Epigenetic consequences of cancer treatments is an underexplored area of research. Instillations of BCG mycobacteria into the bladder to stimulate an immune response is an established treatment for non-muscle invasive bladder cancer (NMIBC). Immune cells, especially when activated, have the ability to change the microenvironment of cancer via cytokines and reactive oxygen species in a way that could influence epigenetic mechanisms of surrounding cells. Aberrant DNA methylation of sites around the centromere has also been correlated with genome instability.
Our research was an hypothesis-free exploration of epigenetic and structural changes in bladder cancer cells in response to BCG-activated immune cells. Bladder cancer cells were co-cultured with leukocytes either with or without BCG, in a transwell system designed to prevent physical interactions with bladder cancer cells. Whole genome sequencing of bladder cancer cell lines was carried out on the PromethION 2 Solo instrument by Oxford Nanopore Technologies, which, in addition to DNA sequencing, can also detect DNA modifications. In addition to methylation of CpG sites (5mC), methylation of Adenosine sites (m6A) and structural changes to the genome were also investigated.
This research is a novel exploration of immune effects on cancer cell DNA structure and function.