The Gut Microbiome Drives Endogenous T Cell Activation Following CAR-T Cell Therapy

Abstract Chimeric antigen receptor (CAR)-T cell therapy has become a promising clinical approach against hematological malignancies, but patients receiving CAR-T cell therapy still presented inconsistent clinical outcomes and are complicated by incomplete tumor eradication. The gut microbiome has shown strong correlation with the therapeutic outcomes of CAR-T cell therapy. However, the underlying mechanism of how gut microbiota affect CAR-T cell therapeutic potency remained undetermined. In this study, we established a syngeneic CD19+ murine lymphoma model which allows for the evaluation of both endogenous immune cells and gut microbiota following CD19-CD28ζ CAR-T therapy. Using single-cell transcriptomic analyses, we report that CAR-T cell infusion led to the activation of peripheral and gut-infiltrating endogenous CD8+ T cells towards an effector-like phenotype. In parallel, 16S RNA sequencing revealed substantial alterations of gut microbiota post-infusion. The composition of gut bacteria was associated with the activation status of endogenous CD8+ T cells and responsiveness to CAR-T therapy. More specifically, we identified gut bacteria strains Turicibacter and Parvibactor as critical determinants towards effective CAR-T treatment. Supplementation of these species of gut bacteria during CAR-T cell therapy led to superior antitumor efficacy. Furthermore, both strains facilitated CAR-T therapy-induced activation of endogenous CD8+ T cells, enhancing their capability to express activation-associated surface markers as well as tumor-lysis potency. In summary, our results demonstrate that gut microbiome plays an essential role in endogenous immune activation after CAR-T therapy and provide specific targets for therapeutic interventions.