A genome-scale screen for synthetic drivers of T cell proliferation

The engineering of autologous patient T cells for adoptive cell therapies has revolutionized the treatment of several types of cancer(1). However, further improvements are needed to increase response and cure rates. CRISPR-based loss-of-function screens have been limited to negative regulators of T cell functions(2-4) and raise safety concerns owing to the permanent modification of the genome. Here we identify positive regulators of T cell functions through overexpression of around 12,000 barcoded human open reading frames (ORFs). The top-ranked genes increased the proliferation and activation of primary human CD4(+) and CD8(+) T cells and their secretion of key cytokines such as interleukin-2 and interferon-gamma. In addition, we developed the single-cell genomics method OverCITE-seq for high-throughput quantification of the transcriptome and surface antigens in ORF-engineered T cells. The top-ranked ORF-lymphotoxin-beta receptor (LTBR)-is typically expressed in myeloid cells but absent in lymphocytes. When overexpressed in T cells, LTBR induced profound transcriptional and epigenomic remodelling, leading to increased T cell effector functions and resistance to exhaustion in chronic stimulation settings through constitutive activation of the canonical NF-kappa B pathway. LTBR and other highly ranked genes improved the antigen-specific responses of chimeric antigen receptor T cells and gamma delta T cells, highlighting their potential for future cancer-agnostic therapies(5). Our results provide several strategies for improving next-generation T cell therapies by the induction of synthetic cell programmes.

Automated summary

Engineering autologous T cells has significantly improved cancer treatment. CRISPR-based loss-of-function screens have limitations and safety concerns. In this study, overexpression of specific genes enhanced T cell functions and a new method called OverCITE-seq was developed for analyzing genetically engineered T cells. LTBR, a highly ranked gene, showed increased T cell effector functions and resistance to exhaustion. These findings have potential implications for future T cell therapies.