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Inanc B, Fang Q, Andrews JF, Zeng X, Clark J, Li J, Dey NB, Ibrahim M, Sykora P, Yu Z, Braganza A, Verheij M, Jonkers J, Yates NA, Vens C, Sobol RW. TRIP12 governs DNA Polymerase β involvement in DNA damage response and repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588474. [PMID: 38645048 PMCID: PMC11030427 DOI: 10.1101/2024.04.08.588474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The multitude of DNA lesion types, and the nuclear dynamic context in which they occur, present a challenge for genome integrity maintenance as this requires the engagement of different DNA repair pathways. Specific 'repair controllers' that facilitate DNA repair pathway crosstalk between double strand break (DSB) repair and base excision repair (BER), and regulate BER protein trafficking at lesion sites, have yet to be identified. We find that DNA polymerase β (Polβ), crucial for BER, is ubiquitylated in a BER complex-dependent manner by TRIP12, an E3 ligase that partners with UBR5 and restrains DSB repair signaling. Here we find that, TRIP12, but not UBR5, controls cellular levels and chromatin loading of Polβ. Required for Polβ foci formation, TRIP12 regulates Polβ involvement after DNA damage. Notably, excessive TRIP12-mediated shuttling of Polβ affects DSB formation and radiation sensitivity, underscoring its precedence for BER. We conclude that the herein discovered trafficking function at the nexus of DNA repair signaling pathways, towards Polβ-directed BER, optimizes DNA repair pathway choice at complex lesion sites.
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Krishna Rao V, Paul S, Gulkis M, Shen Z, Nair H, Singh A, Li C, Sharma AK, Çağlayan M, Das C, Das B, Kundu CN, Narayan S, Guchhait SK. Molecular editing of NSC-666719 enabling discovery of benzodithiazinedioxide-guanidines as anticancer agents. RSC Med Chem 2024; 15:937-962. [PMID: 38516586 PMCID: PMC10953490 DOI: 10.1039/d3md00648d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
DNA polymerase β (Polβ) is crucial for the base excision repair (BER) pathway of DNA damage repair and is an attractive target for suppressing tumorigenesis as well as chemotherapeutic intervention of cancer. In this study, a unique strategy of scaffold-hopping-based molecular editing of a bioactive agent NSC-666719 was investigated, which led to the development of new molecular motifs with Polβ inhibitory activity. NSC compound and its analogs (two series) were prepared, focusing on pharmacophore-based molecular diversity. Most compounds showed higher activities than the parent NSC-666719 and exhibited effects on apoptosis. The inhibitory activity of Polβ was evaluated in both in vitro reconstituted and in vivo intact cell systems. Compound 10e demonstrated significant Polβ interaction and inhibition characteristics, including direct, non-covalent, reversible, and comparable binding affinity. The investigated approach is useful, and the discovered novel analogs have a high potential for developing as anticancer therapeutics.
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Affiliation(s)
- Vajja Krishna Rao
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
| | - Subarno Paul
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Zhihang Shen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Haritha Nair
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Amandeep Singh
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Arun K Sharma
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Chinmay Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Biswajit Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Chanakya N Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Satya Narayan
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Sankar K Guchhait
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
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Wang R, Sun Y, Li C, Xue Y, Ba X. Targeting the DNA Damage Response for Cancer Therapy. Int J Mol Sci 2023; 24:15907. [PMID: 37958890 PMCID: PMC10648182 DOI: 10.3390/ijms242115907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Over the course of long-term evolution, cells have developed intricate defense mechanisms in response to DNA damage; these mechanisms play a pivotal role in maintaining genomic stability. Defects in the DNA damage response pathways can give rise to various diseases, including cancer. The DNA damage response (DDR) system is instrumental in safeguarding genomic stability. The accumulation of DNA damage and the weakening of DDR function both promote the initiation and progression of tumors. Simultaneously, they offer opportunities and targets for cancer therapeutics. This article primarily elucidates the DNA damage repair pathways and the progress made in targeting key proteins within these pathways for cancer treatment. Among them, poly (ADP-ribose) polymerase 1 (PARP1) plays a crucial role in DDR, and inhibitors targeting PARP1 have garnered extensive attention in anticancer research. By delving into the realms of DNA damage and repair, we aspire to explore more precise and effective strategies for cancer therapy and to seek novel avenues for intervention.
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Affiliation(s)
- Ruoxi Wang
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (R.W.); (Y.S.)
| | - Yating Sun
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (R.W.); (Y.S.)
| | - Chunshuang Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
| | - Yaoyao Xue
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
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4
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Mechanisms of Drug Resistance in Ovarian Cancer and Associated Gene Targets. Cancers (Basel) 2022; 14:cancers14246246. [PMID: 36551731 PMCID: PMC9777152 DOI: 10.3390/cancers14246246] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
In the United States, over 100,000 women are diagnosed with a gynecologic malignancy every year, with ovarian cancer being the most lethal. One of the hallmark characteristics of ovarian cancer is the development of resistance to chemotherapeutics. While the exact mechanisms of chemoresistance are poorly understood, it is known that changes at the cellular and molecular level make chemoresistance challenging to treat. Improved therapeutic options are needed to target these changes at the molecular level. Using a precision medicine approach, such as gene therapy, genes can be specifically exploited to resensitize tumors to therapeutics. This review highlights traditional and novel gene targets that can be used to develop new and improved targeted therapies, from drug efflux proteins to ovarian cancer stem cells. The review also addresses the clinical relevance and landscape of the discussed gene targets.
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Abstract
Base excision repair (BER) is one of the major DNA repair pathways used to fix a myriad of cellular DNA lesions. The enzymes involved in BER, including DNA polymerase β (Polβ), have been identified and characterized, but how they act together to efficiently perform BER has not been fully understood. Through gel electrophoresis, mass spectrometry, and kinetic analysis, we discovered that the two enzymatic activities of Polβ can be interlocked, rather than functioning independently from each other, when processing DNA intermediates formed in BER. The finding prompted us to hypothesize a modified BER pathway. Through conventional and time-resolved X-ray crystallography, we solved 11 high-resolution crystal structures of cross-linked Polβ complexes and proposed a detailed chemical mechanism for Polβ’s 5′-deoxyribose-5-phosphate lyase activity. Base excision repair (BER) is a major cellular pathway for DNA damage repair. During BER, DNA polymerase β (Polβ) is hypothesized to first perform gap-filling DNA synthesis by its polymerase activity and then cleave a 5′-deoxyribose-5-phosphate (dRP) moiety via its dRP lyase activity. Through gel electrophoresis and kinetic analysis of partial BER reconstitution, we demonstrated that gap-filling DNA synthesis by the polymerase activity likely occurred after Schiff base formation but before β-elimination, the two chemical reactions catalyzed by the dRP lyase activity. The Schiff base formation and β-elimination intermediates were trapped by sodium borohydride reduction and identified by mass spectrometry and X-ray crystallography. Presteady-state kinetic analysis revealed that cross-linked Polβ (i.e., reduced Schiff base) exhibited a 17-fold higher polymerase efficiency than uncross-linked Polβ. Conventional and time-resolved X-ray crystallography of cross-linked Polβ visualized important intermediates for its dRP lyase and polymerase activities, leading to a modified chemical mechanism for the dRP lyase activity. The observed interlocking enzymatic activities of Polβ allow us to propose an altered mechanism for the BER pathway, at least under the conditions employed. Plausibly, the temporally coordinated activities at the two Polβ active sites may well be the reason why Polβ has both active sites embedded in a single polypeptide chain. This proposed pathway suggests a corrected facet of BER and DNA repair, and may enable alternative chemical strategies for therapeutic intervention, as Polβ dysfunction is a key element common to several disorders.
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Gujarathi S, Zafar MK, Liu X, Eoff RL, Zheng G. A Facile Semisynthesis and Evaluation of Garcinoic Acid and Its Analogs for the Inhibition of Human DNA Polymerase β. Molecules 2020; 25:E5847. [PMID: 33322249 PMCID: PMC7763917 DOI: 10.3390/molecules25245847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/17/2022] Open
Abstract
Garcinoic acid has been identified as an inhibitor of DNA polymerase β (pol β). However, no structure-activity relationship (SAR) studies of garcinoic acid as a pol β inhibitor have been conducted, in part due to the lack of an efficient synthetic method for this natural product and its analogs. We developed an efficient semi-synthetic method for garcinoic acid and its analogs by starting from natural product δ-tocotrienol. Our preliminary SAR studies provided a valuable insight into future discovery of garcinoic acid-based pol β inhibitors.
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Affiliation(s)
- Satheesh Gujarathi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.G.); (X.L.)
| | - Maroof Khan Zafar
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (M.K.Z.); (R.L.E.)
| | - Xingui Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.G.); (X.L.)
| | - Robert L. Eoff
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (M.K.Z.); (R.L.E.)
| | - Guangrong Zheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.G.); (X.L.)
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
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7
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Yu X, Weng T, Gu C, Yang H. Comparison of gene regulatory networks to identify pathogenic genes for lymphoma. J Bioinform Comput Biol 2020; 18:2050029. [PMID: 33131362 DOI: 10.1142/s0219720020500298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lymphoma is the most complicated cancer that can be divided into several tens of subtypes. It may occur in any part of body that has lymphocytes, and is closely correlated with diverse environmental factors such as the ionizing radiation, chemocarcinogenesis, and virus infection. All the environmental factors affect the lymphoma through genes. Identifying pathogenic genes for lymphoma is consequently an essential task to understand its complexity in a unified framework. In this paper, we propose a new method to expose high-confident edges in gene regulatory networks (GRNs) for a total of 32 organs, called Filtered GRNs (f-GRNs), comparison of which gives us a proper reference for the Lymphoma, i.e. the B-lymphocytes cells, whose f-GRN is closest with that for the Lymphoma. By using the Gene Ontology and Biological Process analysis we display the differences of the two networks' hubs in biological functions. Matching with the Genecards shows that most of the hubs take part in the genetic information transmission and expression, except a specific gene of Retinoic Acid Receptor Alpha (RARA) that encodes the retinoic acid receptor. In the lymphoma, the genes in the RARA ego-network are involved in two cancer pathways, and the RARA is present only in these cancer pathways. For the lymphoid B cells, however, the genes in the RARA ego-network do not participate in cancer-related pathways.
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Affiliation(s)
- Xiao Yu
- Department of Systems Science, University of Shanghai for Science and Technology, Jungong Road No. 516, Shanghai 200093, P. R. China
| | - Tongfeng Weng
- Department of Systems Science, University of Shanghai for Science and Technology, Jungong Road No. 516, Shanghai 200093, P. R. China
| | - Changgui Gu
- Department of Systems Science, University of Shanghai for Science and Technology, Jungong Road No. 516, Shanghai 200093, P. R. China
| | - Huijie Yang
- Department of Systems Science, University of Shanghai for Science and Technology, Jungong Road No. 516, Shanghai 200093, P. R. China
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8
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Non-muscle invasive bladder cancer tissues have increased base excision repair capacity. Sci Rep 2020; 10:16371. [PMID: 33004944 PMCID: PMC7529820 DOI: 10.1038/s41598-020-73370-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/15/2020] [Indexed: 12/26/2022] Open
Abstract
The molecular mechanisms underlying the development and progression of bladder cancer (BC) are complex and have not been fully elucidated. Alterations in base excision repair (BER) capacity, one of several DNA repair mechanisms assigned to preserving genome integrity, have been reported to influence cancer susceptibility, recurrence, and progression, as well as responses to chemotherapy and radiotherapy. We report herein that non-muscle invasive BC (NMIBC) tissues exhibit increased uracil incision, abasic endonuclease and gap-filling activities, as well as total BER capacity in comparison to normal bladder tissue from the same patient (p < 0.05). No significant difference was detected in 8-oxoG incision activity between cancer and normal tissues. NMIBC tissues have elevated protein levels of uracil DNA glycosylase, 8-oxoguanine DNA glycosylase, AP endonuclease 1 and DNA polymerase β protein. Moreover, the fold increase in total BER and the individual BER enzyme activities were greater in high-grade tissues than in low-grade NMIBC tissues. These findings suggest that enhanced BER activity may play a role in the etiology of NMIBC and that BER proteins could serve as biomarkers in disease prognosis, progression or response to genotoxic therapeutics, such as Bacillus Calmette–Guérin.
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Guffanti F, Alvisi MF, Caiola E, Ricci F, De Maglie M, Soldati S, Ganzinelli M, Decio A, Giavazzi R, Rulli E, Damia G. Impact of ERCC1, XPF and DNA Polymerase β Expression on Platinum Response in Patient-Derived Ovarian Cancer Xenografts. Cancers (Basel) 2020; 12:cancers12092398. [PMID: 32847049 PMCID: PMC7564949 DOI: 10.3390/cancers12092398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
Platinum resistance is an unmet medical need in ovarian carcinoma. Molecular biomarkers to predict the response to platinum-based therapy could allow patient stratification and alternative therapeutic strategies early in clinical management. Sensitivity and resistance to platinum therapy are partially determined by the tumor’s intrinsic DNA repair activities, including nucleotide excision repair (NER) and base excision repair (BER). We investigated the role of the NER proteins—ERCC1, XPF, ERCC1/XPF complex—and of the BER protein DNA polymerase β, as possible biomarkers of cisplatin (DDP) response in a platform of recently established patient-derived ovarian carcinoma xenografts (OC-PDXs). ERCC1 and DNA polymerase β protein expressions were measured by immunohistochemistry, the ERCC1/XPF foci number was detected by proximity ligation assay (PLA) and their mRNA levels by real-time PCR. We then correlated the proteins, gene expression and ERCC1/XPF complexes with OC-PDXs’ response to platinum. To the best of our knowledge, this is the first investigation of the role of the ERCC1/XPF complex, detected by PLA, in relation to the response to DDP in ovarian carcinoma. None of the proteins in the BER and NER pathways studied predicted platinum activity in this panel of OC-PDXs, nor did the ERCC1/XPF foci number. These results were partially explained by the experimental evidence that the ERCC1/XPF complex increases after DDP treatment and this possibly better associates with the cancer cells’ abilities to activate the NER pathway to repair platinum-induced damage than its basal level. Our findings highlight the need for DNA functional assays to predict the response to platinum-based therapy.
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Affiliation(s)
- Federica Guffanti
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (F.G.); (E.C.); (F.R.)
| | - Maria Francesca Alvisi
- Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.F.A.); (E.R.)
| | - Elisa Caiola
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (F.G.); (E.C.); (F.R.)
| | - Francesca Ricci
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (F.G.); (E.C.); (F.R.)
| | - Marcella De Maglie
- Mouse and Animal Pathology Lab (MAPLab), Filarete Foundation, Department of Veterinary Medicine, University of Milan, 20139 Milan, Italy;
| | - Sabina Soldati
- Department of Veterinary Pathology, University of Milan, 20133 Milan, Italy;
| | - Monica Ganzinelli
- Unit of Thoracic Oncology, Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Alessandra Decio
- Laboratory of Cancer Metastasis Therapeutics, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (A.D.); (R.G.)
| | - Raffaella Giavazzi
- Laboratory of Cancer Metastasis Therapeutics, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (A.D.); (R.G.)
| | - Eliana Rulli
- Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.F.A.); (E.R.)
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (F.G.); (E.C.); (F.R.)
- Correspondence: ; Tel.: +39-0239014234
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10
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Alvisi MF, Ganzinelli M, Linardou H, Caiola E, Lo Russo G, Cecere FL, Bettini AC, Psyrri A, Milella M, Rulli E, Fabbri A, De Maglie M, Romanelli P, Murray S, Ndembe G, Broggini M, Garassino MC, Marabese M. Predicting the Role of DNA Polymerase β Alone or with KRAS Mutations in Advanced NSCLC Patients Receiving Platinum-Based Chemotherapy. J Clin Med 2020; 9:jcm9082438. [PMID: 32751518 PMCID: PMC7465625 DOI: 10.3390/jcm9082438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 01/17/2023] Open
Abstract
Clinical data suggest that only a subgroup of non-small cell lung cancer (NSCLC) patients has long-term benefits after front-line platinum-based therapy. We prospectively investigate whether KRAS status and DNA polymerase β expression could help identify patients responding to platinum compounds. Prospectively enrolled, advanced NSCLC patients treated with a first-line regimen containing platinum were genotyped for KRAS and centrally evaluated for DNA polymerase β expression. Overall survival (OS), progression-free survival (PFS), and the objective response rate (ORR) were recorded. Patients with KRAS mutations had worse OS (hazard ratio (HR): 1.37, 95% confidence interval (95% CI): 0.70–2.27). Negative DNA polymerase β staining identified a subgroup with worse OS than patients expressing the protein (HR: 1.43, 95% CI: 0.57–3.57). The addition of KRAS to the analyses further worsened the prognosis of patients with negative DNA polymerase β staining (HR: 1.67, 95% CI: 0.52–5.56). DNA polymerase β did not influence PFS and ORR. KRAS may have a negative role in platinum-based therapy responses in NSCLC, but its impact is limited. DNA polymerase β, when not expressed, might indicate a group of patients with poor outcomes. KRAS mutations in tumors not expressing DNA polymerase β further worsens survival. Therefore, these two biomarkers together might well identify patients for whom alternatives to platinum-based chemotherapy should be used.
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Affiliation(s)
- Maria Francesca Alvisi
- Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.F.A.); (E.R.)
| | - Monica Ganzinelli
- Unit of Thoracic Oncology, Medical Oncology Department 1, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; (M.G.); (G.L.R.); (M.C.G.)
| | - Helena Linardou
- 4th Oncology Department, Metropolitan Hospital, 18547 Athens, Greece;
| | - Elisa Caiola
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (E.C.); (G.N.)
| | - Giuseppe Lo Russo
- Unit of Thoracic Oncology, Medical Oncology Department 1, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; (M.G.); (G.L.R.); (M.C.G.)
| | - Fabiana Letizia Cecere
- Division of Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | | | - Amanda Psyrri
- Section of Oncology, Department of Internal Medicine, Attikon Hospital, National Kapodistrian University of Athens, 12462 Athens, Greece;
| | - Michele Milella
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, 37126 Verona, Italy;
| | - Eliana Rulli
- Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (M.F.A.); (E.R.)
| | - Alessandra Fabbri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Marcella De Maglie
- Mouse & Animal Pathology Lab, Fondazione Filarete, 20139 Milan, Italy; (M.D.M.); (P.R.)
- Department of Veterinary Medicine, University of Milan, 20122 Milan, Italy
| | - Pierpaolo Romanelli
- Mouse & Animal Pathology Lab, Fondazione Filarete, 20139 Milan, Italy; (M.D.M.); (P.R.)
- Department of Veterinary Medicine, University of Milan, 20122 Milan, Italy
| | | | - Gloriana Ndembe
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (E.C.); (G.N.)
| | - Massimo Broggini
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (E.C.); (G.N.)
- Correspondence: (M.B.); (M.M.); Tel.: +39-0239014585 (M.B.); +39-0239014236 (M.M.)
| | - Marina Chiara Garassino
- Unit of Thoracic Oncology, Medical Oncology Department 1, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; (M.G.); (G.L.R.); (M.C.G.)
| | - Mirko Marabese
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (E.C.); (G.N.)
- Correspondence: (M.B.); (M.M.); Tel.: +39-0239014585 (M.B.); +39-0239014236 (M.M.)
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11
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Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion. Biochem J 2020; 477:937-951. [PMID: 32039434 DOI: 10.1042/bcj20190906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 01/06/2023]
Abstract
The cisplatin-1,2-d(GpG) (Pt-GG) intrastrand cross-link is the predominant DNA lesion generated by cisplatin. Cisplatin has been shown to predominantly induce G to T mutations and Pt-GG permits significant misincorporation of dATP by human DNA polymerase β (polβ). In agreement, polβ overexpression, which is frequently observed in cancer cells, is linked to cisplatin resistance and a mutator phenotype. However, the structural basis for the misincorporation of dATP opposite Pt-GG is unknown. Here, we report the first structures of a DNA polymerase inaccurately bypassing Pt-GG. We solved two structures of polβ misincorporating dATP opposite the 5'-dG of Pt-GG in the presence of Mg2+ or Mn2+. The Mg2+-bound structure exhibits a sub-optimal conformation for catalysis, while the Mn2+-bound structure is in a catalytically more favorable semi-closed conformation. In both structures, dATP does not form a coplanar base pairing with Pt-GG. In the polβ active site, the syn-dATP opposite Pt-GG appears to be stabilized by protein templating and pi stacking interactions, which resembles the polβ-mediated dATP incorporation opposite an abasic site. Overall, our results suggest that the templating Pt-GG in the polβ active site behaves like an abasic site, promoting the insertion of dATP in a non-instructional manner.
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12
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Vasquez JL, Lai Y, Annamalai T, Jiang Z, Zhang M, Lei R, Zhang Z, Liu Y, Tse-Dinh YC, Agoulnik IU. Inhibition of base excision repair by natamycin suppresses prostate cancer cell proliferation. Biochimie 2020; 168:241-250. [PMID: 31756402 PMCID: PMC6926147 DOI: 10.1016/j.biochi.2019.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022]
Abstract
Prostate cancer (PCa) progression is characterized by increased expression and transcriptional activity of the androgen receptor (AR). In the advanced stages of prostate cancer, AR significantly upregulates the expression of genes involved in DNA repair. Upregulation of expression for base excision repair (BER) related genes is associated with poor patient survival. Thus, inhibition of the BER pathway may prove to be an effective therapy for prostate cancer. Using a high throughput BER capacity screening assay, we sought to identify BER inhibitors that can synergize with castration therapy. An FDA-approved drug library was screened to identify inhibitors of BER using a fluorescence-based assay suitable for HTS. A gel-based secondary assay confirmed the reduction of BER capacity by compounds identified in the primary screen. Five compounds were then selected for further testing in the independently derived, androgen-dependent prostate cancer cell lines, LNCaP and LAPC4, and in the nonmalignant prostate derived cell lines PNT1A and RWPE1. Further analysis led to the identification of a lead compound, natamycin, as an effective inhibitor of key BER enzymes DNA polymerase β (pol β) and DNA Ligase I (LIG I). Natamycin significantly inhibited proliferation of PCa cells in an androgen depleted environment at 1 μM concentration, however, growth inhibition did not occur with nonmalignant prostate cell lines, suggesting that BER inhibition may improve efficacy of the castration therapies.
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Affiliation(s)
- Judy L Vasquez
- Department of Human and Molecular Genetics, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
| | - Zhongliang Jiang
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, 33199, USA
| | - Manqi Zhang
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, 33199, USA
| | - Ruipeng Lei
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, 33199, USA
| | - Zunzhen Zhang
- Department of Occupational and Environmental Health, Sichuan University West China School of Public Health, Chengdu, Sichuan, China
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA; Biochemistry Ph.D. Program, Florida International University, Miami, FL, 33199, USA.
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA; Biochemistry Ph.D. Program, Florida International University, Miami, FL, 33199, USA.
| | - Irina U Agoulnik
- Department of Human and Molecular Genetics, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA; Biochemistry Ph.D. Program, Florida International University, Miami, FL, 33199, USA; Department of Cellular and Molecular Biology, Baylor College of Medicine, USA.
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13
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Koag MC, Jung H, Lee S. Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J Am Chem Soc 2019; 141:4584-4596. [PMID: 30817143 DOI: 10.1021/jacs.8b08551] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reactive oxygen species attack DNA to produce 7,8-dihyro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as major lesions. The structural basis for the mutagenicity of oxoG, which induces G to T mutations, is well understood. However, the structural basis for the mutagenic potential of oxoA, which induces A to C mutations, remains poorly understood. To gain insight into oxoA-induced mutagenesis, we conducted kinetic studies of human DNA polymerases β and η replicating across oxoA and structural studies of polβ incorporating dTTP/dGTP opposite oxoA. While polη readily bypassed oxoA, it incorporated dGTP opposite oxoA with a catalytic specificity comparable to that of correct insertion, underscoring the promutagenic nature of the major oxidative adenine lesion. Polη and polβ incorporated dGTP opposite oxoA ∼170-fold and ∼100-fold more efficiently than that opposite dA, respectively, indicating that the 8-oxo moiety greatly facilitated error-prone replication. Crystal structures of polβ showed that, when paired with an incoming dTTP, the templating oxoA adopted an anti conformation and formed Watson-Crick base pair. When paired with dGTP, oxoA adopted a syn conformation and formed a Hoogsteen base pair with Watson-Crick-like geometry, highlighting the dual-coding potential of oxoA. The templating oxoA was stabilized by Lys280-mediated stacking and hydrogen bonds. Overall, these results provide insight into the mutagenic potential and dual-coding nature of the major oxidative adenine lesion.
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Affiliation(s)
- Myong-Chul Koag
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hunmin Jung
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Seongmin Lee
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
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14
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Kumar M, Shukla VK, Misra PK, Raman MJ. Dysregulated Expression and Subcellular Localization of Base Excision Repair (BER) Pathway Enzymes in Gallbladder Cancer. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2018; 7:119-132. [PMID: 30276167 PMCID: PMC6148499 DOI: 10.22088/ijmcm.bums.7.2.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/14/2018] [Indexed: 01/06/2023]
Abstract
Base excision repair (BER) pathway is one of the repair systems that has an impact on radiotherapy and chemotherapy for cancer patients. The molecular pathogenesis of gallbladder cancer is not known extensively. In the present study we investigated whether the expression of AP endonuclease 1 (APE1) and DNA polymerase β (DNA pol β), key enzymes of BER pathway has any clinical significance with gallbladder carcinogenesis. 41 gallbladder cancer, 27 chronic cholecystitis, and 3 normal gallbladder specimens were analyzed for the expression of APE1 and DNA polymerase β by western blotting, and subcellular localization studied by immunohistochemistry. The enzymatic activity of APE1 was also studied. The correlations with expression of the above proteins with clinical-pathological characteristics of gallbladder cancer patients were analyzed. The integrated density value ratio (relative expression) of total APE1 (37 kDa + 35 kDa variant) analyzed in the three groups of tissues, was 0.76±0.03 in normal gallbladder, 0.91±0.08 in chronic cholecystitis, and 1.12±0.05 in gallbladder cancer. APE1 was found to be up-regulated in 80% of gallbladder carcinoma samples (P = 0.01). A positive trend of APE1 expression with tumor stage and lymph node positivity was observed. The enzymatic activity of APE1 was found higher in gallbladder cancer samples in comparison with chronic cholecystitis. The integrated density value ratio of DNA polymerase β for normal gallbladder, chronic cholecystitis and gallbladder cancer tissue samples were 0.46±0.03, 0.7±0.06 and 1.33±0.1, respectively. DNA polymerase β was found to be upregulated in almost all gallbladder carcinoma samples (P =0.0001), and its expression was negatively correlated with age (P=0.02). DNA polymerase β expression showed a positive trend with tumor stage and nuclear differentiation of gallbladder cancer. It may be concluded that alteration of these BER pathway proteins may be the causal factors for carcinogenesis of gallbladder, and has targeted therapeutic potential.
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Affiliation(s)
- Manoj Kumar
- Cytogenetics laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India.,School of Biological and Environmental Sciences, Faculty of Basic Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Vijay Kumar Shukla
- Department of General Surgery, Institute of Medical Science, Banaras Hindu University, Varanasi, India
| | - Pravas Kumar Misra
- Departments of Pathology and Surgery, Indian Railways Cancer Institute and Research Centre, Varanasi, Uttar Pradesh, India
| | - Mercy Jacob Raman
- Cytogenetics laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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15
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Kou Y, Koag MC, Lee S. Structural and Kinetic Studies of the Effect of Guanine N7 Alkylation and Metal Cofactors on DNA Replication. Biochemistry 2018; 57:5105-5116. [PMID: 29957995 DOI: 10.1021/acs.biochem.8b00331] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A wide variety of endogenous and exogenous alkylating agents attack DNA to preferentially generate N7-alkylguanine (N7-alkylG) adducts. Studies of the effect of N7-alkylG lesions on biological processes have been difficult in part because of complications arising from the chemical lability of the positively charged N7-alkylG, which can readily produce secondary lesions. To assess the effect of bulky N7-alkylG on DNA replication, we prepared chemically stable N7-benzylguanine (N7bnG)-containing DNA and evaluated nucleotide incorporation opposite the lesion by human DNA polymerase β (polβ), a model enzyme for high-fidelity DNA polymerases. Kinetic studies showed that the N7-benzyl-G lesion greatly inhibited dCTP incorporation by polβ. The crystal structure of polβ incorporating dCTP opposite N7bnG showed a Watson-Crick N7bnG:dCTP structure. The polβ-N7bnG:dCTP structure showed an open protein conformation, a relatively disordered dCTP, and a lack of catalytic metal, which explained the inefficient nucleotide incorporation opposite N7bnG. This indicates that polβ is sensitive to major groove adducts in the templating base side and deters nucleotide incorporation opposite bulky N7-alkylG adducts by adopting a catalytically incompetent conformation. Substituting Mg2+ for Mn2+ induced an open-to-closed conformational change due to the presence of catalytic metal and stably bound dCTP and increased the catalytic efficiency by ∼10-fold, highlighting the effect of binding of the incoming nucleotide and catalytic metal on protein conformation and nucleotidyl transfer reaction. Overall, these results suggest that, although bulky alkyl groups at guanine-N7 may not alter base pairing properties of guanine, the major groove-positioned lesions in the template could impede nucleotidyl transfer by some DNA polymerases.
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Affiliation(s)
- Yi Kou
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Myong-Chul Koag
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Seongmin Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
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16
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Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD. Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues. Chem Res Toxicol 2017; 30:1993-2001. [PMID: 28862449 PMCID: PMC6494084 DOI: 10.1021/acs.chemrestox.7b00173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Members of the nucleoside analogue class of cancer therapeutics compete with canonical nucleotides to disrupt numerous cellular processes, including nucleotide homeostasis, DNA and RNA synthesis, and nucleotide metabolism. Nucleoside analogues are triphosphorylated and subsequently inserted into genomic DNA, contributing to the efficacy of therapeutic nucleosides in multiple ways. In some cases, the altered base acts as a mutagen, altering the DNA sequence to promote cellular death; in others, insertion of the altered nucleotide triggers DNA repair pathways, which produce lethal levels of cytotoxic intermediates such as single and double stranded DNA breaks. As a prerequisite to many of these biological outcomes, the modified nucleotide must be accommodated in the DNA polymerase active site during nucleotide insertion. Currently, the molecular contacts that mediate DNA polymerase insertion of modified nucleotides remain unknown for multiple therapeutic compounds, despite decades of clinical use. To determine how modified bases are inserted into duplex DNA, we used mammalian DNA polymerase β (pol β) to visualize the structural conformations of four therapeutically relevant modified nucleotides, 6-thio-2'-deoxyguanosine-5'-triphosphate (6-TdGTP), 5-fluoro-2'-deoxyuridine-5'-triphosphate (5-FdUTP), 5-formyl-deoxycytosine-5'-triphosphate (5-FodCTP), and 5-formyl-deoxyuridine-5'-triphosphate (5-FodUTP). Together, the structures reveal a pattern in which the modified nucleotides utilize Watson-Crick base pairing interactions similar to that of unmodified nucleotides. The nucleotide modifications were consistently positioned in the major groove of duplex DNA, accommodated by an open cavity in pol β. These results provide novel information for the rational design of new therapeutic nucleoside analogues and a greater understanding of how modified nucleotides are tolerated by polymerases.
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Affiliation(s)
| | | | | | | | - Bret D. Freudenthal
- Corresponding Author 4015 Wahl Hall West, Laboratory of Genome Maintenance and Structural Biology, Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center Kansas City, Kansas 66160. Phone: 913-588-5560,
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17
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Nemec AA, Abriola L, Merkel JS, de Stanchina E, DeVeaux M, Zelterman D, Glazer PM, Sweasy JB. DNA Polymerase Beta Germline Variant Confers Cellular Response to Cisplatin Therapy. Mol Cancer Res 2017; 15:269-280. [PMID: 28074003 DOI: 10.1158/1541-7786.mcr-16-0227-t] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 12/31/2022]
Abstract
Resistance to cancer chemotherapies leads to deadly consequences, yet current research focuses only on the roles of somatically acquired mutations in this resistance. The mutational status of the germline is also likely to play a role in the way cells respond to chemotherapy. The carrier status for the POLB rs3136797 germline mutation encoding P242R DNA polymerase beta (Pol β) is associated with poor prognosis for lung cancer, specifically in response to treatment with cisplatin. Here, it is revealed that the P242R mutation is sufficient to promote resistance to cisplatin in human cells and in mouse xenografts. Mechanistically, P242R Pol β acts as a translesion polymerase and prefers to insert the correct nucleotide opposite cisplatin intrastrand cross-links, leading to the activation of the nucleotide excision repair (NER) pathway, removal of crosslinks, and resistance to cisplatin. In contrast, wild-type (WT) Pol β preferentially inserts the incorrect nucleotide initiating mismatch repair and cell death. Importantly, in a mouse xenograft model, tumors derived from lung cancer cells expressing WT Pol β displayed a slower rate of growth when treated with cisplatin, whereas tumors expressing P242R Pol β had no response to cisplatin. Pol β is critical for mediating crosstalk in response to cisplatin. The current data strongly suggest that the status of Pol β influences cellular responses to crosslinking agents and that Pol β is a promising biomarker to predict responses to specific chemotherapies. Finally, these results highlight that the genetic status of the germline is a critical factor in the response to cancer treatment.Implications: Pol β has prognostic biomarker potential in the treatment of cancer with cisplatin and perhaps other intrastrand crosslinking agents. Mol Cancer Res; 15(3); 269-80. ©2017 AACR.
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Affiliation(s)
- Antonia A Nemec
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut. .,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Laura Abriola
- Center for Molecular Discovery, Yale University, West Haven, Connecticut
| | - Jane S Merkel
- Center for Molecular Discovery, Yale University, West Haven, Connecticut
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michelle DeVeaux
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Daniel Zelterman
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut. .,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
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18
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Ray D, Kidane D. Gut Microbiota Imbalance and Base Excision Repair Dynamics in Colon Cancer. J Cancer 2016; 7:1421-30. [PMID: 27471558 PMCID: PMC4964126 DOI: 10.7150/jca.15480] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/18/2016] [Indexed: 12/15/2022] Open
Abstract
Gut microbiota are required for host nutrition, energy balance, and regulating immune homeostasis, however, in some cases, this mutually beneficial relationship becomes twisted (dysbiosis), and the gut flora can incite pathological disorders including colon cancer. Microbial dysbiosis promotes the release of bacterial genotoxins, metabolites, and causes chronic inflammation, which promote oxidative DNA damage. Oxidized DNA base lesions are removed by base excision repair (BER), however, the role of this altered function of BER, as well as microbiota-mediated genomic instability and colon cancer development, is still poorly understood. In this review article, we will discuss how dysbiotic microbiota induce DNA damage, its impact on base excision repair capacity, the potential link of host BER gene polymorphism, and the risk of dysbiotic microbiota mediated genomic instability and colon cancer.
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Affiliation(s)
- Debolina Ray
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
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19
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Caiola E, Salles D, Frapolli R, Lupi M, Rotella G, Ronchi A, Garassino MC, Mattschas N, Colavecchio S, Broggini M, Wiesmüller L, Marabese M. Base excision repair-mediated resistance to cisplatin in KRAS(G12C) mutant NSCLC cells. Oncotarget 2015; 6:30072-87. [PMID: 26353932 PMCID: PMC4745782 DOI: 10.18632/oncotarget.5019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/20/2015] [Indexed: 01/22/2023] Open
Abstract
KRAS mutations in NSCLC are supposed to indicate a poor prognosis and poor response to anticancer treatments but this feature lacks a mechanistic basis so far. In tumors, KRAS was found to be mutated mostly at codons 12 and 13 and a pool of mutations differing in the base alteration and the amino acid substitution have been described. The different KRAS mutations may differently impact on cancerogenesis and drug sensitivity. On this basis, we hypothesized that a different KRAS mutational status in NSCLC patients determines a different profile in the tumor response to treatments. In this paper, isogenic NSCLC cell clones expressing mutated forms of KRAS were used to determine the response to cisplatin, the main drug used in the clinic against NSCLC. Cells expressing the KRAS(G12C) mutation were found to be less sensitive to treatment both in vitro and in vivo. Systematic analysis of drug uptake, DNA adduct formation and DNA damage responses implicated in cisplatin adducts removal revealed that the KRAS(G12C) mutation might be particular because it stimulates Base Excision Repair to rapidly remove platinum from DNA even before the formation of cross-links. The presented results suggest a different pattern of sensitivity/resistance to cisplatin depending on the KRAS mutational status and these data might provide proof of principle for further investigations on the role of the KRAS status as a predictor of NSCLC response.
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Affiliation(s)
- Elisa Caiola
- Laboratory of Molecular Pharmacology, Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
| | - Daniela Salles
- Department of Obstetrics and Gynecology of the University of Ulm, Ulm, Germany
| | - Roberta Frapolli
- Laboratory of Cancer Pharmacology, Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
| | - Monica Lupi
- Laboratory of Cancer Pharmacology, Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
| | - Giuseppe Rotella
- Department of Environmental Health Sciences, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
| | - Anna Ronchi
- Centro Nazionale Informazione Tossicologiche, Fondazione Salvatore Maugeri I.R.C.C.S., Pavia, Italy
| | - Marina Chiara Garassino
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nikola Mattschas
- Department of Obstetrics and Gynecology of the University of Ulm, Ulm, Germany
| | - Stefano Colavecchio
- Laboratory of Molecular Pharmacology, Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
| | - Massimo Broggini
- Laboratory of Molecular Pharmacology, Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology of the University of Ulm, Ulm, Germany
| | - Mirko Marabese
- Laboratory of Molecular Pharmacology, Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
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20
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Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna CE. Two Scaffolds from Two Flips: (α,β)/(β,γ) CH2/NH "Met-Im" Analogues of dTTP. Org Lett 2015; 17:2586-9. [PMID: 25970636 PMCID: PMC4672865 DOI: 10.1021/acs.orglett.5b00799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel α,β-CH2 and β,γ-NH (1a) or α,β-NH and β,γ-CH2 (1b) "Met-Im" dTTPs were synthesized via monodemethylation of triethyl-dimethyl phosphorimido-bisphosphonate synthons (4a, 4b), formed via a base-induced [1,3]-rearrangement of precursors (3a, 3b) in a reaction with dimethyl or diethyl phosphochloridate. Anomerization during final bromotrimethylsilane (BTMS) deprotection after Mitsunobu conjugation with dT was avoided by microwave conditions. 1a was 9-fold more potent in inhibiting DNA polymerase β, attributed to an NH-group interaction with R183 in the active site.
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Affiliation(s)
- Anastasia P. Kadina
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Keriann Oertell
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Vinod K. Batra
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Myron F. Goodman
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
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21
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DNA polymerases β and λ and their roles in cell. DNA Repair (Amst) 2015; 29:112-26. [DOI: 10.1016/j.dnarep.2015.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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22
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TCRP1 contributes to cisplatin resistance by preventing Pol β degradation in lung cancer cells. Mol Cell Biochem 2014; 398:175-83. [PMID: 25260657 DOI: 10.1007/s11010-014-2217-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
Cisplatin (DDP) is the first-line chemotherapy drug widely used for the treatment of lung cancer patients, whereas the majority of cancer patients will eventually show resistance to DDP. The mechanisms responsible for DDP resistance are not fully understood. Tongue cancer resistance-associated protein 1 (TCRP1) gene was recently cloned and reported to specially mediate DDP resistance in human oral squamous cell carcinoma (OSCC) cells. However, the mechanisms of TCRP1-mediated DDP resistance are far from clear, and whether TCRP1 participates in DDP resistance in lung cancer cells remains unknown. Here, we show that TCRP1 contributes to DDP resistance in lung cancer cells. Knockdown of TCRP1 sensitizes the cells to DDP and increases the DDP-induced DNA damage. We have identified that Pol β is associated with DDP resistance, and Pol β knockdown delays the repair of DDP-induced DNA damage in A549/DDP cells. We find TCRP1 interacts with Pol β in lung cancer cells. Moreover, TCRP1 knockdown decreases the level of Pol β and increases the level of its ubiquitination. These results suggest that TCRP1 contributes to DDP resistance through the prevention of Pol β degradation in lung cancer cells. These findings provide new insights into chemoresistance and may contribute to prevention and reversal of DDP resistance in treatment of lung cancer in the future.
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23
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Koag MC, Lai L, Lee S. Structural basis for the inefficient nucleotide incorporation opposite cisplatin-DNA lesion by human DNA polymerase β. J Biol Chem 2014; 289:31341-8. [PMID: 25237188 DOI: 10.1074/jbc.m114.605451] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Human DNA polymerase β (polβ) has been suggested to play a role in cisplatin resistance, especially in polβ-overexpressing cancer cells. Polβ has been shown to accurately albeit slowly bypass the cisplatin-1,2-d(GpG) (Pt-GG) intramolecular cross-link in vitro. Currently, the structural basis for the inefficient Pt-GG bypass mechanism of polβ is unknown. To gain structural insights into the mechanism, we determined two ternary structures of polβ incorporating dCTP opposite the templating Pt-GG lesion in the presence of the active site Mg(2+) or Mn(2+). The Mg(2+)-bound structure shows that the bulky Pt-GG adduct is accommodated in the polβ active site without any steric hindrance. In addition, both guanines of the Pt-GG lesion form Watson-Crick base pairing with the primer terminus dC and the incoming dCTP, providing the structural basis for the accurate bypass of the Pt-GG adduct by polβ. The Mn(2+)-bound structure shows that polβ adopts a catalytically suboptimal semiclosed conformation during the insertion of dCTP opposite the templating Pt-GG, explaining the inefficient replication across the Pt-GG lesion by polβ. Overall, our studies provide the first structural insights into the mechanism of the potential polβ-mediated cisplatin resistance.
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Affiliation(s)
- Myong-Chul Koag
- From the Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas 78712
| | - Lara Lai
- From the Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas 78712
| | - Seongmin Lee
- From the Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas 78712
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DNA polymerase beta overexpression correlates with poor prognosis in esophageal cancer patients. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-5956-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Zhao W, Wu M, Lai Y, Deng W, Liu Y, Zhang Z. Involvement of DNA polymerase β overexpression in the malignant transformation induced by benzo[a]pyrene. Toxicology 2013; 309:73-80. [PMID: 23652152 DOI: 10.1016/j.tox.2013.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/27/2013] [Accepted: 04/27/2013] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To explore the relationship between DNA polymerase β (pol β) overexpression and benzo[a]pyrene (BaP) carcinogenesis. METHODS Firstly, mouse embryonic fibroblasts that express wild-type level of DNA polymerase β (pol β cell) and high level of pol β (pol β oe cell) were treated by various concentrations of BaP to determine genetic instability induced by BaP under differential expression levels of pol β. Secondly, malignant transformation of pol β cells by low concentration of BaP (20 μM) was determined by soft agar colony formation assay and transformation focus assay. Thirdly, the mRNA and protein levels of BaP-transformed pol β cells (named pol β-T cells) was measured by reverse transcriptase-polymerase chain reaction (RT-PCR) and western blot, and the genetic instability of these cells were examined by HPRT gene mutation assay and random amplified polymorphic DNA (RAPD) assay. RESULTS Pol β cells were successfully transformed into malignant pol β-T cells by an exposure to low concentration of BaP for 6 months. Pol β-T cells exhibited increased levels of pol β gene expression, HPRT gene mutation frequency and polymorphisms of RAPD products that were comparable to those of pol β oe cells. CONCLUSION Pol β overexpression and its-associated genetic instability may play a key role in BaP carcinogenesis.
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Affiliation(s)
- Wei Zhao
- Department of Environmental Health, West China School of Public Health, Sichuan University, Chengdu, Sichuan, People's Republic of China
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26
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Sousa MML, Zub KA, Aas PA, Hanssen-Bauer A, Demirovic A, Sarno A, Tian E, Liabakk NB, Slupphaug G. An inverse switch in DNA base excision and strand break repair contributes to melphalan resistance in multiple myeloma cells. PLoS One 2013; 8:e55493. [PMID: 23405159 PMCID: PMC3566207 DOI: 10.1371/journal.pone.0055493] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/23/2012] [Indexed: 12/02/2022] Open
Abstract
Alterations in checkpoint and DNA repair pathways may provide adaptive mechanisms contributing to acquired drug resistance. Here, we investigated the levels of proteins mediating DNA damage signaling and -repair in RPMI8226 multiple myeloma cells and its Melphalan-resistant derivative 8226-LR5. We observed markedly reduced steady-state levels of DNA glycosylases UNG2, NEIL1 and MPG in the resistant cells and cross-resistance to agents inducing their respective DNA base lesions. Conversely, repair of alkali-labile sites was apparently enhanced in the resistant cells, as substantiated by alkaline comet assay, autoribosylation of PARP-1, and increased sensitivity to PARP-1 inhibition by 4-AN or KU58684. Reduced base-excision and enhanced single-strand break repair would both contribute to the observed reduction in genomic alkali-labile sites, which could jeopardize productive processing of the more cytotoxic Melphalan-induced interstrand DNA crosslinks (ICLs). Furthermore, we found a marked upregulation of proteins in the non-homologous end-joining (NHEJ) pathway of double-strand break (DSB) repair, likely contributing to the observed increase in DSB repair kinetics in the resistant cells. Finally, we observed apparent upregulation of ATR-signaling and downregulation of ATM-signaling in the resistant cells. This was accompanied by markedly increased sensitivity towards Melphalan in the presence of ATR-, DNA-PK, or CHK1/2 inhibitors whereas no sensitizing effect was observed subsequent to ATM inhibition, suggesting that replication blocking lesions are primary triggers of the DNA damage response in the Melphalan resistant cells. In conclusion, Melphalan resistance is apparently contributed by modulation of the DNA damage response at multiple levels, including downregulation of specific repair pathways to avoid repair intermediates that could impair efficient processing of cytotoxic ICLs and ICL-induced DSBs. This study has revealed several novel candidate biomarkers for Melphalan sensitivity that will be included in targeted quantitation studies in larger patient cohorts to validate their value in prognosis as well as targets for replacement- or adjuvant therapies.
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Affiliation(s)
- Mirta M. L. Sousa
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- The Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kamila Anna Zub
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- The KG Jebsen Center for Myeloma Research, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Per Arne Aas
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Audun Hanssen-Bauer
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Aida Demirovic
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antonio Sarno
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Erming Tian
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Laboratory of Myeloma Genetics, Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Nina B. Liabakk
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- The Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- The KG Jebsen Center for Myeloma Research, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- * E-mail:
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Sharma S, Helchowski CM, Canman CE. The roles of DNA polymerase ζ and the Y family DNA polymerases in promoting or preventing genome instability. Mutat Res 2012. [PMID: 23195997 DOI: 10.1016/j.mrfmmm.2012.11.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer cells display numerous abnormal characteristics which are initiated and maintained by elevated mutation rates and genome instability. Chromosomal DNA is continuously surveyed for the presence of damage or blocked replication forks by the DNA Damage Response (DDR) network. The DDR is complex and includes activation of cell cycle checkpoints, DNA repair, gene transcription, and induction of apoptosis. Duplicating a damaged genome is associated with elevated risks to fork collapse and genome instability. Therefore, the DNA damage tolerance (DDT) pathway is also employed to enhance survival and involves the recruitment of translesion DNA synthesis (TLS) polymerases to sites of replication fork blockade or single stranded DNA gaps left after the completion of replication in order to restore DNA to its double stranded form before mitosis. TLS polymerases are specialized for inserting nucleotides opposite DNA adducts, abasic sites, or DNA crosslinks. By definition, the DDT pathway is not involved in the actual repair of damaged DNA, but provides a mechanism to tolerate DNA lesions during replication thereby increasing survival and lessening the chance for genome instability. However this may be associated with increased mutagenesis. In this review, we will describe the specialized functions of Y family polymerases (Rev1, Polη, Polι and Polκ) and DNA polymerase ζ in lesion bypass, mutagenesis, and prevention of genome instability, the latter due to newly appreciated roles in DNA repair. The recently described role of the Fanconi anemia pathway in regulating Rev1 and Polζ-dependent TLS is also discussed in terms of their involvement in TLS, interstrand crosslink repair, and homologous recombination.
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Affiliation(s)
- Shilpy Sharma
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Corey M Helchowski
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Christine E Canman
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States.
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28
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DNA polymerase beta promoter mutations affect gene transcription, translation and the sensitivity of esophageal cancer cells to cisplatin treatment. Mol Biol Rep 2012; 40:1333-9. [PMID: 23117284 DOI: 10.1007/s11033-012-2177-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/08/2012] [Indexed: 01/30/2023]
Abstract
The ability of a promoter to initiate transcription is important for the control of gene expression. Mutations in the DNA polymerase beta (po1β) promoter may affect the transcription of this gene; however, the relationship between these mutations and the upregulation of the expression of po1β remains unclear. Therefore, in the present study, three po1β promoter mutants (M1, -37 C→A; M2, -114 G→A, -37 C→A; M3, -194 T→C) were generated to examine the effect of promoter mutations on polβ gene expression and sensitivity to cisplatin. We found that the M1 and M2 mutant polβ promoter constructs showed higher RLA than the wild-type polβ promoter (P < 0.01), whereas the activity of the M3 polβ promoter did not differ significantly from that of the wild-type polβ promoter (P > 0.05). The expression levels of polβ mRNA and protein were significantly higher (P < 0.01) and the sensitivity to cisplatin was significantly lower (P < 0.05) in Eca9706(-/-)-M1 and Eca9706(-/-)-M2 cells than in Eca9706(-/-)-W. The expression levels of polβ mRNA and protein and the sensitivity to cisplatin were not significantly different between Eca9706(-/-)-M3 and Eca9706(-/-)-W cells (P > 0.05).These results revealed that specific mutations of the polymerase beta gene promoter significantly enhanced the gene's transcriptional activity. These mutations correspondingly increased the gene's mRNA and protein product, at the same time reduced the esophageal cancer cells' sensitivity to cisplatin.
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29
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Fenske AE, Glaesener S, Bokemeyer C, Thomale J, Dahm-Daphi J, Honecker F, Dartsch DC. Cisplatin resistance induced in germ cell tumour cells is due to reduced susceptibility towards cell death but not to altered DNA damage induction or repair. Cancer Lett 2012; 324:171-8. [DOI: 10.1016/j.canlet.2012.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/09/2012] [Accepted: 05/11/2012] [Indexed: 11/26/2022]
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30
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Sun SJ, Feng L, Zhao GQ, Dong ZM. HAX-1 promotes the chemoresistance, invasion, and tumorigenicity of esophageal squamous carcinoma cells. Dig Dis Sci 2012; 57:1838-46. [PMID: 22451114 DOI: 10.1007/s10620-012-2108-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 02/21/2012] [Indexed: 01/07/2023]
Abstract
BACKGROUND HAX-1 is an anti-apoptotic factor and regulates the expression of DNA pol β. Interestingly, DNA polymerase pol β is overexpressed in esophageal squamous cell carcinoma (ESCC). However, the functional role of HAX-1 in ESCC remains unclear. AIMS To investigate the role of HAX-1 in chemoresistance, invasion, and tumorigenicity of ESCC. METHODS Lentivirus-mediated overexpression or knockdown of HAX-1 was employed to establish ESCC EC9706 cell lines that expressed HAX-1 at different levels. The biological behaviors of these engineered cells were characterized in vitro and in vivo using a xenograft nude mice model. In addition, HAX-1 and pol β expression in the tumor tissues was detected by RT-PCR and immunohistochemistry. RESULTS HAX-1 overexpression promoted cell proliferation and resistance against cisplatin, increased cell invasion and suppressed apoptosis along with increased pol β expression. Conversely, HAX-1 knockdown inhibited the malignant phenotypes of EC9706 cells. The xenograft nude mice model demonstrated that HAX-1 overexpression or depletion led to increased or decreased tumor growth in vivo, respectively. Furthermore, a positive correlation of HAX-1 and pol β expression in the tumor tissues was observed. CONCLUSIONS HAX-1 promotes the proliferation, chemoresistance, invasion, and tumorigenicity of ESCC, and this is correlated with increased poly β expression. HAX-1 may represent a potential target to overcome the resistance and metastasis of ESCC.
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Affiliation(s)
- Sa-jia Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
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31
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Barakat KH, Gajewski MM, Tuszynski JA. DNA polymerase beta (pol β) inhibitors: a comprehensive overview. Drug Discov Today 2012; 17:913-20. [PMID: 22561893 DOI: 10.1016/j.drudis.2012.04.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/19/2012] [Accepted: 04/19/2012] [Indexed: 11/25/2022]
Abstract
Base excision repair (BER) is the fundamental pathway responsible for the elimination of damaged DNA bases and repair of DNA single-strand breaks generated spontaneously or produced by DNA-damaging agents. Among the essential enzymes that are required to achieve the BER reaction is DNA polymerase beta (pol β), which has been regarded as a potential therapeutic target. More than 60 pol β-inhibitors have been identified so far; however, most of them are either not potent or not specific enough to become a drug. In this article we compile an essential knowledge base regarding the structures, the modes of inhibition and the activities of these pharmacologically interesting molecules.
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Affiliation(s)
- Khaled H Barakat
- Department of Physics, University of Alberta, Edmonton, AB, Canada.
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32
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Kothandapani A, Dangeti VSMN, Brown AR, Banze LA, Wang XH, Sobol RW, Patrick SM. Novel role of base excision repair in mediating cisplatin cytotoxicity. J Biol Chem 2011; 286:14564-74. [PMID: 21357694 DOI: 10.1074/jbc.m111.225375] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using isogenic mouse embryonic fibroblasts and human cancer cell lines, we show that cells defective in base excision repair (BER) display a cisplatin-specific resistant phenotype. This was accompanied by enhanced repair of cisplatin interstrand cross-links (ICLs) and ICL-induced DNA double strand breaks, but not intrastrand adducts. Cisplatin induces abasic sites with a reduced accumulation in uracil DNA glycosylase (UNG) null cells. We show that cytosines that flank the cisplatin ICLs undergo preferential oxidative deamination in vitro, and AP endonuclease 1 (APE1) can cleave the resulting ICL DNA substrate following removal of the flanking uracil. We also show that DNA polymerase β has low fidelity at the cisplatin ICL site after APE1 incision. Down-regulating ERCC1-XPF in BER-deficient cells restored cisplatin sensitivity. Based on our results, we propose a novel model in which BER plays a positive role in maintaining cisplatin cytotoxicity by competing with the productive cisplatin ICL DNA repair pathways.
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Affiliation(s)
- Anbarasi Kothandapani
- Department of Biochemistry and Cancer Biology, University of Toledo, Health Science Campus, Toledo, Ohio 43614, USA
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33
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Barakat K, Tuszynski J. Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta. J Mol Graph Model 2011; 29:702-16. [DOI: 10.1016/j.jmgm.2010.12.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/02/2010] [Accepted: 12/06/2010] [Indexed: 11/26/2022]
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34
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Kennedy EM, Gavegnano C, Nguyen L, Slater R, Lucas A, Fromentin E, Schinazi RF, Kim B. Ribonucleoside triphosphates as substrate of human immunodeficiency virus type 1 reverse transcriptase in human macrophages. J Biol Chem 2010; 285:39380-91. [PMID: 20924117 PMCID: PMC2998149 DOI: 10.1074/jbc.m110.178582] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Indexed: 01/04/2023] Open
Abstract
We biochemically simulated HIV-1 DNA polymerization in physiological nucleotide pools found in two HIV-1 target cell types: terminally differentiated/non-dividing macrophages and activated/dividing CD4(+) T cells. Quantitative tandem mass spectrometry shows that macrophages harbor 22-320-fold lower dNTP concentrations and a greater disparity between ribonucleoside triphosphate (rNTP) and dNTP concentrations than dividing target cells. A biochemical simulation of HIV-1 reverse transcription revealed that rNTPs are efficiently incorporated into DNA in the macrophage but not in the T cell environment. This implies that HIV-1 incorporates rNTPs during viral replication in macrophages and also predicts that rNTP chain terminators lacking a 3'-OH should inhibit HIV-1 reverse transcription in macrophages. Indeed, 3'-deoxyadenosine inhibits HIV-1 proviral DNA synthesis in human macrophages more efficiently than in CD4(+) T cells. This study reveals that the biochemical landscape of HIV-1 replication in macrophages is unique and that ribonucleoside chain terminators may be a new class of anti-HIV-1 agents specifically targeting viral macrophage infection.
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Affiliation(s)
- Edward M. Kennedy
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Christina Gavegnano
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Laura Nguyen
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Rebecca Slater
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Amanda Lucas
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Emilie Fromentin
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Raymond F. Schinazi
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Baek Kim
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
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35
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Belousova EA, Lavrik OI. DNA polymerases β and λ and their roles in DNA replication and repair. Mol Biol 2010. [DOI: 10.1134/s0026893310060014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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36
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Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE. Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. J Am Chem Soc 2010; 132:7617-25. [PMID: 20465217 PMCID: PMC2891752 DOI: 10.1021/ja909370k] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta,gamma-fluoromethylene analogues of nucleotides are considered to be useful mimics of the natural substrates, but direct structural evidence defining their active site interactions has not been available, including the influence of the new chiral center introduced at the CHF carbon, as in beta,gamma-fluoromethylene-dGTP, which forms an active site complex with DNA polymerase beta, a repair enzyme that plays an important role in base excision repair (BER) and oncogenesis. We report X-ray crystallographic results for a series of beta,gamma-CXY dGTP analogues, where X,Y = H, F, Cl, Br, and/or CH(3). For all three R/S monofluorinated analogues examined (CHF, 3/4; CCH(3)F, 13/14; CClF 15/16), a single CXF-diastereomer (3, 13, 16) is observed in the active site complex, with the CXF fluorine atom at a approximately 3 A (bonding) distance to a guanidinium N of Arg183. In contrast, for the CHCl, CHBr, and CHCH(3) analogues, both diasteromers (6/7, 8/9, 10/11) populate the dGTP site in the enzyme complex about equally. The structures of the bound dichloro (5) and dimethyl (12) analogue complexes indicate little to no steric effect on the placement of the bound nucleotide backbone. The results suggest that introduction of a single fluorine atom at the beta,gamma-bridging carbon atom of these dNTP analogues enables a new, stereospecific interaction within the preorganized active site complex that is unique to fluorine. The results also provide the first diverse structural data set permitting an assessment of how closely this class of dNTP analogues mimics the conformation of the parent nucleotide within the active site complex.
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Affiliation(s)
- Vinod K. Batra
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - William A. Beard
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Boris A. Kashemirov
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Thomas G. Upton
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Myron F. Goodman
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Charles E. McKenna
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
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Wong JHY, Brown JA, Suo Z, Blum P, Nohmi T, Ling H. Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4. EMBO J 2010; 29:2059-69. [PMID: 20512114 DOI: 10.1038/emboj.2010.101] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/27/2010] [Indexed: 01/17/2023] Open
Abstract
Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG DNA. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3'G (first insertion) and 5'G (second insertion) of Pt-GG, and the primer extension beyond the lesion site. We observed a dynamic process, in which the lesion was converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4. The DNA translocation-coupled conformational change may account for additional inhibition on the second insertion reaction. The structures illustrate that Pt-GG disturbs the replicating base pair in the active site, which reduces the catalytic efficiency and fidelity. The in vivo relevance of Dpo4-mediated Pt-GG bypass was addressed by a dpo-4 knockout strain of Sulfolobus solfataricus, which exhibits enhanced sensitivity to cisplatin and proteomic alterations consistent with genomic stress.
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Affiliation(s)
- Jimson H Y Wong
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
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38
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Yang J, Parsons J, Nicolay NH, Caporali S, Harrington CF, Singh R, Finch D, D'Atri S, Farmer PB, Johnston PG, McKenna WG, Dianov G, Sharma RA. Cells deficient in the base excision repair protein, DNA polymerase beta, are hypersensitive to oxaliplatin chemotherapy. Oncogene 2009; 29:463-8. [PMID: 19838217 DOI: 10.1038/onc.2009.327] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A significant proportion of human cancers overexpress DNA polymerase beta (Pol beta), the major DNA polymerase involved in base excision repair. The underlying mechanism and biological consequences of overexpression of this protein are unknown. We examined whether Pol beta, expressed at levels found in tumor cells, is involved in the repair of DNA damage induced by oxaliplatin treatment and whether the expression status of this protein alters the sensitivity of cells to oxaliplatin. DNA damage induced by oxaliplatin treatment of HCT116 and HT29 colon cancer cells was observed to be associated with the stabilization of Pol beta protein on chromatin. In comparison with HCT116 colon cancer cells, isogenic oxaliplatin-resistant (HCT-OR) cells were found to have higher constitutive levels of Pol beta protein, faster in vitro repair of a DNA substrate containing a single nucleotide gap and faster repair of 1,2-GG oxaliplatin adduct levels in cells. In HCT-OR cells, small interfering RNA knockdown of Pol beta delayed the repair of oxaliplatin-induced DNA damage. In a different model system, Pol beta-deficient fibroblasts were less able to repair 1,2-GG oxaliplatin adducts and were hypersensitive to oxaliplatin treatment compared with isogenic Pol beta-expressing cells. Consistent with previous studies, Pol beta-deficient mouse fibroblasts were not hypersensitive to cisplatin treatment. These data provide the first link between oxaliplatin sensitivity and DNA repair involving Pol beta. They demonstrate that Pol beta modulates the sensitivity of cells to oxaliplatin treatment.
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Affiliation(s)
- J Yang
- Cancer Research UK-Medical Research Council Gray Institute for Radiation Oncology & Biology, University of Oxford, Oxford, Oxon OX37DQ, UK
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39
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Iwatsuki M, Mimori K, Yokobori T, Tanaka F, Tahara K, Inoue H, Baba H, Mori M. A platinum agent resistance gene, POLB, is a prognostic indicator in colorectal cancer. J Surg Oncol 2009; 100:261-6. [PMID: 19330779 DOI: 10.1002/jso.21275] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Recent progress in chemotherapy with platinum agents has improved clinical outcome in colorectal cancer (CRC), but there are no useful markers to predict the efficacy of such agents. DNA polymerase beta (POLB) mediates the efficacy of chemotherapy through DNA repair machinery. We analyzed the significance of POLB expression in CRC chemotherapy and its potential as a prognostic indicator. METHODS Using microarray, POLB was found to be overexpressed in CRC cells compared with corresponding normal colon epithelial cells. We determined the susceptibility of POLB-suppressed cells to cisplatin and oxaliplatin. We evaluated POLB mRNA expression in 97 CRC cases to determine the clinicopathologic significance of POLB expression. RESULTS We found the suppression of POLB altered the in vitro susceptibility to cisplatin but not to oxaliplatin. In 97 CRC cases, lymph node metastasis, distant metastasis and TNM classification were significantly greater in the high POLB group than in the low group (P < 0.05). Patients with high POLB expression had significantly poorer prognosis than those with low expression (P < 0.05). CONCLUSIONS The data indicate POLB is overexpressed in CRC cases with high malignant potential. We suggest POLB could be useful as a predictive marker for selection of patients responsive to cisplatin.
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Affiliation(s)
- Masaaki Iwatsuki
- Department of Surgical Oncology, Medical Institute of Bioregulation, Kyushu University, Beppu 874-0838, Japan
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40
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Yoshizawa K, Jelezcova E, Brown AR, Foley JF, Nyska A, Cui X, Hofseth LJ, Maronpot RM, Wilson SH, Sepulveda AR, Sobol RW. Gastrointestinal hyperplasia with altered expression of DNA polymerase beta. PLoS One 2009; 4:e6493. [PMID: 19654874 PMCID: PMC2716528 DOI: 10.1371/journal.pone.0006493] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 07/07/2009] [Indexed: 01/13/2023] Open
Abstract
Background Altered expression of DNA polymerase β (Pol β) has been documented in a large percentage of human tumors. However, tumor prevalence or predisposition resulting from Pol β over-expression has not yet been evaluated in a mouse model. Methodology/Principal Findings We have recently developed a novel transgenic mouse model that over-expresses Pol β. These mice present with an elevated incidence of spontaneous histologic lesions, including cataracts, hyperplasia of Brunner's gland and mucosal hyperplasia in the duodenum. In addition, osteogenic tumors in mice tails, such as osteoma and osteosarcoma were detected. This is the first report of elevated tumor incidence in a mouse model of Pol β over-expression. These findings prompted an evaluation of human gastrointestinal tumors with regard to Pol β expression. We observed elevated expression of Pol β in stomach adenomas and thyroid follicular carcinomas, but reduced Pol β expression in esophageal adenocarcinomas and squamous carcinomas. Conclusions/Significance These data support the hypothesis that balanced and proficient base excision repair protein expression and base excision repair capacity is required for genome stability and protection from hyperplasia and tumor formation.
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Affiliation(s)
- Katsuhiko Yoshizawa
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- Department of Pathology II, Kansai Medical University, Moriguchi, Osaka, Japan
| | - Elena Jelezcova
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine & University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Ashley R. Brown
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine & University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Julie F. Foley
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Abraham Nyska
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Xiangli Cui
- Department of Pharmaceutical and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, United States of America
| | - Lorne J. Hofseth
- Department of Pharmaceutical and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, United States of America
| | - Robert M. Maronpot
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Antonia R. Sepulveda
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert W. Sobol
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine & University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Faumont N, Le Clorennec C, Teira P, Goormachtigh G, Coll J, Canitrot Y, Cazaux C, Hoffmann JS, Brousset P, Delsol G, Feuillard J, Meggetto F. Regulation of DNA polymerase beta by the LMP1 oncoprotein of EBV through the nuclear factor-kappaB pathway. Cancer Res 2009; 69:5177-85. [PMID: 19491276 DOI: 10.1158/0008-5472.can-08-2866] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The repair DNA polymerase beta (Polbeta), when overexpressed, plays a critical role in generating genetic instability via its interference with the genomic replication program. Up-regulation of Polbeta has been reported in many tumor types that exhibit genetic aberrations, including EBV-related B-cell lymphomas. However, the mechanisms responsible for its overexpression have never been examined. Here, we report that both expression and activity of Polbeta, in EBV-immortalized B cells, are induced by several natural genetic variants of LMP1, an oncoprotein associated with the vast majority of EBV-related tumors. Conversely, we found that the expression of Polbeta decreased when LMP1 signaling was down-regulated by a dominant negative of LMP1 or an inhibitor of the nuclear factor-kappaB (NF-kappaB) pathway, the main transduction pathway activated by LMP1, strongly supporting a role of NF-kappaB in the LMP1-mediated Polbeta regulation. Using electrophoretic mobility shift assay experiments from several EBV-immortalized B-cell nuclear extracts, we identified an LMP1-dependent p50/c-Rel heterodimer on a proximal kappaB binding site (-211 to -199nt) of the Polbeta promoter. This result was correlated with a specific Polbeta kappaB transcriptional activity. Taken together, our data enlighten a new mechanism responsible for Polbeta overexpression in EBV-infected cells, mediated by LMP1 and dependent on NF-kappaB activation.
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Affiliation(s)
- Nathalie Faumont
- Institut National de la Sante et de la Recherche Medicale-U563, CPTP
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42
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Aag-initiated base excision repair drives alkylation-induced retinal degeneration in mice. Proc Natl Acad Sci U S A 2009; 106:888-93. [PMID: 19139400 DOI: 10.1073/pnas.0807030106] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Vision loss affects >3 million Americans and many more people worldwide. Although predisposing genes have been identified their link to known environmental factors is unclear. In wild-type animals DNA alkylating agents induce photoreceptor apoptosis and severe retinal degeneration. Alkylation-induced retinal degeneration is totally suppressed in the absence of the DNA repair protein alkyladenine DNA glycosylase (Aag) in both differentiating and postmitotic retinas. Moreover, transgenic expression of Aag activity restores the alkylation sensitivity of photoreceptors in Aag null animals. Aag heterozygotes display an intermediate level of retinal degeneration, demonstrating haploinsufficiency and underscoring that Aag expression confers a dominant retinal degeneration phenotype.
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43
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Kaminski R, Darbinyan A, Merabova N, Deshmane SL, White MK, Khalili K. Protective role of Puralpha to cisplatin. Cancer Biol Ther 2008; 7:1926-35. [PMID: 18927497 DOI: 10.4161/cbt.7.12.6938] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The nucleic acid-binding protein Puralpha is involved at stalled DNA replication forks, in double-strand break (DSB) DNA repair and the cellular response to DNA replication stress. Puralpha also regulates homologous recombination-directed DNA repair (HRR). RESULTS Cells lacking Puralpha showed enhanced sensitivity to cisplatin as evaluated by assays for cell viability and cell clonogenicity. This was seen both in Puralpha-negative MEFs and in human glioblastoma cells treated with siRNA directed against Puralpha. MEFs lacking Puralpha also showed enhanced H2AX phosphorylation in response to cisplatin. Repair of a reporter plasmid that had been treated with cisplatin was decreased in a reactivation assay using Puralpha-negative MEFs and the capacity of nuclear extracts from Puralpha-negative MEFs to perform non-homologous end-joining in vitro was also impaired. METHODS We investigated the effects of the DNA damage-inducing cancer chemotherapeutic agent cisplatin on mouse embryo fibroblasts (MEFs) from PURA(-/-) knockout mice that lack Puralpha. CONCLUSIONS Puralpha has a role in the cellular response to cisplatin-induced DNA damage and may provide new therapeutic modalities for cisplatin-resistant tumors.
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Affiliation(s)
- Rafal Kaminski
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, USA
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44
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Trivedi RN, Wang XH, Jelezcova E, Goellner EM, Tang JB, Sobol RW. Human methyl purine DNA glycosylase and DNA polymerase beta expression collectively predict sensitivity to temozolomide. Mol Pharmacol 2008; 74:505-16. [PMID: 18477668 DOI: 10.1124/mol.108.045112] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Overexpression of N-methylpurine DNA glycosylase (MPG) has been suggested as a possible gene therapy approach to sensitize tumor cells to the cell-killing effects of temozolomide, an imidazotetrazine-class chemotherapeutic alkylating agent. In the present study, we show that both elevated MPG expression and short hairpin RNA-mediated loss of DNA polymerase beta (Pol beta) expression in human breast cancer cells increases cellular sensitivity to temozolomide. Resistance to temozolomide is restored by complementation of either wild-type human Pol beta or human Pol beta with an inactivating mutation specific to the polymerase active site yet functional for 5'-deoxyribose-phosphate (5'dRP) lyase activity. These genetic and cellular studies uniquely demonstrate that overexpression of MPG causes an imbalance in base excision repair (BER), leading to an accumulation of cytotoxic 5'dRP lesions, and that the 5'dRP lyase activity of Pol beta is required to restore resistance to temozolomide. These results imply that Pol beta-dependent 5'dRP lyase activity is the rate-limiting step in BER in these cells and suggests that BER is a tightly balanced pathway for the repair of alkylated bases such as N7-methylguanine and N3-methyladenine. Furthermore, we find that 5'dRP-mediated cell death is independent of caspase-3 activation and does not induce the formation of autophagosomes, as measured by green fluorescent protein-light chain 3 localization. The experiments presented herein suggest that it will be important to investigate whether an active BER pathway could be partially responsible for the temozolomide-mediated resistance seen in some tumors and that balanced BER protein expression and overall BER capacity may help predict sensitivity to temozolomide.
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Affiliation(s)
- Ram N Trivedi
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213-1863, USA
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45
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Hazan C, Boudsocq F, Gervais V, Saurel O, Ciais M, Cazaux C, Czaplicki J, Milon A. Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: towards the design of higher-affinity inhibitors. BMC STRUCTURAL BIOLOGY 2008; 8:22. [PMID: 18416825 PMCID: PMC2375893 DOI: 10.1186/1472-6807-8-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 04/16/2008] [Indexed: 11/17/2022]
Abstract
BACKGROUND DNA polymerase beta (pol beta), the error-prone DNA polymerase of single-stranded DNA break repair as well as base excision repair pathways, is overexpressed in several tumors and takes part in chemotherapeutic agent resistance, like that of cisplatin, through translesion synthesis. For this reason pol beta has become a therapeutic target. Several inhibitors have been identified, but none of them presents a sufficient affinity and specificity to become a drug. The fragment-based inhibitor design allows an important improvement in affinity of small molecules. The initial and critical step for setting up the fragment-based strategy consists in the identification and structural characterization of the first fragment bound to the target. RESULTS We have performed docking studies of pamoic acid, a 9 micromolar pol beta inhibitor, and found that it binds in a single pocket at the surface of the 8 kDa domain of pol beta. However, docking studies provided five possible conformations for pamoic acid in this site. NMR experiments were performed on the complex to select a single conformation among the five retained. Chemical Shift Mapping data confirmed pamoic acid binding site found by docking while NOESY and saturation transfer experiments provided distances between pairs of protons from the pamoic acid and those of the 8 kDa domain that allowed the identification of the correct conformation. CONCLUSION Combining NMR experiments on the complex with docking results allowed us to build a three-dimensional structural model. This model serves as the starting point for further structural studies aimed at improving the affinity of pamoic acid for binding to DNA polymerase beta.
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Affiliation(s)
- Corinne Hazan
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
| | - François Boudsocq
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
| | - Virginie Gervais
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
| | - Olivier Saurel
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
| | - Marion Ciais
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
| | - Christophe Cazaux
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
| | - Jerzy Czaplicki
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
| | - Alain Milon
- University of Toulouse, UPS; IPBS (Institute of Pharmacology and Structural Biology), 205 route de Narbonne, 31077 Toulouse, France
- CNRS, IPBS, UMR5089, Toulouse, France
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46
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CHIP-Mediated Degradation and DNA Damage-Dependent Stabilization Regulate Base Excision Repair Proteins. Mol Cell 2008; 29:477-87. [DOI: 10.1016/j.molcel.2007.12.027] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 08/24/2007] [Accepted: 12/03/2007] [Indexed: 11/24/2022]
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47
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McKenna CE, Kashemirov BA, Upton TG, Batra VK, Goodman MF, Pedersen LC, Beard WA, Wilson SH. (R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. J Am Chem Soc 2007; 129:15412-3. [PMID: 18031037 PMCID: PMC2677377 DOI: 10.1021/ja072127v] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
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48
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Sarnowska E, Grzybowska EA, Sobczak K, Konopiński R, Wilczyńska A, Szwarc M, Sarnowski TJ, Krzyżosiak WJ, Siedlecki JA. Hairpin structure within the 3'UTR of DNA polymerase beta mRNA acts as a post-transcriptional regulatory element and interacts with Hax-1. Nucleic Acids Res 2007; 35:5499-510. [PMID: 17704138 PMCID: PMC2018635 DOI: 10.1093/nar/gkm502] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aberrant expression of DNA polymerase beta, a key enzyme involved in base excision repair, leads to genetic instability and carcinogenesis. Pol beta expression has been previously shown to be regulated at the level of transcription, but there is also evidence of post-transcriptional regulation, since rat transcripts undergo alternative polyadenylation, and the resulting 3'UTR contain at least one regulatory element. Data presented here indicate that RNA of the short 3'UTR folds to form a strong secondary structure (hairpin). Its regulatory role was established utilizing a luciferase-based reporter system. Further studies led to the identification of a protein factor, which binds to this element-the anti-apoptotic, cytoskeleton-related protein Hax-1. The results of in vitro binding analysis indicate that the formation of the RNA-protein complex is significantly impaired by disruption of the hairpin motif. We demonstrate that Hax-1 binds to Pol beta mRNA exclusively in the form of a dimer. Biochemical analysis revealed the presence of Hax-1 in mitochondria, but also in the nuclear matrix, which, along with its transcript-binding properties, suggests that Hax-1 plays a role in post-transcriptional regulation of expression of Pol beta.
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Affiliation(s)
- Elżbieta Sarnowska
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Ewa A. Grzybowska
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
- *To whom correspondence should be addressed. +48 22 546 23 68+48 22 644 02 09
| | - Krzysztof Sobczak
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Ryszard Konopiński
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Anna Wilczyńska
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Maria Szwarc
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Tomasz J. Sarnowski
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Włodzimierz J. Krzyżosiak
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Janusz A. Siedlecki
- Cancer Center Institute, Roentgena 5, 02-781 Warsaw, Institute of Bioorganic Chemistry, PAS, Noskowskiego 12/14, 61-704, Poznań and Institute of Biochemistry and Biophysics, PAS, Pawińskiego 5A, 02-106, Warsaw, Poland
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49
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Stewart DJ. Mechanisms of resistance to cisplatin and carboplatin. Crit Rev Oncol Hematol 2007; 63:12-31. [PMID: 17336087 DOI: 10.1016/j.critrevonc.2007.02.001] [Citation(s) in RCA: 455] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 01/25/2007] [Accepted: 02/02/2007] [Indexed: 02/08/2023] Open
Abstract
While cisplatin and carboplatin are active versus most common cancers, epithelial malignancies are incurable when metastatic. Even if an initial response occurs, acquired resistance due to mutations and epigenetic events limits efficacy. Resistance may be due to excess of a resistance factor, to saturation of factors required for tumor cell killing, or to mutation or alteration of a factor required for tumor cell killing. Platinum resistance could arise from decreased tumor blood flow, extracellular conditions, reduced platinum uptake, increased efflux, intracellular detoxification by glutathione, etc., decreased binding (e.g., due to high intracellular pH), DNA repair, decreased mismatch repair, defective apoptosis, antiapoptotic factors, effects of several signaling pathways, or presence of quiescent non-cycling cells. In lung cancer, flattening of dose-response curves at higher doses suggests that efficacy is limited by exhaustion of something required for cell killing, and several clinical observations suggest epigenetic events may play a major role in resistance.
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Affiliation(s)
- David J Stewart
- Section of Experimental Therapeutics, Department of Thoracic/Head & Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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50
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Sharma RA, Dianov GL. Targeting base excision repair to improve cancer therapies. Mol Aspects Med 2007; 28:345-74. [PMID: 17706275 DOI: 10.1016/j.mam.2007.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 05/30/2007] [Accepted: 06/05/2007] [Indexed: 01/05/2023]
Abstract
Most commonly used cancer therapies, particularly ionizing radiation and certain classes of cytotoxic chemotherapies, cause cell death by damaging DNA. Base excision repair (BER) is the major system responsible for the removal of corrupt DNA bases and repair of DNA single strand breaks generated spontaneously and induced by exogenous DNA damaging factors such as certain cancer therapies. In this review, the physico-chemical properties of the proteins involved in BER are discussed with particular emphasis on molecular mechanisms coordinating repair processes. The aim of this review is to apply extensive knowledge that currently exists regarding the biochemical mechanisms involved in human BER to the molecular biology of current therapies for cancer. It is anticipated that the application of this knowledge will translate into the development of novel effective therapies for improving existing treatments such as radiation therapy and oxaliplatin chemotherapy.
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Affiliation(s)
- Ricky A Sharma
- Radiation Oncology & Biology, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
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