Robert C. A. M. van Waardenburg

DNA repair mechanisms involved in gemcitabine cytotoxicity and in the interaction between gemcitabine and cisplatin

The influence of DNA repair mechanisms on the interaction between gemcitabine and cisplatin was studied using a panel of Chinese hamster ovary (CHO) cell lines deficient in one of the following repair pathways: base excision repair (BER), nucleotide excision repair (NER), homologous recombination (HR) and non-homologous end joining (NHEJ). NER and HR are known to be involved in platinum-DNA adduct repair. Single agent experiments demonstrated that each of the repair deficient cell lines had a similar sensitivity towards gemcitabine as the parental cell lines, whereas the NER- and HR-deficient lines showed increased sensitivity towards cisplatin. Furthermore, in the parental cell lines, the administration sequence cisplatin followed by gemcitabine was synergistic, whereas the reversed schedule showed additivity and simultaneous administration revealed antagonistic cytotoxicity. In the repair deficient cell lines, using this synergistic schedule of cisplatin followed by gemcitabine, loss of synergy was observed in the NER- and HR-deficient cell lines. However, the magnitude of the effect in the NER-deficient cells was small. The sensitivity to the combination of cisplatin and gemcitabine shown by the BER- and NHEJ-deficient cell lines did not differ significantly from that of the parental cell line. Cellular accumulation of platinum as well as the formation of GG- and AG-intrastrand adducts in the parental line and in the HR-deficient line were not affected by gemcitabine. In conclusion, our results indicate that BER, NER, HR, and NHEJ are most likely incapable of modulating the cytotoxicity of gemcitabine, and that HR is involved in the synergistic interaction between cisplatin and gemcitabine in our cell system.

Defects in SUMO (small ubiquitin-related modifier) conjugation and deconjugation alter cell sensitivity to DNA topoisomerase I-induced DNA damage

Eukaryotic DNA topoisomerase I (Top1p) has important functions in DNA replication, transcription, and recombination. This enzyme also constitutes the cellular target of camptothecin (CPT), which induces S-phase-dependent cytotoxicity. To define cellular pathways that regulate cell sensitivity to Top1p-induced DNA lesions, we described a yeast genetic screen for conditional tah (top1T722A-hypersensitive) mutants with enhanced sensitivity to low levels of the CPT mimetic mutant top1T722A (Reid, R. J., Fiorani, P., Sugawara, M., and Bjornsti, M. A. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 11440–11445; Fiorani, P., Reid, R. J., Schepis, A., Jacquiau, H. R., Guo, H., Thimmaiah, P., Benedetti, P., and Bjornsti, M. A. (2004) J. Biol. Chem. 279, 21271–21281). Here we report that tah mutant ubc9–10 harbors a hypomorphic allele of UBC9, which encodes the essential SUMO (small ubiquitin-related modifier) E2-conjugating enzyme. The same conditional ubc9P123L mutant was also isolated in an independent screen for enhanced sensitivity to a distinct Top1p poison, Top1N726Hp. The ubc9–10 mutant exhibited a decrease in global protein sumoylation and increased sensitivity to a wide range of DNA-damaging agents independent of Top1p. Deletion of the Ulp2 SUMO protease failed to restore ubc9–10 cell resistance to Top1p poisons or hydroxyurea yet adversely affected wild-type TOP1 cell genetic stability and sensitivity to hydroxyurea. Moreover, although mutation of different consensus SUMO sites in the N terminus and linker region of yeast Top1p failed to recapitulate ubc9–10 mutant phenotypes, they revealed distinct and subtle effects on cell sensitivity to CPT. These results provide insights into the complexities of SUMO conjugation and the confounding effects of SUMO modification on Top1p function and cell sensitivity to genotoxic agents.

Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress.

ABSTRACT Covalent modification with SUMO alters protein function, intracellular localization, or protein-protein interactions. Target recognition is determined, in part, by the SUMO E2 enzyme, Ubc9, while Siz/Pias E3 ligases may facilitate select interactions by acting as substrate adaptors. A yeast conditional Ubc9P123L mutant was viable at 36°C yet exhibited enhanced sensitivity to DNA damage. To define functional domains in Ubc9 that dictate cellular responses to genotoxic stress versus those necessary for cell viability, a 1.75-Å structure of yeast Ubc9 that demonstrated considerable conservation of backbone architecture with human Ubc9 was solved. Nevertheless, differences in side chain geometry/charge guided the design of human/yeast chimeras, where swapping domains implicated in (i) binding residues within substrates that flank canonical SUMOylation sites, (ii) interactions with the RanBP2 E3 ligase, and (iii) binding of the heterodimeric E1 and SUMO had distinct effects on cell growth and resistance to DNA-damaging agents. Our findings establish a functional interaction between N-terminal and substrate-binding domains of Ubc9 and distinguish the activities of E3 ligases Siz1 and Siz2 in regulating cellular responses to genotoxic stress.

Topoisomerase I levels in white blood cells of patients with ovarian cancer treated with paclitaxel-cisplatin-topotecan in a phase I study.

Topotecan stabilizes the topoisomerase I (Topo I) cleavable complex. We measured Topo I levels in white blood cells of patients with ovarian cancer treated with topotecan. Topotecan was given i.v. daily ×5 q 3 weeks in combination with paclitaxel (1 day before topotecan) and cisplatin (just prior topotecan). Our aim was to correlate Topo I levels to pharmacokinetics and toxicity. Topo I levels were determined using Western blotting and were expressed relative to the Topo I level present in 10 μ g cell lysate of the human IGROV1 ovarian cancer cell line. We found no correlation between Topo I levels and (non-)hematological toxicity. Topo I levels after the fifth topotecan infusion were significantly negatively correlated with the AUC of topotecan (R  =−0.64, p =0.026), in contrast with Topo I levels prior to (R  =−0.25, p =0.4) and after (R  =−0.30, p =0.3) the first topotecan infusion. Topo I levels after the fifth topotecan infusion (48±27%, mean±SD) were higher than Topo I levels prior to and after the first topotecan infusion (3.0±4.7 and 2.7±3.6%, respectively) (p =0.001). In conclusion, we detected a significant inverse correlation between Topo I level and topotecan AUC at day 5, and we found increasing Topo I levels during a daily ×5 schedule of treatment with topotecan.

Abstract 1075: JQ1 induces DNA damage, inhibits expression of DNA repair proteins, and synergizes with PARP inhibitors in pancreatic cancer cells

Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer. PDAC is a highly aggressive tumor with a 5-year survival of The goal of the current study was to develop effective combination therapy for PDAC by identifying agents that might be combined with the BET bromodomain inhibitor JQ1, which we have shown to inhibit the growth in vivo of PDAC patient derived xenografts (PDX). Expression profile analysis of tumors from vehicle control and JQ1 treated mice revealed that JQ1 inhibited the expression of multiple gene products involved in DNA repair. Notably, JQ1 inhibited expression of DNA double-strand break (DSB) repair proteins BRCA2 and Ku80. Immunohistochemical staining confirmed down-regulation of expression of both proteins in tumors of mice treated with JQ1. Further, immunoblot and immunofluorescence analyses demonstrated that decreased expression of BRCA2 and Ku80 was coincident with increased levels of DNA damage, as reflected by expression of the DNA DSB marker gamma-H2AX. Data generated in vivo in three independent PDX models corroborated in vitro data generated using pancreatic cancer cell lines BxPC3 and Panc1. The data suggest that JQ1 induces DNA damage by inhibiting DNA repair. Because DNA repair deficiency sensitizes cells to PARP inhibitors, we hypothesized that JQ1-induced DNA repair deficiency would sensitize PDAC cells to PARP inhibitors. To address this hypothesis, we exposed Panc1 and BxPC3 to JQ1 or to a PARP 1/2 inhibitor (veliparib or olaparib) or to the combinations, and assessed the efficacy of each. Growth inhibition data, analyzed using Compusyn software and reported as combination indices, demonstrated that the combinations of JQ1 + veliparib or olaparib exert synergistic cytotoxicity. Further, the combination of JQ1 + a PARP inhibitor increased the accumulation of DNA damage in vitro, compared to either agent alone. We conclude that JQ1 induces DNA damage due at least in part to DNA repair deficiency, and propose that this mechanism sensitizes PDAC cells to PARP inhibitors. Citation Format: Aubrey Lynn Miller, Tracy Gamblin, Leona Council, Robert van Waardenburg, Eddy Yang, James Bradner, Karina Yoon. JQ1 induces DNA damage, inhibits expression of DNA repair proteins, and synergizes with PARP inhibitors in pancreatic cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1075. doi:10.1158/1538-7445.AM2017-1075

Biochemical and Genetic Analyses of DNA Topoisomerase 1-Mediated DNA Damage

Eukaryotic DNA topoisomerase 1 (Top1) is a highly conserved enzyme that catalyzes changes in the linkage of DNA strands (reviewed in refs. 1, 2, 3). Such changes in DNA topology are important during cellular processes involving DNA, including DNA replication, recombination, transcription, and chromosome condensation (1, 2, 3). The monomeric Top1 enzyme, encoded by the Top1 gene, binds to duplex DNA and catalyzes the transient cleavage and relegation of a single DNA strand. This is achieved by the nucleophilic attack of the active site tyrosine on a DNA phosphodiester bond to generate a phosphotyrosyl linkage between the enzyme and the 3′-end of the nicked DNA. The formation of this enzyme-linked nick allows for the rotation of the noncovalently held DNA end around phosphodiester bonds in the nonscissile strand to effect changes in DNA linking number. In a second transesterification reaction, the 5′OH DNA end attacks the phosphotyrosyl bond to restore the phosphodiester backbone bond and liberate the enzyme. The formation of a covalent Top1p-DNA complex is the hallmark of topoisomerase-catalyzed reactions and acts to conserve the energy of the cleaved DNA bond such that the concerted nicking and relegation of DNA stands does not require an exogenous energy source, such as adenosine triphosphate (ATP). The type IB enzymes, such as eukaryotic Top1, are distinct from type IA and type II enzymes in the formation of a 3′-phosphotyrosyl bond. Recent structural insights suggest mechanistic similarities between type IB enzymes and tyrosine recombinases, such as Cre and Int, which also form a covalent linkage with a 3′-phosphoryl DNA end (4,5).