Abstract C042: Systematic discovery of logic-gated cell surface targets for enhanced solid tumor CAR therapy through single-cell transcriptomics

作者：Sanna Madan, Tiangen Chang, Andrew Martinez, Alexandra R. Harris, Huaitian Liu, Saugato Rahman Dhruba, Binbin Wang, Padma Sheila Rajagopal, Sanju Sinha, Aravind Srinivasan, Simon Knott, Shahin Sayed, Francis Makokha, Chi‐Ping Day, Gretchen L. Gierach, Stefan Ambs, Alejandro A. Schäffer, Eytan Ruppin · 发表于：Molecular Cancer Therapeutics · 年份：2025 · DOI：10.1158/1535-7163.targ-25-c042 · 研究领域：CAR-T cell therapy research、Advanced Biosensing Techniques and Applications、Nanoplatforms for cancer theranostics

Abstract Background: Current CAR-T therapies for solid tumors are limited by suboptimal target selection, with single antigens failing to address tumor heterogeneity and causing on-target, off-tumor toxicities. Systematic identification of multi-target combinations using logic gates (AND, OR, NOT) represents an untapped approach for discovering safer, more effective CAR immunotherapy targets. Methods: We developed LogiCAR designer, a genetic algorithm-based framework that systematically screens 2,758 cell surface proteins to identify optimal 1-5 gene logic-gated target combinations (i.e., ‘circuits’) from single-cell transcriptomics data. Applied to the largest breast cancer single-cell dataset (∼2 million cells, >620k tumor cells from 342 patients across 17 cohorts), we optimized tumor-targeting efficacy while maintaining safety across 689,601 normal cells from 31 Human Protein Atlas tissues. Comprehensive target validation included RNA and protein expression profiling across major human tissues and tumor microenvironment specificity analysis. Results: Our systematic approach identified novel cell surface targets with superior profiles compared to current clinical candidates. The top 3-gene circuit ('GABRP | PRLR | VTCN1') achieved 60% tumor-targeting efficacy—234% higher than the best clinical trial targets. Newly discovered single targets (ELAPOR1, PRLR, BAMBI, LDLRAD3) demonstrated consistent tumor-specific expression (>2-fold tumor vs. non-tumor cells, p&am...