Abstract 2780: Topoisomerase IIb binding underlies frequently mutated elements in cancer genomes

Abstract Type-II topoisomerases resolve topological stress in DNA through controlled double-strand breaks. While TOP2A is a chemotherapy target in proliferating cells, the ubiquitously expressed TOP2B is a potential off-target. Here we explore roles of TOP2B in mutagenesis by generating DNA-binding maps of TOP2B, CTCF, and RAD21 in human cancer samples and analyzing these maps for driver mutations and mutational processes in 6500 whole cancer genomes. TOP2B-CTCF-RAD21 and TOP2B-RAD21 sites are enriched in somatic mutations and structural variants (SVs), especially at evolutionary conserved sites displaying high transcription and long-range chromatin interactions. TOP2B binding underlies SVs and hotspot mutations in cancer-driving genes such as TP53, MYC, FOXA1, and VHL, and many cis-regulatory elements. We show that the TOP2B-bound mutational hotspot at RMRP drives tumor initiation and growth in vivo. These data highlight TOP2B as a protector of the genome from topological challenges whose aberrant activity promotes driver and passenger mutations in cancer genomes. Citation Format: Jüri Reimand, 1 Christian A. Lee, 1 Robin H. Oh, 2 Zoe P. Klein, 1 Nina Adler, 1 Sana Akhtar Alvi, 3 Ellen Langille, 2 Elisa Pasini, 4 Kevin C. Cheng, 1 Diala Abd-Rabbo, 1 Huayun Hou, 3 Ricky Tsai, 2 Mamatha Bhat, 1 Daniel Schramek, 2 Michael D. Wilson, 3 Liis Uusküla-Reimand3. Topoisomerase IIb binding underlies frequently mutated elements in cancer genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2780.