Abstract 15: Massively parallel base-editing screens to map variant effects on anti-tumor hallmarks of primary human T cells and improve cell-based cancer immunotherapies
Authors: Walsh Zachary Hudson , Shah Parin , Kothapalli Neeha , Nikolenyi Gergo , Shah Shivem , Leuzzi Giuseppe , Vasan Neil , AlQuarishi Mohammed , Ciccia Alberto , Melms Johannes , Izar Benjamin 
Published: March 2024

Base editing enables precise generation of single nucleotide variants, but large-scale screening in primary human T cells has been limited by low editing efficiency. Here, we developed a high-throughput approach for highly efficient, massively parallel adenine and cytosine base-editor screening in primary human T cells. We performed multiple large-scale pooled screens editing 108 genes with central functions in T cells and whole-gene tiling mutagenesis of selected genes. All screens were functionally read out to capture the effect of variants on hallmarks of T cell anti-tumor immunity, including activation, proliferation, long-term persistence, and cytokine production. We discovered a broad landscape of gain-of-function and loss-of-function mutations and characterized their impact across multiple axes of T cell functions. Among others, we identified gain-of-function mutations in PIK3CD and its regulatory subunit PIK3R1, LCK, AKT1, and loss-of-function mutants of CTLA-4, driving increased T cell polyfunctionality. We validated several of these mutations by probing downstream signaling and functional outputs. To demonstrate the feasibility of using such screen results for improving cell-based cancer immunotherapies, we used human T cells with engineered T cell receptors recognizing specific epitopes in melanoma models. We base-edited these T cells with mutations identified in our screens and demonstrate that these mutations indeed significantly enhance cytotoxic cytokine production and tumor-lytic capacity with minimal off-target activity. Lastly, we also provide proof-of-feasibility for high-efficiency combinatorial base-editing in T cells. This study presents a framework for large-scale base editing screens with multi-dimensional functional readouts in cells that are typically difficult to molecularly engineer in a precise manner. This work also has important therapeutic implications: T cells are the substrate for clinically active cell-based therapies, such as adoptive transfer of tumor-infiltrating lymphocytes (TILs) or chimeric-receptor antigen T (CAR-T) cells. Our screen-informed base editing to achieve an improved T cell product against melanoma exemplifies the therapeutic power of generating synthetic protein variants that improve a wide range of existing and future T cell-based cancer immunotherapies.

Citation Format: Zachary Hudson Walsh, Parin Shah, Neeha Kothapalli, Gergo Nikolenyi, Shivem Shah, Giuseppe Leuzzi, Neil Vasan, Mohammed AlQuarishi, Alberto Ciccia, Johannes Melms, Benjamin Izar. Massively parallel base-editing screens to map variant effects on anti-tumor hallmarks of primary human T cells and improve cell-based cancer immunotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 15.