Abstract 2672: Response to anti-PD-1 based therapy in metastatic melanoma patients is associated with the diversity and composition of the gut microbiome
Authors: Gopalakrishnan Vancheswaran , Spencer Christine , Reuben Alexandre , Prieto Peter , Vicente Diego , Karpinets Tatiana V. , Hudgens Courtney W. , Hutchinson Diane S. , Tetzlaff Michael , Lazar Alexander , Davies Michael A. , Gershenwald Jeffrey E. , Jenq Robert , Hwu Patrick , Sharma Padmanee , Allison James , Futreal Andrew , Ajami Nadim , Petrosino Joseph , Daniel-MacDougall Carrie , Wargo Jennifer A. 
Published: July 2017

Abstract
Background: Melanoma therapy has benefitted greatly from immune checkpoint blockade, although responses are variable and not always durable. There is a growing appreciation of the role of the microbiome in cancer-related outcomes and recent evidence in murine models suggests that modulation of the gut microbiome may enhance responses to immune checkpoint blockade in melanoma. However this has not been investigated in patients. Here, we demonstrate that differential bacterial “signatures” exist in the gut microbiome of responders (R) and non-responders (NR) to anti-PD-1 therapy, and that insights gained could be used to derive actionable strategies to enhance responses.
Methods: We collected buccal (n=105) and stool (n=53) samples from a cohort of anti-PD-1 treated metastatic melanoma patients (n=110). Patients were classified as either R or NR based on RECIST criteria, and 16S rDNA, and whole-genome shotgun sequencing was performed to characterize the diversity, composition and functional capabilities of the microbiomes. Immune profiling (via 7-marker IHC panel of CD3, CD8, PD-1, PD-L1, Granzyme B, RORγT and FoxP3) and cytokine analyses were also performed on available tumors and serum samples at baseline.
Results: In these studies, we observed significant differences in the diversity and composition of the gut microbiome in R versus NR to PD-1 blockade at baseline, but no clear differences in buccal microbiomes. Specifically, R had a significantly higher alpha diversity compared to NR (p=0.017), and the Ruminococcaceae family of the Clostridiales order was enriched in R whereas Prevotellaceae family of the Bacteroidales order was enriched in NR. Immune profiling demonstrated significantly increased immune infiltrates in baseline tumor samples of R, with a positive correlation between CD8, CD3, PD-1 and FoxP3 T-cell density and abundance of specific bacteria enriched in R (e.g. Faecalibacterium). Low diversity was also associated with elevated levels of chronic inflammation markers in the serum at baseline. Lastly, we saw differentially abundant metabolic pathways in the gut microbiomes of R (pyrimidine nucleotide biosynthesis, fatty acid biosynthesis, shikimate pathway) vs NR (Tricarboxylic acid cycle, assimilatory sulphate and nitrate reduction, tryptophan biosynthesis).
Conclusion: Differences exist in the diversity and composition of the gut microbiome in R vs NR to anti-PD-1 therapy and these microbiota could bridge the gap between host metabolism and anti-tumor immunity. These results have far-reaching implications and suggest that modifications to the gut microbiome could potentially enhance therapeutic responses to immune checkpoint blockade.
Citation Format: Vancheswaran Gopalakrishnan, Christine Spencer, Alexandre Reuben, Peter Prieto, Diego Vicente, Tatiana V. Karpinets, Courtney W. Hudgens, Diane S. Hutchinson, Michael Tetzlaff, Alexander Lazar, Michael A. Davies, Jeffrey E. Gershenwald, Robert Jenq, Patrick Hwu, Padmanee Sharma, James Allison, Andrew Futreal, Nadim Ajami, Joseph Petrosino, Carrie Daniel-MacDougall, Jennifer A. Wargo. Response to anti-PD-1 based therapy in metastatic melanoma patients is associated with the diversity and composition of the gut microbiome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2672. doi:10.1158/1538-7445.AM2017-2672