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Gao Y, Cui Y. Optimizing clinico-genomic disease prediction across ancestries: a machine learning strategy with Pareto improvement. Genome Med 2024; 16:76. [PMID: 38835075 DOI: 10.1186/s13073-024-01345-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Accurate prediction of an individual's predisposition to diseases is vital for preventive medicine and early intervention. Various statistical and machine learning models have been developed for disease prediction using clinico-genomic data. However, the accuracy of clinico-genomic prediction of diseases may vary significantly across ancestry groups due to their unequal representation in clinical genomic datasets. METHODS We introduced a deep transfer learning approach to improve the performance of clinico-genomic prediction models for data-disadvantaged ancestry groups. We conducted machine learning experiments on multi-ancestral genomic datasets of lung cancer, prostate cancer, and Alzheimer's disease, as well as on synthetic datasets with built-in data inequality and distribution shifts across ancestry groups. RESULTS Deep transfer learning significantly improved disease prediction accuracy for data-disadvantaged populations in our multi-ancestral machine learning experiments. In contrast, transfer learning based on linear frameworks did not achieve comparable improvements for these data-disadvantaged populations. CONCLUSIONS This study shows that deep transfer learning can enhance fairness in multi-ancestral machine learning by improving prediction accuracy for data-disadvantaged populations without compromising prediction accuracy for other populations, thus providing a Pareto improvement towards equitable clinico-genomic prediction of diseases.
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Affiliation(s)
- Yan Gao
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
- Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Yan Cui
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
- Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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2
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Asadi-Tarani M, Darashti A, Javadi M, Rezaei M, Saravani M, Salimi S. The effects of ANRIL polymorphisms on colorectal cancer, tumor stage, and tumor grade among Iranian population. Mol Biol Rep 2024; 51:486. [PMID: 38578390 DOI: 10.1007/s11033-024-09420-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is a type of neoplasm, developing in the colon or rectum. The exact etiology of CRC is not well known, but the role of genetic, epigenetic, and environmental factors are established in its pathogenesis. Therefore, the aim of this research was to explore the effects of ANRIL polymorphisms on the CRC and its clinical findings. METHODS AND RESULTS The peripheral blood specimens were collected from 142 CRC patients and 225 controls referred to Milad Hospital, Tehran, Iran. PCR- RFLP method was used to analyze ANRIL rs1333040, rs10757274 rs4977574, and rs1333048 polymorphisms. The ANRIL rs1333040 polymorphism was related to a higher risk of CRC in the co-dominant, dominant, and log-additive models. ANRIL rs10757274, rs4977574, and rs1333048 polymorphisms showed no effect on CRC susceptibility. The CGAA and TGGA haplotypes of ANRIL rs1333040/ rs10757274/ rs4977574/rs1333048 polymorphisms were associated with the higher and the lower risk of CRC respectively. The rs1333040 polymorphism was associated with higher TNM stages (III and IV). The frequency of ANRIL rs10757274 polymorphism was lower in CRC patients over 50 years of age only in the dominant model. In addition, the rs10757274 was associated with well differentiation in CRC patients. CONCLUSION The ANRIL rs1333040 polymorphism was associated with a higher risk of CRC and higher TNM stages. ANRIL rs10757274 polymorphism was associated with the well-differentiated tumor in CRC.
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Affiliation(s)
- Mina Asadi-Tarani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | | | - Mahnaz Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Saravani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saeedeh Salimi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Zhang L, Xiong Y, Zhang J, Feng Y, Xu A. Systematic proteome-wide Mendelian randomization using the human plasma proteome to identify therapeutic targets for lung adenocarcinoma. J Transl Med 2024; 22:330. [PMID: 38576019 PMCID: PMC10993587 DOI: 10.1186/s12967-024-04919-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the predominant histological subtype of lung cancer and the leading cause of cancer-related mortality. Identifying effective drug targets is crucial for advancing LUAD treatment strategies. METHODS This study employed proteome-wide Mendelian randomization (MR) and colocalization analyses. We collected data on 1394 plasma proteins from a protein quantitative trait loci (pQTL) study involving 4907 individuals. Genetic associations with LUAD were derived from the Transdisciplinary Research in Cancer of the Lung (TRICL) study, including 11,245 cases and 54,619 controls. We integrated pQTL and LUAD genome-wide association studies (GWASs) data to identify candidate proteins. MR utilizes single nucleotide polymorphisms (SNPs) as genetic instruments to estimate the causal effect of exposure on outcome, while Bayesian colocalization analysis determines the probability of shared causal genetic variants between traits. Our study applied these methods to assess causality between plasma proteins and LUAD. Furthermore, we employed a two-step MR to quantify the proportion of risk factors mediated by proteins on LUAD. Finally, protein-protein interaction (PPI) analysis elucidated potential links between proteins and current LUAD medications. RESULTS We identified nine plasma proteins significantly associated with LUAD. Increased levels of ALAD, FLT1, ICAM5, and VWC2 exhibited protective effects, with odds ratios of 0.79 (95% CI 0.72-0.87), 0.39 (95% CI 0.28-0.55), 0.91 (95% CI 0.72-0.87), and 0.85 (95% CI 0.79-0.92), respectively. Conversely, MDGA2 (OR, 1.13; 95% CI 1.08-1.19), NTM (OR, 1.12; 95% CI 1.09-1.16), PMM2 (OR, 1.35; 95% CI 1.18-1.53), RNASET2 (OR, 1.15; 95% CI 1.08-1.21), and TFPI (OR, 4.58; 95% CI 3.02-6.94) increased LUAD risk. Notably, none of the nine proteins showed evidence of reverse causality. Bayesian colocalization indicated that RNASET2, TFPI, and VWC2 shared the same variant with LUAD. Furthermore, NTM and FLT1 demonstrated interactions with targets of current LUAD medications. Additionally, FLT1 and TFPI are currently under evaluation as therapeutic targets, while NTM, RNASET2, and VWC2 are potentially druggable. These findings shed light on LUAD pathogenesis, highlighting the tumor-promoting effects of RNASET2, TFPI, and NTM, along with the protective effects of VWC2 and FLT1, providing a significant biological foundation for future LUAD therapeutic targets. CONCLUSIONS Our proteome-wide MR analysis highlighted RNASET2, TFPI, VWC2, NTM, and FLT1 as potential drug targets for further clinical investigation in LUAD. However, the specific mechanisms by which these proteins influence LUAD remain elusive. Targeting these proteins in drug development holds the potential for successful clinical trials, providing a pathway to prioritize and reduce costs in LUAD therapeutics.
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Affiliation(s)
- Long Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yajun Xiong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuying Feng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Aiguo Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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Duncan MS, Diaz-Zabala H, Jaworski J, Tindle HA, Greevy RA, Lipworth L, Hung RJ, Freiberg MS, Aldrich MC. Interaction between Continuous Pack-Years Smoked and Polygenic Risk Score on Lung Cancer Risk: Prospective Results from the Framingham Heart Study. Cancer Epidemiol Biomarkers Prev 2024; 33:500-508. [PMID: 38227004 PMCID: PMC10988206 DOI: 10.1158/1055-9965.epi-23-0571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/13/2023] [Accepted: 01/11/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Lung cancer risk attributable to smoking is dose dependent, yet few studies examining a polygenic risk score (PRS) by smoking interaction have included comprehensive lifetime pack-years smoked. METHODS We analyzed data from participants of European ancestry in the Framingham Heart Study Original (n = 454) and Offspring (n = 2,470) cohorts enrolled in 1954 and 1971, respectively, and followed through 2018. We built a PRS for lung cancer using participant genotyping data and genome-wide association study summary statistics from a recent study in the OncoArray Consortium. We used Cox proportional hazards regression models to assess risk and the interaction between pack-years smoked and genetic risk for lung cancer adjusting for European ancestry, age, sex, and education. RESULTS We observed a significant submultiplicative interaction between pack-years and PRS on lung cancer risk (P = 0.09). Thus, the relative risk associated with each additional 10 pack-years smoked decreased with increasing genetic risk (HR = 1.56 at one SD below mean PRS, HR = 1.48 at mean PRS, and HR = 1.40 at one SD above mean PRS). Similarly, lung cancer risk per SD increase in the PRS was highest among those who had never smoked (HR = 1.55) and decreased with heavier smoking (HR = 1.32 at 30 pack-years). CONCLUSIONS These results suggest the presence of a submultiplicative interaction between pack-years and genetics on lung cancer risk, consistent with recent findings. Both smoking and genetics were significantly associated with lung cancer risk. IMPACT These results underscore the contributions of genetics and smoking on lung cancer risk and highlight the negative impact of continued smoking regardless of genetic risk.
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Affiliation(s)
- Meredith S. Duncan
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hector Diaz-Zabala
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James Jaworski
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hilary A. Tindle
- Geriatric Research Education and Clinical Centers (GRECC), Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
- Division of Internal Medicine, Vanderbilt University Medical Center, Nashville Tennessee
| | - Robert A. Greevy
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Loren Lipworth
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rayjean J. Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Matthew S. Freiberg
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Geriatric Research Education and Clinical Centers (GRECC), Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Melinda C. Aldrich
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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Chen X, Wang S, Shen W. The causal relationship between severe mental illness and risk of lung carcinoma. Medicine (Baltimore) 2024; 103:e37355. [PMID: 38489734 PMCID: PMC10939700 DOI: 10.1097/md.0000000000037355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 03/17/2024] Open
Abstract
Observational studies have suggested a link between severe mental illness (SMI) and risk of lung carcinoma (LC); however, causality has not been established. In this study, we conducted a two-sample, two-step Mendelian randomization (MR) investigation to uncover the etiological influence of SMI on LC risk and quantify the mediating effects of known modifiable risk factors. We obtained summary-level datasets for schizophrenia, major depressive disorder (MDD), and bipolar disorder (BD) from the Psychiatric Genomics Consortium (PGC). Data on single nucleotide polymorphisms (SNPs) associated with lung carcinoma (LC) were sourced from a recent large meta-analysis by McKay et al. We employed two-sample MR and two-step MR utilizing the inverse variance weighted method for causal estimation. Sensitivity tests were conducted to validate causal relationships. In two-sample MR, we identified schizophrenia as a risk factor for LC (OR = 1.06, 95% CI 1.02-1.11, P = 3.48E-03), while MDD (OR = 1.18, 95% CI 0.98-1.42, P = .07) and BD (OR = 1.07, 95% CI 0.99-1.15, P = .09) showed no significant association with LC. In the two-step MR, smoking accounted for 24.66% of the schizophrenia-LC risk association, and alcohol consumption explained 7.59% of the effect. Schizophrenia is a risk factor for lung carcinoma, and smoking and alcohol consumption are the mediating factors in this causal relationship. LC screening should be emphasized in individuals with schizophrenia, particularly in those who smoke and consume alcohol regularly.
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Affiliation(s)
- Xiaohan Chen
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Shudan Wang
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Weiyu Shen
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
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Wang X, Zhang Z, Ding Y, Chen T, Mucci L, Albanes D, Landi MT, Caporaso NE, Lam S, Tardon A, Chen C, Bojesen SE, Johansson M, Risch A, Bickeböller H, Wichmann HE, Rennert G, Arnold S, Brennan P, McKay JD, Field JK, Shete SS, Le Marchand L, Liu G, Andrew AS, Kiemeney LA, Zienolddiny-Narui S, Behndig A, Johansson M, Cox A, Lazarus P, Schabath MB, Aldrich MC, Hung RJ, Amos CI, Lin X, Christiani DC. Impact of individual level uncertainty of lung cancer polygenic risk score (PRS) on risk stratification. Genome Med 2024; 16:22. [PMID: 38317189 PMCID: PMC10840262 DOI: 10.1186/s13073-024-01298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 01/26/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Although polygenic risk score (PRS) has emerged as a promising tool for predicting cancer risk from genome-wide association studies (GWAS), the individual-level accuracy of lung cancer PRS and the extent to which its impact on subsequent clinical applications remains largely unexplored. METHODS Lung cancer PRSs and confidence/credible interval (CI) were constructed using two statistical approaches for each individual: (1) the weighted sum of 16 GWAS-derived significant SNP loci and the CI through the bootstrapping method (PRS-16-CV) and (2) LDpred2 and the CI through posteriors sampling (PRS-Bayes), among 17,166 lung cancer cases and 12,894 controls with European ancestry from the International Lung Cancer Consortium. Individuals were classified into different genetic risk subgroups based on the relationship between their own PRS mean/PRS CI and the population level threshold. RESULTS Considerable variances in PRS point estimates at the individual level were observed for both methods, with an average standard deviation (s.d.) of 0.12 for PRS-16-CV and a much larger s.d. of 0.88 for PRS-Bayes. Using PRS-16-CV, only 25.0% of individuals with PRS point estimates in the lowest decile of PRS and 16.8% in the highest decile have their entire 95% CI fully contained in the lowest and highest decile, respectively, while PRS-Bayes was unable to find any eligible individuals. Only 19% of the individuals were concordantly identified as having high genetic risk (> 90th percentile) using the two PRS estimators. An increased relative risk of lung cancer comparing the highest PRS percentile to the lowest was observed when taking the CI into account (OR = 2.73, 95% CI: 2.12-3.50, P-value = 4.13 × 10-15) compared to using PRS-16-CV mean (OR = 2.23, 95% CI: 1.99-2.49, P-value = 5.70 × 10-46). Improved risk prediction performance with higher AUC was consistently observed in individuals identified by PRS-16-CV CI, and the best performance was achieved by incorporating age, gender, and detailed smoking pack-years (AUC: 0.73, 95% CI = 0.72-0.74). CONCLUSIONS Lung cancer PRS estimates using different methods have modest correlations at the individual level, highlighting the importance of considering individual-level uncertainty when evaluating the practical utility of PRS.
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Affiliation(s)
- Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, 667 Huntington Ave, Boston, MA, 02115, USA
| | - Ziwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA
| | - Tony Chen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Lorelei Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Demetrios Albanes
- 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
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen Lam
- Department of Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Department of Epidemiology, University of Washington School of Public Health, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Angela Risch
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, and Cancer Cluster Salzburg, Salzburg, Austria
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
| | - Gadi Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Carmel, Haifa, Israel
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James D McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sanjay S Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Angeline S Andrew
- Department of Epidemiology, Department of Community and Family Medicine, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Lambertus A Kiemeney
- Department for Health Evidence, Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Annelie Behndig
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | | | - Angie Cox
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Melinda C Aldrich
- Department of Medicine, Department of Biomedical Informatics and Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, 667 Huntington Ave, Boston, MA, 02115, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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Enjo-Barreiro JR, Ruano-Ravina A, Pérez-Ríos M, Kelsey K, Barros-Dios JM, Varela-Lema L. Genome Wide Association Studies in Small-Cell Lung Cancer. A Systematic Review. Clin Lung Cancer 2024; 25:9-17. [PMID: 37940411 DOI: 10.1016/j.cllc.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/28/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
Small cell lung cancer (SCLC) is one of the deadliest forms of lung cancer, but few information exists regarding the role of genetics, particularly on Genome Wide Association Studies (GWAS). The aim of the study is to explore the evidence available obtained through GWAS studies for SCLC using a systematic review. We performed a literature search in the main databases until July 31st, 2023. We included all human based studies on GWAS for lung cancer which presented results for SCLC. Only studies with participants diagnosed of SCLC with anatomopathological confirmation were included. Fourteen studies were identified; 8 studies showed a relationship between ASCL1 overexpression and SCLC, which may regulate CHRNA5/A3/B4 cluster, producing a consequent nAChR overexpression. Nine papers, including 8 of the previous, found a positive association between SNPs located in chromosome 15 and SCLC. The most important cluster of genes found is CHRNA5/A3/B4 but the mechanism for the role of these genes is unclear. Kyoto Encyclopaedia of Genes and Genome (KEGG) shows that these receptors were found to be overexpressed where nicotine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-Nitrosonornicotine (NNN) acts, involving different routes in SCLC carcinogenesis.
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Affiliation(s)
- José Ramón Enjo-Barreiro
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain; Service of Preventive Medicine, A Coruña University Teaching Hospital Complex, A Coruña, Spain
| | - Alberto Ruano-Ravina
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Santiago de Compostela, Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain.
| | - Mónica Pérez-Ríos
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Santiago de Compostela, Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain
| | - Karl Kelsey
- Department of Epidemiology, Brown School of Public Health, Brown University, Providence, RI
| | - Juan Miguel Barros-Dios
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Santiago de Compostela, Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain
| | - Leonor Varela-Lema
- Department of Preventive Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Santiago de Compostela, Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain
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8
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Enjo-Barreiro JR, Ruano-Ravina A, Diz-de-Almeida S, Cruz R, Quintela I, Rey-Brandariz J, Carracedo Á, Kelsey K, Provencio M, Barros-Dios J, Varela-Lema L, Pérez-Ríos M. A Genome-Wide Association Study of Small Cell Lung Cancer. Arch Bronconeumol 2023; 59:645-650. [PMID: 37500326 DOI: 10.1016/j.arbres.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Abstract
INTRODUCTION Small cell lung cancer (SCLC) comprises 10-15% of all lung cancer cases and is the most aggressive histological type. Survival is poor and the molecular landscape of this disease is extraordinarily complex. The objective of this paper was to perform a Genome-Wide Association Study (GWAS) of this disease using a case-control study specifically designed for small cell lung cancer (SCLC). METHODS Incident cases were consecutively recruited from 8 hospitals from different regions of Spain. Controls were recruited from the same hospitals using a frequency sampling based on age and sex distribution of cases. Biological samples were obtained along with detailed information on cases and controls lifestyle, including tobacco and radon exposure. RESULTS We included 271 SCLC cases and 557 controls. We found evidence (p-values<10-5) of an association in the complete dataset for several loci, while MAP4 showed a significant association in the gene-based analysis. Pathway analysis suggested that ATR, ATRIP, MCM4, MCM5, ORC4, RPA3 and CDC25A genes have a role on the onset of SCLC. CONCLUSION This study provides biological evidence for pathways related to SCLC, offering novel loci for further research.
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Affiliation(s)
- José Ramón Enjo-Barreiro
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Spain
| | - Alberto Ruano-Ravina
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain.
| | - Silvia Diz-de-Almeida
- Grupo de Medicina Xenómica CIBERER-Instituto de Salud Carlos III (U-711), Centro Singular de Investigación en Medicina Molecular y Enfermedades Cronicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Raquel Cruz
- Grupo de Medicina Xenómica CIBERER-Instituto de Salud Carlos III (U-711), Centro Singular de Investigación en Medicina Molecular y Enfermedades Cronicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inés Quintela
- Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Julia Rey-Brandariz
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica CIBERER-Instituto de Salud Carlos III (U-711), Centro Singular de Investigación en Medicina Molecular y Enfermedades Cronicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Karl Kelsey
- Department of Epidemiology and Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Mariano Provencio
- Department of Medical Oncology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - Juan Barros-Dios
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain
| | - Leonor Varela-Lema
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain
| | - Mónica Pérez-Ríos
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública - CIBERESP), Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela - IDIS), Santiago de Compostela, Spain
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9
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Fan J, Hong T, Zhao X, Liang S, Zhu M, Jiang Y, Jin G, Hu Z, Ma H, Dai J, Shen H. A two-stage genome-wide association study identified four potential early-onset nonsmall cell lung cancer risk loci based on 26,652 participants in Chinese population. Mol Carcinog 2023; 62:1263-1270. [PMID: 37232355 DOI: 10.1002/mc.23561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/28/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023]
Abstract
Early-onset lung cancer is rare with an increasing incidence rate. Although several genetic variants have been identified for it with candidate gene approaches, no genome-wide association study (GWAS) has been reported. In this study, a two-stage strategy was adopted: firstly we performed a GWAS to identify variants associated with early-onset nonsmall-cell lung cancer (NSCLC) risk using 2556 cases (age ≤ 50 years) and 13,327 controls by logistic regression model. To further discriminate younger cases from older ones, we took a case-case analysis for the promising variants with above early-onset cases and 10,769 cases (age > 50 years) by Cox regression model. After combining these results, we identified four early-onset NSCLC susceptibility loci at 5p15.33 (rs2853677, odds ratio [OR] = 1.48, 95% confidence interval [CI]: 1.36-1.60, Pcase-control = 3.58 × 10-21 ; hazard ratio [HR] = 1.10, 95% CI: 1.04-1.16, Pcase-case = 6.77 × 10-4 ), 5p15.1 (rs2055817, OR = 1.24, 95% CI: 1.15-1.35, Pcase-control = 1.39 × 10-7 ; HR = 1.08, 95% CI: 1.02-1.14, Pcase-case = 6.90 × 10-3 ), 6q24.2 (rs9403497, OR = 1.24, 95% CI: 1.15-1.35, Pcase-control = 1.61 × 10-7 ; HR = 1.11, 95% CI: 1.05-1.17, Pcase-case = 3.60 × 10-4 ) and 12q14.3 (rs4762093, OR = 1.31, 95% CI: 1.18-1.45, Pcase-control = 1.90 × 10-7 ; HR = 1.10, 95% CI: 1.03-1.18, Pcase-case = 7.49 × 10-3 ). Except for 5p15.33, other loci were found to be associated with NSCLC risk for the first time. All of them had stronger effects in younger patients than in older ones. These results provide a promising overview for early-onset NSCLC genetics.
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Affiliation(s)
- Jingyi Fan
- Department of Epidemiology, Center for Global Health, School of Public Health, Gusu School, 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
- Health Management Center, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Tongtong Hong
- Department of Epidemiology, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, Nanjing, China
- Institute of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiaoyu Zhao
- Department of Epidemiology, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Shuang Liang
- Department of Epidemiology, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Gusu School, 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
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Gusu School, 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, Center for Global Health, School of Public Health, Gusu School, 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, Center for Global Health, School of Public Health, Gusu School, 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
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Gusu School, 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, Center for Global Health, School of Public Health, Gusu School, 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, Center for Global Health, School of Public Health, Gusu School, 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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10
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Xu J, Xu W, Choi J, Brhane Y, Christiani DC, Kothari J, McKay J, Field JK, Davies MPA, Liu G, Amos CI, Hung RJ, Briollais L. Large-scale whole exome sequencing studies identify two genes,CTSL and APOE, associated with lung cancer. PLoS Genet 2023; 19:e1010902. [PMID: 37738239 PMCID: PMC10516417 DOI: 10.1371/journal.pgen.1010902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/07/2023] [Indexed: 09/24/2023] Open
Abstract
Common genetic variants associated with lung cancer have been well studied in the past decade. However, only 12.3% heritability has been explained by these variants. In this study, we investigate the contribution of rare variants (RVs) (minor allele frequency <0.01) to lung cancer through two large whole exome sequencing case-control studies. We first performed gene-based association tests using a novel Bayes Factor statistic in the International Lung Cancer Consortium, the discovery study (European, 1042 cases vs. 881 controls). The top genes identified are further assessed in the UK Biobank (European, 630 cases vs. 172 864 controls), the replication study. After controlling for the false discovery rate, we found two genes, CTSL and APOE, significantly associated with lung cancer in both studies. Single variant tests in UK Biobank identified 4 RVs (3 missense variants) in CTSL and 2 RVs (1 missense variant) in APOE stongly associated with lung cancer (OR between 2.0 and 139.0). The role of these genetic variants in the regulation of CTSL or APOE expression remains unclear. If such a role is established, this could have important therapeutic implications for lung cancer patients.
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Affiliation(s)
- Jingxiong Xu
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Wei Xu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yonathan Brhane
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - David C. Christiani
- T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Jui Kothari
- Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - John K. Field
- Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Michael P. A. Davies
- Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Geoffrey Liu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I. Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rayjean J. Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Laurent Briollais
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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11
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Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
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Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
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12
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Wu X, Huang G, Li W, Chen Y. Ethnicity-specific association between TERT rs2736100 (A > C) polymorphism and lung cancer risk: a comprehensive meta-analysis. Sci Rep 2023; 13:13271. [PMID: 37582820 PMCID: PMC10427644 DOI: 10.1038/s41598-023-40504-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/11/2023] [Indexed: 08/17/2023] Open
Abstract
The rs2736100 (A > C) polymorphism of the second intron of Telomerase reverse transcriptase (TERT) has been confirmed to be closely associated with the risk of Lung cancer (LC), but there is still no unified conclusion on the results of its association with LC. This study included Genome-wide association studies (GWAS) and case-control studies reported so far on this association between TERT rs2736100 polymorphism and LC to clarify such a correlation with LC and the differences in it between different ethnicities and different types of LC. Relevant literatures published before May 7, 2022 on 'TERT rs2736100 polymorphism and LC susceptibility' in PubMed, EMbase, CENTRAL, MEDLINE databases were searched through the Internet, and data were extracted. Statistical analysis of data was performed in Revman5.3 software, including drawing forest diagrams, drawing funnel diagrams and so on. Sensitivity and publication bias analysis were performed in Stata 12.0 software. The C allele of TERT rs2736100 was associated with the risk of LC (Overall population: [OR] = 1.21, 95%CI [1.17, 1.25]; Caucasians: [OR] = 1.11, 95%CI [1.06, 1.17]; Asians: [OR] = 1.26, 95%CI [1.21, 1.30]), and Asians had a higher risk of LC than Caucasians (C vs. A: Caucasians: [OR] = 1.11 /Asians: [OR]) = 1.26). The other gene models also showed similar results. The results of stratified analysis of LC patients showed that the C allele was associated with the risk of Non-small-cell lung carcinoma (NSCLC) and Lung adenocarcinoma (LUAD), and the risk of NSCLC and LUAD in Asians was higher than that in Caucasians. The C allele was associated with the risk of Lung squamous cell carcinoma (LUSC) and Small cell lung carcinoma(SCLC) in Asians but not in Caucasians. NSCLC patients ([OR] = 1.27) had a stronger correlation than SCLC patients ([OR] = 1.03), and LUAD patients ([OR] = 1.32) had a stronger correlation than LUSC patients ([OR] = 1.09).In addition, the C allele of TERT rs2736100 was associated with the risk of LC, NSCLC and LUAD in both smoking groups and non-smoking groups, and the risk of LC in non-smokers of different ethnic groups was higher than that in smokers. In the Asians, non-smoking women were more at risk of developing LUAD. The C allele of TERT rs2736100 is a risk factor for LC, NSCLC, and LUAD in different ethnic groups, and the Asian population is at a more common risk. The C allele is a risk factor for LUSC and SCLC in Asians but not in Caucasians. And smoking is not the most critical factor that causes variation in TERT rs2736100 to increase the risk of most LC (NSCLC, LUAD). Therefore, LC is a multi-etiological disease caused by a combination of genetic, environmental and lifestyle factors.
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Affiliation(s)
- Xiaozheng Wu
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Gao Huang
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Wen Li
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Yunzhi Chen
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China.
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13
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Shi J, Shiraishi K, Choi J, Matsuo K, Chen TY, Dai J, Hung RJ, Chen K, Shu XO, Kim YT, Landi MT, Lin D, Zheng W, Yin Z, Zhou B, Song B, Wang J, Seow WJ, Song L, Chang IS, Hu W, Chien LH, Cai Q, Hong YC, Kim HN, Wu YL, Wong MP, Richardson BD, Funderburk KM, Li S, Zhang T, Breeze C, Wang Z, Blechter B, Bassig BA, Kim JH, Albanes D, Wong JYY, Shin MH, Chung LP, Yang Y, An SJ, Zheng H, Yatabe Y, Zhang XC, Kim YC, Caporaso NE, Chang J, Ho JCM, Kubo M, Daigo Y, Song M, Momozawa Y, Kamatani Y, Kobayashi M, Okubo K, Honda T, Hosgood DH, Kunitoh H, Patel H, Watanabe SI, Miyagi Y, Nakayama H, Matsumoto S, Horinouchi H, Tsuboi M, Hamamoto R, Goto K, Ohe Y, Takahashi A, Goto A, Minamiya Y, Hara M, Nishida Y, Takeuchi K, Wakai K, Matsuda K, Murakami Y, Shimizu K, Suzuki H, Saito M, Ohtaki Y, Tanaka K, Wu T, Wei F, Dai H, Machiela MJ, Su J, Kim YH, Oh IJ, Lee VHF, Chang GC, Tsai YH, Chen KY, Huang MS, Su WC, Chen YM, Seow A, Park JY, Kweon SS, Chen KC, Gao YT, Qian B, Wu C, Lu D, Liu J, Schwartz AG, Houlston R, Spitz MR, Gorlov IP, Wu X, Yang P, Lam S, Tardon A, Chen C, Bojesen SE, Johansson M, Risch A, Bickeböller H, Ji BT, Wichmann HE, Christiani DC, Rennert G, Arnold S, Brennan P, McKay J, Field JK, Shete SS, Le Marchand L, Liu G, Andrew A, Kiemeney LA, Zienolddiny-Narui S, Grankvist K, Johansson M, Cox A, Taylor F, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Jeon HS, Jiang SS, Sung JS, Chen CH, Hsiao CF, Jung YJ, Guo H, Hu Z, Burdett L, Yeager M, Hutchinson A, Hicks B, Liu J, Zhu B, Berndt SI, Wu W, Wang J, Li Y, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Wang WC, Xu J, Guan P, Tan W, Yu CJ, Yang G, Sihoe ADL, Chen Y, Choi YY, Kim JS, Yoon HI, Park IK, Xu P, He Q, Wang CL, Hung HH, Vermeulen RCH, Cheng I, Wu J, Lim WY, Tsai FY, Chan JKC, Li J, Chen H, Lin HC, Jin L, Liu J, Sawada N, Yamaji T, Wyatt K, Li SA, Ma H, Zhu M, Wang Z, Cheng S, Li X, Ren Y, Chao A, Iwasaki M, Zhu J, Jiang G, Fei K, Wu G, Chen CY, Chen CJ, Yang PC, Yu J, Stevens VL, Fraumeni JF, Chatterjee N, Gorlova OY, Hsiung CA, Amos CI, Shen H, Chanock SJ, Rothman N, Kohno T, Lan Q. Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population. Nat Commun 2023; 14:3043. [PMID: 37236969 PMCID: PMC10220065 DOI: 10.1038/s41467-023-38196-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications.
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Affiliation(s)
- Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tzu-Yu Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - 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
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Young Tae Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Clinical Epidemiology and Center of Evidence Based Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Bao Song
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Jie Seow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Li-Hsin Chien
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee Nam Kim
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Maria Pik Wong
- Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Brian Douglas Richardson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Karen M Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Shilan Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University Medical Center, Washington, DC, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jin Hee Kim
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Lap Ping Chung
- Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, China
| | - She-Juan An
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yasushi Yatabe
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasuneup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jiang Chang
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - James Chung Man Ho
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Medical Oncology and Cancer Center, and Center for Advanced Medicine against Cancer, Shiga University of Medical Science, Shiga, Japan
| | - Minsun Song
- Department of Statistics & Research Institute of Natural Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Kobayashi
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Okubo
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayuki Honda
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Dean H Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Hideo Kunitoh
- Department of Medical Oncology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yuichiro Ohe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Graduate School of Medicine, Akita University, Akita, Japan
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kimihiro Shimizu
- Department of Surgery, Division of General Thoracic Surgery, Shinshu University School of Medicine Asahi, Nagano, Japan
| | - Hiroyuki Suzuki
- Department of Chest Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoichi Ohtaki
- Department of Integrative center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Kazumi Tanaka
- Department of Integrative center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Tangchun Wu
- Institute of Occupational Medicine and Ministry of Education Key Lab for Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jian Su
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasuneup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Victor Ho Fun Lee
- Department of Clinical Oncology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Gee-Chen Chang
- School of Medicine and Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Internal Medicine, Division of Pulmonary Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ying-Huang Tsai
- Department of Respiratory Therapy, Chang Gung University, Taoyuan, Taiwan
- Department of Pulmonary and Critical Care, Xiamen Chang Gung Hospital, Xiamen, China
| | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, E-Da Cancer Hospital, I-Shou University and Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wu-Chou Su
- Department of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, and school of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
- Jeonnam Regional Cancer Center, Chonnam National University, Hwasun, Republic of Korea
| | - Kun-Chieh Chen
- Department of Internal Medicine, Division of Pulmonary Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Biyun Qian
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chen Wu
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianjun Liu
- Genome Institute of Singapore, Agency of Science, Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Margaret R Spitz
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
| | - Ivan P Gorlov
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
| | - Xifeng Wu
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stig E Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Angela Risch
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Helmholtz Center Munich, Institute of Epidemiology, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | | | | | | | - Paul Brennan
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | | | - Sanjay S Shete
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | | | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | | | | | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Lazarus
- Washington State University College of Pharmacy, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hyo-Sung Jeon
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Shih Sheng Jiang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jae Sook Sung
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Chung-Hsing Chen
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chin-Fu Hsiao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yoo Jin Jung
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Huan Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Jia Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Junwen Wang
- Department of Biochemistry, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Genomic Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuqing Li
- Department of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Jin Eun Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Kyong Hwa Park
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Sook Whan Sung
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Li Liu
- Department of Oncology, Cancer Center, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Chang Hyun Kang
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Wen Tan
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Gong Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | | | - Ying Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yi Young Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jun Suk Kim
- Department of Internal Medicine, Division of Medical Oncology, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ho-Il Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - In Kyu Park
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ping Xu
- Department of Oncology, Wuhan Iron and Steel (Group) Corporation Staff-Worker Hospital, Wuhan, China
| | - Qincheng He
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Chih-Liang Wang
- Department of Pulmonary and Critical Care, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsiao-Han Hung
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Roel C H Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Junjie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Fang-Yu Tsai
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Qujing, China
| | - Hongyan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hsien-Chih Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - 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
| | - Meng Zhu
- 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
| | - Zhehai Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Ann Chao
- Center for Global Health, National Cancer Institute, Bethesda, MD, USA
| | - Motoki Iwasaki
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Junjie Zhu
- Shanghai Pulmonary Hospital, Shanghai, China
| | | | - Ke Fei
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, China
| | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chien-Jen Chen
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jinming Yu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | | | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Olga Y Gorlova
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Christopher I Amos
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - 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
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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14
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Yan H, Jin X, Zhang C, Zhu C, He Y, Du X, Feng G. Associations between diet and incidence risk of lung cancer: A Mendelian randomization study. Front Nutr 2023; 10:1149317. [PMID: 37063327 PMCID: PMC10102585 DOI: 10.3389/fnut.2023.1149317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
BackgroundObservational studies have revealed associations between diet and lung cancer. However, it is unclear whether the association is disturbed by confounding factors. We used a two-sample Mendelian randomization (MR) method to characterize the associations between diet and the lung cancer risk (including 3 subtypes: lung adenocarcinoma (LA), squamous cell lung carcinoma (SqCLC), and small cell lung cancer (SCLC)).Materials and methodsData on 20 diets were screened from the UK Biobank. Lung cancer data came from a large meta-analysis of 85,716 individuals. The inverse-variance weighted method was used as the main analysis. Sensitivity analysis was also used to explain the different multiplicity patterns of the final model.ResultsOur results showed significant evidence that 3 diets were associated with lung cancer [odds ratio (OR): 0.271, 95% confidence interval (CI): 0.150–0.488, p = 1.46 × 10−4, dried fruit; OR: 3.010, 95% CI: 1.608–5.632, p = 5.70 × 10−4, beer] and SqCLC (OR: 0.135, 95% CI: 0.062–0.293, p = 2.33 × 10−5, dried fruit; OR: 0.485, 95% CI: 0.328–0.717, p = 2.9 × 10−4, cheese). There were also suggestive correlations between 5 dietary intakes and lung cancer (OR: 0.441, 95% CI: 0.250–0.778, p = 0.008, cereal; OR: 2.267, 95% CI: 1.126–4.564, p = 0.022, beef), LA (OR: 0.494, 95% CI: 0.285–0.858, p = 0.012, dried fruit; OR: 3.536, 95% CI: 1.546–8.085, p = 0.003, beer) and SCLC (OR: 0.006, 95% CI: 0.000–0.222, p = 0.039, non-oily fish; OR: 0.239, 95% CI: 0.086–0.664, p = 0.006, dried fruit). No other association between diet and lung cancer was observed.ConclusionOur study preliminary found that cheese, dried fruit, and beer intake were significantly associated with the risk of lung cancer or its subtypes, while cereal, beef, and non-oily fish intake were suggestively associated with the risk of lung cancer or its subtypes. Well-designed prospective studies are still needed to confirm our findings in the future.
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Affiliation(s)
- Haihao Yan
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao Jin
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Changwen Zhang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Changjun Zhu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yucong He
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xingran Du
- Department of Infectious Disease, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Xingran Du,
| | - Ganzhu Feng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Ganzhu Feng,
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15
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Mangani D, Yang D, Anderson AC. Learning from the nexus of autoimmunity and cancer. Immunity 2023; 56:256-271. [PMID: 36792572 PMCID: PMC9986833 DOI: 10.1016/j.immuni.2023.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 02/16/2023]
Abstract
The immune system plays critical roles in both autoimmunity and cancer, diseases at opposite ends of the immune spectrum. Autoimmunity arises from loss of T cell tolerance against self, while in cancer, poor immunity against transformed self fails to control tumor growth. Blockade of pathways that preserve self-tolerance is being leveraged to unleash immunity against many tumors; however, widespread success is hindered by the autoimmune-like toxicities that arise in treated patients. Knowledge gained from the treatment of autoimmunity can be leveraged to treat these toxicities in patients. Further, the understanding of how T cell dysfunction arises in cancer can be leveraged to induce a similar state in autoreactive T cells. Here, we review what is known about the T cell response in autoimmunity and cancer and highlight ways in which we can learn from the nexus of these two diseases to improve the application, efficacy, and management of immunotherapies.
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Affiliation(s)
- Davide Mangani
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Mass General Brigham, Boston, MA 02115, USA; Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Universita della Svizzera Italiana, Bellinzona 6500, Switzerland.
| | - Dandan Yang
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Mass General Brigham, Boston, MA 02115, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases, Ann Romney Center for Neurologic Diseases, Harvard Medical School and Mass General Brigham, Boston, MA 02115, USA.
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16
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Yang J, Nie D, Chen Y, Liu Z, Li M, Gong C, Liu Q. The role of smoking and alcohol in mediating the effect of gastroesophageal reflux disease on lung cancer: A Mendelian randomization study. Front Genet 2023; 13:1054132. [PMID: 36726719 PMCID: PMC9885128 DOI: 10.3389/fgene.2022.1054132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/07/2022] [Indexed: 01/19/2023] Open
Abstract
Observational studies have suggested a positive association between gastroesophageal reflux disease and lung cancer, but due to the existence of confounders, it remains undetermined whether gastroesophageal reflux disease (GERD) has a causal association with lung cancer. Therefore, Mendelian randomization (MR) analyses were applied to investigate the relationship between the two conditions. Two-sample Mendelian randomization analysis was utilized with summary genetic data from the European Bioinformatics Institute (602,604 individuals) and International Lung Cancer Consortium, which provides information on lung cancer and its histological subgroups. Furthermore, we used two-step Mendelian randomization and multivariable Mendelian randomization to estimate whether smoking initiation (311,629 cases and 321,173 controls) and alcohol intake frequency (n = 462,346) mediate any effect of gastroesophageal reflux disease on lung cancer risk. The Mendelian randomization analyses indicated that gastroesophageal reflux disease was associated with and significantly increased the risk of lung cancer (ORIVW = 1.35, 95% CI = 1.18-1.54; p = 1.36 × 10-5). Smoking initiation and alcohol intake frequency mediated 35% and 3% of the total effect of gastroesophageal reflux disease on lung cancer, respectively. The combined effect of these two factors accounted for 60% of the total effect. In conclusion, gastroesophageal reflux disease is associated with an increased risk of lung cancer, and interventions to reduce smoking and alcohol intake may reduce the incidence of lung cancer.
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Affiliation(s)
- Jing Yang
- The First Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Duorui Nie
- Graduate school of Hunan University of Chinese Medicine, Changsha, China
| | - Yujing Chen
- The First Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zixing Liu
- The First Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mengzhao Li
- The First Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chun Gong
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, Hunan, China,*Correspondence: Chun Gong, ; Qiong Liu,
| | - Qiong Liu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China,*Correspondence: Chun Gong, ; Qiong Liu,
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Wang Q, Gümüş ZH, Colarossi C, Memeo L, Wang X, Kong CY, Boffetta P. SCLC: Epidemiology, Risk Factors, Genetic Susceptibility, Molecular Pathology, Screening, and Early Detection. J Thorac Oncol 2023; 18:31-46. [PMID: 36243387 PMCID: PMC10797993 DOI: 10.1016/j.jtho.2022.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022]
Abstract
We review research regarding the epidemiology, risk factors, genetic susceptibility, molecular pathology, and early detection of SCLC, a deadly tumor that accounts for 14% of lung cancers. We first summarize the changing incidences of SCLC globally and in the United States among males and females. We then review the established risk factor (i.e., tobacco smoking) and suspected nonsmoking-related risk factors for SCLC, and emphasize the importance of continued effort in tobacco control worldwide. Review of genetic susceptibility and molecular pathology suggests different molecular pathways in SCLC development compared with other types of lung cancer. Last, we comment on the limited utility of low-dose computed tomography screening in SCLC and on several promising blood-based molecular biomarkers as potential tools in SCLC early detection.
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Affiliation(s)
- Qian Wang
- University Hospitals Seidman Cancer Center, Cleveland, Ohio.
| | - Zeynep H Gümüş
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Thoracic Oncology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Cristina Colarossi
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, Catania, Italy
| | - Lorenzo Memeo
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, Catania, Italy
| | - Xintong Wang
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chung Yin Kong
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paolo Boffetta
- Department of Family, Population & Preventive Medicine, Stony Brook University, Stony Brook, New York; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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18
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Zou K, Sun P, Huang H, Zhuo H, Qie R, Xie Y, Luo J, Li N, Li J, He J, Aschebrook-Kilfoy B, Zhang Y. Etiology of lung cancer: Evidence from epidemiologic studies. JOURNAL OF THE NATIONAL CANCER CENTER 2022. [DOI: 10.1016/j.jncc.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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19
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Barnett GC, Kerns SL, Dorling L, Fachal L, Aguado-Barrera ME, Martínez-Calvo L, Jandu HK, Welsh C, Tyrer J, Coles CE, Haviland JS, Parker C, Gómez-Caamaño A, Calvo-Crespo P, Sosa-Fajardo P, Burnet NG, Summersgill H, Webb A, De Ruysscher D, Seibold P, Chang-Claude J, Talbot CJ, Rattay T, Parliament M, De Ruyck K, Rosenstein BS, Pharoah PDP, Dunning AM, Vega A, West CML. No Association Between Polygenic Risk Scores for Cancer and Development of Radiation Therapy Toxicity. Int J Radiat Oncol Biol Phys 2022; 114:494-501. [PMID: 35840111 DOI: 10.1016/j.ijrobp.2022.06.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE Our aim was to test whether updated polygenic risk scores (PRS) for susceptibility to cancer affect risk of radiation therapy toxicity. METHODS AND MATERIALS Analyses included 9,717 patients with breast (n=3,078), prostate (n=5,748) or lung (n=891) cancer from Radiogenomics and REQUITE Consortia cohorts. Patients underwent potentially curative radiation therapy and were assessed prospectively for toxicity. Germline genotyping involved genome-wide single nucleotide polymorphism (SNP) arrays with nontyped SNPs imputed. PRS for each cancer were generated by summing literature-identified cancer susceptibility risk alleles: 352 breast, 136 prostate, and 24 lung. Weighted PRS were generated using log odds ratio (ORs) for cancer susceptibility. Standardized total average toxicity (STAT) scores at 2 and 5 years (breast, prostate) or 6 to 12 months (lung) quantified toxicity. Primary analysis tested late STAT, secondary analyses investigated acute STAT, and individual endpoints and SNPs using multivariable regression. RESULTS Increasing PRS did not increase risk of late toxicity in patients with breast (OR, 1.000; 95% confidence interval [CI], 0.997-1.002), prostate (OR, 0.99; 95% CI, 0.98-1.00; weighted PRS OR, 0.93; 95% CI, 0.83-1.03), or lung (OR, 0.93; 95% CI, 0.87-1.00; weighted PRS OR, 0.68; 95% CI, 0.45-1.03) cancer. Similar results were seen for acute toxicity. Secondary analyses identified rs138944387 associated with breast pain (OR, 3.05; 95% CI, 1.86-5.01; P = 1.09 × 10-5) and rs17513613 with breast edema (OR, 0.94; 95% CI, 0.92-0.97; P = 1.08 × 10-5). CONCLUSIONS Patients with increased polygenic predisposition to breast, prostate, or lung cancer can safely undergo radiation therapy with no anticipated excess toxicity risk. Some individual SNPs increase the likelihood of a specific toxicity endpoint, warranting validation in independent cohorts and functional studies to elucidate biologic mechanisms.
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Affiliation(s)
- Gillian C Barnett
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom.
| | - Sarah L Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, New York
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Miguel E Aguado-Barrera
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Santiago de Compostela, A Coruña, Spain; Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Laura Martínez-Calvo
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Santiago de Compostela, A Coruña, Spain; Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Harkeran K Jandu
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ceilidh Welsh
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Charlotte E Coles
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom
| | - Joanne S Haviland
- Clinical Trials and Statistics Unit, Institute of Cancer Research, London, United Kingdom
| | - Christopher Parker
- Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago de Compostela, Spain
| | - Patricia Calvo-Crespo
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago de Compostela, Spain
| | - Paloma Sosa-Fajardo
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago de Compostela, Spain
| | - Neil G Burnet
- Proton Beam Therapy Centre, Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Holly Summersgill
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Adam Webb
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Dirk De Ruysscher
- Department of Radiation Oncology (Maastro Clinic), Maastricht University Medical Center, GROW School for Oncology and Developmental Biology, Maastricht, The Netherlands; Radiation Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany
| | - Christopher J Talbot
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Tim Rattay
- Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Matthew Parliament
- Division of Radiation Oncology, Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
| | - Kim De Ruyck
- Departments of Basic Medical Sciences and Radiotherapy, Ghent University Hospital, Ghent, Belgium
| | - Barry S Rosenstein
- Departments of Radiation Oncology and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Ana Vega
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Santiago de Compostela, A Coruña, Spain; Biomedical Network on Rare Diseases (CIBERER), Spain
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust, Manchester, United Kingdom
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Yan H, Jin X, Yin L, Zhu C, Feng G. Investigating Causal Associations of Circulating Micronutrients Concentrations with the Risk of Lung Cancer: A Mendelian Randomization Study. Nutrients 2022; 14:nu14214569. [PMID: 36364831 PMCID: PMC9655558 DOI: 10.3390/nu14214569] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Previous observational studies have suggested that the effect of diet-derived circulating micronutrient concentrations on lung cancer (LC) risk is controversial. We conducted a two-sample Mendelian randomization (MR) analysis to investigate the causal relationship between circulating micronutrient concentrations and the overall risk of LC and three LC subtypes (namely lung adenocarcinoma (LA), squamous cell lung cancer (SqCLC), and small cell lung cancer (SCLC)). The instrumental variables (IVs) of 11 micronutrients (beta-carotene, calcium, copper, folate, lycopene, magnesium, phosphorus, retinol, selenium, zinc, and vitamin B6) were screened from the published genome-wide association studies (GWAS). Summary statistics related to LC and its subtypes came from the largest meta-analysis, including 29,266 cases and 56,450 controls. Inverse-variance weighted (IVW) method is used as the main MR analysis, and the sensitivity analysis is carried out to ensure the MR assumptions. This MR study found suggestive evidence that genetically predicted 6 circulating micronutrient concentrations was correlated with the risk of overall LC (odds ratio (OR): 1.394, 95% confidence interval (CI): 1.041–1.868, p = 0.026, phosphorus), LA (OR: 0.794, 95% CI: 0.634–0.995, p = 0.045, beta-carotene; OR: 0.687, 95%CI: 0.494–0.957, p = 0.026, calcium), SqCLC (OR: 0.354, 95% CI: 0.145–0.865, p = 0.023, retinol), and SCLC (OR: 1.267, 95% CI: 1.040–1.543, p = 0.019, copper; OR: 0.801, 95% CI: 0.679–0.944, p = 0.008, zinc). We found no evidence that other micronutrients are associated with the risk of overall LC or its subtypes. Our study suggested that the increase in circulating beta-carotene, calcium, retinol, and zinc concentration may reduce the risk of LC; the increase in circulating copper and phosphorus concentration may be related to the increased risk of LC. In the future, larger replication samples of LC genetic data and larger micronutrient-related GWAS will be needed to verify our findings.
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Affiliation(s)
- Haihao Yan
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Xiao Jin
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Linlin Yin
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Changjun Zhu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Ganzhu Feng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
- Correspondence:
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Coronary artery disease and cancer: a significant resemblance. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:187. [PMID: 36071253 DOI: 10.1007/s12032-022-01789-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/01/2022] [Indexed: 10/14/2022]
Abstract
Cancer and coronary artery disease (CAD) are two of the most common causes of death, and they frequently coexist, especially as the world's population ages. CAD can develop prior to or following cancer diagnosis, as well as a side effect of cancer treatment. CAD develops as complex interactions of lifestyle and hereditary variables, just like the development of the most complex and non-communicable diseases. Cancer is caused by both external/acquired factors (tobacco, food, physical activity, alcohol consumption, epigenetic alterations) and internal/inherited factors (genetic mutations, hormones, and immunological diseases). The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (Cas9) system has recently emerged as a strong tool for gene therapy for both cancer as well as CAD treatment due to its great accuracy and efficiency. A deeper understanding of the complex link between CAD and cancer should lead to better prevention, faster detection, and safer treatment strategies.
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22
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Zhang R, Shen S, Wei Y, Zhu Y, Li Y, Chen J, Guan J, Pan Z, Wang Y, Zhu M, Xie J, Xiao X, Zhu D, Li Y, Albanes D, Landi MT, Caporaso NE, Lam S, Tardon A, Chen C, Bojesen SE, Johansson M, Risch A, Bickeböller H, Wichmann HE, Rennert G, Arnold S, Brennan P, McKay JD, Field JK, Shete SS, Le Marchand L, Liu G, Andrew AS, Kiemeney LA, Zienolddiny-Narui S, Behndig A, Johansson M, Cox A, Lazarus P, Schabath MB, Aldrich MC, Dai J, Ma H, Zhao Y, Hu Z, Hung RJ, Amos CI, Shen H, Chen F, Christiani DC. A Large-Scale Genome-Wide Gene-Gene Interaction Study of Lung Cancer Susceptibility in Europeans With a Trans-Ethnic Validation in Asians. J Thorac Oncol 2022; 17:974-990. [PMID: 35500836 PMCID: PMC9512697 DOI: 10.1016/j.jtho.2022.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Although genome-wide association studies have been conducted to investigate genetic variation of lung tumorigenesis, little is known about gene-gene (G × G) interactions that may influence the risk of non-small cell lung cancer (NSCLC). METHODS Leveraging a total of 445,221 European-descent participants from the International Lung Cancer Consortium OncoArray project, Transdisciplinary Research in Cancer of the Lung and UK Biobank, we performed a large-scale genome-wide G × G interaction study on European NSCLC risk by a series of analyses. First, we used BiForce to evaluate and rank more than 58 billion G × G interactions from 340,958 single-nucleotide polymorphisms (SNPs). Then, the top interactions were further tested by demographically adjusted logistic regression models. Finally, we used the selected interactions to build lung cancer screening models of NSCLC, separately, for never and ever smokers. RESULTS With the Bonferroni correction, we identified eight statistically significant pairs of SNPs, which predominantly appeared in the 6p21.32 and 5p15.33 regions (e.g., rs521828C6orf10 and rs204999PRRT1, ORinteraction = 1.17, p = 6.57 × 10-13; rs3135369BTNL2 and rs2858859HLA-DQA1, ORinteraction = 1.17, p = 2.43 × 10-13; rs2858859HLA-DQA1 and rs9275572HLA-DQA2, ORinteraction = 1.15, p = 2.84 × 10-13; rs2853668TERT and rs62329694CLPTM1L, ORinteraction = 0.73, p = 2.70 × 10-13). Notably, even with much genetic heterogeneity across ethnicities, three pairs of SNPs in the 6p21.32 region identified from the European-ancestry population remained significant among an Asian population from the Nanjing Medical University Global Screening Array project (rs521828C6orf10 and rs204999PRRT1, ORinteraction = 1.13, p = 0.008; rs3135369BTNL2 and rs2858859HLA-DQA1, ORinteraction = 1.11, p = 5.23 × 10-4; rs3135369BTNL2 and rs9271300HLA-DQA1, ORinteraction = 0.89, p = 0.006). The interaction-empowered polygenetic risk score that integrated classical polygenetic risk score and G × G information score was remarkable in lung cancer risk stratification. CONCLUSIONS Important G × G interactions were identified and enriched in the 5p15.33 and 6p21.32 regions, which may enhance lung cancer screening models.
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Affiliation(s)
- Ruyang Zhang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts; China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Sipeng Shen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts; China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, People's Republic of China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yongyue Wei
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts; China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ying Zhu
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Jiajin Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jinxing Guan
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zoucheng Pan
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yuzhuo Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Meng Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Junxing Xie
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Xiangjun Xiao
- The Institute for Clinical and Translational Research, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Dakai Zhu
- The Institute for Clinical and Translational Research, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Yafang Li
- The Institute for Clinical and Translational Research, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen Lam
- Department of Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Department of Epidemiology, University of Washington School of Public Health, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Angela Risch
- Department of Biosciences and Cancer Cluster Salzburg, University of Salzburg, Salzburg, Austria
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
| | - Gadi Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Carmel, Haifa, Israel
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James D McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sanjay S Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Angeline S Andrew
- Department of Epidemiology, Department of Community and Family Medicine, Dartmouth Geisel School of Medicine, Hanover, New Hampshire
| | - Lambertus A Kiemeney
- Department for Health Evidence, Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Annelie Behndig
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | | | - Angela Cox
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, Washington
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yang Zhao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhibin Hu
- China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, People's Republic of China; Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- The Institute for Clinical and Translational Research, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Hongbing Shen
- China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, People's Republic of China; Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China.
| | - David C Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts; Pulmonary and Critical Care Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition. Genes (Basel) 2022; 13:genes13071224. [PMID: 35886007 PMCID: PMC9317577 DOI: 10.3390/genes13071224] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
The microbiome is the collection of all microbial genes and can be investigated by sequencing highly variable regions of 16S ribosomal RNA (rRNA) genes. Evidence suggests that environmental factors and host genetics may interact to impact human microbiome composition. Identifying host genetic variants associated with human microbiome composition not only provides clues for characterizing microbiome variation but also helps to elucidate biological mechanisms of genetic associations, prioritize genetic variants, and improve genetic risk prediction. Since a microbiota functions as a community, it is best characterized by β diversity; that is, a pairwise distance matrix. We develop a statistical framework and a computationally efficient software package, microbiomeGWAS, for identifying host genetic variants associated with microbiome β diversity with or without interacting with an environmental factor. We show that the score statistics have positive skewness and kurtosis due to the dependent nature of the pairwise data, which makes p-value approximations based on asymptotic distributions unacceptably liberal. By correcting for skewness and kurtosis, we develop accurate p-value approximations, whose accuracy was verified by extensive simulations. We exemplify our methods by analyzing a set of 147 genotyped subjects with 16S rRNA microbiome profiles from non-malignant lung tissues. Correcting for skewness and kurtosis eliminated the dramatic deviation in the quantile–quantile plots. We provided preliminary evidence that six established lung cancer risk SNPs were collectively associated with microbiome composition for both unweighted (p = 0.0032) and weighted (p = 0.011) UniFrac distance matrices. In summary, our methods will facilitate analyzing large-scale genome-wide association studies of the human microbiome.
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Long E, Patel H, Byun J, Amos CI, Choi J. Functional studies of lung cancer GWAS beyond association. Hum Mol Genet 2022; 31:R22-R36. [PMID: 35776125 DOI: 10.1093/hmg/ddac140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately forty-five genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries, and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.
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Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Spiliopoulou P, Yang SC, Bruce JP, Wang BX, Berman HK, Pugh TJ, Siu LL. All is not lost: learning from 9p21 loss in cancer. Trends Immunol 2022; 43:379-390. [DOI: 10.1016/j.it.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
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Morales Berstein F, McCartney DL, Lu AT, Tsilidis KK, Bouras E, Haycock P, Burrows K, Phipps AI, Buchanan DD, Cheng I, Martin RM, Davey Smith G, Relton CL, Horvath S, Marioni RE, Richardson TG, Richmond RC. Assessing the causal role of epigenetic clocks in the development of multiple cancers: a Mendelian randomization study. eLife 2022; 11:e75374. [PMID: 35346416 PMCID: PMC9049976 DOI: 10.7554/elife.75374] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background Epigenetic clocks have been associated with cancer risk in several observational studies. Nevertheless, it is unclear whether they play a causal role in cancer risk or if they act as a non-causal biomarker. Methods We conducted a two-sample Mendelian randomization (MR) study to examine the genetically predicted effects of epigenetic age acceleration as measured by HannumAge (nine single-nucleotide polymorphisms (SNPs)), Horvath Intrinsic Age (24 SNPs), PhenoAge (11 SNPs), and GrimAge (4 SNPs) on multiple cancers (i.e. breast, prostate, colorectal, ovarian and lung cancer). We obtained genome-wide association data for biological ageing from a meta-analysis (N = 34,710), and for cancer from the UK Biobank (N cases = 2671-13,879; N controls = 173,493-372,016), FinnGen (N cases = 719-8401; N controls = 74,685-174,006) and several international cancer genetic consortia (N cases = 11,348-122,977; N controls = 15,861-105,974). Main analyses were performed using multiplicative random effects inverse variance weighted (IVW) MR. Individual study estimates were pooled using fixed effect meta-analysis. Sensitivity analyses included MR-Egger, weighted median, weighted mode and Causal Analysis using Summary Effect Estimates (CAUSE) methods, which are robust to some of the assumptions of the IVW approach. Results Meta-analysed IVW MR findings suggested that higher GrimAge acceleration increased the risk of colorectal cancer (OR = 1.12 per year increase in GrimAge acceleration, 95% CI 1.04-1.20, p = 0.002). The direction of the genetically predicted effects was consistent across main and sensitivity MR analyses. Among subtypes, the genetically predicted effect of GrimAge acceleration was greater for colon cancer (IVW OR = 1.15, 95% CI 1.09-1.21, p = 0.006), than rectal cancer (IVW OR = 1.05, 95% CI 0.97-1.13, p = 0.24). Results were less consistent for associations between other epigenetic clocks and cancers. Conclusions GrimAge acceleration may increase the risk of colorectal cancer. Findings for other clocks and cancers were inconsistent. Further work is required to investigate the potential mechanisms underlying the results. Funding FMB was supported by a Wellcome Trust PhD studentship in Molecular, Genetic and Lifecourse Epidemiology (224982/Z/22/Z which is part of grant 218495/Z/19/Z). KKT was supported by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme) and by the Hellenic Republic's Operational Programme 'Competitiveness, Entrepreneurship & Innovation' (OΠΣ 5047228). PH was supported by Cancer Research UK (C18281/A29019). RMM was supported by the NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). RMM is a National Institute for Health Research Senior Investigator (NIHR202411). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. GDS and CLR were supported by the Medical Research Council (MC_UU_00011/1 and MC_UU_00011/5, respectively) and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). REM was supported by an Alzheimer's Society project grant (AS-PG-19b-010) and NIH grant (U01 AG-18-018, PI: Steve Horvath). RCR is a de Pass Vice Chancellor's Research Fellow at the University of Bristol.
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Affiliation(s)
- Fernanda Morales Berstein
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College LondonLondonUnited Kingdom
- Department of Hygiene and Epidemiology, School of Medicine, University of IoanninaIoanninaGreece
| | - Emmanouil Bouras
- Department of Hygiene and Epidemiology, School of Medicine, University of IoanninaIoanninaGreece
| | - Philip Haycock
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Epidemiology, School of Public Health, University of WashingtonSeattleUnited States
| | - Daniel D Buchanan
- Department of Clinical Pathology, Melbourne Medical School, University of MelbourneParkvilleAustralia
| | - Iona Cheng
- Cancer Prevention Institute of CaliforniaFremontUnited States
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of BristolBristolUnited Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Biostatistics, Fielding School of Public Health, University of California, Los AngelesLos AngelesUnited States
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
- Novo Nordisk Research CentreOxfordUnited Kingdom
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
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27
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Rosenberger A, Muttray N, Hung RJ, Christiani DC, Caporaso NE, Liu G, Bojesen SE, Le Marchand L, Albanes D, Aldrich MC, Tardon A, Fernández-Tardón G, Rennert G, Field JK, Davies MPA, Liloglou T, Kiemeney LA, Lazarus P, Wendel B, Haugen A, Zienolddiny S, Lam S, Schabath MB, Andrew AS, Duell EJ, Arnold SM, Goodman GE, Chen C, Doherty JA, Taylor F, Cox A, Woll PJ, Risch A, Muley TR, Johansson M, Brennan P, Landi MT, Shete SS, Amos CI, Bickeböller H. Gene-gene interaction of AhRwith and within the Wntcascade affects susceptibility to lung cancer. Eur J Med Res 2022; 27:14. [PMID: 35101137 PMCID: PMC8805279 DOI: 10.1186/s40001-022-00638-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/07/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Aberrant Wnt signalling, regulating cell development and stemness, influences the development of many cancer types. The Aryl hydrocarbon receptor (AhR) mediates tumorigenesis of environmental pollutants. Complex interaction patterns of genes assigned to AhR/Wnt-signalling were recently associated with lung cancer susceptibility. AIM To assess the association and predictive ability of AhR/Wnt-genes with lung cancer in cases and controls of European descent. METHODS Odds ratios (OR) were estimated for genomic variants assigned to the Wnt agonist and the antagonistic genes DKK2, DKK3, DKK4, FRZB, SFRP4 and Axin2. Logistic regression models with variable selection were trained, validated and tested to predict lung cancer, at which other previously identified SNPs that have been robustly associated with lung cancer risk could also enter the model. Furthermore, decision trees were created to investigate variant × variant interaction. All analyses were performed for overall lung cancer and for subgroups. RESULTS No genome-wide significant association of AhR/Wnt-genes with overall lung cancer was observed, but within the subgroups of ever smokers (e.g., maker rs2722278 SFRP4; OR = 1.20; 95% CI 1.13-1.27; p = 5.6 × 10-10) and never smokers (e.g., maker rs1133683 Axin2; OR = 1.27; 95% CI 1.19-1.35; p = 1.0 × 10-12). Although predictability is poor, AhR/Wnt-variants are unexpectedly overrepresented in optimized prediction scores for overall lung cancer and for small cell lung cancer. Remarkably, the score for never-smokers contained solely two AhR/Wnt-variants. The optimal decision tree for never smokers consists of 7 AhR/Wnt-variants and only two lung cancer variants. CONCLUSIONS The role of variants belonging to Wnt/AhR-pathways in lung cancer susceptibility may be underrated in main-effects association analysis. Complex interaction patterns in individuals of European descent have moderate predictive capacity for lung cancer or subgroups thereof, especially in never smokers.
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Affiliation(s)
- Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany.
- Institut Für Genetische Epidemiologie, Universitätsmedizin Göttingen, Humboldtallee 32, 37073, Göttingen, Germany.
| | - Nils Muttray
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health and Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Geoffrey Liu
- Medical Oncology and Medical Biophysics, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Medicine and Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo, ISPA and CIBERESP, Oviedo, Spain
| | | | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool, Liverpool, UK
| | - Michael P A Davies
- Department of Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool, Liverpool, UK
| | - Triantafillos Liloglou
- Department of Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool, Liverpool, UK
| | - Lambertus A Kiemeney
- Departments of Health Evidence and Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Bernadette Wendel
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Aage Haugen
- National Institute of Occupational Health, Oslo, Norway
| | | | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Angeline S Andrew
- Department of Epidemiology, Geisel School of Medicine, Hanover, NH, USA
| | - Eric J Duell
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | | | - Chu Chen
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer A Doherty
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Penella J Woll
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | - Thomas R Muley
- Member of the German Center for Lung Research (DZL), Translational Lung Research Center (TLRC) Heidelberg, Heidelberg, Germany
- Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | | | - 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, US National Institutes of Health, Bethesda, MD, USA
| | - Sanjay S Shete
- Department of Biostatistics, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
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Gormley M, Dudding T, Kachuri L, Burrows K, Chong AHW, Martin RM, Thomas SJ, Tyrrell J, Ness AR, Brennan P, Munafò MR, Pring M, Boccia S, Olshan AF, Diergaarde B, Hung RJ, Liu G, Tajara EH, Severino P, Toporcov TN, Lacko M, Waterboer T, Brenner N, Smith GD, Vincent EE, Richmond RC. Investigating the effect of sexual behaviour on oropharyngeal cancer risk: a methodological assessment of Mendelian randomization. BMC Med 2022; 20:40. [PMID: 35094705 PMCID: PMC8802428 DOI: 10.1186/s12916-022-02233-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/04/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human papilloma virus infection is known to influence oropharyngeal cancer (OPC) risk, likely via sexual transmission. However, sexual behaviour has been correlated with other risk factors including smoking and alcohol, meaning independent effects are difficult to establish. We aimed to evaluate the causal effect of sexual behaviour on the risk of OPC using Mendelian randomization (MR). METHODS Genetic variants robustly associated with age at first sex (AFS) and the number of sexual partners (NSP) were used to perform both univariable and multivariable MR analyses with summary data on 2641 OPC cases and 6585 controls, obtained from the largest available genome-wide association studies (GWAS). Given the potential for genetic pleiotropy, we performed a number of sensitivity analyses: (i) MR methods to account for horizontal pleiotropy, (ii) MR of sexual behaviours on positive (cervical cancer and seropositivity for Chlamydia trachomatis) and negative control outcomes (lung and oral cancer), (iii) Causal Analysis Using Summary Effect estimates (CAUSE), to account for correlated and uncorrelated horizontal pleiotropic effects, (iv) multivariable MR analysis to account for the effects of smoking, alcohol, risk tolerance and educational attainment. RESULTS In univariable MR, we found evidence supportive of an effect of both later AFS (IVW OR = 0.4, 95%CI (0.3, 0.7), per standard deviation (SD), p = < 0.001) and increasing NSP (IVW OR = 2.2, 95%CI (1.3, 3.8) per SD, p = < 0.001) on OPC risk. These effects were largely robust to sensitivity analyses accounting for horizontal pleiotropy. However, negative control analysis suggested potential violation of the core MR assumptions and subsequent CAUSE analysis implicated pleiotropy of the genetic instruments used to proxy sexual behaviours. Finally, there was some attenuation of the univariable MR results in the multivariable models (AFS IVW OR = 0.7, 95%CI (0.4, 1.2), p = 0.21; NSP IVW OR = 0.9, 95%CI (0.5 1.7), p = 0.76). CONCLUSIONS Despite using genetic variants strongly related sexual behaviour traits in large-scale GWAS, we found evidence for correlated pleiotropy. This emphasizes a need for multivariable approaches and the triangulation of evidence when performing MR of complex behavioural traits.
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Affiliation(s)
- Mark Gormley
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK.
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Tom Dudding
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Linda Kachuri
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, USA
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Amanda H W Chong
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- University Hospitals Bristol and Weston NHS Foundation Trust National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Steven J Thomas
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK
- University Hospitals Bristol and Weston NHS Foundation Trust National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Jessica Tyrrell
- University of Exeter Medical School, RILD Building, RD&E Hospital, Exeter, UK
| | - Andrew R Ness
- University Hospitals Bristol and Weston NHS Foundation Trust National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Paul Brennan
- Genetic Epidemiology Group, World Health Organization, International Agency for Research on Cancer, Lyon, France
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- School of Psychological Science, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Miranda Pring
- Bristol Dental Hospital and School, University of Bristol, Bristol, UK
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italia
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, and UPMC Hillman Cancer Center, Pittsburgh, USA
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Geoffrey Liu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, Toronto, Canada
| | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, São Paulo, Brazil
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Tatiana N Toporcov
- Department of Epidemiology, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Martin Lacko
- Department of Otorhinolaryngology and Head and Neck Surgery, Research Institute GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Tim Waterboer
- Infections and Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Nicole Brenner
- Infections and Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emma E Vincent
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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29
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Veiskarami P, Houshmand M, Seifi S, Ansarinejad N, Fardad F, Abbasi B. The effect of CHRNA3 rs1051730 C>T and ABCB1 rs3842 A>G polymorphisms on non-small cell lung cancer and nicotine dependence in Iranian population. Heliyon 2021; 7:e07867. [PMID: 34522797 PMCID: PMC8426517 DOI: 10.1016/j.heliyon.2021.e07867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/14/2020] [Accepted: 08/20/2021] [Indexed: 12/24/2022] Open
Abstract
Aims Lung cancer is still the leading cause of cancer mortality in all over the world. Nicotine and its derivatives are the most well-known carcinogens that participate in both etiology and progression of lung cancer. The objective of the current study was to investigate whether single nucleotide polymorphisms (SNPs) rs1051730C > T in CHRNA3 and rs3842A > G in ABCB1, two genes contributing in the mechanism of disposition and metabolism of nicotine and its derivatives, could modify the risk of developing lung cancer, as well as nicotine dependence in Iranian. Main methods The genotyping analysis for these two SNPs was conducted in a case-control study of 108 lung cancer cases and 120 healthy controls using ARMS-PCR and Tetra-primer ARMS-PCR techniques. The correlation between studied SNPs and lung cancer was assessed by the regression analysis. Key findings We observed a significant association between lung cancer and rs1051730C > T by using four genetic models: allele (OR:1.83; 95% CI:1.24-2.6; p = 0.002), dominant (OR: 2.19; 95% CI:1.27-3.78; p = 0.005), recessive (OR: 2.25; 95% CI: 1.02-4.95; p = 0.043) and additive (TT vs CC: OR:3.25; 95% CI:1.38-7.60; p = 0.007, CT vs CC: OR:1.96; 95% CI:1.10-3.48; p = 0.021). Furthermore, a significant association between this variant and nicotine dependence (OR: 2.27; 95% CI: 1.52-3.39; p = 0.00005) was reported. However, no association was found for rs3842A > G. Significance The results suggested that the CHRNA3 rs1051730C > T via a smoking-dependent manner could modify susceptibility to lung cancer among Iranian population.
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Affiliation(s)
- Parisa Veiskarami
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,Research Center, Knowledge University, Erbil, Kurdistan Region, Iraq
| | - Sharareh Seifi
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nafiseh Ansarinejad
- Department of Hematology and Medical Oncology, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Farshid Fardad
- Department of Hematology and Medical Oncology, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Bahareh Abbasi
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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30
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Pettit RW, Byun J, Han Y, Ostrom QT, Edelson J, Walsh KM, Bondy ML, Hung RJ, McKay JD, Amos CI. The shared genetic architecture between epidemiological and behavioral traits with lung cancer. Sci Rep 2021; 11:17559. [PMID: 34475455 PMCID: PMC8413319 DOI: 10.1038/s41598-021-96685-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023] Open
Abstract
The complex polygenic nature of lung cancer is not fully characterized. Our study seeks to identify novel phenotypes associated with lung cancer using cross-trait linkage disequilibrium score regression (LDSR). We measured pairwise genetic correlation (rg) and SNP heritability (h2) between 347 traits and lung cancer risk using genome-wide association study summary statistics from the UKBB and OncoArray consortium. Further, we conducted analysis after removing genomic regions previously associated with smoking behaviors to mitigate potential confounding effects. We found significant negative genetic correlations between lung cancer risk and dietary behaviors, fitness metrics, educational attainment, and other psychosocial traits. Alcohol taken with meals (rg = - 0.41, h2 = 0.10, p = 1.33 × 10-16), increased fluid intelligence scores (rg = - 0.25, h2 = 0.22, p = 4.54 × 10-8), and the age at which full time education was completed (rg = - 0.45, h2 = 0.11, p = 1.24 × 10-20) demonstrated negative genetic correlation with lung cancer susceptibility. The body mass index was positively correlated with lung cancer risk (rg = 0.20, h2 = 0.25, p = 2.61 × 10-9). This analysis reveals shared genetic architecture between several traits and lung cancer predisposition. Future work should test for causal relationships and investigate common underlying genetic mechanisms across these genetically correlated traits.
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Affiliation(s)
- Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Quinn T Ostrom
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Jacob Edelson
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Melissa L Bondy
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Stanford, CA, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - James D McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Schamschula E, Lahnsteiner A, Assenov Y, Hagmann W, Zaborsky N, Wiederstein M, Strobl A, Stanke F, Muley T, Plass C, Tümmler B, Risch A. Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in PKP3 in lung epithelial cells. Epigenetics 2021; 17:837-860. [PMID: 34415821 PMCID: PMC9423854 DOI: 10.1080/15592294.2021.1959976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the Plakophilin-3 (PKP3) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of PKP3 which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
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Affiliation(s)
| | | | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hagmann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria.,Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Anna Strobl
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Frauke Stanke
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik Heidelberg, University of Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Burkhard Tümmler
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Angela Risch
- Department of Biosciences, University of Salzburg, Salzburg, Austria.,Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Cancer Cluster Salzburg, Salzburg, Austria.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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32
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Behrouzfar K, Burton K, Mutsaers SE, Morahan G, Lake RA, Fisher SA. How to Better Understand the Influence of Host Genetics on Developing an Effective Immune Response to Thoracic Cancers. Front Oncol 2021; 11:679609. [PMID: 34235080 PMCID: PMC8256168 DOI: 10.3389/fonc.2021.679609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023] Open
Abstract
Thoracic cancers pose a significant global health burden. Immune checkpoint blockade therapies have improved treatment outcomes, but durable responses remain limited. Understanding how the host immune system interacts with a developing tumor is essential for the rational development of improved treatments for thoracic malignancies. Recent technical advances have improved our understanding of the mutational burden of cancer cells and changes in cancer-specific gene expression, providing a detailed understanding of the complex biology underpinning tumor-host interactions. While there has been much focus on the genetic alterations associated with cancer cells and how they may impact treatment outcomes, how host genetics affects cancer development is also critical and will greatly determine treatment response. Genome-wide association studies (GWAS) have identified genetic variants associated with cancer predisposition. This approach has successfully identified host genetic risk factors associated with common thoracic cancers like lung cancer, but is less effective for rare cancers like malignant mesothelioma. To assess how host genetics impacts rare thoracic cancers, we used the Collaborative Cross (CC); a powerful murine genetic resource designed to maximize genetic diversity and rapidly identify genes associated with any biological trait. We are using the CC in conjunction with our asbestos-induced MexTAg mouse model, to identify host genes associated with mesothelioma development. Once genes that moderate tumor development and progression are known, human homologues can be identified and human datasets interrogated to validate their association with disease outcome. Furthermore, our CC-MexTAg animal model enables in-depth study of the tumor microenvironment, allowing the correlation of immune cell infiltration and gene expression signatures with disease development. This strategy provides a detailed picture of the underlying biological pathways associated with mesothelioma susceptibility and progression; knowledge that is crucial for the rational development of new diagnostic and therapeutic strategies. Here we discuss the influence of host genetics on developing an effective immune response to thoracic cancers. We highlight current knowledge gaps, and with a focus on mesothelioma, describe the development and application of the CC-MexTAg to overcome limitations and illustrate how the knowledge gained from this unique study will inform the rational design of future treatments of mesothelioma.
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Affiliation(s)
- Kiarash Behrouzfar
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Kimberley Burton
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Steve E. Mutsaers
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Nedlands, WA, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Richard A. Lake
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
| | - Scott A. Fisher
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
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Raniszewska A, Kwiecień I, Rutkowska E, Rzepecki P, Domagała-Kulawik J. Lung Cancer Stem Cells-Origin, Diagnostic Techniques and Perspective for Therapies. Cancers (Basel) 2021; 13:2996. [PMID: 34203877 PMCID: PMC8232709 DOI: 10.3390/cancers13122996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
Lung cancer remains one of the most aggressive solid tumors with an overall poor prognosis. Molecular studies carried out on lung tumors during treatment have shown the phenomenon of clonal evolution, thereby promoting the occurrence of a temporal heterogeneity of the tumor. Therefore, the biology of lung cancer is interesting. Cancer stem cells (CSCs) are involved in tumor initiation and metastasis. Aging is still the most important risk factor for lung cancer development. Spontaneously occurring mutations accumulate in normal stem cells or/and progenitor cells by human life resulting in the formation of CSCs. Deepening knowledge of these complex processes and improving early recognition and markers of predictive value are of utmost importance. In this paper, we discuss the CSC hypothesis with an emphasis on age-related changes that initiate carcinogenesis. We analyze the current literature in the field, describe our own experience in CSC investigation and discuss the technical challenges with special emphasis on liquid biopsy.
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Affiliation(s)
- Agata Raniszewska
- Laboratory of Hematology and Flow Cytometry, Department of Internal Medicine and Hematology, Military Institute of Medicine, 04-141 Warsaw, Poland; (I.K.); (E.R.)
| | - Iwona Kwiecień
- Laboratory of Hematology and Flow Cytometry, Department of Internal Medicine and Hematology, Military Institute of Medicine, 04-141 Warsaw, Poland; (I.K.); (E.R.)
| | - Elżbieta Rutkowska
- Laboratory of Hematology and Flow Cytometry, Department of Internal Medicine and Hematology, Military Institute of Medicine, 04-141 Warsaw, Poland; (I.K.); (E.R.)
| | - Piotr Rzepecki
- Department of Internal Medicine and Hematology, Military Institute of Medicine, 04-141 Warsaw, Poland;
| | - Joanna Domagała-Kulawik
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Banacha 1a Street, 02-097 Warsaw, Poland;
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34
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Li M, Chen R, Ji B, Fan C, Wang G, Yue C, Jin G. RAD52 variants influence NSCLC risk in the Chinese population in a high altitude area. Ther Adv Respir Dis 2021; 14:1753466620918192. [PMID: 32401173 PMCID: PMC7223216 DOI: 10.1177/1753466620918192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) accounts for approximately 80% of diagnosed lung cancer patients. RAD52 has been reported to be associated with the development of squamous cell lung carcinoma. In this study, we assessed the relationships of RAD52 genetic polymorphisms and NSCLC risk among the Chinese population at high altitude. METHODS Eight single nucleotide polymorphisms (SNPs) of RAD52 were genotyped in the Agena MassARRAY platform among 506 NSCLC patients and 510 healthy controls. We examined the association of RAD52 polymorphisms with NSCLC risk using odds ratios (ORs) and 95% confidence intervals (CIs) via multiple genetic models. RESULTS The rs10774474 A allele was related to a decreased risk of NSCLC in a high altitude population of China (OR = 0.82, 95% CI = 0.69-0.98, p = 0.032), whereas mutant alleles of rs1051672, rs7310449, rs1051669, rs6413436, rs4766377 and rs10849605 significantly increased NSCLC risk. Haplotype analysis showed that four haplotypes of RAD52 polymorphisms conferred an enhanced susceptibility to NSCLC (Ars1051672Grs7310449Trs1051669Ars6413436: OR = 1.29, p = 0.021; Grs1051672Ars7310449Crs1051669Grs6413436: OR = 1.21, p = 0.027; Grs4766377Crs12822733Trs10774474Crs10849605: OR = 1.26, p = 0.032; Ars4766377Crs12822733Ars10774474Trs10849605: OR = 1.21, p = 0.032). CONCLUSIONS Our findings suggested the remarkable association of RAD52 polymorphisms with NSCLC risk among the Chinese population in a high altitude area. The reviews of this paper are available via the supplemental material section.
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Affiliation(s)
- Miao Li
- Department of Medicine Oncology, The Fifth People's Hospital of Qinghai Province, Xining, Qinghai, China
| | - Rong Chen
- Department of Medicine Oncology, The Affiliated Hospital of Qinghai University, Xining, Qinghai, China
| | - Baoyan Ji
- Department of Medicine Oncology, The People's Hospital of Qinghai Province, Xining, Qinghai, China
| | - Chunmei Fan
- Department of Science and Education, The Fifth People's Hospital of Qinghai Province, Xining, Qinghai, China
| | - Guanying Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chenli Yue
- Department of Respiratory Medicine, Shaanxi Provincial Corps Hospital of Chinese People's Armed Police Force, Xi'an, Shaanxi, China
| | - Guoquan Jin
- Department of Oncology, The Fifth People's Hospital of Qinghai Province, 166 East Nanshan Road, Xining, Qinghai 810007, China
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35
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Nazarian A, Kulminski AM. Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers. Genes (Basel) 2021; 12:genes12050686. [PMID: 34062886 PMCID: PMC8147355 DOI: 10.3390/genes12050686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/24/2022] Open
Abstract
Almost all complex disorders have manifested epidemiological and clinical sex disparities which might partially arise from sex-specific genetic mechanisms. Addressing such differences can be important from a precision medicine perspective which aims to make medical interventions more personalized and effective. We investigated sex-specific genetic associations with colorectal (CRCa) and lung (LCa) cancers using genome-wide single-nucleotide polymorphisms (SNPs) data from three independent datasets. The genome-wide association analyses revealed that 33 SNPs were associated with CRCa/LCa at P < 5.0 × 10−6 neither males or females. Of these, 26 SNPs had sex-specific effects as their effect sizes were statistically different between the two sexes at a Bonferroni-adjusted significance level of 0.0015. None had proxy SNPs within their ±1 Mb regions and the closest genes to 32 SNPs were not previously associated with the corresponding cancers. The pathway enrichment analyses demonstrated the associations of 35 pathways with CRCa or LCa which were mostly implicated in immune system responses, cell cycle, and chromosome stability. The significant pathways were mostly enriched in either males or females. Our findings provided novel insights into the potential sex-specific genetic heterogeneity of CRCa and LCa at SNP and pathway levels.
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36
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Brainson CF, Huang B, Chen Q, McLouth LE, He C, Hao Z, Arnold SM, Zinner RG, Mullett TW, Bocklage TJ, Orren DK, Villano JL, Durbin EB. Description of a Lung Cancer Hotspot: Disparities in Lung Cancer Histology, Incidence, and Survival in Kentucky and Appalachian Kentucky. Clin Lung Cancer 2021; 22:e911-e920. [PMID: 33958300 DOI: 10.1016/j.cllc.2021.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Kentucky is recognized as the state with the highest lung cancer burden for more than 2 decades, but how lung cancer differs in Kentucky relative to other US populations is not fully understood. PATIENTS AND METHODS We examined lung cancer reported to the Surveillance, Epidemiology, and End Results (SEER) Program by Kentucky and the other SEER regions for patients diagnosed between 2012 and 2016. Our analyses included histologic types, incidence rates, stage at diagnosis, and survival in Kentucky and Appalachian Kentucky relative to other SEER regions. RESULTS We found that both squamous cell carcinomas and small-cell lung cancers represent larger proportions of lung cancer diagnoses in Kentucky and Appalachian Kentucky than they do in the SEER registries. Furthermore, age-adjusted cancer incidence rates were higher in Kentucky for every subtype of lung cancer examined. Most notably, for Appalachian women the rate of small-cell carcinomas was 3.5-fold higher, and for Appalachian men the rate of squamous cell carcinoma was 3.1-fold higher, than the SEER rates. In Kentucky, lung cancers were diagnosed at later stages and lung cancer survival was lower for adenocarcinoma and neuroendocrine carcinomas than in SEER registries. Squamous cell carcinomas and small-cell carcinomas were most lethal in Appalachian Kentucky. CONCLUSION Together, these data highlight the considerable disparities among lung cancer cases in the United States and demonstrate the continuing high burden and poor survival of lung cancer in Kentucky and Appalachian Kentucky. Strategies to identify and rectify causes of these disparities are discussed.
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Affiliation(s)
- Christine F Brainson
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY; Markey Cancer Center, University of Kentucky, Lexington, KY.
| | - Bin Huang
- Markey Cancer Center, University of Kentucky, Lexington, KY; Division of Cancer Biostatistics, College of Medicine, University of Kentucky, Lexington, KY; Kentucky Cancer Registry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Quan Chen
- Markey Cancer Center, University of Kentucky, Lexington, KY; Kentucky Cancer Registry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Laurie E McLouth
- Markey Cancer Center, University of Kentucky, Lexington, KY; Department of Behavioral Science, Center for Health Equity Transformation, College of Medicine, University of Kentucky, Lexington, KY
| | - Chunyan He
- Markey Cancer Center, University of Kentucky, Lexington, KY; Department of Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY
| | - Zhonglin Hao
- Markey Cancer Center, University of Kentucky, Lexington, KY; Department of Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY; Department of Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY
| | - Ralph G Zinner
- Markey Cancer Center, University of Kentucky, Lexington, KY; Department of Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY
| | - Timothy W Mullett
- Department of Surgery, Division of Cardiothoracic Surgery, College of Medicine, University of Kentucky, Lexington, KY
| | - Therese J Bocklage
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY
| | - David K Orren
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY; Markey Cancer Center, University of Kentucky, Lexington, KY
| | - John L Villano
- Markey Cancer Center, University of Kentucky, Lexington, KY; Department of Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY
| | - Eric B Durbin
- Markey Cancer Center, University of Kentucky, Lexington, KY; Kentucky Cancer Registry, Markey Cancer Center, University of Kentucky, Lexington, KY; Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
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Sun R, Xu M, Li X, Gaynor S, Zhou H, Li Z, Bossé Y, Lam S, Tsao MS, Tardon A, Chen C, Doherty J, Goodman G, Bojesen SE, Landi MT, Johansson M, Field JK, Bickeböller H, Wichmann HE, Risch A, Rennert G, Arnold S, Wu X, Melander O, Brunnström H, Le Marchand L, Liu G, Andrew A, Duell E, Kiemeney LA, Shen H, Haugen A, Johansson M, Grankvist K, Caporaso N, Woll P, Teare MD, Scelo G, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Albanes D, Mak R, Barbie D, Brennan P, Hung RJ, Amos CI, Christiani DC, Lin X. Integration of multiomic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer. Genet Epidemiol 2021; 45:99-114. [PMID: 32924180 PMCID: PMC7855632 DOI: 10.1002/gepi.22358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 02/05/2023]
Abstract
Clinical trial results have recently demonstrated that inhibiting inflammation by targeting the interleukin-1β pathway can offer a significant reduction in lung cancer incidence and mortality, highlighting a pressing and unmet need to understand the benefits of inflammation-focused lung cancer therapies at the genetic level. While numerous genome-wide association studies (GWAS) have explored the genetic etiology of lung cancer, there remains a large gap between the type of information that may be gleaned from an association study and the depth of understanding necessary to explain and drive translational findings. Thus, in this study we jointly model and integrate extensive multiomics data sources, utilizing a total of 40 genome-wide functional annotations that augment previously published results from the International Lung Cancer Consortium (ILCCO) GWAS, to prioritize and characterize single nucleotide polymorphisms (SNPs) that increase risk of squamous cell lung cancer through the inflammatory and immune responses. Our work bridges the gap between correlative analysis and translational follow-up research, refining GWAS association measures in an interpretable and systematic manner. In particular, reanalysis of the ILCCO data highlights the impact of highly associated SNPs from nuclear factor-κB signaling pathway genes as well as major histocompatibility complex mediated variation in immune responses. One consequence of prioritizing likely functional SNPs is the pruning of variants that might be selected for follow-up work by over an order of magnitude, from potentially tens of thousands to hundreds. The strategies we introduce provide informative and interpretable approaches for incorporating extensive genome-wide annotation data in analysis of genetic association studies.
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Affiliation(s)
- Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Miao Xu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sheila Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Quebec, Quebec, Canada
| | - Stephen Lam
- British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Department of Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jennifer Doherty
- Department of Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, Geisel School of Medicine, Hanover, New Hampshire, United States of America
| | - Gary Goodman
- Department of Medical Oncology, Swedish Medical Group, Seattle, Washington, United States of America
| | - Stig Egil Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - John K. Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - Angela Risch
- Cancer Cluster Salzburg, University of Salzburg, Salzburg, Austria
- Translational Lung Research Center Heidelberg, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center, German Center for Lung Research, Heidelberg, Germany
| | - Gadi Rennert
- Clalit National Cancer Control Center, Carmel Medical Center, Haifa, Israel
| | - Suzanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Olle Melander
- Unit of Nutrition and Cancer, Catalan Institute of Oncology Barcelona, Spain
- Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - Hans Brunnström
- Laboratory Medicine Region, Skäne University Hospital, Lund, Sweden
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Geoffrey Liu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Angeline Andrew
- Department of Epidemiology, Geisel School of Medicine, Hanover, New Hampshire, United States of America
| | - Eric Duell
- Unit of Nutrition and Cancer, Catalan Institute of Oncology Barcelona, Spain
| | - Lambertus A. Kiemeney
- Faculty of Medical Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Nanjing Medical University, Nanjing, China
| | - Aage Haugen
- National Institute of Occupational Health, Oslo, Norway
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeä University, Umeä, Sweden
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Penella Woll
- Department of Oncology, University of Sheffield, Sheffield, United Kingdom
| | - M. Dawn Teare
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Ghislaine Scelo
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- University of Pittsburgh Medical Center Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington, United States of America
| | - Matthew B. Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Demetrios Albanes
- Russian N.N. Blokhin Cancer Research Centre, Russian Academy of Medical Sciences, Moscow, Russia
| | - Raymond Mak
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - David Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Rayjean J. Hung
- Prosserman Centre for Population Health Research, Sinai Health System, Toronto, Canada
| | - Christopher I. Amos
- Dan L. Duncan Comprehensive Cancer Center and Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - David C. Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
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Maruei-Milan R, Heidari Z, Aryan A, Asadi-Tarani M, Salimi S. Long non-coding RNA ANRIL polymorphisms in papillary thyroid cancer and its severity. Br J Biomed Sci 2021; 78:58-62. [PMID: 33186076 DOI: 10.1080/09674845.2020.1829853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: Long non-coding RNAs are likely to have a role in the pathogenesis of many diseases, including cancer. We hypothesised an effect of certain ANRIL single nucleotide polymorphisms (SNPs) in papillary thyroid cancer. Methods: Genomic ANRIL SNPs in rs11333048, rs4977574, rs1333040 and rs10757274 were determined in 134 papillary thyroid cancer patients and 155 age- and sex-matched controls. Results: None of the ANRIL SNPs were individually linked to papillary thyroid cancer. However, the AAAC haplotype (A from rs11333048, A from rs4977574, A from rs1333040 and C from rs10757274, respectively) showed a protective effect from papillary thyroid cancer whilst the CAAC and CAGT haplotypes were associated with cancer. The rs1333048 CC variant was more frequent in patients with larger tumour size (≥1 cm) in a recessive model (OR 3.4 [95%CI, 1.1-11], P = 0.035). The rs4977574 AC variant was associated with smaller tumour size in an over-dominant model (OR 0.4 [95%CI, 0.2-1.0], P = 0.041). SNPs in rs10757274 (AA: p = 0.045) and rs1333040 (CC: p = 0.019) are linked to a lower likelihood of III-IV cancer stages in dominant or codominant models. Conclusions: Certain haplotypes of ANRIL SNPs are associated with papillary thyroid cancer. ANRIL rs1333048 and rs4977574 variants were associated with larger and smaller tumour sizes, respectively. rs10757274 and rs1333040 variants might lead to lower III-IV cancer stages. These SNPs may be important in the diagnosis of this form of thyroid cancer.
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Affiliation(s)
- R Maruei-Milan
- Departments of Clinical Biochemistry, Zahedan University of Medical Sciences , Zahedan, Iran
| | - Z Heidari
- Department of Internal Medicine, Zahedan University of Medical Sciences , Zahedan, Iran
| | - A Aryan
- Department of Radiology, Zahedan University of Medical Sciences , Zahedan, Iran
| | - M Asadi-Tarani
- Departments of Clinical Biochemistry, Zahedan University of Medical Sciences , Zahedan, Iran
| | - S Salimi
- Departments of Clinical Biochemistry, Zahedan University of Medical Sciences , Zahedan, Iran.,Cellular and Molecular Research Center, Zahedan University of Medical Sciences , Zahedan, Iran
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Ji G, Bao T, Li Z, Tang H, Liu D, Yang P, Li W, Huang Y. Current lung cancer screening guidelines may miss high-risk population: a real-world study. BMC Cancer 2021; 21:50. [PMID: 33430831 PMCID: PMC7802250 DOI: 10.1186/s12885-020-07750-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Despite much research published on lung cancer screening, China has had no large-scale study on the missed diagnosis of lung cancer in a health examination population. We therefore did a real-world study using the current lung cancer screening guidelines to a health examination population in China to determine the proportion of lung cancer cases that have been missed. METHODS A real-world cohort study of screening, with the use of low-dose computed tomography, was conducted among people who took yearly health checkup in health management center of West China Hospital between 2006 and 2017. We respectively used current guidelines including lung cancer screening guidelines of the U.S. Preventive Services Task Force (USPSTF) and expert consensus on low dose spiral CT lung cancer screening in China. RESULTS In a total of 15,996 participants with health examination who completed the baseline screening, 6779 (42.4%) subjects had at least one positive finding, and 142 (2.1%) cases of lung cancer were screened positive. The false positive rate was 97.9%. Of 142 lung cancer cases detected in our study, only 9.2% met the lung cancer screening guidelines proposed by the USPSTF, and 24.4% met that of China. The rates of missed diagnosis were as high as 90.8 and 75.6% respectively. In addition, we did an in-depth analysis by gender. We found that among male patients with lung cancer, the proportion of smokers was 75%, and the proportion of young people under 50 was 23.2%. Among female patients with lung cancer, the proportion of smokers was only 5.8%, and the proportion of young people under 50 was up to 33.3%. CONCLUSIONS The rate of missed diagnosis was as high as 90.8% applying the current lung cancer screening guidelines to the health examination population in China. Further study to determine screening guidelines for targeted populations, is warranted.
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Affiliation(s)
- Guiyi Ji
- Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Bao
- Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhenzhen Li
- Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huairong Tang
- Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dan Liu
- Division of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ping Yang
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Weimin Li
- Division of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Frontiers Science Center for Disease-related Molecular Network, Sichuan University, Chengdu, Sichuan, China.,The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan, China
| | - Yan Huang
- Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Corlin L, Liu C, Lin H, Leone D, Yang Q, Ngo D, Levy D, Cupples LA, Gerszten RE, Larson MG, Vasan RS. Proteomic Signatures of Lifestyle Risk Factors for Cardiovascular Disease: A Cross-Sectional Analysis of the Plasma Proteome in the Framingham Heart Study. J Am Heart Assoc 2021; 10:e018020. [PMID: 33372532 PMCID: PMC7955453 DOI: 10.1161/jaha.120.018020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Background Proteomic biomarkers related to cardiovascular disease risk factors may offer insights into the pathogenesis of cardiovascular disease. We investigated whether modifiable lifestyle risk factors for cardiovascular disease are associated with distinctive proteomic signatures. Methods and Results We analyzed 1305 circulating plasma proteomic biomarkers (assayed using the SomaLogic platform) in 897 FHS (Framingham Heart Study) Generation 3 participants (mean age 46±8 years; 56% women; discovery sample) and 1121 FOS (Framingham Offspring Study) participants (mean age 52 years; 54% women; validation sample). Participants were free of hypertension, diabetes mellitus, and clinical cardiovascular disease. We used linear mixed effects models (adjusting for age, sex, body mass index, and family structure) to relate levels of each inverse-log transformed protein to 3 lifestyle factors (ie, smoking, alcohol consumption, and physical activity). A Bonferroni-adjusted P value indicated statistical significance (based on number of proteins and traits tested, P<4.2×10-6 in the discovery sample; P<6.85×10-4 in the validation sample). We observed statistically significant associations of 60 proteins with smoking (37/40 top proteins validated in FOS), 30 proteins with alcohol consumption (23/30 proteins validated), and 5 proteins with physical activity (2/3 proteins associated with the physical activity index validated). We assessed the associations of protein concentrations with previously identified genetic variants (protein quantitative trait loci) linked to lifestyle-related disease traits in the genome-wide-association study catalogue. The protein quantitative trait loci were associated with coronary artery disease, inflammation, and age-related mortality. Conclusions Our cross-sectional study from a community-based sample elucidated distinctive sets of proteins associated with 3 key lifestyle factors.
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Affiliation(s)
- Laura Corlin
- Boston University Department of MedicineBostonMA
- Department of Public Health and Community MedicineTufts University School of MedicineBostonMA
- Department of Civil and Environmental EngineeringTufts University School of EngineeringMedfordMA
| | - Chunyu Liu
- Boston University School of Public HealthBostonMA
| | | | | | - Qiong Yang
- Boston University School of Public HealthBostonMA
| | - Debby Ngo
- Department of MedicineBeth Israel Deaconess Medical CenterBostonMA
- Harvard Medical SchoolBostonMA
| | - Daniel Levy
- Population Sciences BranchNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMD
- Framingham Heart StudyFraminghamMA
| | - L. Adrienne Cupples
- Boston University School of Public HealthBostonMA
- Framingham Heart StudyFraminghamMA
| | - Robert E. Gerszten
- Department of MedicineBeth Israel Deaconess Medical CenterBostonMA
- Harvard Medical SchoolBostonMA
| | - Martin G. Larson
- Boston University School of Public HealthBostonMA
- Framingham Heart StudyFraminghamMA
| | - Ramachandran S. Vasan
- Boston University Department of MedicineBostonMA
- Boston University School of Public HealthBostonMA
- Framingham Heart StudyFraminghamMA
- Boston University Center for Computing and Data SciencesBostonMA
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Vashi R, Patel BM. Roles of ARF tumour suppressor protein in lung cancer: time to hit the nail on the head! Mol Cell Biochem 2021; 476:1365-1375. [PMID: 33392921 DOI: 10.1007/s11010-020-03996-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
Owing to its poor prognosis, the World Health Organization (WHO) lists lung cancer on top of the list when it comes to growing mortality rates and incidence. Usually, there are two types of lung cancer, small-cell lung cancer (SCLC) and non-small-cell lung cancer (NSCLC), which also includes adenocarcinoma, squamous cell carcinoma and large cell carcinomas. ARF, also known in humans as p14ARF and in the mouse as p19ARF, is a nucleolar protein and a member of INK4, a family of cyclin-independent kinase inhibitors (CKI). These genes are clustered on chromosome number 9p21 within the locus of CDKN2A. NSCLC has reported the role of p14ARF as a potential target. p14ARF has a basic mechanism to inhibit mouse double minute 2 protein that exhibits inhibitory action on p53, a phosphoprotein tumour suppressor, thus playing a role in various tumour-related activities such as growth inhibition, DNA damage, autophagy, apoptosis, cell cycle arrest and others. Extensive cancer research is ongoing and updated reports regarding the role of ARF in lung cancer are available. This article summarizes the available lung cancer ARF data, its molecular mechanisms and its associated signalling pathways. Attempts have been made to show how p14ARF functions in different types of lung cancer providing a thought to look upon ARF as a new target for treating the debilitating condition of lung cancer.
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Affiliation(s)
- Ruju Vashi
- Institute of Pharmacy, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India
| | - Bhoomika M Patel
- Institute of Pharmacy, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India.
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Jin J, Robeson H, Fagan P, Orloff MS. Association of PARP1-specific polymorphisms and haplotypes with non-small cell lung cancer subtypes. PLoS One 2020; 15:e0243509. [PMID: 33284833 PMCID: PMC7721167 DOI: 10.1371/journal.pone.0243509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/20/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE The carcinogenesis role of PARP1 in lung cancer is still not clear. Analysis at allelic levels cannot fully explain the function of PARP1 on lung cancer. Our study aims to further explore the relation between PARP1 haplotypes and lung cancer. MATERIALS AND METHODS DNA and RNA were extracted from non-small cell lung cancer (NSCLC) tumor and adjacent normal fresh frozen tissue. Five PARP1-SNPs were genotyped and PARP1-specific SNPs were imputed using IMPUTE and SHAPEIT software. The SNPs were subjected to allelic, haplotype and SNP-SNP interaction analyses. Correlation between SNPs and mRNA/protein expressions were performed. RESULTS SNP imputation inferred the ungenotyped SNPs and increased the power for association analysis. Tumor tissue samples are more likely to carry rs1805414 (OR = 1.85; 95% CI: 1.12-3.06; P-value: 0.017) and rs1805404 (OR = 2.74; 95%CI 1.19-6.32; P-value: 0.015) compared to normal tissues. Our study is the first study to show that haplotypes comprising of 5 SNPs on PARP1 (rs1136410, rs3219073, rs1805414, rs1805404, rs1805415) is able to differentiate the NSCLC tumor from normal tissues. Interaction between rs3219073, rs1805415, and rs1805414 were significantly associated with the NSCLC tumor with OR ranging from 3.61-6.75; 95%CI from 1.82 to 19.9; P-value<0.001. CONCLUSION PARP1 haplotypes may serve as a better predictor in lung cancer development and prognosis compared to single alleles.
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Affiliation(s)
- Jing Jin
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Heather Robeson
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Pebbles Fagan
- Department of Health Behavior and Health Education, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Center for the Studies of Tobacco, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Mohammed S. Orloff
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Center for the Studies of Tobacco, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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Potential Genes Associated with the Survival of Lung Adenocarcinoma Were Identified by Methylation. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:7103412. [PMID: 34007304 PMCID: PMC8108640 DOI: 10.1155/2020/7103412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022]
Abstract
Background Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer. The purpose of this study is to search for genes related to the prognosis of LUAD through methylation based on a linear mixed model (LMM). Methods Gene expression, methylation, and survival data of LUAD patients were downloaded from the TCGA database. Based on the LMM model, the GEMMA algorithm was used to screen the predictive genes related to LUAD survival. The Cox model was used to further screen the predicted genes, and then, protein-protein interaction (PPI) network was constructed. Through the software plugin Cytoscape MCODE 3.8.0, the most closely related genes in the PPI network module were selected for in-depth biological function analysis to further explore the interaction and correlation between genes. Results We screened out 97 predictive genes from 18,834 genes and eliminated one gene associated with lung squamous cell carcinoma from previous studies, leaving 96 genes. The MCODE and the Kaplan-Meier curve analysis were used to finally identify two genes ASB16 and NEDD4 that are related to the prognosis of LUAD. Conclusions The newly identified two genes associated with the prognosis of LUAD may provide a basis for the treatment of patients.
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Chen J, Loukola A, Gillespie NA, Peterson R, Jia P, Riley B, Maes H, Dick DM, Kendler KS, Damaj MI, Miles MF, Zhao Z, Li MD, Vink JM, Minica CC, Willemsen G, Boomsma DI, Qaiser B, Madden PAF, Korhonen T, Jousilahti P, Hällfors J, Gelernter J, Kranzler HR, Sherva R, Farrer L, Maher B, Vanyukov M, Taylor M, Ware JJ, Munafò MR, Lutz SM, Hokanson JE, Gu F, Landi MT, Caporaso NE, Hancock DB, Gaddis NC, Baker TB, Bierut LJ, Johnson EO, Chenoweth M, Lerman C, Tyndale R, Kaprio J, Chen X. Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes. Nicotine Tob Res 2020; 22:900-909. [PMID: 31294817 DOI: 10.1093/ntr/ntz099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION FTND (Fagerstrӧm test for nicotine dependence) and TTFC (time to smoke first cigarette in the morning) are common measures of nicotine dependence (ND). However, genome-wide meta-analysis for these phenotypes has not been reported. METHODS Genome-wide meta-analyses for FTND (N = 19,431) and TTFC (N = 18,567) phenotypes were conducted for adult smokers of European ancestry from 14 independent cohorts. RESULTS We found that SORBS2 on 4q35 (p = 4.05 × 10-8), BG182718 on 11q22 (p = 1.02 × 10-8), and AA333164 on 14q21 (p = 4.11 × 10-9) were associated with TTFC phenotype. We attempted replication of leading candidates with independent samples (FTND, N = 7010 and TTFC, N = 10 061), however, due to limited power of the replication samples, the replication of these new loci did not reach significance. In gene-based analyses, COPB2 was found associated with FTND phenotype, and TFCP2L1, RELN, and INO80C were associated with TTFC phenotype. In pathway and network analyses, we found that the interconnected interactions among the endocytosis, regulation of actin cytoskeleton, axon guidance, MAPK signaling, and chemokine signaling pathways were involved in ND. CONCLUSIONS Our analyses identified several promising candidates for both FTND and TTFC phenotypes, and further verification of these candidates was necessary. Candidates supported by both FTND and TTFC (CHRNA4, THSD7B, RBFOX1, and ZNF804A) were associated with addiction to alcohol, cocaine, and heroin, and were associated with autism and schizophrenia. We also identified novel pathways involved in cigarette smoking. The pathway interactions highlighted the importance of receptor recycling and internalization in ND. IMPLICATIONS Understanding the genetic architecture of cigarette smoking and ND is critical to develop effective prevention and treatment. Our study identified novel candidates and biological pathways involved in FTND and TTFC phenotypes, and this will facilitate further investigation of these candidates and pathways.
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Affiliation(s)
- Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Anu Loukola
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Nathan A Gillespie
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Roseann Peterson
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Peilin Jia
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX
| | - Brien Riley
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Hermine Maes
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Daniella M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA
| | - Kenneth S Kendler
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - M Imad Damaj
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Michael F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Zhongming Zhao
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jacqueline M Vink
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Behavioural Science Institute, Radboud University, Nijmegen, the Netherlands
| | - Camelia C Minica
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Beenish Qaiser
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Tellervo Korhonen
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Finland
| | | | - Jenni Hällfors
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Joel Gelernter
- Department of Psychiatry, Yale University, New Haven, CT
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Richard Sherva
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Lindsay Farrer
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Brion Maher
- Department of Mental Health, Johns Hopkins University, Baltimore, MD
| | - Michael Vanyukov
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Michelle Taylor
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Jenifer J Ware
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Sharon M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - John E Hokanson
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Fangyi Gu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Maria T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Neil E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Dana B Hancock
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC
| | - Nathan C Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, Madison, WI
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO
| | - Eric O Johnson
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC.,Fellow Program, RTI International, Research Triangle Park, NC
| | - Meghan Chenoweth
- Centre for Addiction and Mental Health, and Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Caryn Lerman
- Center for Interdisciplinary Research on Nicotine Addiction, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Rachel Tyndale
- Centre for Addiction and Mental Health, and Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV.,Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA.,Department of Psychology, University of Nevada Las Vegas, Las Vegas, NV
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Baumeister SE, Leitzmann MF, Bahls M, Meisinger C, Amos CI, Hung RJ, Teumer A, Baurecht H. Physical Activity Does Not Lower the Risk of Lung Cancer. Cancer Res 2020; 80:3765-3769. [PMID: 32646967 PMCID: PMC11141401 DOI: 10.1158/0008-5472.can-20-1127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/28/2020] [Accepted: 06/23/2020] [Indexed: 11/16/2022]
Abstract
Observational studies have suggested that physical activity might lower the risk of lung cancer in former and current smokers, but not in never-smokers. Using genetic instruments for self-reported and accelerometer-measured physical activity traits implemented through two-sample Mendelian randomization (MR), we sought to strengthen the evidence for causality. We used 18 genome-wide significant (P < 5 × 10-8) single-nucleotide polymorphisms (SNP) for self-reported moderate-to-vigorous physical activity and seven SNP for accelerometer-measured ("average acceleration") physical activity from up to 377,234 UK Biobank participants and evaluated these in relation to risk using 29,266 lung cancer cases (including 11,273 adenocarcinomas, 7,426 squamous cell carcinoma, and 2,664 small-cell carcinoma cases) and 56,450 controls. MR analysis suggested no effect of self-reported physical activity [OR (95% confidence interval (CI)) = 0.67 (0.42-1.05); P = 0.081; Q-value = 0.243] and accelerometer-measured activity [OR (95% CI) = 0.98 (0.93-1.03); P = 0.372; Q-value = 0.562] on lung cancer. There was no evidence for associations of physical activity with histologic types and lung cancer in ever and never smokers. Replication analysis using genetic instruments from a different genome-wide study and sensitivity analysis to address potential pleiotropic effects led to no substantive change in estimates. Collectively, these findings do not support a protective relationship between physical activity and the risk of lung cancer. SIGNIFICANCE: A new genetic study provides little evidence that recommending physical activity would help prevent lung cancer.
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Affiliation(s)
- Sebastian-Edgar Baumeister
- Chair of Epidemiology, LMU München, UNIKA-T Augsburg, Augsburg, Germany.
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Michael F Leitzmann
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Martin Bahls
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Christa Meisinger
- Chair of Epidemiology, LMU München, UNIKA-T Augsburg, Augsburg, Germany
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | | | - Alexander Teumer
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
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46
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DNA Mismatch Repair Gene Variants in Sporadic Solid Cancers. Int J Mol Sci 2020; 21:ijms21155561. [PMID: 32756484 PMCID: PMC7432688 DOI: 10.3390/ijms21155561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
The phenotypic effects of single nucleotide polymorphisms (SNPs) in the development of sporadic solid cancers are still scarce. The aim of this review was to summarise and analyse published data on the associations between SNPs in mismatch repair genes and various cancers. The mismatch repair system plays a unique role in the control of the genetic integrity and it is often inactivated (germline and somatic mutations and hypermethylation) in cancer patients. Here, we focused on germline variants in mismatch repair genes and found the outcomes rather controversial: some SNPs are sometimes ascribed as protective, while other studies reported their pathological effects. Regarding the complexity of cancer as one disease, we attempted to ascertain if particular polymorphisms exert the effect in the same direction in the development and treatment of different malignancies, although it is still not straightforward to conclude whether polymorphisms always play a clear positive role or a negative one. Most recent and robust genome-wide studies suggest that risk of cancer is modulated by variants in mismatch repair genes, for example in colorectal cancer. Our study shows that rs1800734 in MLH1 or rs2303428 in MSH2 may influence the development of different malignancies. The lack of functional studies on many DNA mismatch repair SNPs as well as their interactions are not explored yet. Notably, the concerted action of more variants in one individual may be protective or harmful. Further, complex interactions of DNA mismatch repair variations with both the environment and microenvironment in the cancer pathogenesis will deserve further attention.
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47
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Poulet C, Njock MS, Moermans C, Louis E, Louis R, Malaise M, Guiot J. Exosomal Long Non-Coding RNAs in Lung Diseases. Int J Mol Sci 2020; 21:E3580. [PMID: 32438606 PMCID: PMC7279016 DOI: 10.3390/ijms21103580] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Within the non-coding genome landscape, long non-coding RNAs (lncRNAs) and their secretion within exosomes are a window that could further explain the regulation, the sustaining, and the spread of lung diseases. We present here a compilation of the current knowledge on lncRNAs commonly found in Chronic Obstructive Pulmonary Disease (COPD), asthma, Idiopathic Pulmonary Fibrosis (IPF), or lung cancers. We built interaction networks describing the mechanisms of action for COPD, asthma, and IPF, as well as private networks for H19, MALAT1, MEG3, FENDRR, CDKN2B-AS1, TUG1, HOTAIR, and GAS5 lncRNAs in lung cancers. We identified five signaling pathways targeted by these eight lncRNAs over the lung diseases mentioned above. These lncRNAs were involved in ten treatment resistances in lung cancers, with HOTAIR being itself described in seven resistances. Besides, five of them were previously described as promising biomarkers for the diagnosis and prognosis of asthma, COPD, and lung cancers. Additionally, we describe the exosomal-based studies on H19, MALAT1, HOTAIR, GAS5, UCA1, lnc-MMP2-2, GAPLINC, TBILA, AGAP2-AS1, and SOX2-OT. This review concludes on the need for additional studies describing the lncRNA mechanisms of action and confirming their potential as biomarkers, as well as their involvement in resistance to treatment, especially in non-cancerous lung diseases.
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Affiliation(s)
- Christophe Poulet
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
| | - Makon-Sébastien Njock
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Catherine Moermans
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Edouard Louis
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Gastroenterology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Renaud Louis
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Michel Malaise
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
| | - Julien Guiot
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
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48
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Bossé Y, Li Z, Xia J, Manem V, Carreras-Torres R, Gabriel A, Gaudreault N, Albanes D, Aldrich MC, Andrew A, Arnold S, Bickeböller H, Bojesen SE, Brennan P, Brunnstrom H, Caporaso N, Chen C, Christiani DC, Field JK, Goodman G, Grankvist K, Houlston R, Johansson M, Johansson M, Kiemeney LA, Lam S, Landi MT, Lazarus P, Le Marchand L, Liu G, Melander O, Rennert G, Risch A, Rosenberg SM, Schabath MB, Shete S, Song Z, Stevens VL, Tardon A, Wichmann HE, Woll P, Zienolddiny S, Obeidat M, Timens W, Hung RJ, Joubert P, Amos CI, McKay JD. Transcriptome-wide association study reveals candidate causal genes for lung cancer. Int J Cancer 2020; 146:1862-1878. [PMID: 31696517 PMCID: PMC7008463 DOI: 10.1002/ijc.32771] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/17/2022]
Abstract
We have recently completed the largest GWAS on lung cancer including 29,266 cases and 56,450 controls of European descent. The goal of our study has been to integrate the complete GWAS results with a large-scale expression quantitative trait loci (eQTL) mapping study in human lung tissues (n = 1,038) to identify candidate causal genes for lung cancer. We performed transcriptome-wide association study (TWAS) for lung cancer overall, by histology (adenocarcinoma, squamous cell carcinoma and small cell lung cancer) and smoking subgroups (never- and ever-smokers). We performed replication analysis using lung data from the Genotype-Tissue Expression (GTEx) project. DNA damage assays were performed in human lung fibroblasts for selected TWAS genes. As expected, the main TWAS signal for all histological subtypes and ever-smokers was on chromosome 15q25. The gene most strongly associated with lung cancer at this locus using the TWAS approach was IREB2 (pTWAS = 1.09E-99), where lower predicted expression increased lung cancer risk. A new lung adenocarcinoma susceptibility locus was revealed on 9p13.3 and associated with higher predicted expression of AQP3 (pTWAS = 3.72E-6). Among the 45 previously described lung cancer GWAS loci, we mapped candidate target gene for 17 of them. The association AQP3-adenocarcinoma on 9p13.3 was replicated using GTEx (pTWAS = 6.55E-5). Consistent with the effect of risk alleles on gene expression levels, IREB2 knockdown and AQP3 overproduction promote endogenous DNA damage. These findings indicate genes whose expression in lung tissue directly influences lung cancer risk.
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Affiliation(s)
- Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Canada
- Department of Molecular Medicine, Laval University, Quebec City, Canada
| | - Zhonglin Li
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Canada
| | - Jun Xia
- Baylor College of Medicine, The Institute for Clinical and Translational Research, Houston, TX
| | - Venkata Manem
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Canada
| | | | - Aurélie Gabriel
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Nathalie Gaudreault
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Canada
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Melinda C Aldrich
- Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN
| | - Angeline Andrew
- Department of Neurology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center Goettingen, Goettingen, Germany
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - David C Christiani
- Program in Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - John K Field
- Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool Institute of Translational Medicine, Liverpool, United Kingdom
| | - Gary Goodman
- Public Health Sciences Division, Swedish Cancer Institute, Seattle, WA
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umea, Sweden
| | - Richard Houlston
- German Research Center for Environmental Health, Institute for Cancer Research, London, United Kingdom
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Pullman, WA
| | - Loic Le Marchand
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI
| | - Geoffrey Liu
- Epidemiology Division, Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | - Gadi Rennert
- Technion Faculty of Medicine, Carmel Medical Center, Haifa, Israel
| | - Angela Risch
- Cancer Center Cluster Salzburg at PLUS, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Matthew B Schabath
- Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Sanjay Shete
- Epidemiology, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Zhuoyi Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | | | - Adonina Tardon
- Faculty of Medicine, University of Oviedo and CIBERESP, Oviedo, Spain
| | - H-Erich Wichmann
- Institute of Epidemiology, Helmholtz Center Munich, Oberschleißheim, Germany
| | - Penella Woll
- Academic Unit of Clinical Oncology, University of Sheffield, Sheffield, United Kingdom
| | | | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Quebec City, Canada
| | - Christopher I Amos
- Baylor College of Medicine, The Institute for Clinical and Translational Research, Houston, TX
| | - James D McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
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Jha P. The hazards of smoking and the benefits of cessation: a critical summation of the epidemiological evidence in high-income countries. eLife 2020; 9:49979. [PMID: 32207405 PMCID: PMC7093109 DOI: 10.7554/elife.49979] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/14/2020] [Indexed: 12/15/2022] Open
Abstract
In high-income countries, the biggest cause of premature death, defined as death before 70 years, is smoking of manufactured cigarettes. Smoking-related disease was responsible for about 41 million deaths in the United States, United Kingdom and Canada, cumulatively, from 1960 to 2020. Every million cigarettes smoked leads to one death in the US and Canada, but slightly more than one death in the UK. The 21st century hazards reveal that smokers who start smoking early in adult life and do not quit lose a decade of life expectancy versus non-smokers. Cessation, particularly before age 40 years, yields large reductions in mortality risk. Up to two-thirds of deaths among smokers are avoidable at non-smoking death rates, and former smokers have about only a quarter of the excess risk of death compared to current smokers. The gap between scientific and popular understanding of smoking hazards is surprisingly large.
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Affiliation(s)
- Prabhat Jha
- Centre for Global Health Research, Dalla Lana School of Public Health and Unity Health, Toronto, University of Toronto, Ontario, Canada
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50
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de Alencar VTL, Formiga MN, de Lima VCC. Inherited lung cancer: a review. Ecancermedicalscience 2020; 14:1008. [PMID: 32104210 PMCID: PMC7039693 DOI: 10.3332/ecancer.2020.1008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the most common cancer worldwide and has high rates of mortality. The major risk factor associated with this disease is tobacco smoke, but approximately 10%-25% of all lung cancer cases occur in patients who have never smoked. Data suggest that lung cancer in never-smokers has a different molecular profile, tumour microenvironment and epidemiology than that in smokers. Several risk factors have been associated with its occurrence, and the possibility of inherited predisposition is becoming clearer. A better understanding of this disease is essential for the future development of personalised screening, diagnosis and treatment approaches, with consequent reduction of mortality. In this review, we discuss historical studies of lung cancer in never-smokers and the currently available evidence of inherited predisposition to this disease.
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Affiliation(s)
| | - Maria Nirvana Formiga
- AC Camargo Cancer Center, R Prof Antônio Prudente, 211 São Paulo, SP 01509-010, Brazil
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