Exploring the emerging role of the microbiome in cancer immunotherapy

Abstract

The activity of the commensal microbiota significantly impacts human health and has been linked to the development of many diseases, including cancer. Gnotobiotic animal models have shown that the microbiota has many effects on host physiology, including on the development and regulation of immune responses. More recently, evidence has indicated that the microbiota can more specifically influence the outcome of cancer immunotherapy. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes have shown promise in mouse studies. Ongoing endeavors are translating these pre-clinical findings to early stage clinical testing. In this review we summarize 1) basic methodologies and considerations for studies of host-microbiota interactions; 2) experimental evidence towards a causal link between gut microbiota composition and immunotherapeutic efficacy; 3) possible mechanisms governing the microbiota-mediated impact on immunotherapy efficacy. Moving forward, there is need for a deeper understanding of the underlying biological mechanisms that link specific bacterial strains to host immunity. Integrating microbiome effects with other tumor and host factors regulating immunotherapy responsiveness versus resistance could facilitate optimization of therapeutic outcomes.

Keywords: 16S rRNA gene sequencing; Anti-PD-1; Germ-free mice; Gut microbiome; Immune checkpoint blockade; Immunotherapy; Metagenomics; Microbiome-based therapy.

Fig. 1

Possible mechanisms linking the gut microbiota to anti-tumor immunity. The composition of the gut microbiome may impact immunotherapy efficacy by either acting as (1) an immunosuppressive or (2) an immunostimulatory factor via various non-mutually exclusive mechanisms. (1) Certain commensal bacteria may suppress anti-tumor immunity by skewing immune subset balances towards suppressive phenotypes such as Tregs and MDSCs. Locally in mucosal sites, induction of immunosuppressive cells could be mediated by cytokines released by host cells (such as gut epithelium or immune cells) in response to microbial sensing. Immunosuppressive effects in distant sites, such as active immunosuppression in the TME, could be mediated by trafficking of locally induced suppressor cells. Additionally, bacterial metabolites with immunosuppressive properties might be released into the circulation and promote immunosuppressive cell functions in the TdLN and TME. Chronic inflammation caused by continuous stimulation by PAMPs/MAMPs or epithelial injury could also ultimately contribute to immunosuppression over time. (2) The immunostimulatory effects of the gut microbiota could be mediated by augmented antigenicity, adjuvanticity, or bystander T cell activation. (a) Antigenicity: Cross-reactive T cells driven by bacterial antigens that additionally recognize tumor-associated antigens is one conceivable mechanism. Luminal bacteria or bacterial antigens can be internalized by DCs in the LP via trans-endothelial dendrites extending through the epithelium into the lumen. Goblet cells and M cells can also serve as portals to deliver bacterial antigens to mucosal APCs. Alternatively, disruption of barrier function may allow for the translocation of luminal bacteria and bacterial antigens. Antigen-loaded DCs can migrate from the LP to the MLN and possibly to distant sites such as the TdLN, where they may prime cross-reactive anti-tumor CD8⁺ or CD4⁺ T cells, enhancing cytotoxic T lymphocyte (CTL) function in the TME. (b) Adjuvanticity: PAMPs/MAMPs may condition DCs to be more potent T cell activators, for instance by upregulating costimulatory molecule expression, enhancing antigen presentation, or boosting type I IFN production. Some microbial metabolites could alter immune cell function epigenetically or otherwise to poise innate and adaptive cells in a heightened activation state. (c) Bystander activation: A heightened inflammatory state in the TME driven by pro-inflammatory cytokines released in response to bacterial stimuli may contribute to tumor cell killing by T cell help provided by bacteria-specific T cells to tumor antigen-specific T cells

Fig. 2

Microbiota-oriented interventions to improve immunotherapy treatment. While stable on a global scale, the gut microbiota regularly undergoes small fluctuations and is amenable to strategies which could shape the commensal community to either help improve patient response rates to immunotherapy or prevent treatment-related toxicity such as colitis. These approaches range from complex community transfers in the form of (a) fecal microbiota transplantation (FMT) which may have many effects on the recipient, to delivery of (g) a single microbial metabolite with a specific immune-modulatory effect. Additional approaches include (b) modulating macronutrient or prebiotic intake to shift bacterial communities, (c) targeting broad classes of bacteria with antibiotics, (d) administration of a select number of known beneficial bacterial species, or (e) a single defined bacterial isolate. Bacteriophages (f) or viruses that infect and kill selected bacteria, could also be used as a means of selectively depleting a detrimental bacterial population