Composition of the gut microbiome is associated with response and toxicity following anti-CD19 CAR T cell therapy

The intestinal microbiome is associated with clinical outcomes after anti-CD19 CAR T cell therapy in patients with B-cell malignancies.

What is the relevant background?

The intestinal microbiome has emerged as an important endogenous factor that is associated with outcomes in cancer and cancer therapy. Studies have confirmed that the intestinal microbiome can modulate the anti-tumor immune response to chemotherapy, radiotherapy, immune checkpoint blockade, allogeneic hematopoietic cell transplantation, and adoptive cellular therapy [1,….12]. Cellular immunotherapy with CD19-targeted chimeric antigen receptor (CAR) T cells has provided new therapeutic options for patients with high-risk hematologic malignancies [13,14,15,16]. Yet, patients may experience disease relapse or CAR-mediated toxicity, cytokine release syndrome (CRS) or immune effector cell-associated neurotoxicity syndrome (ICANS) [17,18,19,20,21,22]. The contribution of the intestinal microbiome on the function of CAR T cell anti-tumor activity and toxicity is unknown.


What did we investigate?

In a multi-center study between Memorial Sloan Kettering Cancer Center and the University of Pennsylvania, we analyzed the association between clinical outcomes and (1) antibiotic exposure prior to CAR T cell infusion and (2) the composition and diversity of the fecal microbiome.


What did we report about antibiotic exposure?

For evaluation of antibiotic exposure, we retrospectively collected clinical data and antibiotic exposures from patients with acute lymphoblastic leukemia (ALL, n=91) and non-Hodgkin lymphoma (NHL, n=137) treated with investigational or commercial CD19 CAR T cells at both centers. We focused our analysis on anaerobe-targeting antibiotics used in the setting of neutropenic fever: piperacillin-tazobactam, imipenem-cilastatin, and meropenem (here referred to as “P-I-M”). We found that overall survival (OS) was significantly decreased following CAR T cell infusion in patients exposed to P-I-M. We queried whether patients exposed to P-I-M had worse fitness or more aggressive disease. In in a multivariate model, we found that exposure to P-I-M, higher pre-lymphodepletion lactate dehydrogenase, and worse ECOG performance status were strong predictors of decreased OS. Exposure to P-I-M was also associated with increased ICANS but not CRS in patients in the combined NHL and ALL cohort as well as in patients with NHL.


What did we report about the fecal microbiome?

For assessment of the fecal microbiome, we prospectively collected baseline fecal samples prior to cell infusion from CD19 CAR T cells recipients (n=48). Samples were submitted for 16S ribosomal RNA sequencing of the V4-V5 region as well as metagenomic shotgun sequencing. In comparison to healthy controls (n=30), CD19 CAR T cell treated patients had an altered fecal microbiome before cell infusion as noted by lower alpha-diversity, increased frequency of bacterial dominance, and distinct bacterial composition. We evaluated the association of bacterial taxa and complete response and toxicity. Specifically, we found that species within the class Clostridia were associated with Day 100 complete response through both untargeted and targeted analysis of 16S sequencing. Metagenomic shotgun sequencing also identified that specific metabolic pathways were associated with Day 100 complete response as well as toxicity. 


How is our study impactful?

In summary, our findings indicate that antibiotic exposure prior to CD19 CAR T cells is associated with poor outcomes, including decrease OS and increased ICANS. Our results also highlight that biomarkers of the intestinal microbiome in baseline fecal samples of CD19 CAR T cell recipients are associated with efficacy and toxicity therapy. These data provide insights as to how the intestinal microbiome can be harnessed to improve clinical outcomes of patients treated with cellular therapies.


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