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

Microbial valerate has been linked to a condition known as CAR T dysbiosis, which negatively impacts the effectiveness of CAR T-cell therapy in treating B-cell lymphoma. This discovery stems from two separate studies conducted on CAR-T candidate cohorts. The research found that lower levels of valerate in stool samples were associated with a dysbiotic gut microbiome, characterized by a decline in fiber-fermenting commensals and an absence of carbohydrate-fermentation, SCFA-biosynthesis, and amino-acid metabolism pathways.

Further analysis of single-cell RNA sequencing data from 42 lymphoma patients, taking into account their exposure to piperacillin-tazobactam/imipenem/meropenem (PIM), revealed that CAR T-cell products exposed to PIM exhibited a CD4-skewed profile. This CD4-skewed CAR T-cell product showed significantly elevated AP-1/immediate-early gene (IEG) and cellular activation signatures, which were directly linked to a poorer progression-free survival rate.

Ex vivo conditioning of CAR T-cells with valerate led to a unique chromatin and transcription factor program, distinct from that induced by butyrate or propionate. This valerate-driven program was characterized by the engagement of the KLF/SP/EGR family, the opening of the KLF4 promoter, and the broad induction of AP-1/IEG and MHC class II transcripts.

Conversely, butyrate induced a broader chromatin remodeling, with gains in TBX21/EOMES/NF-{kappa}B and a closure of the KLF2 promoter. Propionate, on the other hand, triggered an NFY-centered program, favoring low-mitochondrial-content states.

Untargeted metabolomics confirmed the uptake and mitochondrial {beta}-oxidation of valerate in CAR T-cells. Dietary sodium valerate supplementation in mice bearing A20 lymphoma, after receiving meropenem treatment, significantly reduced tumor burden and extended survival compared to CAR T-cells alone. These findings suggest that stool valerate can serve as a bedside-deployable biomarker for dysbiosis-imprinted CAR T-cell dysfunction, and that ex vivo or dietary valerate supplementation can be a clinically feasible approach to enhance CAR-T anti-tumor function in patients with disrupted gut microbiomes.