Abstract LB062: Identifying novel targets for CAR-T therapies from single cell RNA-sequencing data

Abstract Chimeric antigen receptor T (CAR-T) cell therapies have revolutionized cancer treatment. While CAR-T has yielded tremendous clinical success for patients with liquid tumors, its potential remains to be unleashed against solid tumors. One key challenge is identifying optimal targets for these therapies: cell surface proteins that are expressed highly and uniformly by a tumor’s constituent malignant cells, and minimally so by healthy tissues. Employing a systematic, data-driven analysis, we first charted the landscape of existing CAR-T targets in the clinic, identifying the leading targets in each indication based on tumor selectivity and safety metrics. Next, from patient tumor single cell transcriptomics data, we performed a genome wide search across many different solid tumor types to identify new and candidate CAR-T targets with better selectivity and safety scores than extant ones. Remarkably, in almost all indications, we could not find such better targets, testifying to the near optimality of the current target space, at least in accordance with our measures. However, one striking exception is HPV-negative head and neck squamous cell carcinoma (HNSC), for which there is currently a dearth of existing CAR-T targets in clinics. Specifically, our investigation has discovered 20 novel CAR-T targets for treating HNSC and one for treating glioblastoma more precisely and safely. Citation Format: Sanna Madan, Sanju Sinha, Alejandro A. Schäffer, Eytan Ruppin. Identifying novel targets for CAR-T therapies from single cell RNA-sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB062.