1
|
Roy R. Simultaneous Short- and Long-Patch Base Excision Repair (BER) Assay in Live Mammalian Cells. Methods Mol Biol 2023; 2701:3-19. [PMID: 37574472 DOI: 10.1007/978-1-0716-3373-1_1] [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] [Indexed: 08/15/2023]
Abstract
The base excision repair (BER) pathway repairs small, non-bulky DNA lesions, including oxidized, alkylated, and deaminated bases, and is responsible for the removal of at least 20,000 DNA lesions per cell per day. BER is initiated by DNA damage-specific DNA glycosylases that excise the damaged base and generates an abasic (AP) site or single-strand breaks, which are subsequently repaired in mammalian cells either by single-nucleotide (SN) or multiple-nucleotide incorporation via the SN-BER or long-patch BER (LP-BER) pathway, respectively. This chapter describes a plaque-based host cell reactivation (PL-HCR) assay system for measuring BER mechanisms in live mammalian cells using a plasmid-based assay. After transfection of a phagemid (M13mp18) containing a single modified base (representative BER DNA substrates) within a restriction site into human cells, restriction digestions detect the presence or absence (complete repair) of the adduct by the transformation of the digestion products into E. coli and counting the transformants as plaques. To monitor the patch size, different plasmids are constructed containing C:A mismatches within different restriction sites (inhibiting digestion) at various distances on both sides (5' or 3') of the modified base-containing restriction sites. Using this assay, the percentage of repair events that occur via 5' and 3' patch formation can be quantified.
Collapse
Affiliation(s)
- Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
| |
Collapse
|
2
|
Hu M, Wang Q, Liu B, Ma Q, Zhang T, Huang T, Lv Z, Wang R. Chronic Kidney Disease and Cancer: Inter-Relationships and Mechanisms. Front Cell Dev Biol 2022; 10:868715. [PMID: 35663394 PMCID: PMC9158340 DOI: 10.3389/fcell.2022.868715] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/26/2022] [Indexed: 12/20/2022] Open
Abstract
Chronic kidney disease (CKD) has been recognized as an increasingly serious public health problem globally over the decades. Accumulating evidence has shown that the incidence rate of cancer was relatively higher in CKD patients than that in general population, which, mechanistically, may be related to chronic inflammation, accumulation of carcinogenic compounds, oxidative stress, impairment of DNA repair, excessive parathyroid hormone and changes in intestinal microbiota, etc. And in patients with cancer, regardless of tumor types or anticancer treatment, it has been indicated that the morbidity and incidence rate of concomitant CKD was also increased, suggesting a complex inter-relationship between CKD and cancer and arousing increasing attention from both nephrologists and oncologists. This narrative review focused on the correlation between CKD and cancer, and underlying molecular mechanisms, which might provide an overview of novel interdisciplinary research interests and the potential challenges related to the screening and treatment of CKD and cancer. A better understanding of this field might be of help for both nephrologists and oncologists in the clinical practice.
Collapse
Affiliation(s)
- Mengsi Hu
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Nephrology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qianhui Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Bing Liu
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Nephrology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qiqi Ma
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tingwei Zhang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tongtong Huang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhimei Lv
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Nephrology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Zhimei Lv, ; Rong Wang,
| | - Rong Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Nephrology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Zhimei Lv, ; Rong Wang,
| |
Collapse
|
3
|
Wu HC, Kehm R, Santella RM, Brenner DJ, Terry MB. DNA repair phenotype and cancer risk: a systematic review and meta-analysis of 55 case-control studies. Sci Rep 2022; 12:3405. [PMID: 35233009 PMCID: PMC8888613 DOI: 10.1038/s41598-022-07256-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 02/15/2022] [Indexed: 01/01/2023] Open
Abstract
DNA repair phenotype can be measured in blood and may be a potential biomarker of cancer risk. We conducted a systematic review and meta-analysis of epidemiological studies of DNA repair phenotype and cancer through March 2021. We used random-effects models to calculate pooled odds ratios (ORs) of cancer risk for those with the lowest DNA repair capacity compared with those with the highest capacity. We included 55 case–control studies that evaluated 12 different cancers using 10 different DNA repair assays. The pooled OR of cancer risk (all cancer types combined) was 2.92 (95% Confidence Interval (CI) 2.49, 3.43) for the lowest DNA repair. Lower DNA repair was associated with all studied cancer types, and pooled ORs (95% CI) ranged from 2.02 (1.43, 2.85) for skin cancer to 7.60 (3.26, 17.72) for liver cancer. All assays, except the homologous recombination repair assay, showed statistically significant associations with cancer. The effect size ranged from 1.90 (1.00, 3.60) for the etoposide-induced double-strand break assay to 5.06 (3.67, 6.99) for the γ-H2AX assay. The consistency and strength of the associations support the use of these phenotypic biomarkers; however large-scale prospective studies will be important for understanding their use related to age and screening initiation.
Collapse
Affiliation(s)
- Hui-Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, 630 West 168th St., Room P&S 16-421E, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
| | - Rebecca Kehm
- Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, 630 West 168th St., Room P&S 16-421E, New York, NY, 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, 630W 168th Street, New York, NY, 10032, USA
| | - Mary Beth Terry
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, 630 West 168th St., Room P&S 16-421E, New York, NY, 10032, USA.,Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY, USA
| |
Collapse
|
4
|
Ge J, Ngo LP, Kaushal S, Tay IJ, Thadhani E, Kay JE, Mazzucato P, Chow DN, Fessler JL, Weingeist DM, Sobol RW, Samson LD, Floyd SR, Engelward BP. CometChip enables parallel analysis of multiple DNA repair activities. DNA Repair (Amst) 2021; 106:103176. [PMID: 34365116 PMCID: PMC8439179 DOI: 10.1016/j.dnarep.2021.103176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/28/2022]
Abstract
DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these applications of the CometChip platform, we expand the utility of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities.
Collapse
Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, United States
| | - Ian J Tay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elina Thadhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jennifer E Kay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Danielle N Chow
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jessica L Fessler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David M Weingeist
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Robert W Sobol
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, United States; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, United States
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Scott R Floyd
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27514, United States
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
| |
Collapse
|
5
|
Toprani SM, Bitounis D, Qiansheng H, Oliveira N, Ng KW, Tay CY, Nagel ZD, Demokritou P. High-Throughput Screening Platform for Nanoparticle-Mediated Alterations of DNA Repair Capacity. ACS NANO 2021; 15:4728-4746. [PMID: 33710878 PMCID: PMC8111687 DOI: 10.1021/acsnano.0c09254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The potential genotoxic effects of engineered nanomaterials (ENMs) may occur through the induction of DNA damage or the disruption of DNA repair processes. Inefficient DNA repair may lead to the accumulation of DNA lesions and has been linked to various diseases, including cancer. Most studies so far have focused on understanding the nanogenotoxicity of ENM-induced damages to DNA, whereas the effects on DNA repair have been widely overlooked. The recently developed fluorescence multiplex-host-cell reactivation (FM-HCR) assay allows for the direct quantification of multiple DNA repair pathways in living cells and offers a great opportunity to address this methodological gap. Herein an FM-HCR-based method is developed to screen the impact of ENMs on six major DNA repair pathways using suspended or adherent cells. The sensitivity and efficiency of this DNA repair screening method were demonstrated in case studies using primary human small airway epithelial cells and TK6 cells exposed to various model ENMs (CuO, ZnO, and Ga2O3) at subcytotoxic doses. It was shown that ENMs may inhibit nucleotide-excision repair, base-excision repair, and the repair of oxidative damage by DNA glycosylases in TK6 cells, even in the absence of significant genomic DNA damage. It is of note that the DNA repair capacity was increased by some ENMs, whereas it was suppressed by others. Overall, this method can be part of a multitier, in vitro hazard assessment of ENMs as a functional, high-throughput platform that provides insights into the interplay of the properties of ENMs, the DNA repair efficiency, and the genomic stability.
Collapse
Affiliation(s)
- Sneh M Toprani
- John B Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
| | - Huang Qiansheng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Nathalia Oliveira
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
| | - Kee Woei Ng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Environmental Chemistry and Materials Centre, Nanyang Environment and Water Research Institution, 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore
| | - Chor Yong Tay
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zachary D Nagel
- John B Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
| |
Collapse
|
6
|
Ma L, Liang B, Yang Y, Chen L, Liu Q, Zhang A. hOGG1 promoter methylation, hOGG1 genetic variants and their interactions for risk of coal-borne arsenicosis: A case-control study. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 75:103330. [PMID: 32004920 DOI: 10.1016/j.etap.2020.103330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
To identify the effect of hOGG1 methylation, Ser326Cys polymorphism and their interactions on the risk of coal-borne arsenicosis, 113 coal-borne arsenicosis subjects and 55 reference subjects were recruited. Urinary arsenic contents were analyzed with ICP-MS. hOGG1 methylation and Ser326Cys polymorphism was measured by mehtylation-specific PCR and restriction fragment length polymorphism PCR in PBLCs, respectively. The results showed that the prevalence of methylated hOGG1 and variation genotype (326 Ser/Cys & 326 Cys/Cys) were increased with raised levels of urinary arsenic in arsenicosis subjects. Increased prevalence of methylated hOGG1 and variation genotype were associated with raised risk of arsenicosis. Moreover, the results revealed that variant genotype might increase the susceptibility to hOGG1 methylation. The interactions of methylated hOGG1 and variation genotype were also found to contribute to increased risk of arsenicosis. Taken together, hOGG1 hypermethylation, hOGG1 variants and their interactions might be potential biomarkers for evaluating risk of coal-borne arsenicosis.
Collapse
Affiliation(s)
- Lu Ma
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
| | - Bing Liang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
| | - Yuan Yang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
| | - Liyuan Chen
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
| | - Qizhan Liu
- The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, PR China.
| | - Aihua Zhang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
| |
Collapse
|
7
|
Zhang H, Ba S, Yang Z, Wang T, Lee JY, Li T, Shao F. Graphene Quantum Dot-Based Nanocomposites for Diagnosing Cancer Biomarker APE1 in Living Cells. ACS APPLIED MATERIALS & INTERFACES 2020; 12:13634-13643. [PMID: 32129072 DOI: 10.1021/acsami.9b21385] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
As an essential DNA repair enzyme, apurinic/apyrimidinic endonuclease 1 (APE1) is overexpressed in most human cancers and is identified as a cancer diagnostic and predictive biomarker for cancer risk assessment, diagnosis, prognosis, and prediction of treatment efficacy. Despite its importance in cancer, however, it is still a significant challenge nowadays to sense abundance variation and monitor enzymatic activity of this biomarker in living cells. Here, we report our construction of biocompatible functional nanocomposites, which are a combination of meticulously designed unimolecular DNA and fine-sized graphene quantum dots. Upon utilization of these nanocomposites as diagnostic probes, massive accumulation of fluorescence signal in living cells can be triggered by merely a small amount of cellular APE1 through repeated cycles of enzymatic catalysis. Most critically, our delicate structural designs assure that these graphene quantum dot-based nanocomposites are capable of sensing cancer biomarker APE1 in identical type of cells under different cell conditions and can be applied to multiple cancerous cells in a highly sensitive and specific manners. This work not only brings about new methods for cytology-based cancer screening but also lays down a general principle for fabricating diagnostic probes that target other endogenous biomarkers in living cells.
Collapse
Affiliation(s)
- Hao Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Sai Ba
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Zhaoqi Yang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tianxiang Wang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Jasmine Yiqin Lee
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Tianhu Li
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fangwei Shao
- ZJU-UIUC Institute, Zhejiang University, Haining, Zhejiang 314400, China
| |
Collapse
|
8
|
Paz-Elizur T, Leitner-Dagan Y, Meyer KB, Markus B, Giorgi FM, O’Reilly M, Kim H, Evgy Y, Fluss R, Freedman LS, Rintoul RC, Ponder B, Livneh Z. DNA Repair Biomarker for Lung Cancer Risk and its Correlation With Airway Cells Gene Expression. JNCI Cancer Spectr 2020; 4:pkz067. [PMID: 32064457 PMCID: PMC7012022 DOI: 10.1093/jncics/pkz067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/23/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Improving lung cancer risk assessment is required because current early-detection screening criteria miss most cases. We therefore examined the utility for lung cancer risk assessment of a DNA Repair score obtained from OGG1, MPG, and APE1 blood tests. In addition, we examined the relationship between the level of DNA repair and global gene expression. METHODS We conducted a blinded case-control study with 150 non-small cell lung cancer case patients and 143 control individuals. DNA Repair activity was measured in peripheral blood mononuclear cells, and the transcriptome of nasal and bronchial cells was determined by RNA sequencing. A combined DNA Repair score was formed using logistic regression, and its correlation with disease was assessed using cross-validation; correlation of expression to DNA Repair was analyzed using Gene Ontology enrichment. RESULTS DNA Repair score was lower in case patients than in control individuals, regardless of the case's disease stage. Individuals at the lowest tertile of DNA Repair score had an increased risk of lung cancer compared to individuals at the highest tertile, with an odds ratio (OR) of 7.2 (95% confidence interval [CI] = 3.0 to 17.5; P < .001), and independent of smoking. Receiver operating characteristic analysis yielded an area under the curve of 0.89 (95% CI = 0.82 to 0.93). Remarkably, low DNA Repair score correlated with a broad upregulation of gene expression of immune pathways in patients but not in control individuals. CONCLUSIONS The DNA Repair score, previously shown to be a lung cancer risk factor in the Israeli population, was validated in this independent study as a mechanism-based cancer risk biomarker and can substantially improve current lung cancer risk prediction, assisting prevention and early detection by computed tomography scanning.
Collapse
Affiliation(s)
- Tamar Paz-Elizur
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Leitner-Dagan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kerstin B Meyer
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Barak Markus
- Bioinformatics Unit, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Federico M Giorgi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Martin O’Reilly
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hyunjin Kim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Yentl Evgy
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Fluss
- Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center, Tel Hashomer, Israel
| | - Laurence S Freedman
- Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center, Tel Hashomer, Israel
| | - Robert C Rintoul
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Thoracic Oncology, Royal Papworth Hospital, Cambridge, UK
| | - Bruce Ponder
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
9
|
Sears CR. DNA repair as an emerging target for COPD-lung cancer overlap. Respir Investig 2019; 57:111-121. [PMID: 30630751 DOI: 10.1016/j.resinv.2018.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/14/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023]
Abstract
Cigarette smoking is the leading cause of lung cancer and chronic obstructive pulmonary disease (COPD). Many of the detrimental effects of cigarette smoke have been attributed to the development of DNA damage, either directly from chemicals contained in cigarette smoke or as a product of cigarette smoke-induced inflammation and oxidative stress. In this review, we discuss the environmental, epidemiological, and physiological links between COPD and lung cancer and the likely role of DNA damage and repair in COPD and lung cancer development. We explore alterations in DNA damage repair by DNA repair proteins and pathways. We discuss emerging data supporting a key role for the DNA repair protein, xeroderma pigmentosum group C (XPC), in cigarette smoke-induced COPD and early lung cancer development. Understanding the interplay between cigarette smoke, DNA damage repair, COPD, and lung cancer may lead to prognostic tools and new, potentially targetable, pathways for lung cancer prevention and treatment.
Collapse
Affiliation(s)
- Catherine R Sears
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, Indiana; The Richard L. Roudebush Veterans Affairs Medical Center; 980W, Walnut Street, Walther Hall, C400, Indianapolis, IN, 46202, USA.
| |
Collapse
|
10
|
Vlahopoulos S, Adamaki M, Khoury N, Zoumpourlis V, Boldogh I. Roles of DNA repair enzyme OGG1 in innate immunity and its significance for lung cancer. Pharmacol Ther 2018; 194:59-72. [PMID: 30240635 DOI: 10.1016/j.pharmthera.2018.09.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytokines are pivotal mediators of the immune response, and their coordinated expression protects host tissue from excessive damage and oxidant stress. Nevertheless, the development of lung pathology, including asthma, chronic obstructive pulmonary disease, and ozone-induced lung injury, is associated with oxidant stress; as evidence, there is a significant increase in levels of the modified guanine base 7,8-dihydro-8-oxoguanine (8-oxoG) in the genome. 8-OxoG is primarily recognized by 8-oxoguanine glycosylase 1 (OGG1), which catalyzes the first step in the DNA base excision repair pathway. However, oxidant stress in the cell transiently halts enzymatic activity of substrate-bound OGG1. The stalled OGG1 facilitates DNA binding of transactivators, including NF-κB, to their cognate sites to enable expression of cytokines and chemokines, with ensuing recruitments of inflammatory cells. Hence, defective OGG1 will modulate the coordination between innate and adaptive immunity through excessive oxidant stress and cytokine dysregulation. Both oxidant stress and cytokine dysregulation constitute key elements of oncogenesis by KRAS, which is mechanistically coupled to OGG1. Thus, analysis of the mechanism by which OGG1 modulates gene expression helps discern between beneficial and detrimental effects of oxidant stress, exposes a missing functional link as a marker, and yields a novel target for lung cancer.
Collapse
Affiliation(s)
- Spiros Vlahopoulos
- Ηoremeio Research Laboratory, First Department of Paediatrics, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Maria Adamaki
- Biomedical Applications Unit, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Nikolas Khoury
- Biomedical Applications Unit, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Istvan Boldogh
- Departments of Microbiology and Immunology and the Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States
| |
Collapse
|
11
|
Programming of Cell Resistance to Genotoxic and Oxidative Stress. Biomedicines 2018; 6:biomedicines6010005. [PMID: 29301323 PMCID: PMC5874662 DOI: 10.3390/biomedicines6010005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 12/23/2017] [Accepted: 12/31/2017] [Indexed: 12/23/2022] Open
Abstract
Different organisms, cell types, and even similar cell lines can dramatically differ in resistance to genotoxic stress. This testifies to the wide opportunities for genetic and epigenetic regulation of stress resistance. These opportunities could be used to increase the effectiveness of cancer therapy, develop new varieties of plants and animals, and search for new pharmacological targets to enhance human radioresistance, which can be used for manned deep space expeditions. Based on the comparison of transcriptomic studies in cancer cells, in this review, we propose that there is a high diversity of genetic mechanisms of development of genotoxic stress resistance. This review focused on possibilities and limitations of the regulation of the resistance of normal cells and whole organisms to genotoxic and oxidative stress by the overexpressing of stress-response genes. Moreover, the existing experimental data on the effect of such overexpression on the resistance of cells and organisms to various genotoxic agents has been analyzed and systematized. We suggest that the recent advances in the development of multiplex and highly customizable gene overexpression technology that utilizes the mutant Cas9 protein and the abundance of available data on gene functions and their signal networks open new opportunities for research in this field.
Collapse
|
12
|
In vivo measurements of interindividual differences in DNA glycosylases and APE1 activities. Proc Natl Acad Sci U S A 2017; 114:E10379-E10388. [PMID: 29122935 DOI: 10.1073/pnas.1712032114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The integrity of our DNA is challenged with at least 100,000 lesions per cell on a daily basis. Failure to repair DNA damage efficiently can lead to cancer, immunodeficiency, and neurodegenerative disease. Base excision repair (BER) recognizes and repairs minimally helix-distorting DNA base lesions induced by both endogenous and exogenous DNA damaging agents. Levels of BER-initiating DNA glycosylases can vary between individuals, suggesting that quantitating and understanding interindividual differences in DNA repair capacity (DRC) may enable us to predict and prevent disease in a personalized manner. However, population studies of BER capacity have been limited because most methods used to measure BER activity are cumbersome, time consuming and, for the most part, only allow for the analysis of one DNA glycosylase at a time. We have developed a fluorescence-based multiplex flow-cytometric host cell reactivation assay wherein the activity of several enzymes [four BER-initiating DNA glycosylases and the downstream processing apurinic/apyrimidinic endonuclease 1 (APE1)] can be tested simultaneously, at single-cell resolution, in vivo. Taking advantage of the transcriptional properties of several DNA lesions, we have engineered specific fluorescent reporter plasmids for quantitative measurements of 8-oxoguanine DNA glycosylase, alkyl-adenine DNA glycosylase, MutY DNA glycosylase, uracil DNA glycosylase, and APE1 activity. We have used these reporters to measure differences in BER capacity across a panel of cell lines collected from healthy individuals, and to generate mathematical models that predict cellular sensitivity to methylmethane sulfonate, H2O2, and 5-FU from DRC. Moreover, we demonstrate the suitability of these reporters to measure differences in DRC in multiple pathways using primary lymphocytes from two individuals.
Collapse
|
13
|
Zeng Y, Zhu J, Qin H, Shen D, Lei Z, Li W, Ding Z, Huang JA, Liu Z. Methylated +322-327 CpG site decreases hOGG1 mRNA expression in non-small cell lung cancer. Oncol Rep 2017; 38:529-537. [PMID: 28586012 DOI: 10.3892/or.2017.5690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/26/2017] [Indexed: 11/06/2022] Open
Abstract
hOGG1 plays a role in several disease pathways, including various cancers. Despite such functional importance, how hOGG1 is regulated at the transcriptional level in human non-small cell lung cancer (NSCLC) remains unknown, particularly via DNA methylation changes. We obtained NSCLC tissues and adjacent non-cancerous tissues and examined hOGG1 mRNA expression levels. NSCLC cells were treated with 5-Aza to test whether DNA methylation can influence the expression of hOGG1. The MassARRAY EpiTYPER and luciferase reporter gene assays were used to define the functional region of the hOGG1 gene (including CpG sites). Finally, ChIP assay was utilized to verify transcription factor binding to the hOGG1 5'-UTR region. Our previous studies supported the idea that the methylation of the hOGG1 gene promoter region occurs frequently in NSCLC. Treatment with 5-Aza, a demethylating agent, led to a significant restoration of hOGG1 expression in NSCLC cell lines. Quantitative PCR and MassARRAY EpiTYPER assays demonstrated that methylation of the +322-327 CpG site in the 5'-UTR region of hOGG1 was higher in NSCLC tissues compared with adjacent non-cancerous tissues. Notably, the methylation level of +322-327 site (T/N) was inversely correlated with that of hOGG1 mRNA level (T/N) in 25 NSCLC tissues. ChIP assay and in silico prediction showed an association between the +322-327 CpG site and Sp1, which has been reported to be an activator of transcription. Importantly, luciferase reporter gene and ChIP assays showed that +322-327 CpG site methylation particularly reduced the recruitment of Sp1 to the 5'-UTR sequence in hOGG1 and reduced transcriptional activity ~50%. In summary, we have demonstrated that hOGG1 mRNA is downregulated in NSCLC tissues. Moreover, we identified that the methylated +322-327 CpG site in the hOGG1 5'-UTR is associated with reduced expression of hOGG1 by decreasing the recruitment of Sp1 to the 5'-UTR of hOGG1.
Collapse
Affiliation(s)
- Yuanyuan Zeng
- Department of Respiratory Medicine, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jianjie Zhu
- Department of Respiratory Medicine, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Hualong Qin
- Department of Cardiothoracic surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Dan Shen
- Department of Respiratory Medicine, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Zhe Lei
- Suzhou Key Laboratory for Molecular Cancer Genetics, Suzhou, Jiangsu, P.R. China
| | - Wei Li
- Department of Oncology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Zongli Ding
- Department of Respiratory Medicine, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jian-An Huang
- Department of Respiratory Medicine, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Zeyi Liu
- Department of Respiratory Medicine, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| |
Collapse
|
14
|
Huang R, Wei Y, Hung RJ, Liu G, Su L, Zhang R, Zong X, Zhang ZF, Morgenstern H, Brüske I, Heinrich J, Hong YC, Kim JH, Cote M, Wenzlaff A, Schwartz AG, Stucker I, Mclaughlin J, Marcus MW, Davies MPA, Liloglou T, Field JK, Matsuo K, Barnett M, Thornquist M, Goodman G, Wang Y, Chen S, Yang P, Duell EJ, Andrew AS, Lazarus P, Muscat J, Woll P, Horsman J, Teare MD, Flugelman A, Rennert G, Zhang Y, Brenner H, Stegmaier C, van der Heijden EHFM, Aben K, Kiemeney L, Barros-Dios J, Pérez-Ríos M, Ruano-Ravina A, Caporaso NE, Bertazzi PA, Landi MT, Dai J, Hongbing Shen H, Fernandez-Tardon G, Rodriguez-Suarez M, Tardon A, Christiani DC. Associated Links Among Smoking, Chronic Obstructive Pulmonary Disease, and Small Cell Lung Cancer: A Pooled Analysis in the International Lung Cancer Consortium. EBioMedicine 2016; 2:1677-85. [PMID: 26870794 PMCID: PMC4740296 DOI: 10.1016/j.ebiom.2015.09.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 01/17/2023] Open
|
15
|
Maynard S, Hejl AM, Dinh TST, Keijzers G, Hansen ÅM, Desler C, Moreno-Villanueva M, Bürkle A, Rasmussen LJ, Waldemar G, Bohr VA. Defective mitochondrial respiration, altered dNTP pools and reduced AP endonuclease 1 activity in peripheral blood mononuclear cells of Alzheimer's disease patients. Aging (Albany NY) 2016; 7:793-815. [PMID: 26539816 PMCID: PMC4637207 DOI: 10.18632/aging.100810] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AIMS Accurate biomarkers for early diagnosis of Alzheimer's disease (AD) are badly needed. Recent reports suggest that dysfunctional mitochondria and DNA damage are associated with AD development. In this report, we measured various cellular parameters, related to mitochondrial bioenergetics and DNA damage, in peripheral blood mononuclear cells (PBMCs) of AD and control participants, for biomarker discovery. METHODS PBMCs were isolated from 53 patients with AD of mild to moderate degree and 30 age-matched healthy controls. Tests were performed on the PBMCs from as many of these participants as possible. We measured glycolysis and mitochondrial respiration fluxes using the Seahorse Bioscience flux analyzer, mitochondrial ROS production using flow cytometry, dNTP levels by way of a DNA polymerization assay, DNA strand breaks using the Fluorometric detection of Alkaline DNA Unwinding (FADU) assay, and APE1 incision activity (in cell lysates) on a DNA substrate containing an AP site (to estimate DNA repair efficiency). RESULTS In the PBMCs of AD patients, we found reduced basal mitochondrial oxygen consumption, reduced proton leak, higher dATP level, and lower AP endonuclease 1 activity, depending on adjustments for gender and/or age. CONCLUSIONS This study reveals impaired mitochondrial respiration, altered dNTP pools and reduced DNA repair activity in PBMCs of AD patients, thus suggesting that these biochemical activities may be useful as biomarkers for AD.
Collapse
Affiliation(s)
- Scott Maynard
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne-Mette Hejl
- Department of Neurology, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thuan-Son T Dinh
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Guido Keijzers
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Åse M Hansen
- Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark.,The National Research Centre for the Working Environment, 2100 Copenhagen, Denmark
| | - Claus Desler
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Alexander Bürkle
- Molecular Toxicology Group, University of Konstanz, D-78457 Konstanz, Germany
| | - Lene J Rasmussen
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Gunhild Waldemar
- Department of Neurology, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Vilhelm A Bohr
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, 2200 Copenhagen, Denmark.,Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224-6825, USA
| |
Collapse
|
16
|
Couto PG, Bastos-Rodrigues L, Carneiro JG, Guieiro F, Bicalho MA, Leidenz FB, Bicalho AJ, Friedman E, De Marco L. DNA Base-Excision Repair Genes OGG1 and NTH1 in Brazilian Lung Cancer Patients. Mol Diagn Ther 2016; 19:389-95. [PMID: 26400813 DOI: 10.1007/s40291-015-0164-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Lung cancer is the leading global cause of cancer-related mortality and is associated with poor prognosis. To improve survival rates of lung cancer patients, better understanding of tumorigenic mechanisms is necessary, which may lead to development of new therapeutic strategies. The hOGG1 and NTH1 genes act in the DNA BER repair pathway and their involvement in lung cancer pathogenesis has been analyzed in several populations. METHODS We analyzed targeted regions of the hOGG1 and NTH1 genes in 96 Brazilian patients with non-small-cell lung cancer (NSCLC) and 89 cancer-free, ethnically matched controls. RESULTS The NTH1 c.98G>T polymorphism rs2302172 (p = 0.02 and p = 0.02 for allele and genotype frequency between cases and controls, respectively) and the 140-17C> T variant (rs2233518) (p = 0.02 and p = 0.02 for allele and genotype frequency between cases and controls, respectively) were detected in four lung cancer cases (4 %) while the NTH1 Q131K (C391A) polymorphism was found in seven lung cancer cases (7 %) (p = 0.001 and p = 0.008, for allele and genotype frequency between cases and controls, respectively). None of these sequence variants were detected in controls. The Ser326Cys (C1245G, rs1052133) polymorphism in the OGG1 gene was detected in 42 % of analyzed NSCLC patients and in 34 % of the controls (p = 0.11 and p = 0.25 for allele and genotype frequency between cases and controls, respectively). CONCLUSIONS Our study provides preliminary evidence that polymorphisms in OGG1 do not contribute to development of NSCLC in Brazilian patients and that NTH1 polymorphisms may be associated with NSCLC pathogenesis.
Collapse
Affiliation(s)
- Patricia G Couto
- Department of Surgery, Universidade Federal de Minas Gerais, Av. Alfredo Balena 190, Room 114, Belo Horizonte, 30130-100, Brazil
| | - Luciana Bastos-Rodrigues
- Universidade Federal de Juiz de Fora, Campus Governador Valadares, Governador Valadares, Minas Gerais, Brazil
| | - Juliana G Carneiro
- Faculty of Medical Science, Centro de Ensino Superior e Desenvolvimento, Campina Grande, Brazil
| | - Fernanda Guieiro
- Department of Surgery, Universidade Federal de Minas Gerais, Av. Alfredo Balena 190, Room 114, Belo Horizonte, 30130-100, Brazil
| | | | - Franciele B Leidenz
- Department of Surgery, Universidade Federal de Minas Gerais, Av. Alfredo Balena 190, Room 114, Belo Horizonte, 30130-100, Brazil
| | - Ana J Bicalho
- Department of Surgery, Universidade Federal de Minas Gerais, Av. Alfredo Balena 190, Room 114, Belo Horizonte, 30130-100, Brazil
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Luiz De Marco
- Department of Surgery, Universidade Federal de Minas Gerais, Av. Alfredo Balena 190, Room 114, Belo Horizonte, 30130-100, Brazil.
| |
Collapse
|
17
|
Wang M, Liu H, Liu Z, Yi X, Bickeboller H, Hung RJ, Brennan P, Landi MT, Caporaso N, Christiani DC, Doherty JA, Amos CI, Wei Q. Genetic variant in DNA repair gene GTF2H4 is associated with lung cancer risk: a large-scale analysis of six published GWAS datasets in the TRICL consortium. Carcinogenesis 2016; 37:888-896. [PMID: 27288692 PMCID: PMC5008248 DOI: 10.1093/carcin/bgw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 12/15/2022] Open
Abstract
DNA repair pathways maintain genomic integrity and stability, and dysfunction of DNA repair leads to cancer. We hypothesize that functional genetic variants in DNA repair genes are associated with risk of lung cancer. We performed a large-scale meta-analysis of 123,371 single nucleotide polymorphisms (SNPs) in 169 DNA repair genes obtained from six previously published genome-wide association studies (GWASs) of 12160 lung cancer cases and 16838 controls. We calculated odds ratios (ORs) with 95% confidence intervals (CIs) using the logistic regression model and used the false discovery rate (FDR) method for correction of multiple testing. As a result, 14 SNPs had a significant odds ratio (OR) for lung cancer risk with P FDR < 0.05, of which rs3115672 in MSH5 (OR = 1.20, 95% CI = 1.14-1.27) and rs114596632 in GTF2H4 (OR = 1.19, 95% CI = 1.12-1.25) at 6q21.33 were the most statistically significant (P combined = 3.99×10(-11) and P combined = 5.40×10(-10), respectively). The MSH5 rs3115672, but not GTF2H4 rs114596632, was strongly correlated with MSH5 rs3131379 in that region (r (2) = 1.000 and r (2) = 0.539, respectively) as reported in a previous GWAS. Importantly, however, the GTF2H4 rs114596632 T, but not MSH5 rs3115672 T, allele was significantly associated with both decreased DNA repair capacity phenotype and decreased mRNA expression levels. These provided evidence that functional genetic variants of GTF2H4 confer susceptibility to lung cancer.
Collapse
Affiliation(s)
- Meilin Wang
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 21116, China
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaohua Yi
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Heike Bickeboller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai hospital, Toronto, Ontario, Canada
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, 69372 Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - David C. Christiani
- Department of Environmental Health and
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA 02115, USA and
| | - Jennifer Anne Doherty
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - The TRICL Research Team
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 21116, China
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai hospital, Toronto, Ontario, Canada
- Genetic Epidemiology Group, International Agency for Research on Cancer, 69372 Lyon, France
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Department of Environmental Health and
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA 02115, USA and
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Christopher I. Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
18
|
Sevilya Z, Leitner-Dagan Y, Pinchev M, Kremer R, Elinger D, Lejbkowicz F, Rennert HS, Freedman LS, Rennert G, Paz-Elizur T, Livneh Z. Development of APE1 enzymatic DNA repair assays: low APE1 activity is associated with increase lung cancer risk. Carcinogenesis 2015; 36:982-91. [PMID: 26045303 PMCID: PMC4552243 DOI: 10.1093/carcin/bgv082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/29/2015] [Indexed: 01/23/2023] Open
Abstract
We developed radioactivity-based and fluorescence-based assays for the DNA repair enzyme APE1 and showed that its decreased activity is associated with increased lung cancer risk. This suggests that ‘bad DNA repair’ rather than ‘bad luck’ is involved in cancer etiology. The key role of DNA repair in removing DNA damage and minimizing mutations makes it an attractive target for cancer risk assessment and prevention. Here we describe the development of a robust assay for apurinic/apyrimidinic (AP) endonuclease 1 (APE1; APEX1), an essential enzyme involved in the repair of oxidative DNA damage. APE1 DNA repair enzymatic activity was measured in peripheral blood mononuclear cell protein extracts using a radioactivity-based assay, and its association with lung cancer was determined using conditional logistic regression with specimens from a population-based case–control study with 96 lung cancer cases and 96 matched control subjects. The mean APE1 enzyme activity in case patients was 691 [95% confidence interval (CI) = 655–727] units/ng protein, significantly lower than in control subjects (mean = 793, 95% CI = 751–834 units/ng protein, P = 0.0006). The adjusted odds ratio for lung cancer associated with 1 SD (211 units) decrease in APE1 activity was 2.0 (95% CI = 1.3–3.1; P = 0.002). Comparison of radioactivity- and fluorescence-based assays showed that the two are equivalent, indicating no interference by the fluorescent tag. The APE1Asp148Glu SNP was associated neither with APE1 enzyme activity nor with lung cancer risk. Taken together, our results indicate that low APE1 activity is associated with lung cancer risk, consistent with the hypothesis that ‘bad DNA repair’, rather than ‘bad luck’, is involved in cancer etiology. Such assays may be useful, along with additional DNA repair biomarkers, for risk assessment of lung cancer and perhaps other cancers, and for selecting individuals to undergo early detection techniques such as low-dose CT.
Collapse
Affiliation(s)
- Ziv Sevilya
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Research, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Yael Leitner-Dagan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Research, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - Ran Kremer
- Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel and
| | - Dalia Elinger
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Research, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Flavio Lejbkowicz
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - Laurence S Freedman
- Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Research, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - Tamar Paz-Elizur
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Research, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Zvi Livneh
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Research, Sheba Medical Center, Tel Hashomer 52621, Israel
| |
Collapse
|
19
|
Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
Collapse
|
20
|
Leitner-Dagan Y, Sevilya Z, Pinchev M, Kremer R, Elinger D, Rennert HS, Schechtman E, Freedman L, Rennert G, Livneh Z, Paz-Elizur T. Enzymatic MPG DNA repair assays for two different oxidative DNA lesions reveal associations with increased lung cancer risk. Carcinogenesis 2014; 35:2763-70. [PMID: 25355292 DOI: 10.1093/carcin/bgu214] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA repair is a major mechanism for minimizing mutations and reducing cancer risk. Here, we present the development of reproducible and specific enzymatic assays for methylpurine DNA glycosylase (MPG) repairing the oxidative lesions 1,N6-ethenoadenine (εA) and hypoxanthine (Hx) in peripheral blood mononuclear cells protein extracts. Association of these DNA repair activities with lung cancer was determined using conditional logistic regression with specimens from a population-based case-control study with 96 lung cancer cases and 96 matched control subjects. The mean MPG-εA in case patients was 15.8 units/μg protein (95% CI 15.3-16.3), significantly higher than in control subjects-15.1 (14.6-15.5), *P = 0.011. The adjusted odds ratio for lung cancer associated with a one SD increase in MPG-εA activity (2.48 units) was significantly bigger than 1 (OR = 1.6, 95% CI = 1.1-2.4; *P = 0.013). When activity of OGG1, a different DNA repair enzyme for oxidative damage, was included in the model, the estimated odds ratio/SD for a combined MPG-εA-OGG1 score was 2.6 (95% CI 1.6-4.2) *P = 0.0001, higher than the odds ratio for each single assay. The MPG enzyme activity assays described provide robust functional risk biomarkers, with increased MPG-εA activity being associated with increased lung cancer risk, similar to the behavior of MPG-Hx. This underscores the notion that imbalances in DNA repair, including high DNA repair, usually perceived as beneficial, can cause cancer risk. Such DNA repair risk biomarkers may be useful for risk assessment of lung cancer and perhaps other cancer types, and for early detection techniques such as low-dose CT.
Collapse
Affiliation(s)
- Yael Leitner-Dagan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel, Department of Industrial Engineering and Management, Ben Gurion University of the Negev, Beer Sheva 84105, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center Tel Hashomer 52621, Israel
| | - Ziv Sevilya
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel, Department of Industrial Engineering and Management, Ben Gurion University of the Negev, Beer Sheva 84105, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center Tel Hashomer 52621, Israel
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - Ran Kremer
- Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel
| | - Dalia Elinger
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel, Department of Industrial Engineering and Management, Ben Gurion University of the Negev, Beer Sheva 84105, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center Tel Hashomer 52621, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - Edna Schechtman
- Department of Industrial Engineering and Management, Ben Gurion University of the Negev, Beer Sheva 84105, Israel and
| | - Laurence Freedman
- Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center Tel Hashomer 52621, Israel
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel
| | - Zvi Livneh
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel, Department of Industrial Engineering and Management, Ben Gurion University of the Negev, Beer Sheva 84105, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center Tel Hashomer 52621, Israel
| | - Tamar Paz-Elizur
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Community Medicine and Epidemiology, Carmel Medical Center, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, and Clalit Health Services National Cancer Control Center, Haifa, Israel, Department of General Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel, Department of Industrial Engineering and Management, Ben Gurion University of the Negev, Beer Sheva 84105, Israel and Biostatistics Unit, Gertner Institute for Epidemiology and Public Health Policy Sheba Medical Center Tel Hashomer 52621, Israel
| |
Collapse
|
21
|
Nagel ZD, Chaim IA, Samson LD. Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research. DNA Repair (Amst) 2014; 19:199-213. [PMID: 24780560 DOI: 10.1016/j.dnarep.2014.03.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Why does a constant barrage of DNA damage lead to disease in some individuals, while others remain healthy? This article surveys current work addressing the implications of inter-individual variation in DNA repair capacity for human health, and discusses the status of DNA repair assays as potential clinical tools for personalized prevention or treatment of disease. In particular, we highlight research showing that there are significant inter-individual variations in DNA repair capacity (DRC), and that measuring these differences provides important biological insight regarding disease susceptibility and cancer treatment efficacy. We emphasize work showing that it is important to measure repair capacity in multiple pathways, and that functional assays are required to fill a gap left by genome wide association studies, global gene expression and proteomics. Finally, we discuss research that will be needed to overcome barriers that currently limit the use of DNA repair assays in the clinic.
Collapse
Affiliation(s)
- Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
22
|
Berwick M. Predicted for greatness: 1994 molecule of the year--the DNA repair enzyme. Cancer Prev Res (Phila) 2014; 7:375-7. [PMID: 24654230 DOI: 10.1158/1940-6207.capr-14-0050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lung cancer mortality is the highest of any cancer. Primary prevention has stalled, however, new lung cancer screening trials of low-dose computerized tomography (LDCT) have shown that the mortality from lung cancer can be reduced by up to 20% among current and former smokers. There are potential harms that must be taken into account when evaluating any screening program. With LDCT, there is a 90% rate of false positives and the potential for high doses of radiation from subsequent workup of benign lesions. The development of biomarkers that might refine the ability of screening to identify individuals at high risk for developing and dying from lung cancer is a ripe area for investigation. Sevilya and colleagues have developed a highly promising set of biomarkers of DNA repair capacity that may satisfy that goal. The large estimate of risk, the thoughtful combination of functional assays of DNA repair capacity, and the population-based design of the study make it reasonable to test these biomarkers in a larger study.
Collapse
Affiliation(s)
- Marianne Berwick
- University of New Mexico, 2703 Frontier Avenue, Suite 190, Albuquerque, NM 87131.
| |
Collapse
|