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

Camara-Pena, S.; Rodriguez-Marquez, P.; Planell, N.; Calleja-Cervantes, M. E.; Jordana-Urriza, L.; Cinnirella, G.; Reich-Zeliger, S.; Rodriguez-Otero, P.; Tamariz, E.; Ochoa, I.; Yosef, N.; Rodriguez-Madoz, J. R.; Prosper, F.; Hernaez, M.

2025-10-13 bioinformatics
10.1101/2025.10.11.681788 bioRxiv
Show 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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The top 4 journals account for 50% of the predicted probability mass.

1
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9
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2.2%
10
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Top 0.9%
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11
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1.9%
12
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13
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1.8%
15
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16
Science
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Top 7%
1.1%
17
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1.1%
18
eLife
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19
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Top 2%
1.0%
20
Proceedings of the National Academy of Sciences
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1.0%
21
Cell Reports
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Top 26%
0.9%
22
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23
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25
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28
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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.