Abstract 4082: Expression of Chimeric Antigen Receptor Therapy Targets in Subpopulations Detected by Single-Cell Sequencing of Normal Cells May Contribute to Off-Tumor Toxicity

Abstract Chimeric antigen receptor (CAR)-engineered cell therapy, which leverages genetically modified immune cells to generate a tailored immune response, has revolutionized cancer treatment (Dougan et al., 2021; Hong et al., 2020). The number, type and indications of clinical trials for CAR-engineered cell therapies have increased rapidly in recent years (MacKay et al., 2020). However, serious and potentially life-threaten toxicities, such as on-target, off-tumor effects, remain a major limitation of CAR-engineered cell therapies (Dougan et al., 2021; MacKay et al., 2020). To better understand the effects of CAR-directed immunotherapy, a systematic single-cell-level dissection of the expression of divergent CAR targets in various cell types across different normal tissues is urgently required. We analyzed the expression of 591 CAR targets, including 71 that were employed in clinical trials up to January 2021 and 520 that were predicted to have favorable safety profiles (MacKay et al., 2020), in two independent single-cell cohorts, including 342,755 adult cell scRNA-seq data from human cell landscape (HCL) based on Microwell-seq (Han et al., 2020), and 84,363 adult cell scRNA-seq data from adult human cell atlas (AHCA) based on 10× Genomics (He et al., 2020). We used a stringent cutoff by defining a CAR target as a potentially risky gene (PRG) if it was measurable in more than 100 non-immune cells and more than 2% of the total cells in at least three normal tissues. We identified 92 and 88 PRGs from HCL and AHCA by employing this criterion, with 57 PRGs shared in both HCL and AHCA datasets (hypergeometric test p = 7.17×10-29), suggesting the robustness of our analysis. To aid the research community in the design of CAR targets, we developed a user-friendly data portal, CAR target gene toxicity at single-cell level (CARTSC) (https://hanlab.tamhsc.edu/CARTSC/), to allow for browsing and searching the single target and logical ‘and’ design switch expressions at the single-cell level. Citation Format: Ying Jing, Yuan Liu, Qiang Li, Leng Han. Expression of chimeric antigen receptor therapy targets in subpopulations detected by single-cell sequencing of normal cells may contribute to off-tumor toxicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4082.