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Zhang T, Xue Y, Su S, Altouma V, Ho K, Martindale JL, Lee SK, Shen W, Park A, Zhang Y, De S, Gorospe M, Wang W. RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames. Nucleic Acids Res 2024; 52:885-905. [PMID: 38000373 PMCID: PMC10810208 DOI: 10.1093/nar/gkad1122] [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] [Received: 06/20/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
RNA-binding proteins (RBPs) with intrinsically disordered regions (IDRs) are linked to multiple human disorders, but their mechanisms of action remain unclear. Here, we report that one such protein, Nocte, is essential for Drosophila eye development by regulating a critical gene expression cascade at translational level. Knockout of nocte in flies leads to lethality, and its eye-specific depletion impairs eye size and morphology. Nocte preferentially enhances translation of mRNAs with long upstream open reading frames (uORFs). One of the key Nocte targets, glass mRNA, encodes a transcription factor critical for differentiation of photoreceptor neurons and accessory cells, and re-expression of Glass largely rescued the eye defects caused by Nocte depletion. Mechanistically, Nocte counteracts long uORF-mediated translational suppression by promoting translation reinitiation downstream of the uORF. Nocte interacts with translation factors eIF3 and Rack1 through its BAT2 domain, and a Nocte mutant lacking this domain fails to promote translation of glass mRNA. Notably, de novo mutations of human orthologs of Nocte have been detected in schizophrenia patients. Our data suggest that Nocte family of proteins can promote translation reinitiation to overcome long uORFs-mediated translational suppression, and disruption of this function can lead to developmental defects and neurological disorders.
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Affiliation(s)
- Tianyi Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Valerie Altouma
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Katherine Ho
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung-Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aaron Park
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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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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Wen S, Wei H, Li M, Zhong S, Cheng Y, Huang W, Wang D, Shu Y. Genetic variants in BAT2 are associated with immune responsiveness to influenza vaccination. Front Genet 2023; 14:1059447. [PMID: 36845396 PMCID: PMC9951381 DOI: 10.3389/fgene.2023.1059447] [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: 10/01/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
Background: Influenza is a global public health problem for its detrimental impact on human health. Annual vaccination is the most effective prevention of influenza infection. Identifying host genetic factors associated with the responsiveness to influenza vaccines can provide clues for developing more effective influenza vaccines. In this study, we aimed to explore whether the single nucleotide polymorphisms in BAT2 are associated with the antibody responses to influenza vaccines. Method: A nested case-control study was conducted in this research. 1968 healthy volunteers were enrolled and 1,582 of them from a Chinese Han population were eligible for further research. According to the hemagglutination inhibition titers of subjects against all influenza vaccine strains, a total of 227 low responders and 365 responders were included in the analysis. Six tag single nucleotide polymorphisms in the coding region of BAT2 were selected and genotyped using the MassARRAY technology platform. Univariable and multivariable analyses were conducted to evaluate the relationship between variants and antibody responses to influenza vaccination. Results: Multivariable logistic regression analysis showed that, compared with the BAT2 rs1046089GG genotype, the GA + AA genotype was correlated with decreased risk of low responsiveness to influenza vaccines after adjusting for gender and age (p = 1.12E-03, OR = .562, 95%CI: .398-.795). rs9366785 GA + AA genotype was associated with a higher risk of low responsiveness to influenza vaccination compared with the GG genotype (p = .003, OR = 1.854, 95%CI: 1.229-2.799). The haplotype consisting of BAT2 rs2280801-rs10885-rs1046089-rs2736158-rs1046080-rs9366785 CCAGAG was correlated with a higher level of antibody response to influenza vaccines compared with haplotype CCGGAG (p < .001, OR = .37, 95%CI: .23-.58). Conclusion: Genetic variants in BAT2 were statistically associated with the immune response to influenza vaccination among the Chinese population. Identifying these variants will provide clues for further research on novel broad-spectrum influenza vaccines, and improve the individualized influenza vaccination scheme.
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Affiliation(s)
- Simin Wen
- Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China
| | - Hejiang Wei
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Mao Li
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Shuyi Zhong
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yanhui Cheng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Weijuan Huang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, China,*Correspondence: Dayan Wang, ; Yuelong Shu,
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China,Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, China,*Correspondence: Dayan Wang, ; Yuelong Shu,
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Long E, Patel H, Byun J, Amos CI, Choi J. Functional studies of lung cancer GWAS beyond association. Hum Mol Genet 2022; 31:R22-R36. [PMID: 35776125 DOI: 10.1093/hmg/ddac140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately forty-five genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries, and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.
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Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Liu X, Zhang Y, Wang Z, Liu L, Zhang G, Li J, Ren Z, Dong Z, Yu Z. PRRC2A Promotes Hepatocellular Carcinoma Progression and Associates with Immune Infiltration. J Hepatocell Carcinoma 2021; 8:1495-1511. [PMID: 34881207 PMCID: PMC8646232 DOI: 10.2147/jhc.s337111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) has high morbidity and poor prognosis due to the propensity of recurrence and metastasis. Emerging studies have confirmed that proline-rich coiled-coil2A (PRRC2A) plays a crucial role in tumorigenesis and immunoregulation. However, its expression status and biological functions in HCC remain poorly documented. Methods The presence and prognostic value of PRRC2A were determined by a tissue microarray (TMA) cohort and multiple databases, mainly from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Clinical Proteomic Tumor Analysis Consortium (CPTAC). Functional enrichment analysis was applied to identify the mechanisms of PRRC2A in HCC. The biological function of PRRC2A in HCC progression in vitro was determined by CCK-8, colony formation, EdU, transwell migration and invasion assays. Moreover, the Estimation of STromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE), single-sample gene set enrichment analysis (ssGSEA), tumor immune dysfunction and exclusion (TIDE) algorithms, immunophenoscore (IPS) and public available immunotherapy cohorts were performed to classify their associations with tumor-infiltrating immune cells and immunotherapy. Results PRRC2A was upregulated in HCC at both mRNA and protein levels. High PRRC2A expression was correlated with poor prognosis and could be an independent risk factor. Functional enrichment analysis demonstrated that elevated PRRC2A was significantly correlated with the activation of various oncogenic pathways. Additionally, in vitro experiments confirmed that silencing PRRC2A could suppress the proliferation and metastasis capacities of HCC cells. More importantly, PRRC2A was negatively associated with many anti-tumor immune cells, but positively related to the expression of markers of exhaustive T cells. And HCC patients with high PRRC2A were more likely to be nonresponsive to immunotherapy. Conclusion This study explored the predictive value and biological roles of PRRC2A in HCC progression and indicated that it might be a potential biomarker for HCC patients and a predictor for immunotherapy.
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Affiliation(s)
- Xin Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Yize Zhang
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Zenghan Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Liwen Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Guizhen Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Jianhao Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Zihui Dong
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Zujiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China.,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
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6
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Zhou W, Zhu W, Tong X, Ming S, Ding Y, Li Y, Li Y. CHRNA5 rs16969968 polymorphism is associated with lung cancer risk: A meta-analysis. CLINICAL RESPIRATORY JOURNAL 2020; 14:505-513. [PMID: 32049419 DOI: 10.1111/crj.13165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 02/08/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVE To evaluate the genetic association between rs16969968 and lung cancer risk by meta-analysis. DATA SOURCE We searched eligible studies from MEDLINE, Web of Science and EMBASE up to Dec, 2017. STUDY SELECTION Association studies concerning rs16969968 and lung cancer risk were included. We assessed the association strength between this polymorphism and risk of lung cancer by calculating odds ratios (OR) and 95% confidence interval (95%CI). RESULTS A total of 26 data sets comprising 30 772 lung cancers and 90 954 controls were included. rs16969968 was found to be associated with lung cancer risk in population of European ancestry in all models (A vs. G: OR = 1.30, 95%CI 1.27-1.33, P < 0.001; AA + GA vs. GG: OR = 1.38, 95%CI 1.33-1.43, P < 0.001; AA vs. GG + GA: OR = 1.45, 95%CI 1.38-1.53, P < 0.001), consistent with previous genome-wide association study (GWAS). However, no association was observed in Asians (A vs. G: OR = 1.19. 95%CI 0.95-1.49, P = 0.131). The minor allele A may increase the risk of lung cancer in both smokers (OR = 1.33, 95%CI 1.29-1.39, P < 0.001) and nonsmokers (OR = 1.25, 95%CI 1.12-1.39, P < 0.001). There was no obvious publication bias in all analyses. CONCLUSIONS Our analysis provided more evidence that rs16969968 is a susceptibility locus of lung cancer in the Caucasians and that it may be not associated with the risk in the Asians.
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Affiliation(s)
- Wei Zhou
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Wenjie Zhu
- Department of Integrative Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xunliang Tong
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Shuhong Ming
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Yong Ding
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Yi Li
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Yanming Li
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
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Jones CC, Bradford Y, Amos CI, Blot WJ, Chanock SJ, Harris CC, Schwartz AG, Spitz MR, Wiencke JK, Wrensch MR, Wu X, Aldrich MC. Cross-Cancer Pleiotropic Associations with Lung Cancer Risk in African Americans. Cancer Epidemiol Biomarkers Prev 2019; 28:715-723. [PMID: 30894353 PMCID: PMC6449205 DOI: 10.1158/1055-9965.epi-18-0935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/02/2018] [Accepted: 12/31/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Identifying genetic variants with pleiotropic associations across multiple cancers can reveal shared biologic pathways. Prior pleiotropic studies have primarily focused on European-descent individuals. Yet population-specific genetic variation can occur, and potential pleiotropic associations among diverse racial/ethnic populations could be missed. We examined cross-cancer pleiotropic associations with lung cancer risk in African Americans. METHODS We conducted a pleiotropic analysis among 1,410 African American lung cancer cases and 2,843 controls. We examined 36,958 variants previously associated (or in linkage disequilibrium) with cancer in prior genome-wide association studies. Logistic regression analyses were conducted, adjusting for age, sex, global ancestry, study site, and smoking status. RESULTS We identified three novel genomic regions significantly associated (FDR-corrected P <0.10) with lung cancer risk (rs336958 on 5q14.3, rs7186207 on 16q22.2, and rs11658063 on 17q12). On chromosome16q22.2, rs7186207 was significantly associated with reduced risk [OR = 0.43; 95% confidence interval (CI), 0.73-0.89], and functional annotation using GTEx showed rs7186207 modifies DHODH gene expression. The minor allele at rs336958 on 5q14.3 was associated with increased lung cancer risk (OR = 1.47; 95% CI, 1.22-1.78), whereas the minor allele at rs11658063 on 17q12 was associated with reduced risk (OR = 0.80; 95% CI, 0.72-0.90). CONCLUSIONS We identified novel associations on chromosomes 5q14.3, 16q22.2, and 17q12, which contain HNF1B, DHODH, and HAPLN1 genes, respectively. SNPs within these regions have been previously associated with multiple cancers. This is the first study to examine cross-cancer pleiotropic associations for lung cancer in African Americans. IMPACT Our findings demonstrate novel cross-cancer pleiotropic associations with lung cancer risk in African Americans.
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Affiliation(s)
- Carissa C Jones
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuki Bradford
- School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | | | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Margaret R Spitz
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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Feky SEE, Ibrahim FA, Haroun M, Ahmmad MAR, Elnaggar M, Elghandour S, Moneim NAAE. Genetic Variation of <i>hTERT</i>, Leukocyte Telomere Length and the Risk of Breast Cancer: A Case-Control Study in Egyptian Females. ADVANCES IN BREAST CANCER RESEARCH 2019; 08:61-76. [DOI: 10.4236/abcr.2019.82005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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9
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Ji X, Bossé Y, Landi MT, Gui J, Xiao X, Qian D, Joubert P, Lamontagne M, Li Y, Gorlov I, de Biasi M, Han Y, Gorlova O, Hung RJ, Wu X, McKay J, Zong X, Carreras-Torres R, Christiani DC, Caporaso N, Johansson M, Liu G, Bojesen SE, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Chen C, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB, Andrew AS, Shen H, Hong YC, Yuan JM, Bertazzi PA, Pesatori AC, Ye Y, Diao N, Su L, Zhang R, Brhane Y, Leighl N, Johansen JS, Mellemgaard A, Saliba W, Haiman C, Wilkens L, Fernandez-Somoano A, Fernandez-Tardon G, van der Heijden EHFM, Kim JH, Dai J, Hu Z, Davies MPA, Marcus MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Doherty J, Goodman GE, Cox A, Taylor F, Woll P, Brüske I, Manz J, Muley T, Risch A, Rosenberger A, Grankvist K, Johansson M, Shepherd F, Tsao MS, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Koh WP, Gao YT, Houlston R, McLaughlin J, Stevens V, Nickle DC, Obeidat M, Timens W, Zhu B, Song L, Artigas MS, Tobin MD, Wain LV, Gu F, Byun J, Kamal A, Zhu D, Tyndale RF, Wei WQ, Chanock S, Brennan P, Amos CI. Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk. Nat Commun 2018; 9:3221. [PMID: 30104567 PMCID: PMC6089967 DOI: 10.1038/s41467-018-05074-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 05/01/2018] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) identified the chromosome 15q25.1 locus as a leading susceptibility region for lung cancer. However, the pathogenic pathways, through which susceptibility SNPs within chromosome 15q25.1 affects lung cancer risk, have not been explored. We analyzed three cohorts with GWAS data consisting 42,901 individuals and lung expression quantitative trait loci (eQTL) data on 409 individuals to identify and validate the underlying pathways and to investigate the combined effect of genes from the identified susceptibility pathways. The KEGG neuroactive ligand receptor interaction pathway, two Reactome pathways, and 22 Gene Ontology terms were identified and replicated to be significantly associated with lung cancer risk, with P values less than 0.05 and FDR less than 0.1. Functional annotation of eQTL analysis results showed that the neuroactive ligand receptor interaction pathway and gated channel activity were involved in lung cancer risk. These pathways provide important insights for the etiology of lung cancer.
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Grants
- P30 CA023108 NCI NIH HHS
- P30 CA076292 NCI NIH HHS
- U01 CA063464 NCI NIH HHS
- P50 CA070907 NCI NIH HHS
- R01 CA111703 NCI NIH HHS
- UM1 CA182876 NCI NIH HHS
- UL1 TR000117 NCATS NIH HHS
- P20 CA090578 NCI NIH HHS
- U19 CA148127 NCI NIH HHS
- P20 GM103534 NIGMS NIH HHS
- UL1 TR000445 NCATS NIH HHS
- R01 LM012012 NLM NIH HHS
- R01 CA092824 NCI NIH HHS
- R35 CA197449 NCI NIH HHS
- UM1 CA164973 NCI NIH HHS
- U01 CA167462 NCI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01 CA144034 NCI NIH HHS
- P20 RR018787 NCRR NIH HHS
- S10 RR025141 NCRR NIH HHS
- R01 CA074386 NCI NIH HHS
- R01 CA176568 NCI NIH HHS
- K07 CA172294 NCI NIH HHS
- P50 CA119997 NCI NIH HHS
- G0902313 Medical Research Council
- R01 CA063464 NCI NIH HHS
- P01 CA033619 NCI NIH HHS
- R01 HL133786 NHLBI NIH HHS
- P30 CA177558 NCI NIH HHS
- P50 CA090578 NCI NIH HHS
- U01 HG004798 NHGRI NIH HHS
- R01 CA151989 NCI NIH HHS
- 001 World Health Organization
- 202849/Z/16/Z Wellcome Trust
- UM1 CA167462 NCI NIH HHS
- U01 CA164973 NCI NIH HHS
- This work was supported by National Institutes of Health (NIH) for the research of lung cancer (grant P30CA023108, P20GM103534 and R01LM012012); Trandisciplinary Research in Cancer of the Lung (TRICL) (grant U19CA148127); UICC American Cancer Society Beginning Investigators Fellowship funded by the Union for International Cancer Control (UICC) (to X.Ji). CAPUA study. This work was supported by FIS-FEDER/Spain grant numbers FIS-01/310, FIS-PI03-0365, and FIS-07-BI060604, FICYT/Asturias grant numbers FICYT PB02-67 and FICYT IB09-133, and the University Institute of Oncology (IUOPA), of the University of Oviedo and the Ciber de Epidemiologia y Salud Pública. CIBERESP, SPAIN. The work performed in the CARET study was supported by the The National Institute of Health / National Cancer Institute: UM1 CA167462 (PI: Goodman), National Institute of Health UO1-CA6367307 (PIs Omen, Goodman); National Institute of Health R01 CA111703 (PI Chen), National Institute of Health 5R01 CA151989-01A1(PI Doherty). The Liverpool Lung project is supported by the Roy Castle Lung Cancer Foundation. The Harvard Lung Cancer Study was supported by the NIH (National Cancer Institute) grants CA092824, CA090578, CA074386 The Multiethnic Cohort Study was partially supported by NIH Grants CA164973, CA033619, CA63464 and CA148127 The work performed in MSH-PMH study was supported by The Canadian Cancer Society Research Institute (020214), Ontario Institute of Cancer and Cancer Care Ontario Chair Award to R.J.H. and G.L. and the Alan Brown Chair and Lusi Wong Programs at the Princess Margaret Hospital Foundation. NJLCS was funded by the State Key Program of National Natural Science of China (81230067), the National Key Basic Research Program Grant (2011CB503805), the Major Program of the National Natural Science Foundation of China (81390543). Norway study was supported by Norwegian Cancer Society, Norwegian Research Council The Shanghai Cohort Study (SCS) was supported by National Institutes of Health R01 CA144034 (PI: Yuan) and UM1 CA182876 (PI: Yuan). The Singapore Chinese Health Study (SCHS) was supported by National Institutes of Health R01 CA144034 (PI: Yuan) and UM1 CA182876 (PI: Yuan). The work in TLC study has been supported in part the James & Esther King Biomedical Research Program (09KN-15), National Institutes of Health Specialized Programs of Research Excellence (SPORE) Grant (P50 CA119997), and by a Cancer Center Support Grant (CCSG) at the H. Lee Moffitt Cancer Center and Research Institute, an NCI designated Comprehensive Cancer Center (grant number P30-CA76292) The Vanderbilt Lung Cancer Study – BioVU dataset used for the analyses described was obtained from Vanderbilt University Medical Center’s BioVU, which is supported by institutional funding, the 1S10RR025141-01 instrumentation award, and by the Vanderbilt CTSA grant UL1TR000445 from NCATS/NIH. Dr. Aldrich was supported by NIH/National Cancer Institute K07CA172294 (PI: Aldrich) and Dr. Bush was supported by NHGRI/NIH U01HG004798 (PI: Crawford). The Copenhagen General Population Study (CGPS) was supported by the Chief Physician Johan Boserup and Lise Boserup Fund, the Danish Medical Research Council and Herlev Hospital. The NELCS study: Grant Number P20RR018787 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). The MDACC study was supported in part by grants from the NIH (P50 CA070907, R01 CA176568) (to X. Wu), Cancer Prevention & Research Institute of Texas (RP130502) (to X. Wu), and The University of Texas MD Anderson Cancer Center institutional support for the Center for Translational and Public Health Genomics. The study in Lodz center was partially funded by Nofer Institute of Occupational Medicine, under task NIOM 10.13: Predictors of mortality from non-small cell lung cancer - field study. Kentucky Lung Cancer Research Initiative was supported by the Department of Defense [Congressionally Directed Medical Research Program, U.S. Army Medical Research and Materiel Command Program] under award number: 10153006 (W81XWH-11-1-0781). Views and opinions of, and endorsements by the author(s) do not reflect those of the US Army or the Department of Defense. This research was also supported by unrestricted infrastructure funds from the UK Center for Clinical and Translational Science, NIH grant UL1TR000117 and Markey Cancer Center NCI Cancer Center Support Grant (P30 CA177558) Shared Resource Facilities: Cancer Research Informatics, Biospecimen and Tissue Procurement, and Biostatistics and Bioinformatics. The Resource for the Study of Lung Cancer Epidemiology in North Trent (ReSoLuCENT) study was funded by the Sheffield Hospitals Charity, Sheffield Experimental Cancer Medicine Centre and Weston Park Hospital Cancer Charity. FT was supported by a clinical PhD fellowship funded by the Yorkshire Cancer Research/Cancer Research UK Sheffield Cancer Centre. The authors would like to thank the staff at the Respiratory Health Network Tissue Bank of the FRQS for their valuable assistance with the lung eQTL dataset at Laval University. The lung eQTL study at Laval University was supported by the Fondation de l’Institut universitaire de cardiologie et de pneumologie de Québec, the Respiratory Health Network of the FRQS, the Canadian Institutes of Health Research (MOP - 123369). Y.B. holds a Canada Research Chair in Genomics of Heart and Lung Diseases. The research undertaken by M.D.T., L.V.W. and M.S.A. was partly funded by the National Institute for Health Research (NIHR). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. M.D.T. holds a Medical Research Council Senior Clinical Fellowship (G0902313).
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Affiliation(s)
- Xuemei Ji
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, G1V 4G5, Canada
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, G1V 4G5, Canada
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Jiang Gui
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - David Qian
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Philippe Joubert
- 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
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Ivan Gorlov
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Mariella de Biasi
- Annenberg School of Communication, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Younghun Han
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Olga Gorlova
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, M5T 3L9, Canada
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 CEDEX 08, France
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, M5T 3L9, Canada
| | - Robert Carreras-Torres
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 CEDEX 08, France
| | - David C Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, 02115, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, 02115, MA, USA
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 CEDEX 08, France
| | - Geoffrey Liu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, M5T 3L9, Canada
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Herlev 2730, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200 København N, Denmark
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Ringvej 75, Copenhagen, Herlev 2730, Denmark
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, 96813, HI, USA
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, 37073, Germany
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, 37203, TN, USA
| | - William S Bush
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, 37203, TN, USA
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, 44106, OH, USA
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo, Oviedo, 33006, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Campus del Cristo s/n, Oviedo, 33006, Spain
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center, Haifa, 34361, Israel
- Faculty of Medicine, Technion, Haifa, 34361, Israel
| | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - M Dawn Teare
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, UK
| | - Lambertus A Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, 6525 EZ, The Netherlands
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, 99210-1495, WA, USA
| | - Aage Haugen
- National Institute of Occupational Health, 0033, Gydas vei 8, 0033, Oslo, Norway
| | - Stephen Lam
- British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, V5Z1L3, Canada
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, 33612, FL, USA
| | - Angeline S Andrew
- Department of Epidemiology, Geisel School of Medicine, 1 Medical Center Drive, Hanover, 03755, NH, USA
| | - 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, 101 Longmian Ave, Nanjing, 211166, PR China
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, 1 Gwanak-ro, Gwanak-gu, Seoul, 151 742, Republic of Korea
| | - Jian-Min Yuan
- University of Pittsburgh Cancer Institute, Pittsburgh, 15232, PA, USA
| | - Pier A Bertazzi
- Department of Preventive Medicine, IRCCS Foundation Ca'Granda Ospedale Maggiore Policlinico, Milan, 20133, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, 20133, Italy
| | - Angela C Pesatori
- Department of Preventive Medicine, IRCCS Foundation Ca'Granda Ospedale Maggiore Policlinico, Milan, 20133, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, 20133, Italy
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Nancy Diao
- Department of Environmental Health, Harvard School of Public Health, Boston, 02115, MA, USA
| | - Li Su
- Department of Environmental Health, Harvard School of Public Health, Boston, 02115, MA, USA
| | - Ruyang Zhang
- Department of Environmental Health, Harvard School of Public Health, Boston, 02115, MA, USA
- 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, 101 Longmian Ave, Nanjing, 211166, PR China
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, M5T 3L9, Canada
| | - Natasha Leighl
- University Health Network-The Princess Margaret Cancer Centre, 600 University Avenue, Toronto, M5G 2C4, Canada
| | - Jakob S Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, 2730, Denmark
| | - Anders Mellemgaard
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, 2730, Denmark
| | - Walid Saliba
- Clalit National Cancer Control Center, Carmel Medical Center, Haifa, 34361, Israel
- Faculty of Medicine, Technion, Haifa, 34361, Israel
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, 90033, CA, USA
| | - Lynne Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, 96813, HI, USA
| | - Ana Fernandez-Somoano
- Faculty of Medicine, University of Oviedo, Oviedo, 33006, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Campus del Cristo s/n, Oviedo, 33006, Spain
| | - Guillermo Fernandez-Tardon
- Faculty of Medicine, University of Oviedo, Oviedo, 33006, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Campus del Cristo s/n, Oviedo, 33006, Spain
| | - Erik H F M van der Heijden
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, 6525 EZ, The Netherlands
| | - Jin Hee Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Juncheng Dai
- 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, 101 Longmian Ave, Nanjing, 211166, PR China
| | - Zhibin Hu
- 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, 101 Longmian Ave, Nanjing, 211166, PR China
| | - Michael P A Davies
- Roy Castle Lung Cancer Research Programme, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, UK
| | - Michael W Marcus
- Roy Castle Lung Cancer Research Programme, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, UK
| | - Hans Brunnström
- Department of Pathology, Lund University, Lund, 222 41, Sweden
| | - Jonas Manjer
- Faculty of Medicine, Lund University, Lund, 22100, Sweden
| | - Olle Melander
- Faculty of Medicine, Lund University, Lund, 22100, Sweden
| | - David C Muller
- School of Public Health, St Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Kim Overvad
- Faculty of Medicine, Lund University, Lund, 22100, Sweden
| | | | - Rosario Tumino
- Cancer Registry and Histopathology Department, "Civic-M.P. Arezzo" Hospital, ASP, Ragusa, 97100, Italy
| | - Jennifer Doherty
- Department of Epidemiology, Geisel School of Medicine, 1 Medical Center Drive, Hanover, 03755, NH, USA
- Fred Hutchinson Cancer Research Center, Seattle, 98109-1024, WA, USA
| | - Gary E Goodman
- Fred Hutchinson Cancer Research Center, Seattle, 98109-1024, WA, USA
- Swedish Medical Group, Arnold Pavilion, Suite 200, Seattle, 98104, WA, USA
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Penella Woll
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Irene Brüske
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Germany
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, D-85764, Germany
| | - Thomas Muley
- Thoraxklinik at University Hospital Heidelberg, Heidelberg, 69126, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, 69120, Germany
| | - Angela Risch
- Cancer Cluster Salzburg, University of Salzburg, Salzburg, 5020, Austria
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, 37073, Germany
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, 901 85, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Umeå University, Umeå, 901 85, Sweden
| | | | | | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, First Floor, 800 Rose Street, Lexington, 40508, KY, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, 33612, KY, USA
| | - Ciprian Bolca
- Institute of Pneumology "Marius Nasta", Bucharest, RO-050159, Romania
| | - Ivana Holcatova
- 1st Faculty of Medicine, Charles University, Kateřinská 32, Prague, 121 08 Praha 2, Czech Republic
| | - Vladimir Janout
- 1st Faculty of Medicine, Charles University, Kateřinská 32, Prague, 121 08 Praha 2, Czech Republic
| | - Milica Kontic
- Clinical Center of Serbia, Clinic for Pulmonology, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Institute-Oncology Center, Warsaw, 02-781, Poland
| | - Anush Mukeria
- Department of Epidemiology and Prevention, Russian N.N. Blokhin Cancer Research Centre, Moscow, 115478, Russian Federation
| | - Simona Ognjanovic
- International Organization for Cancer Prevention and Research, Belgrade, 11070, Serbia
| | - Tadeusz M Orlowski
- Department of Surgery, National Tuberculosis and Lung Diseases Research Institute, Warsaw, PL-01-138, Poland
| | - Ghislaine Scelo
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 CEDEX 08, France
| | - Beata Swiatkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, 91-348, Poland
| | - David Zaridze
- Department of Epidemiology and Prevention, Russian N.N. Blokhin Cancer Research Centre, Moscow, 115478, Russian Federation
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, 5021, Norway
| | - Vidar Skaug
- National Institute of Occupational Health, 0033, Gydas vei 8, 0033, Oslo, Norway
| | - Shanbeh Zienolddiny
- National Institute of Occupational Health, 0033, Gydas vei 8, 0033, Oslo, Norway
| | - Eric J Duell
- Unit of Nutrition and Cancer, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, 08908, Spain
| | - Lesley M Butler
- University of Pittsburgh Cancer Institute, Pittsburgh, 15232, PA, USA
| | - Woon-Puay Koh
- Duke-NUS Medical School, Singapore, 119077, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, 2200, China
| | | | | | | | - David C Nickle
- Department of Genetics and Pharmacogenomics, Merck Research Laboratories, Boston, 02115-5727, MA, USA
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, St Paul's Hospital, The University of British Columbia, Vancouver, V6Z 1Y6, BC, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, GRIAC, University of Groningen, University Medical Center Groningen, Groningen, NL - 9713 GZ, The Netherlands
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Leicester Respiratory Biomedical Research Unit, National Institute for Health Research (NIHR), Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Leicester Respiratory Biomedical Research Unit, National Institute for Health Research (NIHR), Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Leicester Respiratory Biomedical Research Unit, National Institute for Health Research (NIHR), Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Dakai Zhu
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, M5S 1A8, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, M5T 1R8, ON, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M6J 1H4, ON, Canada
| | - Wei-Qi Wei
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, 37235, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 CEDEX 08, France
| | - Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03750, NH, USA.
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, 77030, TX, USA.
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Li Z, Pu Z, Fan J, Li N, Zhu M, Zhang J, Wang Y, Geng L, Cheng Y, Ma H, Jin G, Dai J, Hu Z, Shen H. Fine mapping in TERT-CLPTM1L region identified three independent lung cancer susceptibility signals: A large-scale multi-ethnic population study. Mol Carcinog 2018; 57:1289-1299. [PMID: 29809284 DOI: 10.1002/mc.22843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022]
Abstract
Genome-wide association studies (GWAS) and fine mapping studies have identified multiple lung cancer susceptibility variants in TERT-CLPTM1L region. However, it is still unclear about the relationship between these risk variants and the independent lung cancer risk signals in this region. Therefore, we evaluated the independent susceptibility signals for lung cancer and explored the potential functional variants in this region. Sequential conditional analysis was used to detect the independent susceptibility loci based on four lung cancer GWAS datasets with 12 843 lung cases and 12 639 controls. Comprehensively functional annotations were performed for each independent signal. Three independent susceptibility signals were identified in multi-ethnic population. For the first signal, rs2736100 showed the most significant association with lung cancer risk (C > A, OR = 0.82, 95%CI: 0.79-0.85, P = 1.98 × 10-25 ). Rs36019446 was the top-ranked site (A > G, OR = 0.88, 95%CI: 0.84-0.92, P = 1.74 × 10-9 ) in the second signal. For the third signal, rs326048 was the leading SNP (A > G, OR = 0.91, 95%CI: 0.87-0.95, P = 1.38 × 10-5 ). The following subgroup analysis found the same three loci among Asian population. Further, we compared the difference between various subgroup populations. Functional annotations revealed that rs2736100, rs27996 (r2 = 0.85 with rs36019446) and rs326049 (r2 = 0.73 with rs326048) could be potential functional variants in these three risk signals, respectively. In conclusion, although multiple variants have been found associated with lung cancer risk in TERT-CLPTM1L region, our findings indicated that there are three independent lung cancer susceptibility signals in this region.
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Affiliation(s)
- Zhihua Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhening Pu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingyi Fan
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ni Li
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiahui Zhang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuzhuo Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Liguo Geng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yang Cheng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
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11
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Jones CC, Bush WS, Crawford DC, Wenzlaff AS, Schwartz AG, Wiencke JK, Wrensch MR, Blot WJ, Chanock SJ, Grogan EL, Aldrich MC. Germline Genetic Variants and Lung Cancer Survival in African Americans. Cancer Epidemiol Biomarkers Prev 2017; 26:1288-1295. [PMID: 28619829 DOI: 10.1158/1055-9965.epi-16-0998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/14/2017] [Accepted: 05/17/2017] [Indexed: 11/16/2022] Open
Abstract
Background: African Americans have the highest lung cancer mortality in the United States. Genome-wide association studies (GWASs) of germline variants influencing lung cancer survival have not yet been conducted with African Americans. We examined five previously reported GWAS catalog variants and explored additional genome-wide associations among African American lung cancer cases.Methods: Incident non-small cell lung cancer cases (N = 286) in the Southern Community Cohort Study were genotyped on the Illumina HumanExome BeadChip. We used Cox proportional hazards models to estimate HRs and 95% confidence intervals (CIs) for overall mortality. Two independent African American studies (N = 316 and 298) were used for replication.Results: One previously reported variant, rs1878022 on 12q23.3, was significantly associated with mortality (HR = 0.70; 95% CI: 0.54-0.92). Replication findings were in the same direction, although attenuated (HR = 0.87 and 0.94). Meta-analysis had a HR of 0.83 (95% CI, 0.71-0.97). Analysis of common variants identified an association between chromosome 6q21.33 and mortality (HR = 0.46; 95% CI, 0.33-0.66).Conclusions: We identified an association between rs1878022 in CMKLR1 and lung cancer survival. However, our results in African Americans have a different direction of effect compared with a prior study in European Americans, suggesting a different genetic architecture or presence of gene-environment interactions. We also identified variants on chromosome 6 within the gene-rich HLA region, which has been previously implicated in lung cancer risk and survival.Impact: We found evidence that inherited genetic risk factors influence lung cancer survival in African Americans. Replication in additional populations is necessary to confirm potential genetic differences in lung cancer survival across populations. Cancer Epidemiol Biomarkers Prev; 26(8); 1288-95. ©2017 AACR.
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Affiliation(s)
- Carissa C Jones
- Department of Thoracic Surgery, Vanderbilt University Medical School, Nashville, Tennessee.,Vanderbilt Genetics Institute, Vanderbilt University Medical School, Nashville, Tennessee
| | - William S Bush
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dana C Crawford
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Angela S Wenzlaff
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - William J Blot
- Division of Epidemiology, Vanderbilt University Medical School, Nashville, Tennessee.,International Epidemiology Institute, Rockville, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Eric L Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical School, Nashville, Tennessee.,Tennessee Valley Health System Veterans Affairs, Nashville, Tennessee
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical School, Nashville, Tennessee. .,Vanderbilt Genetics Institute, Vanderbilt University Medical School, Nashville, Tennessee.,Division of Epidemiology, Vanderbilt University Medical School, Nashville, Tennessee
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12
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Dong J, Cheng Y, Zhu M, Wen Y, Wang C, Wang Y, Geng L, Shen W, Liu J, Li Z, Zhang J, Ma H, Dai J, Jin G, Hu Z, Shen H. Fine mapping of chromosome 5p15.33 identifies novel lung cancer susceptibility loci in Han Chinese. Int J Cancer 2017; 141:447-456. [PMID: 28335076 DOI: 10.1002/ijc.30702] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 03/05/2017] [Accepted: 03/07/2017] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies in European and Asian populations have consistently identified chromosome 5p15.33 as a lung cancer susceptibility region. To investigate further the genetic architecture of common variants in this region, we conducted a two-stage fine-mapping analysis discovered by targeted resequencing of 200 cases and 300 controls individually, and validated in multiethnic lung cancer Genome wide association studies (GWASs) with 12,843 cases and 12,639 controls. Two independent variants were identified in approximate conditional analysis with GCTA and consistently validated in lung cancer GWASs in both Asian and European populations. These were rs10054203 in TERT (resequencing: OR = 1.69, p = 2.70 × 10-4 ; validation: OR = 1.34, p = 2.10 × 10-23 for Asian, and OR = 1.09, p = 6.00 × 10-3 for European), and rs397640 in CLPTM1L (resequencing: OR = 0.37, p = 1.19 × 10-4 ; validation: OR = 0.75, p = 5.89 × 10-8 for Asian, and OR = 0.90, p = 2.40 × 10-2 for European). Expression quantitative trait loci analysis showed the risk allele (C) of rs10054203 was significantly associated with lower mRNA expression of CTD-2245Ef15.3 (p = 0.019) and Tubulin Polymerization-Promoting Protein (TPPP, p = 0.031) in 167 lung tissues. In conclusion, in this largest and first resequencing-based fine-mapping analysis of 5p15.33 region in Han Chinese, we identified two novel variants associated with lung cancer susceptibility. Further validation studies and functional work is required to confirm the roles of the newly discovered variants.
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Affiliation(s)
- Jing Dong
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yang Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yang Wen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yuzhuo Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Liguo Geng
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jia Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhihua Li
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jiahui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
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13
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Ribero S, Mangino M, Bataille V. Skin phenotypes can offer some insight about the association between telomere length and cancer susceptibility. Med Hypotheses 2016; 97:7-10. [PMID: 27876133 DOI: 10.1016/j.mehy.2016.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/03/2016] [Accepted: 10/18/2016] [Indexed: 11/26/2022]
Abstract
The role of telomere biology in cancer has been studied for a wide variety of different cancers but the association with telomere length has been controversial. This is because some cancers have been found to be associated with longer telomeres in circulating white cells whilst other cancer types are more common in individuals with shorter telomeres. Hence, there has been some skepticism as to whether telomere length may be helpful in estimating cancer risk. For melanoma, however, results have been fairly consistent showing that longer telomeres are associated with an increased risk. This link was first discovered because of a link between longer telomeres and a high number of naevi. In contrast, for cutaneous squamous cell carcinomas, the relationship is reversed with higher risk in individuals with shorter telomeres. Differences in skin phenotypes with the presence of high number of naevi versus photoageing with solar elastosis and solar keratoses have already been valuable for dermatologists as the former phenotype is associated with melanoma whilst the latter is more common in patients with squamous cell carcinoma of the skin. The hypothesis is that the differences in cutaneous phenotypes already observed by dermatologists for skin cancers may, in fact, be useful as well for cancer prediction in general as it may reflect underlying telomere biology. This manuscript will address the evidence for links between telomere biology, skin phenotypes and cancer risk.
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Affiliation(s)
- S Ribero
- Department of Twin Research and Genetic Epidemiology, King's College London, UK; Department of Medical Sciences, University of Turin, Turin, Italy.
| | - M Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, UK
| | - V Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, UK; Department of Dermatology, West Herts NHS Trust, Herts, UK
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14
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Zanetti KA, Wang Z, Aldrich M, Amos CI, Blot WJ, Bowman ED, Burdette L, Cai Q, Caporaso N, Chung CC, Gillanders EM, Haiman CA, Hansen HM, Henderson BE, Kolonel LN, Marchand LL, Li S, McNeill LH, Ryan BM, Schwartz AG, Sison JD, Spitz MR, Tucker M, Wenzlaff AS, Wiencke JK, Wilkens L, Wrensch MR, Wu X, Zheng W, Zhou W, Christiani D, Palmer JR, Penning TM, Rieber AG, Rosenberg L, Ruiz-Narvaez EA, Su L, Vachani A, Wei Y, Whitehead AS, Chanock SJ, Harris CC. Genome-wide association study confirms lung cancer susceptibility loci on chromosomes 5p15 and 15q25 in an African-American population. Lung Cancer 2016; 98:33-42. [PMID: 27393504 PMCID: PMC4939239 DOI: 10.1016/j.lungcan.2016.05.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 01/09/2023]
Abstract
OBJECTIVES Genome-wide association studies (GWAS) of lung cancer have identified regions of common genetic variation with lung cancer risk in Europeans who smoke and never-smoking Asian women. This study aimed to conduct a GWAS in African Americans, who have higher rates of lung cancer despite smoking fewer cigarettes per day when compared with Caucasians. This population provides a different genetic architecture based on underlying African ancestry allowing the identification of new regions and exploration of known regions for finer mapping. MATERIALS AND METHODS We genotyped 1,024,001 SNPs in 1737 cases and 3602 controls in stage 1, followed by a replication phase of 20 SNPs (p<1.51×10(-5)) in an independent set of 866 cases and 796 controls in stage 2. RESULTS AND CONCLUSION In the combined analysis, we confirmed two loci to be associated with lung cancer that achieved the threshold of genome-wide significance: 15q25.1 marked by rs2036527 (p=1.3×10(-9); OR=1.32; 95% CI=1.20-1.44) near CHRNA5, and 5p15.33 marked by rs2853677 (p=2.8×10(-9); OR=1.28; 95% CI=1.18-1.39) near TERT. The association with rs2853677 is driven by the adenocarcinoma subtype of lung cancer (p=1.3×10(-8); OR=1.37; 95% CI=1.23-1.54). No SNPs reached genome-wide significance for either of the main effect models examining smoking - cigarettes per day and current or former smoker. Our study was powered to identify strong risk loci for lung cancer in African Americans; we confirmed results previously reported in African Americans and other populations for two loci near plausible candidate genes, CHRNA5 and TERT, on 15q25.1 and 5p15.33 respectively, are associated with lung cancer. Additional work is required to map and understand the biological underpinnings of the strong association of these loci with lung cancer risk in African Americans.
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Affiliation(s)
- Krista A Zanetti
- Division of Cancer Control and Population Sciences, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Melinda Aldrich
- Division of Epidemiology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, TN 37232, USA; Department of Thoracic Surgery, Vanderbilt University Medical Center, 609 Oxford House, 1313 21st Ave South, Nashville, TN 37232-4682, USA.
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine, 1 Rope Ferry Road, Dartmouth, Lebanon, NH 03755-1404, USA.
| | - William J Blot
- Division of Epidemiology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, TN 37232, USA.
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Building 37, Room 3068A, Bethesda, MD 20892, USA.
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Qiuyin Cai
- Division of Epidemiology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, TN 37232, USA.
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Elizabeth M Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California and Norris Comprehensive Cancer Center, 1975 Zonal Avenue, Los Angeles, CA 90033, USA.
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, 505 Parnassus Ave., Room 779 M, San Francisco, San Francisco, CA 94143-00112, USA.
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California and Norris Comprehensive Cancer Center, 1975 Zonal Avenue, Los Angeles, CA 90033, USA
| | - Laurence N Kolonel
- Epidemiology Program, Cancer Research Center, University of Hawaii, 701 Ilalo Street, Honolulu, HI 96813, USA.
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, 701 Ilalo Street, Honolulu, HI 96813, USA.
| | - Shengchao Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Lorna Haughton McNeill
- Department of Health Disparities Research, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 91, Houston, TX 77030, USA.
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Building 37, Room 3068A, Bethesda, MD 20892, USA.
| | - Ann G Schwartz
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, Detroit, MI 48201, USA.
| | - Jennette D Sison
- Department of Neurological Surgery, University of California, 505 Parnassus Ave., Room 779 M, San Francisco, San Francisco, CA 94143-00112, USA.
| | - Margaret R Spitz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Mail Stop BCM225, Houston, TX 77030, USA.
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Angela S Wenzlaff
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, Detroit, MI 48201, USA.
| | - John K Wiencke
- Department of Neurological Surgery, University of California, 505 Parnassus Ave., Room 779 M, San Francisco, San Francisco, CA 94143-00112, USA.
| | - Lynne Wilkens
- Epidemiology Program, Cancer Research Center, University of Hawaii, 701 Ilalo Street, Honolulu, HI 96813, USA.
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California, 505 Parnassus Ave., Room 779 M, San Francisco, San Francisco, CA 94143-00112, USA.
| | - Xifeng Wu
- Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Unit 1340, PO Box 301439, Houston, TX 77230-1439, USA.
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, TN 37232, USA.
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - David Christiani
- Harvard School of Public Health, Massachusetts General Hospital/Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
| | - Julie R Palmer
- Slone Epidemiology Cancer Center at Boston University, 1010 Commonwealth Avenue, 4th Floor, Boston, MA 02215, USA.
| | - Trevor M Penning
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, 3535 Market Street, Mezzanine, Philadelphia PA 19104, USA; Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 3535 Market Street, Mezzanine, Philadelphia PA 19104, USA.
| | - Alyssa G Rieber
- Department of General Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.
| | - Lynn Rosenberg
- Slone Epidemiology Cancer Center at Boston University, 1010 Commonwealth Avenue, 4th Floor, Boston, MA 02215, USA.
| | - Edward A Ruiz-Narvaez
- Slone Epidemiology Cancer Center at Boston University, 1010 Commonwealth Avenue, 4th Floor, Boston, MA 02215, USA.
| | - Li Su
- Harvard School of Public Health, Massachusetts General Hospital/Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
| | - Anil Vachani
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, 3535 Market Street, Mezzanine, Philadelphia PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 3535 Market Street, Mezzanine, Philadelphia, PA 19104, USA.
| | - Yongyue Wei
- Harvard School of Public Health, Massachusetts General Hospital/Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
| | - Alexander S Whitehead
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, 3535 Market Street, Mezzanine, Philadelphia PA 19104, USA; Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 3535 Market Street, Mezzanine, Philadelphia PA 19104, USA.
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892, USA.
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Building 37, Room 3068A, Bethesda, MD 20892, USA.
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15
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Polymorphisms in human telomerase reverse transcriptase (hTERT) gene and susceptibility to gastric cancer in a Turkish population: Hospital-based case-control study. Gene 2016; 585:84-92. [PMID: 27016301 DOI: 10.1016/j.gene.2016.03.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 03/19/2016] [Indexed: 12/19/2022]
Abstract
Erosion of telomeres, tandem nucleotide repeats (TTAGGG)n that cap the end of eukaryotic chromosomes, has been related with carcinogenesis. The human telomerase reverse transcriptase (hTERT) gene is encoded the rate-limiting catalytic subunit of the telomerase complexes, which is essential for the protection of telomeric DNA length and chromosomal stability. The purpose of this study was to examine the effect of four functional single nucleotide polymorphisms (SNPs) of hTERT (rs2736109 G>A, rs2735940 T>C, rs2853669 A>G and rs2736100 T>G) on susceptibility to gastric cancer (GC) in Turkish population. The genotype frequency of hTERT rs2736109 G>A, rs2735940 T>C, rs2853669 A>G and rs2736100 T>G polymorphisms were determined by using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and TaqMan methods in 104 subjects with GC and 209 healthy control subjects. We found that hTERT rs2736109 G>A (AA+AG vs. GG OR=1.68 95% CI=1.01-2.81, P=0.04), rs2735940 T>C (CC vs. CT+TT: OR=2.53 95% CI=1.01-6.13, P=0.03), and rs2736100 T>G (TT vs. TG+GG: OR=2.27 95% CI=1.23-4.17, P=0.006) polymorphisms were associated with risk of GC. In the haplotype analysis, hTERT Grs2736109/Trs2735940/Ars2853669/Grs2736100 haplotype was also related with an increased risk of GC (OR=1.75; 95% CI: 1.05-2.93, P=0.03). Because this is the first study regarding the hTERT rs2736109 G>A, rs2735940 T>C, rs2853669 A>G and rs2736100 T>G polymorphisms and the risk of GC susceptibility in the literature, further independent studies are needed to verify our results in a larger sample sizes, as well as in patients of different populations.
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16
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David SP, Wang A, Kapphahn K, Hedlin H, Desai M, Henderson M, Yang L, Walsh KM, Schwartz AG, Wiencke JK, Spitz MR, Wenzlaff AS, Wrensch MR, Eaton CB, Furberg H, Mark Brown W, Goldstein BA, Assimes T, Tang H, Kooperberg CL, Quesenberry CP, Tindle H, Patel MI, Amos CI, Bergen AW, Swan GE, Stefanick ML. Gene by Environment Investigation of Incident Lung Cancer Risk in African-Americans. EBioMedicine 2016; 4:153-61. [PMID: 26981579 PMCID: PMC4776066 DOI: 10.1016/j.ebiom.2016.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/22/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified polymorphisms linked to both smoking exposure and risk of lung cancer. The degree to which lung cancer risk is driven by increased smoking, genetics, or gene-environment interactions is not well understood. METHODS We analyzed associations between 28 single nucleotide polymorphisms (SNPs) previously associated with smoking quantity and lung cancer in 7156 African-American females in the Women's Health Initiative (WHI), then analyzed main effects of top nominally significant SNPs and interactions between SNPs, cigarettes per day (CPD) and pack-years for lung cancer in an independent, multi-center case-control study of African-American females and males (1078 lung cancer cases and 822 controls). FINDINGS Nine nominally significant SNPs for CPD in WHI were associated with incident lung cancer (corrected p-values from 0.027 to 6.09 × 10(-5)). CPD was found to be a nominally significant effect modifier between SNP and lung cancer for six SNPs, including CHRNA5 rs2036527[A](betaSNP*CPD = - 0.017, p = 0.0061, corrected p = 0.054), which was associated with CPD in a previous genome-wide meta-analysis of African-Americans. INTERPRETATION These results suggest that chromosome 15q25.1 variants are robustly associated with CPD and lung cancer in African-Americans and that the allelic dose effect of these polymorphisms on lung cancer risk is most pronounced in lighter smokers.
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Affiliation(s)
- Sean P. David
- Division of General Medical Disciplines, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Ange Wang
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Kristopher Kapphahn
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Haley Hedlin
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Manisha Desai
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Michael Henderson
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Lingyao Yang
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Kyle M. Walsh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- Program in Cancer Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Ann G. Schwartz
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - John K. Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Margaret R. Spitz
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Angela S. Wenzlaff
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - Margaret R. Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Charles B. Eaton
- Center for Primary Care and Prevention, Department of Family Medicine, Warren Alpert Medical School of Brown University, Pawtucket, RI, United States
| | - Helena Furberg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - W. Mark Brown
- Division of Public Health Sciences, Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, NC, United States
| | - Benjamin A. Goldstein
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, United States
| | - Themistocles Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Charles L. Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | | | - Hilary Tindle
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Manali I. Patel
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Christopher I. Amos
- Departments of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | | | - Gary E. Swan
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Marcia L. Stefanick
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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Schwartz AG, Cote ML. Epidemiology of Lung Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 893:21-41. [PMID: 26667337 DOI: 10.1007/978-3-319-24223-1_2] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lung cancer continues to be one of the most common causes of cancer death despite understanding the major cause of the disease: cigarette smoking. Smoking increases lung cancer risk 5- to 10-fold with a clear dose-response relationship. Exposure to environmental tobacco smoke among nonsmokers increases lung cancer risk about 20%. Risks for marijuana and hookah use, and the new e-cigarettes, are yet to be consistently defined and will be important areas for continued research as use of these products increases. Other known environmental risk factors include exposures to radon, asbestos, diesel, and ionizing radiation. Host factors have also been associated with lung cancer risk, including family history of lung cancer, history of chronic obstructive pulmonary disease and infections. Studies to identify genes associated with lung cancer susceptibility have consistently identified chromosomal regions on 15q25, 6p21 and 5p15 associated with lung cancer risk. Risk prediction models for lung cancer typically include age, sex, cigarette smoking intensity and/or duration, medical history, and occupational exposures, however there is not yet a risk prediction model currently recommended for general use. As lung cancer screening becomes more widespread, a validated model will be needed to better define risk groups to inform screening guidelines.
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Affiliation(s)
- Ann G Schwartz
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Michele L Cote
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
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18
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Kachuri L, Amos CI, McKay JD, Johansson M, Vineis P, Bueno-de-Mesquita H, Boutron-Ruault MC, Johansson M, Quirós J, Sieri S, Travis RC, Weiderpass E, Le Marchand L, Henderson BE, Wilkens L, Goodman GE, Chen C, Doherty JA, Christiani DC, Wei Y, Su L, Tworoger S, Zhang X, Kraft P, Zaridze D, Field JK, Marcus MW, Davies MP, Hyde R, Caporaso NE, Landi MT, Severi G, Giles GG, Liu G, McLaughlin JR, Li Y, Xiao X, Fehringer G, Zong X, Denroche RE, Zuzarte PC, McPherson JD, Brennan P, Hung RJ. Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci. Carcinogenesis 2016; 37:96-105. [PMID: 26590902 PMCID: PMC4715236 DOI: 10.1093/carcin/bgv165] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/02/2015] [Accepted: 11/13/2015] [Indexed: 01/01/2023] Open
Abstract
Chromosome 5p15.33 has been identified as a lung cancer susceptibility locus, however the underlying causal mechanisms were not fully elucidated. Previous fine-mapping studies of this locus have relied on imputation or investigated a small number of known, common variants. This study represents a significant advance over previous research by investigating a large number of novel, rare variants, as well as their underlying mechanisms through telomere length. Variants for this fine-mapping study were identified through a targeted deep sequencing (average depth of coverage greater than 4000×) of 576 individuals. Subsequently, 4652 SNPs, including 1108 novel SNPs, were genotyped in 5164 cases and 5716 controls of European ancestry. After adjusting for known risk loci, rs2736100 and rs401681, we identified a new, independent lung cancer susceptibility variant in LPCAT1: rs139852726 (OR = 0.46, P = 4.73×10(-9)), and three new adenocarcinoma risk variants in TERT: rs61748181 (OR = 0.53, P = 2.64×10(-6)), rs112290073 (OR = 1.85, P = 1.27×10(-5)), rs138895564 (OR = 2.16, P = 2.06×10(-5); among young cases, OR = 3.77, P = 8.41×10(-4)). In addition, we found that rs139852726 (P = 1.44×10(-3)) was associated with telomere length in a sample of 922 healthy individuals. The gene-based SKAT-O analysis implicated TERT as the most relevant gene in the 5p15.33 region for adenocarcinoma (P = 7.84×10(-7)) and lung cancer (P = 2.37×10(-5)) risk. In this largest fine-mapping study to investigate a large number of rare and novel variants within 5p15.33, we identified novel lung and adenocarcinoma susceptibility loci with large effects and provided support for the role of telomere length as the potential underlying mechanism.
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Affiliation(s)
- Linda Kachuri
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5T 3L9, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7, Canada
| | - Christopher I. Amos
- Department of Community and Family Medicine, Center for Genomic Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03766, USA
| | - James D. McKay
- International Agency for Research on Cancer, Lyon, CEDEX 08, 69372, France
| | - Mattias Johansson
- International Agency for Research on Cancer, Lyon, CEDEX 08, 69372, France
| | - Paolo Vineis
- Human Genetics Foundation (HuGeF), 10126Torino, Italy
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - H.Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, 3584 CX Utrecht, The Netherlands
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London SW7 2AZ, UK
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Marie-Christine Boutron-Ruault
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), U1018, Lifestyle, Genes and Health: Integrative Trans-Generational Epidemiology, 94805 Villejuif, France
- Université Paris Sud, UMRS 1018 94805, Villejuif, France
- Institut Gustave RoussyF-94805, Villejuif, France
| | - Mikael Johansson
- Department of Radiation Sciences, Umeå University, Umeå SE-901 87, Sweden
| | - J.Ramón Quirós
- Public Health Directorate Asturias, CP 33006 Oviedo, Spain
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, 9037 Tromsø, Norway
- Department of Research, Cancer Registry of Norway, 0379 Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
- Genetic Epidemiology Group, Folkhälsan Research Center, Helsinki FI-00014, Finland
| | | | | | - Lynne Wilkens
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Gary E. Goodman
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jennifer A. Doherty
- Department of Community and Family Medicine, Center for Genomic Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03766, USA
| | - David C. Christiani
- Departments of Environmental Health and Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Yongyue Wei
- Departments of Environmental Health and Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Li Su
- Departments of Environmental Health and Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shelley Tworoger
- Departments of Environmental Health and Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter Kraft
- Departments of Biostatistics and Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - David Zaridze
- Russian Cancer Research Center, Moscow 115478, Russia
| | - John K. Field
- Roy Castle Lung Cancer Research Programme, University of Liverpool Cancer Research Centre Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Michael W. Marcus
- Roy Castle Lung Cancer Research Programme, University of Liverpool Cancer Research Centre Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Michael P.A. Davies
- Roy Castle Lung Cancer Research Programme, University of Liverpool Cancer Research Centre Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Russell Hyde
- Roy Castle Lung Cancer Research Programme, University of Liverpool Cancer Research Centre Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Gianluca Severi
- Human Genetics Foundation (HuGeF), 10126Torino, Italy
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), U1018, Lifestyle, Genes and Health: Integrative Trans-Generational Epidemiology, 94805 Villejuif, France
- Université Paris Sud, UMRS 1018 94805, Villejuif, France
- Institut Gustave RoussyF-94805, Villejuif, France
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne 3010, Australia
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne 3010, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne 3004, Australia
| | - Geoffrey Liu
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7, Canada
- Ontario Cancer Institute, Princess Margaret Cancer Center, Toronto, Ontario M5G 0A3, Canada
| | - John R. McLaughlin
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5T 3L9, Canada
- Public Health Ontario, Toronto, Ontario M5G 1V2, Canada, and
| | - Yafang Li
- Department of Community and Family Medicine, Center for Genomic Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03766, USA
| | - Xiangjun Xiao
- Department of Community and Family Medicine, Center for Genomic Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03766, USA
| | - Gord Fehringer
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5T 3L9, Canada
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5T 3L9, Canada
| | - Robert E. Denroche
- Genome Technologies, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Philip C. Zuzarte
- Genome Technologies, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - John D. McPherson
- Genome Technologies, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, CEDEX 08, 69372, France
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5T 3L9, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7, Canada
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Fiscella K, Winters P, Farah S, Sanders M, Mohile SG. Do Lung Cancer Eligibility Criteria Align with Risk among Blacks and Hispanics? PLoS One 2015; 10:e0143789. [PMID: 26618478 PMCID: PMC4664289 DOI: 10.1371/journal.pone.0143789] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/10/2015] [Indexed: 12/31/2022] Open
Abstract
Background Black patients have higher lung cancer risk despite lower pack years of smoking. We assessed lung cancer risk by race, ethnicity, and sex among a nationally representative population eligible for lung cancer screening based on Medicare criteria. Methods We used data from the National Health and Nutrition Examination Survey, 2007–2012 to assess lung cancer risk by sex, race and ethnicity among persons satisfying Medicare age and pack-year smoking eligibility criteria for lung cancer screening. We assessed Medicare eligibility based on age (55–77 years) and pack-years (≥30). We assessed 6-year lung cancer risk using a risk prediction model from Prostate, Lung, Colorectal and Ovarian Cancer Screening trial that was modified in 2012 (PLCOm2012). We compared the proportions of eligible persons by sex, race and ethnicity using Medicare criteria with a risk cut-point that was adjusted to achieve comparable total number of persons eligible for screening. Results Among the 29.7 million persons aged 55–77 years who ever smoked, we found that 7.3 million (24.5%) were eligible for lung cancer screening under Medicare criteria. Among those eligible, Blacks had statistically significant higher (4.4%) and Hispanics lower lung cancer risk (1.2%) than non-Hispanic Whites (3.2%). At a cut-point of 2.12% risk for lung screening eligibility, the percentage of Blacks and Hispanics showed statistically significant changes. Blacks eligible rose by 48% and Hispanics eligible declined by 63%. Black men and Hispanic women were affected the most. There was little change in eligibility among Whites. Conclusion Medicare eligibility criteria for lung cancer screening do not align with estimated risk for lung cancer among Blacks and Hispanics. Data are urgently needed to determine whether use of risk-based eligibility screening improves lung cancer outcomes among minority patients.
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Affiliation(s)
- Kevin Fiscella
- Department of Family Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY, United States of America
- * E-mail:
| | - Paul Winters
- Department of Family Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Subrina Farah
- Department of Family Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Mechelle Sanders
- Department of Family Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Supriya G. Mohile
- Department of Medicine, Division of Oncology, University of Rochester Medical Center and the Wilmot Cancer Center, Rochester, NY, United States of America
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Ji X, Gui J, Han Y, Brennan P, Li Y, McKay J, Caporaso NE, Bertazzi PA, Landi MT, Amos CI. The role of haplotype in 15q25.1 locus in lung cancer risk: results of scanning chromosome 15. Carcinogenesis 2015; 36:1275-83. [PMID: 26282330 PMCID: PMC4635666 DOI: 10.1093/carcin/bgv118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/16/2015] [Accepted: 08/06/2015] [Indexed: 11/13/2022] Open
Abstract
The role of haplotypes and the interaction of haplotypes and smoking in lung cancer risk have not been well characterized. We analyzed data from an Italian population-based, case-control study with 1815 lung cancer patients and 1959 healthy controls in discovery, and performed a validation using a case-control study with 2983 lung cancer patients and 3553 healthy controls of European ancestry for replication. Sliding window haplotype analysis within chromosome 15, evaluating 4722250 haplotypes and pair-wise haplotype analysis identified that CHRNA5 rs588765-rs16969968 was the most significant haplotype associated with lung cancer risk (omnibus P = 8.35×10(-15) in discovery and 7.26×10(-14) in replication), and improved the prediction of case status over that provided by the individual SNPs rs16969968 or rs588765 (likelihood ratio test P = 0.006 for rs16969968 and 3.83×10(-14) for rs588765 in discovery, 0.009 for rs16969968 and 4.62×10(-13) for rs588765 in replication, compared with rs588765-rs16969968). Compared with the wild-type homozygous diplotype, CA/CA homozygote exhibited an approximately 2-fold increase risk for lung cancer (OR = 2.12; 95% CI 1.46-3.07 in discovery, and OR = 2.01; 95% CI 1.51-2.67 in replication). Even among never-smokers, CA/CA homozygote showed an increased risk of lung cancer with borderline significance in discovery (adjusted OR = 1.75, 95% CI 0.96-3.19) and statistical significance in replication (adjusted OR = 2.10, 95% CI 1.12-3.96), compared with combined genotypes (CG/CG + CG/TG). Accordingly, rs588765-rs16969968 may be a genetic marker to lung cancer risk, even among never-smokers.
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Affiliation(s)
- Xuemei Ji
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
- International Agency for Research on Cancer, 69372 Lyon, France
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences and Community Health, Department of Preventive Medicine, University of Milan, Fondazione IRCCS Ca’ Granda Policlinico Hospital, 20122 Milan, Italy
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
- International Agency for Research on Cancer, 69372 Lyon, France
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences and Community Health, Department of Preventive Medicine, University of Milan, Fondazione IRCCS Ca’ Granda Policlinico Hospital, 20122 Milan, Italy
| | - Younghun Han
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
- International Agency for Research on Cancer, 69372 Lyon, France
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences and Community Health, Department of Preventive Medicine, University of Milan, Fondazione IRCCS Ca’ Granda Policlinico Hospital, 20122 Milan, Italy
| | - Paul Brennan
- International Agency for Research on Cancer, 69372 Lyon, France
| | - Yafang Li
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
- International Agency for Research on Cancer, 69372 Lyon, France
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences and Community Health, Department of Preventive Medicine, University of Milan, Fondazione IRCCS Ca’ Granda Policlinico Hospital, 20122 Milan, Italy
| | - James McKay
- International Agency for Research on Cancer, 69372 Lyon, France
| | - Neil E. Caporaso
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pier Alberto Bertazzi
- Department of Clinical Sciences and Community Health, Department of Preventive Medicine, University of Milan, Fondazione IRCCS Ca’ Granda Policlinico Hospital, 20122 Milan, Italy
| | - Maria Teresa Landi
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher I. Amos
- *To whom correspondence should be addressed. Tel: +1 603 603 650 1729. Fax: +1 603 653 6698;
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Xu ZW, Wang GN, Dong ZZ, Li TH, Cao C, Jin YH. CHRNA5 rs16969968 Polymorphism Association with Risk of Lung Cancer - Evidence from 17,962 Lung Cancer Cases and 77,216 Control Subjects. Asian Pac J Cancer Prev 2015; 16:6685-90. [DOI: 10.7314/apjcp.2015.16.15.6685] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Jin G, Zhu M, Yin R, Shen W, Liu J, Sun J, Wang C, Dai J, Ma H, Wu C, Yin Z, Huang J, Higgs BW, Xu L, Yao Y, Christiani DC, Amos CI, Hu Z, Zhou B, Shi Y, Lin D, Shen H. Low-frequency coding variants at 6p21.33 and 20q11.21 are associated with lung cancer risk in Chinese populations. Am J Hum Genet 2015; 96:832-40. [PMID: 25937444 DOI: 10.1016/j.ajhg.2015.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/24/2015] [Indexed: 11/29/2022] Open
Abstract
Genome-wide association studies have successfully identified a subset of common variants associated with lung cancer risk. However, these variants explain only a fraction of lung cancer heritability. It has been proposed that low-frequency or rare variants might have strong effects and contribute to the missing heritability. To assess the role of low-frequency or rare variants in lung cancer development, we analyzed exome chips representing 1,348 lung cancer subjects and 1,998 control subjects during the discovery stage and subsequently evaluated promising associations in an additional 4,699 affected subjects and 4,915 control subjects during the replication stages. Single-variant and gene-based analyses were carried out for coding variants with a minor allele frequency less than 0.05. We identified three low-frequency missense variants in BAT2 (rs9469031, c.1544C>T [p.Pro515Leu]; odds ratio [OR] = 0.55, p = 1.28 × 10(-10)), FKBPL (rs200847762, c.410C>T [p.Pro137Leu]; OR = 0.25, p = 9.79 × 10(-12)), and BPIFB1 (rs6141383, c.850G>A [p.Val284Met]; OR = 1.72, p = 1.79 × 10(-7)); these variants were associated with lung cancer risk. rs9469031 in BAT2 and rs6141383 in BPIFB1 were also associated with the age of onset of lung cancer (p = 0.001 and 0.006, respectively). BAT2 and FKBPL at 6p21.33 and BPIFB1 at 20q11.21 were differentially expressed in lung tumors and paired normal tissues. Gene-based analysis revealed that FKBPL, in which two independent variants were identified, might account for the association with lung cancer risk at 6p21.33. Our results highlight the important role low-frequency variants play in lung cancer susceptibility and indicate that candidate genes at 6p21.33 and 20q11.21 are potentially biologically relevant to lung carcinogenesis.
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Affiliation(s)
- Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention, and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jia Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jie Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chen Wu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110001, China
| | | | | | - Lin Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | | | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Christopher I Amos
- Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03755, USA
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention, and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110001, China
| | - Yongyong Shi
- Ministry of Education Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongxin Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention, and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China.
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23
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Etokebe GE, Zienolddiny S, Kupanovac Z, Enersen M, Balen S, Flego V, Bulat-Kardum L, Radojčić-Badovinac A, Skaug V, Bakke P, Haugen A, Dembic Z. Association of the FAM46A gene VNTRs and BAG6 rs3117582 SNP with non small cell lung cancer (NSCLC) in Croatian and Norwegian populations. PLoS One 2015; 10:e0122651. [PMID: 25884493 PMCID: PMC4401550 DOI: 10.1371/journal.pone.0122651] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 02/11/2015] [Indexed: 12/25/2022] Open
Abstract
We analyzed for associations between a variable number of tandem repeat (VNTR) polymorphism in the Family with sequence similarity 46, member A (FAM46A) gene and a single nucleotide polymorphism (rs3117582) in the BCL2-Associated Athanogene 6 (BAG6) with non small cell lung cancer in Croatian and Norwegian subjects. A total of 503 (262 Croatian and 241Norwegian) non small cell lung cancer patients and 897 controls (568 Croatian and 329 Norwegian) were analyzed. We found that the frequency of allele b (three VNTR repeats) of FAM46A gene was significantly increased in the patients compared to the healthy controls in the Croatian and the combined Croatian and Norwegian subjects. Genotype frequencies of cd (four and five VNTR repeats) and cc (four VNTR repeats homozygote) of the FAM46A gene were significantly decreased in the patients compared to the healthy controls in the Croatian and Norwegian subjects, respectively. Logistic regression analyses revealed FAM46A genotype cc to be an independent predictive factor for non small cell lung cancer risk in the Norwegian subjects after adjustment for age, gender and smoking status. This is the first study to suggest an association between the FAM46A gene VNTR polymorphisms and non small cell lung cancer. We found also that BAG6 rs3117582 SNP was associated with non small cell lung cancer in the Norwegian subjects and the combined Croatian-Norwegian subjects corroborating the earlier finding that BAG6 rs3117582 SNP was associated with lung cancer in Europeans. Logistic regression analyses revealed that genotypes and alleles of BAG6 were independent predictive factor for non small cell lung cancer risk in the Norwegian and combined Croatian-Norwegian subjects, after adjustment for age and gender.
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Affiliation(s)
- Godfrey Essien Etokebe
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- * E-mail:
| | - Shanbeh Zienolddiny
- Department of Chemical and Biological Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Zeljko Kupanovac
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Section of Pulmology, Department of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | - Morten Enersen
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Sanja Balen
- Institute for Transfusion Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | - Veljko Flego
- Section of Pulmology, Department of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | - Ljiljana Bulat-Kardum
- Section of Pulmology, Department of Internal Medicine, Clinical Hospital Center, University of Rijeka, Rijeka, Croatia
| | | | - Vidar Skaug
- Department of Chemical and Biological Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Per Bakke
- Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Aage Haugen
- Department of Chemical and Biological Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Zlatko Dembic
- Institute for Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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24
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Yang H, Li J, Tang R, Liu Y, Shao Y, Huang Q, Shi J. Telomere reverse transcriptase (TERT) rs2735940 increases cancer risk. Med Sci Monit 2015; 21:612-6. [PMID: 25716168 PMCID: PMC4354426 DOI: 10.12659/msm.893087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background Telomerase reverse transcriptase (TERT) rs2735940 polymorphism was found to be associated with increased cancer risk. However, recent studies reported controversial results. The aim of our study was to detect its relationship with cancer risk. Material/Methods EMBASE and PubMed databases were searched for all publications until October 2014. ORs and 95% CIs were applied to investigate the association in the random-effects model. Results Thirteen case-control studies with 19385 cases and 17558 controls were included in this study. We found a significant association between cancer risk and TERT rs2735940 polymorphism (OR=1.06, 95% CI 1.02–1.11, P=0.005). In the subgroup analysis by ethnicity, a marginal association was found in Caucasians (OR=1.05, 95% CI 1.00–1.10, P=0.05), but not in Asians (OR=1.01, 95% CI 0.82–1.24, P=0.93). In the subgroup analysis by cancer site, this polymorphism was significantly associated with lung cancer risk (OR=1.08, 95% CI 1.02–1.13, P=0.004). Conclusions TERT rs2735940 polymorphism was significantly associated with cancer risk, especially lung cancer.
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Affiliation(s)
- Hui Yang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shanxi, China (mainland)
| | - Jing Li
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shanxi, China (mainland)
| | - Ruihua Tang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shanxi, China (mainland)
| | - Yaxiong Liu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shanxi, China (mainland)
| | - Yan Shao
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shanxi, China (mainland)
| | - Qingsheng Huang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shanxi, China (mainland)
| | - Junling Shi
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shanxi, China (mainland)
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25
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Abstract
Regular smoking is the major risk factor for cardiovascular disease and cancers, and thus is one of the most preventable causes of morbidity and mortality worldwide. Intake of nicotine, its central nervous system effects, and its metabolism are regulated by biological pathways; some of these are well known, but others are not. Genetic studies offer a method for developing insights into the genes contributing to those pathways. In recent years, large genome-wide association study (GWAS) meta-analyses have consistently revealed that the strongest genetic contribution to smoking-related traits comes from variation in the nicotinic receptor subunit genes. Many other genes, including those coding for enzymes involved in nicotine metabolism, also have been implicated. However, the proportion of phenotypic variance explained by the identified genetic variants is very modest. This review intends to cover progress made in genetics and genetic epidemiology of smoking behavior in recent years, and focuses on studies revealing the nicotinic receptor gene cluster on chromosome 15q25. Evidence supporting the involvement of a novel pathway in the shared pathophysiology of nicotine dependence and schizophrenia is also briefly reviewed. A summary of the current knowledge on gene-environment interactions involved in smoking behavior is included.
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26
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Eldholm V, Haugen A, Zienolddiny S. CTCF mediates the TERT enhancer-promoter interactions in lung cancer cells: identification of a novel enhancer region involved in the regulation of TERT gene. Int J Cancer 2013; 134:2305-13. [PMID: 24174344 DOI: 10.1002/ijc.28570] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/19/2013] [Accepted: 10/18/2013] [Indexed: 01/18/2023]
Abstract
Telomerase activation is a hallmark of cancer. Although the regulation of the telomerase reverse transcriptase catalytic subunit (TERT), the rate-limiting factor for telomerase activity, has been studied intensively it remains incompletely understood. In cells devoid of telomerase activity, TERT is embedded in a region of condensed chromatin and the chromatin remodeling protein CCCTC-binding factor (CTCF) has been implicated in the inhibition of TERT expression. The importance of TERT activation for cellular immortalization and carcinogenesis is attested by the fact that the gene is expressed in more than 90% of immortal cell lines and tumors and that gain of TERT is the most frequent amplification event in early stage lung cancer. This study was designed to study the mechanisms of regulation of the TERT gene expression by the CTCF transcription factor in three human lung cancer cell lines, A427, A549 and H838. Depletion of CTCF by siRNA resulted in reduced TERT mRNA levels in two (A427 and A549) of the three cell lines. A novel enhancer element was identified approximately 4.5 kb upstream of the TERT transcription start site. Chromatin immunoprecipitation experiments revealed recruitment of CTCF to this enhancer element. Chromosome conformation capture experiments demonstrated the presence of CTCF-dependent chromatin loops between this enhancer element and the TERT proximal promoter in A427 and A549 cell lines. In summary, the results show that CTCF plays an important role in maintaining TERT expression in a subset of human lung cancer cell lines. This role may be due to CTCF-dependent enhancer-promoter interactions.
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Affiliation(s)
- Vegard Eldholm
- Department of Chemical and Biological Work Environment, National Institute of Occupational Health, Oslo, Norway
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27
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Powell CA, Halmos B, Nana-Sinkam SP. Update in lung cancer and mesothelioma 2012. Am J Respir Crit Care Med 2013; 188:157-66. [PMID: 23855692 PMCID: PMC3778761 DOI: 10.1164/rccm.201304-0716up] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/01/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Charles A Powell
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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