Investigating the Impact of the Microbiome on CAR T-Cell Therapy Outcomes

Chimeric antigen receptor (CAR) T-cell therapy is a groundbreaking treatment for hematologic malignancies, particularly B-cell malignancies. However, 60% of patients who receive CAR T-cell therapy experience relapse of their underlying disease within 12 months of treatment, explained Melody Smith, MD, MS, a medical oncologist and hematologist at Stanford Medicine, during her presentation at the American Association for Cancer Research Immunotherapy (AACR IO) Conference in Los Angeles, California.¹

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“There’s a long tail [in the graph] of patients who survive, but still, late relapses may occur in addition to cytokine release syndrome [CRS] and immune effector cell–associated neurotoxicity syndrome [ICANS],” Smith said during the AACR IO presentation. “These [toxicities] are limitations that we have certainly developed much more adept ways to diagnose and treat, but [they are] another limitation of note.”¹

Given these challenges, ongoing research and advancements in immunotherapy are crucial to improving patient outcomes, optimizing long-term efficacy, and mitigating adverse effects. Continued innovation will be key to expanding the potential of CAR T-cell therapy and enhancing its role in cancer treatment.¹

The Evolution of CAR T-Cell Therapy

A pivotal breakthrough in the development of CAR T-cell therapy was the introduction of the costimulatory receptor CD28 into the CAR vector by Michel Sadelain, MD, PhD, director of the Columbia Initiative in Cell Engineering and Therapy at Columbia University in New York, New York. This development significantly enhanced CAR T-cell functionality, according to Smith.¹

“My comentor during my postdoc in the lab, Michel Sadelain, MD, PhD, initially introduced the costimulatory receptor CD28 to the CAR vector,” Smith said. “Now we have CAR T cells that are really broad in therapeutic implications for patients with blood cancers.”¹

As of November 2024, 7 CAR T-cell therapies have received FDA approval, Smith explained. CD19-targeted CAR T-cell therapies include axicabtagene ciloleucel (Yescarta; Kite), brexucabtagene autoleucel (Tecartus; Kite), tisagenlecleucel (Kymriah; Novartis), lisocabtagene maraleucel (Breyanzi; Juno Therapeutics, Inc), and obecabtagene autoleucel (Aucatzyl; Autolus Therapeutics plc). In addition, 2 B-cell maturation antigen (BCMA)-targeted CAR T-cell therapies have been approved for multiple myeloma.¹

The evolution of CAR T-cell therapy, driven by innovative research and clinical advancements, underscores its growing impact on the treatment landscape for hematologic malignancies. With ongoing developments and new targets emerging, the future of CAR T-cell therapy holds promise for expanding efficacy and accessibility to a broader range of patients.¹

The Role of the Intestinal Microbiome in CAR T-Cell Therapy Outcomes

In Smith’s research over the past several years, she has explored the intricate relationship between the intestinal microbiome and the efficacy and toxicity of CAR T-cell therapy. Previous studies have established robust connections between the microbiome and clinical outcomes in allogeneic hematopoietic cell transplantation and immune checkpoint blockade; however, before Smith’s research, no data had been published on the role of the intestinal microbiome in CAR T-cell therapy.¹

“So, I asked the question: What impact do host extrinsic and intrinsic factors that alter the intestinal microbiome have on CAR T-cell efficacy and toxicity?” Smith said. “So, we developed an antibiotic cohort through a collaboration between Memorial Sloan Kettering [MSK] Cancer Center and the University of Pennsylvania [UPenn], and we asked whether the exposure to specific antibiotics in the 4 weeks prior to CAR T-cell therapy was associated with clinical outcomes.”¹

Smith had been based at MSK until August 2021, when she left for a position at Stanford. But while at MSK, she conducted this research in collaboration with UPenn.¹

“We had a pretty large cohort of CD19 CAR T-cell recipients; 228 patients contributed from both centers, and we first retrospectively assessed this question,” Smith said. “First, when asking the question regarding antibiotic exposure, we wanted to highlight antibiotics, not because other medications don’t alter the microbiome or potentially induce dysbiosis, but [because] antibiotics are one of the main culprits. But even within the category of antibiotics, not all antibiotics are equally dysbiotic or disruptive.”¹

Smith explained that one of the most common exposures in the 4-week period before CAR T-cell therapy was trimethoprim/sulfamethoxazole, which is often given to patients who are neutropenic for prevention of Pneumocystis jirovecii pneumonia (PCP). However, Smith noted that PCP was found to not alter the microbiome to the same degree as antibiotics such as piperacillin-tazobactam (Zosyn; Pfizer Inc), imipenem-cilastatin (Primaxin; Merck), and meropenem (Merrem; Pfizer Inc), which Smith collectively referred to as PIM.1,2

When looking at data from patients who had any antibiotic exposure, Smith explained that patients exposed to any antibiotic in the 4 weeks before CAR T-cell therapy had decreased overall survival (OS).¹ “But then to drill down onto the antibiotics that we thought might be more disruptive to the gut, we looked at PIM, and we saw that 20% of the patients in our cohort were exposed to PIM in that time period, so we then evaluated the impact of PIM on OS,” Smith said.¹

Smith explained that when looking at PIM exposure, they found that exposure to PIM antibiotics in the 4 weeks before infusion was associated with significantly worse OS and progression-free survival, particularly in patients with non-Hodgkin lymphoma.1 This effect was independent of the CAR T-cell costimulatory domain (CD28 vs 41BB).^1,2

Compared with cefepime, which does not primarily target obligate anaerobes, PIM exposure was linked to worse OS, suggesting a microbiome-related mechanism. Additionally, PIM exposure was associated with increased incidence of ICANS but not CRS.^1,2

To further elucidate the microbiome’s role in CAR T-cell therapy outcomes, Smith’s team analyzed fecal microbiome samples from CAR T-cell recipients. Compared with healthy individuals, CAR T-cell recipients exhibited statistically significant reductions in alpha diversity and compositional differences in beta diversity. Bayesian analysis identified a trend between higher Ruminococcus abundance and improved day-100 complete response rates. Other studies have highlighted Bacteroides fragilis and various Clostridioides species as potentially beneficial for CAR T-cell response.^1,2

According to Smith, these findings suggest that microbiome composition and antibiotic exposure influence CAR T-cell efficacy and toxicity, highlighting potential implications for antibiotic stewardship in patients receiving CAR T-cell therapy. However, Smith noted further research is needed to validate these findings in larger cohorts and explore microbiome-related mechanisms in CAR T-cell therapy outcomes.^1,2

Longitudinal Analysis and Mechanistic Insights

In Smith’s ongoing research, she aims to capture longitudinal changes in the microbiome of CAR T-cell recipients.¹

“Our ongoing studies at Stanford are looking at prospective banking of our patients who receive CAR T cells—not just those who receive CD19 but also BCMA-targeted commercial [CAR T] and some of our investigational studies,” Smith said.¹

From the perspective of the correlative analysis, Smith explained that her team now has more robust longitudinal data to characterize the microbiome in CAR T-cell recipients, showing how the fecal alpha diversity changes over time.¹ “We also see the beta diversity changing over time as patients are exposed likely to antibiotics in inpatient stays and clustering more disparately in the weeks post CAR T-cell therapy,” Smith said. “It seems like it starts to return back to baseline, and we are collecting data all the way through month 3, looking at these longitudinal changes to develop deeper insights for our CAR T-cell recipients.”¹

Smith explained that her lab also engages in preclinical studies utilizing germ-free and specific pathogen-free mice to explore mechanistic links between microbial metabolites and CAR T-cell function. These studies aim to identify potential microbiome-based therapeutic interventions, according to Smith.¹ “We are really excited about our preclinical studies that are starting to reveal regulatory mechanisms, and I look forward to sharing that in the future,” Smith said.¹

REFERENCES

1. Smith M. Interrogating the impact of the intestinal microbiome on CAR T cell therapy. Presented at: American Association of Cancer Research Immunotherapy Conference; February 2-26, 2025; Los Angeles, California.

2. Smith M, Dai A, Ghilardi G, et al. Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy. Nat Med. 2022;28(4):713-723. doi:10.1038/s41591-022-01702-9