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Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Mol Biol Evol 2024; 41:msae036. [PMID: 38376487 PMCID: PMC10919930 DOI: 10.1093/molbev/msae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | | | | | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maylie Gonzales
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cara Argus
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jennifer Bolin
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mark E Berres
- University of Wisconsin Biotechnology Center, Bioinformatics Resource Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - John Steill
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott A Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Bogdan M Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Alexander Ionkov
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Kalpana Raja
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Aimee Lang
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Magnus Wolf
- Institute for Evolution and Biodiversity (IEB), University of Muenster, 48149, Muenster, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
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Wang G, Li Y, Pan R, Yin X, Jia C, She Y, Huang L, Yang G, Chi H, Tian G. XRCC1: a potential prognostic and immunological biomarker in LGG based on systematic pan-cancer analysis. Aging (Albany NY) 2024; 16:872-910. [PMID: 38217545 PMCID: PMC10817400 DOI: 10.18632/aging.205426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
X-ray repair cross-complementation group 1 (XRCC1) is a pivotal contributor to base excision repair, and its dysregulation has been implicated in the oncogenicity of various human malignancies. However, a comprehensive pan-cancer analysis investigating the prognostic value, immunological functions, and epigenetic associations of XRCC1 remains lacking. To address this knowledge gap, we conducted a systematic investigation employing bioinformatics techniques across 33 cancer types. Our analysis encompassed XRCC1 expression levels, prognostic and diagnostic implications, epigenetic profiles, immune and molecular subtypes, Tumor Mutation Burden (TMB), Microsatellite Instability (MSI), immune checkpoints, and immune infiltration, leveraging data from TCGA, GTEx, CELL, Human Protein Atlas, Ualcan, and cBioPortal databases. Notably, XRCC1 displayed both positive and negative correlations with prognosis across different tumors. Epigenetic analysis revealed associations between XRCC1 expression and DNA methylation patterns in 10 cancer types, as well as enhanced phosphorylation. Furthermore, XRCC1 expression demonstrated associations with TMB and MSI in the majority of tumors. Interestingly, XRCC1 gene expression exhibited a negative correlation with immune cell infiltration levels, except for a positive correlation with M1 and M2 macrophages and monocytes in most cancers. Additionally, we observed significant correlations between XRCC1 and immune checkpoint gene expression levels. Lastly, our findings implicated XRCC1 in DNA replication and repair processes, shedding light on the precise mechanisms underlying its oncogenic effects. Overall, our study highlights the potential of XRCC1 as a prognostic and immunological pan-cancer biomarker, thereby offering a novel target for tumor immunotherapy.
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Affiliation(s)
- Guobing Wang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Medical Clinical Laboratory, Yibin Hospital of T.C.M, Yibin, China
| | - Yunyue Li
- Queen Mary College, Medical School of Nanchang University, Nanchang, China
| | - Rui Pan
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Xisheng Yin
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Congchao Jia
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Yuchen She
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Luling Huang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, OH 45701, USA
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Qiao R, Sang S, Teng J, Zhong H, Li H, Han B. Genetic Polymorphisms of ACE1 Rs4646994 Associated with Lung Cancer in Patients with Pulmonary Nodules: A Case-Control Study. Biomedicines 2023; 11:1549. [PMID: 37371643 DOI: 10.3390/biomedicines11061549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Currently, many detection methods have high sensitivity to the diagnosis of lung cancer. However, some postoperative patients with pulmonary nodules are eventually diagnosed as having benign nodules. The ideal evaluation of an individual with a pulmonary nodule would expedite therapy for a malignant nodule and minimize testing for those with a benign nodule. METHODS This case-control study is designed to explore the relationship between ACE1 rs4646994 polymorphism and the risk of lung cancer in patients with pulmonary nodules, for which 400 individuals with lung cancer and benign pulmonary nodules were included. A DNA extraction kit was used to extract DNA from peripheral blood. The relationship between ACE1 rs4646994 and the risk of lung cancer in patients with pulmonary nodules was determined by the chi-square test, logistic regression analysis and cross analysis. RESULTS The results showed that after adjusting for age and gender confounding factors, the risk of lung cancer in patients with pulmonary nodules carrying the DD genotype was more than three times that of the I carriers (II + ID) genotype (OR = 3.035, 95% CI, 1.252-7.356, p = 0.014). There was no significant difference between lung squamous cell carcinoma and lung adenocarcinoma in the polymorphism of ACE1 rs4646994 (p > 0.05). We also found that the ACE1 rs4646994 DD genotype frequency was inversely correlated with the risk of EGFR mutation in lung adenocarcinoma patients. CONCLUSIONS Our study indicated that ACE1 rs4646994 polymorphism increases the risk of lung cancer in patients with pulmonary nodules from China.
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Affiliation(s)
- Rong Qiao
- Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Siyao Sang
- MOE Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiajun Teng
- Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Hua Zhong
- Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
- Fudan-Datong Institute of Chinese Origin, Datong 037006, China
| | - Baohui Han
- Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
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Yang F, Zhou L, Chen J, Luo Y, Wang Y. Survival association of XRCC1 for patients with head and neck squamous cell carcinoma: A systematic review and meta-analysis. Front Genet 2023; 13:1035910. [PMID: 36685969 PMCID: PMC9849232 DOI: 10.3389/fgene.2022.1035910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Epidemiologic studies have demonstrated that X-ray repair cross-complementary group 1 (XRCC1) is one of the susceptibility factors in head and neck squamous cell carcinoma (HNSCC) patients. However, its clinical prognostic impact remains controversial. Thus, a meta-analysis was performed to clarify the association between XRCC1 and the survival outcomes in HNSCC patients. Methods: Following the Preferred Reporting Items or Systematic Reviews Meta Analyses (PRISMA) 2020 guidelines, literature searches were systematically performed in PubMed, EMBASE, Web of Science, Wanfang, and Chinese National Knowledge Infrastructure (CNKI) databases with manual retrieval. Hazard ratios (HRs) and 95% confidence intervals (CIs) were collected to estimate the correlation between XRCC1 and the survival outcomes of HNSCC patients. Results: Ten studies including 1995 HNSCC patients who satisfied the inclusion and exclusion criteria were included in this meta-analysis. Pooled analysis indicated that XRCC1 Arg399Gln and XRCC1 high protein expression were significantly correlated with poor overall survival with HR of 1.31 (95% CIs: 1.03-1.66, p = 0.027) and 2.32 (95% CIs: 1.55-3.48 p = 0.000) in HNSCC patients. In addition, our results demonstrated that XRCC1 was significantly associated with poor progression-free survival (HR = 1.42, 95% CIs: 1.15-1.75, p = 0.001) in HNSCC patients. ConclusionThis meta-analysis demonstrated that XRCC1 Arg399Gln and XRCC1 high protein expression increase the risk of poor survival for HNSCC patients. XRCC1 is a potential therapeutic target for HNSCC.
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Zhou S, Zhu Q, Liu H, Jiang S, Zhang X, Peng C, Yang G, Li J, Cheng L, Zhong R, Zeng Q, Miao X, Lu Q. Associations of polycyclic aromatic hydrocarbons exposure and its interaction with XRCC1 genetic polymorphism with lung cancer: A case-control study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118077. [PMID: 34523522 DOI: 10.1016/j.envpol.2021.118077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Humans are extensively exposed to polycyclic aromatic hydrocarbons (PAHs) daily via multiple pathways. Epidemiological studies have demonstrated that occupational exposure to PAHs increases the risk of lung cancer, but related studies in the general population are limited. Hence, we conducted a case-control study among the Chinese general population to investigate the associations between PAHs exposure and lung cancer risk and analyze the modifications of genetic polymorphisms in DNA repair genes. In this study, we enrolled 122 lung cancer cases and 244 healthy controls in Wuhan, China. Urinary PAHs metabolites were determined by gas chromatography-mass spectrometry, and rs25487 in X-ray repair cross-complementation 1 (XRCC1) gene was genotyped by the Agena Bioscience MassARRAY System. Then, multivariable logistic regression models were performed to estimate the potential associations. We found that urinary hydroxynaphthalene (OH-Nap), hydroxyphenanthrene (OH-Phe) and the sum of hydroxy PAHs (∑OH-PAHs) levels were significantly higher in lung cancer cases than those in controls. After adjusting for gender, age, BMI, smoking status, smoking pack-years, drinking status and family history, urinary ∑OH-Nap and ∑OH-Phe levels were positively associated with lung cancer risk, with dose-response relationships. Compared with those in the lowest tertiles, individuals in the highest tertiles of ∑OH-Nap and ∑OH-Phe had a 2.13-fold (95% CI: 1.10, 4.09) and 2.45-fold (95% CI: 1.23, 4.87) increased risk of lung cancer, respectively. Effects of gender, age, smoking status and smoking pack-years on the associations of PAHs exposure with lung cancer risk were shown in the subgroup analysis. Furthermore, associations of urinary ∑OH-Nap and ∑OH-PAHs levels with lung cancer risk were modified by XRCC1 rs25487 (Pinteraction ≤ 0.025), and were more pronounced in wild-types of rs25487. These findings suggest that environmental exposure to naphthalene and phenanthrene is associated with increased lung cancer risk, and polymorphism of XRCC1 rs25487 might modify the naphthalene exposure-related lung cancer effect.
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Affiliation(s)
- Shuang Zhou
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qiuqi Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Huimin Liu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Shunli Jiang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China; Key Laboratory of Occupational Health and Environmental Medicine, Department of Public Health, Jining Medical University, 133 Hehua Road, Jining, Shandong, 272067, China
| | - Xu Zhang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Cheng Peng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Guanlin Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Road, Wuhan, Hubei, 430030, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Road, Wuhan, Hubei, 430030, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qiang Zeng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Xiaoping Miao
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China
| | - Qing Lu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China.
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Liu Y, Zheng C, Huang Y, He M, Xu WW, Li B. Molecular mechanisms of chemo- and radiotherapy resistance and the potential implications for cancer treatment. MedComm (Beijing) 2021; 2:315-340. [PMID: 34766149 PMCID: PMC8554658 DOI: 10.1002/mco2.55] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is a leading cause of death worldwide. Surgery is the primary treatment approach for cancer, but the survival rate is very low due to the rapid progression of the disease and presence of local and distant metastasis at diagnosis. Adjuvant chemotherapy and radiotherapy are important components of the multidisciplinary approaches for cancer treatment. However, resistance to radiotherapy and chemotherapy may result in treatment failure or even cancer recurrence. Radioresistance in cancer is often caused by the repair response to radiation-induced DNA damage, cell cycle dysregulation, cancer stem cells (CSCs) resilience, and epithelial-mesenchymal transition (EMT). Understanding the molecular alterations that lead to radioresistance may provide new diagnostic markers and therapeutic targets to improve radiotherapy efficacy. Patients who develop resistance to chemotherapy drugs cannot benefit from the cytotoxicity induced by the prescribed drug and will likely have a poor outcome with these treatments. Chemotherapy often shows a low response rate due to various drug resistance mechanisms. This review focuses on the molecular mechanisms of radioresistance and chemoresistance in cancer and discusses recent developments in therapeutic strategies targeting chemoradiotherapy resistance to improve treatment outcomes.
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Affiliation(s)
- Ya‐Ping Liu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education InstitutesInstitute of Life and Health EngineeringJinan UniversityGuangzhouP. R. China
| | - Can‐Can Zheng
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education InstitutesInstitute of Life and Health EngineeringJinan UniversityGuangzhouP. R. China
| | - Yun‐Na Huang
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering MedicineNational Engineering Research Center of Genetic MedicineInstitute of BiomedicineCollege of Life Science and TechnologyJinan UniversityGuangzhouP. R. China
| | - Ming‐Liang He
- Department of Biomedical SciencesCity University of Hong KongHong KongChina
| | - Wen Wen Xu
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering MedicineNational Engineering Research Center of Genetic MedicineInstitute of BiomedicineCollege of Life Science and TechnologyJinan UniversityGuangzhouP. R. China
| | - Bin Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education InstitutesInstitute of Life and Health EngineeringJinan UniversityGuangzhouP. R. China
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Polymorphic Variants in 5'-UTR Regions of the RAD51 Gene are Associated With RAD51 Expression and Triple-Negative Breast Cancer (TNBC): A Case-Control Study. Appl Immunohistochem Mol Morphol 2021; 29:270-276. [PMID: 33417321 DOI: 10.1097/pai.0000000000000900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/24/2020] [Indexed: 11/26/2022]
Abstract
Breast cancer is a heterogeneous disease at morphologic and molecular levels, which is considered the most commonly occurring cancer in women. RAD51, a DNA-repairing protein, involves homologous recombination and has a vital role in genome stability. Polymorphism of the RAD51 gene, and its overexpression, has been proposed to be associated with the development of breast cancer. Overexpression of RAD51 in many types of human cancer including metastatic breast cancer may signify its potential use as a biomarker. Considering the numerous reports on the role of the 5'-UTR-RAD51 polymorphism in breast cancer, this study aimed to investigate the utility of RAD51 gene expression and its variants G135C and G172T as a possible foretelling factor of breast cancer development. DNA sequencing and immunohistochemistry of RAD51 were conducted on 103 samples from patients diagnosed with sporadic breast cancer and 80 samples from a control group. The results demonstrated that the RAD51 variants, G135C and G172T, were significantly presented in the breast cancer tissue compared with the control group. RAD51 expression was mainly shown in the cytoplasm of malignant cells (56% of cases) and significantly correlated with p53 and G135C, C135C variants. Moreover, the occurrence of the G172T variant was significantly associated with the expression of estrogen receptor. Interestingly, 21/26 (81%) of the triple-negative breast cancer showed G135C and C135C genotypes that were significantly associated with the expression of RAD51 (73%). In conclusion, the G135C and C135C variants together with the cytoplasmic expression of RAD51 may have clinical potential as a prognostic predictor for breast cancer development and aggressiveness.
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Jin J, Robeson H, Fagan P, Orloff MS. Association of PARP1-specific polymorphisms and haplotypes with non-small cell lung cancer subtypes. PLoS One 2020; 15:e0243509. [PMID: 33284833 PMCID: PMC7721167 DOI: 10.1371/journal.pone.0243509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/20/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE The carcinogenesis role of PARP1 in lung cancer is still not clear. Analysis at allelic levels cannot fully explain the function of PARP1 on lung cancer. Our study aims to further explore the relation between PARP1 haplotypes and lung cancer. MATERIALS AND METHODS DNA and RNA were extracted from non-small cell lung cancer (NSCLC) tumor and adjacent normal fresh frozen tissue. Five PARP1-SNPs were genotyped and PARP1-specific SNPs were imputed using IMPUTE and SHAPEIT software. The SNPs were subjected to allelic, haplotype and SNP-SNP interaction analyses. Correlation between SNPs and mRNA/protein expressions were performed. RESULTS SNP imputation inferred the ungenotyped SNPs and increased the power for association analysis. Tumor tissue samples are more likely to carry rs1805414 (OR = 1.85; 95% CI: 1.12-3.06; P-value: 0.017) and rs1805404 (OR = 2.74; 95%CI 1.19-6.32; P-value: 0.015) compared to normal tissues. Our study is the first study to show that haplotypes comprising of 5 SNPs on PARP1 (rs1136410, rs3219073, rs1805414, rs1805404, rs1805415) is able to differentiate the NSCLC tumor from normal tissues. Interaction between rs3219073, rs1805415, and rs1805414 were significantly associated with the NSCLC tumor with OR ranging from 3.61-6.75; 95%CI from 1.82 to 19.9; P-value<0.001. CONCLUSION PARP1 haplotypes may serve as a better predictor in lung cancer development and prognosis compared to single alleles.
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Affiliation(s)
- Jing Jin
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Heather Robeson
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Pebbles Fagan
- Department of Health Behavior and Health Education, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Center for the Studies of Tobacco, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Mohammed S. Orloff
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Center for the Studies of Tobacco, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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Oliveira de Araújo Melo C, Cidália Vieira T, Duarte Gigonzac MA, Soares Fortes J, Moreira Duarte SS, da Cruz AD, Silva DDME. Evaluation of polymorphisms in repair and detoxification genes in alcohol drinkers and non-drinkers using capillary electrophoresis. Electrophoresis 2019; 41:254-258. [PMID: 31886888 DOI: 10.1002/elps.201900193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 02/03/2023]
Abstract
Alcohol use disorder (AUD) causes about 3.3 million deaths around the world each year. It is the primary risk factor for the global burden of diseases in American countries. Long-term abuse of alcohol induces numerous molecular and biochemical changes in tissues exposed to alcohol. The toxic effects of alcohol are mediated by DNA damage through various mechanisms, such as induction of oxidative damage, DNA adducts, crosslinks, and DNA strand breaks. The main aim of the current study was to compare the frequency of SNP polymorphisms in XRCC1 (rs7997782) and GSTP1 (rs1695) genes involved in DNA repair of single strand breaks (SSB) and xenobiotic detoxification between alcohol addicts and a control group comprised of non-drinkers. Genetic polymorphisms were identified following allelic specific PCR designed to generate the amplicons containing the variants. Then amplicons were sequenced, and sequences were aligned against the human genome reference deposited in GenBank using the CLC Sequence Viewer software (version 7.6.1). The GG homozygotes in rs1695 (GSTP1) were significantly (p = 0.023) 3.8x more frequent among those with AUD when compared to the control group. No SNP variation was observed in rs7997782 (XRCC1). rs1695 variant has been associated with susceptibility to various diseases, including those related to alcohol consumption.
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Affiliation(s)
- Caroline Oliveira de Araújo Melo
- Federal University of Goiás, Goiânia, GO, Brazil.,Postgraduate Program in Genetics/Replicon Research Center, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil
| | - Thaís Cidália Vieira
- Postgraduate Program in Genetics/Replicon Research Center, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil.,Laboratory of Human Cytogenetics and Molecular Genetics, Goiás State Health Secretary, Goiânia, GO, Brazil.,Goiás State University - Campus Goiânia, GO, Brazil
| | - Marc Alexandre Duarte Gigonzac
- Postgraduate Program in Genetics/Replicon Research Center, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil.,Laboratory of Human Cytogenetics and Molecular Genetics, Goiás State Health Secretary, Goiânia, GO, Brazil.,Goiás State University - Campus Goiânia, GO, Brazil
| | - Jakeline Soares Fortes
- Postgraduate Program in Genetics/Replicon Research Center, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil
| | - Sabrina Sara Moreira Duarte
- Federal University of Goiás, Goiânia, GO, Brazil.,Postgraduate Program in Genetics/Replicon Research Center, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Federal University of Goiás, Goiânia, GO, Brazil.,Postgraduate Program in Genetics/Replicon Research Center, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil.,Laboratory of Human Cytogenetics and Molecular Genetics, Goiás State Health Secretary, Goiânia, GO, Brazil
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10
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Ezzeldin N, El-Lebedy D, Mohammed A. Gene-environment and gene-gene interactions between CHRNA3 rs1051730, XRCC1 rs25487, and ERCC1 rs735482 variants highly elevate the risk of lung cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0034-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Gene-gene and gene-environment interactions play an important role in cancer susceptibility. In this work, we studied the association of XRCC1 rs25487, ERCC1 rs735482, and CHRNA3 rs1051730 variants with lung cancer and assessed the modulatory effect of potential interaction between these variants on disease risk.
Results
In this study, 86 primary lung cancer patients and 64 control subjects were genotyped for CHRNA3 rs1051730, XRCC1 rs25487, and ERCC1 rs735482 by real-time PCR. The frequency of the three studied variants was higher among lung cancer patients than in control subjects, but with no statistical significance. ERCC1 rs735482 variant was associated with 6.9-fold increased risk to develop lung cancer among smokers (p = 0.03). Concomitant presence of CHRNA3 and ERCC1 wild alleles was associated with 2.7-fold elevated risk of lung cancer (p < 0.0001), while concomitant presence of CHRNA3 rs1051730 variant allele with ERCC1 wild allele was associated with 20-fold elevated risk (p < 0.000). Concomitant presence of both variants, ERCC1 rs735482 and CHRNA3 rs1051730, was associated with 9.9-fold elevated risk (p < 0.0001). Meanwhile, the concomitant presence of XRCC1 rs25487 with either ERCC1 rs735482 or CHRNA3 rs1051730 or both was not associated with increased risk of the disease.
Conclusion
Our results emphasize the role of gene-gene interaction in the pathogenesis of lung cancer. Large-scale further studies to clarify the underlying mechanisms are needed.
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11
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Bhardwaj A, Bahl C, Sharma S, Singh N, Behera D. Interactive potential of genetic polymorphism in Xenobiotic metabolising and DNA repair genes for predicting lung cancer predisposition and overall survival in North Indians. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2017; 826:15-24. [PMID: 29412865 DOI: 10.1016/j.mrgentox.2017.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/18/2017] [Accepted: 12/15/2017] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Cancer, a multi-step, multifactorial and multi-gene disease, not only damages the genomic integrity of the cell but also hinders the DNA repair mechanisms of the body. Gene-gene and gene environment interactions amongst the genetic polymorphisms together modulate the susceptibility towards a cancer. We have studied the high order gene interactions between the genetic polymorphism of detoxifying genes (CYP1A1, Ahr, XRCC and GST1) that play a key role in the metabolism of the xenobiotics and have been proved to be prognostic markers for lung cancer METHODS: 237 cases and 250 controls have been genotyped using PCR-RFLP technique. In order to find out the association, unconditional logistic regression approach was used and to analyse high order interactions MDR and CART was used. RESULTS In the MDR analysis, the best model was one factor model which included GSTM1 (CVC 10/10, Prediction error = 0.43, p < .001). The best three factor model comprised of XRCC1 632, XRCC1 206, GSTM1 (CVC 10/10, Prediction error = 0.45, p < .0001). The CART analysis exhibited that Node 1 carrying mutant type of GSTM1 imposed the highest risk towards lung cancer (OR = 11.0, 95%C.I. = 6.05-20.03, p = .000001). Wild type of GSTM1 when combined with mutant type of CYP1A1 M2 and XRCC1 632, an 8 fold risk towards lung cancer was observed (95%C.I. = 4.07-16.29, p = .00001). The high order interactions were used to predict the prognosis of lung cancer patients. Of all the genetic variants, XRCC1 632, GSTM1 and AhR rs2066853 was the most important determinant of overall survival of lung cancer patients CONCLUSION: Through the study we introduced the concept of polygenic approach to get an insight about the various polymorphic variants in determining cancer susceptibility. Lesser number of subjects were found in the high risk subgroups. Further studies with larger sample size are required to warranty the above findings.
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Affiliation(s)
- Apurva Bhardwaj
- Department of Biotechnology, Thapar University, Patiala, Punjab-147002, India
| | - Charu Bahl
- Department of Biotechnology, Thapar University, Patiala, Punjab-147002, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar University, Patiala, Punjab-147002, India.
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 14, Chandigarh, India
| | - Digamber Behera
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 14, Chandigarh, India
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12
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Tasnim T, Al-Mamun MMA, Nahid NA, Islam MR, Apu MNH, Bushra MU, Rabbi SNI, Nahar Z, Chowdhury JA, Ahmed MU, Islam MS, Hasnat A. Genetic variants of SULT1A1 and XRCC1 genes and risk of lung cancer in Bangladeshi population. Tumour Biol 2017; 39:1010428317729270. [PMID: 29110586 DOI: 10.1177/1010428317729270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is one of the most frequently occurring cancers throughout the world as well as in Bangladesh. This study aimed to correlate the prognostic and/or predictive value of functional polymorphisms in SULT1A1 (rs9282861) and XRCC1 (rs25487) genes and lung cancer risk in Bangladeshi population. A case-control study was conducted which comprises 202 lung cancer patients and 242 healthy volunteers taking into account the age, sex, and smoking status. After isolation of genomic DNA, genotyping was done by polymerase chain reaction-restriction fragment length polymorphism method and the lung cancer risk was evaluated as odds ratio that was adjusted for age, sex, and smoking status. A significant association was found between SULT1A1 rs9282861 and XRCC1 rs25487 polymorphisms and lung cancer risk. In case of rs9282861 polymorphism, Arg/His (adjusted odds ratio = 5.06, 95% confidence interval = 3.05-8.41, p < 0.05) and His/His (adjusted odds ratio = 3.88, 95% confidence interval = 2.20-6.82, p < 0.05) genotypes were strongly associated with increased risk of lung cancer in comparison to the Arg/Arg genotype. In case of rs25487 polymorphism, Arg/Gln heterozygote (adjusted odds ratio = 4.57, 95% confidence interval = 2.79-7.46, p < 0.05) and Gln/Gln mutant homozygote (adjusted odds ratio = 4.99, 95% confidence interval = 2.66-9.36, p < 0.05) were also found to be significantly associated with increased risk of lung cancer. This study demonstrates that the presence of His allele and Gln allele in case of SULT1A1 rs9282861 and XRCC1 rs25487, respectively, involve in lung cancer prognosis in Bangladeshi population.
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Affiliation(s)
- Tasnova Tasnim
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh.,3 Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Mir Md Abdullah Al-Mamun
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Noor Ahmed Nahid
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Md Reazul Islam
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Mohd Nazmul Hasan Apu
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Most Umme Bushra
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | | | - Zabun Nahar
- 3 Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Jakir Ahmed Chowdhury
- 4 Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Maizbha Uddin Ahmed
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Safiqul Islam
- 5 Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Abul Hasnat
- 1 Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
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13
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Meng Q, Wang S, Tang W, Wu S, Gao N, Zhang C, Cao X, Li X, Zhang Z, Aschner M, Jin H, Huang Y, Chen R. XRCC1 mediated the development of cervival cancer through a novel Sp1/Krox-20 swich. Oncotarget 2017; 8:86217-86226. [PMID: 29156789 PMCID: PMC5689679 DOI: 10.18632/oncotarget.21040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/09/2017] [Indexed: 01/18/2023] Open
Abstract
Cervical cancer is the second leading cause of mortality among women. Impairment of the base excision repair (BER) pathway is one of the major causes of the initiation and progression of cervical cancer. However, whether the polymorphisms of the BER pathway components (i.e., HOGG1, XRCC1, ADPRT, and APE1) can affect the risk of cervical cancer remains unknown. Herein, we applied a hospital-based case-control study covering two independent cohorts and a subsequent functional assay to determine the roles of the single nucleotide polymorphisms (SNPs) of the BER pathway genes in cervical cancer. Results indicated that the XRCC1 rs3213245 (-77TC) TT genotype was associated with an increased risk of cervical cancer. The immunohistochemistry assay showed that XRCC1 protein expression levels were upregulated in cervical cancer patients with the XRCC1 rs3213245 CC genotype compared with the CT or TT genotypes. Further, results from ChIP assay showed that Sp1 could bind to the −77 site and that the rs3213245 C genotype promoted the binding of Sp1 to the XRCC1 promoter. Moreover, ChIP/Re-ChIP assays revealed that transcription factor Krox-20 was recruited to the XRCC1 rs3213245 mutation region and regulated the transcription of the XRCC1 gene by interacting with Sp1, ultimately mediated cervical cancer development. In summary, the findings indicated that the functional XRCC1 SNP rs3213245 was associated with the risk of cervical cancer based on the Sp1/Krox-20 switch.
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Affiliation(s)
- Qingtao Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Weiyan Tang
- Medical Oncology, Jiangsu Cancer Hospital, Nanjing, China
| | - Shenshen Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Na Gao
- Institute of Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
| | - Chengcheng Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Xiaoli Cao
- Clinical Lab, Nantong Tumor Hospital, Nantong, China
| | - Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hua Jin
- Core Laboratory, Nantong Tumor Hospital, Nantong, China
| | - Yue Huang
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China.,State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
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14
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Sujitha SP, Kumar DT, Doss CGP, Aavula K, Ramesh R, Lakshmanan S, Gunasekaran S, Anilkumar G. DNA Repair Gene (XRCC1) Polymorphism (Arg399Gln) Associated with Schizophrenia in South Indian Population: A Genotypic and Molecular Dynamics Study. PLoS One 2016; 11:e0147348. [PMID: 26824244 PMCID: PMC4732819 DOI: 10.1371/journal.pone.0147348] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/31/2015] [Indexed: 01/20/2023] Open
Abstract
This paper depicts the first report from an Indian population on the association between the variant Arg399Gln of XRCC1 locus in the DNA repair system and schizophrenia, the debilitating disease that affects 1% of the world population. Genotypic analysis of a total of 523 subjects (260 patients and 263 controls) revealed an overwhelming presence of Gln399Gln in the case subjects against the controls (P < 0.0068), indicating significant level of association of this nsSNP with schizophrenia; the Gln399 allele frequency was also perceptibly more in cases than in controls (p < 0.003; OR = 1.448). The results of the genotypic studies were further validated using pathogenicity and stability prediction analysis employing computational tools [I-Mutant Suite, iStable, PolyPhen2, SNAP, and PROVEAN], with a view toassess the magnitude of deleteriousness of the mutation. The pathogenicity analysis reveals that the nsSNP could be deleterious inasmuch as it could affect the functionality of the gene, and interfere with protein function. Molecular dynamics simulation of 60ns was performed using GROMACS to analyse structural change due to a mutation (Arg399Gln) that was never examined before. RMSD, RMSF, hydrogen bonds, radius of gyration and SASA analysis showedthe existence of asignificant difference between the native and the mutant protein. The present study gives astrong indication that the XRCC1 locus deserves serious attention, as it could be a potential candidatecontributing to the etio-pathogenesis of the disease.
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Affiliation(s)
- S. P. Sujitha
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - D. Thirumal Kumar
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - C. George Priya Doss
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - K. Aavula
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - R. Ramesh
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - S. Lakshmanan
- Department of Psychiatry, Government Vellore Medical College, Vellore, India
| | - S. Gunasekaran
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - G. Anilkumar
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
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15
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Ghosh S, Ghosh S, Bankura B, Saha ML, Maji S, Ghatak S, Pattanayak AK, Sadhukhan S, Guha M, Nachimuthu SK, Panda CK, Maity B, Das M. Association of DNA repair and xenobiotic pathway gene polymorphisms with genetic susceptibility to gastric cancer patients in West Bengal, India. Tumour Biol 2016; 37:9139-49. [PMID: 26768611 DOI: 10.1007/s13277-015-4780-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/29/2015] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer is one of the most common malignancies in India. DNA repair gene or xenobiotic pathway gene polymorphisms have recently been shown to affect individual susceptibility to gastric cancer. Here, the possible interaction between common polymorphisms in X-ray repair cross complementing group I (XRCC1) gene and glutathione S-transferase (GST) genes (GSTM1, GSTT1 and GSTP1), smoking and alcohol consumption and overall survival in gastric cancer patients were evaluated. In this population-based case control study, 70 gastric cancer patients and 82 healthy controls were enrolled. The epidemiological data were collected by a standard questionnaire, and blood samples were collected from each individual. XRCC1 Arg194Trp, Arg280His and Arg399Gln polymorphisms were determined by polymerase chain reaction and direct DNA sequencing. GSTM1 and GSTT1 null polymorphisms and GSTP1 Ile105Val polymorphism were identified by multiplex polymerase chain reaction and restriction fragment length polymorphism (RFLP), respectively. The risk of gastric cancer was significantly elevated in individuals with XRCC1 Arg/Gln +Gln/Gln (p = 0.031; odds ratio = 2.32; 95 % confidence interval (CI) 1.07-5.06) and GSTP1 Val/Val genotype (p = 0.009; odds ratio = 8.64; 95 % CI 1.84-40.55). An elevated risk for GC was observed in smokers and alcohol consumers carrying GSTP1 Ile/Val +Val/Val genotype (p = 0.041; odds ratio = 3.71; 95 % CI 0.98-14.12; p = 0.002; odds ratio = 12.31; 95 % CI 1.71-88.59). These findings suggest that XRCC1 rs25487 and GSTP1 rs1695 can be considered as a risk factor associated with gastric cancer and might be used as a molecular marker for evaluating the susceptibility of the disease.
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Affiliation(s)
- Soumee Ghosh
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Sudakshina Ghosh
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Biswabandhu Bankura
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Makhan Lal Saha
- Department of Surgery, Institute of Post Graduate Medical Education & Research, 244 A.J.C Bose Road, Kolkata, 700 020, West Bengal, India
| | - Suvendu Maji
- Department of Surgery, Institute of Post Graduate Medical Education & Research, 244 A.J.C Bose Road, Kolkata, 700 020, West Bengal, India
| | - Souvik Ghatak
- Department of Biotechnology, Mizoram University, Tanhril, Aizawl, Mizoram, P.O. Box No. 190, India
| | - Arup Kumar Pattanayak
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Susanta Sadhukhan
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Manalee Guha
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Senthil Kumar Nachimuthu
- Department of Biotechnology, Mizoram University, Tanhril, Aizawl, Mizoram, P.O. Box No. 190, India
| | - Chinmay Kumar Panda
- Department of Oncogene Regulation and Viral Associated Human Cancer, Chittaranjan Cancer Research Institute, 37, S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India
| | - Biswanath Maity
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Madhusudan Das
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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16
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Al-Zoubi MS, Mazzanti CM, Zavaglia K, Hamad MA, Armogida I, Lisanti MP, Bevilacqua G. Homozygous T172T and Heterozygous G135C Variants of Homologous Recombination Repairing Protein RAD51 are Related to Sporadic Breast Cancer Susceptibility. Biochem Genet 2015; 54:83-94. [DOI: 10.1007/s10528-015-9703-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/21/2015] [Indexed: 12/30/2022]
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17
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Yoo SS, Jin C, Jung DK, Choi YY, Choi JE, Lee WK, Lee SY, Lee J, Cha SI, Kim CH, Seok Y, Lee E, Park JY. Putative functional variants of XRCC1 identified by RegulomeDB were not associated with lung cancer risk in a Korean population. Cancer Genet 2014; 208:19-24. [PMID: 25592768 DOI: 10.1016/j.cancergen.2014.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 11/03/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
Abstract
The Encyclopedia of DNA elements (ENCODE) project revealed that nearby or distantly located non-coding DNA regulates the expression of coding genes. RegulomeDB (http://regulome.stanford.edu) is a new database that can be used to predict whether a variant affects transcription factor binding and gene expression. We investigated the association between lung cancer risk and potentially functional polymorphisms of XRCC1 that were selected using RegulomeDB in a Korean population. A total of 185 polymorphisms of XRCC1 were evaluated using RegulomeDB. Strong evidence suggested that 10 polymorphisms, from among the 185, affected XRCC1 expression with scores of 1a-1f that were based on the RegulomeDB scoring system. The rs2854510 polymorphism was rare in Asians (minor allele frequency < 0.05). Eight polymorphisms were in strong linkage disequilibrium (LD). The rs2854509 polymorphism, which was one of the 8 polymorphisms in LD, and rs7248167, which was not in the LD block, were genotyped in 610 lung cancer patients and 607 age- and sex-matched controls. Additionally, four polymorphisms of XRCC1 (rs25487, rs25489, rs1799782, and rs3213245), which were investigated with regard to their association with lung cancer risk in previous studies, were also genotyped. Two polymorphisms (rs2854509 and rs7248167) that were predicted to affect XRCC1 expression based on their RegulomeDB scores were not associated with lung cancer risk (P = 0.31 and 0.93, respectively). When stratified according to age, gender, smoking status, and tumor histology, the two polymorphisms of XRCC1 were not associated with lung cancer risk. Among the four polymorphisms that were previously studied, only rs25489 of XRCC1 was significantly associated with lung cancer risk (dominant model, adjusted odds ratio = 0.61, 95% confidence interval = 0.46-0.83, P = 0.002). Although RegulomeDB is an attractive tool for predicting the regulatory potential of variants, the two polymorphisms that were selected using RegulomeDB were not associated with lung cancer risk.
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Affiliation(s)
- Seung Soo Yoo
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Chengcheng Jin
- Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Deuk Kju Jung
- Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Yi Young Choi
- Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Won Kee Lee
- Department of Preventive Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Shin Yup Lee
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Jaehee Lee
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Seung Ick Cha
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Chang Ho Kim
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Yangki Seok
- Department of Thoracic Surgery, Kyungpook National University School of Medicine, Daegu, Korea
| | - Eungbae Lee
- Department of Thoracic Surgery, Kyungpook National University School of Medicine, Daegu, Korea
| | - Jae Yong Park
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea; Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea.
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18
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Natukula K, Jamil K, Pingali UR, Attili VSS, Madireddy URN. The codon 399 Arg/Gln XRCC1 polymorphism is associated with lung cancer in Indians. Asian Pac J Cancer Prev 2014; 14:5275-9. [PMID: 24175813 DOI: 10.7314/apjcp.2013.14.9.5275] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The XRCC1 (X-ray repair cross complimenting group-I) gene in BER (base excision repair) pathway is essential for DNA repair process. Polymorphisms in this gene are associated with variations in the repair efficiency which might predispose individuals to development of various cancers. Two variants of XRCC1gene (at codon 399), Gln/Gln and Arg/Gln, have been shown to be related to lowered DNA repair capacity and increased genomic instability in multiple studies. Hence our investigation focused on genotyping these variants to correlate with other multiple risk factors in lung cancer (NSCLC) patients since we hypothesized that these variants of the XRCC1 gene might influence disease susceptibility. MATERIALS AND METHODS We examined the frequency of the polymorphism in one hundred cases and an almost equal number of controls after recording their demographics with a structured questionnaire. Genomic DNA from blood samples was extracted for PCR studies, followed by RFLP to determine the variants. The significance of the data was statistically analyzed. RESULTS The three genotypes in cases and controls were Arg/Arg (40% and 54.45%); Gln/Gln (19% and 9.90%), and Arg/Gln (41.0% and 35.64%) respectively. Among these 3 genotypes, we found Gln/Gln and Arg/Gln to show association with lung cancer. Correlating these genotypes with several parameters, we also found that these two variants were associated with risk in males (p<0.05) and with smoking habits (p<0.05). In females Arg/Gln genotype showed association with stage of the disease (p=0.04). This is the first report in South Indian scenario where Arg399Gln genotypes were found to be associated with stage of the disease in females. CONCLUSIONS It is concluded that XRCC1 genotypes Gln/Gln and Arg/Gln may influence cancer susceptibility in patients with smoking habits and these functional SNPs in XRCC1 gene may act as attractive candidate biomarkers in lung cancer for diagnosis and prognosis.
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Affiliation(s)
- Kirmani Natukula
- Genetics Department, Bhagwan Mahavir Medical Research Centre, Masab tank, India E-mail :
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Wang C, Ai Z. Association of XRCC1 polymorphisms with thyroid cancer risk. Tumour Biol 2014; 35:4791-7. [PMID: 24477575 DOI: 10.1007/s13277-014-1629-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 01/06/2014] [Indexed: 11/28/2022] Open
Abstract
Due to the important role in the DNA repair pathways, numerous studies have been carried out to explore the relationship between the polymorphisms in the X-ray repair cross-complementing group 1 (XRCC1) gene and thyroid cancer risk. But previous reports have produced conflicting results. Thus, we performed an updated comprehensive meta-analysis to better investigate the association of the XRCC1 polymorphisms with thyroid cancer risk. There were a total of nine studies included with 1,621 cases and 3,669 controls examining the effects of the XRCC1 Arg280His, Arg399Gln, and Arg194Trp polymorphisms on the susceptibility of thyroid cancer. In our study, the XRCC1 Arg280His polymorphism was found to be associated with an increased thyroid cancer risk in the Caucasian population [allelic contrast: odds ratio (OR) = 1.38, 95% CI = 1.05-1.80, P(Z) = 0.02, P(Q) = 0.61; dominant model: OR = 1.43, 95% CI = 1.08-1.89, P(Z) = 0.01, P(Q) = 0.57]. The Arg399Gln polymorphism was associated with a significant decreased risk [allelic contrast: OR = 0.73, 95% CI = 0.59-0.92, P(Z) = 0.006, P(Q) = 0.31; dominant model: OR = 0.73, 95% CI = 0.55-0.97, P(Z) = 0.03, P(Q) = 0.33; recessive model: OR = 0.56, 95% CI = 0.34-0.93, P(Z) = 0.02, P(Q) = 0.59], while the Arg194Trp SNP conferred an increased risk for thyroid cancer in the mixed populations [allelic contrast: OR = 1.49, 95% CI = 1.02-2.17, P(Z) = 0.04]. To conclude, the present meta-analysis demonstrated that the polymorphisms in the XRCC1 gene may be associated with developing of thyroid cancer.
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Affiliation(s)
- Cong Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
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Wang JY, Cai Y. X-ray repair cross-complementing group 1 codon 399 polymorphism and lung cancer risk: an updated meta-analysis. Tumour Biol 2013; 35:411-8. [DOI: 10.1007/s13277-013-1057-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 07/24/2013] [Indexed: 11/25/2022] Open
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DNA repair gene XRCC3 Thr241Met polymorphism and hepatocellular carcinoma risk. Tumour Biol 2013; 34:2827-34. [DOI: 10.1007/s13277-013-0841-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/02/2013] [Indexed: 12/16/2022] Open
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Yanatatsaneejit P, Boonsuwan T, Mutirangura A, Kitkumthorn N. XRCC1 gene polymorphisms and risk of ameloblastoma. Arch Oral Biol 2013. [DOI: 10.1016/j.archoralbio.2012.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Yuan T, Wei J, Luo J, Liu M, Deng S, Chen P. Polymorphisms of base-excision repair genes hOGG1 326cys and XRCC1 280His increase hepatocellular carcinoma risk. Dig Dis Sci 2012; 57:2451-7. [PMID: 22565339 DOI: 10.1007/s10620-012-2192-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 04/14/2012] [Indexed: 12/20/2022]
Abstract
BACKGROUND DNA base-excision repair genes hOGG1 and XRCC1 play an important role in preserving genetic stability in mammalian cells against any damage caused by different factors. However, it is unclear whether altered expression and function of these DNA repair genes could lead to hepatocellular carcinoma (HCC) susceptibility. AIMS This study determined the association between polymorphisms of the genes encoding two key proteins of DNA base excision repair (hOGG1 ser326Cys and XRCC1 Arg 280His) and HCC risk. METHODS A total of 350 HCC patients (mean age of 51.1 years) and 400 healthy controls (mean age of 51.4 years) were recruited for analysis of XRCC1 and hOGG1 gene polymorphisms using PCR plus restriction fragment length polymorphism (PCR-RFLP). RESULTS The data showed that the hOGG1 Cys326Cys and Ser326Cys genotypes were associated with increase in HCC risk. In contrast, there was no association between HCC susceptibility and the distribution of XRCC1 His 280 His and Arg280His. However, combination of these two gene polymorphisms (XRCC1-280 Arg and hOGG1-326Cys) is associated with significant induction of HCC risk. In addition, the data also showed that XRCC1 280His polymorphism was associated with HBV infection and HCC family history to increase HCC risk. The hOGG1 326cys genotype was associated with alcohol consumption, tobacco smoke, and HBV infection to increase HCC risk. CONCLUSION The data from the current study demonstrated the association of these two DNA repair gene polymorphisms with HCC risk. Future studies will confirm these data before they can be used as a biomarker for assessing HCC risk.
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Affiliation(s)
- Tao Yuan
- Department of Hepatobiliary Surgery, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing 400042, China
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High risk of benzo[α]pyrene-induced lung cancer in E160D FEN1 mutant mice. Mutat Res 2011; 731:85-91. [PMID: 22155171 DOI: 10.1016/j.mrfmmm.2011.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/18/2011] [Accepted: 11/25/2011] [Indexed: 11/20/2022]
Abstract
Flap endonuclease 1 (FEN1), a member of the Rad2 nuclease family, possesses 5' flap endonuclease (FEN), 5' exonuclease (EXO), and gap-endonuclease (GEN) activities. The multiple, structure-specific nuclease activities of FEN1 allow it to process different intermediate DNA structures during DNA replication and repair. We previously identified a group of FEN1 mutations and single nucleotide polymorphisms that impair FEN1's EXO and GEN activities in human cancer patients. We also established a mouse model carrying the E160D FEN1 mutation, which mimics the mutations seen in humans. FEN1 mutant mice developed spontaneous lung cancer at high frequency at their late life stages. An important unanswered question is whether individuals carrying such FEN1 mutation are more susceptible to tobacco smoke and have an earlier onset of lung cancer. Here, we report our study on E160D mutant mice exposed to benzo[α]pyrene (B[α]P), a major DNA damaging compound found in tobacco smoke. We demonstrate that FEN1 employs its GEN activity to cleave DNA bubble substrates with BP-induced lesions, but the E160D FEN1 mutation abolishes such activity. As a consequence, Mouse cells carrying the E160D mutation display defects in the repair of B[α]P adducts and accumulate DNA double-stranded breaks and chromosomal aberrations upon treatments with B[α]P. Furthermore, more E160D mice than WT mice have an early onset of B[α]P-induced lung adenocarcinoma. All together, our current study suggests that individuals carrying the GEN-deficient FEN1 mutations have high risk to develop lung cancer upon exposure to B[α]P-containing agents such as tobacco smoke.
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Li Z, Guan W, Li MX, Zhong ZY, Qian CY, Yang XQ, Liao L, Li ZP, Wang D. Genetic polymorphism of DNA base-excision repair genes (APE1, OGG1 and XRCC1) and their correlation with risk of lung cancer in a Chinese population. Arch Med Res 2011; 42:226-34. [PMID: 21722819 DOI: 10.1016/j.arcmed.2011.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 03/11/2011] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Reactive oxygen species (ROS) and numerous carcinogens may cause DNA damage including oxidative base lesions that contribute to the risk of lung cancer. The base excision repair (BER) pathway could effectively remove oxidative lesions in which 8-oxoguanine glycosylase-1 (OGG1), x-ray repair cross-complementing 1 (XRCC1), and apurinic/apyimidinic endonuclease 1 (APE1) play key roles. The aim of this study was to analyze the polymorphisms of DNA BER genes (OOG1, XRCC1 and APE1) and explore their associations, and the combined effects of these variants, with risk of lung cancer. METHODS In a hospital-based, case-control study of 455 lung cancer cases and 443 cancer-free hospital controls, the SNPs of OGG1 (Ser326Cys), XRCC1 (Arg399Gln), APE1 (Asp148Glu and -141T/G) were genotyped and analyzed for their correlation with the risk of lung cancer in multivariate logistic regression models. RESULTS Individuals homozygous for the variants APE1 -141GG showed a protective effect for lung cancer overall (OR=0.62; 95% CI: 0.42-0.91; p=0.02) and for lung adenocarcinoma (OR=0.65; 95% CI, 0.44-0.96; p=0.03). When analyzing the combined effects of variant alleles, 84 patients and controls were identified who were homozygous for two or three of the potential protective alleles (i.e., OGG1 326Cys, XRCC1 399Gln and APE1 -141G). ORs were significantly reduced when all patients were analyzed (OR=0.62; 95% CI: 0.38-0.99; p=0.05). CONCLUSIONS The combined effects of polymorphisms within BER genes may contribute to the tumorigenesis of lung cancer.
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Affiliation(s)
- Zheng Li
- Department of Pathology, Third Military Medical University, Chongqing, China
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Shagirova ZM, Kurbatova LA, Shulenina LV, Semyachkina AN, Mikhailov VF, Zasukhina GD. The peculiarities of polymorphism of XPD and XRCC1 repair genes in cells of down and Ehlers-Danlo syndrome patients characterized by increased radiosensitivity. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911050198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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García-Quispes WA, Pérez-Machado G, Akdi A, Pastor S, Galofré P, Biarnés F, Castell J, Velázquez A, Marcos R. Association studies of OGG1, XRCC1, XRCC2 and XRCC3 polymorphisms with differentiated thyroid cancer. Mutat Res 2011; 709-710:67-72. [PMID: 21414327 DOI: 10.1016/j.mrfmmm.2011.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 02/28/2011] [Accepted: 03/02/2011] [Indexed: 10/18/2022]
Abstract
The role of the DNA repair genes OGG1, XRCC1, XRCC2 and XRCC3 on differentiated thyroid cancer (DTC) susceptibility was examined in 881 individuals (402 DTC and 479 controls). DNA repair genes were proposed as candidate genes, since the current data indicate that exposure to ionizing radiation is the only established factor in the development of thyroid cancer, especially when it occurs in early stages of life. We have genotyped DNA repair genes involved in base excision repair (BER) (OGG1, Ser326Cys; XRCC1, Arg280His and Arg399Gln), and homologous recombination repair (HRR) (XRCC2, Arg188His and XRCC3, ISV-14G). Genotyping was carried out using the iPLEX (Sequenom) technique. Multivariate logistic regression analyses were performed in a case-control study design. From all the studied polymorphism, only a positive association (OR=1.58, 95% CI 1.05-2.46, P=0.027) was obtained for XRCC1 (Arg280His). No associations were observed for the other polymorphisms. No effects of the histopathological type of tumor were found when the DTC patients were stratified according to the type of tumor. It must be emphasized that this study include the greater patients group, among the few studies carried out until now determining the role of DNA repair genes in thyroid cancer susceptibility.
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Affiliation(s)
- Wilser-Andrés García-Quispes
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Ginsberg G, Angle K, Guyton K, Sonawane B. Polymorphism in the DNA repair enzyme XRCC1: utility of current database and implications for human health risk assessment. Mutat Res 2011; 727:1-15. [PMID: 21352951 DOI: 10.1016/j.mrrev.2011.02.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/10/2011] [Accepted: 02/16/2011] [Indexed: 11/29/2022]
Abstract
Genetic polymorphisms are increasingly recognized as sources of variability not only in toxicokinetic but also in toxicodynamic response to environmental agents. XRCC1 is involved in base excision repair (BER) of DNA; it has variant genotypes that are associated with modified repair function. This analysis focuses on four polymorphisms: three in the coding region that affect protein structure and one in an upstream regulatory sequence that affects gene expression. The Arg399Gln variant is the most widely studied with evidence supporting a quantitative effect of genotype on phenotype. The homozygous variant (Gln/Gln) can have 3-4-fold diminished capacity to remove DNA adducts and oxidized DNA damage. This variant is relatively common in Caucasians and Asians where approximately 10% are homozygous variant. In contrast, the Arg194Trp variant appears to protect against genotoxic effects although the degree to which DNA repair is enhanced by this polymorphism is uncertain. The homozygous variant is rare in Caucasians and African Americans but it is present at 7% in Asians. A third coding region polymorphism at codon 280 appears to decrease repair function but additional quantitative information is needed and the homozygous variant is rare across populations studied. A polymorphism in an upstream promoter binding sequence (-77T>C) appears to lower XRCC1 levels by decreasing gene expression. Based upon genotype effect on phenotype and allele frequency, the current analysis finds that the codon 399 and upstream (-77) polymorphisms have the greatest potential to affect the toxicodynamic response to DNA damaging agents. However, the implications for risk assessment are limited by the likelihood that polymorphisms in multiple BER genes interact to modulate DNA repair.
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Affiliation(s)
- Gary Ginsberg
- Connecticut Dept of Public Health, Hartford, CT, United States.
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DNA repair gene X-ray repair cross complementing group 1 Arg194Trp polymorphism on the risk of lung cancer: a meta-analysis on 22 studies. J Thorac Oncol 2011; 5:1741-7. [PMID: 20975374 DOI: 10.1097/jto.0b013e3181f0c409] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND DNA repair gene X-ray repair cross complementing group 1 (XRCC1) Arg194Trp polymorphism has been investigated widely on lung cancer risk. However, the results are inconclusive. To derive a more precise estimation of the relationship between XRCC1 Arg194Trp polymorphism and lung cancer risk, we performed this meta-analysis. METHODS An electronic search of the database PubMed, Embase, and Chinese National Knowledge Infrastructure was performed. The odds ratio (OR) was pooled by STATA 10.1. Subgroup analyses by ethnicity, gender, smoking, and histologic types of lung cancer were performed. RESULTS Twenty-two studies including 7515 cases and 9560 controls were identified ultimately. The pooled OR for total population showed that homozygous Trp/Trp variant genotype could increase lung cancer risk compared with the homozygous wild Arg/Arg genotype (OR = 1.22, 95% confidence interval [CI] = 1.04-1.44, p = 0.01); however, heterozygote Arg/Trp variant genotype could decrease lung cancer risk (OR = 0.91, 95% CI = 0.85-0.99, p = 0.02). Subgroup analyses by ethnicity confirmed the result that homozygous Trp/Trp variant genotype increased lung cancer risk in Asians (OR = 1.19, 95% CI = 1.01-1.41, p = 0.04) but not in whites. It was interesting to find that both the heterozygote Arg/Trp and the combined Trp/Trp + Arg/Trp variant genotypes could decrease the risk of lung cancer in whites (OR = 0.83, 95% CI = 0.72-0.96, p = 0.01; OR = 0.85, 95% CI = 0.74-0.98, p = 0.03, respectively) but not in Asians. Subgroup analyses by gender, smoking, and histologic types of lung cancer did not indicate any significant difference between cases and controls, excepted for male population, which carried heterozygote Arg/Trp variant genotype that could decrease lung cancer risk (OR = 0.54, 95% CI = 0.31-0.95, p = 0.03). CONCLUSIONS Homozygous Trp/Trp variant genotype of XRCC1 Arg194Trp polymorphism could increase lung cancer risk in total population, especially in Asians. However, the heterozygote Arg/Trp variant genotype might decrease the risk of lung cancer, especially in whites.
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An association between DNA repair gene polymorphisms and survival in patients with resected non-small cell lung cancer. Mol Biol Rep 2010; 38:5231-41. [PMID: 21188533 DOI: 10.1007/s11033-010-0674-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
Abstract
DNA repair genetic polymorphisms have been studied extensively in relation to lung cancer susceptibility, but much less is known about their role in clinical outcome modulation. In this report, we examined effect of the XPA -4G>A, XPD Asp312Asn, Leu751Gln, hHR23B Ala249Val, XPG Asp1104His, XRCC1 Arg399Gln, XRCC2 -4234G>C and XRCC3 Thr241Met polymorphisms on overall survival in 162 patients with resected non-small cell lung cancer (NSCLC). The XRCC3 Met/Met genotype was significantly associated with increased risk of death among all patients and men in uni- and multivariate analyses. The risk was higher for adenocarcinoma patients possessing the XRCC3 Met/Met or XRCC1 Gln/Gln genotypes, although their frequency was small. The XRCC1 399Gln allele was also associated with poor prognosis in stage II-IIIA and among older individuals. Men homozygous for the XPD 312 Asn/Asn had significantly better survival with the risk of death being at borderline significance in uni- and multivariate models. Younger cases and ever smokers smoking less than median pack-years showed significantly increased risk of death associated with the XPA -4A allele. A presence of one or two XRCC2 -4234C alleles had a protective effect in males and ever smokers with lower cumulative smoking dose, although the CC genotype was rarely observed. When number of combined risk alleles was considered, we found that carriers of >4 adverse alleles were at significantly increased risk of death in uni- and multivariate models. Therefore, our results indicate that selected genetic polymorphisms in DNA repair genes may influence overall survival in resected NSCLC.
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Liu L, Yuan P, Wu C, Zhang X, Wang F, Guo H, Zhong R, Xu Y, Wu J, Yu D, Wu T, Zhang X, Nie S, Miao X, Lin D. Assessment of XPD Lys751Gln and XRCC1 T-77C polymorphisms in advanced non-small-cell lung cancer patients treated with platinum-based chemotherapy. Lung Cancer 2010; 73:110-5. [PMID: 21129812 DOI: 10.1016/j.lungcan.2010.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 10/13/2010] [Accepted: 11/01/2010] [Indexed: 02/07/2023]
Abstract
Polymorphisms in DNA repair genes were thought to represent important determinants of platinum drug efficacy. This study tested whether XPD Lys751Gln and XRCC1 T-77C polymorphisms were associated with survival in platinum-treated patients with advanced non-small-cell lung cancer (NSCLC). In this study, 199 advanced NSCLC patients with platinum-based chemotherapy were recruited. During the median 26.5 months of follow-up, patients with the XPD 751Lys/Lys genotype had a median survival time of 17.0 months (95% CI, 14.5-19.6 months), not much longer than those carried Lys/Gln heterozygote (12.0 months; 95% CI, 3.4-20.6 months; log-rank test, P=0.542). In Cox proportional hazards model, no significant associations were found between XPD Lys751Gln polymorphism and survival. For XRCC1 T-77C polymorphism, the median survival of patients with TC+CC genotype (18 months; 95% CI, 13.5-22.5 months) was similar to those with the TT genotype (16.0 months; 95% CI, 13.3-18.7 months; log-rank test, P=0.399). XRCC1 T-77C polymorphism was not associated with survival in Cox proportional hazards model. Additionally, the analysis for combination of these two polymorphisms also showed no prognostic significance for NSCLC. Our findings indicated that neither XPD Lys751Gln nor XRCC1 T-77C could be genetic determinant for prognosis of advanced NSCLC patients treated with platinum-based chemotherapy.
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Affiliation(s)
- Li Liu
- Department of Epidemiology and Biostatistics, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
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Kim M, Kang HG, Lee SY, Lee HC, Lee EB, Choi YY, Lee WK, Cho S, Jin G, Jheon HS, Son JW, Lee MH, Jung DK, Cha SI, Kim CH, Kang YM, Kam S, Jung TH, Jheon S, Park JY. Comprehensive analysis of DNA repair gene polymorphisms and survival in patients with early stage non-small-cell lung cancer. Cancer Sci 2010; 101:2436-42. [PMID: 20731661 PMCID: PMC11159840 DOI: 10.1111/j.1349-7006.2010.01699.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
This study was conducted to analyze a comprehensive panel of single nucleotide polymorphisms (SNP) in DNA repair genes to determine the relationship between polymorphisms and the survival outcome of patients with early stage non-small-cell lung cancer (NSCLC). Three hundred and ten consecutive patients with surgically resected NSCLC were enrolled. Forty-eight SNP in 27 DNA repair genes were genotyped and their associations with overall survival (OS) and disease-free survival (DFS) were analyzed. Individually, six SNP exhibited significant associations with survival outcome. When the six SNP were combined, OS and DFS decreased as the number of bad genotypes increased (P(trend) <0.0001 for both). Patients with three, and four or five bad genotypes had a significantly worse OS and DFS compared with those carrying zero or one bad genotypes (adjusted hazard ratio [aHR] for OS=3.53, 95% confidence interval [CI]=1.25-9.97, P=0.02, and aHR for DFS=3.31, 95% CI=1.41-7.76, P=0.006; and aHR for OS=5.47, 95% CI=1.87-16.00, P=0.002, and aHR for DFS=4.42, 95% CI=1.82-10.74, P=0.001, respectively). These findings suggest that the six SNP identified can be used as prognostic markers for patients with surgically resected early stage NSCLC.
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Affiliation(s)
- Min Kim
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, South Korea
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Martin SA, Hewish M, Lord CJ, Ashworth A. Genomic instability and the selection of treatments for cancer. J Pathol 2010; 220:281-9. [PMID: 19890832 DOI: 10.1002/path.2631] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A critical link exists between DNA mutation and chromosomal rearrangements (genomic instability) and cancer development. This genomic instability can manifest itself as small changes at the nucleotide level or as gross chromosomal alterations. Mutations in the genes that encode DNA damage response proteins are responsible for a variety of genomic instability syndromes including hereditary non-polyposis colorectal carcinoma, Bloom's syndrome, ataxia-telangiectasia, BRCA-associated breast and ovarian cancers and Fanconi anaemia. Similarly, epigenetic silencing of genes associated with the maintenance of genomic stability have also been implicated in the pathogenesis of cancer. Here, we discuss how different tumours may be classified not only by tumour site but also by the type of underlying genetic instability. This type of classification may assist in the optimization of existing treatment regimens as well as informing the development of new therapeutic approaches.
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Affiliation(s)
- Sarah A Martin
- CRUK Gene Function Laboratory, Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
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Sabitha K, Reddy MV, Jamil MK. Mutations in XRCC1 Gene Alters the Genetic Risks of Head and Neck Cancer Patients. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/ijcr.2009.58.68] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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