Recurrent mutations in topoisomerase IIα cause a previously undescribed mutator phenotype in human cancers

Abstract

Topoisomerases nick and reseal DNA to relieve torsional stress associated with transcription and replication and to resolve structures such as knots and catenanes. Stabilization of the yeast Top2 cleavage intermediates is mutagenic in yeast, but whether this extends to higher eukaryotes is less clear. Chemotherapeutic topoisomerase poisons also elevate cleavage, resulting in mutagenesis. Here, we describe p.K743N mutations in human topoisomerase hTOP2α and link them to a previously undescribed mutator phenotype in cancer. Overexpression of the orthologous mutant protein in yeast generated a characteristic pattern of 2- to 4-base pair (bp) duplications resembling those in tumors with p.K743N. Using mutant strains and biochemical analysis, we determined the genetic requirements of this mutagenic process and showed that it results from trapping of the mutant yeast yTop2 cleavage complex. In addition to 2- to 4-bp duplications, hTOP2α p.K743N is also associated with deletions that are absent in yeast. We call the combined pattern of duplications and deletions ID_TOP2α. All seven tumors carrying the hTOP2α p.K743N mutation showed ID_TOP2α, while it was absent from all other tumors examined (n = 12,269). Each tumor with the ID_TOP2α signature had indels in several known cancer genes, which included frameshift mutations in tumor suppressors PTEN and TP53 and an activating insertion in BRAF. Sequence motifs found at ID_TOP2α mutations were present at 80% of indels in cancer-driver genes, suggesting that ID_TOP2α mutagenesis may contribute to tumorigenesis. The results reported here shed further light on the role of topoisomerase II in genome instability.

Topography of mutational signatures in human cancer

“…At least six mutational signatures were predominately enriched in early replicating regions: SBS6 attributed to mismatched repair (enriched in early replicating regions in 2 out of 3 cancer types; 2/3), SBS11 attributed to temozolomide therapy (1/1), SBS15 due to DNA mismatch repair deficiency (1/1), SBS16 (2/2) and ID11 (3/5) both associated with alcohol consumption, and SBS84 (1/1) due to aberrant activities of activation-induced (AID) cytidine deaminases. ID17 signature, most probably due to TOP2A mutations (Boot et al, 2022), was also enriched in early replicating regions in oesophageal squamous cell carcinoma.…”

An overview of mutational and copy number signatures in human cancer

“…Experimental works have also revealed the compendium of in vitro-induced mutational signatures and the vulnerabilities of human stem cells to different endogenous and exogenous mutagens. Importantly, examination of mutational signatures has brought significant insights into the interactions between mismatch repair and replication; enzymatic deamination by AID/APOBEC3; transcription-coupled repair; transcription-coupled damage; topoisomerases and DNA repair; clustered mutagenesis and genomic rearrangements; and many others [25][26][27][28][29][30][31].…”

SUMO: A Swiss Army Knife for Eukaryotic Topoisomerases

“…Eukaryotic topoisomerase I appears to be particularly prone to trapping by DNA damage, and abasic sites also efficiently trap TOP2 in vitro (reviewed by Nitiss et al (2019 )). In addition, mutations in topoisomerases can impair the enzyme’s ability to carry out re-ligation ( Levin et al, 1993 ; Stantial et al, 2020 ; Boot et al, 2022 ).…”