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Association between polymorphism in CDKN2B-AS1 gene and its interaction with smoking on the risk of lung cancer in a Chinese population. Hum Genomics 2019; 13:58. [PMID: 31775885 PMCID: PMC6880550 DOI: 10.1186/s40246-019-0240-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 01/06/2023] Open
Abstract
Background Long non-coding RNAs became the hot spots in the carcinogenesis of various tumors. This case-control study evaluated the association between the rs2151280 in lncRNA CDKN2B-AS1 and lung cancer risk. Methods This study included 507 lung cancer patients and 542 healthy individuals. Odds ratios and their 95% confidence intervals were calculated by unconditional logistic regression analysis to evaluate the association between the rs2151280 and lung cancer risk. Results Compared with individuals carrying TT genotype, individuals carrying CC genotype of rs2151280 had a decreased risk of lung cancer (OR = 0.640, 95%CI = 0.421–0.972, P = 0.036). In the recessive model, rs2151280 CC genotype was observed to reduce the risk of lung cancer (OR = 0.684). C allele was associated with non-small cell lung cancer risk (OR = 0.674). The rs2151280 was significantly associated with lung adenocarcinoma risk (CCvsTT: OR = 0.567, 95%CI = 0.333–0.965, P = 0.037; CCvsTC+TT: OR = 0.543, 95%CI 0.330–0.893, P = 0.016, respectively). However, there was no significant association between rs2151280 and lung squamous cell carcinoma risk in five models. The quantitative analysis suggested that there were no significant interactions of rs2151280 with smoking exposure to lung cancer susceptibility. Conclusions This hospital-based case-control study suggested that CDKN2B-AS1 rs2151280 T>C was associated with the risk of lung cancer.
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Translational Molecular Approaches in Substance Abuse Research. Handb Exp Pharmacol 2019; 258:31-60. [PMID: 31628598 DOI: 10.1007/164_2019_259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Excessive abuse of psychoactive substances is one of the leading contributors to morbidity and mortality worldwide. In this book chapter, we review translational research strategies that are applied in the pursuit of new and more effective therapeutics for substance use disorder (SUD). The complex, multidimensional nature of psychiatric disorders like SUD presents difficult challenges to investigators. While animal models are critical for outlining the mechanistic relationships between defined behaviors and genetic and/or molecular changes, the heterogeneous pathophysiology of brain diseases is uniquely human, necessitating the use of human studies and translational research schemes. Translational research describes a cross-species approach in which findings from human patient-based data can be used to guide molecular genetic investigations in preclinical animal models in order to delineate the mechanisms of reward circuitry changes in the addicted state. Results from animal studies can then inform clinical investigations toward the development of novel treatments for SUD. Here we describe the strategies that are used to identify and functionally validate genetic variants in the human genome which may contribute to increased risk for SUD, starting from early candidate gene approaches to more recent genome-wide association studies. We will next examine studies aimed at understanding how transcriptional and epigenetic dysregulation in SUD can persistently alter cellular function in the disease state. In our discussion, we then focus on examples from the literature illustrating molecular genetic methodologies that have been applied to studies of different substances of abuse - from alcohol and nicotine to stimulants and opioids - in order to exemplify how these approaches can both delineate the underlying molecular systems driving drug addiction and provide insights into the genetic basis of SUD.
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Triphuridet N, Henschke C. Landscape on CT screening for lung cancer in Asia. LUNG CANCER (AUCKLAND, N.Z.) 2019; 10:107-124. [PMID: 31686936 PMCID: PMC6777900 DOI: 10.2147/lctt.s192643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022]
Abstract
Lung cancer remains the leading cause of cancer incidence and mortality worldwide. Approximately 60% of the world's new cases of lung cancer and deaths from it are expected in Asia in 2018. Currently, lung cancer screening using low-dose computed tomography (LDCT) is recommended for heavy smokers in North America, Europe and some countries in Asia. Tobacco smoking being the major risk factor for lung cancer, but in Asia, lung cancer in never-smokers (LCINS) is also a concern. This paper reviews on lung cancer incidence, mortality, etiology, smoking in Asia, and systematic reviews on LDCT lung cancer screening studies, including ongoing projects and recommendation on lung cancer screening in Asia. Some of the earliest studies of LDCT lung cancer screening worldwide were in Asia. Many countries in Asia have developed LDCT screening studies in various high-risk participants. Currently, there are several ongoing large-scale lung cancer screening trials to evaluate the efficacy of LDCT screening for never-smokers and light smokers, as well as heavy smokers, and to evaluate the feasibility of population-based LDCT lung cancer screening.
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Affiliation(s)
- Natthaya Triphuridet
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Claudia Henschke
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Bhat GR, Bhat A, Verma S, Sethi I, Shah R, Sharma V, Dar KA, Abrol D, Kaneez S, Kaul S, Ganju R, Kumar R. Association of newly identified genetic variant rs2853677 of TERT with non-small cell lung cancer and leukemia in population of Jammu and Kashmir, India. BMC Cancer 2019; 19:493. [PMID: 31126249 PMCID: PMC6533689 DOI: 10.1186/s12885-019-5685-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 05/08/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Telomere genetics has recently been emerged as an important field in molecular oncology. Various genome-wide association studies in different population groups have revealed that polymorphisms in Telomere maintenance gene (TERT) gene located on 5p15.33 is associated with susceptibility to leukemia and lung cancer risk. However, association of TERT with leukemia and lung cancer risk in north Indian population groups is still unknown. This study observed the association between genetic variant rs2853677 of TERT and leukemia and lung cancer in the state of Jammu and Kashmir, India. METHODS A total of 781 subjects, out of which 381 cases (203 leukemic patients and 178 non-small cell lung cancer patients NSCLC) and 400 healthy controls were recruited for the study. Genetic variant rs2853677of TERT was detected using the real-time and Taqman Chemistry. Hardy-Weinberg Equilibrium was assessed using the chi square test. The allele and genotype- specific risks were estimated as odds ratio with 95% confidence interval. RESULTS We observed that variant rs2853677 was strongly associated with lung cancer and leukemia risk with an odds ratio (OR) =1.8 (1.03-3.2 at 95% CI); p value (adjusted) = 0.03; odds ratio (OR) =2.9 (1.4-5.5.at 95% CI); p value (adjusted) = 0.002, respectively. CONCLUSION The results of this study suggested that rs2853677 of TERT signifies association in multiple cancers and suggests that it can become potential marker for diagnosis of non-small cell lung cancer and leukemia. The study will provide an insight in understanding the genetic etiology and highlights the role of telomere-associated pathways in non-small cell lung cancer and leukemia. However, it would be quite interesting to explore the contribution of this variant in other cancers as well.
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Affiliation(s)
- Gh Rasool Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Amrita Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Sonali Verma
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Itty Sethi
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ruchi Shah
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Khursheed A Dar
- Chest Disease Hospital, Government Medical College, Srinagar, India
| | - Deepak Abrol
- Department of Radiotherapy, Government Medical College, Jammu, India
| | - Subiya Kaneez
- Department of Radiotherapy, Government Medical College, Srinagar, India
| | - Sandeep Kaul
- Department of surgical Oncology, Shri Mata Vaishno Devi Narayana Super speciality hospital, kata, India
| | - Ramesh Ganju
- Department of Pathology, College of Medicine, The OHIO State University, Columbus, USA
| | - Rakesh Kumar
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
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Precision oncology of lung cancer: genetic and genomic differences in Chinese population. NPJ Precis Oncol 2019; 3:14. [PMID: 31069257 PMCID: PMC6499836 DOI: 10.1038/s41698-019-0086-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/15/2019] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the lung cancer genome has experienced rapid growth over the past decade. Genome-wide association studies and sequencing studies have identified dozens of genetic variants and somatic mutations implicated in the development of lung cancer in both Chinese and Caucasian populations. With the accumulating evidence, heterogeneities in lung cancer susceptibility were observed in different ethnicities. In this review, the progress on germline-based genetic variants and somatic-based genomic mutations associated with lung cancer and the differences between Chinese and Caucasian populations were systematically summarized. In the analysis of the genetic predisposition to lung cancer, 6 susceptibility loci were shared by Chinese and Caucasian populations (3q28, 5p15, 6p21, 9p21.3, 12q13.13 and 15q25), 14 loci were specific to the Chinese population (1p36.32, 5q31.1, 5q32, 6p21.1, 6q22.2, 6p21.32, 7p15.3, 10p14, 10q25.2, 12q23.1, 13q22, 17q24.3, 20q13.2, and 22q12), and 12 loci were specific to the Caucasian population (1p31.1, 2q32.1, 6q27, 8p21.1, 8p12, 10q24.3, 11q23.3, 12p13.33, 13q13.1, 15q21.1, 20q13.33 and 22q12.1). In the analysis of genomic and somatic alterations, different mutation rates were observed for EGFR (Chinese: 39–59% vs. TCGA: 14%), KRAS (Chinese: 7–11% vs. TCGA: 31%), TP53 (Chinese: 44% vs. TCGA: 53%), CDKN2A (Chinese: 22% vs. TCGA: 15%), NFE2L2 (Chinese: 28% vs. TCGA: 17%), STK11 (Chinese: 4–7% vs. TCGA: 16%), KEAP1 (Chinese: 3–5% vs. TCGA: 18%), and NF1 (Chinese: <2% vs. TCGA: 12%). In addition, frequently amplified regions encompassing genes involved in cytoskeletal organization or focal adhesion were identified only in Chinese patients. These results provide a comprehensive description of the genetic and genomic differences in lung cancer susceptibility between Chinese and Caucasian populations and may contribute to the development of precision medicine for lung cancer treatment and prevention.
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Integrated Somatic and Germline Whole-Exome Sequencing Analysis in Women with Lung Cancer after a Previous Breast Cancer. Cancers (Basel) 2019; 11:cancers11040441. [PMID: 30925779 PMCID: PMC6520745 DOI: 10.3390/cancers11040441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/12/2019] [Accepted: 03/25/2019] [Indexed: 12/11/2022] Open
Abstract
Women treated for breast cancer (BC) are at risk of developing secondary tumors, such as lung cancer (LC). Since rare germline variants have been linked to multiple cancer development, we hypothesized that BC survivors might be prone to develop LC as a result of harboring rare variants. Sixty patients with LC with previous BC (the study population; SP) and 53 women with either BC or LC and no secondary cancer (control population; CP) were enrolled. Whole exome sequencing was performed in both tumors and unaffected tissues from 28/60 SP patients, and in germline DNA from 32/53 CP. Candidate genes were validated in the remaining individuals from both populations. We found two main mutational signature profiles: S1 (C>T) in all BCs and 16/28 LCs, and S2 (C>A) which is strongly associated with smoking, in 12/28 LCs. The burden test over rare germline variants in S1-LC vs CP identified 248 genes. Validation confirmed GSN as significantly associated with LC in never-smokers. In conclusion, our data suggest two signatures involved in LC onset in women with previous BC. One of these signatures is linked to smoking. Conversely, regardless of smoking habit, in a subgroup of BC survivors genetic susceptibility may contribute to LC risk.
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Li Y, Xiang C, Shen N, Deng L, Luo X, Yuan P, Ji Z, Li J, Cheng L. Functional polymorphisms on chromosome 5p15.33 disturb telomere biology and confer the risk of non‐small cell lung cancer in Chinese population. Mol Carcinog 2019; 58:913-921. [DOI: 10.1002/mc.22980] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/10/2019] [Accepted: 01/18/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ying Li
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Cheng Xiang
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Na Shen
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Lingyan Deng
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xia Luo
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Peihong Yuan
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Zhi Ji
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jiaoyuan Li
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Liming Cheng
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Huyghe JR, Bien SA, Harrison TA, Kang HM, Chen S, Schmit SL, Conti DV, Qu C, Jeon J, Edlund CK, Greenside P, Wainberg M, Schumacher FR, Smith JD, Levine DM, Nelson SC, Sinnott-Armstrong NA, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Bamia C, Banbury BL, Baron JA, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Chirlaque MD, Cho SH, Connolly CM, Cross AJ, Cuk K, Curtis KR, de la Chapelle A, Doheny KF, Duggan D, Easton DF, Elias SG, Elliott F, English DR, Feskens EJM, Figueiredo JC, Fischer R, FitzGerald LM, Forman D, Gala M, Gallinger S, Gauderman WJ, Giles GG, Gillanders E, Gong J, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hampel H, Harlid S, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Hunter DJ, Ibañez-Sanz G, Idos GE, Ingersoll R, Jackson RD, Jacobs EJ, Jenkins MA, Joshi AD, Joshu CE, Keku TO, Key TJ, Kim HR, Kobayashi E, Kolonel LN, Kooperberg C, Kühn T, Küry S, Kweon SS, Larsson SC, Laurie CA, Le Marchand L, Leal SM, Lee SC, Lejbkowicz F, Lemire M, Li CI, Li L, Lieb W, Lin Y, Lindblom A, Lindor NM, Ling H, Louie TL, Männistö S, Markowitz SD, Martín V, Masala G, McNeil CE, Melas M, Milne RL, Moreno L, Murphy N, Myte R, Naccarati A, Newcomb PA, Offit K, Ogino S, Onland-Moret NC, Pardini B, Parfrey PS, Pearlman R, Perduca V, Pharoah PDP, Pinchev M, Platz EA, Prentice RL, Pugh E, Raskin L, Rennert G, Rennert HS, Riboli E, Rodríguez-Barranco M, Romm J, Sakoda LC, Schafmayer C, Schoen RE, Seminara D, Shah M, Shelford T, Shin MH, Shulman K, Sieri S, Slattery ML, Southey MC, Stadler ZK, Stegmaier C, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Thomas SS, Toland AE, Trichopoulou A, Ulrich CM, Van Den Berg DJ, van Duijnhoven FJB, Van Guelpen B, van Kranen H, Vijai J, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Win AK, Wolf CR, Wolk A, Woods MO, Wu AH, Zaidi SH, Zanke BW, Zhang Q, Zheng W, Scacheri PC, Potter JD, Bassik MC, Kundaje A, Casey G, Moreno V, Abecasis GR, Nickerson DA, Gruber SB, Hsu L, Peters U. Discovery of common and rare genetic risk variants for colorectal cancer. Nat Genet 2019; 51:76-87. [PMID: 30510241 PMCID: PMC6358437 DOI: 10.1038/s41588-018-0286-6] [Citation(s) in RCA: 326] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/22/2018] [Indexed: 12/17/2022]
Abstract
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
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Affiliation(s)
- Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jihyoun Jeon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peyton Greenside
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Michael Wainberg
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David M Levine
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Kristin Anderson
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Bamia
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | | | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, CA, USA
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria-Dolores Chirlaque
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, Murcia, Spain
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - Charles M Connolly
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Katarina Cuk
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, AZ, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Faye Elliott
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rocky Fischer
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
| | - Liesel M FitzGerald
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - David Forman
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John S Grove
- University of Hawaii Cancer Research Center, Honolulu, HI, USA
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robert W Haile
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Philipp Hofer
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Wan-Ling Hsu
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Gemma Ibañez-Sanz
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Gastroenterology Department, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Gregory E Idos
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roxann Ingersoll
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca D Jackson
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Emiko Kobayashi
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laurence N Kolonel
- Office of Public Health Studies, University of Hawaii Manoa, Honolulu, HI, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Flavio Lejbkowicz
- The Clalit Health Services, Personalized Genomic Service, Carmel, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Li Li
- Center for Community Health Integration and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Hua Ling
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tin L Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University, and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Vicente Martín
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Biomedicine Institute (IBIOMED), University of León, León, Spain
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute of Cancer Research, Prevention and Clinical Network - ISPRO, Florence, Italy
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Marilena Melas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robin Myte
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Patrick S Parfrey
- The Clinical Epidemiology Unit, Memorial University Medical School, Newfoundland, Canada
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France
- CESP (Inserm U1018), Facultés de Medicine Université Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Miguel Rodríguez-Barranco
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Escuela Andaluza de Salud Pública. Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada, Universidad de Granada, Granada, Spain
| | - Jane Romm
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Tameka Shelford
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Korea
| | | | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Duncan C Thomas
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sushma S Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - David J Van Den Berg
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Henk van Kranen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aung Ko Win
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - C Roland Wolf
- School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Syed H Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Brent W Zanke
- Division of Hematology, University of Toronto, Toronto, Ontario, Canada
| | - Qing Zhang
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
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Ding X, Chen Y, Yang J, Li G, Niu H, He R, Zhao J, Ning H. Characteristics of Familial Lung Cancer in Yunnan-Guizhou Plateau of China. Front Oncol 2018; 8:637. [PMID: 30619770 PMCID: PMC6305406 DOI: 10.3389/fonc.2018.00637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
Background: Lung cancer has inherited susceptibility and show familial aggregation, the characteristics of familial lung cancer exhibit population heterogeneity. Despite previous studies, familial lung cancer in China's Yunnan-Guizhou plateau remains understudied. Methods: Between 2015 and 2017, 1,023 lung cancer patients (residents of Yunnan-Guizhou plateau) were enrolled with no limitation on other parameters, 152 subjects had familial lung cancer. Clinicopathologic parameters were analyzed and compared, 4,754 lung cancer patients from NCI-GDC were used to represent a general population. Results: Familial lung cancer (FLC) subjects showed unique characters: early-onset; increased rate of female, adenocarcinoma, stage IV and other cancer history; unbalance in anatomic sites; all ruling out significant difference in smoking status. Unbalanced distribution of co-existing diseases or symptoms was also discovered. FLC patients were more likely to develop benign lesions (polyps, nodules, cysts) early in life, especially early-growth of multiple pulmonary nodules at higher frequency. Typical diseases with family history like diabetes and hypertension were also increased in FLC population. Compared to GDC data, our subject population was younger: the age peak of our FLC group was in 50-59; our sporadic group had an age peak around 60; while GDC patients' age peak was in 60-69. Importantly, the biggest difference happened in age 40-49: our FLC group and sporadic group had 3 times and 2 times higher ratio than GDC population, respectively. Moreover, the age peaks of our FLC males and FLC females were both in 50-59; while our sporadic females had the age peak in 50-59, much earlier than sporadic males (around 60-69); reflecting gender-specific or age-specific characters in our subject population. Conclusions: Familial lung cancer in China's Yunnan-Guizhou plateau showed unique clinicopathologic characters, differences were found in gender, age, histologic type, TNM stage and co-existing diseases or symptoms. Identification of hereditary factors which lead to increased lung cancer risk will be a challenge of both scientific and clinical significance.
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Affiliation(s)
- Xiaojie Ding
- Key Laboratory of Lung Cancer Research of Kunming Medical University, Kunming, China.,Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
| | - Ying Chen
- Key Laboratory of Lung Cancer Research of Kunming Medical University, Kunming, China.,Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
| | - Jiapeng Yang
- Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
| | - Guangjian Li
- Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
| | - Huatao Niu
- Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
| | - Rui He
- Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
| | - Jie Zhao
- Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
| | - Huanqi Ning
- Yunnan Cancer Hospital and The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
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Esai Selvan M, Klein RJ, Gümüş ZH. Rare, Pathogenic Germline Variants in Fanconi Anemia Genes Increase Risk for Squamous Lung Cancer. Clin Cancer Res 2018; 25:1517-1525. [PMID: 30425093 DOI: 10.1158/1078-0432.ccr-18-2660] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/05/2018] [Accepted: 11/08/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Lung cancer is the leading cause of cancer deaths worldwide, with substantially better prognosis in early-stage as opposed to late-stage disease. Identifying genetic factors for lung squamous cell carcinoma (SqCC) risk will enable their use in risk stratification, and personalized intensive surveillance, early detection, and prevention strategies for high-risk individuals. EXPERIMENTAL DESIGN We analyzed whole-exome sequencing datasets of 318 cases and 814 controls (discovery cohort) and then validated our findings in an independent cohort of 444 patients and 3,479 controls (validation cohort), all of European descent. We also combined all the samples from both cohorts, which, after principal component analysis (PCA) and population stratification, included 765 cases and 4,344 controls (combined cohort). We focused on rare, pathogenic variants found in the ClinVar database and used penalized logistic regression to identify genes in which such variants are enriched in cases. All statistical tests were two-sided. RESULTS We observed an overall enrichment of rare, deleterious germline variants in Fanconi anemia genes in cases with SqCC [joint analysis odds ratio (OR) = 3.08; P = 1.4e-09; 95% confidence interval (CI), 2.2-4.3]. Consistent with previous studies, BRCA2 in particular exhibited an increased overall burden of rare, deleterious variants (joint OR = 3.2; P = 8.7e-08; 95% CI, 2.1-4.7). More importantly, rare, deleterious germline variants were enriched in Fanconi anemia genes even without the BRCA2 rs11571833 variant that is strongly enriched in lung SqCC cases (joint OR = 2.76; P = 7.0e-04; 95% CI, 1.6-4.7). CONCLUSIONS These findings can be used toward the development of a genetic diagnostic test in the clinic to identify SqCC high-risk individuals, who can benefit from personalized programs, improving prognosis.
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Affiliation(s)
- Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
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Chen YX, Guo Y, Dong SS, Chen XF, Chen JB, Zhang YJ, Yao S, Thynn HN, Zhi L, Yang TL. Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females. J Cancer 2018; 9:3858-3866. [PMID: 30410588 PMCID: PMC6218761 DOI: 10.7150/jca.22855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 02/24/2018] [Indexed: 12/14/2022] Open
Abstract
Although genome-wide association studies (GWASs) have identified some risk single-nucleotide polymorphisms in East Asian never-smoking females, the unexplained missing heritability is still required to be investigated. Runs of homozygosity (ROHs) are thought to be a type of genetic variation acting on human complex traits and diseases. We detected ROHs in 8,881 East Asian never-smoking women. The summed ROHs were used to fit a logistic regression model which noteworthily revealed a significant association between ROHs and the decreased risk of lung cancer (P < 0.05). We identified 4 common ROHs regions located at 2p22.1, which were significantly associated with decreased risk of lung cancer (P = 2.00 × 10-4 - 1.35 × 10-4). Functional annotation was conducted to investigate the regulatory function of ROHs. The common ROHs were overlapped with potential regulatory elements, such as active epigenome elements and chromatin states in lung-derived cell lines. SOS1 and ARHGEF33 were significantly up-regulated as the putative target genes of the identified ROHs in lung cancer samples according to the analysis of differently expressed genes. Our results suggest that ROHs could act as recessive contributing factors and regulatory elements to influence the risk of lung cancer in never-smoking East Asian females.
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Affiliation(s)
- Yi-Xiao Chen
- Department of Joint Surgery, Honghui Hospital; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, P. R. China.,Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
| | - Liqiang Zhi
- Department of Joint Surgery, Honghui Hospital; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Tie-Lin Yang
- Department of Joint Surgery, Honghui Hospital; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, P. R. China.,Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, P. R. China
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Planchard D, Popat S, Kerr K, Novello S, Smit EF, Faivre-Finn C, Mok TS, Reck M, Van Schil PE, Hellmann MD, Peters S. Metastatic non-small cell lung cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 2018; 29:iv192-iv237. [PMID: 30285222 DOI: 10.1093/annonc/mdy275] [Citation(s) in RCA: 1415] [Impact Index Per Article: 235.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- D Planchard
- Department of Medical Oncology, Thoracic Group, Gustave-Roussy Villejuif, France
| | - S Popat
- Royal Marsden Hospital, London
| | - K Kerr
- Aberdeen Royal Infirmary, Aberdeen University Medical School, Aberdeen, UK
| | - S Novello
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - E F Smit
- Thoracic Oncology Service, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - C Faivre-Finn
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - T S Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - M Reck
- LungenClinic Airway Research Center North (ARCN), German Center for Lung Research, Grosshansdorf, Germany
| | - P E Van Schil
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital and Antwerp University, Antwerp, Belgium
| | | | - S Peters
- Medical Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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64
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Ferreiro-Iglesias A, Lesseur C, McKay J, Hung RJ, Han Y, Zong X, Christiani D, Johansson M, Xiao X, Li Y, Qian DC, Ji X, Liu G, Caporaso N, Scelo G, Zaridze D, Mukeriya A, Kontic M, Ognjanovic S, Lissowska J, Szołkowska M, Swiatkowska B, Janout V, Holcatova I, Bolca C, Savic M, Ognjanovic M, Bojesen SE, Wu X, Albanes D, Aldrich MC, Tardon A, Fernandez-Somoano A, Fernandez-Tardon G, Le Marchand L, Rennert G, Chen C, Doherty J, Goodman G, Bickeböller H, Wichmann HE, Risch A, Rosenberger A, Shen H, Dai J, Field JK, Davies M, Woll P, Teare MD, Kiemeney LA, van der Heijden EHFM, Yuan JM, Hong YC, Haugen A, Zienolddiny S, Lam S, Tsao MS, Johansson M, Grankvist K, Schabath MB, Andrew A, Duell E, Melander O, Brunnström H, Lazarus P, Arnold S, Slone S, Byun J, Kamal A, Zhu D, Landi MT, Amos CI, Brennan P. Fine mapping of MHC region in lung cancer highlights independent susceptibility loci by ethnicity. Nat Commun 2018; 9:3927. [PMID: 30254314 PMCID: PMC6156406 DOI: 10.1038/s41467-018-05890-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/30/2018] [Indexed: 12/19/2022] Open
Abstract
The basis for associations between lung cancer and major histocompatibility complex genes is not completely understood. Here the authors further consider genetic variation within the MHC region in lung cancer patients and identify independent associations within HLA genes that explain MHC lung cancer associations in Europeans and Asian populations. Lung cancer has several genetic associations identified within the major histocompatibility complex (MHC); although the basis for these associations remains elusive. Here, we analyze MHC genetic variation among 26,044 lung cancer patients and 20,836 controls densely genotyped across the MHC, using the Illumina Illumina OncoArray or Illumina 660W SNP microarray. We impute sequence variation in classical HLA genes, fine-map MHC associations for lung cancer risk with major histologies and compare results between ethnicities. Independent and novel associations within HLA genes are identified in Europeans including amino acids in the HLA-B*0801 peptide binding groove and an independent HLA-DQB1*06 loci group. In Asians, associations are driven by two independent HLA allele sets that both increase risk in HLA-DQB1*0401 and HLA-DRB1*0701; the latter better represented by the amino acid Ala-104. These results implicate several HLA–tumor peptide interactions as the major MHC factor modulating lung cancer susceptibility.
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Affiliation(s)
- Aida Ferreiro-Iglesias
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 cedex 08, France
| | - Corina Lesseur
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 cedex 08, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 cedex 08, France
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Sinai Health System, University of Toronto, Toronto, M5G 1X5, Canada
| | - Younghun Han
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute of Sinai Health System, University of Toronto, Toronto, M5G 1X5, Canada
| | - David Christiani
- Department of Environmental Health, Harvard TH Chan School of Public Health, Massachusetts General Hospital/ Harvard Medical School, Boston, 02115, MA, USA
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 cedex 08, France
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - David C Qian
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Xuemei Ji
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Geoffrey Liu
- Lunenfeld-Tanenbaum Research Institute of Sinai Health System, University of Toronto, Toronto, M5G 1X5, Canada
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892-9768, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 cedex 08, France
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, 115478, Russian Federation
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow, 115478, Russian Federation
| | | | - Simona Ognjanovic
- International Organization for Cancer Prevention and Research, Belgrade, 11070, Serbia
| | - Jolanta Lissowska
- M. Sklodowska-Curie Cancer Center, Institute of Oncology, Warsaw, 02-034, Poland
| | - Małgorzata Szołkowska
- Department of Pathology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, 01-138, Poland
| | - Beata Swiatkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, 91-348, Poland
| | - Vladimir Janout
- Faculty of Medicine, University of Olomouc, Olomouc, 701 03, Czech Republic
| | - Ivana Holcatova
- 2nd Faculty of Medicine, Institute of Public Health and Preventive Medicine, Charles University, Prague, CZ 128 00, Czech Republic
| | - Ciprian Bolca
- Institute of Pneumology "Marius Nasta", Bucharest, RO-050159, Romania
| | - Milan Savic
- Department of Thoracic Surgery Clinical Center of Serbia Belgrade, Belgrade, 11000, Serbia
| | - Miodrag Ognjanovic
- International Organization for Cancer Prevention and Research, Belgrade, 11070, Serbia
| | - Stig Egil Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen, 2730, Denmark.,Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, 2730, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2730, Denmark
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892-9768, MD, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, 37232-4682, TA, USA
| | - Adonina Tardon
- University of Oviedo and CIBERESP, Faculty of Medicine, Oviedo, 33006, Spain
| | | | | | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, 96813, HI, USA
| | - Gadi Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, 3525433, Israel
| | - Chu Chen
- Department of Epidemiology, University of Washington School of Public Health and Community Medicine, Seattle, 98195, WA, USA
| | - Jennifer Doherty
- Department of Epidemiology, University of Washington School of Public Health and Community Medicine, Seattle, 98195, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | | | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, 37073, Germany
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig Maximilians University, Munich, D-85764, Germany.,Helmholtz Center Munich, Institute of Epidemiology 2, Munich, D-85764, Germany.,Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, D-80333, Germany
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, 5020, Austria.,Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, 69120, Germany.,German Center for Lung Research (DZL), Heidelberg, 69121, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, 37073, Germany
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, L3 9TA, UK
| | - Michael Davies
- Institute of Translational Medicine, University of Liverpool, Liverpool, L3 9TA, UK
| | - Penella Woll
- Department of Oncology, University of Sheffield, Sheffield, S10 2RX, UK
| | - M Dawn Teare
- School of Health and Related Research, University Of Sheffield, England, S1 4DA, UK
| | | | | | - Jian-Min Yuan
- University of Pittsburgh Cancer Institute, Pittsburgh, 15232, PA, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, 110-799, Republic of Korea
| | - Aage Haugen
- National Institute of Occupational Health, Oslo, N-0033, Norway
| | | | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, V5Z 1M9, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Mikael Johansson
- Department of Radiation Sciences, Umeå University, Umeå, 901 85, Sweden
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, 901 85, Sweden
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, 33612, FL, USA
| | - Angeline Andrew
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Eric Duell
- Unit of Nutrition and Cancer, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, 08908, Spain
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö, 221 00, Sweden.,Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Hans Brunnström
- Laboratory Medicine Region Skåne, Department of Clinical Sciences Lund, Pathology, Lund University, Lund, 221 00, Sweden
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, 99202, WA, USA
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, 40536-0098, KY, USA
| | - Stacey Slone
- University of Kentucky, Markey Cancer Center, Lexington, 40536-0098, KY, USA
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Dakai Zhu
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, 20892-9768, MD, USA
| | - Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, 03755, NH, USA
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, 69372 cedex 08, France.
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65
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Byun J, Schwartz AG, Lusk C, Wenzlaff AS, de Andrade M, Mandal D, Gaba C, Yang P, You M, Kupert EY, Anderson MW, Han Y, Li Y, Qian D, Stilp A, Laurie C, Nelson S, Zheng W, Hung RJ, Gaborieau V, Mckay J, Brennan P, Caporaso NE, Landi MT, Wu X, McLaughlin JR, Brhane Y, Bossé Y, Pinney SM, Bailey-Wilson JE, Amos CI. Genome-wide association study of familial lung cancer. Carcinogenesis 2018; 39:1135-1140. [PMID: 29924316 PMCID: PMC6148967 DOI: 10.1093/carcin/bgy080] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/12/2018] [Accepted: 06/18/2018] [Indexed: 12/27/2022] Open
Abstract
To identify genetic variation associated with lung cancer risk, we performed a genome-wide association analysis of 685 lung cancer cases that had a family history of two or more first or second degree relatives compared with 744 controls without lung cancer that were genotyped on an Illumina Human OmniExpressExome-8v1 array. To ensure robust results, we further evaluated these findings using data from six additional studies that were assembled through the Transdisciplinary Research on Cancer of the Lung Consortium comprising 1993 familial cases and 33 690 controls. We performed a meta-analysis after imputation of all variants using the 1000 Genomes Project Phase 1 (version 3 release date September 2013). Analyses were conducted for 9 327 222 SNPs integrating data from the two sources. A novel variant on chromosome 4p15.31 near the LCORL gene and an imputed rare variant intergenic between CDKN2A and IFNA8 on chromosome 9p21.3 were identified at a genome-wide level of significance for squamous cell carcinomas. Additionally, associations of CHRNA3 and CHRNA5 on chromosome 15q25.1 in sporadic lung cancer were confirmed at a genome-wide level of significance in familial lung cancer. Previously identified variants in or near CHRNA2, BRCA2, CYP2A6 for overall lung cancer, TERT, SECISPB2L and RTEL1 for adenocarcinoma and RAD52 and MHC for squamous carcinoma were significantly associated with lung cancer.
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Affiliation(s)
- Jinyoung Byun
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Christine Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | | | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Colette Gaba
- University of Toledo Dana Cancer Center, Toledo, OH, USA
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | - Younghun Han
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - Yafang Li
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - David Qian
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
| | - Adrienne Stilp
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Cathy Laurie
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Sarah Nelson
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Wenying Zheng
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Valerie Gaborieau
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - James Mckay
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xifeng Wu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Yonathan Brhane
- Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Susan M Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Joan E Bailey-Wilson
- National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Christopher I Amos
- Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
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66
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Yang C, Stueve TR, Yan C, Rhie SK, Mullen DJ, Luo J, Zhou B, Borok Z, Marconett CN, Offringa IA. Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell epigenomes. Epigenomics 2018; 10:1167-1187. [PMID: 30212242 DOI: 10.2217/epi-2018-0003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
AIM To identify functional lung adenocarcinoma (LUAD) risk SNPs. MATERIALS & METHODS Eighteen validated LUAD risk SNPs (p ≤ 5 × 10-8) and 930 SNPs in high linkage disequilibrium (r2 > 0.5) were integrated with epigenomic information from primary human alveolar epithelial cells. Enhancer-associated SNPs likely affecting transcription factor-binding sites were predicted. Three SNPs were functionally investigated using luciferase assays, expression quantitative trait loci and cancer-specific expression. RESULTS Forty-seven SNPs mapped to putative enhancers; 11 located to open chromatin. Of these, seven altered predicted transcription factor-binding motifs. Rs6942067 showed allele-specific luciferase expression and expression quantitative trait loci analysis indicates that it influences expression of DCBLD1, a gene that encodes an unknown membrane protein and is overexpressed in LUAD. CONCLUSION Integration of candidate LUAD risk SNPS with epigenomic marks from normal alveolar epithelium identified numerous candidate functional LUAD risk SNPs including rs6942067, which appears to affect DCBLD1 expression. Data deposition: Data are provided in GEO record GSE84273.
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Affiliation(s)
- Chenchen Yang
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Theresa Ryan Stueve
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA.,Department of Preventive Medicine, University of Southern California, CA 90089, USA
| | - Chunli Yan
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Suhn K Rhie
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Daniel J Mullen
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Jiao Luo
- Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Department of Medicine, Division of Pulmonary & Critical Care & Sleep Medicine, University of Southern California, CA 90089, USA
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA.,Department of Medicine, Division of Pulmonary & Critical Care & Sleep Medicine, University of Southern California, CA 90089, USA.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, CA 90089, USA
| | - Zea Borok
- Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA.,Department of Medicine, Division of Pulmonary & Critical Care & Sleep Medicine, University of Southern California, CA 90089, USA.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, CA 90089, USA
| | - Crystal N Marconett
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
| | - Ite A Offringa
- Department of Surgery, University of Southern California, CA 90089, USA.,Department of Biochemistry & Molecular Medicine, University of Southern California, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, CA 90089, USA
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67
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O’Brien TD, Jia P, Aldrich MC, Zhao Z. Lung Cancer: One Disease or Many. Hum Hered 2018; 83:65-70. [PMID: 29864749 PMCID: PMC6261707 DOI: 10.1159/000488942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/03/2018] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE Lung cancer is classified as a single entity comprised of multiple histological subtypes. But how similar are these subtypes on a genetic level? This paper aims to address this question through a concise overview of germline and somatic differences between small cell lung cancer, lung adenocarcinoma, and lung squamous cell carcinoma. METHODS We reveal the weak overlap found between these 3 lung cancer subtypes using published data from one of the largest germline genetic studies on lung cancer to date and somatic mutation data from Catalogue of Somatic Mutations in Cancer (COSMIC). RESULTS These data indicate that these 3 subtypes share very little with each other at the genetic level. At the germline SNP level, only 24 independent SNPs from 2 chromosomes were shared across all 3 subtypes. We also demonstrate that only 30 unique cancer-specific mutations overlap the 3 subtypes from COSMIC, and that this is fewer than overlapping mutations chosen at random. Finally, we show that only 3 somatic mutational signatures are shared between these 3 subtypes. CONCLUSION This paper highlights that these 3 lung cancer subtypes may be distinct diseases at the genetic level. In the era of precision medicine, we feel that these genomic differences will be of utmost importance in the choice of lung cancer therapy in the future.
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Affiliation(s)
- Timothy D. O’Brien
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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68
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Wang Z, Wei Y, Zhang R, Su L, Gogarten SM, Liu G, Brennan P, Field JK, McKay JD, Lissowska J, Swiatkowska B, Janout V, Bolca C, Kontic M, Scelo G, Zaridze D, Laurie CC, Doheny KF, Pugh EK, Marosy BA, Hetrick KN, Xiao X, Pikielny C, Hung RJ, Amos CI, Lin X, Christiani DC. Multi-Omics Analysis Reveals a HIF Network and Hub Gene EPAS1 Associated with Lung Adenocarcinoma. EBioMedicine 2018; 32:93-101. [PMID: 29859855 PMCID: PMC6021270 DOI: 10.1016/j.ebiom.2018.05.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
Recent technological advancements have permitted high-throughput measurement of the human genome, epigenome, metabolome, transcriptome, and proteome at the population level. We hypothesized that subsets of genes identified from omic studies might have closely related biological functions and thus might interact directly at the network level. Therefore, we conducted an integrative analysis of multi-omic datasets of non-small cell lung cancer (NSCLC) to search for association patterns beyond the genome and transcriptome. A large, complex, and robust gene network containing well-known lung cancer-related genes, including EGFR and TERT, was identified from combined gene lists for lung adenocarcinoma. Members of the hypoxia-inducible factor (HIF) gene family were at the center of this network. Subsequent sequencing of network hub genes within a subset of samples from the Transdisciplinary Research in Cancer of the Lung-International Lung Cancer Consortium (TRICL-ILCCO) consortium revealed a SNP (rs12614710) in EPAS1 associated with NSCLC that reached genome-wide significance (OR = 1.50; 95% CI: 1.31-1.72; p = 7.75 × 10-9). Using imputed data, we found that this SNP remained significant in the entire TRICL-ILCCO consortium (p = .03). Additional functional studies are warranted to better understand interrelationships among genetic polymorphisms, DNA methylation status, and EPAS1 expression.
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Affiliation(s)
- Zhaoxi Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yongyue Wei
- Department of Epidemiology, Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruyang Zhang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Su
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephanie M Gogarten
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - Paul Brennan
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - James D McKay
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - Vladimir Janout
- Department of Epidemiology and Public Health, University of Ostrava, University of Olomouc, Olomouc, Czech Republic
| | - Ciprian Bolca
- Thoracic Surgery Division, "Marius Nasta" National Institute of Pneumology, Bucharest, Romania
| | - Milica Kontic
- Clinic of Pulmonology, Clinical Center of Serbia (KCS), Belgrade, Serbia
| | - Ghislaine Scelo
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Cathy C Laurie
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth K Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Beth A Marosy
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kurt N Hetrick
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Claudio Pikielny
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 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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70
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Cui P, Zhao Y, Chu X, He N, Zheng H, Han J, Song F, Chen K. SNP rs2071095 in LincRNA H19 is associated with breast cancer risk. Breast Cancer Res Treat 2018; 171:161-171. [PMID: 29737472 DOI: 10.1007/s10549-018-4814-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/03/2018] [Indexed: 01/05/2023]
Abstract
PURPOSE An increasing number of long intergenic non-coding RNAs (lincRNAs) appear to play critical roles in cancer development and progression. To assess the association between SNPs that reside in regions of lincRNAs and breast cancer risk, we performed a large case-control study in China. METHODS We carried out a two-stage case-control study including 2881 breast cancer cases and 3220 controls. In stage I, we genotyped 17 independent (r2 < 0.5) SNPs located in 6 tumor-related lincRNAs by using the TaqMan platform. In stage II, SNPs potentially associated with breast cancer risk were replicated in an independent population. Quantitative real-time PCR was used to measure H19 levels in tissues from 228 breast cancer patients with different genotypes. RESULTS We identified 2 SNPs significantly associated with breast cancer risk in stage I (P < 0.05), but not significantly replicated in stage II. We combined the data from stage I and stage II, and found that, compared with the rs2071095 CC genotype, AA and CA + AA genotypes were associated with significantly decreased risk of breast cancer (adjusted OR 0.83, 95% CI 0.69-0.99; adjusted OR 0.88, 95% CI 0.80-0.98, respectively). Stratified analyses showed that rs2071095 was associated with breast cancer risk in estrogen receptor (ER)-positive patients (P = 0.002), but not in ER-negative ones (P = 0.332). Expression levels of H19 in breast cancer cases with AA genotype were significantly lower than those with CC genotype. CONCLUSIONS We identified that rs2071095 may contribute to the susceptibility of breast cancer in Chinese women via affecting H19 expression. The mechanisms underlying the association remain to be investigated.
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Affiliation(s)
- Ping Cui
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy in Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy in Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy in Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Na He
- Department of Cancer Biobank, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Centre of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy in Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Fengju Song
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy in Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China.
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy in Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China.
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71
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Zanetti D, Weale ME. Transethnic differences in GWAS signals: A simulation study. Ann Hum Genet 2018; 82:280-286. [PMID: 29733446 DOI: 10.1111/ahg.12251] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 01/15/2018] [Accepted: 03/14/2018] [Indexed: 02/01/2023]
Abstract
Genome-wide association studies (GWASs) have allowed researchers to identify thousands of single nucleotide polymorphisms (SNPs) and other variants associated with particular complex traits. Previous studies have reported differences in the strength and even the direction of GWAS signals across different populations. These differences could be due to a combination of (1) lack of power, (2) allele frequency differences, (3) linkage disequilibrium (LD) differences, and (4) true differences in causal variant effect sizes. To determine whether properties (1)-(3) on their own might be sufficient to explain the patterns previously noted in strong GWAS signals, we simulated case-control data of European, Asian and African ancestry, applying realistic allele frequencies and LD from 1000 Genomes data but enforcing equal causal effect sizes across populations. Much of the observed differences in strong GWAS signals could indeed be accounted for by allele frequency and LD differences, enhanced by the Euro-centric SNP bias and lower SNP coverage found in older GWAS panels. While we cannot rule out a role for true transethnic effect size differences, our results suggest that strong causal effects may be largely shared among human populations, motivating the use of transethnic data for fine-mapping.
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Affiliation(s)
- Daniela Zanetti
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, CA, USA.,Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
| | - Michael E Weale
- Department of Medical & Molecular Genetics, King's College London, London, UK
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72
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Kennedy AE, Ozbek U, Dorak MT. What has GWAS done for HLA and disease associations? Int J Immunogenet 2018; 44:195-211. [PMID: 28877428 DOI: 10.1111/iji.12332] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/16/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022]
Abstract
The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations. Another layer of complexity is provided to the region by the extreme structural variation and copy number variations. While the HLA-B gene has the highest number of alleles, the HLA-DR/DQ subregion is structurally most variable and shows the highest number of disease associations. Reliance on a single reference sequence has complicated the design, execution and analysis of GWAS for the MHC region and not infrequently, the MHC region has even been excluded from the analysis of GWAS data. Here, we contrast features of the MHC region with the rest of the genome and highlight its complexities, including its functional polymorphisms beyond those determined by single nucleotide polymorphisms or single amino acid residues. One of the several issues with customary GWAS analysis is that it does not address this additional layer of polymorphisms unique to the MHC region. We highlight alternative approaches that may assist with the analysis of GWAS data from the MHC region and unravel associations with all functional polymorphisms beyond single SNPs. We suggest that despite already showing the highest number of disease associations, the true extent of the involvement of the MHC region in disease genetics may not have been uncovered.
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Affiliation(s)
- A E Kennedy
- Center for Research Strategy, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - U Ozbek
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M T Dorak
- Head of School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Kingston-upon-Thames, UK
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73
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Bossé Y, Amos CI. A Decade of GWAS Results in Lung Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:363-379. [PMID: 28615365 PMCID: PMC6464125 DOI: 10.1158/1055-9965.epi-16-0794] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Genome-wide association studies (GWAS) were successful to identify genetic factors robustly associated with lung cancer. This review aims to synthesize the literature in this field and accelerate the translation of GWAS discoveries into results that are closer to clinical applications. A chronologic presentation of published GWAS on lung cancer susceptibility, survival, and response to treatment is presented. The most important results are tabulated to provide a concise overview in one read. GWAS have reported 45 lung cancer susceptibility loci with varying strength of evidence and highlighted suspected causal genes at each locus. Some genetic risk loci have been refined to more homogeneous subgroups of lung cancer patients in terms of histologic subtypes, smoking status, gender, and ethnicity. Overall, these discoveries are an important step for future development of new therapeutic targets and biomarkers to personalize and improve the quality of care for patients. GWAS results are on the edge of offering new tools for targeted screening in high-risk individuals, but more research is needed if GWAS are to pay off the investment. Complementary genomic datasets and functional studies are needed to refine the underlying molecular mechanisms of lung cancer preliminarily revealed by GWAS and reach results that are medically actionable. Cancer Epidemiol Biomarkers Prev; 27(4); 363-79. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec, Canada.
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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74
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Xu Y, Wang Y, Liu H, Kang X, Li W, Wei Q. Genetic variants of genes in the Notch signaling pathway predict overall survival of non-small cell lung cancer patients in the PLCO study. Oncotarget 2018; 7:61716-61727. [PMID: 27557513 PMCID: PMC5308685 DOI: 10.18632/oncotarget.11436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/11/2016] [Indexed: 12/17/2022] Open
Abstract
The Notch signaling pathway has been shown to have biological significance and therapeutic application in non-small cell lung cancer (NSCLC). We hypothesize that genetic variants of genes in the Notch signaling pathway are associated with overall survival (OS) of NSCLC patients. To test this hypothesis, we performed multivariate Cox proportional hazards regression analysis to evaluate associations of 19,571 single nucleotide polymorphisms (SNPs) in 132 Notch pathway genes with OS of 1,185 NSCLC patients available from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial. We found that five potentially functional tagSNPs in four genes (i.e., ADAM12 rs10794069 A > G, DTX1 rs1732793 G > A, TLE1 rs199731120 C > CA, TLE1 rs35970494 T > TC and E2F3 rs3806116 G > T) were associated with a poor OS, with a variant-allele attributed hazards ratio (HR) of 1.27 [95% confidence interval (95% CI) = 1.13–1.42, P = 3.62E-05], 1.30 (1.14–1.49, 8.16E-05), 1.40 (1.16–1.68, 3.47E-04), 1.27 (1.11–1.44, 3.38E-04), and 1.21 (1.09–1.33, 2.56E-04), respectively. Combined analysis of these five risk genotypes revealed that the genetic score 0–5 was associated with the adjusted HR in a dose-response manner (Ptrend = 3.44E-13); individuals with 2–5 risk genotypes had an adjusted HR of 1.56 (1.34–1.82, 1.46E-08), compared with those with 0–1 risk genotypes. Larger studies are needed to validate our findings.
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Affiliation(s)
- Yinghui Xu
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozheng Kang
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Thoracic Surgery I, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Wei Li
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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O'Brien TD, Jia P, Caporaso NE, Landi MT, Zhao Z. Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels. Genome Med 2018; 10:16. [PMID: 29486777 PMCID: PMC5828003 DOI: 10.1186/s13073-018-0522-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/13/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). These subtypes are mainly classified by physiological and pathological characteristics, although there is increasing evidence of genetic and molecular differences as well. Although some work has been done at the somatic level to explore the genetic and biological differences among subtypes, little work has been done that interrogates these differences at the germline level to characterize the unique and shared susceptibility genes for each subtype. METHODS We used single-nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) of European samples to interrogate the similarity of the subtypes at the SNP, gene, pathway, and regulatory levels. We expanded these genotyped SNPs to include all SNPs in linkage disequilibrium (LD) using data from the 1000 Genomes Project. We mapped these SNPs to several lung tissue expression quantitative trait loci (eQTL) and enhancer datasets to identify regulatory SNPs and their target genes. We used these genes to perform a biological pathway analysis for each subtype. RESULTS We identified 8295, 8734, and 8361 SNPs with moderate association signals for LUAD, LUSC, and SCLC, respectively. Those SNPs had p < 1 × 10- 3 in the original GWAS or were within LD (r2 > 0.8, Europeans) to the genotyped SNPs. We identified 215, 320, and 172 disease-associated genes for LUAD, LUSC, and SCLC, respectively. Only five genes (CHRNA5, IDH3A, PSMA4, RP11-650 L12.2, and TBC1D2B) overlapped all subtypes. Furthermore, we observed only two pathways from the Kyoto Encyclopedia of Genes and Genomes shared by all subtypes. At the regulatory level, only three eQTL target genes and two enhancer target genes overlapped between all subtypes. CONCLUSIONS Our results suggest that the three lung cancer subtypes do not share much genetic signal at the SNP, gene, pathway, or regulatory level, which differs from the common subtype classification based upon histology. However, three (CHRNA5, IDH3A, and PSMA4) of the five genes shared between the subtypes are well-known lung cancer genes that may act as general lung cancer genes regardless of subtype.
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Affiliation(s)
- Timothy D O'Brien
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Zhongming Zhao
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA. .,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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76
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Hao Y, Yan L, Ke E, Wang H, He J. Birth in winter can reduce the risk of lung cancer: A retrospective study of the birth season of patients with lung cancer in Beijing area, China. Chronobiol Int 2018; 34:511-518. [PMID: 28426385 DOI: 10.1080/07420528.2017.1305964] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The season of birth is an important risk factor for several diseases. We explored the relationship between birth season and lung cancer. In this population-based retrospective study, we focused on patients with lung cancer who had registered at the Beijing Institute for Cancer Research from 2003 to 2012. In total, 33,025 patients were divided into five subgroups based on their histologic classification, and these five subgroups were compared with the general population (i.e., the permanent resident population of Beijing in 2013). A binary logistic regression method with sex and age as control factors was used to evaluate the relationship between birth season and lung cancer; P < 0.01 was statistically significant. Taking winter as a reference in our analysis of the relationship between season of birth and lung cancer, we found that people who were born in other seasons had a higher probability of developing lung cancer (spring: odds ratio [OR] = 1.06, 95% confidence interval [CI] = 1.03-1.09; summer: OR = 1.07, 95% CI = 1.04-1.10; autumn: OR = 1.06, 95% CI = 1.03-1.09) (P < 0.01). Among the five subgroups, persons with squamous cell carcinoma who were born in summer were more likely to develop lung cancer than those who were born in winter (OR = 1.09, 95% CI = 1.02-1.15, P = 0.006). The other subgroups showed no correlation with season of birth (P > 0.01). This study demonstrates that for people born in winter, the risks of developing lung cancer and squamous cell carcinoma are comparatively lower than those for people born in other seasons. Differences in immune function and the maternal nutrition status during pregnancy of people born in different seasons may explain this finding.
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Affiliation(s)
- Yu Hao
- a Preclinical School of Medicine, Beijing University of Chinese Medicine , Beijing , China
| | - Long Yan
- a Preclinical School of Medicine, Beijing University of Chinese Medicine , Beijing , China
| | - ErQinFu Ke
- a Preclinical School of Medicine, Beijing University of Chinese Medicine , Beijing , China
| | - Hong Wang
- a Preclinical School of Medicine, Beijing University of Chinese Medicine , Beijing , China
| | - Juan He
- a Preclinical School of Medicine, Beijing University of Chinese Medicine , Beijing , China
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Mocellin S, Tropea S, Benna C, Rossi CR. Circadian pathway genetic variation and cancer risk: evidence from genome-wide association studies. BMC Med 2018; 16:20. [PMID: 29455641 PMCID: PMC5817863 DOI: 10.1186/s12916-018-1010-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dysfunction of the circadian clock and single polymorphisms of some circadian genes have been linked to cancer susceptibility, although data are scarce and findings inconsistent. We aimed to investigate the association between circadian pathway genetic variation and risk of developing common cancers based on the findings of genome-wide association studies (GWASs). METHODS Single nucleotide polymorphisms (SNPs) of 17 circadian genes reported by three GWAS meta-analyses dedicated to breast (Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) Consortium; cases, n = 15,748; controls, n = 18,084), prostate (Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE) Consortium; cases, n = 14,160; controls, n = 12,724) and lung carcinoma (Transdisciplinary Research In Cancer of the Lung (TRICL) Consortium; cases, n = 12,160; controls, n = 16,838) in patients of European ancestry were utilized to perform pathway analysis by means of the adaptive rank truncated product (ARTP) method. Data were also available for the following subgroups: estrogen receptor negative breast cancer, aggressive prostate cancer, squamous lung carcinoma and lung adenocarcinoma. RESULTS We found a highly significant statistical association between circadian pathway genetic variation and the risk of breast (pathway P value = 1.9 × 10-6; top gene RORA, gene P value = 0.0003), prostate (pathway P value = 4.1 × 10-6; top gene ARNTL, gene P value = 0.0002) and lung cancer (pathway P value = 6.9 × 10-7; top gene RORA, gene P value = 2.0 × 10-6), as well as all their subgroups. Out of 17 genes investigated, 15 were found to be significantly associated with the risk of cancer: four genes were shared by all three malignancies (ARNTL, CLOCK, RORA and RORB), two by breast and lung cancer (CRY1 and CRY2) and three by prostate and lung cancer (NPAS2, NR1D1 and PER3), whereas four genes were specific for lung cancer (ARNTL2, CSNK1E, NR1D2 and PER2) and two for breast cancer (PER1, RORC). CONCLUSIONS Our findings, based on the largest series ever utilized for ARTP-based gene and pathway analysis, support the hypothesis that circadian pathway genetic variation is involved in cancer predisposition.
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Affiliation(s)
- Simone Mocellin
- Department of Surgery Oncology and Gastroenterology, University of Padova, Via Giustiniani 2, 35128, Padova, Italy. .,Istituto Oncologico Veneto, IOV-IRCCS, Padova, Italy.
| | | | - Clara Benna
- Department of Surgery Oncology and Gastroenterology, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Carlo Riccardo Rossi
- Department of Surgery Oncology and Gastroenterology, University of Padova, Via Giustiniani 2, 35128, Padova, Italy.,Istituto Oncologico Veneto, IOV-IRCCS, Padova, Italy
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78
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Noell G, Faner R, Agustí A. From systems biology to P4 medicine: applications in respiratory medicine. Eur Respir Rev 2018; 27:27/147/170110. [PMID: 29436404 PMCID: PMC9489012 DOI: 10.1183/16000617.0110-2017] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022] Open
Abstract
Human health and disease are emergent properties of a complex, nonlinear, dynamic multilevel biological system: the human body. Systems biology is a comprehensive research strategy that has the potential to understand these emergent properties holistically. It stems from advancements in medical diagnostics, “omics” data and bioinformatic computing power. It paves the way forward towards “P4 medicine” (predictive, preventive, personalised and participatory), which seeks to better intervene preventively to preserve health or therapeutically to cure diseases. In this review, we: 1) discuss the principles of systems biology; 2) elaborate on how P4 medicine has the potential to shift healthcare from reactive medicine (treatment of illness) to predict and prevent illness, in a revolution that will be personalised in nature, probabilistic in essence and participatory driven; 3) review the current state of the art of network (systems) medicine in three prevalent respiratory diseases (chronic obstructive pulmonary disease, asthma and lung cancer); and 4) outline current challenges and future goals in the field. Systems biology and network medicine have the potential to transform medical research and practicehttp://ow.ly/r3jR30hf35x
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Affiliation(s)
- Guillaume Noell
- Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Rosa Faner
- Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Alvar Agustí
- Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain .,CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain.,Respiratory Institute, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
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79
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Feng Y, Wang Y, Liu H, Liu Z, Mills C, Owzar K, Xie J, Han Y, Qian DC, Hung Rj RJ, Brhane Y, McLaughlin J, Brennan P, Bickeböller H, Rosenberger A, Houlston RS, Caporaso N, Landi MT, Brüske I, Risch A, Ye Y, Wu X, Christiani DC, Amos CI, Wei Q. Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer. Mol Carcinog 2018; 57:216-224. [PMID: 29071797 PMCID: PMC6128286 DOI: 10.1002/mc.22748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/21/2017] [Accepted: 09/29/2017] [Indexed: 01/18/2023]
Abstract
The P38MAPK pathway participates in regulating cell cycle, inflammation, development, cell death, cell differentiation, and tumorigenesis. Genetic variants of some genes in the P38MAPK pathway are reportedly associated with lung cancer risk. To substantiate this finding, we used six genome-wide association studies (GWASs) to comprehensively investigate the associations of 14 904 single nucleotide polymorphisms (SNPs) in 108 genes of this pathway with lung cancer risk. We identified six significant lung cancer risk-associated SNPs in two genes (CSNK2B and ZAK) after correction for multiple comparisons by a false discovery rate (FDR) <0.20. After removal of three CSNK2B SNPs that are located in the same locus previously reported by GWAS, we performed the LD analysis and found that rs3769201 and rs7604288 were in high LD. We then chose two independent representative SNPs of rs3769201 and rs722864 in ZAK for further analysis. We also expanded the analysis by including these two SNPs from additional GWAS datasets of Harvard University (984 cases and 970 controls) and deCODE (1319 cases and 26 380 controls). The overall effects of these two SNPs were assessed using all eight GWAS datasets (OR = 0.92, 95%CI = 0.89-0.95, and P = 1.03 × 10-5 for rs3769201; OR = 0.91, 95%CI = 0.88-0.95, and P = 2.03 × 10-6 for rs722864). Finally, we performed an expression quantitative trait loci (eQTL) analysis and found that these two SNPs were significantly associated with ZAK mRNA expression levels in lymphoblastoid cell lines. In conclusion, the ZAK rs3769201 and rs722864 may be functional susceptibility loci for lung cancer risk.
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Affiliation(s)
- Yun Feng
- Department of Respiration, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Coleman Mills
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute and Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Jichun Xie
- Duke Cancer Institute and Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Younghun Han
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - David C Qian
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - Rayjean J Hung Rj
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Irene Brüske
- Helmholtz Centre Munich, German Research Centre for Environmental Health, Institute of Epidemiology I, Neuherberg, Germany
| | - Angela Risch
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David C Christiani
- Massachusetts General Hospital, Boston, Massachusetts
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Christopher I Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
- Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
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80
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Du Y, Hao X, Liu X. Low expression of long noncoding RNA CDKN2B-AS1 in patients with idiopathic pulmonary fibrosis predicts lung cancer by regulating the p53-signaling pathway. Oncol Lett 2018. [PMID: 29541247 PMCID: PMC5835920 DOI: 10.3892/ol.2018.7910] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The present study aimed to investigate the expression of long non-coding RNA (lncRNA) cyclin dependent kinase inhibitor-2B-antisense RNA 1 CDKN2B-AS1 in patients with peripheral blood of idiopathic pulmonary fibrosis (IPF). A total of 24 patients with IPF and 24 healthy controls were included in the study, four patients with IPF and four healthy controls were selected randomly to extract RNA. There were no other diseases such as hypertension and diabetes in the two groups. RNA from peripheral blood was extracted by high-throughput sequencing and bioinformatics analysis was performed. Based on selected differentially expressed lncRNA and mRNA, gene ontology analysis was performed to screen out the tumor-associated mRNA. A total of 20 samples were chosen to avoid variance due to individual differences. A total of 20 patients with IPF, and 20 controls were further studied, RNA extracted from peripheral blood was used to verify the lncRNA and mRNA levels. A total of 440 lncRNAs were identified to be upregulated and 1,376 downregulated according to the screening results of differential expression. High-throughput sequencing and bioinformatics analysis demonstrated that the expression of CDKN2B-AS1 decreased significantly in patients with IPF compared with healthy controls. The adjacent gene mRNA of CDKN2B-AS1 was identified as CDKN2A, an important anti-oncogene, which is concentrated on the p53 signaling-pathway according to the Kyoto Encyclopedia of Genes and Genomes database. CDKN2A mRNA expression levels were lower in patients with IPF and higher in the control group. The expression of CDKN2B-AS1 and CDKN2A mRNA was significantly lower in IPF group compared with in the control group (P<0.05). The results suggest the expression of the CDKN2B-AS1 and adjacent gene, CDKN2A, are downregulated in the peripheral blood of patients with IPF, which activates the p53-signaling pathway to promote lung cancer formation.
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Affiliation(s)
- Yufeng Du
- Department of Geriatric Diseases, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xiaoyan Hao
- Department of Geriatric Diseases, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xuejun Liu
- Department of Geriatric Diseases, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
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81
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Ramsey AT, Chen LS, Hartz SM, Saccone NL, Fisher SL, Proctor EK, Bierut LJ. Toward the implementation of genomic applications for smoking cessation and smoking-related diseases. Transl Behav Med 2018; 8:7-17. [PMID: 29385591 PMCID: PMC6065540 DOI: 10.1093/tbm/ibx060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The incorporation of genomic information into routine care settings is a burgeoning area for investigation in behavioral medicine. The past decade has witnessed rapid advancements in knowledge of genetic biomarkers associated with smoking behaviors and tobacco-related morbidity and mortality, providing the basis for promising genomic applications in clinical and community settings. We assessed the current state of readiness for implementing genomic applications involving variation in the α5 nicotinic cholinergic receptor subunit gene CHRNA5 and smoking outcomes (behaviors and related diseases) using a process that could be translatable to a wide range of genomic applications in behavioral medicine. We reviewed the scientific literature involving CHRNA5 genetic variation and smoking cessation, and then summarized and synthesized a chain of evidence according to analytic validity, clinical validity, clinical utility, and ethical, legal, and social implications (ACCE), a well-established set of criteria used to evaluate genomic applications. Our review identified at least three specific genomic applications for which implementation may be considered, including the use of CHRNA5 genetic test results for informing disease risk, optimizing smoking cessation treatment, and motivating smoking behavior change. For these genomic applications, we rated analytic validity as convincing, clinical validity as adequate, and clinical utility and ethical, legal, and social implications as inadequate. For clinical genomic applications involving CHRNA5 variation and smoking outcomes, research efforts now need to focus on establishing clinical utility. This approach is compatible with pre-implementation research, which is also needed to accelerate translation, improve innovation design, and understand and refine system processes involved in implementation. This study informs the readiness to incorporate smoking-related genomic applications in real-world settings and facilitates cross-disciplinary collaboration to accelerate the integration of evidence-based genomics in behavioral medicine.
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Affiliation(s)
- Alex T Ramsey
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sherri L Fisher
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Enola K Proctor
- Brown School of Social Work, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
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82
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Zuber V, Jönsson EG, Frei O, Witoelar A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, Smeland OB, Dieset I, Fanous AH, Desikan RS, Küry S, Bézieau S, Dale AM, Mills IG, Andreassen OA. Identification of shared genetic variants between schizophrenia and lung cancer. Sci Rep 2018; 8:674. [PMID: 29330379 PMCID: PMC5766533 DOI: 10.1038/s41598-017-16481-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 11/14/2017] [Indexed: 02/02/2023] Open
Abstract
Epidemiology studies suggest associations between schizophrenia and cancer. However, the underlying genetic mechanisms are not well understood, and difficult to identify from epidemiological data. We investigated if there is a shared genetic architecture between schizophrenia and cancer, with the aim to identify specific overlapping genetic loci. First, we performed genome-wide enrichment analysis and second, we analyzed specific loci jointly associated with schizophrenia and cancer by the conjunction false discovery rate. We analyzed the largest genome-wide association studies of schizophrenia and lung, breast, prostate, ovary, and colon-rectum cancer including more than 220,000 subjects, and included genetic association with smoking behavior. Polygenic enrichment of associations with lung cancer was observed in schizophrenia, and weak enrichment for the remaining cancer sites. After excluding the major histocompatibility complex region, we identified three independent loci jointly associated with schizophrenia and lung cancer. The strongest association included nicotinic acetylcholine receptors and is an established pleiotropic locus shared between lung cancer and smoking. The two other loci were independent of genetic association with smoking. Functional analysis identified downstream pleiotropic effects on epigenetics and gene-expression in lung and brain tissue. These findings suggest that genetic factors may explain partly the observed epidemiological association of lung cancer and schizophrenia.
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Affiliation(s)
- Verena Zuber
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway ,0000000121885934grid.5335.0MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Erik G. Jönsson
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 1937 0626grid.4714.6Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - Oleksandr Frei
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Aree Witoelar
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Wesley K. Thompson
- 0000 0001 2107 4242grid.266100.3Department of Psychiatry, University of California, San Diego, La Jolla, CA USA
| | - Andrew J. Schork
- 0000 0001 2107 4242grid.266100.3Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Cognitive Sciences Graduate Program, University of California, San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Center for Human Development, University of California at San Diego, La Jolla, CA USA
| | - Francesco Bettella
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Yunpeng Wang
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- 0000 0004 1936 7443grid.7914.bNORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway ,0000 0004 0389 8485grid.55325.34Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Olav B. Smeland
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ingrid Dieset
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ayman H. Fanous
- 0000 0001 0693 2202grid.262863.bDepartment of Psychiatry, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Rahul S. Desikan
- 0000 0001 2297 6811grid.266102.1Department of Radiology, University of California, San Francisco, San Francisco, CA USA
| | - Sébastien Küry
- 0000 0004 0472 0371grid.277151.7CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, CEDEX 1 France
| | - Stéphane Bézieau
- 0000 0004 0472 0371grid.277151.7CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, CEDEX 1 France
| | - Anders M. Dale
- 0000 0001 2107 4242grid.266100.3Department of Psychiatry, University of California, San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Center for Human Development, University of California at San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Department of Neurosciences, University of California, San Diego, La Jolla, CA USA
| | - Ian G. Mills
- 0000 0004 0389 8485grid.55325.34Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Department of Cancer Prevention, Institute of Cancer Research and Department of Urology, Oslo University Hospital, Oslo, Norway ,0000 0004 0374 7521grid.4777.3Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, BT9 7AE UK ,0000 0004 1936 8948grid.4991.5Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Ole A. Andreassen
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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83
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Bierut LJ, Tyndale RF. Preparing the Way: Exploiting Genomic Medicine to Stop Smoking. Trends Mol Med 2018; 24:187-196. [PMID: 29307500 DOI: 10.1016/j.molmed.2017.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 12/10/2017] [Indexed: 12/15/2022]
Abstract
Clinical medicine of the future is poised to use an individual's genomic data to predict disease risk and guide clinical care. The treatment of cigarette smoking and tobacco use disorder represents a prime area for genomics implementation. The genes CHRNA5 and CYP2A6 are strong genomic contributors that alter the risk of heaviness of smoking, tobacco use disorder, and smoking-related diseases in humans. These biomarkers have proven analytical and clinical validity, and evidence for their clinical utility continues to grow. We propose that these biomarkers harbor the potential of enabling the identification of elevated disease risk in smokers, personalizing smoking cessation treatments, and motivating behavioral changes. We must prepare for the integration of genomic applications into clinical care of patients who smoke.
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Affiliation(s)
- Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH) and Departments of Psychiatry, Pharmacology and Toxicology, University of Toronto, Toronto, M5S 1A8, Ontario, Canada
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84
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Sud A, Kinnersley B, Houlston RS. Genome-wide association studies of cancer: current insights and future perspectives. Nat Rev Cancer 2017; 17:692-704. [PMID: 29026206 DOI: 10.1038/nrc.2017.82] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWAS) provide an agnostic approach for investigating the genetic basis of complex diseases. In oncology, GWAS of nearly all common malignancies have been performed, and over 450 genetic variants associated with increased risks have been identified. As well as revealing novel pathways important in carcinogenesis, these studies have shown that common genetic variation contributes substantially to the heritable risk of many common cancers. The clinical application of GWAS is starting to provide opportunities for drug discovery and repositioning as well as for cancer prevention. However, deciphering the functional and biological basis of associations is challenging and is in part a barrier to fully unlocking the potential of GWAS.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
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85
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Gu F, Zhang H, Hyland PL, Berndt S, Gapstur SM, Wheeler W, Ellipse Consortium T, Amos CI, Bezieau S, Bickeböller H, Brenner H, Brennan P, Chang-Claude J, Conti DV, Doherty JA, Gruber SB, Harrison TA, Hayes RB, Hoffmeister M, Houlston RS, Hung RJ, Jenkins MA, Kraft P, Lawrenson K, McKay J, Markt S, Mucci L, Phelan CM, Qu C, Risch A, Rossing MA, Wichmann HE, Shi J, Schernhammer E, Yu K, Landi MT, Caporaso NE. Inherited variation in circadian rhythm genes and risks of prostate cancer and three other cancer sites in combined cancer consortia. Int J Cancer 2017; 141:1794-1802. [PMID: 28699174 PMCID: PMC5907928 DOI: 10.1002/ijc.30883] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/15/2017] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Circadian disruption has been linked to carcinogenesis in animal models, but the evidence in humans is inconclusive. Genetic variation in circadian rhythm genes provides a tool to investigate such associations. We examined associations of genetic variation in nine core circadian rhythm genes and six melatonin pathway genes with risk of colorectal, lung, ovarian and prostate cancers using data from the Genetic Associations and Mechanisms in Oncology (GAME-ON) network. The major results for prostate cancer were replicated in the Prostate, Lung, Colorectal and Ovarian (PLCO) cancer screening trial, and for colorectal cancer in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). The total number of cancer cases and controls was 15,838/18,159 for colorectal, 14,818/14,227 for prostate, 12,537/17,285 for lung and 4,369/9,123 for ovary. For each cancer site, we conducted gene-based and pathway-based analyses by applying the summary-based Adaptive Rank Truncated Product method (sARTP) on the summary association statistics for each SNP within the candidate gene regions. Aggregate genetic variation in circadian rhythm and melatonin pathways were significantly associated with the risk of prostate cancer in data combining GAME-ON and PLCO, after Bonferroni correction (ppathway < 0.00625). The two most significant genes were NPAS2 (pgene = 0.0062) and AANAT (pgene = 0.00078); the latter being significant after Bonferroni correction. For colorectal cancer, we observed a suggestive association with the circadian rhythm pathway in GAME-ON (ppathway = 0.021); this association was not confirmed in GECCO (ppathway = 0.76) or the combined data (ppathway = 0.17). No significant association was observed for ovarian and lung cancer. These findings support a potential role for circadian rhythm and melatonin pathways in prostate carcinogenesis. Further functional studies are needed to better understand the underlying biologic mechanisms.
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Affiliation(s)
- Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | | | | | | | | | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center Göttingen, Göttingen, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David V Conti
- Keck School of Medicine, University of South California, Los Angeles, CA
| | | | - Stephen B Gruber
- Keck School of Medicine, University of South California, Los Angeles, CA
| | - Tabitha A Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Richard B Hayes
- Department of Population Health, New York University School of Medicine, New York, NY
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H Chan School of Public Health, Boston, MA
| | | | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Sarah Markt
- Department of Epidemiology, Harvard T.H Chan School of Public Health, Boston, MA
| | - Lorelei Mucci
- Department of Epidemiology, Harvard T.H Chan School of Public Health, Boston, MA
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Population Sciences Division, Moffitt Cancer Center, Tampa, FL
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Angela Risch
- Division of Molecular Biology, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
- Translational Lung Research Center, Heidelberg, Germany within the German Center for Lung Research (DZL), Giessen, Germany
- Division of Epigenomics and Cancer Risk Factors, DKFZ German Cancer Research Center, Heidelberg, Germany
| | - Mary Anne Rossing
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Bavaria, Germany
- Helmholtz Center Munich, Institute of Epidemiology II, Neuherberg, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Eva Schernhammer
- Department of Epidemiology, Harvard T.H Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Department of Epidemiology, Medical University of Vienna, Vienna, Austria
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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86
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Liu C, Cui H, Gu D, Zhang M, Fang Y, Chen S, Tang M, Zhang B, Chen H. Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies. Lung Cancer 2017; 113:18-29. [PMID: 29110844 DOI: 10.1016/j.lungcan.2017.08.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023]
Abstract
A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.
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Affiliation(s)
- Caiyang Liu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China
| | - Huijie Cui
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Dongqing Gu
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Min Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yanfei Fang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Siyu Chen
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Mingshuang Tang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China.
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87
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Couto PP, Bastos-Rodrigues L, Schayek H, Melo FM, Lisboa RGC, Miranda DM, Vilhena A, Bale AE, Friedman E, De Marco L. Spectrum of germline mutations in smokers and non-smokers in Brazilian non-small-cell lung cancer (NSCLC) patients. Carcinogenesis 2017; 38:1112-1118. [DOI: 10.1093/carcin/bgx089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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88
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Wang J, Liu Q, Yuan S, Xie W, Liu Y, Xiang Y, Wu N, Wu L, Ma X, Cai T, Zhang Y, Sun Z, Li Y. Genetic predisposition to lung cancer: comprehensive literature integration, meta-analysis, and multiple evidence assessment of candidate-gene association studies. Sci Rep 2017; 7:8371. [PMID: 28827732 PMCID: PMC5567126 DOI: 10.1038/s41598-017-07737-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 07/04/2017] [Indexed: 01/03/2023] Open
Abstract
More than 1000 candidate-gene association studies on genetic susceptibility to lung cancer have been published over the last two decades but with few consensuses for the likely culprits. We conducted a comprehensive review, meta-analysis and evidence strength evaluation of published candidate-gene association studies in lung cancer up to November 1, 2015. The epidemiological credibility of cumulative evidence was assessed using the Venice criteria. A total of 1018 publications with 2910 genetic variants in 754 different genes or chromosomal loci were eligible for inclusion. Main meta-analyses were performed on 246 variants in 138 different genes. Twenty-two variants from 21 genes (APEX1 rs1130409 and rs1760944, ATM rs664677, AXIN2 rs2240308, CHRNA3 rs6495309, CHRNA5 rs16969968, CLPTM1L rs402710, CXCR2 rs1126579, CYP1A1 rs4646903, CYP2E1 rs6413432, ERCC1 rs11615, ERCC2 rs13181, FGFR4 rs351855, HYKK rs931794, MIR146A rs2910164, MIR196A2 rs11614913, OGG1 rs1052133, PON1 rs662, REV3L rs462779, SOD2 rs4880, TERT rs2736098, and TP53 rs1042522) showed significant associations with lung cancer susceptibility with strong cumulative epidemiological evidence. No significant associations with lung cancer risk were found for other 150 variants in 98 genes; however, seven variants demonstrated strong cumulative evidence. Our findings provided the most updated summary of genetic risk effects on lung cancer and would help inform future research direction.
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Affiliation(s)
- Junjun Wang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Qingyun Liu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Shuai Yuan
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Weijia Xie
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Yuan Liu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Ying Xiang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Na Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Long Wu
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Xiangyu Ma
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Tongjian Cai
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Yao Zhang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China.,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Zhifu Sun
- Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China. .,Center for Clinical Epidemiology and Evidence-Based Medicine, Third Military Medical University, Chongqing, People's Republic of China.
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89
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Wichmann HE. Epidemiology in Germany-general development and personal experience. Eur J Epidemiol 2017; 32:635-656. [PMID: 28815360 DOI: 10.1007/s10654-017-0290-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Did you ever hear about epidemiology in Germany? Starting from an epidemiological desert the discipline has grown remarkably, especially during the last 10-15 years: research institutes have been established, research funding has improved, multiple curriculae in Epidemiology and Public Health are offered. This increase has been quite steep, and now the epidemiological infrastructure is much better. Several medium-sized and even big population cohorts are ongoing, and the number and quality of publications from German epidemiologists has reached a respectable level. My own career in epidemiology started in the field of environmental health. After German reunification I concentrated for many years on environmental problems in East Germany and observed the health benefits after improvement of the situation. Later, I concentrated on population-based cohorts in newborns (GINI/LISA) and adults (KORA, German National Cohort), and on biobanking. This Essay describes the development in Germany after worldwar 2, illustrated by examples of research results and build-up of epidemiological infractructures worth mentioning.
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Affiliation(s)
- Heinz-Erich Wichmann
- Institute of Epidemiology, 2, Helmholtz Center Munich, Munich, Germany. .,Chair of Epidemiology, University of Munich, Munich, Germany.
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90
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Akhtar N, Bansal JG. Risk factors of Lung Cancer in nonsmoker. Curr Probl Cancer 2017; 41:328-339. [PMID: 28823540 DOI: 10.1016/j.currproblcancer.2017.07.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/12/2017] [Accepted: 07/17/2017] [Indexed: 12/18/2022]
Abstract
Generally, the cause of lung cancer is attributed to tobacco smoking. But many of the new lung cancer cases have been reported in nonsmokers. Apart from smoking; air pollution, environmental exposure, mutations, and single-nucleotide polymorphisms are known to be associated with lung cancer. Improper diet, alcohol consumption, marijuana smoking, estrogen, infections with human papillomavirus (HPV), HIV, and Epstein-Barr virus are suggested to be linked with lung cancer but clear evidences to ascertain their relation is not available. This article provides a comprehensive review of various risk factors and the underlying molecular mechanisms responsible for increasing the incidence of lung cancer. The pathologic, histologic, and genetic differences exist with lung cancer among smokers and nonsmokers. A better understanding of the risk factors, differences in pathology and molecular features of lung cancer in smokers and nonsmokers and the mode of action of various carcinogens will facilitate the prevention and management of lung cancer.
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Affiliation(s)
- Nahid Akhtar
- Department of Bioengineering and Biosciences, Lovely Professional University (LPU), Phagwara, Punjab, India
| | - Jeena Gupta Bansal
- Department of Bioengineering and Biosciences, Lovely Professional University (LPU), Phagwara, Punjab, India.
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91
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McKay JD, Hung RJ, Han Y, Zong X, Carreras-Torres R, Christiani DC, Caporaso NE, Johansson M, Xiao X, Li Y, Byun J, Dunning A, Pooley KA, Qian DC, Ji X, Liu G, Timofeeva MN, Bojesen SE, Wu X, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, 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 CA, Wilkens LR, Fernandez-Somoano A, Fernandez-Tardon G, van der Heijden HF, 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 JA, Barnett MP, Chen C, Goodman GE, Cox A, Taylor F, Woll P, Brüske I, Wichmann HE, Manz J, Muley TR, Risch A, Rosenberger A, Grankvist K, Johansson M, Shepherd FA, 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 RS, McLaughlin J, Stevens VL, Joubert P, Lamontagne M, Nickle DC, Obeidat M, Timens W, Zhu B, Song L, Kachuri L, Artigas MS, Tobin MD, Wain LV, Rafnar T, Thorgeirsson TE, Reginsson GW, Stefansson K, Hancock DB, Bierut LJ, Spitz MR, Gaddis NC, Lutz SM, Gu F, Johnson EO, Kamal A, Pikielny C, Zhu D, Lindströem S, Jiang X, Tyndale RF, Chenevix-Trench G, Beesley J, Bossé Y, Chanock S, Brennan P, Landi MT, Amos CI. Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes. Nat Genet 2017; 49:1126-1132. [PMID: 28604730 PMCID: PMC5510465 DOI: 10.1038/ng.3892] [Citation(s) in RCA: 397] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 05/10/2017] [Indexed: 12/15/2022]
Abstract
Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma. Gene expression quantitative trait locus (eQTL) analysis in 1,425 normal lung tissue samples highlights RNASET2, SECISBP2L and NRG1 as candidate genes. Other loci include genes such as a cholinergic nicotinic receptor, CHRNA2, and the telomere-related genes OFBC1 and RTEL1. Further exploration of the target genes will continue to provide new insights into the etiology of lung cancer.
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Affiliation(s)
- James D. McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Younghun Han
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | | | - David C. Christiani
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Karen A. Pooley
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - David C. Qian
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Xuemei Ji
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Geoffrey Liu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Maria N. Timofeeva
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Stig E. Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Germany
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center
| | - William S. Bush
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Adonina Tardon
- University of Oviedo and CIBERESP, Faculty of Medicine, Campus del Cristo s/n, 33006 Oviedo, Spain
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - M. Dawn Teare
- School of Health and Related Research, University of Sheffield, England, UK
| | - John K. Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, Washington, USA
| | - Aage Haugen
- National Institute of Occupational Health, Oslo, Norway
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, Canada
| | - Matthew B. Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- University of Pittsburgh Cancer Institute, Pittsburgh, USA
| | - Pier Alberto Bertazzi
- Department of Preventive Medicine, IRCCS Foundation Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health – DISCCO, University of Milan, Milan, Italy
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health – DISCCO, University of Milan, Milan, Italy
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Nancy Diao
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Li Su
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Ruyang Zhang
- Department of Environmental Health, Harvard TH Chan School of Public Health, and Massachusetts General Hospital/Harvard Medical School, Boston, MA. 02115
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Natasha Leighl
- University Health Network- The Princess Margaret Cancer Centre, Toronto, CA
| | - Jakob S. Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Anders Mellemgaard
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Walid Saliba
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ana Fernandez-Somoano
- University of Oviedo and CIBERESP, Faculty of Medicine, Campus del Cristo s/n, 33006 Oviedo, Spain
| | | | | | - Jin Hee Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, Gwangjin-gu, Seoul, 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, Nanjing, P.R. 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, Nanjing, P.R. China
| | - Michael PA Davies
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael W. Marcus
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Jonas Manjer
- Faculty of Medicine, Lund University, Lund, Sweden
| | | | - David C. Muller
- School of Public Health, St Mary’s Campus, Imperial College London, UK
| | - Kim Overvad
- Section for Epidemiology, Department of Public Health, Aarhus University, Denmark
| | | | - Rosario Tumino
- Tumino. Molecular and Nutritional Epidemiology Unit CSPO (Cancer Research and Prevention Centre), Scientific Institute of Tuscany, Florence, Italy
| | - Jennifer A. Doherty
- Department of Epidemiology, Geisel School of Medicine, Hanover, NH
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Matt P. Barnett
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Angela Cox
- Department of Oncology, University of Sheffield, Sheffield, UK
| | - Fiona Taylor
- Department of Oncology, University of Sheffield, Sheffield, UK
| | - Penella Woll
- Department of Oncology, University of Sheffield, Sheffield, UK
| | - Irene Brüske
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Germany
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas R. Muley
- Thoraxklinik at University Hospital Heidelberg
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
| | - Angela Risch
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Thoraxklinik at University Hospital Heidelberg
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
- University of Salzburg and Cancer Cluster Salzburg, Austria
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Germany
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | | | | | - Susanne M. Arnold
- University of Kentucky, Markey Cancer Center, Lexington, Kentucky, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Ciprian Bolca
- Institute of Pneumology “Marius Nasta”, Bucharest, Romania
| | - Ivana Holcatova
- 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Milica Kontic
- Clinical Center of Serbia, Belgrade. School of Medicine, University of Belgrade
| | - Jolanta Lissowska
- M. Sklodowska-Curie Cancer Center, Institute of Oncology, Warsaw, Poland
| | - Anush Mukeria
- Department of Epidemiology and Prevention, Russian N.N.Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Simona Ognjanovic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - Tadeusz M. Orlowski
- Department of Surgery, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Ghislaine Scelo
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - David Zaridze
- Department of Epidemiology and Prevention, Russian N.N.Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Vidar Skaug
- National Institute of Occupational Health, Oslo, Norway
| | | | - Eric J. Duell
- Unit of Nutrition and Cancer, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | | | - Woon-Puay Koh
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, China
| | | | | | | | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Maxime Lamontagne
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - David C. Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, MA, USA
| | - Ma’en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Wim Timens
- University of Groningen, Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, The Netherlands
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Linda Kachuri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - SpiroMeta Consortium
- SpiroMeta Consortium see Supplemental Materials for full list of participating members
| | | | | | | | | | - Dana B. Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, North Carolina, USA
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Nathan C. Gaddis
- Research Computing Division, RTI International, Research Triangle Park, North Carolina, USA
| | - Sharon M. Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Eric O. Johnson
- Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, North Carolina, USA
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Claudio Pikielny
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Dakai Zhu
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH
| | - Sara Lindströem
- Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Health Sciences Bldg., F-247B, Box 357236, Seattle, WA 98195
| | - Xia Jiang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115
| | - Rachel F. Tyndale
- Departments of Pharmacology and Toxicology & Psychiatry, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | | | - Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Molecular Medicine, Laval University, Québec, Canada
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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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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93
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Carreras-Torres R, Johansson M, Haycock PC, Wade KH, Relton CL, Martin RM, Davey Smith G, Albanes D, Aldrich MC, Andrew A, Arnold SM, Bickeböller H, Bojesen SE, Brunnström H, Manjer J, Brüske I, Caporaso NE, Chen C, Christiani DC, Christian WJ, Doherty JA, Duell EJ, Field JK, Davies MPA, Marcus MW, Goodman GE, Grankvist K, Haugen A, Hong YC, Kiemeney LA, van der Heijden EHFM, Kraft P, Johansson MB, Lam S, Landi MT, Lazarus P, Le Marchand L, Liu G, Melander O, Park SL, Rennert G, Risch A, Haura EB, Scelo G, Zaridze D, Mukeriya A, Savić M, Lissowska J, Swiatkowska B, Janout V, Holcatova I, Mates D, Schabath MB, Shen H, Tardon A, Teare MD, Woll P, Tsao MS, Wu X, Yuan JM, Hung RJ, Amos CI, McKay J, Brennan P. Obesity, metabolic factors and risk of different histological types of lung cancer: A Mendelian randomization study. PLoS One 2017; 12:e0177875. [PMID: 28594918 PMCID: PMC5464539 DOI: 10.1371/journal.pone.0177875] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/04/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Assessing the relationship between lung cancer and metabolic conditions is challenging because of the confounding effect of tobacco. Mendelian randomization (MR), or the use of genetic instrumental variables to assess causality, may help to identify the metabolic drivers of lung cancer. METHODS AND FINDINGS We identified genetic instruments for potential metabolic risk factors and evaluated these in relation to risk using 29,266 lung cancer cases (including 11,273 adenocarcinomas, 7,426 squamous cell and 2,664 small cell cases) and 56,450 controls. The MR risk analysis suggested a causal effect of body mass index (BMI) on lung cancer risk for two of the three major histological subtypes, with evidence of a risk increase for squamous cell carcinoma (odds ratio (OR) [95% confidence interval (CI)] = 1.20 [1.01-1.43] and for small cell lung cancer (OR [95%CI] = 1.52 [1.15-2.00]) for each standard deviation (SD) increase in BMI [4.6 kg/m2]), but not for adenocarcinoma (OR [95%CI] = 0.93 [0.79-1.08]) (Pheterogeneity = 4.3x10-3). Additional analysis using a genetic instrument for BMI showed that each SD increase in BMI increased cigarette consumption by 1.27 cigarettes per day (P = 2.1x10-3), providing novel evidence that a genetic susceptibility to obesity influences smoking patterns. There was also evidence that low-density lipoprotein cholesterol was inversely associated with lung cancer overall risk (OR [95%CI] = 0.90 [0.84-0.97] per SD of 38 mg/dl), while fasting insulin was positively associated (OR [95%CI] = 1.63 [1.25-2.13] per SD of 44.4 pmol/l). Sensitivity analyses including a weighted-median approach and MR-Egger test did not detect other pleiotropic effects biasing the main results. CONCLUSIONS Our results are consistent with a causal role of fasting insulin and low-density lipoprotein cholesterol in lung cancer etiology, as well as for BMI in squamous cell and small cell carcinoma. The latter relation may be mediated by a previously unrecognized effect of obesity on smoking behavior.
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Affiliation(s)
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
| | - Philip C. Haycock
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Kaitlin H. Wade
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Richard M. Martin
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- National Institute for Health Research Biomedical Research Unit in Nutrition, Diet and Lifestyle at University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Demetrius Albanes
- Metabolic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Rockville, Maryland, United States of America
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Angeline Andrew
- Norris Cotton Cancer Center, Lebanon, New Hampshire, United States of America
| | - Susanne M. Arnold
- University of Kentucky Markey Cancer Center, Lexington, Kentucky, United States of America
| | | | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans Brunnström
- Laboratory Medicine Region Skåne, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jonas Manjer
- Laboratory Medicine Region Skåne, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Neil E. Caporaso
- Genetic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Rockville, Maryland, United States of America
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David C. Christiani
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health and Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - W. Jay Christian
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jennifer A. Doherty
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire, United States of America
| | - Eric J. Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - John K. Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Michael P. A. Davies
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Michael W. Marcus
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Gary E. Goodman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Aage Haugen
- National Institute of Occupational Health, Oslo, Norway
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | | | | | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | | | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Maria Teresa Landi
- Genetic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Rockville, Maryland, United States of America
| | - Philip Lazarus
- Washington State University College of Pharmacy, Spokane, Washington, United States of America
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Geoffrey Liu
- Ontario Cancer Institute, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Sungshim L. Park
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gad Rennert
- Clalit National Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Ghislaine Scelo
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, The Russian Federation
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow, The Russian Federation
| | - Milan Savić
- Department of Thoracic Surgery, Clinical Center of Serbia, Belgrade, Serbia
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Institute – Oncology Center, Warsaw, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - Vladimir Janout
- Department of Epidemiology and Public Health, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Matthew B. Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Adonina Tardon
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo and CIBERESP, Oviedo, Spain
| | - M Dawn Teare
- University of Sheffield, Sheffield, United Kingdom
| | - Penella Woll
- University of Sheffield, Sheffield, United Kingdom
| | | | - Xifeng Wu
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jian-Min Yuan
- Division of Cancer Control and Population Science, University of Pittsburgh Cancer Institute; and Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Christopher I. Amos
- Department of Biomedical Data Science, Geisel School of medicine, Dartmouth College, Lebanon, New Hampshire, United States of America
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
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Yin J, Liu H, Liu Z, Owzar K, Han Y, Su L, Wei Y, Hung RJ, Brhane Y, McLaughlin J, Brennan P, Bickeboeller H, Rosenberger A, Houlston RS, Caporaso N, Landi MT, Heinrich J, Risch A, Christiani DC, Amos CI, Wei Q. Pathway-analysis of published genome-wide association studies of lung cancer: A potential role for the CYP4F3 locus. Mol Carcinog 2017; 56:1663-1672. [PMID: 28150878 PMCID: PMC5423820 DOI: 10.1002/mc.22622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 01/30/2017] [Indexed: 12/14/2022]
Abstract
The fatty acids (FAs) metabolism is suggested to play a pivotal role in the development of lung cancer, and we explored that by conducting a pathway-based analysis. We performed a meta-analysis of published datasets of six genome wide association studies (GWASs) from the Transdisciplinary Research in Cancer of the Lung (TRICL) consortium, which included 12 160 cases with lung cancer and 16 838 cancer-free controls. A total of 30 722 single-nucleotide polymorphisms (SNPs) from 317 genes relevant to FA metabolic pathways were identified. An additional dataset from the Harvard Lung Cancer Study with 984 cases and 970 healthy controls was also added to the final meta-analysis. In the initial meta-analysis, 26 of 28 SNPs that passed false discovery rate multiple tests were mapped to the CYP4F3 gene. Among the 26 top ranked hits was a proxy SNP, CYP4F3 rs4646904 (P = 8.65 × 10-6 , FDR = 0.018), which is suggested to change splicing pattern/efficiency and to be associated with gene expression levels. However, after adding data of rs4646904 from the Harvard GWAS, the significance in the combined analysis was reduced to P = 3.52 × 10-3 [odds ratio (OR) = 1.07, 95% confidence interval (95%CI) = 1.03-1.12]. Interestingly, the small Harvard dataset also pointed to the same direction of the association in subgroups of smokers (OR = 1.07) and contributed to a combined OR of 1.13 (95% CI = 1.06-1.20, P = 6.70 × 10-5 ). The results suggest that a potentially functional SNP in CYP4F3 (rs4646904) may contribute to the etiology of lung cancer, especially in smokers. Additional mechanistic studies are warranted to unravel the potential biological significance of the finding.
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Affiliation(s)
- Jieyun Yin
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, 199 Ren Ai Road, Suzhou, China
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC
| | - Younghun Han
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Li Su
- Massachusetts General Hospital, Boston, MA
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Yongyue Wei
- Massachusetts General Hospital, Boston, MA
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Heike Bickeboeller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Neil Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Maria Teresa Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joachim Heinrich
- Helmholtz Centre Munich, German Research Centre for Environmental Health, Institute of Epidemiology I, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich, Ludwig Maximilian University Munich, Munich, Germany
| | - Angela Risch
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
- Department of Epigenomics and Cancer Risk Factors, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - David C. Christiani
- Massachusetts General Hospital, Boston, MA
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Christopher I. Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
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95
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Toth R, Scherer D, Kelemen LE, Risch A, Hazra A, Balavarca Y, Issa JPJ, Moreno V, Eeles RA, Ogino S, Wu X, Ye Y, Hung RJ, Goode EL, Ulrich CM. Genetic Variants in Epigenetic Pathways and Risks of Multiple Cancers in the GAME-ON Consortium. Cancer Epidemiol Biomarkers Prev 2017; 26:816-825. [PMID: 28115406 PMCID: PMC6054308 DOI: 10.1158/1055-9965.epi-16-0728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 11/16/2022] Open
Abstract
Background: Epigenetic disturbances are crucial in cancer initiation, potentially with pleiotropic effects, and may be influenced by the genetic background.Methods: In a subsets (ASSET) meta-analytic approach, we investigated associations of genetic variants related to epigenetic mechanisms with risks of breast, lung, colorectal, ovarian and prostate carcinomas using 51,724 cases and 52,001 controls. False discovery rate-corrected P values (q values < 0.05) were considered statistically significant.Results: Among 162,887 imputed or genotyped variants in 555 candidate genes, SNPs in eight genes were associated with risk of more than one cancer type. For example, variants in BABAM1 were confirmed as a susceptibility locus for squamous cell lung, overall breast, estrogen receptor (ER)-negative breast, and overall prostate, and overall serous ovarian cancer; the most significant variant was rs4808076 [OR = 1.14; 95% confidence interval (CI) = 1.10-1.19; q = 6.87 × 10-5]. DPF1 rs12611084 was inversely associated with ER-negative breast, endometrioid ovarian, and overall and aggressive prostate cancer risk (OR = 0.93; 95% CI = 0.91-0.96; q = 0.005). Variants in L3MBTL3 were associated with colorectal, overall breast, ER-negative breast, clear cell ovarian, and overall and aggressive prostate cancer risk (e.g., rs9388766: OR = 1.06; 95% CI = 1.03-1.08; q = 0.02). Variants in TET2 were significantly associated with overall breast, overall prostate, overall ovarian, and endometrioid ovarian cancer risk, with rs62331150 showing bidirectional effects. Analyses of subpathways did not reveal gene subsets that contributed disproportionately to susceptibility.Conclusions: Functional and correlative studies are now needed to elucidate the potential links between germline genotype, epigenetic function, and cancer etiology.Impact: This approach provides novel insight into possible pleiotropic effects of genes involved in epigenetic processes. Cancer Epidemiol Biomarkers Prev; 26(6); 816-25. ©2017 AACR.
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Affiliation(s)
- Reka Toth
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Scherer
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Linda E Kelemen
- Medical University of South Carolina and Hollings Cancer Center, Charleston, South Carolina
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Cancer Research and Epigenetics, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Aditi Hazra
- Brigham and Women's Hospital, Harvard Medical School, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yesilda Balavarca
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Victor Moreno
- Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | | | - Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- University of Toronto, Toronto, Canada
| | - Ellen L Goode
- Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Cornelia M Ulrich
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Huntsman Cancer Institute, Salt Lake City, Utah
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96
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Wang F, Li H, Long J, Ye S. Clinicopathological significance of p14 ARF expression in lung cancer: a meta-analysis. Onco Targets Ther 2017; 10:2491-2499. [PMID: 28507441 PMCID: PMC5428763 DOI: 10.2147/ott.s131954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND p14ARF, a tumor suppressor protein, encoded by the p16 tumor suppressor gene, has been reported to be associated with the clinicopathological features of lung cancer. However, the evaluated outcomes were inconsistent and remained inconclusive. In this study, we conducted a meta-analysis to clarify the significance of p14ARF expression in lung cancer pathogenesis. MATERIALS AND METHODS Electronic databases, PubMed, Web of Knowledge, Embase, and CNKI, were retrieved to collect relevant articles with inclusion and exclusion criteria. Using Stata 12.0 software, 95% confidence intervals (CIs) and odds ratios (ORs) were calculated. RESULTS A total of 15 eligible case-control studies that evaluated the relationship between p14ARF expression and lung cancer were included in the meta-analysis. The results demonstrated that there were significant associations between p14ARF expression and the risk of non-small-cell lung cancer (NSCLC), lung adenocarcinoma, and lung squamous carcinoma (for NSCLC, OR =11.02, 95% CI =5.30-22.92; for lung adenocarcinoma, OR =7.28, 95% CI =3.92-13.50; and for lung squamous carcinoma, OR =14.40, 95% CI =2.83-73.24). In the stratified analysis based on race, significant associations between p14ARF expression and lung cancer risk were found in Chinese population and Caucasians (for Chinese population, OR = 7.02, 95% CI =4.48-11.00 and for Caucasians, OR =4.19, 95% CI =1.42-12.38). Furthermore, the expression of p14ARF was significantly associated with the TNM-stage of lung cancer in Chinese population (OR =2.07, 95% CI =1.38-3.10). CONCLUSION p14ARF expression was significantly associated with the risk of lung cancer. In addition, the data of the meta-analysis showed that there was a significant correlation between p14ARF expression and the TNM-stage of lung cancer in Chinese population.
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Affiliation(s)
- Fang Wang
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou City, Guangdong Province, People’s Republic of China
| | - Heping Li
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou City, Guangdong Province, People’s Republic of China
| | - Jianting Long
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou City, Guangdong Province, People’s Republic of China
| | - Sheng Ye
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou City, Guangdong Province, People’s Republic of China
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97
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Liu H, Liu Z, Wang Y, Stinchcombe TE, Owzar K, Han Y, Hung RJ, Brhane Y, McLaughlin J, Brennan P, Bickeböller H, Rosenberger A, Houlston RS, Caporaso N, Landi MT, Brüske I, Risch A, Wu X, Ye Y, Christiani DC, Amos CI, Wei Q. Functional variants in DCAF4 associated with lung cancer risk in European populations. Carcinogenesis 2017; 38:541-551. [PMID: 28383684 PMCID: PMC6074950 DOI: 10.1093/carcin/bgx033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/13/2017] [Accepted: 03/24/2017] [Indexed: 11/14/2022] Open
Abstract
Cullin-RING ubiquitin ligases (CRLs) responsible for substrate specificity of ubiquitination play a key role in cell-cycle control and DNA damage response. In this study, we assessed associations between 16 599 SNPs in 115 CRL genes and lung cancer risk by using summary data of six published genome-wide association studies (GWASs) of 12 160 cases and 16 838 cases of European ancestry. As a result, we identified three independent SNPs in DCAF4 (rs117781739, rs12587742 and rs2240980) associated with lung cancer risk (odds ratio = 0.91, 1.09 and 1.09, respectively; 95% confidence interval = 0.88-0.95, 1.05-1.14 and 1.05-1.13, respectively; and P = 3.99 × 10-6, 4.97 × 10-5 and 1.44 × 10-5, respectively) after multiple comparison correction by a false discovery rate <0.05. Since SNP rs12587742 is located within the promoter region and one CpG island of DCAF4, we further performed in silico functional analyses and found that the rs12587742 variant A allele was associated with an increased mRNA expression (P = 2.20 × 10-16, 1.79 × 10-13 and 0.001 in blood cells, normal lung tissues and tumor tissues of lung squamous carcinoma, respectively) and a decreased methylation status (P = 2.48 × 10-9 and 0.032 in adipose and lung tumor tissues, respectively). Moreover, evidence from differential expression analyses further supported an oncogenic effect of DCAF4 on lung cancer, with higher mRNA levels in both lung squamous carcinoma and adenocarcinoma (P = 4.48 × 10-11 and 1.22 × 10-9, respectively) than in adjacent normal tissues. Taken together, our results suggest that rs12587742 is associated with an increased lung cancer risk, possibly by up-regulating mRNA expression and decreasing methylation status of DCAF4.
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Affiliation(s)
- Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas E Stinchcombe
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Younghun Han
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5,Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5,Canada
| | | | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, 69372 Lyon, France
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Richard S Houlston
- Division of Genetics and Epidemiology, the Institute of Cancer Research, London SW7 3RP, UK
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irene Brüske
- Helmholtz Centre Munich, German Research Centre for Environmental Health, Institute of Epidemiology I, 85764 Neuherberg, Germany
| | - Angela Risch
- Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David C Christiani
- Massachusetts General Hospital, Boston, MA 02114, USA and
- Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA
| | - Christopher I Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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98
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Richmond-Rakerd LS, Otto JM, Slutske WS, Ehlers CL, Wilhelmsen KC, Gizer IR. A Novel Tobacco Use Phenotype Suggests the 15q25 and 19q13 Loci May be Differentially Associated With Cigarettes per Day and Tobacco-Related Problems. Nicotine Tob Res 2017; 19:426-434. [PMID: 27663783 PMCID: PMC5968625 DOI: 10.1093/ntr/ntw260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/22/2016] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Tobacco use is associated with variation at the 15q25 gene cluster and the cytochrome P450 (CYP) genes CYP2A6 and CYP2B6. Despite the variety of outcomes associated with these genes, few studies have adopted a data-driven approach to defining tobacco use phenotypes for genetic association analyses. We used factor analysis to generate a tobacco use measure, explored its incremental validity over a simple indicator of tobacco involvement: cigarettes per day (CPD), and tested both phenotypes in a genetic association study. METHODS Data were from the University of California, San Francisco Family Alcoholism Study (n = 1942) and a Native American sample (n = 255). Factor analyses employed a broad array of tobacco use variables to establish the candidate phenotype. Subsequently, we conducted tests for association with variants in the nicotinic acetylcholine receptor and CYP genes. We explored associations with CPD and our measure. We then examined whether the variants most strongly associated with our measure remained associated after controlling for CPD. RESULTS Analyses identified one factor that captured tobacco-related problems. Variants at 15q25 were significantly associated with CPD after multiple testing correction (rs938682: p = .00002, rs1051730: p = .0003, rs16969968: p = .0003). No significant associations were obtained with the tobacco use phenotype; however, suggestive associations were observed for variants in CYP2B6 near CYP2A6 (rs45482602: ps = .0082, .0075) and CYP4Z2P (rs10749865: ps = .0098, .0079). CONCLUSIONS CPD captures variation at 15q25. Although strong conclusions cannot be drawn, these finding suggest measuring additional dimensions of problems may detect genetic variation not accounted for by smoking quantity. Replication in independent samples will help further refine phenotype definition efforts. IMPLICATIONS Different facets of tobacco-related problems may index unique genetic risk. CPD, a simple measure of tobacco consumption, is associated with variants at the 15q25 gene cluster. Additional dimensions of tobacco problems may help to capture variation at 19q13. Results demonstrate the utility of adopting a data-driven approach to defining phenotypes for genetic association studies of tobacco involvement and provide results that can inform replication efforts.
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Affiliation(s)
- Leah S Richmond-Rakerd
- Department of Psychological Sciences, University of Missouri, Columbia, MO
- Alcoholism Research Center at Washington University School of Medicine, St. Louis, MO
| | - Jacqueline M Otto
- Department of Psychological Sciences, University of Missouri, Columbia, MO
- Alcoholism Research Center at Washington University School of Medicine, St. Louis, MO
| | - Wendy S Slutske
- Department of Psychological Sciences, University of Missouri, Columbia, MO
- Alcoholism Research Center at Washington University School of Medicine, St. Louis, MO
| | - Cindy L Ehlers
- Department of Molecular and Cellular Neurosciences (CLE), The Scripps Research Institute, La Jolla, CA
| | - Kirk C Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ian R Gizer
- Department of Psychological Sciences, University of Missouri, Columbia, MO
- Alcoholism Research Center at Washington University School of Medicine, St. Louis, MO
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99
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Zuber V, Bettella F, Witoelar A, Andreassen OA, Mills IG, Urbanucci A. Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. BMC Genomics 2017; 18:270. [PMID: 28359301 PMCID: PMC5374680 DOI: 10.1186/s12864-017-3620-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/11/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Epigenetic information can be used to identify clinically relevant genomic variants single nucleotide polymorphisms (SNPs) of functional importance in cancer development. Super-enhancers are cell-specific DNA elements, acting to determine tissue or cell identity and driving tumor progression. Although previous approaches have been tried to explain risk associated with SNPs in regulatory DNA elements, so far epigenetic readers such as bromodomain containing protein 4 (BRD4) and super-enhancers have not been used to annotate SNPs. In prostate cancer (PC), androgen receptor (AR) binding sites to chromatin have been used to inform functional annotations of SNPs. RESULTS Here we establish criteria for enhancer mapping which are applicable to other diseases and traits to achieve the optimal tissue-specific enrichment of PC risk SNPs. We used stratified Q-Q plots and Fisher test to assess the differential enrichment of SNPs mapping to specific categories of enhancers. We find that BRD4 is the key discriminant of tissue-specific enhancers, showing that it is more powerful than AR binding information to capture PC specific risk loci, and can be used with similar effect in breast cancer (BC) and applied to other diseases such as schizophrenia. CONCLUSIONS This is the first study to evaluate the enrichment of epigenetic readers in genome-wide associations studies for SNPs within enhancers, and provides a powerful tool for enriching and prioritizing PC and BC genetic risk loci. Our study represents a proof of principle applicable to other diseases and traits that can be used to redefine molecular mechanisms of human phenotypic variation.
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Affiliation(s)
- Verena Zuber
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Francesco Bettella
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Aree Witoelar
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - the CRUK GWAS
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- PCUK Movember Centre of Excellence, CCRCB, Queen’s University, Belfast, UK
| | - the TRICL Consortium
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- PCUK Movember Centre of Excellence, CCRCB, Queen’s University, Belfast, UK
| | - Ole A. Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ian G. Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- PCUK Movember Centre of Excellence, CCRCB, Queen’s University, Belfast, UK
| | - Alfonso Urbanucci
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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100
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Rosenberger A, Sohns M, Friedrichs S, Hung RJ, Fehringer G, McLaughlin J, Amos CI, Brennan P, Risch A, Brüske I, Caporaso NE, Landi MT, Christiani DC, Wei Y, Bickeböller H. Gene-set meta-analysis of lung cancer identifies pathway related to systemic lupus erythematosus. PLoS One 2017; 12:e0173339. [PMID: 28273134 PMCID: PMC5342225 DOI: 10.1371/journal.pone.0173339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/20/2017] [Indexed: 02/03/2023] Open
Abstract
INTRODUCTION Gene-set analysis (GSA) is an approach using the results of single-marker genome-wide association studies when investigating pathways as a whole with respect to the genetic basis of a disease. METHODS We performed a meta-analysis of seven GSAs for lung cancer, applying the method META-GSA. Overall, the information taken from 11,365 cases and 22,505 controls from within the TRICL/ILCCO consortia was used to investigate a total of 234 pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. RESULTS META-GSA reveals the systemic lupus erythematosus KEGG pathway hsa05322, driven by the gene region 6p21-22, as also implicated in lung cancer (p = 0.0306). This gene region is known to be associated with squamous cell lung carcinoma. The most important genes driving the significance of this pathway belong to the genomic areas HIST1-H4L, -1BN, -2BN, -H2AK, -H4K and C2/C4A/C4B. Within these areas, the markers most significantly associated with LC are rs13194781 (located within HIST12BN) and rs1270942 (located between C2 and C4A). CONCLUSIONS We have discovered a pathway currently marked as specific to systemic lupus erythematosus as being significantly implicated in lung cancer. The gene region 6p21-22 in this pathway appears to be more extensively associated with lung cancer than previously assumed. Given wide-stretched linkage disequilibrium to the area APOM/BAG6/MSH5, there is currently simply not enough information or evidence to conclude whether the potential pleiotropy of lung cancer and systemic lupus erythematosus is spurious, biological, or mediated. Further research into this pathway and gene region will be necessary.
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Affiliation(s)
- Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Melanie Sohns
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefanie Friedrichs
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Gord Fehringer
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | | | - Christopher I. Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Angela Risch
- Division of Molecular Biology, University Salzburg, Salzburg, Austria
| | - Irene Brüske
- Institute of Epidemiology I, Helmholtz Center Munich, Munich, Germany
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - David C. Christiani
- Harvard University School of Public Health, Boston, Massachusetts, United States of America
| | - Yongyue Wei
- Harvard University School of Public Health, Boston, Massachusetts, United States of America
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
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