Role of microbiome in cancer and inflammation

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

In our studies, we extensively use mice deficient for immune or inflammation-related genes and it is always difficult to distinguish a direct effect of those genes on the colitis, cancer and response to therapy , or an indirect one through the regulation of the intestinal microbiota. We have established methods for the determination of mouse microbioma using 454 sequencing or MiSeq sequencing of 16 RNA, metagenomic analysis using NextSeq sequencing, and cytofluorimetric analysis of FISH labeling of specific bacterial types and we have established a Microbiome core for providing these technologies as a service to the NIH community. We work extensively with germ free mice, gnotobiotic mice with defined intestinal flora, and mice reconstitute after antibiotic treatment. Initially we studied the role of the intestinal microbiota in experimental models of colitis and colitis-associated cancer using mice genetically deficient for inflammation-controlling genes such as MyD88, IL-18, TNF, TLRs, and others. In these mice the genetic defects induce a dysbiosis that can be transferred to normal mice by co-housing or fecal transplant and enhance susceptibility to chemical carcinogenesis. The bacterial species responsible of this increased susceptibility to carcinogenesis and their mechanism of action are being investigated. The role of commensal microbiota in energetic alteration associated with cancer (i.e. obesity, cachexia, anorexia, cancer treatment, irradiation) has been initiated in murine experimental models and in observational clinical experimentation. We were among the very first to show that Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment (Science 342:967-970). The gut microbiome influences both local and systemic inflammation. Although the role of inflammation in cancer is well documented, whether commensal bacteria can exert distant effects on the inflammation in the sterile tumor microenvironment remains unclear. Here we show that microbiota perturbation impairs the response of subcutaneous cancers to CpG-oligonucleotide-immunotherapy or platinum chemotherapy. In antibiotic-treated or germ-free mice, decreased cytokine production from tumor-infiltrating monocyte-derived cells following CpG-ODN treatment reduced tumor necrosis, whereas deficient chemotherapy-induced production of reactive oxygen species by myeloid cells impaired genotoxicity and tumor destruction. Thus, optimal response to cancer immunotherapy and chemotherapy requires an intact commensal microbiota that acts distantly by modulating myeloid-derived cell function in the tumor microenvironment. These findings underscore the importance of the microbiota in the outcome of disease treatment. Many laboratories have extended our results to cancer immunotherapy in patients and suggested that the microbiome composition determine the ability of patients with melanoma and other type of cancer to respond to anti-PD1 therapy. However, the different studies have identified different types of bacteria has been responsible for this effect and the mechanisms remain unclear. We have extended the analysis to a large cohort of melanoma patients at the University of Pittsburgh and we are starting to elucidate the reason of the discordant results in the various group and to identify common mechanisms. In collaboration with MD Anderson cancer center we have established that patients with a high fiber diet respond better to anti-PD1 therapy and we have studied the mechanisms underlying this effect in mouse studies. In collaboration with the University of Pittsburgh Cancer Center we have treated 14 anti-PD1 refractory melanoma patients with a fecal microbiota transplant from PD1-responsive patients and in almost half of the patients the rapidly progressive tumors stabilized or significantly responded to the continued anti-PD1 therapy. The mechanisms underlying this effect are being studied with microbiome, cytokine and metabolomic studies. Intestinal Microbiota Signatures Predict Are Associated with Clinical Outcome and Immune-related Adverse Events in PD-1 Treated Melanoma Patients: The gut microbiome is has been proposed to be a biomarker and a driver of response to immune checkpoint blockade therapy in cancer. However, reported microbial signatures were inconsistent. By analyzing a new melanoma patient cohort, along with four previously published datasets, and by addressing the sources of variation contributing to statistical noise, we identified signatures of beneficial and detrimental taxa that potentially contribute to the resistance to anti-PD1 therapy and development of immune-related adverse events (irAEs). Time-to-event analyses identified an optimal time post-treatment that maximally separatedin which maximal separation of the microbiota composition near the beginning of treatment was observed between responders and non-responders. We observed different degrees of association between human enteric microbial communities (microbiotypes) and patients' response status. Microbiotypes had non-uniform geographic distribution, contributing to discrepancies between cohorts. Data from the new cohort and combined meta-analysis of the five melanoma cohorts identified a beneficial signature comprised of members of Actinobacteria phylum and of Lachnospiraceae and Ruminococcaceae families, while detrimental signature included Bacteroidetes and Proteobacteria phyla, and Streptococcaceae. Gram-negative bacteria and lipopolysaccharide were associated with an inflammatory host gene signature, increased neutrophil-to-lymphocyte ratio, and unfavorable clinical outcome. Increased abundance of Lachnospiraceae and Streptococcaceae was associated with distinct irAEs, and favorable and unfavorable clinical outcomes, respectively. Altogether our study identifies robust signatures of beneficial and detrimental microbes associated with the resistance to anti-PD1 therapy, clarifies causes of inconsistencies between cohorts and provides a novel roadmap for the future clinical microbiome studies.Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients: Anti-programmed cell death protein 1 (PD-1) therapy provides long-term clinical benefits to patients with advanced melanoma. The composition of the gut microbiota correlates with anti-PD-1 efficacy in preclinical models and cancer patients. To investigate whether resistance to anti-PD-1 can be overcome by changing the gut microbiota, this clinical trial evaluated the safety and efficacy of responder-derived fecal microbiota transplantation (FMT) together with anti-PD-1 in patients with PD-1-refractory melanoma. This combination was well tolerated, provided clinical benefit in 6 of 15 patients, and induced rapid and durable microbiota perturbation. Responders exhibited increased abundance of taxa that were previously shown to be associated with response to anti-PD-1, increased CD8(+) T cell activation, and decreased frequency of interleukin-8-expressing myeloid cells. Responders had distinct proteomic and metabolomic signatures, and transkingdom network analyses confirmed that the gut microbiome regulated these changes. Collectively, our findings show that FMT and anti-PD-1 changed the gut microbiome and reprogrammed the tumor microenvironment to overcome resistance to anti-PD-1 in a subset of PD-1 advanced melanoma.