Adverse gut microbiome promotes resistance immune checkpoint inhibitors via chronic inflammation

Project summary/abstract Immune checkpoint inhibitors (ICI) transformed oncological care for multiple cancers. Yet, 80% of ICI patients will eventually fail therapy. Colossal efforts are invested in overcoming ICI resistance. A promising candidate is the gut microbiome which was associated with ICI clinical outcomes. I led a seminal clinical trial in which the gut microbiome of patients with ICI refractory metastatic melanoma was modulated via fecal microbiota transplantation (FMT). FMT and ICI re-induction resulted in increased intra-tumoral infiltration of CD8+ T-cells and objective clinical response rates of 30%. However, microbiome modulation remains far from wide clinical use. While FMT showed consistent clinical efficacy, it is not feasible outside of major academic centers; and some probiotics have been associated with a deleterious effect on ICI efficacy. Therapies that mimic the microbiome effect on the immune system can enhance ICI efficacy while omitting FMT obstacles. However, the development of such therapies is hindered since the mechanisms driving the gut microbiome's effect on anti-tumoral immunity remain unknown. In this proposal, I will test the hypothesis that an adverse microbiome induces a state of chronic inflammation that impedes ICI efficacy. FMT from donors with favorable microbiomes promotes anti-tumoral immunity by disrupting the net inflammatory signaling; hence, attenuating inflammation by direct immune re-programming can mimic the FMT effect. To test this, I propose the following research plan. In Aim 1, I will determine the effect of microbial-induced inflammation on anti-tumoral immunity by analyzing longitudinal stool, serum, gut, and tumor samples from a unique cohort of 33 patients with ICI- refractory melanoma (n=20) and microsatellite-instability high cancers (MSI-H, n=13) who participated in clinical trials of FMT and ICI re-induction (NCT03353402 and NCT04729322, respectively). Spatial transcriptomics of gut and tumor samples will be used to demonstrate FMT-induced immune dynamics and to test my sub-hypothesis that microbial inflammatory signals are mediated via myeloid antigen-presenting cells (APC). In Aim 2, I will determine the immune system's ability to override microbial signals. I will conduct FMT from cancer patients who responded and did not respond to ICI into CD11c-Cre+ Stat3f/f (Stat3Δ/Δ) mice that have dendritic cells with hyper-activated toll-like receptors (TLR) signaling. This experiment will test the ability of an immune system with a chronic inflamed state to overcome the beneficial effect of FMT from a donor with a favorable microbiome. To re-program the immune system to override the effect of adverse microbiome- mediated inflammation and hence overcome ICI resistance, I will compare the immune activity and tumor growth of mice undergoing FMT versus mice treated with a combination of ICI and interleukin (IL)-1b blockade; since IL-1b secretion can be a product of TLR activation and our previous work showed that an adverse microbiome induces IL-1-mediates gut inflammation. Overcoming ICI resistance by microbial-derived inflammatory signal blockade can enhance the clinical efficacy of ICI in patients with various cancer types.