Dietary modulation of the gut microbiome as an immunoregulatory intervention

The commensal microbiota is an important source of inter-subject heterogeneity and can impact human health through modulation of host immunity. Because the abundance and metabolic functions of various gut microbes are affected by dietary elements, recent studies in Cell and Science test the links between diet, microbiota, and immune system modulation.

Cancer and the Microbiome-Influence of the Commensal Microbiota on Cancer, Immune Responses, and Immunotherapy

The commensal microbiota has been implicated in the regulation of a diverse array of physiological processes, both within the gastrointestinal tract and at distant tissue sites. Cancer is no exception, and distinct aspects of the microbiota have been reported to have either pro- or anti-tumor effects. The functional role of the microbiota in regulating not only mucosal but also systemic immune responses has led to investigations into the impact on cancer immunotherapies, particularly with agents targeting the immunologic checkpoints PD-1 and CTLA-4. Microbial sequencing and reconstitution of germ-free mice have indicated both positive and negative regulatory bacteria likely exist, which either promote or interfere with immunotherapy efficacy. These collective findings have led to the development of clinical trials pursuing microbiome-based therapeutic interventions, with the hope of expanding immunotherapy efficacy. This review summarizes recent knowledge about the relationship between the host microbiota and cancer and anti-tumor immune response, with implications for cancer therapy.

Investigating microbiome-based anti-tumor immune modulation using patient-derived mouse models

Growing data supports that the gut microbiota can impact cancer immunotherapy. We previously found certain bacterial taxa associated with response to immune checkpoint blockade. These correlations warrant deeper mechanistic studies using tractable mouse models to establish the role of the microbiota in determining immunotherapy efficacy.

To understand how the microbiota affects anti-tumor immunity we generated patient-based microbiota models. Germ-free mice were colonized using patient feces, bred, and subsequent generations studied using transplantable tumor models. We focused on two representative patient-based models: one from a responder (R) to immunotherapy and one from a non-responder (NR).

Mice established from the R demonstrated greater benefit from anti-PD-L1 therapy compared to NR colonized mice and had superior CD8+ T cell responses with greater accumulation of tumor-specific CD8+ T cells and increased proliferation. In addition, compared to NR-derived mice, R-derived mice had increased intra-tumoral CD103+ dendritic cells (DCs), as well as increased BATF3-lineage DCs in the mesenteric lymph nodes and spleen. In agreement with a stronger anti-tumor immune response, R mice had higher circulating levels of IFN-γ, IL-12p70, and CXCL5 compared to NR mice.

To identify potential systemic signals originating from the gut microbiome and capable of altering global immune populations we profiled serum using an unbiased metabolomics-based approach. We found distinct metabolite profiles in the R- and NR-derived mice, suggesting potential bacteria-derived or -modified metabolite modulating immune function. These data support a role for the gut microbiome determining host sensitivity to cancer immunotherapy.

Exploring the emerging role of the microbiome in cancer immunotherapy

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.

The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients

Anti-PD-1-based immunotherapy has had a major impact on cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients' microbiome, which has been shown to affect antitumor immunity and immunotherapy efficacy in preclinical mouse models. We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment, through an integration of 16S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria. A significant association was observed between commensal microbial composition and clinical response. Bacterial species more abundant in responders included Bifidobacterium longum, Collinsella aerofaciens, and Enterococcus faecium. Reconstitution of germ-free mice with fecal material from responding patients could lead to improved tumor control, augmented T cell responses, and greater efficacy of anti-PD-L1 therapy. Our results suggest that the commensal microbiome may have a mechanistic impact on antitumor immunity in human cancer patients.

Innate immune signaling and regulation in cancer immunotherapy

A pre-existing T cell-inflamed tumor microenvironment has prognostic utility and also can be predictive for response to contemporary cancer immunotherapies. The generation of a spontaneous T cell response against tumor-associated antigens depends on innate immune activation, which drives type I interferon (IFN) production. Recent work has revealed a major role for the STING pathway of cytosolic DNA sensing in this process. This cascade of events contributes to the activation of Batf3-lineage dendritic cells (DCs), which appear to be central to anti-tumor immunity. Non-T cell-inflamed tumors lack chemokines for Batf3 DC recruitment, have few Batf3 DCs, and lack a type I IFN gene signature, suggesting that failed innate immune activation may be the ultimate cause for lack of spontaneous T cell activation and accumulation. With this information in hand, new strategies for triggering innate immune activation and Batf3 DC recruitment are being developed, including novel STING agonists for de novo immune priming. Ultimately, the successful development of effective innate immune activators should expand the fraction of patients that can respond to immunotherapies, such as with checkpoint blockade antibodies.

Differential migration of myeloid-derived suppressor cell subsets to tumor-draining lymph nodes in a murine model of breast cancer (P2014)

Myeloid-derived suppressor cells (MDSC) expand in cancer and suppress the anti-tumor immune response. MDSC are morphologically and functionally divided into monocytic (MO-MDSC) and polymorphonuclear (PMN-MDSC) subsets, identified as CD11b+Ly-6G-Ly-6Chigh and CD11b+Ly-6G+Ly-6Clow, respectively. MDSC accumulate primarily in the blood and spleen, but their suppressive function is limited to the tumor and tumor-draining lymph nodes (TDLN). We sought to determine the involvement of adhesion molecules in MDSC migration to TDLN using the 4T1 murine breast cancer model. Both MDSC subsets expressed L-selectin and LFA-1, although L-selectin levels were higher on MO-MDSC. To determine whether this differential L-selectin expression affected MDSC migration to TDLN, we analyzed tissue distribution and in vivo migration of wild type and L-selectin-deficient MDSC. In the blood and spleen of wild type mice, the PMN-MDSC subset predominated (MO-MDSC/PMN-MDSC ratio of 0.1), while the MO-MDSC subset predominated in the TDLN (ratio of 1.5). By contrast, in L-selectin-deficient mice, the MO-MDSC/PMN-MDSC ratios in the TDLN (0.3) and in the blood and spleen (0.1) were similar. This differential tissue distribution was consistent with increased TDLN entry of wild type, but not L-selectin-deficient, MO-MDSC relative to PMN-MDSC in adoptive transfer experiments. Taken together, these results suggest a migratory preference of MO-MDSC to the TDLN dependent on L-selectin.