Topoisomerase IIb binding delineates localized mutational processes and driver mutations in cancer genomes

Type-II topoisomerases resolve topological stress in DNA by inducing and repairing double-strand breaks in a coordinated fashion. While topoisomerases are chemotherapy targets linked to therapy-related genotoxicity, TOP2B is uniquely positioned to influence mutagenesis through its activity in non-dividing cells and sensitivity to topoisomerase poisons. Here, to understand the role of TOP2B in mutagenesis and cancer driver mechanisms, we generated unique DNA-binding maps of TOP2B, CTCF, and RAD21 in human liver cancer samples using chromatin immunoprecipitation sequencing (ChIP-seq). Next, we conducted a systematic analysis of these genome-wide maps for cancer driver mutations and somatic mutational processes across a dataset of 6500 whole cancer genomes representing 18 major cancer types. We show that TOP2B-CTCF-RAD21 and TOP2B-RAD21 sites are enriched in somatic small mutations (SNVs, indels) as well as structural variants (SVs), particularly at sites with evolutionary conservation, high transcription and long-range chromatin interactions. When focusing on evolutionarily selected genes using a systematic driver analysis, TOP2B binding appears to underlie SVs and hotspot mutations in cancer-driving genes such as TP53, MYC, FOXA1, and VHL, and many frequently mutated non-coding regions. We show that the TOP2B-bound mutational hotspot at RMRP is a novel non-coding driver mutation that causes tumor initiation and growth in vivo and leads to transcriptional deregulation of migration and cell adhesion pathways. Together, these data highlights TOP2B as a safeguard of the genome integrity and a marker of mutational processes and hotspots in cancer, underscoring implications for cancer genomics research.