Exploring the Role of Gut Microbiome in Cancer Therapy

Jennifer Leigh McQuade, MD

Emerging research suggests a potential role of the gut microbiome in cancer development and in determining therapy efficacy. Research focusing on enhancing treatment efficacy by modulating the gut microbiome is ongoing.

Source of Biomarkers

In humans, the gut microbiota serves many functions. The normal gut microbiota metabolizes nutrients and drugs, maintains the gut mucosal barrier integrity, protects against pathogens, and trains and develops the immune system.¹ The gut microbiome has been implicated in many human pathologies.

“In the past 5 years, the gut microbiome and its effect on the immune system have led to it becoming a source of biomarkers that can predict response to cancer therapy and potentially be modified as therapy itself,” said Karla Lee, SpR, a clinical research fellow and PhD candidate at King’s College, London, England, United Kingdom, during an interview with Targeted Therapies in Oncology™. Lee’s area of study focuses on gut microbiota in oncology research.

The gut microbiome represents a new age of holistic cancer treatment. Whereas in the past, biomarkers to predict therapy response were tumor-centric and involved characterizing tumor mutational load, metabolism, and sensitivity to immune effectors, the gut microbiota is a new, nontumor-centric area with therapeutic potential.²

“What makes the gut microbiome really exciting is that it is modifiable and in terms of treatment it is something patients can [affect] on their own to improve their odds of response to therapy,” said Jennifer Leigh McQuade, MD, an assistant professor of melanoma medical oncology at The University of Texas MD Anderson Cancer Center in Houston during an interview with Targeted Therapies in Oncology™.

It is important for clinicians to grasp how the gut microbiome may affect tumor progression. The gut microbiota consists of approximately 100 trillion microbes existing in a stable state that interact with the host immune system.³ Disruption of the stable commensal bacteria results in an unstable state of dysbiosis that may lead to tumorigenesis. Observational studies have shown bacteremia from Streptococcus gallolyticus has been associated with an increased risk of developing colorectal cancer.⁴ Although mechanisms are still being understood, some pathogenic bacteria are thought to induce host DNA damage, cause oxidative stress damage, or inhibit host antitumor responses by acting on the tumor microenvironment.⁵

In addition to its unique association with tumorigenesis, the gut microbiome’s interaction with intestinal epithelium affects host immunity and may thereby affect the tumor microenvironment. In animal models, mice lacking intestinal microbiota have severe defects in immunity, an absent mucous layer, altered IgA secretion (IgA blocks bacterial adherence to epithelial cells), and reduced size and functionality of Peyer patches and draining mesenteric lymph nodes.⁶

“Given the important role of the gut microbiota in maintaining host immunity, it has been theorized that alterations of the gut microbiome can affect immune responses within the tumor microenvironment,” Lee said. Cancer cells manipulate and suppress immune cells to persist. In fact, development of immune checkpoint inhibitors (ICI) has changed cancer therapy by inhibiting tumoral immunosuppression within the tumor microenvironment and allowing effector cells to attack tumor cells.⁷ However, ICIs are not universally effective across all cancers.

“It is important to determine when ICIs are and are not effective,” said McQuade, whose focus of research is on dietary modulation of the microbiome for oncotherapy. Given its immunologic effects, exploration of the gut microbiome for biomarkers has allowed for identification of microbiome signatures that help determine when ICIs are effective.⁸ Characterization of the microbiome identifies features in those who do or do not respond to ICI therapy. In those situations, the microbiome can be modulated to create an environment for response to ICI therapy.

Cancer Etiology and Treatment

A recent study analyzing the intratumoral microbiome in patients with colorectal cancer identified an abundance of Akkermansia in younger patients that was absent in elderly patients.⁹ Furthermore, younger patients had better overall survival (OS), suggesting that the presence of Akkermansia has a role in determining clinical outcomes from colorectal cancer. Similarly, in patients with colorectal cancer, numbers of Fusobacterium nucleatum increase as cancer progresses.¹⁰ It has been shown that F nucleatum suppresses host lymphocytes and natural killer cells by binding to the inhibitory immune receptor TIGIT.¹¹ “It has become clear that the gut microbiome has an important role to play in the etiology or treatment of many cancer subtypes,” Lee said.

Not only is the microbiome associated with clinical outcomes, but it can also affect the efficacy of cancer therapies such as chemotherapy. F nucleatum has been associated with oxaliplatin chemotherapy resistance in patients with colorectal cancer.¹¹ Also, lung tumor–bearing mice treated with cisplatin and gut microbiota–depleting antibiotics developed larger tumors and had poorer survival.¹² However, certain bacteria may improve chemotherapy response. Cyclophosphamide therapy was improved when combined with commensal bacteria such as Lactobacillus johnsonii and Enterococcus hirae.¹³ The combination converted naïve T cells to proinflammatory Th17 cells and ultimately improved cyclophosphamide efficacy.

ICI Efficacy

“Similar to its effect on chemotherapy, the gut microbiota has also been shown to affect ICI efficacy,” McQuade said. The gut microbiota primes cells for an effective immune response. T cells are inhibited in the tumor microenvironment. Bacteria such as Bifidobacterium pseudolongum produce metabolites like inosine, which helps to activate T cells that are normally restricted in the tumor microenvironment.¹⁴ Inosine supplementation enhanced the antitumor efficacy of ICI.¹⁵ “Sometimes we focus too much on who the bugs are as opposed to what they are doing,” said McQuade.

Much research has focused on identifying microbiome biomarkers that affect ICI efficacy. Specific examples help to explain the association of the gut bacteria and metabolites with ICI efficacy.

In murine models, Sivan et al showed the efficacy of anti–PD-L1 antibodies in melanoma was improved in the presence of gut microbiome enriched with Bifidobacterium spp.¹⁶ It was shown that when

Bifidobacterium species are combined with anti–PD-L1 antibodies, there was enhanced CD8+ T-cell priming and accumulation in

the tumor microenvironment that inhibited melanoma growth. “Most research involves associations of microbiota with ICI efficacy. This study showed the potential for selected microbiota as therapy in conjunction with ICIs, giving microbiota manipulation practical value,” McQuade said. Moreover, it was shown that patients with melanoma treated with anti–PD-1/anti–PD-L1 ICI had lower OS and progression-free survival (PFS) when treated with antibiotics.⁹

A study investigating phase 2 neoadjuvant trials of anti–PD-1/anti-CTLA-4 antibodies for melanoma, non–small cell lung cancer, and sarcoma saw that among all cancers, an abundance of Ruminococcus was higher in responders and had an increase in B-cell signatures not seen in patients with a low abundance of Ruminococcus.¹⁷ Several examples have shown that strains of bacteria are associated with ICI therapy outcomes and can potentially be used both to predict response to ICI therapy and in conjunction with therapy to improve patient outcomes.

Gut Microbiome Modulation Techniques for Enhanced ICI Response

“What is exciting about the microbiome is that it is inherently modifiable. We can’t change our germline genome or tumor genome, but we can change our gut microbiome. We are starting to see that microbiomodulation certainly holds promise,” McQuade said.

Microbiome modulation by supplementing bacteria and metabolites in patients who do not respond to ICI therapy has shown potential to inhibit cancer progression and augment the efficacy of immunotherapies.² The administration of live bacterial specimens like Bifidobacterium and Lactobacillus can influence anti-inflammatory cytokine levels, degrade carcinogens, activate phagocytes to eliminate early-stage cancer cells, and produce short chain fatty acids that affect cell death and proliferation.¹⁸

Fecal microbiota transplantation (FMT) from PD-1 responders with favorable gut microbiome or from a young person with healthy gut microbiome could potentially be transplanted into PD-1–resistant patients. A phase 1 study (NCT03353402) assessed the safety and feasibility of anti–PD-1 refractory melanoma with reinduction of anti–PD-1 inhibitors after FMT. Of 10 patients, 3 responded (1 complete, 2 partial).¹⁹ “These results, although only 30% efficacious, give meaning to microbiome manipulation and FMT therapy,” said McQuade. FMT was associated with favorable changes in immune cell infiltrates and gene expression profiles.¹⁹ FMT studies show that the microbiome is modifiable and there is potential to overcome resistance with the prior immunotherapy. “These are very exciting results, although early studies,” stated Lee.

Similarly, a study showed that patients with cancer who responded to anti–PD-1 therapy were rich in Akkermansia. Replenishing those deficient in Akkermansia with FMT has shown an improvement in anti–PD-1 efficacy in previous nonresponders.⁹

In patients with acute myeloid leukemia treated with intensive chemotherapy and antibiotics, a phase 2 study (NCT02928523) showed autologous fecal microbiota transfer was safe and effective to restore richness and diversity in the gut microbiome.²⁰

A recent study (NCT03829111) showed patients with renal cell carcinoma treated with either anti–CTLA-4/anti–PD-1 therapy alone or in conjunction with CBM588, a bifidogenic live bacterial product, had enhanced clinical outcomes. PFS was significantly longer in patients receiving ICI therapy with CBM588 than without (12.7 months vs 2.5 months, P = .001), without a significant difference in toxicity.²¹ “Larger studies are needed to elucidate the mechanism of action, but the results are promising,” noted Lee.

The use of antibiotics such as vancomycin to decrease harmful gram-positive bacteria but not affecting gram-negative bacteria such as Bacteroides enhanced the efficacy of anti–CTLA-4 therapy.²² This has led to bacteriophages designed to target only detrimental and pathogenic bacteria as another therapeutic strategy. In mouse models, a bacteriophage that killed F nucleatum led to reduced immunosuppressive myeloid-derived suppressor cells in the tumor microenvironment and prolonged OS time when coupled with ICIs.²³

Although FMT has been the focus of therapy and bacteriophage research is ongoing, other mechanisms for microbiota modulation exist. A novel microbiome-derived therapeutic vaccine used in conjunction with ICI therapy in patients with adrenocortical carcinoma was safe and induced an immune response.²⁴

“I think that one massively neglected area in oncology is diet, and this is obviously very closely related to the gut microbiome in many ways. Diet is the most modifiable factor affecting the development and condition of the gut microbiome,” Lee said. Similarly, McQuade has focused her research on dietary manipulation for improved outcomes in cancer treatment.

“Patients with higher habitual consumption of fiber have improved response to immunotherapy,” McQuade noted. High fiber intake and elimination of animal fats can increase immune-promoting bacteria like Faecalibacterium prausnitzii and decrease detrimental bacteria like Bacteroidales.²⁵

The daily use of probiotics is controversial. Probiotics may decrease biologic diversity in individuals and can alter cytokine profiles.²⁶ For example, in colorectal cancer, treatment with Lactobacillus acidophilus and Bifidobacterium lactis led to an abundance of butyrate-producing bacteria within the tumor. Furthermore, pretreatment with a preoperative probiotic in patients with colorectal cancer altered cytokine profiles with lower numbers of cytokines assessed at time of mucosal resection, giving mixed results.²⁶

Reducing ICI Toxicity

A major challenge with ICI treatment involves treatment-related toxicities leading to delays and discontinuation of treatment. One-third of all patients undergoing anti–CTLA-4 therapy experience intestinal inflammation. The combination of anti–CTLA-4 and anti–PD-1 blockade may result in high-grade toxicity requiring hospitalization in more than 50% of patients receiving treatment.²⁷ “Anyone who has worked in immune oncology understands how devastating and unpredictable immune-related adverse events (irAEs) can be. I would love to see more gut microbiome studies that focus on toxicity,” Lee said.

Recently, in advanced gastric carcinoma, the gut microbiome was analyzed for predictors of anti–PD-1 induced toxicity in patients treated with nivolumab (Opdivo).²⁸ Arthrobacter was identified as a candidate marker for skin eruptions, as patients with high levels of Arthrobacter experienced this symptom more frequently. Single-nucleotide polymorphisms were also identified, including NLRC5 and IL6R for skin toxicity and NOTCH1 and SEMA4D with diarrhea.

Patients treated with anti–CTLA-4 antibodies have shown, in preclinical models, oral gavage of Bacteroides fragilis and Burkholderia cepacia benefit in reducing irAEs and lessened toxicity scores.²⁹

In human cohorts, patients with melanoma treated with anti–CTLA-4 therapy who were colitis-free had enriched Bacteroides and many genetic pathways involved in polyamine transport and B vitamin synthesis compared with those who developed colitis. However, an abundance of F prausnitzii and other Firmicutes had a higher risk of colitis on anti–CTLA-4 therapy.^30,31

Several ongoing trials are determining how to prevent toxicity in patients with renal cancer treated with immunotherapy by using FMT to reduce or prevent posttherapeutic toxic effects.^31,32 The gut microbiota can be altered by a defined mixture of live intestinal bacterial cultures from a healthy donor used in conjunction with immunotherapy. Similarly, FMT and drug-based metabolic modulators like metformin, nivolumab, and pembrolizumab (Keytruda) are being studied to optimize the microbiota in conjunction with immunotherapy. ^33,34

Challenges in Microbiome Modulation

“When I first started working in this area there was hope that we would identify a simple microbe or group of microbes associated with response that could then be readily translated to a therapy of some type. However, it has become quite clear that it is not going to be quite so simple, and it is likely that signatures of response may be quite personalized,” said Lee.

In patients being treated with anti–PD-1 therapy across different cancers, the bacteria that affect drug efficacy are not the same. In one study, Bifidobacterium longum and Collinsella aerofaciens were identified in responders, and in another study the Ruminococcaceae family was identified, and a third identified Bacteroides thetaiotaomicron and F prausnitzii. It is likely that more bacteria will vary among different cancers and gut ecology.^17,34

“Understanding the disparity in taxa and identifying common functional metabolites may help determine specific aspects of the microbiome that can optimally improve ICI efficacy,” said McQuade. Newer immunotherapies may need to be designed with a microbiome-modulating therapeutic element like a probiotic supplement or metabolite to reduce variability in ICI response.

“With the complexity of the tumor microenvironment and genetic determinants involved, there will not be a single predictor of therapeutic response or toxicity. Complicated risk scores taking all these factors into

account will likely be needed to determine optimized response,” McQuade said. “Everyone who responds to therapy is not because of their microbiome, and everyone who doesn’t respond is not because of their microbiome.”

Dietary modulation to modify gut composition can potentially change the therapeutic paradigm for patients who do not respond to immunotherapy, chemotherapy, radiotherapy, or surgery.³⁵ The ketogenic diet has shown effective management of latestage glioblastoma multiforme by arresting tumor cell growth and reducing symptoms and prevalence of edema.^36,37 The ketogenic diet has facilitated nontoxic drug delivery to tumor sites with lower dosages needed to achieve therapeutic effects. Following a ketogenic diet reshapes gut composition.

Complex Relationship

The microbiome is complex and has potential to predict response to cancer therapy and be manipulated to affect the tumor microenvironment. Current research has focused on identifying microbes involved in cancer therapy. “Given the complex interactions of the gut with immune and cancer cells, the challenge will be to find an ideal combination of bacteria and metabolites to affect the tumor microenvironment, and how to ideally introduce this combination for cancer treatment and maintenance,” Lee said. The modulation of gut microbiota will represent a novel and important adjunct to current anticancer therapeutic modalities.

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