Single-cell-guided identification of logic-gated antigen combinations for designing effective and safe CAR therapy

作者：Sanna Madan, Tiangen Chang, Alexandra R. Harris, Huaitian Liu, Andrew Martinez, 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：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2025 · DOI：10.1101/2025.03.19.644074 · 被引用次数：7 · 研究领域：CAR-T cell therapy research、Single-cell and spatial transcriptomics、Microfluidic and Bio-sensing Technologies

Abstract Chimeric antigen receptor (CAR) T-cell therapy has revolutionized the treatment of hematological malignancies. However, its application in solid tumors remains limited because single targets are unlikely to suffice due to tumor antigen heterogeneity and off-tumor toxicities. To overcome these obstacles, we developed LogiCAR designer , a computational approach that utilizes single-cell transcriptomics data from patient tumors to systematically identify the cancer-specific antigen circuits with logic gates (“AND,” “OR,” and “NOT”) that target the majority of cancer cells in a tumor while sparing normal cells and tissues as much as possible. LogiCAR designer efficiently scales to higher-order antigen combinations involving up to five genes. Applied to a large-scale dataset encompassing approximately 2 million cells (including > 620k tumor cells) from 342 clinical patient samples across all major breast cancer subtypes, LogiCAR designer identified antigen circuits with enhanced tumor-targeting efficacy and improved safety profiles compared to both previously reported circuits and single-target therapies in clinical trials. However, even these optimized shared circuits still proved insufficient for some patients. We hence systematically studied LogiCAR designer ’s ability to identify highly effective CAR circuits that are individualized to each patient. Remarkably, such personalized CAR circuits provide estimated tumor-targeting efficacy tantamount to complete response...