TOP2A substitution enhances topoisomerase activity and causes transcriptional dysfunction in glioblastoma patients

High grade gliomas (HGGs) are aggressive, primary brain tumors with poor clinical outcomes. To better understand glioma pathobiology and find potential therapeutic susceptibilities, we designed a custom- panel 664 cancer- and epigenetics-related genes and employed targeted next generation sequencing to study the genomic landscape of somatic and germline variants in 182 glioma samples of different malignancy grades. Besides known alterations in TP53, IDH1, ATRX, EGFR genes, we found several novel variants that can be potential drivers in gliomas. In four patients from the Polish glioma cohort, we identified a novel recurrent mutation in the TOP2A gene coding for Topoisomerase 2A in glioblastomas (GBM, WHO grade IV gliomas). The mutation results in a substitution of glutamic acid (E) 948 to glutamine (Q) of TOP2 A and we predicted this E948Q substitution may affect DNA binding and a TOP2A enzymatic activity. Topoisomerases are enzymes that control the higher order DNA structure by introducing transient breaks and rejoining DNA strands. Using recombinant proteins we demonstrated stronger DNA binding and DNA supercoil relaxation activities of the variant proteins. Glioblastoma (GBM) patients with the mutated TOP2A had shorter overall survival than wild type TOP2A GBM patients. Computational analyses of transcriptomic data showed that the GBM samples with the mutated TOP2A have different transcriptomic patterns suggesting higher transcriptomic activity. The results suggest that TOP2A E948Q variant strongly binds to DNA and is more active in comparison to the wild-type protein. Altogether, our findings suggest that the E948Q substitution leads to gain of function by TOP2A.