DDX11 loss causes replication stress and pharmacologically exploitable DNA repair defects

DDX11 encodes an iron–sulfur cluster DNA helicase required for development, mutated, and overexpressed in cancers. Here, we show that loss of DDX11 causes replication stress and sensitizes cancer cells to DNA damaging agents, including poly ADP ribose polymerase (PARP) inhibitors and platinum drugs. We find that DDX11 helicase activity prevents chemotherapy drug hypersensitivity and accumulation of DNA damage. Mechanistically, DDX11 acts downstream of 53BP1 to mediate homology-directed repair and RAD51 focus formation in manners nonredundant with BRCA1 and BRCA2. As a result, DDX11 down-regulation aggravates the chemotherapeutic sensitivity of BRCA1/2-mutated cancers and resensitizes chemotherapy drug–resistant BRCA1/2-mutated cancer cells that regained homologous recombination proficiency. The results further indicate that DDX11 facilitates recombination repair by assisting double strand break resection and the loading of both RPA and RAD51 on single-stranded DNA substrates. We propose DDX11 as a potential target in cancers by creating pharmacologically exploitable DNA repair vulnerabilities.

Faithful DNA replication and DNA repair processes are essential for genome integrity. Inherited mutations in BRCA1 or BRCA2 genes predispose to breast and ovarian cancer, among other types of malignancies such as pancreatic cancers and brain tumors (1). Mechanistically, BRCA1 and BRCA2 are critical for double strand break (DSB) repair by homologous recombination (HR) and for the protection of stalled replication forks by facilitating RAD51 filament formation (2).Tumors with mutations in HR factors, the most widespread being those harboring mutations in BRCA1 and BRCA2, are sensitive to chemotherapeutic drugs that block replication and cause DSBs (3). Platinum drugs, such as cisplatin, create intra- and interstrand adducts that require HR activities for DNA repair during replication and therefore are effective in killing HR-defective cancers. Analysis of the plateau of the survival curve of different cancers revealed that patients often develop resistance, and thus, alternative strategies are needed. The advent of PARP (poly ADP ribose polymerase) inhibitors (PARPi), including olaparib, which exhibit synthetic lethal effects when applied to cells and tumors defective in HR (4, 5), holds significant promise. PARP1, 2, and 3 are required to repair numerous DNA single-strand breaks (SSBs) resulting from oxidative damage and during base excision repair. When PARP enzymes are locally trapped at SSBs, they prevent fork progression and generate DSBs (6), which need to be repaired by BRCA1/2 and other HR factors (4, 5). While the synthetic lethality of PARPi and HR deficiency is being exploited clinically, many BRCA-mutated carcinomas acquire resistance to PARPi (2). Identifying key factors that are functionally linked with BRCA1/2 and/or PARP during replication stress response may indicate useful alternative or combinatorial chemotherapeutic strategies.DDX11 is a conserved iron–sulfur (Fe–S) cluster 5′ to 3′ DNA helicase facilitating chromatin structure and DNA repair in manners that are not fully understood. Biallelic DDX11 mutations in humans cause the developmental disorder Warsaw breakage syndrome (WBS), which presents overlaps with Fanconi anemia in terms of chromosomal instability induced by intra- and interstrand crosslinking (ICL) agents and with cohesinopathies in terms of sister chromatid cohesion defects (7, 8). DDX11 has also strong ties to cancer. Specifically, DDX11 is highly up-regulated or amplified in diverse cancers, such as breast and ovarian cancers, including one-fifth of high-grade serous ovarian cancers (cBioPortal and The Cancer Genome Atlas TCGA]). Moreover, DDX11 is required for the survival of advanced melanomas (9), lung adenocarcinomas (10), and hepatocellular carcinomas (11). In terms of molecular functions, DDX11 interacts physically with the replication fork component Timeless to assist replisome progression and to facilitate epigenetic stability at G-quadruplex (G4) structures and sister chromatid cohesion (12–16). Notably, DDX11 also contributes along 9–1-1, Fanconi anemia factors, and SMC5/6 to prevent cytotoxicity of PARPi and ICLs (17–20). However, if the DNA damage tolerance functions of DDX11 are relevant for tumorigenesis or cancer therapies remains currently unknown.Here, we find that targeting DDX11 sensitizes ovarian and other cancer cell lines to drug therapies involving cisplatin and the PARP inhibitor olaparib. We established DDX11 knockout (KO) in HeLa uterine and U2OS osteosarcoma cancer cell lines and uncovered via chemical drug screens and immunofluorescence of DNA damage markers that they show typical hallmarks of increased replication stress. DDX11 helicase activity and the Fe–S domain are critical to prevent cellular sensitization to olaparib and ICLs and to avert accumulation of DSB markers. Mechanistically, we uncover that DDX11 facilitates homology-directed repair of DSBs and RAD51 focus formation downstream of 53BP1. Importantly, DDX11 is required for viability in BRCA1-depleted cells that are resistant to chemotherapy by concomitant depletion of 53BP1, REV7, and other shieldin components (21, 22), indicating roles for DDX11 in the activated BRCA2-dependent HR pathway, often accounting for the resistance of BRCA1-mutated tumors (2). DDX11 DNA repair function is nonredundant with BRCA1 and BRCA2 pathways, facilitating resection and loading of both RPA and RAD51 on single-stranded DNA substrates. Altogether, our results define a DDX11-mediated DNA repair pathway that creates pharmaceutically targetable vulnerabilities in cancers.