An open CAR-T single-cell atlas to enable in-depth characterization and rational engineering of CAR-T products

Sergio Camara-Peña; Paula Rodríguez-Márquez; Núria Planell; María Eréndira Calleja-Cervantes; Lorea Jordana-Urriza; Giacomo Cinnirella; Shlomit Reich-Zeliger; Paula Rodríguez‐Otero; Luis‐Esteban Tamariz‐Amador; Idoia Ochoa; Nir Yosef; Juan R. Rodríguez-Madoz; Felipe Prósper; Mikel Hernáez

doi:10.1101/2025.10.11.681788

BioinformaticsbioRxivOct 11, 2025

Preprint

An open CAR-T single-cell atlas to enable in-depth characterization and rational engineering of CAR-T products

Sergio Camara-Peña, Paula Rodríguez-Márquez iD, Núria Planell iD, María Eréndira Calleja-Cervantes iD, Lorea Jordana-Urriza iD, Giacomo Cinnirella iD, Shlomit Reich-Zeliger iD, Paula Rodríguez‐Otero iD, Luis‐Esteban Tamariz‐Amador iD, Idoia Ochoa iD, Nir Yosef iD, Juan R. Rodríguez-Madoz iD, Felipe Prósper iD, Mikel Hernáez iD

Abstract

BRIEF ABSTRACTWe built a CAR-T cell functional atlas from over one million cells across 13 studies, integrating data from patients and healthy donors. The atlas captures 11 phenotypes, links infusion product composition with clinical response, and reveals sex- and age-dependent effects, metabolic signatures, and rare ICANS-associated cells. This open-access resource provides a foundation to understand CAR-T cell function and guide the design of next-generation therapies.

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