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Mukerjee N, Maitra S, Roy S, Modak S, Hasan MM, Chakraborty B, Ghosh A, Ghosh A, Kamal MA, Dey A, Ashraf GM, Malik S, Rahman MH, Alghamdi BS, Abuzenadah AM, Alexiou A. Treatments against Polymorphosal discrepancies in Glioblastoma Multiforme. Metab Brain Dis 2023; 38:61-68. [PMID: 36149588 DOI: 10.1007/s11011-022-01082-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/30/2022] [Indexed: 02/03/2023]
Abstract
Glioblastoma (GB) are aggressive tumors that obstruct normal brain function. While the skull cannot expand in response to cancer growth, the growing pressure in the brain is generally the first sign. It can produce more frequent headaches, unexplained nausea or vomiting, blurred peripheral vision, double vision, a loss of feeling or movement in an arm or leg, and difficulty speaking and concentrating; all depend on the tumor's location. GB can also cause vascular thrombi, damaging endothelial cells and leading to red blood cell leakage. Latest studies have revealed the role of single nucleotide polymorphisms (SNPs) in developing and spreading cancers such as GB and breast cancer. Many discovered SNPs are associated with GB, particularly in great abundance in the promoter region, creating polygenetic vulnerability to glioma. This study aims to compile a list of some of the most frequent and significant SNPs implicated with GB formation and proliferation.
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Affiliation(s)
- Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Rahara, Khardah, West Bengal, Kolkata, 700118, India.
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, 2770, Australia.
| | - Swastika Maitra
- Department of Microbiology, Adamas University, Kolkata, 700126, West Bengal, India
| | - Subhradeep Roy
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Rahara, Khardah, West Bengal, Kolkata, 700118, India
| | - Shaswata Modak
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Rahara, Khardah, West Bengal, Kolkata, 700118, India
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Biswajit Chakraborty
- Department of Biochemistry and Biophysics, University of Kalyani Nadia, Kalyani, West Bengal, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Asmita Ghosh
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
- Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee place, Habersham , NSW, 2770, Australia
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand, 834001, India
| | - Md Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Gangwon-do, Wonju, 26426, Korea
| | - Badrah S Alghamdi
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adel Mohammad Abuzenadah
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, NSW, 2770, Australia.
- AFNP Med, 1030, Vienna, Austria.
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Wang Y, Huang X, Su Z, He J, Zhao N, Nie L, Tang Y, Zhao H, Nong Q. The Glu69Asp Polymorphism of EME1 Gene is Associated with an Increased Risk of Hepatocellular Carcinoma in Guangxi Population, China. Int J Gen Med 2022; 15:7855-7866. [PMID: 36281338 PMCID: PMC9587733 DOI: 10.2147/ijgm.s383261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
Background The dysfunction of Essential meiotic endonuclease 1 homolog 1 (EME1) can lead to genomic instability and tumorigenesis. Single nucleotide polymorphisms (SNPs) in the EME1 gene have been reported to be associated with the risk of several cancers, but its association with hepatocellular carcinoma (HCC) has not been investigated. This study aimed to determine the association between EME1 SNPs and the risk of HCC. Methods This study included 645 HCC patients and 649 healthy controls from a Guangxi population of Southern China, and genotyped three functional SNPs (Glu69Asp: rs3760413A>C, Ile350Thr: rs12450550T>C, and rs11868055A>G) of the EME1 gene utilizing the Agena MassARRAY platform. Results The rs3760413C variant genotypes (AC+CC: Glu/Asp+Asp/Asp) conferred a 1.419-fold risk of HCC compared to the AA (Glu/Glu) genotype (adjusted OR = 1.419, 95% CI = 1.017–1.980), and the allele C increased the risk of HCC in a dose-dependent manner (Ptrend = 0.017). Moreover, the effects of the rs3760413C variant genotypes were more pronounced in individuals who drank pond/ditch water (adjusted OR = 3.956, 95% CI = 1.413–11.076) than in those who never drank (P = 0.033). We further observed that a potential carcinogen microcystin-LR induced more DNA oxidative damages in peripheral blood mononuclear cells from the carriers of rs3760413C variant genotypes than those from the subjects with AA genotype (P = 0.006). A nomogram was also constructed combining the rs3760413A>C polymorphism and environmental risk factors for predicting HCC risk with a good discriminatory ability (concordance index = 0.892, 95% CI: 0.874–0.911) and good calibration (mean absolute error = 0.005). Conclusion Our data suggest that the Glu69Asp missense polymorphism (rs3760413) of EME1 gene is associated with the risk of HCC, which may be a susceptible biomarker of HCC in the Guangxi population.
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Affiliation(s)
- Youxin Wang
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Xinglei Huang
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Zhaohui Su
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Junquan He
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Na Zhao
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Liyun Nie
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Yanmei Tang
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Huiliu Zhao
- Department of Clinical Laboratory, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Qingqing Nong
- Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China,Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, People’s Republic of China,Correspondence: Qingqing Nong, Department of Environmental Health, School of Public Health, Guangxi Medical University, Nanning, 530021, People’s Republic of China, Tel +86 771-5358146, Fax +86 771-5350823, Email
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Nageeb AM, Mohamed MM, Ezz El Arab LR, Khalifa MK, Swellam M. Next generation sequencing of BRCA genes in glioblastoma multiform Egyptian patients: a pilot study. Arch Physiol Biochem 2022; 128:809-817. [PMID: 32100578 DOI: 10.1080/13813455.2020.1729814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Germ line mutations of BRCA1 and BRCA2 were correlated with a variety of cancer Authors aimed to use next-generation sequencing (NGS) to detect BRCA1 and BRCA2 germ line mutations in glioblastoma multiform (GBM) Egyptian patients. MATERIALS AND METHODS Genomic DNA was extracted from six GBM cases, amplified using Ion AmpliSeq BRCA1 and BRCA2 panel. DNA libraries were pooled, barcoded and finally sequenced using Ion Torrent Personal Genome Machine sequencer. RESULTS BRCA1 the previously reported rs1799966, rs1799950, rs16941 were found in five cases and they are in a linkage disequilibrium forming two distinct haplotypes, which might support their role in cancer predisposition. Out of the 18 reported variants in BRCA2, three denovo mutations were detected which leads to frame shift. CONCLUSION Further studies on large number of GBM patients and control cases to determine BRCA1 and BRCA2 germline mutations and haplotypes; diagnostic and prognostic role are encouraged.
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Affiliation(s)
- Amira M Nageeb
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, Giza, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, Dokki, Giza, Egypt
| | - Magdy M Mohamed
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Lobna R Ezz El Arab
- Clinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, Giza, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, Dokki, Giza, Egypt
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Liang C, Liu X, Liu C, Xu Y, Geng W, Li J. Integrin α10 regulates adhesion, migration, and osteogenic differentiation of alveolar bone marrow mesenchymal stem cells in type 2 diabetic patients who underwent dental implant surgery. Bioengineered 2022; 13:13252-13268. [PMID: 35635091 PMCID: PMC9275886 DOI: 10.1080/21655979.2022.2079254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Affiliation(s)
- Chao Liang
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Xiu Liu
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Changying Liu
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Yifan Xu
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Wei Geng
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Jun Li
- Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
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Yan S, Gao S, Zhou P. Multi-functions of exonuclease 1 in DNA damage response and cancer susceptibility. RADIATION MEDICINE AND PROTECTION 2021. [DOI: 10.1016/j.radmp.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Guo Z, Liang E, Li W, Jiang L, Zhi F. Essential meiotic structure-specific endonuclease1 ( EME1) promotes malignant features in gastric cancer cells via the Akt/GSK3B/CCND1 pathway. Bioengineered 2021; 12:9869-9884. [PMID: 34719326 PMCID: PMC8810030 DOI: 10.1080/21655979.2021.1999371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA damage plays a key role in various biological processes involved in malignant disease, the role of the DNA damage repair gene EME1 (essential meiotic structure-specific endonuclease 1) in gastric cancer (GC) development is unknown. This work aimed to investigate expression and role of EME1 in tumorigenesis. Quantitative real-time polymerase chain reaction (qRT-PCR), immunoblot, cell viability and dual-luciferase reporter assays, RNAi and gene transfection, and immunofluorescent staining were performed to assess EME1 regulation in GC tumorigenesis. Further, mouse xenografts were established for in vivo mechanistic studies. EME1 was found to be upregulated in both gastric cancer cells and clinically obtained tumors. Additionally, EME1 levels were strongly associated with the differentiation level of GC and lymph node metastasis. In vivo and in vitro knockdown of EME1 markedly suppressed the proliferative, migratory, and invasive abilities of GC cells and enhanced apoptotic cell death and cell cycle arrest rates. Mechanistically, EME1 modulated Akt/GSK3B/CCND1 signaling. MYB may also have contributed to EME1-dependent gastric carcinogenesis. Elevated EME1 expressions may enhance the proliferative and metastatic abilities of GC cells, thereby acting as a tumor-promoting factor via Akt. These findings reveal that EME1 is an important biomarker for GC prognosis and treatment in humans. Abbreviations: Essential meiotic structure-specific endonuclease 1 (EME1); MYB proto-oncogene (MYB); Cell counting kit-8 (CCK-8); 4,6-diamimo-2-phenyl indole (DAPI); Quantitative real-time PCR (qRT-PCR); Gastric cancer (GC); Immunofluorescence (IF); Small interfering RNA (siRNA); Small hairpin RNA (shRNA); Alpha serine threonine-protein kinase (Akt); Glycogen synthase kinase 3 beta (GSK3B); Cyclin D1 (CCND1); Glyceraldehyde-3-phosphate dehydrogenase (GAPDH); Disease-free survival (DFS); Overall survival (OS); Negative controls (NC); American Joint Committee on Cancer (AJCC); Coding sequence (CDS); Lymph node metastasis (LNM); Tris-Buffered Saline-Tween-20 (TBST); Horseradish Peroxidase (HRP); Electrochemiluminescence (ECL); Polyvinylidene Fluoride (PVDF); Excision repair cross complementation group 1 (ERCC1).
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Affiliation(s)
- Zhiguo Guo
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Erbo Liang
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Li
- Department of Endocrinology, Suzhou Hospital of Anhui Medical University, Suzhou, Anhui 234000, China
| | - Leilei Jiang
- Department of Gastroenterology, Suzhou Hospital of Anhui Medical University, Suzhou, Anhui 234000, China
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
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Jung SY, Sobel EM, Pellegrini M, Yu H, Papp JC. Synergistic Effects of Genetic Variants of Glucose Homeostasis and Lifelong Exposures to Cigarette Smoking, Female Hormones, and Dietary Fat Intake on Primary Colorectal Cancer Development in African and Hispanic/Latino American Women. Front Oncol 2021; 11:760243. [PMID: 34692549 PMCID: PMC8529283 DOI: 10.3389/fonc.2021.760243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Disparities in cancer genomic science exist among racial/ethnic minorities. Particularly, African American (AA) and Hispanic/Latino American (HA) women, the 2 largest minorities, are underrepresented in genetic/genome-wide studies for cancers and their risk factors. We conducted on AA and HA postmenopausal women a genomic study for insulin resistance (IR), the main biologic mechanism underlying colorectal cancer (CRC) carcinogenesis owing to obesity. METHODS With 780 genome-wide IR-specific single-nucleotide polymorphisms (SNPs) among 4,692 AA and 1,986 HA women, we constructed a CRC-risk prediction model. Along with these SNPs, we incorporated CRC-associated lifestyles in the model of each group and detected the topmost influential genetic and lifestyle factors. Further, we estimated the attributable risk of the topmost risk factors shared by the groups to explore potential factors that differentiate CRC risk between these groups. RESULTS In both groups, we detected IR-SNPs in PCSK1 (in AA) and IFT172, GCKR, and NRBP1 (in HA) and risk lifestyles, including long lifetime exposures to cigarette smoking and endogenous female hormones and daily intake of polyunsaturated fatty acids (PFA), as the topmost predictive variables for CRC risk. Combinations of those top genetic- and lifestyle-markers synergistically increased CRC risk. Of those risk factors, dietary PFA intake and long lifetime exposure to female hormones may play a key role in mediating racial disparity of CRC incidence between AA and HA women. CONCLUSIONS Our results may improve CRC risk prediction performance in those medically/scientifically underrepresented groups and lead to the development of genetically informed interventions for cancer prevention and therapeutic effort, thus contributing to reduced cancer disparities in those minority subpopulations.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, CA, United States
| | - Eric M. Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA, United States
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Jeanette C. Papp
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Jung SY. Genetic Signatures of Glucose Homeostasis: Synergistic Interplay With Long-Term Exposure to Cigarette Smoking in Development of Primary Colorectal Cancer Among African American Women. Clin Transl Gastroenterol 2021; 12:e00412. [PMID: 34608882 PMCID: PMC8500576 DOI: 10.14309/ctg.0000000000000412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/22/2021] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Insulin resistance (IR)/glucose intolerance is a critical biologic mechanism for the development of colorectal cancer (CRC) in postmenopausal women. Whereas IR and excessive adiposity are more prevalent in African American (AA) women than in White women, AA women are underrepresented in genome-wide studies for systemic regulation of IR and the association with CRC risk. METHODS With 780 genome-wide IR single-nucleotide polymorphisms (SNPs) among 4,692 AA women, we tested for a causal inference between genetically elevated IR and CRC risk. Furthermore, by incorporating CRC-associated lifestyle factors, we established a prediction model on the basis of gene-environment interactions to generate risk profiles for CRC with the most influential genetic and lifestyle factors. RESUTLS In the pooled Mendelian randomization analysis, the genetically elevated IR was associated with 9 times increased risk of CRC, but with lack of analytic power. By addressing the variation of individual SNPs in CRC in the prediction model, we detected 4 fasting glucose-specific SNPs in GCK, PCSK1, and MTNR1B and 4 lifestyles, including smoking, aging, prolonged lifetime exposure to endogenous estrogen, and high fat intake, as the most predictive markers of CRC risk. Our joint test for those risk genotypes and lifestyles with smoking revealed the synergistically increased CRC risk, more substantially in women with longer-term exposure to cigarette smoking. DISCUSSION Our findings may improve CRC prediction ability among medically underrepresented AA women and highlight genetically informed preventive interventions (e.g., smoking cessation; CRC screening to longer-term smokers) for those women at high risk with risk genotypes and behavioral patterns.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, School of Nursing, University of California, Los Angeles, Los Angeles, California, USA; and
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, USA.
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Liu D, Gao Y, Li L, Chen H, Bai L, Qu Y, Zhou B, Yan Y, Zhao Y. Single nucleotide polymorphisms in breast cancer susceptibility gene 1 are associated with susceptibility to lung cancer. Oncol Lett 2021; 21:424. [PMID: 33850565 DOI: 10.3892/ol.2021.12685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 02/10/2021] [Indexed: 12/24/2022] Open
Abstract
BRCA1 is a tumor suppressor that has been found to be involved DNA synthesis during cell replication. In a recent study, the single nucleotide polymorphism (SNP), rs799917, in BRCA1 was found to be associated with the development and progression of various types of tumor. In the present study, the association between rs799917 and susceptibility to lung cancer was evaluated in a Han Chinese population in the Liaoning Province of China. The BRCA1 rs799917 genotypes (C/C, C/T and T/T) were analyzed using TaqMan quantitative PCR in 682 patients with lung cancer and 694 healthy controls, and the results were analyzed using a Student's t-test, a χ2 test and logistic regression analysis. Individuals carrying the C/T or T/T genotype had a lower risk of lung cancer compared with those carrying the C/C genotype [odds ratio (OR), 0.741; P=0.021; and OR, 0.610; P=0.011, respectively). The C/T + T/T genotype group had an even lower risk (OR, 0.709; P=0.005) compared with that in the C/C genotype group. In the stratified analyses of non-smokers, individuals with the C/T or T/T genotype had a lower risk of developing lung cancer compared with that in those carrying the C/C genotype (OR, 0.681; P=0.013; and OR, 0.569; P=0.021, respectively). The stratified analyses of the BRCA1 rs799917 polymorphism based on pathological type, chemotherapy and radiotherapy, showed that in the squamous cell carcinoma, non-chemotherapy and non-radiotherapy subgroups, individuals with the T/T genotype had a lower risk of lung cancer compared with that in those carrying the C/C genotype (OR, 0.454; P=0.007; OR, 0.485; P=0.002; and OR, 0.599; P=0.020, respectively). In conclusion, the T allele of the rs799917 SNP in BRCA1 was associated with a lower risk of lung cancer in the ethnic Han Chinese population in Liaoning Province and may represent a protective factor against lung cancer.
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Affiliation(s)
- Dan Liu
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Ya Gao
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China.,Department of Oncology, Kailuan Hospital, Tangshan, Hebei 063000, P.R. China
| | - Lingling Li
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - He Chen
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Lu Bai
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yanli Qu
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Baosen Zhou
- Department of Epidemiology, China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Ying Yan
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China.,Department of Radiation Oncology, The General Hospital of Shenyang Military Region, Shenyang, Liaoning 110016, P.R. China
| | - Yuxia Zhao
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
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Jung SY, Papp JC, Sobel EM, Pellegrini M, Yu H, Zhang ZF. Pro-inflammatory cytokine polymorphisms in ONECUT2 and HNF4A and primary colorectal carcinoma: a post genome-wide gene-lifestyle interaction study. Am J Cancer Res 2020; 10:2955-2976. [PMID: 33042629 PMCID: PMC7539781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023] Open
Abstract
Immune-related molecular and genetic pathways that are connected to colorectal cancer (CRC) and lifestyles in postmenopausal women are incompletely characterized. In this study, we examined the role of pro-inflammatory biomarkers such as C-reactive protein (CRP) and interleukin-6 (IL-6) in those pathways. Through selection of the best predictive single-nucleotide polymorphisms (SNPs) and lifestyles, our goal was to improve the prediction accuracy and ability for CRC risk. Using large cohort data of postmenopausal women from the Women's Health Initiative Database for Genotypes and Phenotypes Study, we previously conducted a genome-wide association (GWA) for a CRP and IL-6 gene-behavioral interaction study. For the present study, we added GWA-SNPs from outside GWA studies, resulting in a total of 152 SNPs. Together with 41 selected lifestyles, we performed a 2-stage multimodal random survival forest analysis with generalized multifactor dimensionality reduction approach to construct CRC risk profiles. Overall and in obesity strata (by body mass index, waist circumference, waist-to-hip ratio, exercise, and dietary fat intake), we identified the best predictive genetic markers in inflammatory cytokines and lifestyles. Across the strata, 2 SNPs (ONECUT2 rs4092465 and HNF4A rs1800961) and 1 lifestyle factor (relatively short-term past use of oral contraceptives) were the most common and strongest predictive markers for CRC risk. The risk profile that combined those variables exhibited synergistically increased risk for CRC; this pattern appeared more strongly in obese and inactive subgroups. Our results may contribute to improved predictability for CRC and suggest genetically targeted lifestyle interventions for women carrying the inflammatory-risk genotypes, reducing CRC risk.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of CaliforniaLos Angeles, CA 90095, USA
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of CaliforniaLos Angeles, CA 90095, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer CenterHonolulu, HI 96813, USA
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of CaliforniaLos Angeles, CA 90095, USA
- Center for Human Nutrition, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA 90095, USA
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Al-Khatib SM, Abdo N, Al-Eitan LN, Al-Mistarehi AHW, Zahran DJ, Al Ajlouni M, Kewan TZ. The Impact of the Genetic Polymorphism in DNA Repair Pathways on Increased Risk of Glioblastoma Multiforme in the Arab Jordanian Population: A Case-Control Study. APPLICATION OF CLINICAL GENETICS 2020; 13:115-126. [PMID: 32606887 PMCID: PMC7295542 DOI: 10.2147/tacg.s248994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 05/22/2020] [Indexed: 01/06/2023]
Abstract
Introduction Among the Jordanian population, brain tumors are the tenth most common type of cancers in both males and females, comprising 2.8% of all newly diagnosed neoplasms. Diffuse gliomas are the most prevalent and the most aggressive primary brain tumors in adults. The incidence of diffuse gliomas varies among different populations; this variation is partially linked to genetic polymorphisms. The purpose of the study is to examine the association between (BRCA1 rs799917G>A, rs1799966T>C, EXO1 rs1047840G>A, EME1 rs12450550T>C, ERCC2 rs13181T>G, rs1799793C>T, and XRCC1 rs1799782G>A) DNA repair gene polymorphisms and glioblastoma multiforme (GBM) susceptibility, and survival in the Jordanian Arab population. Methods Eighty-four patients diagnosed with glioblastoma multiforme at the King Abdullah University Hospital (KAUH) between 2013 and 2018 and 225 healthy cancer-free control subjects with similar geographic and ethnic backgrounds to the patients were included in the study. Genomic DNA was extracted from the formalin-fixed paraffin-embedded tissues of the subjects. The Sequenom MassARRAY® sequencer system (iPLEX GOLD) was used. The analyses included assessments of population variability and survival. Results This study is the first to address the relationship between BRCA1 rs1799966 and rs799917 SNP, and the risk of GBM among the Arab Jordanian population. The findings of the study show that BRCA1 rs799917 is associated with decreased risk of GBM in the recessive model (AA vs G/G-A/G: OR, 0.46, 95% CI, 0.26-0.82, p=0.01) and the same SNP is associated with increased risk of GBM in the overdominant model (AG vs G/G-A/A: OR, 1.72, 95% CI, 1.02-2.89, p=0.04).
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Affiliation(s)
- Sohaib M Al-Khatib
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Nour Abdo
- Department of Public Health, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Laith N Al-Eitan
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Abdel-Hameed W Al-Mistarehi
- Department of Family Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Deeb Jamil Zahran
- Department of Internal Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Marwan Al Ajlouni
- Department of Public Health, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Tariq Zuheir Kewan
- Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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12
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Kour A, Sambyal V, Guleria K, Singh NR, Uppal MS, Manjari M, Sudan M. Screening of BRCA1 variants c.190T>C, 1307delT, g.5331G>A and c.2612C>T in breast cancer patients from North India. Genet Mol Biol 2020; 43:e20190014. [PMID: 32453341 PMCID: PMC7250277 DOI: 10.1590/1678-4685-gmb-2019-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/22/2019] [Indexed: 12/01/2022] Open
Abstract
The polymorphic variants of BRCA1, which lead to amino acid
substitutions, have a known pathogenic role in breast cancer. The present study
investigated in North Indian breast cancer patients the association of risk with
four reported pathogenic variants of BRCA1: c.190T>C
(p.Cys64Arg), 1307delT, g.5331G>A (p.G1738R) and c.2612C>T (p.Pro871Leu).
Genotyping was done by PCR-RFLP method in 255 clinically confirmed breast cancer
patients and 255 age and gender matched healthy individuals. For c.190T>C,
1307delT and g.5331G>A, all the patients and controls had the wild-type
genotype indicating no association with breast cancer risk. For c.2612C>T
polymorphism, the frequency of the CC, CT, and TT genotypes was 14.5 vs 15.7%,
59.6 vs 53.7% and 25.9 vs 30.6% in breast cancer patients and controls
respectively. The frequency of heterozygotes (CT genotype) was higher in cases
than controls but the difference was not statistically significant. Genetic
model analysis showed no association of the four analyzed BRCA1
variants with breast cancer risk with any model. The studied variants were not
associated with the risk of breast cancer in Punjab, North west India,
suggesting a need for further screening of other BRCA1
variants. It is the first reported study on these 4 variants from India.
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Affiliation(s)
- Akeen Kour
- Guru Nanak Dev University, Department of Human Genetics, Human Cytogenetics Laboratory, Amritsar, Punjab, India
| | - Vasudha Sambyal
- Guru Nanak Dev University, Department of Human Genetics, Human Cytogenetics Laboratory, Amritsar, Punjab, India
| | - Kamlesh Guleria
- Guru Nanak Dev University, Department of Human Genetics, Human Cytogenetics Laboratory, Amritsar, Punjab, India
| | - Neeti Rajan Singh
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah,Department of Surgery, Amritsar, Punjab, India
| | - Manjit Singh Uppal
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah,Department of Surgery, Amritsar, Punjab, India
| | - Mridu Manjari
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah,Department of Pathology, Amritsar, Punjab, India
| | - Meena Sudan
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Department of Radiotherapy, Amritsar, Punjab, India
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13
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Wang Q, He Z, Chen Y. Comprehensive Analysis Reveals a 4-Gene Signature in Predicting Response to Temozolomide in Low-Grade Glioma Patients. Cancer Control 2019; 26:1073274819855118. [PMID: 31167546 PMCID: PMC6558750 DOI: 10.1177/1073274819855118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Low-grade gliomas (LGGs) are a highly heterogeneous group of slow-growing,
lethal, diffusive brain tumors. Temozolomide (TMZ) is a frequently used primary
chemotherapeutic agent for LGGs. Currently there is no consensus as to the
optimal biomarkers to predict the efficacy of TMZ, which calls for
decision-making for each patient while considering molecular profiles. Low-grade
glioma data sets were retrieved from The Cancer Genome Atlas. Cox regression and
survival analyses were applied to identify clinical features significantly
associated with survival. Subsequently, Ordinal logistic regression,
co-expression, and Cox regression analyses were applied to identify genes that
correlate significantly with response rate, disease-free survival, and overall
survival of patients receiving TMZ as primary therapy. Finally, gene expression
and methylation analyses were exploited to explain the mechanism between these
gene expression and TMZ efficacy in LGG patients. Overall survival was
significantly correlated with age, Karnofsky Performance Status score, and
histological grade, but not with IDH1 mutation status. Using 3
distinct efficacy end points, regression and co-expression analyses further
identified a novel 4-gene signature of ASPM, CCNB1, EXO1, and
KIF23 which negatively correlated with response to TMZ
therapy. In addition, expression of the 4-gene signature was associated with
those of genes involved in homologous recombination. Finally, expression and
methylation profiling identified a largely unknown olfactory receptor
OR51F2 as potential mediator of the roles of the 4-gene
signature in reducing TMZ efficacy. Taken together, these findings propose the
4-gene signature as a novel panel of efficacy predictors of TMZ therapy, as well
as potential downstream mechanisms, including homologous recombination, OR51F2,
and DNA methylation independent of MGMT.
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Affiliation(s)
- Qi Wang
- 1 Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Zongze He
- 1 Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Yong Chen
- 1 Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
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14
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Sousa JFD, Serafim RB, Freitas LMD, Fontana CR, Valente V. DNA repair genes in astrocytoma tumorigenesis, progression and therapy resistance. Genet Mol Biol 2019; 43:e20190066. [PMID: 31930277 PMCID: PMC7198033 DOI: 10.1590/1678-4685-gmb-2019-0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/21/2019] [Indexed: 12/26/2022] Open
Abstract
Glioblastoma (GBM) is the most common and malignant type of primary brain tumor,
showing rapid development and resistance to therapies. On average, patients
survive 14.6 months after diagnosis and less than 5% survive five years or more.
Several pieces of evidence have suggested that the DNA damage signaling and
repair activities are directly correlated with GBM phenotype and exhibit
opposite functions in cancer establishment and progression. The functions of
these pathways appear to present a dual role in tumorigenesis and cancer
progression. Activation and/or overexpression of ATRX, ATM and RAD51 genes were
extensively characterized as barriers for GBM initiation, but paradoxically the
exacerbated activity of these genes was further associated with cancer
progression to more aggressive stages. Excessive amounts of other DNA repair
proteins, namely HJURP, EXO1, NEIL3, BRCA2, and BRIP, have also been connected
to proliferative competence, resistance and poor prognosis. This scenario
suggests that these networks help tumor cells to manage replicative stress and
treatment-induced damage, diminishing genome instability and conferring therapy
resistance. Finally, in this review we address promising new drugs and
therapeutic approaches with potential to improve patient survival. However,
despite all technological advances, the prognosis is still dismal and further
research is needed to dissect such complex mechanisms.
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Affiliation(s)
- Juliana Ferreira de Sousa
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, U.S.A
| | - Rodolfo Bortolozo Serafim
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Laura Marise de Freitas
- Universidade de São Paulo, Instituto de Química, Departamento de Bioquímica, São Paulo, SP, Brazil
| | - Carla Raquel Fontana
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
| | - Valeria Valente
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.,Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil.,Centro de Terapia Celular (CEPID-FAPESP), Ribeirão Preto, SP, Brazil
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15
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Luo F, Wang YZ, Lin D, Li J, Yang K. Exonuclease 1 expression is associated with clinical progression, metastasis, and survival prognosis of prostate cancer. J Cell Biochem 2019; 120:11383-11389. [PMID: 30775798 DOI: 10.1002/jcb.28415] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/16/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Prostate cancer (PCa) is the most prevalent malignancy and the second leading cause of cancer-related deaths in the male population in western countries, and we explored the association between exonuclease 1 (EXO1) expression and clinical progression, metastasis (Met), and survival prognosis of PCa. EXO1 expression of high/low-metastatic patient-derived xenografts model was investigated and clinical correlation and prognosis outcomes were validated. EXO1 in high-metastatic models was significantly increased compared with low-metastatic lines. In memorial sloan-kettering cancer center (MSKCC) cohort, EXO1 expression positively correlated with PCa Met, and patients with high EXO1 had poor biochemical recurrence-free survival in primary PCa cohort. Validation in The Cancer Genome Atlas primary cohort indicated EXO1 expression was significantly associated with lymph node Met and disease-free survival. The overexpression of EXO1 is significantly associated with PCa poor survival outcome, and is a promising biomarker for PCa, especially for primary PCa. A prospective study is clearly needed to validate these findings.
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Affiliation(s)
- Fei Luo
- Department of Urology, Tianjin Union Medical Center, Tianjin, China.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yu-Zhuo Wang
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Dong Lin
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jian Li
- Department of Urology, Tianjin Union Medical Center, Tianjin, China
| | - Kuo Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin, China
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16
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Jung SY, Zhang ZF. The effects of genetic variants related to insulin metabolism pathways and the interactions with lifestyles on colorectal cancer risk. Menopause 2019; 26:771-780. [PMID: 30649085 PMCID: PMC7035960 DOI: 10.1097/gme.0000000000001301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Genetic variants in metabolic signaling pathways may interact with lifestyle factors, such as dietary fatty acids, influencing postmenopausal colorectal cancer (CRC) risk, but these interrelated pathways are not fully understood. METHODS In this study, we examined 54 single-nucleotide polymorphisms (SNPs) in genes related to insulin-like growth factor-I/insulin traits and their signaling pathways and lifestyle factors in relation to postmenopausal CRC, using data from 6,539 postmenopausal women in the Women's Health Initiative Harmonized and Imputed Genome-Wide Association Studies. By employing a two-stage random survival forest analysis, we evaluated the SNPs and lifestyle factors by ranking them according to their predictive value and accuracy for CRC. RESULTS We identified four SNPs (IRS1 rs1801123, IRS1 rs1801278, AKT2 rs3730256, and AKT2 rs7247515) and two lifestyle factors (age and percentage calories from saturated fatty acids) as the top six most influential predictors for CRC risk. We further examined interactive effects of those factors on cancer risk. In the individual SNP analysis, no significant association was observed, but the combination of the four SNPs, age, and percentage calories from saturated fatty acid (≥11% per day) significantly increased the risk of CRC in a gene and lifestyle dose-dependent manner. CONCLUSIONS Our findings provide insight into gene-lifestyle interactions and will enable researchers to focus on individuals with risk genotypes to promote intervention strategies. Our study suggests the careful use of data on potential genetic targets in clinical trials for cancer prevention to reduce the risk for CRC in postmenopausal women.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
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17
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Alyahri N, Abdi S, Khan W, Elrobh M, Addar MH, Babay ZA, Alanazi M, Aldaihan S, Shaik J, Arafah M, Parine NR, Warsy A. Novel Associations between BRCA1 Variants C.181 T>G (Rs28897672) and Ovarian Crisk in Saudi Females. J Med Biochem 2019; 38:13-21. [PMID: 30820179 PMCID: PMC6298454 DOI: 10.2478/jomb-2018-0037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/11/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Mutations in BRCA1 gene have been implicated in ovarian cancers, and BRCA testing may be conducted in high-risk women. This study was designed to determine the frequency of three single nucleotide polymorphisms (SNPs) variants in BRCA1 gene and BRCA1 expression in Saudi females with ovarian cancer. METHODS Expression levels of mRNA of BRCA1 gene were studied in 10 ovarian cancer and 10 normal ovarian tissues, by quantitative real time polymerase chain reaction (qPCR). The study also included 28 females who had suffered from ovarian cancer and had been successfully operated upon and 90 healthy females with no history of cancer. Blood was drawn in EDTA tubes and used for extraction of DNA. The genotyping was carried out using Taqman® SNP Genotyping kit by RT-PCR. The variants investigated included c.871 T>C (rs799917), c.1040 G>A (rs4986852), c.181 T>G (rs28897672) in BRCA1 gene. RESULTS The c.181 T>G (rs28897672) showed significantly different genotype and allele frequencies between the patients and the control subjects (p value = 0.002 and 0.02, respectively). The genotype TG was significantly protective (OR = 0.36, p value = 0.024). The mRNA expression of BRCA1 gene was found to be low in the ovarian cancer tissues. CONCLUSIONS This study showed that c.181 T>G in BRCA1 genes is associated with the development of ovarian cancer in Saudis. More studies are needed to unveil other SNPs that may be associated with ovarian cancer and to understand the mechanism(s) involved in reducing the expression of BRCA1 gene in ovarian cancer tissues.
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Affiliation(s)
- Nora Alyahri
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saba Abdi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wajahatullah Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdul Aziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mohamed Elrobh
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed H. Addar
- Department of Obs/Gyn, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Zeneb A. Babay
- Department of Obs/Gyn, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Alanazi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sooad Aldaihan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jilani Shaik
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Maha Arafah
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Narasimha Reddy Parine
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Arjumand Warsy
- Central Laboratory, Center for Science and Medical Studies for Girls, King Saud University, Riyadh, Saudi Arabia
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18
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Tan S, Qin R, Zhu X, Tan C, Song J, Qin L, Liu L, Huang X, Li A, Qiu X. Associations between single-nucleotide polymorphisms of human exonuclease 1 and the risk of hepatocellular carcinoma. Oncotarget 2018; 7:87180-87193. [PMID: 27894089 PMCID: PMC5349980 DOI: 10.18632/oncotarget.13517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/17/2016] [Indexed: 01/27/2023] Open
Abstract
Human exonuclease 1 (hEXO1) is an important nuclease involved in mismatch repair system that contributes to maintain genomic stability and modulate DNA recombination. This study is aimed to explore the associations between single-nucleotide polymorphisms (SNPs) of hEXO1 and the hereditary susceptibility of hepatocellular carcinoma (HCC). SNPs rs1047840, rs1776148, rs3754093, rs4149867, rs4149963, and rs1776181 of hEXO1 were examined from a hospital-based case-control study including 1,196 cases (HCC patients) and 1,199 controls (non-HCC patients) in Guangxi, China. We found the rs3754093 AG genotype decreased the risk of HCC (OR=0.714, 95% CI: 0.539∼0.946). According to the results of stratification analysis, rs3754093 mutant genotype AG/GG decreased the risk of HCC with some HCC protective factors such as non-smoking, non-alcohol consumption and non-HCC family history, but also decreased the risk of HCC with HBV infection. Moreover, it was correlated to non-tumor metastasis and increased the survival of HCC patients. The results from gene-environment interaction assay indicated all hEXO1 SNPs interacted with smoking, alcohol consumption, HBV infection in pathogenesis of HCC. However, gene-gene interaction assay suggested the interaction between rs3754093 and other 5 SNPs were associated with reducing the HCC risk. These results suggest rs3754093 exhibits a protective activity to decrease the incidence risk of HCC in Guangxi, China. In addition, all SNPs in this study interacted with environment risk factors in pathogenesis of HCC.
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Affiliation(s)
- Shengkui Tan
- Department of Epidemiology, School of Public Health, Guilin Medical University, Guilin 541004, Guangxi, People's Republic of China
| | - Ruoyun Qin
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Xiaonian Zhu
- Department of Epidemiology, School of Public Health, Guilin Medical University, Guilin 541004, Guangxi, People's Republic of China
| | - Chao Tan
- Guangxi Center for Disease Prevention and Control, Nanning 530021, Guangxi, People's Republic of China
| | - Jiale Song
- Department of Epidemiology, School of Public Health, Guilin Medical University, Guilin 541004, Guangxi, People's Republic of China
| | - Linyuan Qin
- Department of Epidemiology, School of Public Health, Guilin Medical University, Guilin 541004, Guangxi, People's Republic of China
| | - Liu Liu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Xiong Huang
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Anhua Li
- Guangxi Center for Disease Prevention and Control, Nanning 530021, Guangxi, People's Republic of China
| | - Xiaoqiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
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19
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Xu GP, Zhao Q, Wang D, Xie WY, Zhang LJ, Zhou H, Chen SZ, Wu LF. The association between BRCA1 gene polymorphism and cancer risk: a meta-analysis. Oncotarget 2018; 9:8681-8694. [PMID: 29492227 PMCID: PMC5823592 DOI: 10.18632/oncotarget.24064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022] Open
Abstract
Many studies have reported that BRCA1 polymorphisms are associated with cancer risk, but the results remain controversial. The purpose of this meta-analysis is to evaluate the relationship between BRCA1 polymorphisms (rs799917, rs1799950, rs1799966, or rs16941) and cancer risk. Relevant studies were identified via a systematic search of the PubMed, Embase, and Web of Science databases up to July 31, 2017. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to examine the strength of the associations. Thirty-five studies published in 19 publications involving 28,094 cases and 50,657 controls were included in this meta-analysis. There was no obvious association between rs799917, rs1799966, or rs16941 polymorphisms and overall cancer risk in any genetic models. However, subgroup analyses revealed that the rs799917 polymorphism could decrease the risk of cervical cancer, esophageal squamous cell carcinoma (ESCC), gastric cancer, and non-Hodgkin lymphoma (NHL) among Asian populations in one or more genetic models and that rs16941 could increase overall cancer risk among Caucasian populations in the homozygote and recessive models. Our meta-analysis also indicated that rs1799950 could decrease the breast cancer (BC) risk among Caucasian populations in the homozygote and recessive models. In summary, our results suggest that BRCA1 polymorphisms may play an important role in the etiology of cancer. However, due to the limited number of studies, these findings should be confirmed by new studies with larger sample sizes that address various types of cancer.
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Affiliation(s)
- Gui-Ping Xu
- Transfusion Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing Zhao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ding Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wen-Yue Xie
- Department of Oncology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li-Jun Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hua Zhou
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shi-Zhi Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li-Fang Wu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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20
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Dai Y, Tang Z, Yang Z, Zhang L, Deng Q, Zhang X, Yu Y, Liu X, Zhu J. EXO1 overexpression is associated with poor prognosis of hepatocellular carcinoma patients. Cell Cycle 2018; 17:2386-2397. [PMID: 30328366 PMCID: PMC6237436 DOI: 10.1080/15384101.2018.1534511] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The roles of exonuclease 1 (EXO1) in hepatocellular carcinoma (HCC) tumorigenesis and progression remain unclear. This study aimed to assess the prognostic value and therapeutic potential of EXO1 in HCC. Exo1 gene copy numbers were obtained from three Oncomine microarray datasets (n = 447). EXO1 mRNA expression was validated by semi-quantitative PCR and QuantiGene® 2.0 assays. Cell growth curve and colony formation were performed to asses the cell proliferation. Clonogenic assay, flow cytometry, and immunofluorescence were adopted to acess the effects of EXO1 knockdown and radiation on cell survival, cell cycle distribution and DNA repair. Western blots were performed to reveal the related mechanism. A significant copy number variation (CNV) of the Exo1 gene was found in HCC specimens in three separate sets of published microarray data. In the 143 cases treated by our team, EXO1 expression levels were elevated (86.71%, 124/143). In addition, EXO1 overexpression was correlated with larger tumor size (P = 0.002), increased lymph node metastasis (P=0.033) and lower Edmondson grade (P = 0.018). High EXO1 expression unfavorably affected overall survival (OS) (P = 0.009). Both univariate and multivariate Cox regression analyses identified EXO1 as an independent predictor of OS (univariate, P = 0.012; multivariate, P = 0.039). Silencing of EXO1 in vitro reduced cell proliferation. EXO1 knockdown further suppressed clonogenic cell survival, abrogated radiation-induced G2/M phase arrest, and enhanced γ-H2AX foci after exposure to irradiation. The accumulation of ataxiatelangiectasia mutated (ATM) might partially regulate the EXO1 related radiosensitivity. In summary, EXO1 could be a promising prognostic marker, with a potential therapeutic value in HCC.
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Affiliation(s)
- Yaoyao Dai
- Department of Hepatology, Shanghai municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zuxiong Tang
- Department of General surgery, the first affiliated hospital of soochow university, suzhou, China
| | - Zongguo Yang
- Department of Central Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lan Zhang
- Department of Hepatology, Shanghai municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Deng
- Department of Central Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaofeng Zhang
- Department of Central Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yongchun Yu
- Department of Central Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xing Liu
- Department of Central Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Biochip Corporation LTD./National Engineering Center for Biochip at Shanghai, Shanghai, China
- CONTACT Xing Liu ; Junfeng Zhu
| | - Junfeng Zhu
- Department of Hepatology, Shanghai municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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21
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Jung SY, Papp JC, Sobel EM, Zhang ZF. Genetic Variants in Metabolic Signaling Pathways and Their Interaction with Lifestyle Factors on Breast Cancer Risk: A Random Survival Forest Analysis. Cancer Prev Res (Phila) 2018; 11:44-51. [PMID: 29074537 PMCID: PMC5754228 DOI: 10.1158/1940-6207.capr-17-0143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/06/2017] [Accepted: 10/18/2017] [Indexed: 12/18/2022]
Abstract
Genetic variants in the insulin-like growth factor-I (IGF-I)/insulin resistance axis may interact with lifestyle factors, influencing postmenopausal breast cancer risk, but these interrelated pathways are not fully understood. In this study, we examined 54 single-nucleotide polymorphisms (SNP) in genes related to IGF-I/insulin phenotypes and signaling pathways and lifestyle factors in relation to postmenopausal breast cancer, using data from 6,567 postmenopausal women in the Women's Health Initiative Harmonized and Imputed Genome-Wide Association Studies. We used a machine-learning method, two-stage random survival forest analysis. We identified three genetic variants (AKT1 rs2494740, AKT1 rs2494744, and AKT1 rs2498789) and two lifestyle factors [body mass index (BMI) and dietary alcohol intake] as the top five most influential predictors for breast cancer risk. The combination of the three SNPs, BMI, and alcohol consumption (≥1 g/day) significantly increased the risk of breast cancer in a gene and lifestyle dose-dependent manner. Our findings provide insight into gene-lifestyle interactions and will enable researchers to focus on individuals with risk genotypes to promote intervention strategies. These data also suggest potential genetic targets in future intervention/clinical trials for cancer prevention in order to reduce the risk for breast cancer in postmenopausal women. Cancer Prev Res; 11(1); 44-51. ©2017 AACR.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, California.
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
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22
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Tomimatsu N, Mukherjee B, Harris JL, Boffo FL, Hardebeck MC, Potts PR, Khanna KK, Burma S. DNA-damage-induced degradation of EXO1 exonuclease limits DNA end resection to ensure accurate DNA repair. J Biol Chem 2017; 292:10779-10790. [PMID: 28515316 PMCID: PMC5491765 DOI: 10.1074/jbc.m116.772475] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/11/2017] [Indexed: 12/22/2022] Open
Abstract
End resection of DNA double-strand breaks (DSBs) to generate 3'-single-stranded DNA facilitates DSB repair via error-free homologous recombination (HR) while stymieing repair by the error-prone non-homologous end joining (NHEJ) pathway. Activation of DNA end resection involves phosphorylation of the 5' to 3' exonuclease EXO1 by the phosphoinositide 3-kinase-like kinases ATM (ataxia telangiectasia-mutated) and ATR (ATM and Rad3-related) and by the cyclin-dependent kinases 1 and 2. After activation, EXO1 must also be restrained to prevent over-resection that is known to hamper optimal HR and trigger global genomic instability. However, mechanisms by which EXO1 is restrained are still unclear. Here, we report that EXO1 is rapidly degraded by the ubiquitin-proteasome system soon after DSB induction in human cells. ATR inhibition attenuated DNA-damage-induced EXO1 degradation, indicating that ATR-mediated phosphorylation of EXO1 targets it for degradation. In accord with these results, EXO1 became resistant to degradation when its SQ motifs required for ATR-mediated phosphorylation were mutated. We show that upon the induction of DNA damage, EXO1 is ubiquitinated by a member of the Skp1-Cullin1-F-box (SCF) family of ubiquitin ligases in a phosphorylation-dependent manner. Importantly, expression of degradation-resistant EXO1 resulted in hyper-resection, which attenuated both NHEJ and HR and severely compromised DSB repair resulting in chromosomal instability. These findings indicate that the coupling of EXO1 activation with its eventual degradation is a timing mechanism that limits the extent of DNA end resection for accurate DNA repair.
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Affiliation(s)
- Nozomi Tomimatsu
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Bipasha Mukherjee
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Janelle Louise Harris
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Francesca Ludovica Boffo
- Department of Molecular Medicine and Medical Biotechnology, Università Federico II, Napoli 80131, Italy, and
| | - Molly Catherine Hardebeck
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Kum Kum Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Sandeep Burma
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390,
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23
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Miao L, Yu Y, Ji Y, Zhang B, Yuan Z, Du Y, Zhu L, Wang R, Chen N, Yuan H. Association between BRCA1 P871L polymorphism and cancer risk: evidence from a meta-analysis. Oncotarget 2017; 8:30587-30594. [PMID: 28427168 PMCID: PMC5444767 DOI: 10.18632/oncotarget.15739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/13/2017] [Indexed: 01/23/2023] Open
Abstract
Breast cancer 1 (BRCA1) gene makes great contributions to the repair of DNA. The association between BRCA1 P871L polymorphism and cancer risk has been investigated in a growing number of studies, but the conclusions are not conclusive. To obtain a comprehensive conclusion, we performed a meta-analysis of 24 studies with 13762 cases and 22388 controls. The pooled results indicated that BRCA1 gene P871L variant decreased risk of overall cancer (homozygous model: odds ratio (OR) = 0.89, 95%confidence interval (CI) = 0.79-1.00; recessive model: OR = 0.89, 95% CI = 0.80-0.99). The stratified analysis observed decreased risk associated with BRCA1 P871L in subgroups among Asians and high score studies, but not Caucasians or low score studies. In conclusion, despite several limitations, this meta-analysis suggested that BRCA1 P871L genetic variation may be associated with decreased susceptibility to cancer.
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Affiliation(s)
- Limin Miao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yang Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yefeng Ji
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Bo Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Zhiyao Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yifei Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Longbiao Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ruixia Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ning Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
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24
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Cherdyntseva N, Gervas P, Voropaeva E, Denisov E, Pisareva L, Malinovskaya E, Maksimov V, Voevoda M, Perinov D, Panferova Y, Cherdyntsev E, Choynzonov E. New variants in the BRCA1 gene in Buryat Mongol breast cancer patients: Report from two families. Cancer Biomark 2017; 18:291-296. [PMID: 27983536 DOI: 10.3233/cbm-161649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The BRCA1 mutations that are endemic to the Slavic population of Russia have not been identified among indigenous peoples, including the Buryats, Tuvinians and Altaians with hereditary breast cancer. OBJECTIVE This study was aimed to identify the mutations that are responsible for the occurrence of hereditary breast cancer in the indigenous population of the Republic of Buryatia. METHODS Mutations in the BRCA1 gene were identified in blood samples by Sanger-based sequencing. RESULTS We identified 11 polymorphisms (10 SNPs and 1 Indel) and 6 new unclassified sequence variants in the BRCA1 gene. In our study three new sequence variants (c.321T>A, c.366T>A, c.4357+2T>A) were found in position of previously described polymorphisms in dbSNPs: rs80357544 (c.321delT), rs190900046 (c.366T>G), and rs80358152 (c.4357+2T>C), respectively. Other three new sequence variants (c.3605A>G, c.1998A>C, and c.80+13A>C) have not been previously described in dbSNP, BIC and Human Gene Mutation Databases. CONCLUSIONS We described six new sequence variants that have never been published in the literature or databases. Further studies are required to confirm the impact of new sequence variants on the risk of breast cancer in the Buryat Mongol population.
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Affiliation(s)
- Nadezda Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia.,Tomsk State University, Tomsk, Russia.,Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia
| | - Polina Gervas
- Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia.,Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia
| | - Elena Voropaeva
- Therapy Research Institute of Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Evgeny Denisov
- Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Lubov Pisareva
- Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia
| | - Elena Malinovskaya
- Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia
| | - Vladimir Maksimov
- Therapy Research Institute of Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Michail Voevoda
- Therapy Research Institute of Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk, Russia
| | | | | | | | - Evgeny Choynzonov
- Cancer Research Institute, Tomsk National Research Medical Centre, Russian Academy of Science, Tomsk, Russia
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25
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Zhang B, Chang K, Ramkissoon S, Tanguturi S, Bi WL, Reardon DA, Ligon KL, Alexander BM, Wen PY, Huang RY. Multimodal MRI features predict isocitrate dehydrogenase genotype in high-grade gliomas. Neuro Oncol 2017; 19:109-117. [PMID: 27353503 PMCID: PMC5193019 DOI: 10.1093/neuonc/now121] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND High-grade gliomas with mutations in the isocitrate dehydrogenase (IDH) gene family confer longer overall survival relative to their IDH-wild-type counterparts. Accurate determination of the IDH genotype preoperatively may have both prognostic and diagnostic value. The current study used a machine-learning algorithm to generate a model predictive of IDH genotype in high-grade gliomas based on clinical variables and multimodal features extracted from conventional MRI. METHODS Preoperative MRIs were obtained for 120 patients with primary grades III (n = 35) and IV (n = 85) glioma in this retrospective study. IDH genotype was confirmed for grade III (32/35, 91%) and IV (22/85, 26%) tumors by immunohistochemistry, spectrometry-based mutation genotyping (OncoMap), or multiplex exome sequencing (OncoPanel). IDH1 and IDH2 mutations were mutually exclusive, and all mutated tumors were collapsed into one IDH-mutated cohort. Cases were randomly assigned to either the training (n = 90) or validation cohort (n = 30). A total of 2970 imaging features were extracted from pre- and postcontrast T1-weighted, T2-weighted, and apparent diffusion coefficient map. Using a random forest algorithm, nonredundant features were integrated with clinical data to generate a model predictive of IDH genotype. RESULTS Our model achieved accuracies of 86% (area under the curve [AUC] = 0.8830) in the training cohort and 89% (AUC = 0.9231) in the validation cohort. Features with the highest predictive value included patient age as well as parametric intensity, texture, and shape features. CONCLUSION Using a machine-learning algorithm, we achieved accurate prediction of IDH genotype in high-grade gliomas with preoperative clinical and MRI features.
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Affiliation(s)
- Biqi Zhang
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Ken Chang
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Shakti Ramkissoon
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Shyam Tanguturi
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Wenya Linda Bi
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - David A Reardon
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Keith L Ligon
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Brian M Alexander
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Patrick Y Wen
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
| | - Raymond Y Huang
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts (B.Z., K.C., R.Y.H.); Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Harvard Medical School, Boston, Massachusetts (S.R., K.L.L.); Department of Pathology, Boston Children's Hospital, Boston, Massachusetts (S.R., K.L.L.); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts(S.R., D.A.R., K.L.L., P.Y.W.); Harvard Radiation Oncology Program, Boston, Massachusetts (S.T.); Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts (W.L.B.); Center of Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (D.A.R., P.Y.W.); Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts (B.M.A.)
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Li Y, Min W, Li M, Han G, Dai D, Zhang L, Chen X, Wang X, Zhang Y, Yue Z, Liu J. Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis. Int J Mol Med 2016; 38:1170-8. [PMID: 27572852 PMCID: PMC5029949 DOI: 10.3892/ijmm.2016.2717] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 08/04/2016] [Indexed: 11/24/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common malignant brain tumor. This study aimed to identify the hub genes and regulatory factors of GBM subgroups by RNA sequencing (RNA-seq) data analysis, in order to explore the possible mechanisms responsbile for the progression of GBM. The dataset RNASeqV2 was downloaded by TCGA-Assembler, containing 169 GBM and 5 normal samples. Gene expression was calculated by the reads per kilobase per million reads measurement, and nor malized with tag count comparison. Following subgroup classification by the non-negative matrix factorization, the differentially expressed genes (DEGs) were screened in 4 GBM subgroups using the method of significance analysis of microarrays. Functional enrichment analysis was performed by DAVID, and the protein-protein interaction (PPI) network was constructed based on the HPRD database. The subgroup-related microRNAs (miRNAs or miRs), transcription factors (TFs) and small molecule drugs were predicted with predefined criteria. A cohort of 19,515 DEGs between the GBM and control samples was screened, which were predominantly enriched in cell cycle- and immunoreaction-related pathways. In the PPI network, lymphocyte cytosolic protein 2 (LCP2), breast cancer 1 (BRCA1), specificity protein 1 (Sp1) and chromodomain-helicase-DNA-binding protein 3 (CHD3) were the hub nodes in subgroups 1–4, respectively. Paired box 5 (PAX5), adipocyte protein 2 (aP2), E2F transcription factor 1 (E2F1) and cAMP-response element-binding protein-1 (CREB1) were the specific TFs in subgroups 1–4, respectively. miR-147b, miR-770-5p, miR-220a and miR-1247 were the particular miRNAs in subgroups 1–4, respectively. Natalizumab was the predicted small molecule drug in subgroup 2. In conclusion, the molecular regulatory mechanisms of GBM pathogenesis were distinct in the different subgroups. Several crucial genes, TFs, miRNAs and small molecules in the different GBM subgroups were identified, which may be used as potential markers. However, further experimental validations may be required.
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Affiliation(s)
- Yanan Li
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Weijie Min
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Mengmeng Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai 200003, P.R. China
| | - Guosheng Han
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Dongwei Dai
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Lei Zhang
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Xin Chen
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Xinglai Wang
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Yuhui Zhang
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Zhijian Yue
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Jianmin Liu
- Department of Neurosurgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
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27
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Associations between Nine Polymorphisms in EXO1 and Cancer Susceptibility: A Systematic Review and Meta-Analysis of 39 Case-control Studies. Sci Rep 2016; 6:29270. [PMID: 27387683 PMCID: PMC4937237 DOI: 10.1038/srep29270] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/15/2016] [Indexed: 12/21/2022] Open
Abstract
An increasing number of studies have highlighted the potential link between EXO1 polymorphisms and cancer risk, although no consensus has yet been obtained. Thus, we aimed to obtain a thorough and current assessment of EXO1 polymorphisms and cancer susceptibility by performing a meta-analysis. A comprehensive literature retrieval was performed on PubMed, EMbase, Web of Science and Wanfang databases. The odds ratio (OR) and 95% confidence interval (CI) were applied to assess the results. Finally, 39 case-control studies of the nine EXO1 polymorphisms that involved 21,651 cases and 21,348 controls met our inclusion criteria. The pooled analysis indicated that the rs1047840 polymorphism conferred a significantly increased susceptibility to cancer in an allelic model. Similarly, the rs3754093, rs1776177, rs9350, rs10802996, rs1635498, rs1776148 and rs851797 polymorphisms were also associated with an increased susceptibility to cancer in an allelic model, respectively, while no significant association was identified for rs1635517 polymorphism. For the rs1047840 polymorphism, in an ethnicity subgroup analysis, a significantly increased susceptibility to cancer for Asians was identified in all the genetic models, and for Caucasians in an allelic model. Our findings provide the evidence that the rs1047840, rs9350, rs10802996, rs1635498, rs1776148, rs1776177, rs3754093 and rs851797 polymorphisms may act as risk factors for cancer.
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Chen ZY, Zheng SR, Zhong JH, Zhuang XD, Zhou JY. Association between three exonuclease 1 polymorphisms and cancer risks: a meta-analysis. Onco Targets Ther 2016; 9:899-910. [PMID: 26966378 PMCID: PMC4770079 DOI: 10.2147/ott.s95258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To date, the results of studies exploring the relation between exonuclease 1 (Exo1) polymorphisms and cancer risks have differed. In this study, we performed a meta-analysis to investigate the effect of the three most extensively studied Exo1 polymorphisms (Pro757Leu, Glu589Lys, and Glu670Gly) on cancer susceptibility. The related studies published before August 5, 2015, were collected by searching the PubMed and EMBASE databases. We found 16 publications containing studies that were eligible for our study, including 10 studies for Pro757Leu polymorphism (4,093 cases and 3,834 controls), 12 studies for Glu589Lys polymorphism (6,479 cases and 6,550 controls), and 7 studies for Glu670Gly polymorphism (3,700 cases and 3,496 controls). Pooled odds ratios and 95% confidence intervals were used to assess the strength of the associations, and all the statistical analyses were calculated using the software program STATA version 12.0. Our results revealed that the Pro757Leu polymorphism was significantly associated with a reduced cancer risk, whereas an inverse association was found for the Glu589Lys polymorphism. Furthermore, subgroup analysis of smoking status indicated that the Glu589Lys polymorphism was significantly associated with an increased cancer risk in smokers, but not in nonsmokers. However, no evidence was found for an association between the Glu670Gly polymorphism and cancer risk. In conclusion, this meta-analysis suggests that the Pro757Leu polymorphism may provide protective effects against cancer, while the Glu589Lys polymorphism may be a risk factor for cancer. Moreover, the Glu670Gly polymorphism may have no influence on cancer susceptibility. In the future, large-scaled and well-designed studies are needed to achieve a more precise and comprehensive result.
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Affiliation(s)
- Zi-Yu Chen
- Department of Clinical Medicine, The First Clinical Medical College, Southern Medical University, Guangzhou, People's Republic of China; Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Si-Rong Zheng
- Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie-Hui Zhong
- Department of Clinical Medicine, The First Clinical Medical College, Southern Medical University, Guangzhou, People's Republic of China; Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Xiao-Duan Zhuang
- Department of Clinical Medicine, The First Clinical Medical College, Southern Medical University, Guangzhou, People's Republic of China; Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Jue-Yu Zhou
- Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
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Pardo-Diaz C, Salazar C, Jiggins CD. Towards the identification of the loci of adaptive evolution. Methods Ecol Evol 2015; 6:445-464. [PMID: 25937885 PMCID: PMC4409029 DOI: 10.1111/2041-210x.12324] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022]
Abstract
1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.
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Affiliation(s)
- Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del RosarioCarrera 24 No 63C-69, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of CambridgeDowning Street, Cambridge, CB2 3EJ, UK
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Bayram S. The exonuclease 1 Glu589Lys gene polymorphism and cancer susceptibility: evidence based on a meta-analysis. Asian Pac J Cancer Prev 2015; 15:2571-6. [PMID: 24761866 DOI: 10.7314/apjcp.2014.15.6.2571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Published studies on the association between the exonuclease 1 (EXO1) Glu589Lys polymorphism and cancer susceptibility have yielded conflicting results. Thus, a meta-analysis of published studies was performed to assess the possible association. MATERIALS AND METHODS All eligible case-control studies published up to January 2013 on the association between the EXO1 Glu589Lys polymorphism and cancer susceptibility were identified by searching PubMed, Web of Science, Science Direct and hand search. Either fixed-effect or random-effect models were used to calculate pooled odds ratios (ORs) with 95% confidence intervals (CIs) using the Comprehensive Meta-Analysis software version 2.2. RESULTS A total of 4,391 cancer cases and 4,339 controls from 10 studies were included. Overall, no significant association between the EXO1 Glu589Lys polymorphism and cancer susceptibility was observed in either genetic model. However; in subgroup analyses by cancer type, a significant association between EXO1 Glu589Lys and lung cancer risk was found (Lys vs Glu: OR=1.23, 95%CI=1.07- 1.41, p heterogeneity=0.05). Further, subgroup analysis by ethnicity indicated that there was a statistically increased cancer risk in Asians (Lys vs Glu: OR=1.42, 95%CI=1.30-1.55, p heterogeneity=0.07; Lys/Lys vs Glu/Glu: OR=1.93, 95%CI=1.20-3.12, p heterogeneity=0.01; Lys/Lys+Glu/Lys vs Glu/Glu: OR=1.52, 95%CI=1.37-1.68, p heterogeneity=0.42; Lys/Lys vs Glu/Lys+Glu/Glu: OR=1.68, 95%CI=1.07-2.65, p heterogeneity=0.02). However, significant association was absent in Caucasians. CONCLUSIONS This meta-analysis suggests, for the first time, that the EXO1 Glu589Lys polymorphism is not associated with overall cancer susceptibility, although marginal associations were found for lung cancer and Asian subgroups. Additional well-designed studies with larger sample size focusing on different ethnicities and cancer types are needed to confirm these findings.
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Affiliation(s)
- Suleyman Bayram
- Adiyaman University, Adiyaman School of Health, Department of Nursing, Adiyaman, Turkey E-mail :
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Potentially functional SNPs (pfSNPs) as novel genomic predictors of 5-FU response in metastatic colorectal cancer patients. PLoS One 2014; 9:e111694. [PMID: 25372392 PMCID: PMC4221105 DOI: 10.1371/journal.pone.0111694] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/29/2014] [Indexed: 12/31/2022] Open
Abstract
5-Fluorouracil (5-FU) and its pro-drug Capecitabine have been widely used in treating colorectal cancer. However, not all patients will respond to the drug, hence there is a need to develop reliable early predictive biomarkers for 5-FU response. Here, we report a novel potentially functional Single Nucleotide Polymorphism (pfSNP) approach to identify SNPs that may serve as predictive biomarkers of response to 5-FU in Chinese metastatic colorectal cancer (CRC) patients. 1547 pfSNPs and one variable number tandem repeat (VNTR) in 139 genes in 5-FU drug (both PK and PD pathway) and colorectal cancer disease pathways were examined in 2 groups of CRC patients. Shrinkage of liver metastasis measured by RECIST criteria was used as the clinical end point. Four non-responder-specific pfSNPs were found to account for 37.5% of all non-responders (P<0.0003). Five additional pfSNPs were identified from a multivariate model (AUC under ROC = 0.875) that was applied for all other pfSNPs, excluding the non-responder-specific pfSNPs. These pfSNPs, which can differentiate the other non-responders from responders, mainly reside in tumor suppressor genes or genes implicated in colorectal cancer risk. Hence, a total of 9 novel SNPs with potential functional significance may be able to distinguish non-responders from responders to 5-FU. These pfSNPs may be useful biomarkers for predicting response to 5-FU.
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Qin TT, Chen T, Zhang Q, Du HN, Shu YQ, Luo K, Zhu LJ. Association between BRCA1 rs799917 polymorphism and breast cancer risk: A meta-analysis of 19,878 subjects. Biomed Pharmacother 2014; 68:905-10. [PMID: 25194442 DOI: 10.1016/j.biopha.2014.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 08/04/2014] [Indexed: 01/24/2023] Open
Abstract
Studies investigating the association between the BRCA1 rs799917 polymorphism and breast cancer risk have reported controversial results. In order to derive a more precise estimation of the relationship, we performed a comprehensive meta-analysis. A total of 8 articles comprising 19,878 subjects were included in this meta-analysis. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were calculated by Stata 11 software. Heterogeneity tests were conducted by Q test with I(2) value, and publication bias assessment was performed by Begg's funnel plot and Egger's test. The pooled results did not show any sufficient evidence approving the association between the BRCA1 rs799917 polymorphism and breast cancer risk in total population (T vs C: OR=1.01, 95% CI=0.97-1.06; TT vs CC: OR=1.03, 95% CI=0.93-1.13; CT vs CC: OR=1.04, 95% CI=0.92-1.16; TT+CT vs CC: OR=1.04, 95% CI=0.94-1.15; TT vs CT+CC: OR=1.03, 95% CI=0.94-1.12). In the further subgroup analyses, no significant associations were found in any comparison models according to ethnicity and source of controls. No publication bias was observed in this meta-analysis. In summary, based on the overall results, this meta-analysis strongly suggests that the BRCA1 rs799917 polymorphism is not associated with breast cancer risk.
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Affiliation(s)
- Ting-ting Qin
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Tao Chen
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Qian Zhang
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Hai-na Du
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Yong-qian Shu
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Kai Luo
- Department of Breast Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.
| | - Ling-jun Zhu
- Department of Medical Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.
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Brodie A, Tovia-Brodie O, Ofran Y. Large scale analysis of phenotype-pathway relationships based on GWAS results. PLoS One 2014; 9:e100887. [PMID: 25007247 PMCID: PMC4090199 DOI: 10.1371/journal.pone.0100887] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 05/28/2014] [Indexed: 12/13/2022] Open
Abstract
The widely used pathway-based approach for interpreting Genome Wide Association Studies (GWAS), assumes that since function is executed through the interactions of multiple genes, different perturbations of the same pathway would result in a similar phenotype. This assumption, however, was not systemically assessed on a large scale. To determine whether SNPs associated with a given complex phenotype affect the same pathways more than expected by chance, we analyzed 368 phenotypes that were studied in >5000 GWAS. We found 216 significant phenotype-pathway associations between 70 of the phenotypes we analyzed and known pathways. We also report 391 strong phenotype-phenotype associations between phenotypes that are affected by the same pathways. While some of these associations confirm previously reported connections, others are new and could shed light on the molecular basis of these diseases. Our findings confirm that phenotype-associated SNPs cluster into pathways much more than expected by chance. However, this is true for <20% (70/368) of the phenotypes. Different types of phenotypes show markedly different tendencies: Virtually all autoimmune phenotypes show strong clustering of SNPs into pathways, while most cancers and metabolic conditions, and all electrophysiological phenotypes, could not be significantly associated with any pathway despite being significantly associated with a large number of SNPs. While this may be due to missing data, it may also suggest that these phenotypes could result only from perturbations of specific genes and not from other perturbations of the same pathway. Further analysis of pathway-associated versus gene-associated phenotypes is, therefore, needed in order to understand disease etiology and in order to promote better drug target selection.
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Affiliation(s)
- Aharon Brodie
- The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel
| | - Oholi Tovia-Brodie
- Department of Cardiology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Yanay Ofran
- The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel
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Du Y, Su T, Zhao L, Tan X, Chang W, Zhang H, Cao G. Associations of polymorphisms in DNA repair genes and MDR1 gene with chemotherapy response and survival of non-small cell lung cancer. PLoS One 2014; 9:e99843. [PMID: 24933103 PMCID: PMC4059653 DOI: 10.1371/journal.pone.0099843] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/19/2014] [Indexed: 12/26/2022] Open
Abstract
Objectives We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementation group 1 (ERCC1) rs11615, xeroderma pigmentosum group D (XPD/ERCC2) rs13181, X-ray repair cross complementing group 1 (XRCC1) rs25487, XRCC3 rs1799794, and breast cancer susceptibility gene 1 (BRCA1) rs1799966 from the DNA repair pathway and multiple drug resistance 1 (MDR1/ABCB1) rs1045642 with response to chemotherapy and survival of non-small cell lung cancer (NSCLC) in a Chinese population. Materials and Methods A total of 352 NSCLC patients were enrolled to evaluate the associations of the six SNPs with response to chemotherapy and overall survival. Logistic regressions were applied to test the associations of genetic polymorphisms with response to chemotherapy in 161 advanced NSCLC patients. Overall survival was analyzed in 161 advanced and 156 early stage NSCLC patients using the Kaplan-Meier method with log-rank test, respectively. Multivariate Cox proportional hazards model was performed to determine the factors independently associated with NSCLC prognosis. Results BRCA1 rs1799966 minor allele C (TC+CC vs. TT, OR = 0.402, 95%CI = 0.204−0.794, p = 0.008) and MDR1/ABCB1 rs1045642 minor allele A (GA +AA vs. GG, OR = 0.478, 95%CI = 0.244−0.934, p = 0.030) were associated with a better response to chemotherapy in advanced NSCLC patients. Survival analyses indicated that BRCA1 rs1799966 TC+CC genotypes were associated with a decreased risk of death (HR = 0.617, 95% CI = 0.402−0.948, p = 0.028) in advanced NSCLC patients, and the association was still significant after the adjustment for covariates. Multivariate Cox regression analysis showed that ERCC1 rs11615 AA genotype (P = 0.020) and smoking (p = 0.037) were associated with increased risks of death in early stage NSCLC patients after surgery. Conclusions Polymorphisms of genes in DNA repair pathway and MDR1 could contribute to chemotherapy response and survival of patients with NSCLC.
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Affiliation(s)
- Yan Du
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Tong Su
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Lijun Zhao
- Department of Pulmonary Medicine, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xiaojie Tan
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Wenjun Chang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
- * E-mail:
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Duan F, Song C, Dai L, Cui S, Zhang X, Zhao X. The significance of Exo1 K589E polymorphism on cancer susceptibility: evidence based on a meta-analysis. PLoS One 2014; 9:e96764. [PMID: 24810280 PMCID: PMC4014567 DOI: 10.1371/journal.pone.0096764] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/07/2014] [Indexed: 12/19/2022] Open
Abstract
The exonuclease1 (Exo1) gene is a key component of mismatch repair (MMR) by resecting the damaged strand, which is the only exonuclease involved in the human MMR system. The gene product is a member of the RAD2 nuclease family and functions in DNA replication, repair and recombination. However, whether Exo1 is required to activate MMR-dependent DNA damage response (DDR) remains unknown, the conclusions of the Exo1 polymorphisms on cancer susceptibility studies were not consistent. We carried out a meta-analysis of 7 case-control studies to clarify the association between the Exo1 K589E polymorphism and cancer risk. Overall,a significant association of the Exo1 K589E polymorphism with cancer risk in all genetic models (Lys vs Glu: OR = 1.51, 95%CI:1.39-1.99, P<0.01; Glu/Lys vs Glu/Glu: OR = 1.43, 95%CI:1.28-1.60, P<0.01; Lys/Lys vs Glu/Glu: OR = 2.45, 95%CI:1.90-3.17, P<0.01; Lys/Lys+Glu/Lys vs Glu/Glu: OR = 1.53, 95%CI:1.38-1.71, P<0.01; Glu/Glu vs Glu/Lys+Lys/Lys: OR = 2.27, 95%CI:1.79-2.89, P<0.01). In the stratified analysis by ethnicity, significantly increased risk was observed in Asian population (Lys vs Glu: OR = 1.53, 95%CI:1.39-1.69, P<0.01; Glu/Lys vs Glu/Glu: OR = 1.50, 95%CI:1.34-1.69, P<0.01; Lys/Lys vs Glu/Glu: OR = 2.48, 95%CI:1.84-3.34, P<0.01; Lys/Lys+Glu/Lys vs Glu/Glu: OR = 1.58, 95%CI:1.41-1.78, P<0.01; Glu/Glu vs Glu/Lys+Lys/Lys: OR = 2.18, 95%CI:1.62-2.93, P<0.01). Subgroup analysis based on smoking suggested Exo1 K589E polymorphism conferred significant risk among smokers (Lys/Lys+Glu/Lys vs Glu/Glu: OR = 2.16, 95%CI:1.77-2.63, P<0.01), but not in non-smokers (Lys/Lys+Glu/Lys vs Glu/Glu: OR = 0.89, 95%CI:0.64-1.24, P = 0.50). In conclusion, Exo1 K589E Lys allele may be used as a novel biomarker for cancer susceptibility, particularly in smokers.
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Affiliation(s)
- Fujiao Duan
- Department of Hospital Infection Management, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou, Henan, China
| | - Chunhua Song
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, Henan, China
| | - Liping Dai
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, Henan, China
| | - Shuli Cui
- College of Professional Study, Northeastern University, Boston, Massachusetts, United States of America
| | - Xiaoqin Zhang
- Department of Hospital Infection Management, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou, Henan, China
| | - Xia Zhao
- Department of Hospital Infection Management, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou, Henan, China
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Adel Fahmideh M, Schwartzbaum J, Frumento P, Feychting M. Association between DNA repair gene polymorphisms and risk of glioma: a systematic review and meta-analysis. Neuro Oncol 2014; 16:807-14. [PMID: 24500421 DOI: 10.1093/neuonc/nou003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Association studies of germline DNA repair single nucleotide polymorphisms (SNPs) and glioma risk have yielded inconclusive results. We therefore performed a systematic review and meta-analysis of studies investigating this association. METHODS We identified 27 eligible studies investigating 105 SNPs in 42 DNA repair genes. Of these, 10 SNPs in 7 genes were analyzed in at least 4 studies and were therefore included in our meta-analysis. The meta-analysis was performed for homozygote comparison, heterozygote comparison, and dominant and recessive models by applying a fixed- or random-effects model. The funnel and forest plots were created using RevMan software. RESULTS We found that SNPs rs3212986 (odds ratio [OR] = 1.35 (1.08-1.68), P = .008), rs13181 (OR = 1.18 (1.06-1.31), P = .002), and rs25487 (OR = 1.12 (1.03-1.22), P = .007) in DNA repair genes ERCC1, ERCC2 (XPD), and XRCC1 may increase the risk of glioma, while polymorphisms rs1136410 (OR = 0.78 (0.68-0.89), P = .0004) and rs12917 (OR = 0.84 (0.73-0.96), P = .01) in PARP1(ADPRT) and MGMT are associated with decreased susceptibility to glioma. No evidence of significant associations between ERCC2 rs1799793, OGG1 rs1052133, XRCC1 rs25489, XRCC1 rs1799782, or XRCC3 rs861539 and risk of glioma was observed. CONCLUSION This study provides evidence that DNA repair genes ERCC1, ERCC2, and XRCC1 might be low-penetrance glioma-risk genes, while MGMT and PARP1 polymorphisms may confer protection against glioma.
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Affiliation(s)
- Maral Adel Fahmideh
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (M.A.F., M.F.); Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio (J.S.); Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (P.F.)
| | - Judith Schwartzbaum
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (M.A.F., M.F.); Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio (J.S.); Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (P.F.)
| | - Paolo Frumento
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (M.A.F., M.F.); Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio (J.S.); Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (P.F.)
| | - Maria Feychting
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (M.A.F., M.F.); Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio (J.S.); Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden (P.F.)
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Abstract
MicroRNA profiling is an important task to investigate miRNA functions and recent technologies such as microarray, single nucleotide polymorphism (SNP), quantitative real-time PCR (qPCR), and next-generation sequencing (NGS) have played a major role for miRNA analysis. In this chapter, we give an overview on statistical approaches for gene expressions, SNP, qPCR, and NGS data including preliminary analyses (pre-processing, differential expression, classification, clustering, exploration of interactions, and the use of ontologies). Our goal is to outline the key approaches with a brief discussion of problems avenues for their solutions and to give some examples for real-world use. Readers will be able to understand the different data formats (expression levels, sequences etc.) and they will be able to choose appropriate methods for their own research and application. On the other hand, we give brief notes on most popular tools/packages for statistical genetic analysis. This chapter aims to serve as a brief introduction to different kinds of statistical methods and also provides an extensive source of references.
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Winham SJ, Biernacka JM. Gene-environment interactions in genome-wide association studies: current approaches and new directions. J Child Psychol Psychiatry 2013; 54:1120-34. [PMID: 23808649 PMCID: PMC3829379 DOI: 10.1111/jcpp.12114] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2013] [Indexed: 01/20/2023]
Abstract
BACKGROUND Complex psychiatric traits have long been thought to be the result of a combination of genetic and environmental factors, and gene-environment interactions are thought to play a crucial role in behavioral phenotypes and the susceptibility and progression of psychiatric disorders. Candidate gene studies to investigate hypothesized gene-environment interactions are now fairly common in human genetic research, and with the shift toward genome-wide association studies, genome-wide gene-environment interaction studies are beginning to emerge. METHODS We summarize the basic ideas behind gene-environment interaction, and provide an overview of possible study designs and traditional analysis methods in the context of genome-wide analysis. We then discuss novel approaches beyond the traditional strategy of analyzing the interaction between the environmental factor and each polymorphism individually. RESULTS Two-step filtering approaches that reduce the number of polymorphisms tested for interactions can substantially increase the power of genome-wide gene-environment studies. New analytical methods including data-mining approaches, and gene-level and pathway-level analyses, also have the capacity to improve our understanding of how complex genetic and environmental factors interact to influence psychologic and psychiatric traits. Such methods, however, have not yet been utilized much in behavioral and mental health research. CONCLUSIONS Although methods to investigate gene-environment interactions are available, there is a need for further development and extension of these methods to identify gene-environment interactions in the context of genome-wide association studies. These novel approaches need to be applied in studies of psychology and psychiatry.
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Affiliation(s)
- Stacey J Winham
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester MN 55905
| | - Joanna M. Biernacka
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester MN 55905,Department of Psychiatry and Psychology, Mayo Clinic, Rochester MN 55905
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Wu HC, Delgado-Cruzata L, Machella N, Wang Q, Santella RM, Terry MB. DNA double-strand break repair genotype and phenotype and breast cancer risk within sisters from the New York site of the Breast Cancer Family Registry (BCFR). Cancer Causes Control 2013; 24:2157-68. [PMID: 24062231 DOI: 10.1007/s10552-013-0292-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 09/13/2013] [Indexed: 12/11/2022]
Abstract
PURPOSE We previously observed that poor DNA repair phenotype is associated with increased breast cancer (BC) risk within families. Here, we examined whether genetic variation in double-strand break repair (DSBR) genes is associated with BC risk and if genotypes are related to phenotype in unaffected women. METHODS Using data from the New York site of the Breast Cancer Family Registry, we investigated 25 single-nucleotide polymorphism (SNPs) involved in DSBR using biospecimens from 337 BC cases and 410 unaffected sister controls. RESULTS Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-2.76) for the combined GA/AA of rs1805377 and 1.69 (95 % CI 1.03-2.77) for rs1056503 TG/GG; these associations were no longer statistically significant in multivariable conditional logistic regression models. When examining the association of SNPs with phenotype, we found that genotypes of XRCC5 rs3834 and rs1051685, which were highly correlated with each other, were associated with end-joining (EJ) capacity; women with the XRCC5 rs3834 GA genotype had better DNA repair as measured by higher levels of EJ capacity (37.8 ± 14.1 % for GA vs. 27.9 ± 11.8 % for GG carriers p = 0.0006). Women with the AA genotype of BRCA1 rs799917 also had higher EJ capacity (35.1 ± 9.2 %) than those with GG (26.4 ± 10.1 %, p = 0.02). CONCLUSIONS Overall, we found that selected DSBR genotypes were associated with phenotype, although they were not associated with BC risk itself, suggesting that phenotypic measures are influenced by endogenous and exogenous factors across the life course and may be better markers than genotypic measures for ascertaining BC risk.
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Affiliation(s)
- Hui-Chen Wu
- Department of Epidemiology, Mailman School of Public Health of Columbia University, 722 West 168th St., 724A, New York, NY, 10032, USA
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Zhao J, Liu L, Zhang A, Chen Q, Fang W, Zeng L, Lu J. Effect of EME1 exon variant Ile350Thr on risk and early onset of breast cancer in southern Chinese women. J Biomed Res 2013; 27:193-201. [PMID: 23720674 PMCID: PMC3664725 DOI: 10.7555/jbr.27.20130013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/22/2013] [Accepted: 03/06/2013] [Indexed: 01/10/2023] Open
Abstract
Essential meiotic endonuclease 1 homolog 1 (EME1) is a key DNA repair protein that participates in the recognition and repair of DNA double-strand breaks. Deficiency of the EME1 gene can lead to spontaneous genomic instability and thus contribute to tumorgenesis. We hypothesized that the exon variants of EME1 confer genetic susceptibility to breast cancer. In a case-control study of 748 breast cancer patients and 778 normal controls, we analyzed the association between two exon variants of EME1 (i.e.,Ile350Thr: rs12450550T > C and Glu69Asp: rs3760413T > G) and breast cancer risk. We found that compared to the common Ile/Ile genotype, the Thr variant genotypes (Thr/Ile + Thr/Thr) conferred a 1.47-fold increased risk of breast cancer (OR=1.47, 95% CI=1.13-1.92). The variant Ile350Thr was also associated with early onset of breast cancer (r = -0.116, P = 0.002). The mean age of onset was 44.4 years for Thr/Thr genotype carriers and 46.5 years for Thr/Ile genotype carriers, which was significantly lower than that (49.4 years) for Ile/Ile genotype carriers (P = 0.006). Moreover, no significant association was observed between the Glu69Asp variant and breast cancer risk. Our findings suggest that the EME1 variant Ile350Thr contributes to an increased risk and early onset of breast cancer.
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Affiliation(s)
- Jianwei Zhao
- The Institute for Chemical Carcinogenesis, the State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 510182, China; ; Baiyun Women and Children Hospital, Guangzhou, Guangdong 510400, China
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Janitza S, Strobl C, Boulesteix AL. An AUC-based permutation variable importance measure for random forests. BMC Bioinformatics 2013; 14:119. [PMID: 23560875 PMCID: PMC3626572 DOI: 10.1186/1471-2105-14-119] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 03/21/2013] [Indexed: 11/30/2022] Open
Abstract
Background The random forest (RF) method is a commonly used tool for classification with
high dimensional data as well as for ranking candidate predictors based on
the so-called random forest variable importance measures (VIMs). However the
classification performance of RF is known to be suboptimal in case of
strongly unbalanced data, i.e. data where response class sizes differ
considerably. Suggestions were made to obtain better classification
performance based either on sampling procedures or on cost sensitivity
analyses. However to our knowledge the performance of the VIMs has not yet
been examined in the case of unbalanced response classes. In this paper we
explore the performance of the permutation VIM for unbalanced data settings
and introduce an alternative permutation VIM based on the area under the
curve (AUC) that is expected to be more robust towards class imbalance. Results We investigated the performance of the standard permutation VIM and of our
novel AUC-based permutation VIM for different class imbalance levels using
simulated data and real data. The results suggest that the new AUC-based
permutation VIM outperforms the standard permutation VIM for unbalanced data
settings while both permutation VIMs have equal performance for balanced
data settings. Conclusions The standard permutation VIM loses its ability to discriminate between
associated predictors and predictors not associated with the response for
increasing class imbalance. It is outperformed by our new AUC-based
permutation VIM for unbalanced data settings, while the performance of both
VIMs is very similar in the case of balanced classes. The new AUC-based VIM
is implemented in the R package party for the unbiased RF variant based on
conditional inference trees. The codes implementing our study are available
from the companion website:
http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html.
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Affiliation(s)
- Silke Janitza
- Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Marchioninistr. 15, D-81377, Munich, Germany.
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Santivasi WL, Xia F. The role and clinical significance of DNA damage response and repair pathways in primary brain tumors. Cell Biosci 2013; 3:10. [PMID: 23388100 PMCID: PMC3573923 DOI: 10.1186/2045-3701-3-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/06/2012] [Indexed: 01/08/2023] Open
Abstract
Primary brain tumors, in particular, glioblastoma multiforme (GBM), continue to have dismal survivability despite advances in treating other neoplasms. The goal of new anti-glioma therapy development is to increase their therapeutic ratios by enhancing tumor control and/or decreasing the severity and incidence of side effects. Because radiotherapy and most chemotherapy agents rely on DNA damage, the cell's DNA damage repair and response (DRR) pathways may hold the key to new therapeutic strategies. DNA double-strand breaks (DSBs) generated by ionizing radiation and chemotherapeutic agents are the most lethal form of damage, and are repaired via either homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways. Understanding and exploitation of the differences in the use of these repair pathways between tumor and normal brain cells will allow for an increase in tumor cell killing and decreased normal tissue damage. A literature review and discussion on new strategies which can improve the anti-glioma therapeutic ratio by differentially targeting HR and NHEJ function in tumor and normal neuronal tissues is the focus of this article.
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Affiliation(s)
- Wil L Santivasi
- Department of Radiation Oncology, The Ohio State University College of Medicine, 072A Starling Loving Hall, 300 W, 10th Avenue, Columbus, OH 43210, USA.
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Walsh KM, Anderson E, Hansen HM, Decker PA, Kosel ML, Kollmeyer T, Rice T, Zheng S, Xiao Y, Chang JS, McCoy LS, Bracci PM, Wiemels JL, Pico AR, Smirnov I, Lachance DH, Sicotte H, Eckel-Passow JE, Wiencke JK, Jenkins RB, Wrensch MR. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genet Epidemiol 2013; 37:222-8. [PMID: 23280628 PMCID: PMC3670948 DOI: 10.1002/gepi.21707] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/13/2012] [Accepted: 11/22/2012] [Indexed: 01/07/2023]
Abstract
Genomewide association studies (GWAS) and candidate-gene studies have implicated single-nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case-control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate-gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P < 0.05), with all associations in the same direction as in previous reports. Several SNP associations showed considerable differences across histologic subtype. All eight successfully replicated associations were first identified by GWAS, although none of the putative risk SNPs from candidate-gene studies was associated in the full case-control sample (all P values > 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes.
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Affiliation(s)
- Kyle M Walsh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
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A single nucleotide polymorphism in EXO1 gene is associated with cervical cancer susceptibility in Chinese patients. Int J Gynecol Cancer 2012; 22:220-5. [PMID: 22146767 DOI: 10.1097/igc.0b013e318234fd8a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The aim of this study was to investigate the association of Exonuclease1 (EXO1) genetic polymorphism and the development of cervical carcinoma. METHODS This study was conducted with 126 patients diagnosed with cervical cancer and 278 people with no cancer history. The polymerase chain reaction-based restriction fragment length polymorphism was used to evaluate the K589E and C908G gene polymorphisms. Unconditional logistic regression analysis was used to estimate the association between the genotypes and the risk for cervical cancer. RESULTS This is the first study on the role of EXO1 K589E (rs1047840) and EXO1 C908G (rs10802996) polymorphisms in cervical cancer in a Chinese population. Our results indicated that the EXO1 K589G polymorphism were significantly associated with the risk for cervical cancer. Compared with the G allele EXO1 K589E, the A allele increased the risk for cervical cancer (adjusted odds ratio, 1.67; 95% confidence interval, 1.13-2.45). By contrast, we have not found a significant association between the EXO1 C908G polymorphism and cervical cancer risk (P = 0.791). CONCLUSION These findings indicate that the SNPs of EXO1 K589E may contribute to cervical cancer carcinogenesis in Chinese populations. A larger population study will need to be carried out to further validate the potential association of EXO1 genetic polymorphism and cervical carcinoma.
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Chen X, Ishwaran H. Random forests for genomic data analysis. Genomics 2012; 99:323-9. [PMID: 22546560 PMCID: PMC3387489 DOI: 10.1016/j.ygeno.2012.04.003] [Citation(s) in RCA: 389] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/11/2012] [Accepted: 04/14/2012] [Indexed: 11/25/2022]
Abstract
Random forests (RF) is a popular tree-based ensemble machine learning tool that is highly data adaptive, applies to "large p, small n" problems, and is able to account for correlation as well as interactions among features. This makes RF particularly appealing for high-dimensional genomic data analysis. In this article, we systematically review the applications and recent progresses of RF for genomic data, including prediction and classification, variable selection, pathway analysis, genetic association and epistasis detection, and unsupervised learning.
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Affiliation(s)
- Xi Chen
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA.
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Abstract
Pathway analysis provides a powerful approach for identifying the joint effect of genes grouped into biologically-based pathways on disease. Pathway analysis is also an attractive approach for a secondary analysis of genome-wide association study (GWAS) data that may still yield new results from these valuable datasets. Most of the current pathway analysis methods focused on testing the cumulative main effects of genes in a pathway. However, for complex diseases, gene-gene interactions are expected to play a critical role in disease etiology. We extended a random forest-based method for pathway analysis by incorporating a two-stage design. We used simulations to verify that the proposed method has the correct type I error rates. We also used simulations to show that the method is more powerful than the original random forest-based pathway approach and the set-based test implemented in PLINK in the presence of gene-gene interactions. Finally, we applied the method to a breast cancer GWAS dataset and a lung cancer GWAS dataset and interesting pathways were identified that have implications for breast and lung cancers.
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Xu L, Doan PC, Wei Q, Liu Y, Li G, Sturgis EM. Association of BRCA1 functional single nucleotide polymorphisms with risk of differentiated thyroid carcinoma. Thyroid 2012; 22:35-43. [PMID: 22136207 PMCID: PMC3263304 DOI: 10.1089/thy.2011.0117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Breast cancer 1, early onset (BRCA1) is a vital DNA repair gene, and the single nucleotide polymorphisms (SNPs) of this gene have been studied in diverse cancer types. In this study, we investigated the association between eight common BRCA1 functional SNPs and the risk of differentiated thyroid carcinoma (DTC). METHODS This cancer center-based case-control study included 303 DTC cases and 511 controls. A polymerase chain reaction-based restriction fragment length polymorphism assay was performed for genotyping. Unconditional logistical regression analysis was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) in single-SNP analysis and haplotype analysis. RESULTS A decreased risk of DTC was found for the A1988G heterozygous AG genotype (adjusted OR=0.63, 95% CI: 0.45-0.87, Bonferroni-adjusted p-value=0.036). AATAATA and ATAA haplotypes that carry C33420T variant allele were associated with reduced papillary thyroid cancer risk (adjusted OR=0.52, 95% CI: 0.33-0.84; adjusted OR=0.62, 95% CI: 0.40-0.95, respectively). Also, having a combination of ≥3 favorable genotypes was associated with a DTC risk reduction (adjusted OR=0.69, 95% CI: 0.50-0.95). The A31875G AG/GG genotype was associated with a 69% reduced risk of multifocal primary tumor in DTC patients (adjusted OR=0.31, 95% CI: 0.12-0.81). CONCLUSION BRCA1 genetic polymorphisms may play a role in DTC risk, while the possible associations warrant confirmation in independent studies.
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Affiliation(s)
- Li Xu
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Phi C. Doan
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Qingyi Wei
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Yanhong Liu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Erich M. Sturgis
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
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Bayram S, Akkız H, Bekar A, Akgöllü E, Yıldırım S. The significance of Exonuclease 1 K589E polymorphism on hepatocellular carcinoma susceptibility in the Turkish population: a case-control study. Mol Biol Rep 2011; 39:5943-51. [PMID: 22205538 DOI: 10.1007/s11033-011-1406-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 12/17/2011] [Indexed: 02/07/2023]
Abstract
Exonuclease 1 (Exo 1) is an important nuclease involved in mismatch repair system that contributes to maintain genomic stability, to modulate DNA recombination, and to mediate cell cycle arrest. A guanine (G)/adenine (A) common single nucleotide polymorphism at first position of codon 589 in Exo 1 gene determines a glutamic acid (Glu, E) to lysine (Lys, K) (K589E) aminoacidic substitution which may alter cancer risk by influencing the activity of Exo 1 protein. Exo 1 K589E polymorphism has been studied in various cancers, but its association with hepatocellular carcinoma (HCC) has yet to be investigated. To determine the association of the Exo 1 K589E polymorphism with the risk of HCC development in a Turkish population, a hospital-based case-control study was designed consisting of 224 subjects with HCC and 224 cancer-free control subjects matched for age, gender, smoking and alcohol status. The genotype frequency of the Exo 1 K589E polymorphism was determined by using a polymerase chain reaction-restriction fragment length polymorphism assay. Our data shows that the Lys/Lys genotype of the Exo 1 K589E polymorphism is associated with increased risk of HCC development in this Turkish population [odds ratio (OR) = 2.15, 95% confidence interval (CI): 1.13-4.09, P = 0.02]. Furthermore, according to stratified analysis, a significant association was observed between the homozygote Lys/Lys genotype and HCC risk in the subgroups of male gender (OR = 2.67, 95% CI: 1.27-5.61, P = 0.009) and patients with non-viral-related HCC (OR = 3.14, 95% CI: 1.09-8.99, P = 0.03). Because our results suggest for the first time that the Lys/Lys homozygote genotype of Exo 1 K589E polymorphism may be a genetic susceptibility factor for HCC in the Turkish population, further independent studies are required to validate our findings in a larger series, as well as in patients of different ethnic origins.
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Affiliation(s)
- Süleyman Bayram
- Department of Nursing, Adıyaman School of Health, Adıyaman University, 02040, Adıyaman, Turkey.
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Unimodal transform of variables selected by interval segmentation purity for classification tree modeling of high-dimensional microarray data. Talanta 2011; 85:1689-94. [DOI: 10.1016/j.talanta.2011.06.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/28/2011] [Accepted: 06/30/2011] [Indexed: 11/20/2022]
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