SCAN1 mutant TDP1 blocks the repair of DSB induced by TOP1 activity during gene transcription and promotes genome reorganisations and cell death in quiescent cells

DNA single-strand breaks (SSBs) are the most common type of DNA damage in quiescent cells, and defects in their repair can lead to hereditary neurological syndromes. A potential endogenous source of SSBs with pathogenic potential is the abortive activity of DNA topoisomerase 1 (TOP1) during transcription. Spinocerebellar ataxia with axonal neuropathy type 1 (SCAN1), is caused by the homozygous mutation H493R in the gene encoding tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that initiates the repair of TOP1-induced SSBs by unlinking the TOP1 peptide from the break end. Notably, transcription-associated TOP1-induced SSBs can be converted into DNA double strand breaks (DSBs) in quiescent cells, with TDP1 also initiating the repair of these breaks. However, the role of TOP1-induced DSBs in the pathology of SCAN1 remains unclear. In this study, we have addressed the impact that SCAN1/H493R mutation, has in the repair of TOP1-induced DSB in quiescent cells. Here we demonstrate that while TDP1 deficiency delays the repair of these breaks, TDP1 H493R completely blocks it. This blockage is accompanied by prolonged covalent trapping of TDP1 H493R to DNA and results in genome instability and increased cell death in quiescent cells. We also demonstrate that tyrosyl-DNA phosphodiesterase 2 (TDP2) can backup TDP1 loss but not SCAN1 TDP1 H493R mutation. Intriguingly, we also unveil that a mutation in catalytic H263 results in a negative dominant effect on TOP1-induced DSB repair. Collectively, our data provide novel insights into the molecular etiology of SCAN1 and support the potential of TOP1-induced DSBs as a main contributor to hereditary neurological syndromes.