve T cell persistenceCombinatorial knockin screens with ∼10,000 transcription factor combinationsBATF-TFAP4 dual knockin construct improves CAR T cell functionin vitroandin vivo