1
|
Walsh ZH, Shah P, Kothapalli N, Shah SB, Nikolenyi G, Brodtman DZ, Leuzzi G, Rogava M, Mu M, Ho P, Abuzaid S, Vasan N, AlQuraishi M, Milner JD, Ciccia A, Melms JC, Izar B. Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens. Nat Biotechnol 2024:10.1038/s41587-024-02235-x. [PMID: 38783148 DOI: 10.1038/s41587-024-02235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Single-nucleotide variants (SNVs) in key T cell genes can drive clinical pathologies and could be repurposed to improve cellular cancer immunotherapies. Here, we perform massively parallel base-editing screens to generate thousands of variants at gene loci annotated with known or potential clinical relevance. We discover a broad landscape of putative gain-of-function (GOF) and loss-of-function (LOF) mutations, including in PIK3CD and the gene encoding its regulatory subunit, PIK3R1, LCK, SOS1, AKT1 and RHOA. Base editing of PIK3CD and PIK3R1 variants in T cells with an engineered T cell receptor specific to a melanoma epitope or in different generations of CD19 chimeric antigen receptor (CAR) T cells demonstrates that discovered GOF variants, but not LOF or silent mutation controls, enhanced signaling, cytokine production and lysis of cognate melanoma and leukemia cell models, respectively. Additionally, we show that generations of CD19 CAR T cells engineered with PIK3CD GOF mutations demonstrate enhanced antigen-specific signaling, cytokine production and leukemia cell killing, including when benchmarked against other recent strategies.
Collapse
Affiliation(s)
- Zachary H Walsh
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Parin Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Neeharika Kothapalli
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shivem B Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gergo Nikolenyi
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - D Zack Brodtman
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Meri Rogava
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael Mu
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia Ho
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Sinan Abuzaid
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Mohammed AlQuraishi
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua D Milner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alberto Ciccia
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Johannes C Melms
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Benjamin Izar
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY, USA.
- Columbia Center for Translational Immunology, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
2
|
Walsh ZH, Shah P, Kothapalli N, Nikolenyi G, Shah SB, Leuzzi G, Mu M, Ho P, Abuzaid S, Brodtman ZD, Vasan N, AlQuraishi M, Milner JD, Ciccia A, Melms JC, Izar B. Massively parallel base editing screens to map variant effects on anti-tumor hallmarks of primary human T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571465. [PMID: 38168306 PMCID: PMC10760091 DOI: 10.1101/2023.12.13.571465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Base editing enables generation of single nucleotide variants, but large-scale screening in primary human T cells is limited due to low editing efficiency, among other challenges 1 . Here, we developed a high-throughput approach for high-efficiency and massively parallel adenine and cytosine base-editor screening in primary human T cells. We performed multiple large-scale screens editing 102 genes with central functions in T cells and full-length tiling mutagenesis of selected genes, and read out variant effects on hallmarks of T cell anti-tumor immunity, including activation, proliferation, and cytokine production. We discovered a broad landscape of gain- and loss-of-function mutations, including in PIK3CD and its regulatory subunit encoded by PIK3R1, LCK , AKT1, CTLA-4 and JAK1 . We identified variants that affected several (e.g., PIK3CD C416R) or only selected (e.g. LCK Y505C) hallmarks of T cell activity, and functionally validated several hits by probing downstream signaling nodes and testing their impact on T cell polyfunctionality and proliferation. Using primary human T cells in which we engineered a T cell receptor (TCR) specific to a commonly presented tumor testis antigen as a model for cellular immunotherapy, we demonstrate that base edits identified in our screens can tune specific or broad T cell functions and ultimately improve tumor elimination while exerting minimal off-target activity. In summary, we present the first large-scale base editing screen in primary human T cells and provide a framework for scalable and targeted base editing at high efficiency. Coupled with multi-modal phenotypic mapping, we accurately nominate variants that produce a desirable T cell state and leverage these synthetic proteins to improve models of cellular cancer immunotherapies.
Collapse
|