The SMC5/6 complex is required for maintenance of genome integrity upon APOBEC3A-mediated replication stress.

Mutational patterns consistent with the activity of the APOBEC3 cytidine deaminases are evident in more than half of human cancer genomes. APOBEC3-mediated mutagenesis is genotoxic when uncontrolled due to accumulation of base mutations, replication stress, and DNA breaks. In particular, the APOBEC3A family member is a potent enzyme with nuclear localization that causes substantial DNA damage in experimental systems and human tumors. However, the spectrum of genome-protective mechanisms that ensure genome stability in cells with active APOBEC3A is unknown. Through a genome-wide functional screen, we identify the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is expressed. Cells depleted of SMC5/6 incurred substantial DNA damage when APOBEC3A was active, as reflected by increased DNA breaks, DNA damage signaling, and defective proliferation. We observed an absence of APOBEC3A mutagenesis in human tumors with dysfunction of SMC5/6, consistent with synthetic lethality. APOBEC3A is known to act on ssDNA at replication forks. We observed increased DNA damage in replicating cells in the absence of SMC5/6, suggestive of replication forks as a source of DNA breaks. We interrogated replication fork dynamics by DNA fiber spreading and found a consistent increase in the length of replication tracks upon APOBEC3A activity across multiple cell lines. Increased replication fork length was dependent on Primpol, consistent with a repriming mechanism downstream of APOBEC3A-induced lesions. Loss of SMC5/6 resulted in abrogation of fork elongation in cells with active APOBEC3A, along with increased DNA breaks. Our findings indicate that increased length of replication forks in response to APOBEC3A is a genome-protective response and is dependent on intact SMC5/6. Therefore, SMC5/6 may be a therapeutic vulnerability in tumors in which APOBEC3A is active.