Microbiota Modulation Offers Hope of Expanding the Benefits of Immunotherapy

Although the microorganisms colonizing our bodies have long been linked to human health and various disease states, an understanding of the potential impact of the microbiota on cancer has just begun to emerge in the past 20 years. Novel strategies to modulate the microbiota are now an area of robust investigation.¹

Components of the microbiota are linked not only to the development of a number of malignancies but also to response to cancer treatment and the risk of therapy-related toxicity.^1,2 Arguably, “one of the most exciting and potentially translational aspects of cancer microbiome research” is the evolving understanding of the impact of the microbiota on outcomes, including the finding that specific gut bacteria are associated with improved response to immune checkpoint inhibitors (ICIs).¹

As interest in the modulation of the microbiota as a potential avenue for the treatment of cancer and other diseases has grown, the FDA has created a new regulatory class to encompass these therapeutics.^3,4 Among the “live biotherapeutic products” (LBPs) in development is fecal microbiota transplantation (FMT). Attention on FMT, already used in the treatment of recurrent Clostridioides difficile infection,⁵ has now turned to its potential in cancer.

An area of intense ongoing research in the ICI field is examining ways to boost these agents’ efficacy, given that only a minority of patients responds to these groundbreaking drugs.⁶ Recently, the first clinical evidence emerged that transplanting the microbiota from a responder could boost the efficacy of ICIs in patients with melanoma who are refractory to these drugs.^7,8

Numerous microbiome-focused biotech companies have sprung up in recent years and are pursuing novel orally administered alternatives to FMT,⁹ using single-strain or multistrain bacterial consortia with strong evidence of potential to enhance patients’ response to cancer therapy.^1,2

These novel LBPs also are being explored in the prevention or management of treatment-related toxicity. The most notable example is graft-vs-host disease (GVHD), a complication associated with hematopoietic stem cell transplantation (HSCT) that causes significant morbidity and mortality in patients with hematologic malignancies.²

Most of the clinical studies evaluating LBPs and other novel approaches to modulating the microbiota in patients with cancer are in the early stages, with academic investigators playing a significant role in the research (Table).

Microbes and Cancer

The concept of modulating the microbiota to promote health and prevent disease started in the early 1900s and has since grown into the multibillion-dollar probiotics industry. Probiotics, defined as bacteria that “confer a health benefit to hosts when consumed in adequate amounts,” are largely marketed as dietary supplements. Free from rigorous regulatory review, the evidence supporting their proposed health claims is often inadequate.²

In the oncology arena, a handful of microorganisms have been directly linked to the development of cancer. Among them are viruses, including human papillomavirus, which is responsible for almost all cases of cervical cancer worldwide,10 and hepatitis B and C viruses, which are major contributing factors to hepatocellular carcinoma.¹¹ Meanwhile, approximately 90% of gastric cancers worldwide are attributable to the bacterium Helicobacter pylori, which is recognized by the World Health Organization as a type I carcinogen.^2,12

Numerous other microbial species likely play a role in the development of cancer. For example, a substantial body of evidence links the bacterium Fusobacterium nucleatum to the development of colorectal cancer (CRC).¹³

Thanks to the ability to rapidly sequence microbial genomes, there is growing appreciation that carcinogenesis involves not just individual microbial species but also may encompass the composition of the microbiota as a whole. In a healthy individual, the gut is typically populated by bacteria of the Lactobacillus, Bacteroides, and Bifidobacterium species, but in patients with CRC there is a global shift in the microbial species that make up the gut microbiome, with an overrepresentation of Fusobacterium, Porphyromonas, Parvimonas, Peptostreptococcus, and Gemella species.¹

These associations have not yet been proven to equal causation, but identifying the mechanisms underlying the link between microbiota disruption and carcinogenesis is a significant focus of ongoing research. The prospect of detecting unique microbial signatures that are predictive of the development of certain cancers offers a tantalizing prospect for cancer diagnosis.^1,14

Microbiota as a Biomarker

In addition to findings about the gut microbiota’s role in cancer development, there is a growing body of evidence demonstrating that microbiota composition and diversity can influence patients’ response to chemotherapy, radiation therapy, and immunotherapy, as well as patient outcomes after HSCT, via a variety of mechanisms.^1,2,15

Conversely, the composition of the microbiota also has been shown to be affected by the use of cancer therapy or associated supportive treatments. Particularly noteworthy in this respect are antibiotics, which are commonly indicated to treat infections that result from the myelosuppressive impact of cancer therapy.¹

Antibiotics could potentially eliminate indigenous microbiota in addition to the pathogenic microorganisms responsible for the infection, which might have unintended negative consequences on patient outcomes. Findings from a recent study that examined the impact of the microbiota and antibiotic use on chimeric antigen receptor (CAR) T-cell therapy outcomes showed that the use of certain antibiotics before CAR T-cell therapy in patients with B-cell malignancies led to worse outcomes.

However, results of another study suggest that the impact of antibiotic use on CAR T-cell therapy outcomes is nuanced. In this study, investigators found that the antibiotic vancomycin was associated with greater CAR T-cell expansion and inflammatory cytokine levels in a small cohort of patients with B-cell acute lymphoblastic leukemia.^16,17

The composition of the microbiota also has been shown to influence the risk of treatment-related toxicity. Several species of gut bacteria have been linked to a reduced incidence of immune-related toxicity. For example, Bacteroidetes are more abundant in patients colitis related to ipilimumab (Yervoy) therapy.² Specific types of gut bacteria also have been shown to be associated with a reduced risk of developing GVHD after allogeneic HSCT.^18-20

Further disentangling the relationship between the microbiota and therapeutic outcomes in cancer could allow specific microbial signatures to serve as biomarkers to predict clinical response and risk of developing complications.

Broadening ICI Efficacy

A particularly exciting avenue of ongoing research relates to potential applications of the microbiota in predicting response to ICIs. A series of studies in mice identified specific groups of bacteria that were associated with improved response to ICIs. Bacteroides species, specifically B fragilis and B thetaiotaomicron, were linked to the antitumor immune response associated with ICIs targeting CTLA-4,²¹ whereas separate studies found that Bifidobacterium and Ruminococcaceae were key to the antitumor response to PD-L1–targeted and PD-1–targeted drugs,^22,23 respectively. That different bacterial taxa were associated with the efficacy of each agent highlights the complexity of the microbiota and the challenge in defining “beneficial” microbial signatures.

Investigators also have demonstrated that tumor-bearing mice whose guts were colonized with feces from patients whose cancer had responded to ICI therapy had better responses to ICIs compared with mice whose guts were colonized with the feces of nonresponders.²³ Another study showed that colonizing the gut of germfree mice with a rationally chosen consortium of 11 human bacterial strains could enhance the efficacy of ICIs.²⁴ These findings have potential implications for the development of novel therapeutic strategies to boost the efficacy of ICIs.

Microbiota-modulating therapies represent an area of intense ongoing research, with perhaps the best-known example being FMT. This process involves the use of donated stool from healthy individuals, which is purified, processed, and then administered to a patient via colonoscopy, enema, or oral capsules.⁵

The results of 2 studies recently published in Science demonstrated the clinical potential of using FMT to promote response to ICIs in patients with ICI-refractory melanoma. In both studies, FMT was derived from donors who had responded to PD-1–targeted therapy and was given, in combination with PD-1–targeted therapy, to patients with melanoma who were refractory to ICIs.

In the first study (NCT03341143), the combination was well tolerated, and clinical benefit was observed in 6 of 15 patients.⁷ In the second study (NCT03353402), clinical responses were observed in 3 of 10 patients, including 2 partial responses (PRs) and 1 complete response (CR).⁸ In both trials, FMT was associated with favorable changes in the microbiota composition, immune cell infiltrates, and the tumor microenvironment (TME).^7,8

Numerous clinical trials of FMT are ongoing, including some testing its potential to boost the efficacy of anticancer therapy, as well as others evaluating FMT for the prevention and management of treatment-related adverse events and the management of acute GVHD (aGVHD).

Next-Generation Probiotics

Although FMT could establish proof of concept for targeting the gut microbiota, it is not without its challenges. There is no standard definition of FMT, and the mechanism underlying its efficacy is poorly understood. Feces contain many species of microorganisms, in addition to other components, such as metabolites, that could have a therapeutic effect.²⁵

FMT is not a traditional drug or medicinal product, and initially it was not regulated by the FDA. In 2012, the agency created a new category for drugs containing live microorganisms that are used for therapeutic purposes, and the use of these LBPs now requires an investigational new drug application.^3,4,25

Despite this increased regulation, FMT has encountered safety issues. In March 2020, the FDA issued a safety alert following infections with pathogenic Escherichia coli strains detected in 6 patients who received investigational FMT products supplied by a stool bank company as treatment for C difficile infection. Additionally, 2 patients with chronic medical conditions died after receiving the FMT product from the stool bank; however, the FDA said the E coli infection was not detected in the stool of 1 of the patients and it was unclear whether the infection contributed to the death of the other. The FDA now mandates additional screening of donor feces for these dangerous strains.^25-27

To overcome some of these challenges, ongoing development of microbiota-modulating therapies is focused on the use of defined single strains or microbial consortia cultivated in the laboratory to produce pure live cultures free from contamination by pathogenic strains.^1,25

Among such products in development is 4D pharma’s MRx0518, which contains a single strain (Enterococcus gallinarum) that has been shown to elicit strong proinflammatory responses in preclinical studies.²⁸ Several clinical trials of MRx0518 are ongoing, including a phase 1/2 study (NCT03637803) with a safety phase (part A) and cohort expansion (part B) evaluating MRx0518 in combination with pembrolizumab (Keytruda) in patients with advanced solid tumors who previously progressed on ICIs.

Among 12 patients with metastatic renal cell carcinoma and non–small cell lung cancer treated during part A of the study, the disease control rate was 42%, including PR in 3 patients and stable disease lasting at least 6 months in 2 additional patients, with a median duration of treatment of 13.2 months among the 5 responders.²⁹

A biomarker analysis revealed that patients who experienced clinical benefit from the combination demonstrated a significantly greater density of CD3+FOXP3+ regulatory T cells and CD3+Ki67+ proliferating T cells in tumors at baseline. Nonresponders had a significantly higher density of CD68+ macrophages in the TME.³⁰

Part B is enrolling 30 patients with each tumor type, and as of February 2021, 24 patients had been enrolled and a safety review of the first 10 patients revealed no dose-limiting toxicities.³¹ Last year, the company also announced plans for a study evaluating MRx0518 in combination with avelumab (Bavencio) for the treatment of patients with urothelial carcinoma in collaboration with Merck and Pfizer.³²

MaaT Pharma is developing several orally administered full-ecosystem microbial therapies known to produce anti-inflammatory short-chain fatty acids.³³ One of these products, MaaT013, is poised to enter phase 3 testing in the ARES trial (NCT04769895) in patients with gastrointestinal (GI) aGVHD refractory to JAK inhibitor therapy with ruxolitinib (Jakafi) and corticosteroids, pending further discussions with the FDA.³⁴

MaaT013 therapy demonstrated safe and effective outcomes for immunocompromised patients with GI aGVHD in results from the phase 2 HERACLES trial (NCT03359980) and an early access program (EAP) in France that were reported at the 63rd American Society of Hematology Annual Meeting and Exposition in December 2021.³⁵

A total of 76 patients with steroid-refractory GI aGVHD were treated in the HERACLES study (n = 24) and the EAP (n = 52; steroid-dependent cases also allowed). In HERACLES, the GI overall response rate (GI-ORR) was 38%, including 5 CRs, 2 very good PRs (VGPRs), and 2 PRs. In the EAP, GI-ORR was 60%, including 16 CRs, 11 VGPRs, and 4 PRs. The 6-month and 12-month overall survival rates were 29% and 25%, respectively, in HERACLES, and 48% and 37%, respectively, in the EAP.³⁵

MaaT Pharma also is testing another microbial therapy, MaaT033, in the phase 1 CIMON trial (NCT04150393) in patients with hematologic malignancies undergoing intensive chemotherapy. The company recently reported that it plans to wrap up the trial early, after promising data from the first 4 cohorts, and progress into a larger phase 2/3 trial in patients with acute myeloid leukemia.³⁶

References

1. Cullin N, Azevedo Antunes C, Straussman R, Stein-Thoeringer CK, Elinav E. Microbiome and cancer. Cancer Cell. 2021;39(10):1317-1341. doi:10.1016/j.ccell.2021.08.006
2. Helmink BA, Khan MAW, Hermann A, Gopalakrishnan V, Wargo JA. The microbiome, cancer, and cancer therapy. Nat Med. 2019;25(3):377-388. doi:10.1038/s41591-019-0377-7
3. Cordaillat-Simmons M, Rouanet A, Pot B. Live biotherapeutic products: the importance of a defined regulatory framework. Exp Mol Med. 2020;52(9):1397-1406. doi:10.1038/s12276-020-0437-6
4. Rouanet A, Bolca S, Bru A, et al. Live biotherapeutic products, aroad map for safety assessment. Front Med (Lausanne). 2020;7:237. doi:10.3389/fmed.2020.00237 
5. Hoffmann DE, Palumbo FB, Ravel J, Rowthorn V, von Rosenvinge E. A proposed definition of microbiota transplantation for regulatory purposes. Gut Microbes. 2017;8(3):208-213. doi:10.1080/19490976.2017.1293223
6. Marin-Acevedo JA, Kimbrough EO, Lou Y. Next generation of immune checkpoint inhibitors and beyond. J Hematol Oncol. 2021;14(1):45. doi:10.1186/s13045-021-01056-8
7. Davar D, Dzutsev AK, McCulloch JA, et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science. 2021;371(6529):595-602. doi:10.1126/science.abf3363
8. Baruch EN, Youngster I, Ben-Betzalel G, et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science. 2021;371(6529):602-609. doi:10.1126/science.abb5920
9. Zipkin M. Fecal microbiota potentiate checkpoint inhibitors, unleash microbiome startups. Nat Biotechnol. 2021;39(5):529-532. doi:10.1038/d41587-021-00002-w
10. Burd EM. Human papillomavirus and cervical cancer. Clin Microbiol Rev. 2003;16(1):1-17. doi:10.1128/CMR.16.1.1-17.2003
11. Ringelhan M, McKeating JA, Protzer U. Viral hepatitis and liver cancer. Philos Trans R Soc Lond B Biol Sci. 2017;372(1732):20160274. doi:10.1098/rstb.2016.0274
12. Knippel RJ, Drewes JL, Sears CL. The cancer microbiome: recent highlights and knowledge gaps. Cancer Discov. 2021;11(10):2378-2395. doi:10.1158/2159-8290.CD-21-0324
13. Wu J, Li Q, Fu X. Fusobacterium nucleatum contributes to the carcinogenesis of colorectal cancer by inducing inflammation and suppressing host immunity. Transl Oncol. 2019;12(6):846-851. doi:10.1016/j.tranon.2019.03.003
14. Jain T, Sharma P, Are AC, Vickers SM, Dudeja V. New insights into the cancer–microbiome–immune axis: decrypting a decade of discoveries. FrontImmunol. 2021;12:622064. doi:10.3389/fimmu.2021.622064 
15. Cheng WY, Wu CY, Yu J. The role of gut microbiota in cancer treatment: friend or foe? Gut. 2020;69(10):1867-1876. doi:10.1136/gutjnl-2020-321153
16. Smith M, Dai A, Ghilardi G, et al. The intestinal microbiota correlates with response and toxicity after CAR T cell therapy in patients with B-cell malignancies. Blood. 2021;138(suppl 1):253. doi:10.1182/blood-2021-153945
17. Ruella M, Uribe-Herranz M, Beghi S, et al. Gut microbiota tuning promotes tumor-associated antigen cross presentation and enhances CAR T antitumor effects. Blood. 2021;138(suppl 1):163. doi:10.1182/blood-2021-151093
18. Holler E, Butzhammer P, Schmid K, et al. Metagenomic analysis of the stool microbiome in patients receiving allogeneic stem cell transplantation: loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal graft-versus-host disease. Biol Blood Marrow Transplant. 2014;20(5):640-645. doi:10.1016/j.bbmt.2014.01.030
19. Kakihana K, Fujioka Y, Suda W, et al. Fecal microbiota transplantation for patients with steroid-resistant acute graft-versus-host disease of the gut. Blood. 2016;128(16):2083-2088. doi:10.1182/blood-2016-05-717652
20. Shono Y, Docampo MD, Peled JU, et al. Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci Transl Med. 2016;8(339):339ra71. doi:10.1126/scitranslmed.aaf2311
21. Vétizou M, Pitt JM, Daillère R, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350(6264):1079-1084. doi:10.1126/science.aad1329
22. Sivan A, Corrales L, Hubert N, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti–PD-L1 efficacy. Science. 2015;350(6264):1084-1089. doi:10.1126/science.aac4255
23. Gopalakrishnan V, Spencer CN, Nezi L, et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2018;359(6371):97-103. doi:10.1126/science.aan4236
24. Tanoue T, Morita S, Plichta DR, et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature. 2019;565(7741):600-605. doi:10.1038/s41586-019-0878-z
25. Merrick B, Allen L, Masirah M Zain N, Forbes B, Shawcross DL, Goldenberg SD. Regulation, risk and safety of faecal microbiota transplant. Infect Prev Pract. 2020;2(3):100069. doi:10.1016/j.infpip.2020.100069
26. Fecal microbiota for transplantation: safety alert -risk of serious adverse events likely due to transmission of pathogenic organisms.FDA. March 12, 2020. Updated April 7, 2020. Accessed February 25, 2022. bit.ly/3McRaLM
27. Update to March 12, 2020 safety alert regarding use of fecal microbiota for transplantation and risk of serious adverse events likely due to transmission of pathogenic organisms. FDA. March 13, 2020. Accessed March 20, 2022. https://bit.ly/3N8IpTt
28. Lauté-Caly DL, Raftis EJ, Cowie P, et al. The flagellin of candidate live biotherapeutic Enterococcus gallinarum MRx0518 is a potent immunostimulant. Sci Rep. 2019;9(1):801. doi:10.1038/s41598-018-36926-8
29. 4D pharma announces clinical benefit data from part A of combination trial of MRx0518 and Keytruda: 42% disease control rate exceeds predefined threshold for expansion. News release. 4D pharma. August 26, 2020. Accessed February 25, 2022. bit.ly/3vfeMsT
30. Parra ER, Adriani M, Lima CFP, et al. 1024P Baseline biomarkers associated with clinical benefit in patients with solid tumors refractory to immune checkpoint inhibitors (ICIs) treated with live biotherapeutic MRx0518 in combination with pembrolizumab. Ann Oncol. 2021;32(suppl 5):S858-S859. doi:10.1016/j.annonc.2021.08.1408
31. Enrollment progressing well for both expanded part B of MRx0518 and Keytruda combination study, and pancreatic cancer study: further analysis of biomarker data in ongoing MRx0518 neoadjuvant monotherapy study. News release. 4D pharma. February 3, 2021. Accessed February 25, 2022. bit.ly/3viiJwV
32. 4D pharma announces clinical trial collaboration and supply agreement with Merck KGaA, Darmstadt, Germany and Pfizer to evaluate MRx0518 in combination with BAVENCIO for the treatment of locally advanced or metastatic urothelial carcinoma. News release. 4D pharma. February 8, 2021. Accessed February 25, 2022. bit.ly/3t6LGcF
33. Pipeline. MaaT Pharma. Accessed February 25, 2022. bit.ly/3IqIKxW
34. MaaT Pharma microbiota as a therapy. MaaT Pharma corporate presentation. January 2022. Accessed March 21, 2022. https://bit.ly/37Rsbhr
35. Malard F, Loschi M, Cluzeau T, et al. Pooled allogenic fecal microbiotherapy MaaT013 for the treatment of steroid-refractory gastrointestinal acute graft-versus-host disease: results from the phase IIa HERACLESstudy and expanded access program. Blood. 2021;138(1):262. doi:10.1182/blood-2021-147709
36. Taylor NP. MaaT wraps up cancer microbiome trial early to power into phase 2/3 this year. January 24, 2022. Accessed February 25, 2022. bit.ly/3BTajxt