Complex mechanisms of topoisomerase II poisons revealed by whole-genome analysis

Topoisomerase II (TOP2) represents a vital enzyme which functions by introducing transient DNA breaks to resolve topological issues in DNA and regulate gene expression. The potentially toxic nature of these DNA breaks made the drugs that stabilize them, TOP2 poisons, into highly successful anticancer agents, and research tools. However, despite decades-long widespread usage of these drugs, not much is known about differences in the genome-wide profiles of DNA breaks caused by them. Here, we generate high-resolution genome-wide maps of DNA breaks induced by seven different TOP2 poisons in a human cancer cell line using the SSiNGLe method developed by our group. We find multiple notable differences even between the drugs with highly similar chemical structures, indicating that each poison targets a specific subpopulation of catalytically engaged TOP2 enzymes bound to DNA. The preferential targeting observed may be partly explained by the distinct local sequence preferences identified for each TOP2 poison. However, our results also indicate that genomic context, chromatin environment, and the heterogeneity of TOP2 cleavage complexes likely contribute. Altogether, this study has potential significant implications for our understanding of the reasons behind the clinical differences among the drugs and the mechanisms of TOP2 function.