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Zhuo Z, Lin A, Zhang J, Chen H, Li Y, Yang Z, Li L, Li S, Cheng J, He J. Genetic variations in base excision repair pathway genes and risk of hepatoblastoma: a seven-center case-control study. Am J Cancer Res 2021; 11:849-857. [PMID: 33791158 DOI: pmid/33791158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatoblastoma is a rare childhood liver cancer without known explicit etiology. Base excision repair (BER) pathway genes have been implicated in the pathophysiology of cancer, yet the role of BER pathway gene single nucleotide polymorphisms (SNPs) on hepatoblastoma risk still awaits to be explored. This study aims to determine whether hepatoblastoma risk be modulated by polymorphisms in the BER pathway genes based on genotyped data from 313 cases and 1446 controls. We applied TaqMan assay to genotype these included samples. We comprehensively genotyped 20 SNPs across six genes of BER, and estimated odds ratio (ORs), 95% confidence intervals (CIs), and P-values of the selected SNPs' contribution to the risk of hepatoblastoma using logistic regression models. Only SNP rs293795 in the hOGG1 gene could significantly enhance hepatoblastoma risk under recessive model (adjusted OR=3.78, 95% CI=1.01-14.17, P=0.047). Stratified analysis revealed that rs159153 TC/CC genotype decreased hepatoblastoma risk in male subgroup. Moreover, rs293795 GG and 1-3 risk genotypes could increase hepatoblastoma risk in clinical stages I+II and male subgroups, respectively. False-positive report probability validated the reliability of the significant results. Our findings provide some clues of a potential risk effect of BER pathway gene hOGG1 SNPs on hepatoblastoma. Further investigation is warranted to confirm these findings and to better elucidate the biological pathways involved.
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Affiliation(s)
- Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University Guangzhou 510623, Guangdong, China
| | - Ao Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University Guangzhou 510623, Guangdong, China
| | - Jiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University Zhengzhou 450052, Henan, China
| | - Huitong Chen
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University Guangzhou 510623, Guangdong, China
| | - Yong Li
- Department of Pediatric Surgery, Hunan Children's Hospital Changsha 410004, Hunan, China
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University Shenyang 110004, Liaoning, China
| | - Li Li
- Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Institute of Pediatrics Research, Yunnan Medical Center for Pediatric Diseases, Kunming Children's Hospital Kunming 650228, Yunnan, China
| | - Suhong Li
- Department of Pathology, Children Hospital and Women Health Center of Shanxi Taiyuan 030013, Shanxi, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an 710004, Shaanxi, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University Guangzhou 510623, Guangdong, China
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Petri net-based model of the human DNA base excision repair pathway. PLoS One 2019; 14:e0217913. [PMID: 31518347 PMCID: PMC6743755 DOI: 10.1371/journal.pone.0217913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/21/2019] [Indexed: 12/14/2022] Open
Abstract
Cellular DNA is daily exposed to several damaging agents causing a plethora of DNA lesions. As a first aid to restore DNA integrity, several enzymes got specialized in damage recognition and lesion removal during the process called base excision repair (BER). A large number of DNA damage types and several different readers of nucleic acids lesions during BER pathway as well as two sub-pathways were considered in the definition of a model using the Petri net framework. The intuitive graphical representation in combination with precise mathematical analysis methods are the strong advantages of the Petri net-based representation of biological processes and make Petri nets a promising approach for modeling and analysis of human BER. The reported results provide new information that will aid efforts to characterize in silico knockouts as well as help to predict the sensitivity of the cell with inactivated repair proteins to different types of DNA damage. The results can also help in identifying the by-passing pathways that may lead to lack of pronounced phenotypes associated with mutations in some of the proteins. This knowledge is very useful when DNA damage-inducing drugs are introduced for cancer therapy, and lack of DNA repair is desirable for tumor cell death.
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Mouzakis KD, Wu T, Haushalter KA. Thermostability and excision activity of polymorphic forms of hOGG1. BMC Res Notes 2019; 12:92. [PMID: 30777129 PMCID: PMC6379936 DOI: 10.1186/s13104-019-4111-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 01/31/2019] [Indexed: 11/11/2022] Open
Abstract
Objectives Reactive oxygen species (ROS) oxidize guanine residues in DNA to form 7,8-dihydro-oxo-2′-deoxyguanosine (8oxoG) lesions in the genome. Human 8-oxoguanine glycosylase-1 (hOGG1) recognizes and excises this highly mutagenic species when it is base-paired opposite a cytosine. We sought to characterize biochemically several hOGG1 variants that have been found in cancer tissues and cell lines, reasoning that if these variants have reduced repair capabilities, they could lead to an increased chance of mutagenesis and carcinogenesis. Results We have over-expressed and purified the R46Q, A85S, R154H, and S232T hOGG1 variants and have investigated their repair efficiency and thermostability. The hOGG1 variants showed only minor perturbations in the kinetics of 8oxoG excision relative to wild-type hOGG1. Thermal denaturation monitored by circular dichroism revealed that R46Q hOGG1 had a significantly lower Tm (36.6 °C) compared to the other hOGG1 variants (40.9 °C to 43.2 °C). Prolonged pre-incubation at 37 °C prior to the glycosylase assay dramatically reduces the excision activity of R46Q hOGG1, has a modest effect on wild-type hOGG1, and a negligible effect on A85S, R154H, and S232T hOGG1. The observed thermolability of hOGG1 variants was mostly alleviated by co-incubation with stoichiometric amounts of competitor DNA. Electronic supplementary material The online version of this article (10.1186/s13104-019-4111-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathryn D Mouzakis
- Department of Chemistry and Biochemistry, Loyola Marymount University, 1 LMU Drive, LSB #284, Los Angeles, CA, 90045, USA
| | - Tiffany Wu
- Vascular & Interventional Specialists of Orange County, 1140 W. La Veta Avenue, Suite 850, Orange, CA, 92868, USA
| | - Karl A Haushalter
- Departments of Chemistry and Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, CA, 91711-5990, USA.
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Zhu J, Jia W, Wu C, Fu W, Xia H, Liu G, He J. Base Excision Repair Gene Polymorphisms and Wilms Tumor Susceptibility. EBioMedicine 2018; 33:88-93. [PMID: 29937070 PMCID: PMC6085508 DOI: 10.1016/j.ebiom.2018.06.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 02/07/2023] Open
Abstract
Base excision repair (BER) is the main mechanism to repair endogenous DNA lesions caused by reactive oxygen species. BER deficiency is linked with cancer susceptibility and premature aging. Single nucleotide polymorphisms (SNPs) within BER genes have been implicated in various human malignancies. Nevertheless, a comprehensive investigation of their association with Wilms tumor susceptibility is lacking. In this study, 145 cases and 531 sex and age-matched healthy controls were recruited. We systematically genotyped 18 potentially functional SNPs in six core BER pathway genes, using a candidate SNP approach. Logistic regression was employed to evaluate odds ratio (OR) and 95% confidence interval (CI) adjusted for age and gender. Several SNPs showed protective effects against Wilms tumor. Significant associations with Wilms tumor susceptibility were shown for hOGG1 rs1052133 (dominant: adjusted OR = 0.66, 95% CI = 0.45-0.96, P = .030), FEN1 rs174538 (dominant: adjusted OR = 0.66, 95% CI = 0.45-0.95, P = .027; recessive: adjusted OR = 0.54, 95% CI = 0.32-0.93 P = .027), and FEN1 rs4246215 (dominant: adjusted OR = 0.55, 95% CI = 0.38-0.80, P = .002) polymorphisms. Stratified analysis was performed by age, gender, and clinical stage. Moreover, there was evidence of functional implication of these significant SNPs suggested by online expression quantitative trait locus (eQTL) analysis. Our findings indicate that common SNPs in BER genes modify susceptibility to Wilms tumor.
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Affiliation(s)
- Jinhong Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China; Department of Clinical Laboratory, Molecular Epidemiology Laboratory, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Wei Jia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Caixia Wu
- Department of Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Wen Fu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Guochang Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China.
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China.
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Fomina EE, Pestryakov PE, Kretov DA, Zharkov DO, Ovchinnikov LP, Curmi PA, Lavrik OI. Inhibition of abasic site cleavage in bubble DNA by multifunctional protein YB-1. J Mol Recognit 2015; 28:117-23. [DOI: 10.1002/jmr.2435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/11/2014] [Accepted: 09/13/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Elizaveta E. Fomina
- Institute of Chemical Biology and Fundamental Medicine; Siberian Branch of Russian Academy of Sciences; Novosibirsk 630090 Russia
| | - Pavel E. Pestryakov
- Institute of Chemical Biology and Fundamental Medicine; Siberian Branch of Russian Academy of Sciences; Novosibirsk 630090 Russia
| | - Dmitry A. Kretov
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR829; Université Evry-Val d'Essonne; Evry France
- Institute of Protein Research; Russian Academy of Sciences; Pushchino Moscow region 142290 Russia
| | - Dmitry O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine; Siberian Branch of Russian Academy of Sciences; Novosibirsk 630090 Russia
- Novosibirsk State University; Novosibirsk 630090 Russia
| | - Lev P. Ovchinnikov
- Institute of Protein Research; Russian Academy of Sciences; Pushchino Moscow region 142290 Russia
| | - Patrick A. Curmi
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR829; Université Evry-Val d'Essonne; Evry France
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine; Siberian Branch of Russian Academy of Sciences; Novosibirsk 630090 Russia
- Novosibirsk State University; Novosibirsk 630090 Russia
- Altai State University; Barnaul 656049 Russia
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Rahmanian S, Taleei R, Nikjoo H. Radiation induced base excision repair (BER): a mechanistic mathematical approach. DNA Repair (Amst) 2014; 22:89-103. [PMID: 25117268 DOI: 10.1016/j.dnarep.2014.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 01/24/2023]
Abstract
This paper presents a mechanistic model of base excision repair (BER) pathway for the repair of single-stand breaks (SSBs) and oxidized base lesions produced by ionizing radiation (IR). The model is based on law of mass action kinetics to translate the biochemical processes involved, step-by-step, in the BER pathway to translate into mathematical equations. The BER is divided into two subpathways, short-patch repair (SPR) and long-patch repair (LPR). SPR involves in replacement of single nucleotide via Pol β and ligation of the ends via XRCC1 and Ligase III, while LPR involves in replacement of multiple nucleotides via PCNA, Pol δ/ɛ and FEN 1, and ligation via Ligase I. A hallmark of IR is the production of closely spaced lesions within a turn of DNA helix (named complex lesions), which have been attributed to a slower repair process. The model presented considers fast and slow component of BER kinetics by assigning SPR for simple lesions and LPR for complex lesions. In the absence of in vivo reaction rate constants for the BER proteins, we have deduced a set of rate constants based on different published experimental measurements including accumulation kinetics obtained from UVA irradiation, overall SSB repair kinetic experiments, and overall BER kinetics from live-cell imaging experiments. The model was further used to calculate the repair kinetics of complex base lesions via the LPR subpathway and compared to foci kinetic experiments for cells irradiated with γ rays, Si, and Fe ions. The model calculation show good agreement with experimental measurements for both overall repair and repair of complex lesions. Furthermore, using the model we explored different mechanisms responsible for inhibition of repair when higher LET and HZE particles are used and concluded that increasing the damage complexity can inhibit initiation of LPR after the AP site removal step in BER.
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Affiliation(s)
- Shirin Rahmanian
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260 P9-02, Stockholm 17176, Sweden
| | - Reza Taleei
- Radiation Physics, MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 94, Houston, TX 77030-4409, USA
| | - Hooshang Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260 P9-02, Stockholm 17176, Sweden.
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Xu X, Wang Y, Guo W, Zhou Y, Lv C, Chen X, Liu K. The significance of the alteration of 8-OHdG in serous ovarian carcinoma. J Ovarian Res 2013; 6:74. [PMID: 24165045 PMCID: PMC3875897 DOI: 10.1186/1757-2215-6-74] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 10/23/2013] [Indexed: 01/11/2023] Open
Abstract
Background Oxidative damage and DNA repair dysfunction are associated with carcinogenesis. 8-OHdG is one of the major oxidative DNA adducts. Present work aims to investigate whether the expression of 8-OHdG and its key repair gene hOGG1 play distinctive role in two types of serous ovarian cancer. Materials and methods 8-OHdG level in DNA from tumor and matched tumor-adjacent normal tissue in 48 high-grade papillary serous carcinomas (HG-SOC), 24 low-grade papillary serous carcinomas (LG-SOC), 20 serous cystadenomas, and 16 non-tumor control ovaries was tested. The Cox proportional hazards model and the log-rank test were used to assess the associations between the 8-OHdG level in two types of serous cancer and patients’ survival. Real-time polymerase chain reaction and protein immunoblot were employed to detect hOGG1 mRNA and protein levels in tumor and adjacent normal tissues. Immunohistochemistry was used to determine the expression of hOGG1 and p53. Results There was no difference of average 8-OHdG/106dG DNA level either between HG-SOC (27.8 ± 8.9), LG-SOC (25.2 ± 7.4) and benign serous cystadenoma (26.5 ± 7.7, p = 0.35); or between the tumor-adjacent normal tissue of HG-SOC (18.8 ± 5.2), LG-SOC (21.4 ± 6.5), benign serous cystadenoma (20.5 ± 9.1) and non-tumor ovary (21.6 ± 4.9, p = 0.62). The 8-OHdG/106dG level was significantly higher in tumor comparing to that in matched normal tissue adjacent to carcinoma in HG-SOC (1.52 ± 0.52, p = 0.02), but not in LG-SOC or benign serous cystadenoma. Increased level of 8-OHdG in tumor DNA was an independent factor of overall survival in serous ovarian carcinoma upon multivariate analysis (p < 0.01). Increased level of 8-OHdG in tumor DNA indicates poorer overall and progression-free survival durations than counterparts (47.3 vs 105.7 months and 13.5 vs 45.3 months, respectively). Protein levels of hOGG1 were remarkably decreased in HG-SOC (p < 0.01), but not in LG-SOC and serous cystadenoma compared with the tissue adjacent to carcinoma. A positive result on p53 immunostaining was associated with lower hOGG1 expression in HG-SOC (p = 0.04). Conclusion Increased 8-OHdG level and decreased expression of hOGG1 in tumor were found in HG-SOC but not LG-SOC. Increased 8-OHdG level in tumor DNA was significantly associated with poorer overall survival and progression-free survival in serous ovarian carcinoma.
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Affiliation(s)
| | | | | | | | | | - Xiaoxiang Chen
- Department of Gynecologic oncology, Jiangsu Institute of Cancer Research, Nanjing, China.
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Gurkan-Cavusoglu E, Avadhani S, Liu L, Kinsella TJ, Loparo KA. Developing an in silico model of the modulation of base excision repair using methoxyamine for more targeted cancer therapeutics. IET Syst Biol 2013; 7:27-37. [PMID: 23847811 DOI: 10.1049/iet-syb.2011.0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Base excision repair (BER) is a major DNA repair pathway involved in the processing of exogenous non-bulky base damages from certain classes of cancer chemotherapy drugs as well as ionising radiation (IR). Methoxyamine (MX) is a small molecule chemical inhibitor of BER that is shown to enhance chemotherapy and/or IR cytotoxicity in human cancers. In this study, the authors have analysed the inhibitory effect of MX on the BER pathway kinetics using a computational model of the repair pathway. The inhibitory effect of MX depends on the BER efficiency. The authors have generated variable efficiency groups using different sets of protein concentrations generated by Latin hypercube sampling, and they have clustered simulation results into high, medium and low efficiency repair groups. From analysis of the inhibitory effect of MX on each of the three groups, it is found that the inhibition is most effective for high efficiency BER, and least effective for low efficiency repair.
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Affiliation(s)
- Evren Gurkan-Cavusoglu
- Department of Electrical Engineering and Computer Science, School of Engineering, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106-7071, USA.
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9
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Taleei R, Nikjoo H. The Non-homologous End-Joining (NHEJ) Pathway for the Repair of DNA Double-Strand Breaks: I. A Mathematical Model. Radiat Res 2013; 179:530-9. [DOI: 10.1667/rr3123.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Stamatelos SK, Androulakis IP, Kong ANT, Georgopoulos PG. A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes. J Theor Biol 2013; 317:244-56. [PMID: 23069314 PMCID: PMC4026948 DOI: 10.1016/j.jtbi.2012.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 07/26/2012] [Accepted: 09/18/2012] [Indexed: 01/09/2023]
Abstract
BACKGROUND A systems engineering approach is presented for describing the kinetics and dynamics that are elicited upon arsenic exposure of human hepatocytes. The mathematical model proposed here tracks the cellular reaction network of inorganic and organic arsenic compounds present in the hepatocyte and analyzes the production of toxicologically potent by-products and the signaling they induce in hepatocytes. METHODS AND RESULTS The present modeling effort integrates for the first time a cellular-level semi-mechanistic toxicokinetic (TK) model of arsenic in human hepatocytes with a cellular-level toxicodynamic (TD) model describing the arsenic-induced reactive oxygen species (ROS) burst, the antioxidant response, and the oxidative DNA damage repair process. The antioxidant response mechanism is described based on the Keap1-independent Nuclear Factor-erythroid 2-related factor 2 (Nrf2) signaling cascade and accounts for the upregulation of detoxifying enzymes. The ROS-induced DNA damage is simulated by coupling the TK/TD formulation with a model describing the multistep pathway of oxidative DNA repair. The predictions of the model are assessed against experimental data of arsenite-induced genotoxic damage to human hepatocytes; thereby capturing in silico the mode of the experimental dose-response curve. CONCLUSIONS The integrated cellular-level TK/TD model presented here provides significant insight into the underlying regulatory mechanism of Nrf2-regulated antioxidant response due to arsenic exposure. While computational simulations are in a fair good agreement with relevant experimental data, further analysis of the system unravels the role of a dynamic interplay among the feedback loops of the system in controlling the ROS upregulation and DNA damage response. This TK/TD framework that uses arsenic as an example can be further extended to other toxic or pharmaceutical agents.
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Affiliation(s)
- Spyros K. Stamatelos
- Environmental and Occupational Health Sciences Institute (EOHSI) A Joint Institute of UMDNJ-Robert Wood Johnson Medical School and Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, United States
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, 720 Rutland Avenue, Baltimore, MD 21205, United States
| | - Ioannis P. Androulakis
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, United States
| | - Ah-Ng Tony Kong
- Department of Pharmaceutics, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, United States
| | - Panos G. Georgopoulos
- Environmental and Occupational Health Sciences Institute (EOHSI) A Joint Institute of UMDNJ-Robert Wood Johnson Medical School and Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, United States
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Greinert R, Volkmer B, Henning S, Breitbart EW, Greulich KO, Cardoso MC, Rapp A. UVA-induced DNA double-strand breaks result from the repair of clustered oxidative DNA damages. Nucleic Acids Res 2012; 40:10263-73. [PMID: 22941639 PMCID: PMC3488256 DOI: 10.1093/nar/gks824] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UVA (320-400 nm) represents the main spectral component of solar UV radiation, induces pre-mutagenic DNA lesions and is classified as Class I carcinogen. Recently, discussion arose whether UVA induces DNA double-strand breaks (dsbs). Only few reports link the induction of dsbs to UVA exposure and the underlying mechanisms are poorly understood. Using the Comet-assay and γH2AX as markers for dsb formation, we demonstrate the dose-dependent dsb induction by UVA in G(1)-synchronized human keratinocytes (HaCaT) and primary human skin fibroblasts. The number of γH2AX foci increases when a UVA dose is applied in fractions (split dose), with a 2-h recovery period between fractions. The presence of the anti-oxidant Naringin reduces dsb formation significantly. Using an FPG-modified Comet-assay as well as warm and cold repair incubation, we show that dsbs arise partially during repair of bi-stranded, oxidative, clustered DNA lesions. We also demonstrate that on stretched chromatin fibres, 8-oxo-G and abasic sites occur in clusters. This suggests a replication-independent formation of UVA-induced dsbs through clustered single-strand breaks via locally generated reactive oxygen species. Since UVA is the main component of solar UV exposure and is used for artificial UV exposure, our results shine new light on the aetiology of skin cancer.
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Affiliation(s)
- R Greinert
- Dermatology Center Buxtehude (DZB), Buxtehude, Germany
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12
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Taleei R, Nikjoo H. Repair of the double-strand breaks induced by low energy electrons: A modelling approach. Int J Radiat Biol 2012; 88:948-53. [DOI: 10.3109/09553002.2012.695098] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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13
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Taleei R, Weinfeld M, Nikjoo H. Single strand annealing mathematical model for double strand break repair. ACTA ACUST UNITED AC 2012. [DOI: 10.7243/2050-1412-1-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Wilson DM, Kim D, Berquist BR, Sigurdson AJ. Variation in base excision repair capacity. Mutat Res 2010; 711:100-12. [PMID: 21167187 DOI: 10.1016/j.mrfmmm.2010.12.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/29/2010] [Accepted: 12/07/2010] [Indexed: 01/20/2023]
Abstract
The major DNA repair pathway for coping with spontaneous forms of DNA damage, such as natural hydrolytic products or oxidative lesions, is base excision repair (BER). In particular, BER processes mutagenic and cytotoxic DNA lesions such as non-bulky base modifications, abasic sites, and a range of chemically distinct single-strand breaks. Defects in BER have been linked to cancer predisposition, neurodegenerative disorders, and immunodeficiency. Recent data indicate a large degree of sequence variability in DNA repair genes and several studies have associated BER gene polymorphisms with disease risk, including cancer of several sites. The intent of this review is to describe the range of BER capacity among individuals and the functional consequences of BER genetic variants. We also discuss studies that associate BER deficiency with disease risk and the current state of BER capacity measurement assays.
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Affiliation(s)
- David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States.
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15
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Crooke PS, Parl FF. A mathematical model for DNA damage and repair. J Nucleic Acids 2010; 2010. [PMID: 20725623 PMCID: PMC2915813 DOI: 10.4061/2010/352603] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 05/27/2010] [Indexed: 11/20/2022] Open
Abstract
In cells, DNA repair has to keep up with DNA damage to maintain the integrity of the genome and prevent mutagenesis and carcinogenesis. While the importance of both DNA damage and repair is clear, the impact of imbalances between both processes has not been studied. In this paper, we created a combined mathematical model for the formation of DNA adducts from oxidative estrogen metabolism followed by base excision repair (BER) of these adducts. The model encompasses a set of differential equations representing the sequence of enzymatic reactions in both damage and repair pathways. By combining both pathways, we can simulate the overall process by starting from a given time-dependent concentration of 17beta-estradiol (E(2)) and 2'-deoxyguanosine, determine the extent of adduct formation and the correction by BER required to preserve the integrity of DNA. The model allows us to examine the effect of phenotypic and genotypic factors such as different concentrations of estrogen and variant enzyme haplotypes on the formation and repair of DNA adducts.
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Affiliation(s)
- Philip S Crooke
- Department of Mathematics, Vanderbilt University, Nashville, TN 37240, USA
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Kinsella TJ. Coordination of DNA mismatch repair and base excision repair processing of chemotherapy and radiation damage for targeting resistant cancers. Clin Cancer Res 2009; 15:1853-9. [PMID: 19240165 DOI: 10.1158/1078-0432.ccr-08-1307] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA damage processing by mismatch repair (MMR) and/or base excision repair (BER) can determine the therapeutic index following treatment of human cancers using radiation therapy and several classes of chemotherapy drugs. Over the last decade, basic and translational cancer research in DNA repair has led to an increased understanding of how these two DNA repair pathways can modify cytotoxicity to chemotherapy and/or ionizing radiation treatments in both normal and malignant tissues. This Molecular Pathways article provides an overview of the current understanding of mechanisms involved in MMR and BER damage processing, including insights into possible coordination of these two DNA repair pathways after chemotherapy and/or ionizing radiation damage. It also introduces principles of systems biology that have been applied to better understand the complexities and coordination of MMR and BER in processing these DNA damages. Finally, it highlights novel therapeutic approaches to target resistant (or DNA damage tolerant) human cancers using chemical and molecular modifiers of chemotherapy and/or ionizing radiation including poly (ADP-ribose) polymerase inhibitors, methoxyamine and iododeoxyuridine (and the prodrug, 5-iodo-2-pyrimidinone-2'-deoxyribose).
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Affiliation(s)
- Timothy J Kinsella
- Case Integrative Cancer Biology Program, Case Western Reserve University, Cleveland, OH, USA.
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17
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Argüelles S, Gómez A, Machado A, Ayala A. A preliminary analysis of within-subject variation in human serum oxidative stress parameters as a function of time. Rejuvenation Res 2008; 10:621-36. [PMID: 18047415 DOI: 10.1089/rej.2006.0528] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of this study was to determine variability at both levels of two serum oxidative stress markers (lipid peroxides and carbonyl concentration) as well as total antioxidant capacity in humans as a function of time. Assays for oxidative stress and antioxidant capacity were repeated in the same individuals three times daily on four particular days over a period of 51 days. The results show a high variation within subject in the concentration of these markers not only when comparing the different days (the morning values can change up to 98%), but also during the day, where the evening values can increase up to 84% with respect to those of the morning. This suggests that several measurements are required to establish the typical oxidative stress status of an individual before studying the potential effect of treatments that possibly influence oxidative damage. The observed changes during the day allowed us to speculate about the optimum temporal antioxidant delivery regimes that minimize the imbalance between oxidants and antioxidants. In the study, only a few general aspects of basic lifestyle habits were controlled. However, the levels of these markers are sensitive to possibly a group of factors. This points to the necessity of using a much bigger population to establish the possible contribution of each lifestyle habits to the concentration of the markers.
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Affiliation(s)
- Sandro Argüelles
- Departamento Bioquímica, Facultad de Farmacia, Universidad de Sevilla, C/Tramontana s/n, Seville, Spain
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18
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Abstract
The DNA in all cells of the human body is subject to damage continuously from exogenous agents, internal cellular processes and spontaneous decomposition. Failure to repair such damage is fundamental to the development of many diseases and to ageing. Fortunately, the vast majority of DNA damage is detected and repaired by one of five complementary DNA repair systems. However, recent studies have shown that even in healthy individuals there is a wide inter-individual variation in DNA repair capacity. Part of this variation can be accounted for by polymorphisms in the genes encoding DNA repair proteins. However, it is probable that environmental factors, including dietary exposure as well as diet-gene interactions, are also responsible for much of the difference in repair capacity between individuals. Whilst there is some evidence from human studies that generalised malnutrition or low intakes of specific nutrients may affect DNA repair, as yet there is limited understanding of the molecular mechanisms through which nutrients can modulate this key cellular process.
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Affiliation(s)
- J Tyson
- Human Nutrition Research Centre, School of Clinical Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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19
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Subba Rao K. Mechanisms of Disease: DNA repair defects and neurological disease. ACTA ACUST UNITED AC 2007; 3:162-72. [PMID: 17342192 DOI: 10.1038/ncpneuro0448] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Accepted: 01/19/2007] [Indexed: 12/20/2022]
Abstract
In this Review, familial and sporadic neurological disorders reported to have an etiological link with DNA repair defects are discussed, with special emphasis placed on the molecular link between the disease phenotype and the precise DNA repair defect. Of the 15 neurological disorders listed, some of which have symptoms of progeria, six--spinocerebellar ataxia with axonal neuropathy-1, Huntington's disease, Alzheimer's disease, Parkinson's disease, Down syndrome and amyotrophic lateral sclerosis--seem to result from increased oxidative stress, and the inability of the base excision repair pathway to handle the damage to DNA that this induces. Five of the conditions (xeroderma pigmentosum, Cockayne's syndrome, trichothiodystrophy, Down syndrome, and triple-A syndrome) display a defect in the nucleotide excision repair pathway, four (Huntington's disease, various spinocerebellar ataxias, Friedreich's ataxia and myotonic dystrophy types 1 and 2) exhibit an unusual expansion of repeat sequences in DNA, and four (ataxia-telangiectasia, ataxia-telangiectasia-like disorder, Nijmegen breakage syndrome and Alzheimer's disease) exhibit defects in genes involved in repairing double-strand breaks. The current overall picture indicates that oxidative stress is a major causative factor in genomic instability in the brain, and that the nature of the resulting neurological phenotype depends on the pathway through which the instability is normally repaired.
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Affiliation(s)
- Kalluri Subba Rao
- Indian Council of Medical Research Centre for Research on Aging and Brain, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India.
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20
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Shin EJ, Chappell E, Pethe V, Hersey K, van der Kwast T, Fleshner N, Bapat B. MYH mutations are rare in prostate cancer. J Cancer Res Clin Oncol 2007; 133:373-8. [PMID: 17219200 DOI: 10.1007/s00432-006-0181-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2006] [Indexed: 01/04/2023]
Abstract
PURPOSE Oxidative stress is considered a risk factor for prostate cancer development and is associated with the production of reactive oxygen species (ROS). The base excision repair gene MYH protects against ROS-mediated damage to DNA. Inherited MYH mutations predispose to colorectal adenomas and cancer. A compromised base-excision repair function due to defective MYH may contribute to prostate carcinogenesis. Here, we examine the genetic contribution of MYH to prostate cancer risk. METHODS Patients diagnosed with high-grade prostatic intraepithelial neoplasia (HGPIN) alone (n = 45), prostate cancer alone (n = 123) or both (n = 82) were screened for the two most common mutations in the MYH gene using PCR-based RFLP analysis. A single patient with an inherited MYH mutation as well as a subset of 26 patients presenting with a family history of colorectal cancer were screened for additional MYH mutations by direct sequencing of the entire coding region. RESULTS Biallelic germline mutations in MYH were not detected among prostate cancer patients. Only a single patient was a heterozygous carrier for the Y165C missense mutation. Allelic deletion or somatic mutation of the remaining MYH allele was not identified in this patient's tumor DNA. Two patients harbored V22M polymorphism and three patients were carriers of Q324H polymorphism. CONCLUSIONS MYH mutations are unlikely to contribute to prostate cancer risk.
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Affiliation(s)
- Eyun-Jung Shin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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21
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Figueroa JD, Malats N, Real FX, Silverman D, Kogevinas M, Chanock S, Welch R, Dosemeci M, Tardón A, Serra C, Carrato A, García-Closas R, Castaño-Vinyals G, Rothman N, García-Closas M. Genetic variation in the base excision repair pathway and bladder cancer risk. Hum Genet 2007; 121:233-42. [PMID: 17203305 DOI: 10.1007/s00439-006-0294-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 11/03/2006] [Indexed: 10/23/2022]
Abstract
Genetic polymorphisms in DNA repair genes may impact individual variation in DNA repair capacity and alter cancer risk. In order to examine the association of common genetic variation in the base-excision repair (BER) pathway with bladder cancer risk, we analyzed 43 single nucleotide polymorphisms (SNPs) in 12 BER genes (OGG1, MUTYH, APEX1, PARP1, PARP3, PARP4, XRCC1, POLB, POLD1, PCNA, LIG1, and LIG3). Using genotype data from 1,150 cases of urinary bladder transitional cell carcinomas and 1,149 controls from the Spanish Bladder Cancer Study we estimated odds ratios (ORs) and 95% confidence intervals (CIs) adjusting for age, gender, region and smoking status. SNPs in three genes showed significant associations with bladder cancer risk: the 8-oxoG DNA glycosylase gene (OGG1), the Poly (ADP-ribose) polymerase family member 1 (PARP1) and the major gap filling polymerase-beta (POLB). Subjects who were heterozygous or homozygous variant for an OGG1 SNP in the promoter region (rs125701) had significantly decreased bladder cancer risk compared to common homozygous: OR (95%CI) 0.78 (0.63-0.96). Heterozygous or homozygous individuals for the functional SNP PARP1 rs1136410 (V762A) or for the intronic SNP POLB rs3136717 were at increased risk compared to those homozygous for the common alleles: 1.24 (1.02-1.51) and 1.30 (1.04-1.62), respectively. In summary, data from this large case-control study suggested bladder cancer risk associations with selected BER SNPs, which need to be confirmed in other study populations.
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Affiliation(s)
- Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, Bethesda, MD, USA.
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Jones IM, Thomas CB, Xi T, Mohrenweiser HW, Nelson DO. Exploration of methods to identify polymorphisms associated with variation in DNA repair capacity phenotypes. Mutat Res 2006; 616:213-20. [PMID: 17145065 DOI: 10.1016/j.mrfmmm.2006.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Elucidating the relationship between polymorphic sequences and risk of common disease is a challenge. For example, although it is clear that variation in DNA repair genes is associated with familial cancer, aging and neurological disease, progress toward identifying polymorphisms associated with elevated risk of sporadic disease has been slow. This is partly due to the complexity of the genetic variation, the existence of large numbers of mostly low frequency variants and the contribution of many genes to variation in susceptibility. There has been limited development of methods to find associations between genotypes having many polymorphisms and pathway function or health outcome. We have explored several statistical methods for identifying polymorphisms associated with variation in DNA repair phenotypes. The model system used was 80 cell lines that had been resequenced to identify variation; 191 single nucleotide substitution polymorphisms (SNPs) are included, of which 172 are in 31 base excision repair pathway genes, 19 in 5 anti-oxidation genes, and DNA repair phenotypes based on single strand breaks measured by the alkaline Comet assay. Univariate analyses were of limited value in identifying SNPs associated with phenotype variation. Of the multivariable model selection methods tested: the easiest that provided reduced error of prediction of phenotype was simple counting of the variant alleles predicted to encode proteins with reduced activity, which led to a genotype including 52 SNPs; the best and most parsimonious model was achieved using a two-step analysis without regard to potential functional relevance: first SNPs were ranked by importance determined by random forests regression (RFR), followed by cross-validation in a second round of RFR modeling that included ever more SNPs in declining order of importance. With this approach six SNPs were found to minimize prediction error. The results should encourage research into utilization of multivariate analytical methods for epidemiological studies of the association of genetic variation in complex genotypes with risk of common diseases.
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Affiliation(s)
- Irene M Jones
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
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Ulrich CM, Nijhout HF, Reed MC. Mathematical Modeling: Epidemiology Meets Systems Biology. Cancer Epidemiol Biomarkers Prev 2006; 15:827-9. [PMID: 16702357 DOI: 10.1158/1055-9965.epi-06-0252] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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