Abstract 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. Citation Format: Liis Uuskula-Reimand, Christian A. Lee, Robin H. Oh, Zoe P. Klein, Nina Adler, Sana Akhtar Alvi, Ellen Langille, Elisa Pasini, Kevin C. Cheng, Evgenija Serafimova, Diala Abd Rabbo, Huayun Hou, Ricky Tsai, Mamatha Bhat, Daniel Schramek, Michael Wilson, Juri Reimand. Topoisomerase IIb binding delineates localized mutational processes and driver mutations in cancer genomes abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 520.
Uusküla-Reimand et al. (Fri,) studied this question.