
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.19.608538
preprint
2
Article
Microbial metabolite-guided CAR T cell engineering enhances anti-tumor immunity via epigenetic-metabolic crosstalk
Staudt Sarah
Nikolka Fabian
Perl Markus
Franz Julia
Leblay Noemie
Yuan Xiaoli-Kat
Warmuth Linda
Fantes Matthias A
Skorpskaite Aiste
Fei Teng http://orcid.org/0000-0001-7888-1715

Bromberg Maria
San Martin-Uriz Patxi
Rodriguez-Madoz Juan Roberto
Ziegler-Martin Kai
Adil-Gholam Nazdar
Benz Pascal
Tran Huu Phuc
Stein-Thoeringer Christoph
Schmitt Michael
Kleigrewe Karin
Freitag Fabian
Riester Zeno
Weber Justus
Mangold Kira
Einsele Hermann
Prosper Felipe
Ellmeier Wilfried http://orcid.org/0000-0001-8192-8481

Busch Dirk
Visekruna Alexander
Slingerland John
Shouval Roni
Hiller Karsten
van den Brink Marcel
Pausch Patrick
Neri Paola
Hudecek Michael
Poeck Hendrik
Luu Maik http://orcid.org/0000-0003-2843-3919

13 9 2024
2024.08.19.608538https://creativecommons.org/licenses/by-nc-nd/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
http://biorxiv.org/lookup/doi/10.1101/2024.08.19.608538
nihpp-2024.08.19.608538.pdf
Emerging data have highlighted a correlation between microbiome composition and cancer immunotherapy outcome. While commensal bacteria and their metabolites are known to modulate the host environment, contradictory effects and a lack of mechanistic understanding impede the translation of microbiome-based therapies into the clinic. In this study, we demonstrate that abundance of the commensal metabolite pentanoate is predictive for survival of chimeric antigen receptor (CAR) T cell patients in two independent cohorts. Its implementation in the CAR T cell manufacturing workflow overcomes solid tumor microenvironments in immunocompetent cancer models by hijacking the epigenetic-metabolic crosstalk, reducing exhaustion and promoting naive-like differentiation. While synergy of clinically relevant drugs mimicked the phenotype of pentanoate-engineered CAR T cells in vitro, in vivo challenge showed inferior tumor control. Metabolic tracing of 13C-pentanoate revealed citrate generation in the TCA cycle via the acetyl- and succinyl-CoA entry points as a unique feature of the C5 aliphatic chain. Inhibition of the ATP-citrate lyase, which links metabolic output and histone acetylation, led to accumulation of pentanoate-derived citrate from the succinyl-CoA route and decreased functionality of SCFA-engineered CAR T cells. Our data demonstrate that microbial metabolites are incorporated as epigenetic imprints and implementation into CAR T cell production might serve as embodiment of the microbiome-host axis benefits for clinical applications.
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pmc
