Emerging Frontiers: The Gut Microbiome's Role in Enhancing Cancer Immunotherapy and Treatment Outcomes

In less than a decade, research has propelled investigations into the gut microbiome in cancer care from a relatively obscure field to a significant focus in cancer treatment, specifically in relation to the microbiome’s pivotal role in cancer prognosis and response to immunotherapy, explained Bertrand Routy, MD, PhD, a hemato-oncologist and associate researcher, cancer axis, CRCHUM; research member, Montreal Cancer Institute; and director of the Immunotherapy and Oncomicrobiome Laboratory and assistant professor in hemato-oncology, Department of Medicine, Université de Montréal in Canada.

During a session at the European Society for Medical Oncology (ESMO) Congress 2024, Routy discussed how clinical research investigating the microbiome’s impact on cancer therapies, particularly immunotherapy, has revealed breakthroughs and future directions for microbiome-based interventions.

In 2018, Routy and his colleagues performed metagenomic sequencing on 100 patients with non-small cell lung cancer (NSCLC), and they observed that responder patients had a unique microbiome composition with enrichment of one commensal bacterium in particular: Akkermansia muciniphila. This observation was then extended and further validated by Routy and his colleagues assessing microbiome composition in a larger cohort of 338 patients with NSCLC.

Following these results, various research groups globally validated the prognostic role of the gut microbiome in melanoma, as well as in the neoadjuvant setting. A meta-analysis of metagenomic studies revealed common bacterial species were enriched in responder patients, such as Faecalibacterium prausnitzii and Akkermansia muciniphila. Conversely, certain bacteria like Enterocluster and Eggerthella lenta were more abundant in non-responders.

the key challenge lies in determining the significance of specific bacterial species and a relevant score to assess potential response to treatment based on their presence. Image Credit: © World of AI - stock.adobe.com

However, the key challenge lies in determining the significance of specific bacterial species and a relevant score to assess potential response to treatment based on their presence at various levels, according to Routy.

“If a patient has 3 good and 4 bad bacteria, how do you create a score [for this],” Routy said during the ESMO session. “We were analyzing 1 bacterium at a time to develop a network analysis.”

In a study published by Derosa et al in Cell in 2024, the investigators noted that they observed 2 bacterial networks in patients with NSCLC (N=254), which they called species interacting groups (SIG). One SIG was increased in non-responder patients with NSCLC, while another network they called SIG2 (consisting of beneficial bacteria) was present at an increased level in responder patients with NSCLC. Based on these 2 bacterial networks, they developed a score they called the TOPOScore, which helped them predict response based on the ratio of these 2 SIG bacterial networks.

“If you have more beneficial bacteria from the SIG2, you have a prolonged overall survival,” Routy said. “Unfortunately, [this] metagenomic [strategy] is not ready for prime time in the clinic [for] routine oncology practice due to the long turnover time, as you need really the best bioinformatician in the world to do the analysis.”

To address this, Routy’s research team partnered with the Norwegian microbiome research company Bio-Me to develop a bacteria polymerase chain reaction (PCR) chip that could rapidly analyze 107 bacteria (some from the TOPOscore from Derosa et al and some from the meta-analysis from Routy’s team) identified as key players in the microbiome. The use of this PCR chip allowed the microbiome composition to be determined far more rapidly than was possible previously.

“The advantage of this PCR chip is you have the results and the microbiome signature within 72 hours. Therefore, we went back to look at surrogate markers of the TOPOscore using this PCR chip,” Routy said. “You see in 2 independent cohorts of [patients with NSCLC], one from France and one from Canada, [that] we were able to reproduce the metagenomic SIG signature with this PCR panel. Therefore, moving forward, this might represent a novel prospective and longitudinal method to monitor microbiome composition.”

However, a second significant finding from this microbiome research was the detrimental impact of broad-spectrum antibiotics on survival of patients. Routy and team observed that in patients with solid tumors who had received antibiotics, they had a reduced overall survival, which was particularly true for patients undergoing immunotherapy or chemotherapy in a cohort of close to 800 patients from Memorial Sloan Kettering (MSK).

Over the last 6 years, more than 100 investigators and studies were published addressing this question of the impact of antibiotic use on overall survival, which allowed for a meta-analysis of 46,000 patients to be conducted looking at the negative role of antibiotics in patients with solid tumors who were treated with immunotherapy. Published by Elkrief et al in Precision Oncology - Nature in 2024, the investigators observed a hazard ratio of 1.7 for reduced survival in patients who took antibiotics before starting immune checkpoint inhibitors (ICIs). Since antibiotics disrupt the microbiome, the use of antibiotics before ICIs was shown to increase the presence of harmful gut bacteria such as Hungatella, Enterocloster, and Veillonella and reduce beneficial species such as Ruminococcaceae, Agathobacter, and Eubacterium.

Mechanistically, antibiotic-related dysbiosis decreases beneficial bacteria in patients with disease that is amenable to immunotherapy and downregulates gut immune checkpoint MAdCAM-1. Specifically, in mice models, antibiotics were observed to downregulate α4β7, which is a gut immune checkpoint that binds to MAdCAM-1. This downregulation causes an exodus of immunosuppressive T cells from the gut and tumor microenvironment, leading to immunosuppression and resistance to anti-PD-1 therapies. To confirm this, the researchers measured soluble MAdCAM-1 levels in patients with NSCLC and confirmed a link between antibiotic use and lower MAdCAM-1, which mirrored the results observed in mice.

“We're working closely with the Centers for Disease Control and Prevention to write firm a recommendation to judiciously prescribe antibiotics,” Routy said. “However, despite our efforts, we see in prospective and retrospective cohorts that still 10% to 15% of patients require antibiotics, therefore, we have to find strategies to overcome this.”

Given the need to reduce antibiotic-related dysbiosis, Routy and his team collaborated with a French biotech company to develop an oral-coated charcoal capsule (DAV132) that absorbs antibiotics in the colon without affecting systemic antibiotic levels. In a phase I randomized clinical trial involving 70 healthy volunteers who received broad-spectrum IV antibiotics (ceftazidime and avibactam [Avycaz; Pfizer and Allergan] and piperacillin and tazobactam [Zosyn; Baxter]), it was demonstrated that the capsule preserved microbiome diversity and protected against antibiotic-induced dysbiosis.

“The paper just got accepted in Nature Communication last week, and the first observation was that the charcoal capsule did not decrease the plasma level of the antibiotic. Conversely, when we look at the microbiome diversity of the healthy volunteer who received the antibiotic, you see that they have a significant decrease of their microbiome diversity, and we know this is deleterious for the patients. In the healthy volunteers who received charcoal plus antibiotic, there is a small decrease of diversity initially, but rapidly they go back to their baseline,” Routy said.

To demonstrate the proof of principle that the charcoal capsule is able to protect the key bacteria, Routy and team performed fecal microbiota transplantation in germ-free mice. They took the feces of the healthy volunteers before they initiated treatment, and compared the groups who either received antibiotic alone or antibiotic plus charcoal capsules.

“When we transferred their feces to the mice, we put a tumor, we gave 4 doses of PD-1, and we were able to observe a strong anti–PD-1 efficacy. Conversely, when we took the feces of the same healthy volunteers at day 6, when the group of antibiotic volunteers were transplanted in mice, we observed a loss of anti–PD-1 efficacy,” Routy said. “Therefore, we created a new therapeutic avenue to overcome antibiotic-induced dysbiosis.”

Fecal microbiota transplantation (FMT) has also shown promise in overcoming immunotherapy resistance. Research conducted by Routy and team in collaboration with Lisa Derosa Institut de Cancérologie Gustave Roussy demonstrated that FMT from patients with renal cell carcinoma who were responders to cancer therapy could enhance the efficacy of immunotherapy treatment. In one trial, they assessed second-line FMT plus single-agent anti–PD-1 in 10 patients and second-line FMT plus single-agent anti–PD-1 in 15 patients, and the objective response rate (ORR) was 30% and 20%, respectively.

“In Canada, we recently published the first first-line combination of FMT plus anti–PD-1 in 20 patients [with melanoma] previously untreated, and once again, you see a very strong [ORR] of 65%,” Routy said. “Galvanized by these results, we recently completed a follow up study called FMT-LUMINate [NCT04951583], which combined, this time, fecal transplantation from healthy volunteers, so the patient received a bowel preparation with PEG Lyte 24 hours before they received their fecal transplant from a donor.”

During FMT-LUMINate, they enrolled 20 patients with NSCLC (receiving pembrolizumab [Keytruda; Merck]), 20 patients with cutaneous melanoma (receiving ipilimumab [Yervoy;Bristol Myers Squibb] + nivolumab [Opdivo; Bristol Myers Squibb]), and 5 patients with uveal melanoma (receiving ipilimumab + nivolumab). The primary objective of the trial was ORR, and the pre-specific ORR for a positive study was 64%. The trial in fact met its primary end point of ORR at 75% (95% CI; 49.1-87.5%). However, the search for a "super donor" with an ideal microbiome has been elusive, underscoring the need for further refinement in this approach, according to Routy.

Additionally, diet plays a role in shaping the gut microbiome. Studies from MD Anderson and research groups in the Netherlands demonstrated that patients with melanoma who consumed more fiber or adhered to a Mediterranean diet had better survival outcomes. In Quebec, patients with NSCLC were found to have a very low median fiber intake, leading researchers to launch a randomized trial aimed at improving dietary habits. Preliminary results from this trial indicated that patients who received monthly nutritional guidance significantly increased their fiber intake, which may potentially influence their microbiome and overall survival.

Altogether, these findings underscore the importance of the gut microbiome as a biomarker for cancer therapy response, particularly in immunotherapy. Judicious use of antibiotics is critical, as antibiotics can induce harmful dysbiosis impacting the efficacy of immunotherapy, but new strategies such as charcoal capsules may offer hope to mitigate these effects. While metagenomic sequencing is still too slow for routine use, rapid technologies such as the use of PCR chips hold promise for more timely and accurate microbiome profiling. Moving forward, longitudinal monitoring of the microbiome could become a routine part of cancer care, much like liquid biopsies, according to Routy.

FMT has shown proof of concept that microbiome modification can enhance immunotherapy; however, new strategies are needed to further refine this approach. Ultimately, a future in which patients with cancer undergo routine microbiome analysis to tailor treatment plans based on microbiome composition is within reach, according to Routy. Furthermore, the hope is that microbiome-based therapies could significantly improve patient outcomes and become a cornerstone of personalized cancer care.

REFERENCE

Routy MB. Exploiting the microbiome to improve treatment outcomes. ESMO Congress 2024; Barcelona, Spain; September 13-17, 2024.