Fecal metagenome analysis in long-term survivors (LTS) of pancreas cancer.

Abstract

e16298 Background: Despite improvements in median survival in pancreas adenocarcinoma (PCa), the 5 year overall survival remains less than 10%. Clinical and tumor genomic characteristics have not differentiated PCa long term survivors (LTS) from unselected patients, however specimens in LTS show enhanced tumor immune response. In preclinical studies, fecal transplant experiments from LTS of PCa reveal delayed tumor growth through unknown mechanisms involving the fecal microbiota (Riquelme Cell 2019). However, features of the fecal microbiome in patients with LTS are unknown. Methods: In this cross-sectional study, comprehensive shotgun metagenomics were performed on stool from PCa patients with LTS (n = 16). LTS was defined as > 4 years from pancreatectomy and all therapy without evidence of recurrence. LTS were compared to control patients with PCa who completed pancreatectomy and chemotherapy (n = 6). Stool was sequenced using an Illumina NextSeq500. Raw reads were processed with Kneaddata for trimming, Kracken2 for taxonomic profiling, Bracken for abundance estimation, and Humann3 for metabolic pathway analyses. Statistical analyses were performed in R with MicrobiomeSeq and Phyloseq for comparison of LTS and controls. Results: At diagnosis, the median age of LTS was 60 with a median time from pancreatectomy of 6 years (4-14 years) at donation. The median age of control patients was 65 with a median disease-free survival of 17 months from pancreatectomy. All patients underwent pancreatectomy and chemotherapy prior to sample donation. No material differences were observed in overall microbial diversity for LTS and controls using Shannon/Simpson indexes. The overall composition of bacteria, eukaryotes, viruses and archaea were similar in LTS relative to controls. Lefse analyses revealed significant enrichment of species relative abundance in LTS for the Ruminococacceae family and the Faecalobacterium genus including the Faecalobacterium prausnitzii species. Enriched species in control patients included Clostridium perfringes. Metabolic pathway analyses of the fecal metagenome of LTS revealed several gene families enriched in Faecalobacterium prausnitzii responsible for starch degradation, ribonucleotide biosynthesis, and thiamin degradation as well gene products from Akermannsia mucinophilia representing unknown pathways. Conclusions: Stool from patients cured from PCa share unique microbial features relative to control populations including enrichment of species in the Faecalobacterium genus and Ruminococacceae family . Interestingly, similar species enrichments are observed in metastatic melanoma patients who respond to PD-1 inhibition (Gopalakrishnan Science 2017). Additional studies are needed to explore underlying immune mediated mechanisms in which the fecal microbiota may influence long term survival in PCa.