Microbial valerate is associated with CAR T dysbiosis and its supplementation enhances CAR T function in B-cell lymphoma

Rehman, L.; Song, W.; Rehman, A.; Singh, K.; Rawat, S. G.; Darbaniyan, F.; Le, C. C.; Aletti, F. M.; Weng, J.; Liu, J.; Cheng, X.; Tang, Y.; Patchva, S.; Richard, M. D.; Chu, F.; Cao, J.; Flowers, C. R.; Shpall, E. J.; Tanner, M. R.; Fahrmann, J.; Elinav, E.; Stein-Thoeringer, C. K.; Jain, M. D.; Jenq, R. R.; Jain, A.; Neelapu, S. S.; Zheng, Y.; Saini, N. Y.

doi:10.64898/2026.09.01.748711

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bioRxiv · 10.64898/2026.09.01.748711

Microbial valerate is associated with CAR T dysbiosis and its supplementation enhances CAR T function in B-cell lymphoma

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Abstract

Anaerobe-depleting antibiotic exposure is associated with inferior progression-free survival after CD19 CAR T-cell therapy in large B-cell lymphoma, yet the cellular mechanisms linking gut dysbiosis to the CAR T-cell product and whether this imprint is reversible have remained undefined. In two independent CAR-T candidate cohorts, low stool valerate at the time of CAR-T eligibility identified a multi-metabolite-deficient dysbiotic gut microbiome state marked by depletion of fiber-fermenting commensals and loss of carbohydrate-fermentation, SCFA-biosynthesis, and amino-acid metabolism pathways. Reanalysis of single-cell RNA sequencing from 42 lymphoma patients stratified by piperacillin-tazobactam/imipenem/meropenem (PIM) exposure revealed that PIM-exposed CAR T-cell products were CD4-skewed, with significantly elevated AP-1/immediate-early gene (IEG) and cellular activation signatures that together predicted inferior progression-free survival. Ex vivo conditioning of CAR T-cells with valerate produced a chromatin and transcription factor program distinct from butyrate or propionate, characterized by KLF/SP/EGR family engagement, KLF4 promoter opening, and broad induction of AP-1/IEG and MHC class II transcripts, whereas butyrate drove broader chromatin remodeling with TBX21/EOMES/NF-{kappa}B gains and KLF2 promoter closure, and propionate induced an NFY-centered program with preferential commitment to low-mitochondrial-content states. Untargeted metabolomics confirmed valerate uptake and mitochondrial {beta}-oxidation in CAR T-cells, while dietary sodium valerate supplementation in meropenem-treated mice bearing A20 lymphoma significantly reduced tumor burden and extended survival compared with CAR T-cells alone. These findings identify stool valerate as a bedside-deployable biomarker of dysbiosis-imprinted CAR T-cell dysfunction and support ex vivo or dietary valerate supplementation as a clinically tractable strategy to improve CAR-T anti-tumor function in patients with disrupted gut microbiomes.

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Rehman, L., Song, W., Rehman, A., Singh, K., Rawat, S. G., Darbaniyan, F., Le, C. C., Aletti, F. M., Weng, J., Liu, J., Cheng, X., Tang, Y., Patchva, S., Richard, M. D., Chu, F., Cao, J., Flowers, C. R., Shpall, E. J., Tanner, M. R., Fahrmann, J., Elinav, E., Stein-Thoeringer, C. K., Jain, M. D., Jenq, R. R., Jain, A., Neelapu, S. S., Zheng, Y., Saini, N. Y.. 2026-09-03. Microbial valerate is associated with CAR T dysbiosis and its supplementation enhances CAR T function in B-cell lymphoma. https://doi.org/10.64898/2026.09.01.748711

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