Wildtype HeLa cells and CRISPR Cas9 TEX264KO treated with CPT

DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that in human cells, lysosomes process Topoisomerase 1-cleavage complexes (TOP1cc) DNA lesion. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of Topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through transient alteration of the nuclear envelope, and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating TOP1cc delivery to lysosomes dependent on MRE11 nuclease and ATR kinase. We found an evolutionary conserved role for selective autophagy in DNA damage repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.