Bladder cancer microbiome and its association with chemoresponse

Rashida Ginwala¹Laura Bukavina^1,2,3Mohit Sindhani⁴Erika Nachman^1,5Suraj Peri¹Jodie Franklin⁶John Drevik⁷Sarah Christianson⁷Alexander Kutikov¹Philip H. Abbosh^1,7*

• ¹Fox Chase Cancer Center, Philadelphia, United States
• ²University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States
• ³School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States
• ⁴India Institute of Technology, Delhi, India
• ⁵Baylor College of Medicine, Houston, Texas, United States
• ⁶Johns Hopkins Medicine, Johns Hopkins University, Baltimore, Maryland, United States
• ⁷Albert Einstein Medical Center, Philadelphia, United States

The microbiome is widely known to cause come types of cancer, modify cancer biology, and impact therapeutic efficacy. Despite the urinary microbiome being one of the most clinically significant microbiomes in human health, it is one of the least well-described. We analyzed raw shotgun sequencing reads from tumors, adjacent normal tissue, and blood from the Cancer Genome Atlas (TCGA) bladder cancer cohort to identify reads originating from known microbiota. Twenty-seven viral and bacterial species were found to be enriched in the tumor samples including sex-specific enrichment of Lactobacillus and Prevotella in female bladder cancer patients which also are prevalent in the normal female genitourinary tract. Using 16S metagenomics data from urine of bladder cancer patients undergoing radical cystectomy and non-cancer controls, we found key differences that distinguish the two groups. Taking advantage of the fact that many patients in the cystectomy cohort underwent neoadjuvant chemotherapy, we also found Granulicatella and Proteus were enriched in patients who did not respond to neoadjuvant chemotherapy while E. Faecalis were enriched in responders. Additionally, we compared microbiome from urine samples to that of the archival diagnostic tumor samples and found 32% overlap between the two . We identify abundant Gammaproteobacteria in urine samples and show that genitourinary flora can detoxify gemcitabine, a commonly used therapy in bladder cancer. Because bladder cancer patients undergoing surgical procedures are exposed to a single dose of peri-procedure antibiotics, we took advantage of a ‘natural experiment’ to measure microbial changes in urology patients receiving a single dose of antibiotics for skin procedures, finding that there are very few changes that persist for 1 month. Additionally, we measured microbial changes during BBN-induced carcinogenesis in a mouse model and observed that changes are more likely related to BBN exposure itself rather than carcinogenesis as changes induced by BBN resolve after BBN withdrawal. In summary, we identify many new relationships between the microbiome and bladder cancer that are clinically relevant and lay the groundwork important functional studies in the future.