Gut Microbiome Influences Response and Toxicity in Anti-CD19 CAR T Cell Therapy

Given the importance of T cell immunity and the gut microbiome in modulating immune responses, the researchers in this study hypothesized that the intestinal microbiome might affect the outcomes of CAR T cell therapy. To test this, they conducted a multi-center study involving retrospective and prospective cohorts of patients. The study examined the impact of antibiotics on the gut microbiome and subsequent clinical outcomes and identified key microbial taxa associated with improved response or toxicity.

The study found that specific bacteria, particularly Ruminococcus, Faecalibacterium, and Bacteroides, were associated with improved response to anti-CD19 CAR T cell therapy in patients with B-cell malignancies. These bacteria, which belong to the class Clostridia, are linked to a Day 100 complete response, likely due to their role in immune modulation. Conversely, exposure to broad-spectrum antibiotics before therapy, particularly piperacillin-tazobactam and meropenem, was associated with worse survival and increased neurotoxicity, underscoring the importance of gut microbiome composition in CAR T therapy outcomes.

One major study finding was the detrimental impact of broad-spectrum antibiotics on patient outcomes. The researchers identified that exposure to certain antibiotics, especially piperacillin/tazobactam, meropenem, and imipenem/cilastatin (referred to as P-I-M), in the four weeks before CAR T cell infusion, was linked to worse overall survival (OS) and progression-free survival (PFS). This antibiotic exposure was also associated with an increased risk of developing ICANS, a serious neurotoxicity. Notably, this effect was observed primarily in patients with NHL rather than ALL, possibly due to differences in disease characteristics and tumor environments.

The use of broad-spectrum antibiotics that target anaerobic bacteria leads to significant changes in the composition of the gut microbiome, contributing to a loss of microbial diversity. The study suggests that the alteration of gut microbiota by these antibiotics may impair the beneficial immune modulation required for effective CAR T cell therapy, thus worsening patient outcomes.

Baseline Microbiome Composition

The researchers also analyzed baseline stool samples from a cohort of CAR T cell recipients to investigate how the composition of the gut microbiome before therapy correlated with clinical outcomes. They found that patients undergoing CAR T cell therapy generally had lower alpha-diversity (a measure of microbial diversity within an individual) compared to healthy controls. In particular, certain beneficial bacterial taxa were significantly depleted in patients, while harmful or opportunistic bacteria, such as Escherichia and Klebsiella, were present at higher levels.

Despite this baseline dysbiosis, the researchers identified key bacterial taxa associated with favorable clinical responses. Specifically, members of the class Clostridia, particularly the genera Ruminococcus, and Faecalibacterium were associated with improved Day 100 complete response (CR) rates. These bacteria are known for their anti-inflammatory properties and their ability to produce short-chain fatty acids, which play a role in regulating immune responses.

The researchers used high-dimensional class comparison techniques, such as linear discriminant analysis (LEfSe), to highlight the differences in microbial composition between responders and non-responders. Higher relative abundances of Ruminococcus bromii and Faecalibacterium prausnitzii were found in patients who achieved complete response by Day 100. These bacteria are obligate anaerobes, which suggests that maintaining a healthy population of anaerobic bacteria in the gut may be crucial for an effective CAR T cell response.

Microbiome and Toxicity

In addition to clinical response, the study also explored the association between the gut microbiome and CAR T cell-related toxicities, such as CRS and ICANS. Interestingly, the same bacterial taxa associated with favorable clinical response—Ruminococcus, Faecalibacterium, and Bacteroides—were also linked to a lower risk of toxicity. The researchers hypothesized that these bacteria may modulate immune responses in a way that enhances the therapeutic effect of CAR T cells while reducing the likelihood of severe inflammatory reactions.

Conversely, the study found that a higher abundance of bacteria from the order Veillonellales and the family Veillonellaceae was associated with decreased CR rates at Day 100, indicating a potential role for these bacteria in promoting immune dysfunction or resistance to CAR T cell therapy.

Mechanisms and Future Directions

To further understand how the gut microbiome influences CAR T cell therapy, the researchers performed metagenomic shotgun sequencing of fecal samples. This analysis revealed that specific microbial metabolic pathways might play a role in modulating CAR T cell response. For example, patients with a complete response showed enrichment in pathways related to peptidoglycan biosynthesis, which is involved in maintaining bacterial cell wall integrity and may influence immune signaling.

The study concludes that maintaining a diverse and balanced gut microbiome, particularly one enriched with beneficial anaerobes like Ruminococcus and Faecalibacterium, may enhance the effectiveness of CAR T cell therapy while reducing the risk of toxicities. These findings underscore the importance of gut health and microbiome composition in cancer immunotherapy, offering potential avenues for improving patient outcomes through microbiome-targeted interventions, such as prebiotics, probiotics, or fecal microbiota transplantation (FMT).

Reference

Smith M, Dai A, Ghilardi G, Amelsberg KV, Devlin SM, Pajarillo R, Slingerland JB, Beghi S, Herrera PS, Giardina P, Clurman A, Dwomoh E, Armijo G, Gomes ALC, Littmann ER, Schluter J, Fontana E, Taur Y, Park JH, Palomba ML, Halton E, Ruiz J, Jain T, Pennisi M, Afuye AO, Perales MA, Freyer CW, Garfall A, Gier S, Nasta S, Landsburg D, Gerson J, Svoboda J, Cross J, Chong EA, Giralt S, Gill SI, Riviere I, Porter DL, Schuster SJ, Sadelain M, Frey N, Brentjens RJ, June CH, Pamer EG, Peled JU, Facciabene A, van den Brink MRM, Ruella M. Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy. Nat Med. 2022 Apr;28(4):713-723. doi: 10.1038/s41591-022-01702-9. Epub 2022 Mar 14. Erratum in: Nat Med. 2023 Nov;29(11):2954. doi: 10.1038/s41591-022-02069-7. PMID: 35288695; PMCID: PMC9434490.