The Role of the Human Microbiome in Immunotherapy

By Ryan M. Weight, DO, MS

Ryan Weight
Ryan Weight, DO, MS
Assistant Professor, Department of Medical Oncology
University of Colorado
Denver, Colorado

Ryan Weight, DO, MS, joined the University of Colorado School of Medicine faculty in 2019 as an assistant professor of medicine with a focus on the treatment of skin malignancies, including melanoma. Prior to this appointment, Dr. Weight served as an assistant professor of medicine at Thomas Jefferson University School of Medicine in Philadelphia.  In 2017, Dr. Weight was appointed leader of the cutaneous malignancy service line within the melanoma division of medical oncology. Dr. Weight established and served as co-director of the Complex Cutaneous Oncology Multidisciplinary Clinic in the Center for Heritable and Connective Tissue Skin Diseases, which brought together dermatology and medical oncology services for the treatment of dysplastic nevus syndrome, patients with a genetic predisposition to skin cancer, erythema bullosum, and others.

Dr. Weight has an interest in the management of immune-related adverse events caused by immune-activating therapies commonly used for the treatment of skin cancers. He served as director of the Immuno-Oncology Clinical Working Group at Thomas Jefferson University (2016- 2018), and as principal investigator for a number of clinical trials focused on the treatment of melanoma, including early phase trials. He has co-authored a multi-center adjuvant study of Nivolumab for the treatment of resected high-risk melanoma patients. 

  November 2, 2017

Mounting evidence suggests that the gut microbiome (or microbiota) plays a fundamental role in the activation, regulation, and function of the immune system. There is ongoing interest in the relationship between not only the gut microbiome and cancer development, but also the role the gut microbiome may play in the variable therapeutic response seen with checkpoint inhibitors and the development of adverse events.

Human Microbiome Basics

Microbes, comprised of bacteria, fungi, viruses, and other prokaryotic and eukaryotic species are found throughout the human body, and live on a wide variety of surfaces including the gastrointestinal tract, skin, dental plaque, saliva, and conjunctiva.1,2 The vast majority of microbes are bacteria and live primarily in the colon, with the bacterial load of the colon at least two orders of magnitude greater than all other regions.1 Microbes that are associated with the digestive-tract are referred to as the gut microbiome.3 Conventional thought indicates the number of symbiotic microbes outweighs nucleated host cells by a factor of 10; however, a recent analysis found that the number of microbes is approximately equal to that of human cells, when all types of human cells are included.1,2

While studies have shown that the first human-microbial interactions occur before birth, much of the microbiome is established from birth through the first several years of life via delivery mode, breast milk, other foods, antibiotic use, and other exposures in the environment.4 By 1-3 years of life, the diversity of a healthy child’s microbiome closely resembles that of an adult; however, the composition and functional potential of the microbiome continues to develop thoughout life.4-6 The Human Microbiome Project found microbial populations greatly vary amongst individuals and there is no one “healthy” microbiome composition.6 However, the diversity and composition of the microbiome (i.e., the number and abundance distribution of distinct types of microbes within a given body habitat) have been linked to both preventing and causing different disease states.5,7

Commensal: A relation between two kinds of organisms in which one obtains food or other benefits from the other without damaging or benefiting i.

Symbiosis: The intimate living together of two dissimilar organisms in a mutually beneficial relationship Source: https://www.merriam-webster.com/dictionary/

While the relationship between microbes and the human host can be commensal, symbiotic/mutualistic, or parasitic, most human microbes are commensal bacteria and exist in homeostatic states with the human host, with each shaping the other.2,5,8,9 Homeostasis is a reflection of a complex interplay between the modulators of microbiome (e.g., antibiotics, probiotics, fecal transplants), host factors (genetics, immune system, hormones), and environmental factors (diet, nutritional state, stress).10

Microbes form complex communities that are integrally linked to host physiology, including digestion and nutrient acquisition, metabolism, host protection from pathogens (barrier immunity), and development and regulation of both the innate and adaptive immune systems.2-6 When microbiome are either commensal or symbiotic with their hosts, the community structure is balanced and beneficial, or in a state of eubiosis.5

Conversely, factors such as antibiotic use, changed diet, and altered host metabolic/nutritional state and immune response can contribute to altered gut microbiome composition and function, disrupting homeostasis. The resultant dysregulation or imbalance of the microbiome-host cell relationship, or dysbiosis, can contribute to disease states, including metabolic, immunological, and infectious diseases.3,5,6,8

Linking the Gut Microbiome and Immuno-Oncology

In the gastrointestinal (GI) tract, the microbiome promotes protective immunity and regulation through a wide variety of mechanisms including, but not limited to: developing gut-associated lymphoid tissue; producing antimicrobial molecules and metabolites that target pathogens; promoting epithelial cell production of antimicrobial peptides; physically reinforcing intercellular tight junctions in the GI epithelium; promoting the induction of effector B and T cells in response to pathogens; stimulating the induction of T regulatory (Treg) cells; and dampening the immune response via immunosuppressive cytokines (e.g., IL-10).2,5,11

For example, microbes are essential for breaking down non-digestible dietary components like fiber; a predominate metabolite of this breakdown process are short chain fatty acids, key players in the induction and performance of Treg cells in the colonic environment, which are essential for the maintenance of self-tolerance.2,9

In the context of cancer, studies have indicated that dysbiosis, including decreases in commensal microbiome diversity and stability, appears to greatly influence the initiation and progression of tumorigenesis.5,12 Conversely, higher levels of urinary enterolignans, considered an important biomarker for microbiome diversity, are associated with greater microbiome diversity as well as reduced cancer risk.13

The composition and diversity of the intestinal microbiome has been shown to mediate various aspects of immunity associated with the anti-tumor response, including enhanced as well as dampened response to chemotherapy and immunotherapy.2,9 As noted by Pippa Corrie, MD, Chair of the National Cancer Research Institute’s Skin Cancer Clinical Studies Group:

“Gut microbes have been shown to influence the role of conventional chemotherapy, so it's probably not surprising that they impact on response to new immunotherapies being used in the clinic. Manipulating the gut flora may be a new strategy to enhance activity of immunotherapy drugs, as well as to manage problematic toxicity in the future.”14

Indeed, a growing body of evidence suggests the gut microbiome is not only central to the variable responses seen with checkpoint inhibitor therapy, but treatment-related changes in microbiome composition may influence the development of side effects.5

Preclinical Findings

A preclinical study assessed the treatment response to programmed death-ligand 1 (PD-L1) inhibitor therapy in mice with syngeneic tumors in both the specific pathogen-free (SGF) and germ-free (GF) environments. Tumor growth in GF mice failed to respond to treatment, whereas, tumor growth was controlled in SGF mice, suggesting the microbiome influenced response to treatment.15

Additional studies have examined the relationship between gut microbiome composition and T cell response to checkpoint therapies in mice with melanoma.16,17 For instance, one study found the antitumor effect of cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) blockade in mice was influenced by the microbiome composition, with efficacy dependent upon the presence of distinct Bacteroidales species (B. fragilis and B. thetaiotaomicron).16

Similarly, another study evaluated the treatment response to PD-L1 checkpoint inhibitor therapy in mice with two distinct types of microbiomes. Mice with gut microbiome high in Bifidobacterium exhibited greater levels of spontaneous anti-tumor T cell response to melanoma compared with mice with lower levels Bifidobacterium. Additionally, the efficacy of PD-L1 checkpoint inhibitor therapy was higher in mice with correspondingly higher levels of Bifidobacterium.17 In each study, transfer of the “responder” microbiome profile to “non-responder” mice elicited improved tumor control, suggesting a role for administration of select microbiomes to improve checkpoint inhibitor efficacy.16-18

Both studies support a role for specific commensal gut microbiome in modulating the response to immuno-oncology therapy, in particular through altering dendritic cell maturation/activity and improving tumor-infiltrating effector T cell function.

Clinical Studies

Recent clinical studies have explored the relationship between the gut microbiome and immuno-oncology therapy response in humans. While different microbiomes were identified across the studies, overall, patients who responded to immuno-oncology therapy had more diversity and different composition of the type of bacteria in their gut microbiome compared with patients who did not respond or respond as well to therapy.14,19-23 Table 1 presents key findings from studies evaluating the relationship between human gut microbiome and response to checkpoint inhibitor therapy, as well as the impact of antibiotic use on outcomes.

Table 1.

Summary of Clinical Studies Evaluating the Role of Gut Microbiome in Response to Checkpoint Inhibitor Therapy

Chaput et al.19 Baseline gut microbiome in metastatic melanoma patients treated with ipilimumab: Relation with clinical response and colitis.

Study Summary

Explores the role of baseline gut microbiome, determined by 16S rRNA gene sequencing, in local systemic anti-tumor response and intestinal toxicity in patients with metastatic melanoma receiving treatment with ipilimumab.

Key Findings

Patients with baseline gut microbiome enriched with Faecaliacterium genus and other Firmicutes had longer progression-free survival and improved overall survival compared to patients with baseline gut microbiome high in Bacteroides. Patients with baseline phylotypes related to Firmicutes experienced increased incidence of ipilimumab-induced colitis compared to patients with baseline Bacteroidetes. Ipilimumab therapy was not associated with significant changes in gut microbiome; i.e., did not induced dysbiosis.

Frankel et al.21 Metagenomic shotgun sequencing (MSS) to identify specific human gut microbes associated with immune checkpoint therapy efficacy in melanoma patients.

Study Summary

Explores whether specific baseline gut microbiome, determined by genomic DNA analysis (MSS) of fecal samples, are associated with improved response to checkpoint inhibitor therapy (nivolumab plus ipilimumab or pembrolizumab alone) in patients with melanoma (N=37).

Key Findings

Twenty-three patients were evaluable. Of these, 8 were classified as responders (RECIST) to checkpoint therapy. Compared with non-responders, MSS indicated responders were significantly enriched with 4 specific gut microbiome, including: Methanobrecibacter smithii; Bacteroides thetaiotamicron; Lactobacillus plantarum; and Eubacterium limosum.

Gopalakrishnan et al.22 Association of diversity and composition of the gut microbiome with differential responses to programmed death-1 (PD-1) based therapy in patients with metastatic melanoma.

Study Summary

Explores whether baseline gut (n=113) and oral (n=222) microbiome, with composition and diversity determined by 16S rRNA gene sequencing, are associated with improved response to PD-1 inhibitor therapy in patients with metastatic melanoma (N=228). When available, tumors underwent pre-treatment immune profiling (CD3, CD8, PD-1, PD-L1, Granzyme B, RORyT, and FoxP3).

Key Findings

Compared with non-responders, patients who responded to treatment with PD-1 inhibitor therapy had greater gut microbiome diversity and notably different composition. No clear differences were observed for oral microbiomes. Baseline immune tumor profiling indicated responders demonstrated significantly increased immune infiltrates, with a positive correlation between CD3, CD8, PD-1, and FoxP3 T-cell density and an abundance of Faecalibacterium.

Wargo et al.23 Association of the diversity and composition of the gut microbiome with responses and survival in metastatic melanoma patients on anti-PD-1 therapy.

Study Summary

Explore whether specific baseline gut microbiome (n=120) and oral microbiome (n=234), determined by 16S rRNA and whole genome shotgun sequencing, are associated with improved response to checkpoint inhibitor therapy in patients with metastatic melanoma (N=221). The majority of patients were treated with PD-1 inhibitor based therapy (n=105). When available, tumors underwent pre-treatment immune profiling.

Key Findings

Compared with non-responders, patients who responded to treatment with PD-1 inhibitor therapy had greater gut microbiome diversity and notably different composition. Responders had a higher abundance of Clostridiales (Ruminococcaceae family), whereas non-responders had a higher abundance of Bacteriodales and much lower diversity. Baseline immune tumor profiling indicated responders demonstrated significantly increased immune infiltrates, with a higher density of CD8+ T cells, which correlated with abundance of specific bacteria enriched in the gut microbiome. Both diversity and abundance of specific bacteria were associated with improved progression free survival.

Derosa et al.20 Antibiotics prescription to decrease progression-free survival (PFS) and overall survival (OS) in patients with advanced cancers treated with PD1/PDL1 immune checkpoint inhibitors.

Study Summary

Antibiotics have been shown to decrease the diversity and change the composition of the gut microbiome. Treatment outcomes were retrospectively evaluated for patients who had received treatment with antibiotics before (2-month period) or within the first month of receiving checkpoint inhibitor therapy (PD-1/PD-L1) for solid malignancies.

Key Findings

The use of antibiotics negatively impacted progression-free survival (PFS) and overall survival (OS). Overall, 29% (51/175) of patients had received antibiotics. Patients who had received antibiotics had significantly shorter PFS and OS compared to those who had not, 3.4 vs 5.2 months (P<0.013) and 12.2 vs 20.8 months (P<0.001), respectively.

Data from both preclinical and clinical studies suggest that specific gut microbiomes may someday serve as biomarkers for identifying patients who might respond to checkpoint inhibitor therapy or be at risk of developing treatment-related adverse events. Findings also suggest the potential merit of altering patients’ gut microbiomes (e.g., prebiotics, probiotics, postbiotics, antibiotics, or fecal transplants) to potentiate the efficacy and mitigate the toxicity of checkpoint inhibitors.5,9,11,14

Relationship Between Gut Microbiome and Immune-Related Adverse Events

While not yet clear, it is believed a variety of factors contribute to the development and severity of immune-related adverse events (irAE) in patients receiving checkpoint inhibitor therapy. These factors include nonspecific immune activation in response to treatment, unveiling of subclinical autoimmunity, host genetics, and microbiome composition.5,24

Data suggest that CTLA-4 checkpoint inhibitors block the inhibitory activity of CTLA-4 on both effector T cells and Treg cells in addition to selective depletion of Treg cell populations in a tumor microenvironment-dependent manner. Widespread depletion of Treg cells has been associated with the development of autoimmune pathologies, which may help explain the development of irAEs in some patients.25

Data exploring the relationship between gut microbiome and irAEs is still relatively limited. However, in a preclinical study with mice, ipilimumab was found to induce dysregulation of the equilibrium at the gut-microbiome interface, resulting in altered microbiome composition and changes in intestinal mucosal barrier, consistent with subclinical colitis.9,16 However, recolonization of the mice with Bacteroides fragilis and Burkholderia cepacia led to reduced toxicity, likely through restoring and enhancing the immuno-suppressive function of Treg cells.9,12,16,26

Another study evaluated the relationship between pre-inflammation fecal microbiome and microbiome composition of patients with malignant melanoma undergoing treatment with ipilimumab and the subsequent development of immune-mediated colitis. In this study, patients with higher abundance of bacteria in the Bacteroidetes phylum (Bacteroidaceas, Rikenallaceae, and Barnesiellaceae) were less likely to develop ipilimumab-induced colitis compared to patients with lower levels of these bacteria. Additionally, patients with higher levels of microbial genetic pathways involved with polyamine transport and vitamin B (B1, B2, B5, and B7) biosynthesis demonstrated a lower risk of developing colitis.27

Such results raise the possibility for specific gut microbiome profiles serving as predictive biomarkers for identifying patients at risk of developing irAEs as well as the development of strategies for manipulating the gut microbiome to reduce irAEs.9,27

Conclusion

The gut microbiome appears to be inextricably linked with both the development of cancer and response to treatment. Yet, numerous questions remain unanswered; therefore, the role of the microbiome in immunotherapy is an area of active research, with the hope of eventually yielding data that will help guide treatment approaches in patients receiving I-O therapy. As succinctly summarized by Jennifer Wargo, MD, MMSc, Associate Professor of Genomic Medicine and Surgical Oncology at the University of Texas MD Anderson Cancer Center in Houston:

“We need concerted research efforts to better understand how the microbiome may influence immune responses, as well as an in-depth view on how we can tweak the microbiome so that more patients can benefit from immunotherapy.”28

References

  1. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533.
  2. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121-141.
  3. Bull MJ, Plummer NT. Part 1: The Human gut microbiome in health and disease. Integr Med (Encinitas). 2014;13(6):17-22.
  4. Hollister EB, Riehle K, Luna RA, et al. Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome. 2015;3:36.
  5. Bhatt AP, Redinbo MR, Bultman SJ. The role of the microbiome in cancer development and therapy. CA Cancer J Clin. 2017;67(4):326-344.
  6. Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med. 2016;8(1):39.
  7. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-214.
  8. Littman DR, Pamer EG. Role of the commensal microbiota in normal and pathogenic host immune responses. Cell Host Microbe. 2011;10(4):311-323.
  9. Pitt JM, Vetizou M, Waldschmitt N, et al. Fine-tuning cancer immunotherapy: Optimizing the gut microbiome. Cancer Res. 2016;76(16):4602-4607.
  10. Eloe-Fadrosh EA, Rasko DA. The human microbiome: from symbiosis to pathogenesis. Ann Rev Med. 2013;64:145-163.
  11. Botticelli A, Zizzarim I, Mazzuca F, Ascierto P, Putignani L, et al. Cross-talk between microbiota and immune fitness to steer and control response to anti PD-1/PDL-1 treatment. Oncotarget. 2017;8(5):10.
  12. Pope JL, Tomkovich S, Yang Y, Jobin C. Microbiota as a mediator of cancer progression and therapy. Transl Res. 2017;179:139-154.
  13. Shiveppa N, Wirth M, Murphy A, Hurley T, Herbert J. Abstract Book of the 42nd ESMO Congress: Abstract 1684P. Association between the Dietary Inflammatory Index (DII), urinary enterolignans and C-reactive protein in the National Health and Nutrition Examination Survey-2003-2008. Ann Oncol. 2017;28(5 ):1.
  14. The ASCO Post. Gut microbes linked to immunotherapy response in patients with melanoma. November 7, 2016; http://www.ascopost.com/News/44100. Accessed Oct. 8, 2017.
  15. Mansfield A, Liu X, Cao S, Bindemen W, Yin P, et al. Abstract Book of the 42nd ESMO Congress: Abstract 1195P. Compromised efficacy of PD-L1 blockade therapy in axenic (germ- free) mice with syngeneic tumors. Ann Oncol. 2017;28(5):1.
  16. Vetizou M, Pitt JM, Daillere R, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350(6264):1079-1084.
  17. 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.
  18. Ratain MJ. Interview with Dr. Gajewski: Manipulating the Microbiome to Improve the Efficacy of Immunotherapy. Clin Adv Hematol and Oncol. 2016;14(6):3.
  19. Chaput N, Lepage P, Coutzac C, et al. Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Ann Oncol. 2017;28(6):1368-1379.
  20. Derosa L, Routy B, Meziquita L, Naltet C, Enot D. Antibiotics prescription to decrease progression-free survival (PFS) and overall survival (OS) in patients with advanced cancers treated with PD1/PDL1 immune checkpoint inhibitors. J Clin Oncol. 2017;35(15):suppl (May 2017) 3015-3015.
  21. Frankel AE, Coughlin LA, Kim J, et al. Metagenomic shotgun sequencing and unbiased metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients. Neoplasia. 2017;19(10):848-855.
  22. Gopalakrishnan K, Spencer C, Reuben A, Karpinets T, Hutchinson D, et al. Association of diversity and composition of the gut microbiome with differential responses to PD-1 based therapy in patients with metastatic melanoma. J Clin Oncol. 2017;35(suppl 7S; abstract 2).
  23. Wargo J, Gopalakrishnan K, Spencer C, Karpinets T, Reuben A, et al. Association of the diversity and composition of the gut microbiome with responses and survival in metastatic melanoma patients on anti-PD-1 therapy. J Clin Oncol. 2017(35):(suppl; abstr 3008).
  24. Abdel-Wahab N, Shah M, Suarez-Almazor ME. Adverse events associated with immune checkpoint blockade in patients with cancer: A systematic review of case reports. PLoS One. 2016;11(7):e0160221.
  25. Simpson TR, Li F, Montalvo-Ortiz W, et al. Fc-dependent depletion of tumor-infiltrating regulatory T cells co-defines the efficacy of anti-CTLA-4 therapy against melanoma. J Exp Med. 2013;210(9):1695-1710.
  26. West NR, Powrie F. Immunotherapy not working? Check your microbiota. Cancer Cell. 2015;28(6):687-689.
  27. Dubin K, Callahan MK, Ren B, et al. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun. 2016;7:10391.
  28. American Society of Clinical Oncology. Response to cancer immunotherapy may depend on gut bacteria. February 21,2017; ASCO (https://www.asco.org/). Accessed Oct. 8, 2017.