ABSTRACT: Association of the commensal urinary microbiome with response to Bacillus Calmette-Guérin (BCG) immunotherapy in nonmuscle invasive bladder cancer.
The standard of care for high-risk non-muscle invasive bladder cancer (NMIBC) is transurethral resection of bladder tumor (TURBT) followed by adjuvant intravesical administration of Bacillus-Calmette Guerin (BCG). BCG treatment provides a marked decrease in cancer recurrence. Nonetheless, approximately 50% of all NMIBC patients experience relapse and disease progression. Recent advancements in microbiome profiling have established the existence of abundant and diverse microbial flora in the urinary bladder. Our group enrolled patients receiving TURBT/BCG therapy for NMIBC. Patients were categorized as responders or non-responders. Urine collected was subjected to DNA isolation and 16S rRNA gene sequencing to determine whether certain phyla correlated with response to therapy. Gammaproteobacteria were more abundant in patients who responded to BCG therapy. Firmicutes were more abundant in patients who relapsed.
When I was an undergraduate, I learned this definition of theory: “A theory is the best explanation of all observable data”. Sometimes, a theory goes for long enough without being challenged. When that occurs, a theory becomes dogma… a stubborn idea that entrenches itself in the minds of college students and tricks them into making faulty assumptions in the real world. But is dogma the best way to view theory? I do not believe so because theory, by the previous definition, is subject to the quality and quantity of the data from which it was formed. Therefore, when better data and more data are derived, the theory, and thus the attached dogma, must be modified and sometimes thrown out altogether.
The popular dogma that a healthy urinary bladder is a sterile environment came to be in the mid-1800’s. A group of famous scientists, not the least of which being Louis Pasteur, performed experiments that are the foundation of this dogma. Urine was taken from healthy individuals and placed in test tubes. Some of the tubes were left open to air, and others were capped. The tubes that were exposed became cloudy as a result of microbial colonization from the air, and the capped tubes remained translucent. Furthermore, culture techniques performed on urine were optimized for growing E. coli and did not result in bacterial growth. From these observations, the scientists concluded that urine was sterile, for that was the best observation of all the observable data. That theory became dogma and lasted for well over 100 years until more and better data became available.
I was fortunate enough to be an undergraduate at an important time in the history of microbiology. I was taking an elective called Microbial Ecology in the Spring of 2011. That was about ten years after the start of the big burst of microbial data that came in the form of genomics. The shotgun sequencing technology designed by the early 2000’s to sequence the entire human genome was quickly adapted to discover and describe thousands of bacterial species present in a huge variety of microbial communities. I chose microbial ecology as an elective because the topic seemed cool and fun. I did not know at that time that I would eventually be studying the microbial ecology of the human bladder.
The microbial communities we discussed in microbial ecology were often found in most of the places you expect to find bacteria: the soil, marine environments, and human skin. I also learned that microbes existed in surprising diversity in extreme environments like deep-sea vents, acid pools, and deep in the crust. Therefore, the big picture idea that I brought with me from microbial ecology is that the microbes are king, and the microbes are EVERYWHERE… except the healthy bladder because the dogma says the healthy bladder is sterile J. The first person I heard challenge this dogma was Dr. Alan Wolfe, one of my professors from my Master’s program. Of course I was skeptical of this heresy called the bladder microbiome. I could not be convinced until I heard that some scientists punctured through the abdomen to collect urine, circumventing any possibility of contamination. I suppose the microbes really are everywhere after all. So by the time I finished my Master’s degree, I accepted Dr. Wolfe’s bladder microbiome theory.
Honestly, my acceptance of the bladder microbiome could not have come at a better time. Study of the human microbiome is still in its youth. Investigating other niches in the body such as the skin and the gut yield data that are so rich that they are complicated, making it difficult to understand the effects caused by certain microbes. A simpler niche with fewer bacterial species would be ideal to develop and validate the tools needed to study the microbiome. The bladder contains many bacterial species, but is not as rich in diversity as these other niches. Thus, our lab is seeking to answer a simple question: do certain bacterial species correlate or anit-correlate with tumor response to BCG, a standard-of-care therapy for bladder cancer patients? 16S rRNA sequencing and shotgun sequencing results suggest that such a correlation may exist. I am currently conducting qPCR in order to validate these results. But the moral of this whole story is: don’t get too attached to a dogma. If you do, you may eventually eat crow.