DNA damage and genome instability by G-quadruplex ligands are mediated by R-loops in human cancer cells

G-quadruplexes (G4s) and R-loops are non-canonical DNA structures that can play regulatory functions of basic nuclear processes and can trigger DNA damage and genome instability. We here show that specific G4 ligands can stabilize G4s and simultaneously increase R-loop levels in human cancer cells likely by spreading DNA:RNA heteroduplexes to adjacent regions containing G4 structures. DNA cleavage and DNA damage response induced by G4 ligands were rescued by overexpression of exogenous RNaseH1 in cancer cells independently of BRCA2 status. The data thus show that R-loops are involved in the induction of DNA damage by chemical G4 stabilization. In addition, G4 ligands trigger the formation of micronuclei, particularly in BRCA2-silenced cancer cells, in an R-loop dependent manner. Our results uncover the mechanism of genome instability caused by G4 ligands and can open to the development of unexpected anticancer strategies using G4-targeted agents. Overall design: Genomic R-loop maps determined by DRIP-seq methodology,in duplicates, in U2OS cells treated with FG and PDS and in untreated control cells. PDS - pyridostatin FG - (2E,2'E)-2,2'-((2,8-diphenyldiimidazo[1,2-a:1',2'-c]pyrimidine-3,9-diyl)bis(methanylylidene))bis(hydrazine-1-carboximidamide)