Ubiquitin-mediated DNA damage response is synthetic lethal with G-quadruplex stabilizer CX-5461

Abstract

CX-5461 is a G-quadruplex (G4) ligand currently in trials with initial indications of clinical activity in cancers with defects in homologous recombination repair. To identify more genetic defects that could sensitize tumors to CX-5461, we tested synthetic lethality for 480 DNA repair and genome maintenance genes to CX-5461, pyridostatin (PDS), a structurally unrelated G4-specific stabilizer, and BMH-21, which binds GC-rich DNA but not G4 structures. We identified multiple members of HRD, Fanconi Anemia pathways, and POLQ, a polymerase with a helicase domain important for G4 structure resolution. Significant synthetic lethality was observed with UBE2N and RNF168, key members of the DNA damage response associated ubiquitin signaling pathway. Loss-of-function of RNF168 and UBE2N resulted in significantly lower cell survival in the presence of CX-5461 and PDS but not BMH-21. RNF168 recruitment and histone ubiquitination increased with CX-5461 treatment, and nuclear ubiquitination response frequently co-localized with G4 structures. Pharmacological inhibition of UBE2N acted synergistically with CX-5461. In conclusion, we have uncovered novel genetic vulnerabilities to CX-5461 with potential significance for patient selection in future clinical trials.

Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy

“…11 , 13 ). Recently, it has been shown that RNF168, which promotes the recruitment of the RAD18-SLF1/2-SMC5/6 pathway to damaged replication forks, is important for signaling the presence of G-quadruplex (G4) DNA structures stabilized by the RNA polymerase I inhibitor, CX5461 47 . Since cells deficient in BRCA1/2 and the cohesin-associated helicase DDX11 are also hypersensitive to this agent 48 , 49 and DDX11 was shown to function with SMC5/6 to repair DNA damage 17 , 50 , 51 , we hypothesized that the RAD18-SLF1/2-SMC5/6 pathway might play a role in suppressing replication stress at sites of stabilized G4 structures.…”

Emerging Roles of RNF168 in Tumor Progression

“…Therefore, RNF168 deficiency leads to the resistance of TOP2α catalytic inhibitor ICRF-193 and the cytotoxic anticancer drug etoposide (VP-16) [ 44 ]. Moreover, deletion of RNF168 inhibits the chromatin ubiquitin pathway and enhances the sensitivity of cancer cells to the bioavailable derivative of quarfloxin CX-5461 [ 45 ]. A recent study showed that a 1,2,3-triazole derivative of quinazoline can directly bind with autophagy-related protein SQSTM1/P62 and E3 ligase RNF168, promote their interaction, and damage the DNA repair mediated by RNF168, thus increasing the sensitivity of colon cancer cell HCT-116 to X-ray radiation.…”

G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions

“…CX-5461 is another G4 ligand that is currently at advanced phase I clinical trials for patients with BRCA1/2 deficient tumors [ 69 ]. Recently, Masud et al demonstrated that inhibition of the critical member of the DNA damage response, UBE2N , acted synergistically with CX-5461 increasing cell toxicity [ 70 ]. Further, this compound has shown the potential to suppress pulmonary arterial hypertension and associated vascular remodeling and pulmonary inflammation by inhibiting the RNA polymerase I [ 71 ].…”