Abstract 129: Biobanking and feasibility considerations for prostate cancer gastrointestinal microbiome studies
Authors: Ernst Sarah E. , Markowski Mark C. , Gupta Anuj , Wheelan Sarah J. , Carter H. Ballentine , Partin Alan W. , Sears Cynthia L. , Sfanos Karen S. 
Published: August 2018

Abstract
The human microbiome may play a role in prostate health and disease as both direct and indirect interactions. Direct interactions between microbiota and prostate cancer include prostate infections, inflammation, prostatitis, and potentially interactions with the urinary microbiome. Indirectly, the gastrointestinal (GI) microbiota may influence prostate cancer via xenobiotic metabolism, augmentation of treatment response, and contributions to systemic inflammation and cytokines. In the present study, we are seeking to understand how different prostate cancer treatments may be affected by the microbial composition of the GI tract. We are currently developing a biorepository of fecal specimens from prostate cancer patients in different clinical states of disease. A key question during the planning phase of this biorepository was if samples can be collected and banked in the form of a rectal swab, instead of the more traditional method of a stool sample. Rectal swabs provide an advantage over collection of stool specimens in that they are easily collected (the patient can self-collect) in a standardized, “on demand” fashion during routine patient visits. Therefore, a pilot study was undertaken to compare the microbial profile of samples collected via both methods from the same individual. We concomitantly collected both stool samples and rectal swabs from 6 patients undergoing active surveillance for prostate cancer at the Johns Hopkins Hospital. All samples were stored at -80°C until we were ready to isolate bacterial DNA. DNA was extracted with a phenol:chloroform based protocol that we have optimized for microbiome studies that includes multiple enzyme digest and bead beating. We conducted Illumina amplicon sequencing of PCR products amplified with universal primers designed against the V6 hypervariable region of the bacterial 16S rRNA gene. We tested our sequencing strategy against Microbiome Reference Standards obtained from American Type Culture Collection (ATCC). The results of our analysis from prostate cancer patients indicated high similarity of bacterial profiles obtained for matched stool and swabs in 4 of the 6 patients. In both of the cases that were dissimilar, there was a greater representation of Enterobacteriaceae in the stool sample versus the swab. We conclude that collection of rectal swabs is a more feasible and convenient means of sampling the GI microbiota in prostate cancer patients, especially when aiming to conduct longitudinal studies with multiple sample collections to correlate microbiota profiles to treatments and/or treatment response. Due to the differences that were identified, we recommend deciding on the sample collection method at the onset of biobanking, and keeping the sampling method consistent throughout.
Citation Format: Sarah E. Ernst, Mark C. Markowski, Anuj Gupta, Sarah J. Wheelan, H. Ballentine Carter, Alan W. Partin, Cynthia L. Sears, Karen S. Sfanos. Biobanking and feasibility considerations for prostate cancer gastrointestinal microbiome studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 129.