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Fang Z, Zhao G, Wang Y, Li F, Ding Z. The updated relationship between the cleft‑lip and palate transmembrane protein‑1‑like rs401681 and lung cancer risk: A systematic review and meta‑analysis. Mol Clin Oncol 2024; 21:70. [PMID: 39113849 PMCID: PMC11304168 DOI: 10.3892/mco.2024.2768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/04/2024] [Indexed: 08/10/2024] Open
Abstract
Currently, the role of cleft-lip and palate transmembrane protein-1-like (CLPTM1L) rs401681 in various tumor types, particularly lung cancer, has garnered significant attention. However, the findings across studies have shown discrepancies. The aim of the present meta-analysis was to provide a more nuanced understanding of the involvement of CLPTM1L rs401681 in lung cancer development. Several electronic databases were systematically searched, including PubMed, Cochrane Library, Embase, Medline, Wanfang, Google Scholar and Chinese National Knowledge Infrastructure. Odds ratios (ORs) and 95% confidence intervals (CIs) were synthesized using random-effects models. Heterogeneity of included studies was assessed using the I2 statistic and Q test. Sensitivity analysis was conducted to evaluate the stability of overall estimates. Moreover, Egger's test was utilized to detect potential publication bias. The collective ORs indicated a significant association between the CLPTM1L rs401681 polymorphism and susceptibility to lung cancer across various genetic comparisons. These encompass allele T vs. allele C (OR=0.93, 95% CI=0.88-0.99, P<0.001), TT + CT vs. CC (OR=0.91, 95% CI=0.87-0.96, P<0.001), TT vs. CC + CT (OR=0.88, 95% CI=0.80-0.96, P<0.001), TT vs. CC (OR=0.84, 95% CI=0.75-0.94, P<0.001) and CT vs. CC (OR=0.84, 95% CI=0.75-0.94, P<0.001). Examination through statistical Q test and I2 statistic revealed pronounced heterogeneity across four genetic comparisons (allele T vs. allele C, TT + CT vs. CC, TT vs. CC and CT vs. CC). Ethnical distinctions emerged as the primary, if not exclusive, sources of the significant heterogeneity. Upon stratification by ethnicity, a notable reduction in heterogeneity was discernible within the Caucasian demographic. However, heterogeneity persisted within the Asian population. Furthermore, lung cancer risks were statistically significantly decreased for individuals possessing allele T through all genetic comparisons within Caucasians; whereas among Asians, significant reduction was observed solely in the TT vs. CC comparison. The present meta-analysis uncovers a significant association between the CLPTM1L rs401681 polymorphism and altered susceptibility to lung cancer.
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Affiliation(s)
- Zemin Fang
- Department of Lung Transplant, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Gaofeng Zhao
- Department of Lung Transplant, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Yuebin Wang
- Department of Lung Transplant, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Fengke Li
- Department of Lung Transplant, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Zhidan Ding
- Department of Lung Transplant, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
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Wu X, Li W, Chen Y. Association of rs401681 (C > T) and rs402710 (C > T) polymorphisms in the CLPTM1L region with risk of lung cancer: a systematic review and meta-analysis. Sci Rep 2024; 14:22603. [PMID: 39349641 PMCID: PMC11442442 DOI: 10.1038/s41598-024-73254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Although many genome-wide association studies (GWAS) have confirmed the negative associations between rs401681[T] / rs402710[T] in the Cleft lip and cleft palate transmembrane protein 1 (CLPTM1L) region and lung cancer (LC) susceptibility in Caucasian and Asian populations, some other studies haven't found these negative associations. The purpose of this study is to clarify the associations between them and LC, as well as the differences in these associations between patients of different ethnicities (Caucasians and Asians), LC subtypes and smoking status. Relevant literatures published before July 7, 2023 in PubMed, EMbase, Web of Science, MEDLINE were searched through the Internet. Statistical analysis of data was performed in Revman 5.3, including drawing forest plots, funnel plots and so on. Sensitivity and publication bias were performed in Stata 14.0. TSA software was performed for the trial sequential analysis (TSA) tests to assess the stability of the results. Registration number: CRD42023407890. A total of 41 literatures (containing 44 studies: 16 studies in Caucasians and 28 studies in Asians) were included in this meta-analysis, including 126476 LC patients and 191648 healthy controls. The results showed that the T allele variants of rs401681 and rs402710 were negatively associated with the risk of LC (rs401681[T]: [OR] = 0.87, 95% CI [0.86, 0.88]; rs402710[T]: [OR] = 0.88, 95% CI [0.86, 0.89]), and the negative associations were stronger in Caucasians than in Asians (Subgroup differences: I2 > 50%). In LC subtypes, the rs401681[T] was negatively associated with the risk of Non-small-cell lung carcinoma (NSCLC), Lung adenocarcinoma (LUAD) and Lung squamous cell carcinoma (LUSC) (P < 0.05), and these negative associations were stronger in Caucasians than in Asians (Subgroup differences: I2 > 50%). The rs402710[T] was negatively associated with the risk of NSCLC, LUAD and LUSC (P < 0.05), and these negative associations in Caucasians were the same as in Asians (Subgroup differences: I2 < 50%). The rs401681[T] was negatively associated with the risk of LC in both smokers and non-smokers (P < 0.05), and the negative association for smokers equals to that of non-smokers (Subgroup differences: P = 0.25, I2 = 24.2%). In LC subtypes, the rs401681[T] was negatively associated with the risks of NSCLC and LUAD in both Caucasian smokers and Asian non-smokers (P < 0.05). The rs402710[T] was negatively associated with the risk of LC in both smokers and non-smokers (P < 0.05), and there was no difference in the strength of this negative risk association between them in Caucasians (Subgroup differences: I2 = 0%). In Asians, this negative association was found to be predominantly among smokers ([OR] = 0.80, 95%CI [0.65, 0.99]). In LC subtypes, the rs402710[T]was negatively associated with the risk of NSCLC in non-smokers, and this negative association was found to be predominantly among non-smokers in Asians ([OR] = 0.75, 95%CI [0.60, 0.94]). The T allele variants of rs401681 and rs402710 are both negatively associated with the risk of developing LC, NSCLC (LUAD, LUSC) in the Caucasian and Asian populations, and the negative associations with the risk of LC are higher in Caucasians. Smoking is an important risk factor for inducing the rs401681 and rs402710 variants and causes LC development in both populations. Other factors like non-smoking are mainly responsible for inducing the development of NSCLC in Asians, and is concentrated in LUAD among Asian non-smoking women.
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Affiliation(s)
- Xiaozheng Wu
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Wen Li
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Yunzhi Chen
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China.
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LoPiccolo J, Gusev A, Christiani DC, Jänne PA. Lung cancer in patients who have never smoked - an emerging disease. Nat Rev Clin Oncol 2024; 21:121-146. [PMID: 38195910 PMCID: PMC11014425 DOI: 10.1038/s41571-023-00844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2023] [Indexed: 01/11/2024]
Abstract
Lung cancer is the most common cause of cancer-related deaths globally. Although smoking-related lung cancers continue to account for the majority of diagnoses, smoking rates have been decreasing for several decades. Lung cancer in individuals who have never smoked (LCINS) is estimated to be the fifth most common cause of cancer-related deaths worldwide in 2023, preferentially occurring in women and Asian populations. As smoking rates continue to decline, understanding the aetiology and features of this disease, which necessitate unique diagnostic and treatment paradigms, will be imperative. New data have provided important insights into the molecular and genomic characteristics of LCINS, which are distinct from those of smoking-associated lung cancers and directly affect treatment decisions and outcomes. Herein, we review the emerging data regarding the aetiology and features of LCINS, particularly the genetic and environmental underpinnings of this disease as well as their implications for treatment. In addition, we outline the unique diagnostic and therapeutic paradigms of LCINS and discuss future directions in identifying individuals at high risk of this disease for potential screening efforts.
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Affiliation(s)
- Jaclyn LoPiccolo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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Huang Y, Bao T, Zhang T, Ji G, Wang Y, Ling Z, Li W. Machine Learning Study of SNPs in Noncoding Regions to Predict Non-small Cell Lung Cancer Susceptibility. Clin Oncol (R Coll Radiol) 2023; 35:701-712. [PMID: 37689528 DOI: 10.1016/j.clon.2023.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/23/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common pathological subtype of lung cancer. Both environmental and genetic factors have been reported to impact the lung cancer susceptibility. We conducted a genome-wide association study (GWAS) of 287 NSCLC patients and 467 healthy controls in a Chinese population using the Illumina Genome-Wide Asian Screening Array Chip on 712,095 SNPs (single nucleotide polymorphisms). Using logistic regression modeling, GWAS identified 17 new noncoding region SNP loci associated with the NSCLC risk, and the top three (rs80040741, rs9568547, rs6010259) were under a stringent p-value (<3.02e-6). Notably, rs80040741 and rs6010259 were annotated from the intron regions of MUC3A and MLC1, respectively. Together with another five SNPs previously reported in Chinese NSCLC patients and another four covariates (e.g., smoking status, age, low dose CT screening, sex), a predictive model by machine learning methods can separate the NSCLC from healthy controls with an accuracy of 86%. This is the first time to apply machine learning method in predicting the NSCLC susceptibility using both genetic and clinical characteristics. Our findings will provide a promising method in NSCLC early diagnosis and improve our understanding of applying machine learning methods in precision medicine.
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Affiliation(s)
- Y Huang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - T Bao
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - T Zhang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - G Ji
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Y Wang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Z Ling
- Chengdu Genepre Technology Co., LTD, Chengdu, Sichuan, China
| | - W Li
- Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Healthy, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan 610041, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chengdu, Sichuan 610041, West China Hospital, China.
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Wu X, Huang G, Li W, Chen Y. Ethnicity-specific association between TERT rs2736100 (A > C) polymorphism and lung cancer risk: a comprehensive meta-analysis. Sci Rep 2023; 13:13271. [PMID: 37582820 PMCID: PMC10427644 DOI: 10.1038/s41598-023-40504-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/11/2023] [Indexed: 08/17/2023] Open
Abstract
The rs2736100 (A > C) polymorphism of the second intron of Telomerase reverse transcriptase (TERT) has been confirmed to be closely associated with the risk of Lung cancer (LC), but there is still no unified conclusion on the results of its association with LC. This study included Genome-wide association studies (GWAS) and case-control studies reported so far on this association between TERT rs2736100 polymorphism and LC to clarify such a correlation with LC and the differences in it between different ethnicities and different types of LC. Relevant literatures published before May 7, 2022 on 'TERT rs2736100 polymorphism and LC susceptibility' in PubMed, EMbase, CENTRAL, MEDLINE databases were searched through the Internet, and data were extracted. Statistical analysis of data was performed in Revman5.3 software, including drawing forest diagrams, drawing funnel diagrams and so on. Sensitivity and publication bias analysis were performed in Stata 12.0 software. The C allele of TERT rs2736100 was associated with the risk of LC (Overall population: [OR] = 1.21, 95%CI [1.17, 1.25]; Caucasians: [OR] = 1.11, 95%CI [1.06, 1.17]; Asians: [OR] = 1.26, 95%CI [1.21, 1.30]), and Asians had a higher risk of LC than Caucasians (C vs. A: Caucasians: [OR] = 1.11 /Asians: [OR]) = 1.26). The other gene models also showed similar results. The results of stratified analysis of LC patients showed that the C allele was associated with the risk of Non-small-cell lung carcinoma (NSCLC) and Lung adenocarcinoma (LUAD), and the risk of NSCLC and LUAD in Asians was higher than that in Caucasians. The C allele was associated with the risk of Lung squamous cell carcinoma (LUSC) and Small cell lung carcinoma(SCLC) in Asians but not in Caucasians. NSCLC patients ([OR] = 1.27) had a stronger correlation than SCLC patients ([OR] = 1.03), and LUAD patients ([OR] = 1.32) had a stronger correlation than LUSC patients ([OR] = 1.09).In addition, the C allele of TERT rs2736100 was associated with the risk of LC, NSCLC and LUAD in both smoking groups and non-smoking groups, and the risk of LC in non-smokers of different ethnic groups was higher than that in smokers. In the Asians, non-smoking women were more at risk of developing LUAD. The C allele of TERT rs2736100 is a risk factor for LC, NSCLC, and LUAD in different ethnic groups, and the Asian population is at a more common risk. The C allele is a risk factor for LUSC and SCLC in Asians but not in Caucasians. And smoking is not the most critical factor that causes variation in TERT rs2736100 to increase the risk of most LC (NSCLC, LUAD). Therefore, LC is a multi-etiological disease caused by a combination of genetic, environmental and lifestyle factors.
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Affiliation(s)
- Xiaozheng Wu
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Gao Huang
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Wen Li
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Yunzhi Chen
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China.
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Cheng C, Hong W, Li Y, Xiao X, McKay J, Han Y, Byun J, Peng B, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeböller H, Wichmann HE, Christiani DC, Rennert G, Arnold S, Goodman G, Field JK, Davies MPA, Shete SS, Le Marchand L, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zhu M, Shen H, Zienolddiny S, Grankvist K, Johansson M, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Brennan P, Li Y, Gorlova O, Gorlov I, Amos CI. Mosaic Chromosomal Alterations Are Associated With Increased Lung Cancer Risk: Insight From the INTEGRAL-ILCCO Cohort Analysis. J Thorac Oncol 2023; 18:1003-1016. [PMID: 37150255 PMCID: PMC10435278 DOI: 10.1016/j.jtho.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/21/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
INTRODUCTION Mosaic chromosomal alterations (mCAs) detected in white blood cells represent a type of clonal hematopoiesis (CH) that is understudied compared with CH-related somatic mutations. A few recent studies indicated their potential link with nonhematological cancers, especially lung cancer. METHODS In this study, we investigated the association between mCAs and lung cancer using the high-density genotyping data from the OncoArray study of INTEGRAL-ILCCO, the largest single genetic study of lung cancer with 18,221 lung cancer cases and 14,825 cancer-free controls. RESULTS We identified a comprehensive list of autosomal mCAs, ChrX mCAs, and mosaic ChrY (mChrY) losses from these samples. Autosomal mCAs were detected in 4.3% of subjects, in addition to ChrX mCAs in 3.6% of females and mChrY losses in 9.6% of males. Multivariable logistic regression analysis indicated that the presence of autosomal mCAs in white blood cells was associated with an increased lung cancer risk after adjusting for key confounding factors, including age, sex, smoking status, and race. This association was mainly driven by a specific type of mCAs: copy-neutral loss of heterozygosity on autosomal chromosomes. The association between autosome copy-neutral loss of heterozygosity and increased risk of lung cancer was further confirmed in two major histologic subtypes, lung adenocarcinoma and squamous cell carcinoma. In addition, we observed a significant increase of ChrX mCAs and mChrY losses in smokers compared with nonsmokers and racial differences in certain types of mCA events. CONCLUSIONS Our study established a link between mCAs in white blood cells and increased risk of lung cancer.
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Affiliation(s)
- Chao Cheng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Wei Hong
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Bo Peng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen Lam
- Department of Integrative Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Angela Risch
- Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany; University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, Kentucky
| | | | - John K Field
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P A Davies
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sanjay S Shete
- Department of Biostatistics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas; Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | - Rayjean J Hung
- Luenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Angeline S Andrew
- Department of Epidemiology, Dartmouth College, Hanover, New Hampshire; Department of Community and Family Medicine, Dartmouth College, Hanover, New Hampshire
| | | | - Meng Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Angela Cox
- Academic Unit of Clinical Oncology University of Sheffield, Weston Park Hospital, Whitham Road, Sheffield, United Kingdom
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C Aldrich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Yong Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.
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Zou K, Sun P, Huang H, Zhuo H, Qie R, Xie Y, Luo J, Li N, Li J, He J, Aschebrook-Kilfoy B, Zhang Y. Etiology of lung cancer: Evidence from epidemiologic studies. JOURNAL OF THE NATIONAL CANCER CENTER 2022; 2:216-225. [PMID: 39036545 PMCID: PMC11256564 DOI: 10.1016/j.jncc.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 12/05/2022] Open
Abstract
Lung cancer is one of the leading causes of cancer incidence and mortality worldwide. While smoking, radon, air pollution, as well as occupational exposure to asbestos, diesel fumes, arsenic, beryllium, cadmium, chromium, nickel, and silica are well-established risk factors, many lung cancer cases cannot be explained by these known risk factors. Over the last two decades the incidence of adenocarcinoma has risen, and it now surpasses squamous cell carcinoma as the most common histologic subtype. This increase warrants new efforts to identify additional risk factors for specific lung cancer subtypes as well as a comprehensive review of current evidence from epidemiologic studies to inform future studies. Given the myriad exposures individuals experience in real-world settings, it is essential to investigate mixture effects from complex exposures and gene-environment interactions in relation to lung cancer and its subtypes.
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Affiliation(s)
- Kaiyong Zou
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peiyuan Sun
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huang Huang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haoran Zhuo
- Yale School of Public Health, New Haven, United States of America
| | - Ranran Qie
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuting Xie
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiajun Luo
- Department of Public Health Sciences, the University of Chicago, Chicago, United States of America
| | - Ni Li
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Li
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Yawei Zhang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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8
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Singh S, Singh N, Baranwal M, Sharma S. Polymorphisms in the MSH2 gene predict poor survival of North Indian lung cancer patients undergoing chemotherapy. Biomark Med 2022; 16:69-82. [PMID: 35081740 DOI: 10.2217/bmm-2021-0565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To estimate if MSH2 polymorphisms, viz. rs63749993, rs2303425, rs2303426, rs4987188, rs2303428 and rs17217772, have any association with clinical outcomes in North Indian lung cancer patients. Materials & methods: PCR-RFLP was used for genotyping 500 cases. Logistic regression and survival analysis was performed by utilizing MedCalc software. Results & conclusion: Our study concluded, adenocarcinoma subjects having heterozygous genotype for rs2303425 have increased survival time (MST = 12.43, p = 0.03). In lung cancer patients undergoing paclitaxel therapy, heterozygous carriers for the rs17217772 polymorphism have reduced survival time (MST = 7.96 vs 2.63 months; HR = 2.09; p = 0.02). For rs63749993 polymorphism undergoing irinotecan therapy, subjects having mutant genotype showed poor survival (13.26 vs 6.06 months; HR = 5.37; p = 0.0004). The results suggest that MSH2 polymorphisms are involved in decreasing overall survival for patients undergoing platinum-based chemotherapy.
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Affiliation(s)
- Sidhartha Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, 160012, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
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9
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Nastase A, Lupo A, Laszlo V, Damotte D, Dima S, Canny E, Alifano M, Popescu I, Klepetko W, Grigoroiu M. Platinum Drug Sensitivity Polymorphisms in Stage III Non-small Cell Lung Cancer With Invasion of Mediastinal Lymph Nodes. Cancer Genomics Proteomics 2021; 17:587-595. [PMID: 32859637 DOI: 10.21873/cgp.20215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND/AIM Patients with stage IIIA (N2) non-small cell lung cancer (NSCLC) with no progression after induction chemotherapy are usually selected for surgery. Nowadays, response to chemotherapy is not predictable. We aimed to identify genomic predictive markers for response to induction chemotherapy in stage IIIA (N2) NSCLC patients. PATIENTS AND METHODS Whole-exome sequencing (WES) was performed on samples from 11 patients with no response after induction chemotherapy and 6 patients with documented pathological response, admitted to the Hotel Dieu Hospital, Paris or Allegemeines Krakenhaus University, Vienna. RESULTS A higher alternative allele frequency was found on SENP5, rs63736860, rs1602 and NCBP2, rs553783 in the non-responder group, and on RGP1, rs1570248, SLFN12L, rs2304968, rs9905892, and GBA2, rs3833700 in the responder group. CONCLUSION These polymorphisms contribute to inter-individual sensibility to chemotherapy response. Interrogation of these genetic variations may have potential applicability when deciding the treatment strategy for patients with stage III NSCLC (N2).
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Affiliation(s)
- Anca Nastase
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Audrey Lupo
- Department of Pathology, Hôpital Cochin, AP-HP, Université de Paris, Paris, France
| | - Victoria Laszlo
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Diane Damotte
- Department of Pathology, Hôpital Cochin, AP-HP, Université de Paris, Paris, France
| | - Simona Dima
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Emelyne Canny
- Department of Pathology, Hôpital Cochin, AP-HP, Université de Paris, Paris, France
| | - Marco Alifano
- Department of Pathology, Hôpital Cochin, AP-HP, Université de Paris, Paris, France
| | - Irinel Popescu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Walter Klepetko
- Department of Thoracic Surgery, Vienna General Hospital, Vienna, Austria
| | - Madalina Grigoroiu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
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10
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Lee AJ, Jung I. Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. Genomics Inform 2021; 19:e3. [PMID: 33840167 PMCID: PMC8042303 DOI: 10.5808/gi.20073] [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: 12/03/2020] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
Functional interpretation of noncoding genetic variants associated with complex human diseases and traits remains a challenge. In an effort to enhance our understanding of common germline variants associated with lung cancer, we categorize regulatory elements based on eight major cell types of human lung tissue. Our results show that 21.68% of lung cancer‒associated risk variants are linked to noncoding regulatory elements, nearly half of which are cell type‒specific. Integrative analysis of high-resolution long-range chromatin interactome maps and single-cell RNA-sequencing data of lung tumors uncovers number of putative target genes of these variants and functionally relevant cell types, which display a potential biological link to cancer susceptibility. The present study greatly expands the scope of functional annotation of lung cancer‒associated genetic risk factors and dictates probable cell types involved in lung carcinogenesis.
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Affiliation(s)
- Andrew J Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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11
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Wu N, Liu S, Li J, Hu Z, Yan S, Duan H, Wu D, Ma Y, Li S, Wang X, Wang Y, Li X, Lu X. Deep sequencing reveals the genomic characteristics of lung adenocarcinoma presenting as ground-glass nodules (GGNs). Transl Lung Cancer Res 2021; 10:1239-1255. [PMID: 33889506 PMCID: PMC8044491 DOI: 10.21037/tlcr-20-1086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background The concept of multi-step progression from atypical adenomatous hyperplasia (AAH) to invasive adenocarcinoma (ADC) has been proposed, and ground-glass nodules (GGNs) may play a critical role during the early lung tumorigenesis. We present the first comprehensive description of the genomic architecture of GGNs to unravel the genetic basis of GGN. Methods We investigated 30 GGN-like lungs ADC by performing >1,000× whole-exome sequencing (WES) and characterized the genomic variations and evaluate the relationship between the clinicopathologic and molecular characteristics in this disease. Results Despite the low somatic mutation burden, GGNs exhibited high intratumor heterogeneity (ITH) characterized by the proportion of subclonal mutations. Different mutagenesis shaped the genomes of GGN during cancer evolution and were mostly featured by molecular clock-like signatures that occur in clonal mutations and defective DNA mismatch signatures that occur in subclonal mutations. Moreover, 10.7–67.1% clonal mutations occurred after whole-genome doubling (WGD), indicating that WGD could be a frequent truncal event in GGNs. Samples with WGD showed higher genomic instability but lower ITH. These GGNs were characterized by recurrent focal copy-number changes that are highly associated with tumorigenesis, with only two genes (EGFR and RBM10) that were recurrently mutated. Additionally, GGNs with different pathological subtypes or computed tomography (CT) features exhibited distinct genetic characteristics. Lepidic predominant or pure GGNs in CT images carried a lower mutation burden and had a relatively stable genome than nonlepidic or mixed GGNs. GGNs with RBM10 mutations tended to accompany a pathologically lepidic pattern, indicating RBM10 may drive the distinct subtype of lung cancer with better prognosis. Conclusions These findings facilitated interpreting the genomic characteristics of GGNs, provided insight into the early stages of lung cancer evolution, and possessed potential clinical significance.
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Affiliation(s)
- Nan Wu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Sixue Liu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Li
- The Precision Medicine Centre of Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhenyu Hu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shi Yan
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hongwei Duan
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dafei Wu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Ma
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shaolei Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xing Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yaqi Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiang Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xuemei Lu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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12
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Potential Genes Associated with the Survival of Lung Adenocarcinoma Were Identified by Methylation. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:7103412. [PMID: 34007304 PMCID: PMC8108640 DOI: 10.1155/2020/7103412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022]
Abstract
Background Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer. The purpose of this study is to search for genes related to the prognosis of LUAD through methylation based on a linear mixed model (LMM). Methods Gene expression, methylation, and survival data of LUAD patients were downloaded from the TCGA database. Based on the LMM model, the GEMMA algorithm was used to screen the predictive genes related to LUAD survival. The Cox model was used to further screen the predicted genes, and then, protein-protein interaction (PPI) network was constructed. Through the software plugin Cytoscape MCODE 3.8.0, the most closely related genes in the PPI network module were selected for in-depth biological function analysis to further explore the interaction and correlation between genes. Results We screened out 97 predictive genes from 18,834 genes and eliminated one gene associated with lung squamous cell carcinoma from previous studies, leaving 96 genes. The MCODE and the Kaplan-Meier curve analysis were used to finally identify two genes ASB16 and NEDD4 that are related to the prognosis of LUAD. Conclusions The newly identified two genes associated with the prognosis of LUAD may provide a basis for the treatment of patients.
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13
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Wang C, Yang D, Zhang X, Zhang X, Yang L, Wang P, Zhou W, Li H, Li Y, Nie H, Li Y. Association of PTEN Gene SNPs rs2299939 With PFS in Patients With Small Cell Lung Cancer Treated With Early Radiotherapy. Front Genet 2020; 11:298. [PMID: 32391045 PMCID: PMC7190978 DOI: 10.3389/fgene.2020.00298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
Lung cancer has higher morbidity and mortality than most cancers. It is common that there are some phenomenons of secondary drug resistance, radiotherapy resistance and poor prognosis during the treatment of small cell lung cancer (SCLC). Recent studies revealed that the single-nucleotide polymorphisms (SNPs) are associated with the curative effect among patients with the same pathological type and stage. Our study analyzed the start time of radiotherapy and the relationship between PTEN gene rs2299939 polymorphisms and survival time among 116 SCLC patients. The results showed that early radiotherapy significantly improved the time of survival in patients compared with late radiotherapy (P = 0.029). Simultaneously, the study found that patients with the rs2299939 AA genotype showed significant sensitivity to both early and late radiotherapy, but early radiotherapy is better. The median survival time of CC genotype patients was 12 months in the early radiotherapy group while it was 9 months in the late radiotherapy group, thus recommending early radiotherapy among these patients. In addition, it was found that rs2299939 could regulate the expression of related genes in peripheral blood and lung tissues by eQTL analysis. This study revealed that the early radiotherapy could prolong the PFS of SCLC and shall be performed in SCLC treatment.
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Affiliation(s)
- Chunbo Wang
- Department of Radiotherapy, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Depeng Yang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Xiaoqing Zhang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Xiaohan Zhang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Lijun Yang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Pingping Wang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyang Zhou
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Huaxin Li
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Yiqun Li
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Huan Nie
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Yu Li
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
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14
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Long C, Lv G, Fu X. Development of a general logistic model for disease risk prediction using multiple SNPs. FEBS Open Bio 2019; 9:2006-2012. [PMID: 31423732 PMCID: PMC6823278 DOI: 10.1002/2211-5463.12722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/08/2019] [Accepted: 08/16/2019] [Indexed: 02/05/2023] Open
Abstract
Human diseases are usually linked to multiloci genetic alterations, including single‐nucleotide polymorphisms (SNPs). Methods to use these SNPs for disease risk prediction (DRP) are of clinical interest. DRP algorithms explored by commercial companies to date have tended to be complex and led to controversial prediction results. Here, we present a general approach for establishing a logistic model‐based DRP algorithm, in which multiple SNP risk factors from different publications are directly used. In particular, the coefficient β of each SNP is set as the natural logarithm of the reported odds ratio, and the constant coefficient β0 is comprehensively determined by the coefficient and frequency of each SNP and the average disease risk in populations. Furthermore, homozygous SNP is considered a dummy variable, and the SNPs are updated (addition, deletion and modification) if necessary. Importantly, we validated this algorithm as a proof of concept: two patients with lung cancer were identified as the maximum risk cases from 57 Chinese individuals. Our logistic model‐based DRP algorithm is apparently more intuitive and self‐evident than the algorithms explored by commercial companies, and it may facilitate DRP commercialization in the era of personalized medicine.
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Affiliation(s)
- Cheng Long
- West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Guanting Lv
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
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15
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Liang Y, Jiang L, Zhong X, Hochwald SN, Wang Y, Huang L, Nie Q, Huang H, Xu JF. Discovery of Aberrant Alteration of Genome in Colorectal Cancer by Exome Sequencing. Am J Med Sci 2019; 358:340-349. [PMID: 31445671 DOI: 10.1016/j.amjms.2019.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND This study analyzed multiple parameters including somatic single nucleotide variations (SNVs), Insertion/Deletions, significantly mutated genes (SMGs), copy number variations and frequently altered pathways aims to discover novel aberrances in the tumorigenesis of colorectal cancer (CRC). MATERIALS AND METHODS Exome sequencing was performed on an Illumina platform to identify novel potential somatic variances in 34 paired tumor and adjacent normal tissues from 17 CRC patients. Results were compared with databases (dbSNP138, 1000 genomes SNP, Hapmap, Catalogue of Somatic Mutation of Cancer and ESP6500) and analyzed. MuSic software was used to identify SMGs. RESULTS In total, 1,637 somatic SNVs in 17 analyzed tumors were identified. Only 7 SNVs were shared by more than 1 tumor, suggesting that over 99% of the analyzed SNVs were independent events. Mutation of KRAS p. G12D and ZNF717 p. L39V were the most common SNVs. Moreover, 10 SMGs namely KRAS, TP53, SMAD4, ZNF717, FBXW7, APC, ZNF493, CDR1, the Armadillo repeat containing 4 (ARMC4) and sulfate-modifying factor 2 (SUMF2) were found. Among those, ZNF717, ZNF493, CDR1, ARMC4 and SUMF2 were novel frequent genes in CRC. For copy number variations analysis, gains in 10q25.3, 1p31.1, 1q44, 10q23.33, 11p15.4 and 20q13.33, and loss of 3q21.3 and 3q29 were frequent aberrations identified in our results. CONCLUSIONS We frequently found novel genes ZNF717, ZNF493, CDR1, ARMC4 and SUMF2 and gains in 10q25.3, which may be functional mutation in CRC. The high-frequency private events such as SNVs confirm the highly heterogeneous mutations found in CRCs. The mutated genes sites in different patients may vary significantly, which may also be more challenging for clinical treatment.
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Affiliation(s)
- Yuanzi Liang
- Department of Clinical Immunology, Institute of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, China
| | | | - Xiaogang Zhong
- Department of Gastrointestinal Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Steven N Hochwald
- Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, New York
| | - Yongsi Wang
- Division of Genome Sequencing, Huayin Medical Laboratory, Guangzhou, Guangdong, China
| | - Lihe Huang
- Department of Laboratory Medicine, Debao County Hospital, Baise, Guangxi, China
| | - Qiumiao Nie
- Wilking Biotechnology Co., Ltd, Nanning, Guangxi, China
| | - Huayi Huang
- Department of Laboratory Medicine and; Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, New York.
| | - Jun-Fa Xu
- Department of Clinical Immunology, Institute of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, China.
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16
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Wen Y, Zhu C, Li N, Li Z, Cheng Y, Dong J, Zhu M, Wang Y, Dai J, Ma H, Jin G, Dai M, Hu Z, Shen H. Fine Mapping in Chromosome 3q28 Identified Two Variants Associated with Lung Cancer Risk in Asian Population. J Cancer 2019; 10:1862-1869. [PMID: 31205543 PMCID: PMC6547980 DOI: 10.7150/jca.28379] [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: 07/08/2018] [Accepted: 01/20/2019] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies (GWASs) have consistently identified chromosome 3q28 as a lung cancer susceptibility region. To further characterize the potential genetic mechanism of the variants in this region, we conducted a fine-mapping study on chromosome 3q28 region. We performed a target resequencing in 200 lung cancer cases and 300 controls in the screening and followed by validation in multi-ethnic lung cancer GWASs with 12,843 cases and 12,639 controls. For our identified novel variants, we conducted expression quantitative trait loci (eQTL) analysis to reveal the potential target genes. Two susceptibility variants were identified (rs4396880: G>A, OR = 0.35, 95%CI: 0.20-0.62, P = 3.01×10-4; and rs3856776: C>T, OR = 2.05, 95%CI: 1.32-3.18, P = 1.49×10-3) and further supported in Asian population (rs4396880: OR = 0.88, P = 7.43×10-6; and rs3856776: OR =1.17, P = 1.64×10-4). The eQTL analysis showed the A allele of rs4396880 was significantly associated with higher mRNA expression of TP63 (P = 1.70×10-4) in lung tissues, while rs3856776 showed significant association with the expression of LEPREL1-AS1 (P = 6.90×10-3), which was the antisense RNA of LEPREL1 and could suppress the translation of LEPREL1. Notably, LEPREL1 was aberrantly downregulated (P = 2.54×10-18) in lung tumor tissues based on TCGA database. In conclusion, this is the first fine-mapping analysis of 3q28 region in Han Chinese, and we found two variants associated with lung cancer susceptibility in Asian population. What's more, rs3856776 was newly identified and might modulate lung cancer susceptibility by suppressing the function of LEPREL1.
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Affiliation(s)
- Yang Wen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chen Zhu
- Zhejiang Provincial Office for Cancer Prevention and Control, Zhejiang Cancer Center/Zhejiang Cancer Hospital, Hangzhou 310004, China
| | - Ni Li
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhihua Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Cheng
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Dong
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuzhuo Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Min Dai
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
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17
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Genome-wide haplotype association study identifies risk genes for non-small cell lung cancer. J Theor Biol 2018; 456:84-90. [PMID: 30096405 DOI: 10.1016/j.jtbi.2018.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Most lung cancer is non-small cell lung cancer (NSCLC), in which malignant cells form in the lung epithelium. Mutations in multiple genes and environmental factors both contribute to NSCLC, and although some NSCLC susceptibility genes have been characterized, the pathogenesis of this disease remains unclear. To identify genes conferring NSCLC risk and determine their associated pathological mechanism, we combined genome-wide haplotype associated analysis with gene prioritization using 224,677 SNPs in 37 NSCLC cell lines and 116 unrelated European individuals. Five candidate genes were identified: ESR1, TGFBR1, INSR, CDH3, and MAP3K5. All of these have previously been implicated in NSCLC, with the exception of CDH3, which can therefore be considered a novel indicator of NSCLC risk. Functional annotation confirmed the relationship between these five genes and NSCLC. Our findings are indicative of the underlying pathological mechanisms of NSCLC and provide information to support future directions in diagnosing and treating NSCLC.
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18
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The TERT rs2736100 polymorphism increases cancer risk: A meta-analysis. Oncotarget 2018; 8:38693-38705. [PMID: 28418878 PMCID: PMC5503564 DOI: 10.18632/oncotarget.16309] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/15/2017] [Indexed: 02/07/2023] Open
Abstract
Abnormal telomerase activity is implicated in cancer initiation and development. The rs2736100 T > G polymorphism in the telomerase reverse transcriptase (TERT) gene, which encodes the telomerase catalytic subunit, has been associated with increased cancer risk. We conducted a meta-analysis to more precisely assess this association. After a comprehensive literature search of the PubMed and EMBASE databases up to November 1, 2016, 61 articles with 72 studies comprising 108,248 cases and 161,472 controls were included in our meta-analysis. Studies were conducted on various cancer types. The TERT rs2736100 polymorphism was associated with increased overall cancer risk in five genetic models [homozygous model (GG vs. TT): odds ratio (OR) = 1.39, 95% confidence interval (95% CI) = 1.26-1.54, P < 0.001; heterozygous model (TG vs. TT): OR = 1.16, 95% CI = 1.11-1.23, P < 0.001; dominant model (TG + GG vs. TT): OR = 1.23, 95% CI = 1.15-1.31, P < 0.001; recessive model (GG vs. TG + TT): OR = 1.25, 95% CI = 1.16-1.35, P < 0.001; and allele contrast model (G vs. T): OR = 1.17, 95% CI = 1.12-1.23, P < 0.001]. A stratified analysis based on cancer type associated the polymorphism with elevated risk of thyroid cancer, bladder cancer, lung cancer, glioma, myeloproliferative neoplasms, and acute myeloid leukemia. Our results confirm that the TERT rs2736100 polymorphism confers increased overall cancer risk.
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Sun H, Wang Y, Chen Y, Li Y, Wang S. pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data. Bioinformatics 2018; 33:1765-1772. [PMID: 28165116 DOI: 10.1093/bioinformatics/btx064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/31/2017] [Indexed: 12/31/2022] Open
Abstract
Motivation DNA methylation plays an important role in many biological processes and cancer progression. Recent studies have found that there are also differences in methylation variations in different groups other than differences in methylation means. Several methods have been developed that consider both mean and variance signals in order to improve statistical power of detecting differentially methylated loci. Moreover, as methylation levels of neighboring CpG sites are known to be strongly correlated, methods that incorporate correlations have also been developed. We previously developed a network-based penalized logistic regression for correlated methylation data, but only focusing on mean signals. We have also developed a generalized exponential tilt model that captures both mean and variance signals but only examining one CpG site at a time. Results In this article, we proposed a penalized Exponential Tilt Model (pETM) using network-based regularization that captures both mean and variance signals in DNA methylation data and takes into account the correlations among nearby CpG sites. By combining the strength of the two models we previously developed, we demonstrated the superior power and better performance of the pETM method through simulations and the applications to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project. The developed pETM method identifies many cancer-related methylation loci that were missed by our previously developed method that considers correlations among nearby methylation loci but not variance signals. Availability and Implementation The R package 'pETM' is publicly available through CRAN: http://cran.r-project.org . Contact sw2206@columbia.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hokeun Sun
- Department of Statistics, Pusan National University, Busan, Korea
| | - Ya Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Yong Chen
- Division of Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
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20
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Bossé Y, Amos CI. A Decade of GWAS Results in Lung Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:363-379. [PMID: 28615365 PMCID: PMC6464125 DOI: 10.1158/1055-9965.epi-16-0794] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Genome-wide association studies (GWAS) were successful to identify genetic factors robustly associated with lung cancer. This review aims to synthesize the literature in this field and accelerate the translation of GWAS discoveries into results that are closer to clinical applications. A chronologic presentation of published GWAS on lung cancer susceptibility, survival, and response to treatment is presented. The most important results are tabulated to provide a concise overview in one read. GWAS have reported 45 lung cancer susceptibility loci with varying strength of evidence and highlighted suspected causal genes at each locus. Some genetic risk loci have been refined to more homogeneous subgroups of lung cancer patients in terms of histologic subtypes, smoking status, gender, and ethnicity. Overall, these discoveries are an important step for future development of new therapeutic targets and biomarkers to personalize and improve the quality of care for patients. GWAS results are on the edge of offering new tools for targeted screening in high-risk individuals, but more research is needed if GWAS are to pay off the investment. Complementary genomic datasets and functional studies are needed to refine the underlying molecular mechanisms of lung cancer preliminarily revealed by GWAS and reach results that are medically actionable. Cancer Epidemiol Biomarkers Prev; 27(4); 363-79. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec, Canada.
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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21
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Snetselaar R, van Oosterhout MFM, Grutters JC, van Moorsel CHM. Telomerase Reverse Transcriptase Polymorphism rs2736100: A Balancing Act between Cancer and Non-Cancer Disease, a Meta-Analysis. Front Med (Lausanne) 2018. [PMID: 29536006 PMCID: PMC5835035 DOI: 10.3389/fmed.2018.00041] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The enzyme telomerase reverse transcriptase (TERT) is essential for telomere maintenance. In replicating cells, maintenance of telomere length is important for the preservation of vital genetic information and prevention of genomic instability. A common genetic variant in TERT, rs2736100 C/A, is associated with both telomere length and multiple diseases. Carriage of the C allele is associated with longer telomere length, while carriage of the A allele is associated with shorter telomere length. Furthermore, some diseases have a positive association with the C and some with the A allele. In this study, meta-analyses were performed for two groups of diseases, cancerous diseases, e.g., lung cancer and non-cancerous diseases, e.g., pulmonary fibrosis, using data from genome-wide association studies and case-control studies. In the meta-analysis it was found that cancer positively associated with the C allele (pooled OR 1.16 [95% CI 1.09–1.23]) and non-cancerous diseases negatively associated with the C allele (pooled OR 0.81 [95% CI 0.65–0.99]). This observation illustrates that the ambiguous role of telomere maintenance in disease hinges, at least in part, on a single locus in telomerase genes. The dual role of this single nucleotide polymorphism also emphasizes that therapeutic agents aimed at influencing telomere maintenance should be used with caution.
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Affiliation(s)
- Reinier Snetselaar
- Interstitial Lung Diseases Center of Excellence, Department of Pulmonology, St Antonius Hospital, Nieuwegein, Netherlands
| | - Matthijs F M van Oosterhout
- Interstitial Lung Diseases Center of Excellence, Department of Pathology, St Antonius Hospital, Nieuwegein, Netherlands
| | - Jan C Grutters
- Interstitial Lung Diseases Center of Excellence, Department of Pulmonology, St Antonius Hospital, Nieuwegein, Netherlands.,Division of Heart and Lung, University Medical Center Utrecht, Utrecht, Netherlands
| | - Coline H M van Moorsel
- Interstitial Lung Diseases Center of Excellence, Department of Pulmonology, St Antonius Hospital, Nieuwegein, Netherlands.,Division of Heart and Lung, University Medical Center Utrecht, Utrecht, Netherlands
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22
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O'Brien TD, Jia P, Caporaso NE, Landi MT, Zhao Z. Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels. Genome Med 2018; 10:16. [PMID: 29486777 PMCID: PMC5828003 DOI: 10.1186/s13073-018-0522-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/13/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). These subtypes are mainly classified by physiological and pathological characteristics, although there is increasing evidence of genetic and molecular differences as well. Although some work has been done at the somatic level to explore the genetic and biological differences among subtypes, little work has been done that interrogates these differences at the germline level to characterize the unique and shared susceptibility genes for each subtype. METHODS We used single-nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) of European samples to interrogate the similarity of the subtypes at the SNP, gene, pathway, and regulatory levels. We expanded these genotyped SNPs to include all SNPs in linkage disequilibrium (LD) using data from the 1000 Genomes Project. We mapped these SNPs to several lung tissue expression quantitative trait loci (eQTL) and enhancer datasets to identify regulatory SNPs and their target genes. We used these genes to perform a biological pathway analysis for each subtype. RESULTS We identified 8295, 8734, and 8361 SNPs with moderate association signals for LUAD, LUSC, and SCLC, respectively. Those SNPs had p < 1 × 10- 3 in the original GWAS or were within LD (r2 > 0.8, Europeans) to the genotyped SNPs. We identified 215, 320, and 172 disease-associated genes for LUAD, LUSC, and SCLC, respectively. Only five genes (CHRNA5, IDH3A, PSMA4, RP11-650 L12.2, and TBC1D2B) overlapped all subtypes. Furthermore, we observed only two pathways from the Kyoto Encyclopedia of Genes and Genomes shared by all subtypes. At the regulatory level, only three eQTL target genes and two enhancer target genes overlapped between all subtypes. CONCLUSIONS Our results suggest that the three lung cancer subtypes do not share much genetic signal at the SNP, gene, pathway, or regulatory level, which differs from the common subtype classification based upon histology. However, three (CHRNA5, IDH3A, and PSMA4) of the five genes shared between the subtypes are well-known lung cancer genes that may act as general lung cancer genes regardless of subtype.
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Affiliation(s)
- Timothy D O'Brien
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Zhongming Zhao
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA. .,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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23
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Tang J, Hu C, Mei H, Peng L, Li H. CLPTM1L gene rs402710 (C > T) and rs401681 (C > T) polymorphisms associate with decreased cancer risk: a meta-analysis. Oncotarget 2017; 8:102446-102457. [PMID: 29254260 PMCID: PMC5731970 DOI: 10.18632/oncotarget.22268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/20/2017] [Indexed: 12/15/2022] Open
Abstract
Cleft lip and palate transmembrane 1-like (CLPTM1L) gene rs402710 (C > T) and rs401681 (C > T) polymorphisms have been widely studied for their potential relation to cancer risk, but studies have produced conflicting results. To systematically evaluate the association between these two polymorphisms and overall cancer risk, we conducted a comprehensive meta-analysis on all relevant articles found in the PubMed and EMBASE databases published prior to May 1, 2017. There were 26 articles with 28 studies, including 30,770 cases and 34,089 controls, for the rs402710 polymorphism and 38 articles with 48 studies, including 67,849 cases and 328,226 controls, for the rs401681 polymorphism. The pooled results indicated that both rs402710 and rs401681 polymorphisms are significantly associated with decreased overall cancer risk. In our stratification analysis, a significant association of the rs402710 polymorphism with lung and bladder cancers was identified among Asian and Caucasian populations in both hospital-based and population-based studies. The rs401681 polymorphism was significantly associated with a decreased risk of lung cancer, bladder cancer, and basal cell carcinoma in Asians and in hospital-based studies. CLPTM1L gene rs402710 and rs401681 polymorphisms thus have a protective association with various types of cancer, especially lung cancer among Asians.
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Affiliation(s)
- Jianzhou Tang
- Department of Biological and Environmental Engineering, Changsha University, Changsha 410003, Hunan, China
| | - Changming Hu
- Department of Molecular Pathology, Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou 510000, Guangdong, China
| | - Hua Mei
- Department of Somatic Stem Cell, Hunan Guangxiu Hospital, Changsha 410002, Hunan, China
| | - Liang Peng
- Department of Biological and Environmental Engineering, Changsha University, Changsha 410003, Hunan, China
| | - Hui Li
- Department of Microbiology and Immunology, Medical School of Jishou University, Jishou 416000, Hunan, China
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24
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Identification of additional loci associated with antibody response to Mycobacterium avium ssp. Paratuberculosis in cattle by GSEA-SNP analysis. Mamm Genome 2017; 28:520-527. [PMID: 28864882 DOI: 10.1007/s00335-017-9714-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 08/27/2017] [Indexed: 10/18/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis: (MAP) causes a contagious chronic infection results in Johne's disease in a wide range of animal species, including cattle. Several genome-wide association studies (GWAS) have been carried out to identify loci putatively associated with MAP susceptibility by testing each marker separately and identifying SNPs that show a significant association with the phenotype, while SNP with modest effects are usually ignored. The objective of this study was to identify modest-effect genes associated with MAP susceptibility using a pathway-based approach. The Illumina BovineSNP50 BeadChip was used to genotype 966 Holstein cows, 483 positive and 483 negative for antibody response to MAP, data were then analyzed using novel SNP-based Gene Set Enrichment Analysis (GSEA-SNP) and validated with Adaptive Rank Truncated Product methodology. An allele-based test was carried out to estimate the statistical association for each marker with the phenotype, subsequently SNPs were mapped to the closest genes, considering for each gene the single variant with the highest value within a window of 50 kb, then pathway-statistics were tested using the GSEA-SNP method. The GO biological process "embryogenesis and morphogenesis" was most highly associated with antibody response to MAP. Within this pathway, five genes code for proteins which play a role in the immune defense relevant to response to bacterial infection. The immune response genes identified would not have been considered using a standard GWAS, thus demonstrating that the pathway approach can extend the interpretation of genome-wide association analyses and identify additional candidate genes for target traits.
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25
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Liu C, Cui H, Gu D, Zhang M, Fang Y, Chen S, Tang M, Zhang B, Chen H. Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies. Lung Cancer 2017; 113:18-29. [PMID: 29110844 DOI: 10.1016/j.lungcan.2017.08.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023]
Abstract
A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.
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Affiliation(s)
- Caiyang Liu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China
| | - Huijie Cui
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Dongqing Gu
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Min Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yanfei Fang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Siyu Chen
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Mingshuang Tang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China.
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26
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Wang J, Liu Q, Yuan S, Xie W, Liu Y, Xiang Y, Wu N, Wu L, Ma X, Cai T, Zhang Y, Sun Z, Li Y. Genetic predisposition to lung cancer: comprehensive literature integration, meta-analysis, and multiple evidence assessment of candidate-gene association studies. Sci Rep 2017; 7:8371. [PMID: 28827732 PMCID: PMC5567126 DOI: 10.1038/s41598-017-07737-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 07/04/2017] [Indexed: 01/03/2023] Open
Abstract
More than 1000 candidate-gene association studies on genetic susceptibility to lung cancer have been published over the last two decades but with few consensuses for the likely culprits. We conducted a comprehensive review, meta-analysis and evidence strength evaluation of published candidate-gene association studies in lung cancer up to November 1, 2015. The epidemiological credibility of cumulative evidence was assessed using the Venice criteria. A total of 1018 publications with 2910 genetic variants in 754 different genes or chromosomal loci were eligible for inclusion. Main meta-analyses were performed on 246 variants in 138 different genes. Twenty-two variants from 21 genes (APEX1 rs1130409 and rs1760944, ATM rs664677, AXIN2 rs2240308, CHRNA3 rs6495309, CHRNA5 rs16969968, CLPTM1L rs402710, CXCR2 rs1126579, CYP1A1 rs4646903, CYP2E1 rs6413432, ERCC1 rs11615, ERCC2 rs13181, FGFR4 rs351855, HYKK rs931794, MIR146A rs2910164, MIR196A2 rs11614913, OGG1 rs1052133, PON1 rs662, REV3L rs462779, SOD2 rs4880, TERT rs2736098, and TP53 rs1042522) showed significant associations with lung cancer susceptibility with strong cumulative epidemiological evidence. No significant associations with lung cancer risk were found for other 150 variants in 98 genes; however, seven variants demonstrated strong cumulative evidence. Our findings provided the most updated summary of genetic risk effects on lung cancer and would help inform future research direction.
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Affiliation(s)
- Junjun Wang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Qingyun Liu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Shuai Yuan
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Weijia Xie
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Yuan Liu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Ying Xiang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Na Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Long Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Xiangyu Ma
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Tongjian Cai
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Yao Zhang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Zhifu Sun
- Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China. .,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China.
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Park SL, Cheng I, Haiman CA. Genome-Wide Association Studies of Cancer in Diverse Populations. Cancer Epidemiol Biomarkers Prev 2017. [PMID: 28637795 DOI: 10.1158/1055-9965.epi-17-0169] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) of cancer have identified more than 700 risk loci, of which approximately 80% were first discovered in European ancestry populations, approximately 15% in East Asians, 3% in multiethnic scans, and less than 1% in African and Latin American populations. These percentages closely mirror the distribution of samples included in the discovery phase of cancer GWAS to date (84% European, 11% East Asian, 4% African, and 1% Latin American ancestry). GWAS in non-European ancestry populations have provided insight into ancestry-specific variation in cancer and have pointed to regions of susceptibility that are of particular importance in certain populations. Uncovering and characterizing cancer risk loci in diverse populations is critical for understanding underlying biological mechanisms and developing future genetic risk prediction models in non-European ancestry populations. New GWAS and continued collaborations will be required to eliminate population inequalities in the number of studies, sample sizes, and variant content on GWAS arrays, and to better align genetic research in cancer to the global distribution of race/ethnicity Cancer Epidemiol Biomarkers Prev; 27(4); 405-17. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Sungshim L Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California.,Stanford Cancer Institute, Palo Alto, California
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
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Zhang Y, Wang DC, Shi L, Zhu B, Min Z, Jin J. Genome analyses identify the genetic modification of lung cancer subtypes. Semin Cancer Biol 2017; 42:20-30. [DOI: 10.1016/j.semcancer.2016.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/08/2016] [Indexed: 12/15/2022]
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29
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Wang C, Nie H, Li Y, Liu G, Wang X, Xing S, Zhang L, Chen X, Chen Y, Li Y. The study of the relation of DNA repair pathway genes SNPs and the sensitivity to radiotherapy and chemotherapy of NSCLC. Sci Rep 2016; 6:26526. [PMID: 27246533 PMCID: PMC4887885 DOI: 10.1038/srep26526] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/04/2016] [Indexed: 12/18/2022] Open
Abstract
To analyze the relation between SNPs in DNA repair pathway-related genes and sensitivity of tumor radio-chemotherapy, 26 SNPs in 20 DNA repair genes were genotyped on 176 patients of NSCLC undertaking radio-chemotherapy treatment. In squamous cell carcinoma (SCC), as the rs2228000, rs2228001 (XPC), rs2273953 (TP73), rs2279744 (MDM2), rs2299939 (PTEN) and rs8178085, rs12334811 (DNA-PKcs) affected the sensitivity to chemotherapy, so did the rs8178085, rs12334811 to radiotherapy. Moreover rs344781, rs2273953 and rs12334811 were related with the survival time of SCC. In general, the “good” genotype GG (rs12334811) showed greater efficacy of radio-chemotherapy and MSF (24 months) on SCC. In adenocarcinoma, as the rs2699887 (PIK3), rs12334811 (DNA-PKcs) influenced the sensitivity to chemotherapy, so did the rs2299939, rs2735343 (PTEN) to radiotherapy. And rs402710, rs80270, rs2279744 and rs2909430 impacted the survival time of the adenocarcinoma patients. Both GG (rs2279744) and AG (rs2909430) showed a shorter survival time (MFS = 6). Additionally, some SNPs such as rs2228000, rs2228001 and rs344781 were found to regulate the expression of DNA repair pathway genes through eQTLs dataset analysis. These results indicate that SNPs in DNA repair pathway genes might regulate the expression and affect the DNA damage repair, and thereby impact the efficacy of radio-chemotherapy and the survival time of NSCLC.
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Affiliation(s)
- Chunbo Wang
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China.,Department of Radiotherapy, Affiliated Tumour Hospital of Harbin Medical University
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Yiqun Li
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Guiyou Liu
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China.,Genome Analysis Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Xu Wang
- Department of Radiotherapy, Beijing Miyun County Hospital
| | - Shijie Xing
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Liping Zhang
- Department of Radiotherapy, Affiliated Tumour Hospital of Harbin Medical University
| | - Xin Chen
- Department of Radiotherapy, Affiliated Tumour Hospital of Harbin Medical University
| | - Yue Chen
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
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Wei R, DeVilbiss FT, Liu W. Genetic Polymorphism, Telomere Biology and Non-Small Lung Cancer Risk. J Genet Genomics 2015; 42:549-561. [PMID: 26554909 DOI: 10.1016/j.jgg.2015.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/03/2015] [Accepted: 08/10/2015] [Indexed: 02/06/2023]
Abstract
Recent genome-wide association studies (GWAS) have identified a number of chromosomal regions associated with the risk of lung cancer. Of these regions, single-nucleotide polymorphisms (SNPs), especially rs2736100 located in the telomerase reverse transcriptase (TERT) gene show unique and significant association with non-small cell lung cancer (NSCLC) in a few subpopulations including women, nonsmokers, East Asians and those with adenocarcinoma. Recent studies have also linked rs2736100 with a longer telomere length and lung cancer risk. In this review, we seek to summarize the relationship between these factors and to further link the underlying telomere biology to lung cancer etiology. We conclude that genetic alleles combined with environmental (e.g., less-smoking) and physiological factors (gender and age) that confer longer telomere length are strong risk factors for NSCLC. This linkage may be particularly relevant in lung adenocarcinoma driven by epidermal growth factor receptor (EGFR) mutations, as these mutations have also been strongly linked to female gender, less-smoking history, adenocarcinoma histology and East Asian ethnicity. By establishing this connection, a strong argument is made for further investigating of the involvement of these entities during the tumorigenesis of NSCLC.
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Affiliation(s)
- Rongrong Wei
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Frank T DeVilbiss
- School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Wanqing Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA.
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Robust Association Tests for the Replication of Genome-Wide Association Studies. BIOMED RESEARCH INTERNATIONAL 2015; 2015:461593. [PMID: 26345547 PMCID: PMC4539975 DOI: 10.1155/2015/461593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/14/2015] [Accepted: 02/14/2015] [Indexed: 11/18/2022]
Abstract
In genome-wide association study (GWAS), robust genetic association tests such as maximum of three CATTs (MAX3), each corresponding to recessive, additive, and dominant genetic models, the minimum p value of Pearson's Chi-square test with 2 degrees of freedom, and CATT based on additive genetic model (MIN2), genetic model selection (GMS), and genetic model exclusion (GME) methods have been shown to provide better power performance under wide range of underlying genetic models. In this paper, we demonstrate how these robust tests can be applied to the replication study of GWAS and how the overall statistical significance can be evaluated using the combined test formed by p values of the discovery and replication studies.
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32
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Fong KM, Daniels M, Goh F, Yang IA, Bowman RV. The current and future roles of genomics. Lung Cancer 2015. [DOI: 10.1183/2312508x.10009614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zhao MM, Zhang Y, Shen L, Ren YW, Li XL, Yin ZH, Zhou BS. Genetic variations in TERT-CLPTM1L genes and risk of lung cancer in a Chinese population. Asian Pac J Cancer Prev 2015; 15:2809-13. [PMID: 24761905 DOI: 10.7314/apjcp.2014.15.6.2809] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study was conducted to investigate the association between single nucleotide polymorphisms (SNPs) in telomerase reverse transcriptase (TERT) and cleft lip and palate transmembrane1-like (CLPTM1L) and lung cancer risk in a Chinese population. METHODS We performed a hospital-based case-control study, including 980 lung cancer cases and 1000 cancer-free controls matched for age and sex. Each case and control was interviewed to collect information by well-trained interviewers. A total of 5 ml of venous blood was collected for genotype testing of TERT rs2736098 and CLPTM1L rs401681 using TaqMan methodology. RESULTS The results revealed that the variant homozygote TERT rs2736098TT was associated with an increased risk of lung cancer (OR=2.017, 95%CI=1.518-2.681), especially lung adenocarcinoma (OR=2.117, 95%CI=1.557-3.043) and small cell carcinoma (OR=1.979, 95%CI: 1.174-3.334), compared with the TERT rs2736098CC genotype. Similar results were observed in non-smokers. CONCLUSION The TERT rs2736098 polymorphism might affect the susceptibility to lung cancer in Chinese populations. The associations need to be verified in larger and different populations.
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Affiliation(s)
- Meng-Meng Zhao
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China E-mail :
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Xun X, Wang H, Yang H, Wang H, Wang B, Kang L, Jin T, Chen C. CLPTM1L genetic polymorphisms and interaction with smoking and alcohol drinking in lung cancer risk: a case-control study in the Han population from northwest China. Medicine (Baltimore) 2014; 93:e289. [PMID: 25526467 PMCID: PMC4603120 DOI: 10.1097/md.0000000000000289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 11/30/2022] Open
Abstract
Genetic variants of cleft lip and palate trans-membrane 1-like (CLPTM1L) genes in the p15.33 region of chromosome 5 were previously identified to influence susceptibility to lung cancer. We examined the association of single nucleotide polymorphisms (SNPs) in CLPTM1L genes with lung cancer and explored their potential effects on the relationship between environmental risk factors (smoking, drinking) and lung cancer in a Chinese Han population. We genotyped 9 single nucleotide polymorphisms (SNPs) of CLPTM1L in a case-control study with 228 lung cancer cases and 301 controls from northwest China. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by unconditional logistic regression. We identified that the minor alleles of rs451360, rs402710, and rs31484 in CLPTM1L were associated with a 0.52-fold, 0.76-fold, and 0.70-fold decreased risk of lung cancer in allelic model analysis, respectively. In the genetic model analysis, we found rs402710 and rs401681 were associated with decreased lung cancer risk. Further stratification analysis showed that rs380286 displayed a significantly decreased lung cancer risk (OR=0.65, P=0.041) in the non-drinkers. In addition, Haplotype "GTTATCTGT" was found to be associated with decreased lung cancer risk (OR=0.50, P=0.033). Our results verified that genetic variants of CLPTM1L contribute to lung cancer susceptibility in the northwest Chinese Han population. Additionally, we found that consumption of alcohol may interact with CLPTM1L polymorphisms to contribute to overall lung cancer susceptibility.
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Affiliation(s)
- Xiaojie Xun
- From the School of Life Sciences, Northwest University, Xi'an, China (XX, HJW, HY, TJ, CC); National Engineering Research Center for Miniaturized Detection Systems, Xi'an, China (HJW, HW, BW, TJ, CC); Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Tibet University for Nationalities, Xianyang, Shaanxi, China (TJ, LK)
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Luo X, Lamsal LP, Xu WJ, Lu J, Lu YJ, Shen Y, Guan Q. Genetic Variant in CLPTM1L Confers Reduced Risk of Lung Cancer: a Replication Study in Chinese and a Meta-analysis. Asian Pac J Cancer Prev 2014; 15:9241-7. [DOI: 10.7314/apjcp.2014.15.21.9241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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36
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Nguyen JDU, Lamontagne M, Couture C, Conti M, Paré PD, Sin DD, Hogg JC, Nickle D, Postma DS, Timens W, Laviolette M, Bossé Y. Susceptibility loci for lung cancer are associated with mRNA levels of nearby genes in the lung. Carcinogenesis 2014; 35:2653-9. [PMID: 25187487 DOI: 10.1093/carcin/bgu184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent studies identified three genetic loci reproducibly associated with lung cancer in populations of European ancestry, namely 15q25, 5p15 and 6p21. The goals of this study are first to confirm whether these loci are associated with lung cancer in a French Canadian population and second to identify disease-associated single nucleotide polymorphisms (SNPs) influencing messenger RNA (mRNA) expression levels of genes in the lung, that is expression quantitative trait loci (eQTLs). SNPs were genotyped in 420 patients undergoing lung cancer surgery and compared with 3151 controls of European ancestry. Genome-wide gene expression levels in non-tumor lung tissues of the same 420 patients were also measured to identify eQTLs. Significant eQTLs were then followed-up in two replication sets (n = 339 and 363). SNPs found in the three susceptibility loci were associated with lung cancer in the French Canadian population. Strong eQTLs were found on chromosome 15q25 with the expression levels of CHRNA5 (P = 2.23 × 10(-) (22) with rs12907966). The CHRNA5-rs12907966 eQTL was convincingly validated in the two replication sets (P = 3.46 × 10(-) (16) and 2.01 × 10(-) (15)). On 6p21, a trend was observed for rs3131379 to be associated with the expression of APOM (P = 3.58 × 10(-) (4)) and validated in the replication sets (P = 1.11 × 10(-) (8) and 6.84 × 10(-) (4)). On 5p15, no significant eQTLs were found. This study confirmed that chromosomes 15q25, 5p15 and 6p21 harbored susceptibility loci for lung cancer in French Canadians. Most importantly, this study suggests that the risk alleles at 15q25 and 6p21 may mediate their effect by regulating the mRNA expression levels of CHRNA5 and APOM in the lung.
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Affiliation(s)
- Justin Dang Uy Nguyen
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec G1V 4G5, Canada
| | - Maxime Lamontagne
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec G1V 4G5, Canada
| | - Christian Couture
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec G1V 4G5, Canada
| | - Massimo Conti
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec G1V 4G5, Canada
| | - Peter D Paré
- UBC James Hogg Research Center and Institute for Heart and Lung Health, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada, Department of Medicine, Respiratory Division and
| | - Don D Sin
- UBC James Hogg Research Center and Institute for Heart and Lung Health, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada, Department of Medicine, Respiratory Division and
| | - James C Hogg
- UBC James Hogg Research Center and Institute for Heart and Lung Health, St Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | | | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, GRIAC Research Institute, Groningen FC41, The Netherlands and
| | - Michel Laviolette
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec G1V 4G5, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec G1V 4G5, Canada, Department of Molecular Medicine, Laval University, Québec G1V 0A6, Canada
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37
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Kim J. Cancer screenee cohort study of the National Cancer Center in South Korea. Epidemiol Health 2014; 36:e2014013. [PMID: 25119453 PMCID: PMC4183059 DOI: 10.4178/epih/e2014013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/06/2014] [Indexed: 12/27/2022] Open
Abstract
The Cancer Screenee Cohort Study was first established in 2002 by the National Cancer Center in South Korea to investigate all possible risk factors related to cancers and to expand biological specimen banking for the development of effective methodologies for cancer detection, diagnosis, and prevention. As of July in 2014, total 41,105 participants were enrolled in this cohort. Data were collected via questionnaire, clinical examination, cancer screening, and biological specimen testing including blood, urine, and exfoliated cervical cells. The highest incidence was found to be thyroid cancer, according to a nested case-control study that was linked to the National Cancer Registry information as of December 31, 2011. Case-control, cross-sectional, and cohort studies have been published using these data since 2009. Diet and nutrition was the most published topic, followed by genetics, hepatitis B virus and liver cancer screening, methodologies, physical activity, obesity, metabolic syndrome, smoking and alcohol consumption, and blood type. Evidence from the Cancer Screenee Cohort Study is highly anticipated to reduce the burden of cancer in the Korean population and aid in the detection, diagnosis, and prevention of cancer.
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Affiliation(s)
- Jeongseon Kim
- Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute, National Cancer Center, Goyang, Korea
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38
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Chen Y, Yu Z, Zhang B, Chang Z, Wang H, Liu Z. CRR9p polymorphism as a protective factor for lung cancer. Tumour Biol 2014; 35:9557-62. [PMID: 24957041 DOI: 10.1007/s13277-014-2198-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/06/2014] [Indexed: 11/26/2022] Open
Abstract
A number of studies have investigated the association between CRR9p polymorphism and risk of lung cancer (LC), yet the role in LC pathogenesis remains unclear owing to inconsistencies across studies. We searched PubMed, Embase, and Web of Science for all medical literature published until January 2014. Pooled odds ratios (ORs) and 95 % confidence intervals (CIs) were obtained by means of the fixed effects model. Data from eight studies satisfying the predesigned inclusion criteria were selected for this meta-analysis. We found a statistically significant evidence for a protective effect on the overall LC risk (TT vs. CC: OR = 0.78, 95 % CI = 0.70-0.87, P het = 0.299; TT vs. CT + CC: OR = 0.81, 95 % CI = 0.73-0.90, P het = 0.113; T vs. C: OR = 0.90, 95 % CI = 0.86-0.95, P het = 0.758; TT + CT vs. CC: OR = 0.92, 95 % CI = 0.87-0.98, P het = 0.892). Both Caucasian and Asian populations were suggested to have a reduced risk of developing such cancer. In the analysis of the association between rs401681 and non-small cell lung cancer (NSCLC) risks, all of the contrast models showed similar results except the CT vs. CC genetic model (OR = 0.93, 95 % CI = 0.84-1.02, P het = 0.568). Our meta-analysis provides supportive evidence that CRR9p polymorphism may influence a risk of LC and NSCLC in a protective model.
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Affiliation(s)
- Yang Chen
- Cancer Center, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, China
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Yang IA, Holloway JW, Fong KM. Genetic susceptibility to lung cancer and co-morbidities. J Thorac Dis 2014; 5 Suppl 5:S454-62. [PMID: 24163739 DOI: 10.3978/j.issn.2072-1439.2013.08.06] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 12/18/2022]
Abstract
Lung cancer is a leading cause of cancer death and disease burden in many countries. Understanding of the biological pathways involved in lung cancer aetiology is required to identify key biomolecules that could be of significant clinical value, either as predictive, prognostic or diagnostic markers, or as targets for the development of novel therapies to treat this disease, in addition to smoking avoidance strategies. Genome-wide association studies (GWAS) have enabled significant progress in the past 5 years in investigating genetic susceptibility to lung cancer. Large scale, multi-cohort GWAS of mainly Caucasian, smoking, populations have identified strong associations for lung cancer mapped to chromosomal regions 15q [nicotinic acetylcholine receptor (nAChR) subunits: CHRNA3, CHRNA5], 5p (TERT-CLPTM1L locus) and 6p (BAT3-MSH5). Some studies in Asian populations of smokers have found similar risk loci, whereas GWAS in never smoking Asian females have identified associations in other chromosomal regions, e.g., 3q (TP63), that are distinct from smoking-related lung cancer risk loci. GWAS of smoking behaviour have identified risk loci for smoking quantity at 15q (similar genes to lung cancer susceptibility: CHRNA3, CHRNA5) and 19q (CYP2A6). Other genes have been mapped for smoking initiation and smoking cessation. In chronic obstructive pulmonary disease (COPD), which is a known risk factor for lung cancer, GWAS in large cohorts have also found CHRNA3 and CHRNA5 single nucleotide polymorphisms (SNPs) mapping at 15q as risk loci, as well as other regions at 4q31 (HHIP), 4q24 (FAM13A) and 5q (HTR4). The overlap in risk loci between lung cancer, smoking behaviour and COPD may be due to the effects of nicotine addiction; however, more work needs to be undertaken to explore the potential direct effects of nicotine and its metabolites in gene-environment interaction in these phenotypes. Goals of future genetic susceptibility studies of lung cancer should focus on refining the strongest risk loci in a wide range of populations with lung cancer, and integrating other clinical and biomarker information, in order to achieve the aim of personalised therapy for lung cancer.
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Affiliation(s)
- Ian A Yang
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia; ; UQ Thoracic Research Centre, The University of Queensland, Brisbane, Australia
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40
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Association between CLPTM1L polymorphisms (rs402710 and rs401681) and lung cancer susceptibility: evidence from 27 case–control studies. Mol Genet Genomics 2014; 289:1001-12. [DOI: 10.1007/s00438-014-0868-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/12/2014] [Indexed: 02/07/2023]
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41
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Genetic polymorphisms of TERT and CLPTM1L and risk of lung cancer: a case-control study in northeast Chinese male population. Med Oncol 2014; 31:18. [PMID: 24861918 DOI: 10.1007/s12032-014-0018-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
Recently, some genome-wide association studies have implicated telomerase reverse transcriptase (TERT) and cleft lip and palate transmembrane 1-like gene (CLPTM1L) in lung cancer development. Here, we present a case-control study that evaluates the genetic effects of TERT-rs2736098 and CLPTM1L-rs401681 variants on the risk of lung cancer development in a Chinese male population. We found that the homozygous variant genetic model of the TERT gene was associated with a significantly increased risk of lung cancer with an adjusted odds ratio (OR) of 1.988. The TERT-rs2736098 T allele was also associated with increased lung cancer risk both in adenocarcinoma and squamous cell carcinoma. No association was found between CLPTM1L-rs401681 and lung cancer risk. However, the joint effect of TERT and CLPTM1L variants increased the risk of lung cancer, especially squamous cell carcinoma, with an adjusted OR of 3.274. However, the exact functional effect of these two variant genes remains unclear, and further investigation is needed in the future.
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Setiawan VW, Schumacher F, Prescott J, Haessler J, Malinowski J, Wentzensen N, Yang H, Chanock S, Brinton L, Hartge P, Lissowska J, Park SL, Cheng I, Bush WS, Crawford DC, Ursin G, Horn-Ross P, Bernstein L, Lu L, Risch H, Yu H, Sakoda LC, Doherty J, Chen C, Jackson R, Yasmeen S, Cote M, Kocarnik JM, Peters U, Kraft P, De Vivo I, Haiman CA, Kooperberg C, Le Marchand L. Cross-cancer pleiotropic analysis of endometrial cancer: PAGE and E2C2 consortia. Carcinogenesis 2014; 35:2068-73. [PMID: 24832084 DOI: 10.1093/carcin/bgu107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified a large number of cancer-associated single nucleotide polymorphisms (SNPs), several of which have been associated with multiple cancer sites suggesting pleiotropic effects and shared biological mechanisms across some cancers. We hypothesized that SNPs associated with other cancers may be additionally associated with endometrial cancer. We examined 213 SNPs previously associated with 14 other cancers for their associations with endometrial cancer in 3758 endometrial cancer cases and 5966 controls of European ancestry from two consortia: Population Architecture Using Genomics and Epidemiology and the Epidemiology of Endometrial Cancer Consortium. Study-specific logistic regression estimates adjusted for age, body mass index and the most significant principal components of genetic ancestry were combined using fixed-effect meta-analysis to evaluate the association between each SNP and endometrial cancer risk. A Bonferroni-corrected P value of 2.35×10(-4) was used to determine statistical significance of the associations. SNP rs7679673, ~6.3kb upstream of TET2 and previously reported to be associated with prostate cancer risk, was associated with endometrial cancer risk in the direction opposite to that for prostate cancer [meta-analysis odds ratio = 0.87 (per copy of the C allele), 95% confidence interval = 0.81, 0.93; P = 7.37×10(-5)] with no evidence of heterogeneity across studies (P heterogeneity = 0.66). This pleiotropic analysis is the first to suggest TET2 as a susceptibility locus for endometrial cancer.
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Affiliation(s)
- Veronica Wendy Setiawan
- Department of Preventive Medicine, Keck School of Medicine, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37235, USA, National Cancer Institute, Bethesda, MD 20892, USA, M.Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland, Cancer Prevention Institute of California, Fremont, CA 94538, USA, Institute of Population Based Cancer Research, Cancer Registry of Norway, N-0304 Oslo, Norway, Division of Cancer Etiology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA, Department of Epidemiology, Yale School of Public Health, New Haven CT 06520, USA, Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Division of Research, Kaiser Permanente Northern California, Oakland, CA 94611, USA, Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA, Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA, Department of Obstetrics and Gynecology, University of California, Davis, CA 95616, USA, Department of Oncology, Wayne State University School of Medicine and Population Studies and Disparities Research, Karmanos Cancer Institute, Detroit, MI 48202, USA and Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37235, USA, National Cancer Institute, Bethesda, MD 20892, USA, M.Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland, Cancer Prevention Institute of California, Fremont, CA 94538, USA, Institute of Population Based Cancer Research, Cancer Registry of Norway, N-0304 Oslo, Norway, Division of Cancer Etiology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA, Department of Epidemiology, Yale School of Public Health, New Haven CT 06520, USA, Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Division of Research, Kaiser Permanente Northern California, Oakland, CA 94611, USA, Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA, Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA, Department of Obstetrics and Gynecology, University of California, Davis, CA 95616, USA, Department of Oncology, Wayne State University School of Medicine and Population Studies and Disparities Research, Karmanos Cancer Institute, Detroit, MI 48202, USA and Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Jennifer Prescott
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jennifer Malinowski
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Hannah Yang
- National Cancer Institute, Bethesda, MD 20892, USA
| | | | | | | | - Jolanta Lissowska
- M.Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - S Lani Park
- Department of Preventive Medicine, Keck School of Medicine, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37235, USA, National Cancer Institute, Bethesda, MD 20892, USA, M.Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland, Cancer Prevention Institute of California, Fremont, CA 94538, USA, Institute of Population Based Cancer Research, Cancer Registry of Norway, N-0304 Oslo, Norway, Division of Cancer Etiology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA, Department of Epidemiology, Yale School of Public Health, New Haven CT 06520, USA, Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Division of Research, Kaiser Permanente Northern California, Oakland, CA 94611, USA, Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA, Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA, Department of Obstetrics and Gynecology, University of California, Davis, CA 95616, USA, Department of Oncology, Wayne State University School of Medicine and Population Studies and Disparities Research, Karmanos Cancer Institute, Detroit, MI 48202, USA and Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, CA 94538, USA
| | - William S Bush
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37235, USA
| | - Dana C Crawford
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37235, USA
| | - Giske Ursin
- Institute of Population Based Cancer Research, Cancer Registry of Norway, N-0304 Oslo, Norway
| | - Pamela Horn-Ross
- Cancer Prevention Institute of California, Fremont, CA 94538, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lingeng Lu
- Department of Epidemiology, Yale School of Public Health, New Haven CT 06520, USA
| | - Harvey Risch
- Department of Epidemiology, Yale School of Public Health, New Haven CT 06520, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Lori C Sakoda
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Division of Research, Kaiser Permanente Northern California, Oakland, CA 94611, USA
| | - Jennifer Doherty
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA
| | - Chu Chen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rebecca Jackson
- Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA
| | - Shagufta Yasmeen
- Department of Obstetrics and Gynecology, University of California, Davis, CA 95616, USA
| | - Michele Cote
- Department of Oncology, Wayne State University School of Medicine and Population Studies and Disparities Research, Karmanos Cancer Institute, Detroit, MI 48202, USA and
| | - Jonathan M Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter Kraft
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Immaculata De Vivo
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37235, USA, National Cancer Institute, Bethesda, MD 20892, USA, M.Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland, Cancer Prevention Institute of California, Fremont, CA 94538, USA, Institute of Population Based Cancer Research, Cancer Registry of Norway, N-0304 Oslo, Norway, Division of Cancer Etiology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA, Department of Epidemiology, Yale School of Public Health, New Haven CT 06520, USA, Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Division of Research, Kaiser Permanente Northern California, Oakland, CA 94611, USA, Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA, Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA, Department of Obstetrics and Gynecology, University of California, Davis, CA 95616, USA, Department of Oncology, Wayne State University School of Medicine and Population Studies and Disparities Research, Karmanos Cancer Institute, Detroit, MI 48202, USA and Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Loic Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
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Tuominen R, Jönsson G, Enerbäck C, Appelqvist F, Olsson H, Ingvar C, Hansson J, Höiom V. Investigation of a putative melanoma susceptibility locus at chromosome 3q29. Cancer Genet 2014; 207:70-4. [PMID: 24721441 DOI: 10.1016/j.cancergen.2014.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/14/2014] [Accepted: 02/18/2014] [Indexed: 12/20/2022]
Abstract
Malignant melanoma, the most fatal form of skin cancer, is currently increasing in incidence in many populations. Approximately 10% of all cases occur in families with an inherited predisposition for melanoma. In Sweden, only a minor portion of such melanoma families carry a mutation in the known melanoma gene CDKN2A, and there is a need to identify additional melanoma susceptibility genes. In a recently performed genome-wide linkage screen, novel loci with suggestive evidence of linkage to melanoma were detected. In this study, we have further analyzed one region on chromosome 3q29. In all, 89 affected and 15 nonaffected family members from 42 melanoma-prone families were genotyped for 34 genetic markers. In a pooled linkage analysis of all 42 families, we detected significant evidence of linkage, with a maximum heterogeneity logarithm of odds (HLOD) score of 3.1 with 83% of the families contributing to the linkage score. The minimum critical region of linkage (defined by a 1LOD score support interval) maps to chromosome 3q29, spans 3.5 Mb of genomic sequence, and harbors 44 identified genes. Sequence variants within this region have previously been associated with cancer susceptibility. This study reports the presence of a putative novel melanoma susceptibility locus in the Swedish population, a finding that needs to be replicated in an independent study on other individuals with familial melanoma. Sequencing of genes in the region may identify novel melanoma-associated mutations.
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Affiliation(s)
- Rainer Tuominen
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Göran Jönsson
- Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
| | - Charlotta Enerbäck
- Division of Cell Biology and Dermatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Frida Appelqvist
- Department of Clinical Genetics, Sahlgrenska University Hospital, Göteborg, Sweden
| | - Håkan Olsson
- Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
| | | | - Johan Hansson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Veronica Höiom
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.
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Imielinski M, Hammerman PS, Thomas R, Meyerson M. Somatic Genome Alterations in Human Lung Cancers. Lung Cancer 2014. [DOI: 10.1002/9781118468791.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Dai X, Deng S, Wang T, Qiu G, Li J, Yang B, Feng W, He X, Deng Q, Ye J, Zhang W, He M, Zhang X, Guo H, Wu T. Associations between 25 lung cancer risk-related SNPs and polycyclic aromatic hydrocarbon-induced genetic damage in coke oven workers. Cancer Epidemiol Biomarkers Prev 2014; 23:986-96. [PMID: 24692499 DOI: 10.1158/1055-9965.epi-13-1251] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified multiple single-nucleotide polymorphisms (SNP) associated with lung cancer. However, whether these SNPs are associated with genetic damage, a crucial event in cancer initiation and evolution, is still unknown. We aimed to establish associations between these SNPs and genetic damage caused by the ubiquitous carcinogens, polycyclic aromatic hydrocarbons (PAH). METHODS We cross-sectionally investigated the associations between SNPs from published GWAS for lung cancer in Asians and PAH-induced genetic damage in 1,557 coke oven workers in China. Urinary PAH metabolites, plasma benzo[a]pyrene-r-7,t-8,c-10-tetrahydrotetrol-albumin (BPDE-Alb) adducts, urinary 8-hydroxydeoxyguanosine (8-OHdG), and micronuclei (MN) frequency were determined by gas chromatography-mass spectrometry, sandwich ELISA, high-performance liquid chromatography, and cytokinesis-block micronucleus assay, respectively. RESULTS 13q12.12-rs753955C was suggestively associated with elevated 8-OHdG levels (P = 0.003). Higher 8-OHdG levels were observed in individuals with rare allele homozygotes (CC) than in TT homozygotes (β, 0.297; 95% confidence interval, 0.124-0.471; P = 0.001). 9p21-rs1333040C, 10p14-rs1663689G, and 15q25.1-rs3813572G were significantly associated with lower MN frequency (P values were 0.002, 0.001, and 0.005, respectively). 10p14-rs1663689G polymorphism downregulated the relationship of the total concentration of PAH metabolites to 8-OHdG levels (Pinteraction = 0.002). TERT-rs2736100G and VTI1A-rs7086803A aggravated the relationship of BPDE-Alb adducts to MN frequency, whereas BPTF-rs7216064G attenuated that correlation (all Pinteraction < 0.001). CONCLUSIONS Lung cancer risk-associated SNPs and their correlations with PAH exposure were associated with 8-OHdG levels and MN frequency. IMPACT Lung cancer risk-associated SNPs might influence one's susceptibility to genetic damage caused by PAHs. Cancer Epidemiol Biomarkers Prev; 23(6); 986-96. ©2014 AACR.
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Affiliation(s)
- Xiayun Dai
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Siyun Deng
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Tian Wang
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Gaokun Qiu
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Jun Li
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Binyao Yang
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Wei Feng
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Xiaosheng He
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Qifei Deng
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Jian Ye
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Wangzhen Zhang
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Meian He
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Xiaomin Zhang
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Huan Guo
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
| | - Tangchun Wu
- Authors' Affiliations: Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health for Incubation, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology; and Institute of Industrial Health, Wuhan Iron and Steel (group) Corporation, Wuhan, Hubei, China
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Wu H, Zhu R. Quantitative assessment of common genetic variants on chromosome 5p15 and lung cancer risk. Tumour Biol 2014; 35:6055-63. [PMID: 24615522 DOI: 10.1007/s13277-014-1802-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/25/2014] [Indexed: 01/17/2023] Open
Abstract
Several genome-wide association studies on lung cancer (LC) have reported similar findings of a new susceptibility locus, 5p15. After that, a number of studies reported that the rs2736100, rs401681, rs402710, and rs31489 polymorphisms at chromosome 5p15 have been implicated in LC risk. However, the studies have yielded contradictory results. To derive a more precise estimation of the relationship, we performed this meta-analysis. Databases including MEDLINE, PubMed, EMBASE, ISI Web of Science, and China National Knowledge Infrastructure (CNKI) were searched to find relevant studies. Odds ratios (ORs) with 95 % confidence intervals (CIs) were used to assess the strength of association. The random effect model was applied, addressing heterogeneity and publication bias. A total of 31 articles involving 72,401 cases and 141,258 controls were included. Overall, significantly elevated LC risk was associated with rs2736100, rs401681, rs402710, and rs31489 polymorphisms when all studies were pooled into the meta-analysis. In the subgroup analysis by ethnicity, sample size, histology, sex, and smoking behavior, significantly increased risks were also detected for these polymorphisms. Our findings demonstrated that these common variations at 5p15 are a risk factor associated with increased LC susceptibility. However, these associations vary between different ethnicity.
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Affiliation(s)
- Hongyu Wu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, People's Republic of China,
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Yang J, Jiao S. Increased lung cancer risk associated with the TERT rs2736100 polymorphism: an updated meta-analysis. Tumour Biol 2014; 35:5763-9. [PMID: 24590268 DOI: 10.1007/s13277-014-1765-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 02/17/2014] [Indexed: 10/25/2022] Open
Abstract
The rs2736100 polymorphism in the telomerase reverse transcriptase (TERT) gene has been implicated in lung cancer risk in multiple populations, but the existing evidence lacks statistical power to draw a convincing conclusion. Therefore, the present study was devised to derive a more precise estimation of the association between rs2736100 and lung cancer risk. The PubMed, Embase, and Web of Science databases were comprehensively searched for papers concerning lung cancer risk in relation to rs2736100. Pooled odds ratios (ORs) and the 95 % confidence intervals (CIs) were appropriately calculated using the fixed or random effects model. Meta-analysis of 20 independent studies involving 39,715 cancer cases and 61,462 control subjects showed statistical evidence for an association between rs2736100 and increased risk of lung cancer. Subgroup analysis by ethnicity demonstrated a significant association among both Asian and Caucasian populations. We additionally found an increased risk of non-small cell lung cancer and lung adenocarcinoma strongly associated with rs2736100. These data provide further evidence supporting a role for genetic susceptibility of TERT rs2736100 in the development of lung cancer.
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Affiliation(s)
- Jihua Yang
- Department of Oncology, Chinese PLA General Hospital, 28# Fuxing Road, Haidian District, Beijing, 100853, People's Republic of China
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48
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Nie W, Zang Y, Chen J, Xiu Q. TERT rs2736100 polymorphism contributes to lung cancer risk: a meta-analysis including 49,869 cases and 73,464 controls. Tumour Biol 2014; 35:5569-74. [PMID: 24535778 DOI: 10.1007/s13277-014-1734-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/05/2014] [Indexed: 11/27/2022] Open
Abstract
Some studies investigated the association of TERT rs2736100 polymorphism with lung cancer (LC). But the results were not consistent. We performed a meta-analysis to examine the association between rs2736100 and LC. Databases including PubMed, EMBASE, Wanfang, and China National Knowledge Infrastructure (CNKI) were searched. Data were extracted, and pooled odds ratios (ORs) with 95 % confidence intervals (CIs) were calculated. A total of 19 studies including 49,869 cases and 73,464 controls were involved in this meta-analysis. Overall, a significant association between TERT rs2736100 polymorphism and LC risk was observed (OR=1.23, 95 % CI 1.18-1.28, P<0.00001). This polymorphism was also significantly associated with LC risk in Asians (OR=1.27, 95 % CI 1.22-1.33, P<0.00001), Caucasians (OR=1.14, 95 % CI 1.10-1.18, P<0.00001), female patients (OR=1.37, 95 % CI 1.24-1.51, P<0.00001), male patients (OR=1.23, 95 % CI 1.15-1.31, P<0.00001), adenocarcinoma patients (OR=1.35, 95 % CI 1.28-1.41, P<0.00001), squamous cell carcinoma patients (OR=1.13, 95 % CI 1.04-1.21, P=0.002), small cell lung cancer patients (OR=1.09, 95 % CI 1.03-1.16, P=0.004), current smokers (OR=1.22, 95 % CI 1.17-1.27, P<0.00001), former smokers (OR=1.14, 95 % CI 1.08-1.21, P<0.0001), and never smokers (OR=1.37, 95 % CI 1.31-1.43, P<0.00001), respectively. This meta-analysis suggested that TERT rs2736100 polymorphism was a risk factor for LC.
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Affiliation(s)
- Wei Nie
- Department of Respiratory Medicine, Shanghai Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
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Association between TERT rs2736100 polymorphism and lung cancer susceptibility: evidence from 22 case-control studies. Tumour Biol 2014; 35:4435-42. [PMID: 24390616 DOI: 10.1007/s13277-013-1583-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/19/2013] [Indexed: 01/02/2023] Open
Abstract
The 5p15.33 locus has been recently identified to associate with multiple cancer types including lung, urinary bladder, prostate, and cervical cancer, based on its critical role in the maintenance of telomere, chromosome stability, and ultimately preventing normal cell malignance. TERT (human telomerase reverse transcriptase) is an attractive candidate gene for the 5p15.33 locus. Recently, a number of case-control studies have been carried out to investigate the relationship between the rs2736100 polymorphism in TERT and genetic susceptibility to lung cancer. However, the results have been inconclusive. To investigate this inconsistency and derive a more precise estimation of the relationship, we conducted a comprehensive meta-analysis of 56,223 cases and 86,680 controls from 22 published studies. Using the random-effects model, we found a significant association between rs2736100 polymorphism and lung cancer risk with per-allele OR of 1.20 (95% CI, 1.16-1.23; P < 10(-5)). Significant results were also observed using dominant and recessive genetic model. Significant results were found in East Asians and Caucasians when stratified by ethnicity in all genetic models. In addition, our data indicate that rs2736100 is involved in lung cancer susceptibility and confer its effect primarily in adenocarcinoma in the subgroup analyses by histological subtype. In the stratified analysis according to sample size, smoking behavior, sex, and age, risks significantly increased for the polymorphism. In conclusion, this meta-analysis demonstrated that TERT rs2736100 polymorphism is a risk factor associated with increased lung cancer susceptibility, particularly for lung adenocarcinoma.
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The SNP rs402710 in 5p15.33 is associated with lung cancer risk: a replication study in Chinese population and a meta-analysis. PLoS One 2013; 8:e76252. [PMID: 24194831 PMCID: PMC3806805 DOI: 10.1371/journal.pone.0076252] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/21/2013] [Indexed: 12/20/2022] Open
Abstract
Background Lung cancer is the most commonly diagnosed cancer and leading cause of cancer mortality in the world. A single nucleotide polymorphism (SNP), rs402710, located in 5p15.33, was firstly identified to be associated with the lung cancer risk in a genome-wide association study. However, some following replication studies yielded inconsistent results. Methodology and Findings A case-control study of 611 cases and 1062 controls in a Chinese population was conducted, and then a meta-analysis integrating the current and previously published studies with a total 31811 cases and 36333 controls was performed to explore the real effect of rs402710 on lung cancer susceptibility. Significant associations between the SNP rs402710 and lung cancer risk were observed in both case-control study and meta-analysis, with ORs equal to 0.77 (95%CI = 0.63–0.95) and 0.83 (95%CI = 0.81–0.86) in dominant model, respectively. By stratified analysis of our case-control study, the associations were also observed in never smoker group and non-small cell lung cancer(NSCLC) group with ORs equal to 0.71 (95%CI = 0.53–0.95) and 0.69 (95%CI = 0.55–0.87), which was remarkable that larger effect of the minor allele T was seen in the two groups than that in overall lung cancer. Besides, the sensitive and cumulative analysis indicated the robust stability of the current results of meta-analysis. Conclusion The results from our replication study and the meta-analysis provided firm evidence that rs402710 T allele significantly contributed to decreased lung cancer risk, and the case-control study implied that the variant may yield stronger effect on NSCLC and never smokers. However, the mechanism underlying the polymorphism conferring susceptibility to lung cancer is warranted to clarify in the follow-up studies.
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