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Li J, Dhilipkannah P, Holden VK, Sachdeva A, Todd NW, Jiang F. Dysregulation of lncRNA MALAT1 Contributes to Lung Cancer in African Americans by Modulating the Tumor Immune Microenvironment. Cancers (Basel) 2024; 16:1876. [PMID: 38791954 PMCID: PMC11119359 DOI: 10.3390/cancers16101876] [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: 04/09/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
African American (AA) populations present with notably higher incidence and mortality rates from lung cancer in comparison to other racial groups. Here, we elucidated the contribution of long non-coding RNAs (lncRNAs) in the racial disparities and their potential clinical applications in both diagnosis and therapeutic strategies. AA patients had elevated plasma levels of MALAT1 and PVT1 compared with cancer-free smokers. Incorporating these lncRNAs as plasma biomarkers, along with smoking history, achieved 81% accuracy in diagnosis of lung cancer in AA patients. We observed a rise in MALAT1 expression, correlating with increased levels of monocyte chemoattractant protein-1 (MCP-1) and CD68, CD163, CD206, indicative of tumor-associated macrophages in lung tumors of AA patients. Forced MALAT1 expression led to enhanced growth and invasiveness of lung cancer cells, both in vitro and in vivo, accompanied by elevated levels of MCP-1, CD68, CD163, CD206, and KI67. Mechanistically, MALAT1 acted as a competing endogenous RNA to directly interact with miR-206, subsequently affecting MCP-1 expression and macrophage activity, and enhanced the tumorigenesis. Targeting MALAT1 significantly reduced tumor sizes in animal models. Therefore, dysregulated MALAT1 contributes to lung cancer disparities in AAs by modulating the tumor immune microenvironment through its interaction with miR-206, thereby presenting novel diagnostic and therapeutic targets.
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Affiliation(s)
- Jin Li
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Pushpa Dhilipkannah
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Van K. Holden
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ashutosh Sachdeva
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nevins W. Todd
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Li J, Dhilipkannah P, Holden VK, Sachdeva A, Todd NW, Jiang F. Dysregulation of lncRNA MALAT1 Contributes to Lung Cancer in African Americans by modulating the tumor immune microenvironment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.04.24305363. [PMID: 38633795 PMCID: PMC11023666 DOI: 10.1101/2024.04.04.24305363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
African American (AA) populations present with notably higher incidence and mortality rates from lung cancer in comparison to other racial groups. Here, we elucidate the contribution of long non-coding RNAs (lncRNAs) in the racial disparities and their potential clinical applications in both diagnosis and therapeutic strategies. AA patients had elevated plasma levels of MALAT1 and PVT1 compared with cancer-free smokers. Incorporating these lncRNAs as plasma biomarkers, along with smoking history, achieved 81% accuracy in diagnosis of lung cancer in AA patients. We observed a rise in MALAT1 expression, correlating with increased levels of monocyte chemoattractant protein-1 (MCP-1) and CD68, CD163, CD206, indicative of tumor-associated macrophages in lung tumors of AA patients. Forced MALAT1 expression led to enhanced growth and invasiveness of lung cancer cells, both in vitro and in vivo, accompanied by elevated levels of MCP-1, CD68, CD163, CD206, and KI67. Mechanistically, MALAT1 acted as a competing endogenous RNA to directly interact with miR-206, subsequently affecting MCP-1 expression and macrophage activity, and enhanced the tumorigenesis. Targeting MALAT1 significantly reduced tumor sizes in animal models. Therefore, dysregulated MALAT1 contributes to lung cancer disparities in AAs by modulating the tumor immune microenvironment through its interaction with miR-206, thereby presenting novel diagnostic and therapeutic targets.
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Gao L, Dhilipkannah P, Holden VK, Deepak J, Sachdeva A, Todd NW, Stass SA, Jiang F. Differential Non-Coding RNA Profiles for Lung Cancer Early Detection in African and White Americans. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.27.24304977. [PMID: 38585975 PMCID: PMC10996737 DOI: 10.1101/2024.03.27.24304977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Introduction Lung cancer leads in cancer-related deaths. Disparities are observed in lung cancer rates, with African Americans (AAs) experiencing disproportionately higher incidence and mortality compared to other ethnic groups. Non-coding RNAs (ncRNAs) play crucial roles in lung tumorigenesis. Our objective was to identify ncRNA biomarkers associated with the racial disparity in lung cancer. Methods Using droplet digital PCR, we examined 93 lung-cancer-associated ncRNAs in the plasma and sputum samples from AA and White American (WA) participants, which included 118 patients and 92 cancer-free smokers. Subsequently, we validated our results with a separate cohort comprising 56 cases and 72 controls. Results In the AA population, plasma showed differential expression of ten ncRNAs, while sputum revealed four ncRNAs when comparing lung cancer patients to the control group. In the WA population, the plasma displayed eleven ncRNAs, and the sputum had five ncRNAs showing differential expression between the lung cancer patients and the control group. For AAs, we identified a three-ncRNA panel (plasma miRs-147b, 324-3p, 422a) diagnosing lung cancer in AAs with 86% sensitivity and 89% specificity. For WAs, a four-ncRNA panel was developed, comprising sputum miR-34a-5p and plasma miRs-103-3p, 126-3p, 205-5p, achieving 88% sensitivity and 87% specificity. These panels remained effective across different stages and histological types of lung tumors and were validated in the independent cohort. Conclusions The ethnicity-related ncRNA signatures have promise as biomarkers to address the racial disparity in lung cancer.
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Leng Q, Dhilipkannah P, Jiang F. Cytokine Signatures for Lung Cancer Diagnosis in African American Populations. J Pers Med 2024; 14:117. [PMID: 38276239 PMCID: PMC10817620 DOI: 10.3390/jpm14010117] [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: 10/31/2023] [Revised: 01/05/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths among both men and women. African Americans (AAs) experience disproportionately higher incidence and mortality compared to other ethnic groups. Cytokines play multifaceted and crucial roles in the initiation, progression, and spread of cancer. Our aim was to identify cytokine biomarkers for the early detection of lung cancer in AAs. We examined eight key cytokines (Interleukin-1, IL-6, IL-8, IL-10, IL-12p70, monocyte chemotactic protein-1 (MCP-1), interferon-gamma (IFN-γ), and tumor necrosis factor-alpha (TNF-α)) in the plasma of 104 lung cancer patients and 48 cancer-free individuals using the FirePlex Immunoassay. These findings were subsequently validated in a separate cohort of 58 cases and 58 controls. IL-8, IFN-γ, and TNF-α exhibited elevated levels in both AA and White American (WA) lung cancer cases. Notably, IL-10 and MCP-1 displayed significant increases specifically in AA lung cancer patients, with MCP-1 levels associated with lung adenocarcinoma cases. Conversely, WA lung cancer patients showed heightened IL-6 levels, particularly linked to lung adenocarcinoma. The combined use of specific cytokines showed promise in lung cancer diagnosis, with IL-8, IL-10, and MCP-1 achieving 76% sensitivity and 79% specificity in AAs and IL-6 and IL-8 combined offering 76% sensitivity and 74% specificity in WAs. These diagnostic biomarkers were validated in the independent cohort. The ethnicity-related cytokine biomarkers hold promise for diagnosing lung cancer in AAs and WAs, potentially addressing the observed racial disparity.
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Affiliation(s)
| | | | - Feng Jiang
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Vakili M, Shirinzadeh-Dastgiri A, Ershadi R, Dastgheib SA, Shiri A, Aghasipour M, Barahman M, Manzourolhojeh M, Aghili K, Neamatzadeh H, Akbarian E. Correlation between rs1800871, rs1800872 and rs1800896 Polymorphisms at IL-10 Gene and Lung Cancer Risk. Asian Pac J Cancer Prev 2024; 25:287-298. [PMID: 38285796 PMCID: PMC10911735 DOI: 10.31557/apjcp.2024.25.1.287] [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: 09/26/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND The tumorigenesis of lung cancer is complicated, and genetic factor may have the role in the malignant transformation of lung cells. IL-10 gene polymorphisms have been evaluated for their potential roles in lung cancer. However, those studies results are controversial. To clarify the effects of IL-10 rs1800871, rs1800872 and rs1800896 polymorphisms on the risk of lung cancer, a meta-analysis was performed with eligible individual studies. METHODS Eligible publications were gathered by retrieving PubMed, Web of Science, Embase, Wan Fang, and CNKI up to September 01, 2023. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of such association. RESULTS A total of 23 studies, including 5950 patients with lung cancer and 8046 healthy controls, were identified in this meta-analysis. Overall, there was no a significant association between the rs1800871, rs1800872 and rs1800896 polymorphisms at IL-10 gene and susceptibility to lung cancer globally when all studies in the pooled into this meta-analysis. Stratified analysis by ethnicity showed that rs1800872 polymorphism was associated with lung cancer among Asians and Caucasians. However, no significant association was identified between the rs1800871 and rs1800896 and risk of lung cancer. CONCLUSIONS Pooled data showed that IL-10 rs1800871, rs1800872 and rs1800896 polymorphisms were not associated with lung cancer globally. Future well-designed large case-control studies with different ethnicities are recommended.
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Affiliation(s)
- Mohammad Vakili
- Department of Surgery, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Ahmad Shirinzadeh-Dastgiri
- Department of Surgery, School of Medicine, Shohadaye Haft-e-Tir Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Reza Ershadi
- Department of Surgery, School of Medicine, Shohadaye Haft-e-Tir Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Seyed Alireza Dastgheib
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Amirmasoud Shiri
- School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Maryam Aghasipour
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Ohio, USA.
| | - Maedeh Barahman
- Department of Radiation Oncology, Firoozgar Hospital, Firoozgar Clinical Research Development Center (FCRDC), Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | - Mohammad Manzourolhojeh
- Department of Medical Laboratory Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Kazem Aghili
- Department of Radiology, Shahid Rahnemoon Hospital , School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Hossein Neamatzadeh
- Mother and Newborn Health Research Center, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Elahe Akbarian
- Children Growth Disorder Research Center, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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Leon C, Manley E, Neely AM, Castillo J, Ramos Correa M, Velarde DA, Yang M, Puente PE, Romero DI, Ren B, Chai W, Gladstone M, Lamango NS, Huang Y, Offringa IA. Lack of racial and ethnic diversity in lung cancer cell lines contributes to lung cancer health disparities. Front Oncol 2023; 13:1187585. [PMID: 38023251 PMCID: PMC10651223 DOI: 10.3389/fonc.2023.1187585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Lung cancer is the leading cause of cancer death in the United States and worldwide, and a major source of cancer health disparities. Lung cancer cell lines provide key in vitro models for molecular studies of lung cancer development and progression, and for pre-clinical drug testing. To ensure health equity, it is imperative that cell lines representing different lung cancer histological types, carrying different cancer driver genes, and representing different genders, races, and ethnicities should be available. This is particularly relevant for cell lines from Black men, who experience the highest lung cancer mortality in the United States. Here, we undertook a review of the available lung cancer cell lines and their racial and ethnic origin. We noted a marked imbalance in the availability of cell lines from different races and ethnicities. Cell lines from Black patients were strongly underrepresented, and we identified no cell lines from Hispanic/Latin(x) (H/L), American Indian/American Native (AI/AN), or Native Hawaiian or other Pacific Islander (NHOPI) patients. The majority of cell lines were derived from White and Asian patients. Also missing are cell lines representing the cells-of-origin of the major lung cancer histological types, which can be used to model lung cancer development and to study the effects of environmental exposures on lung tissues. To our knowledge, the few available immortalized alveolar epithelial cell lines are all derived from White subjects, and the race and ethnicity of a handful of cell lines derived from bronchial epithelial cells are unknown. The lack of an appropriately diverse collection of lung cancer cell lines and lung cancer cell-of-origin lines severely limits racially and ethnically inclusive lung cancer research. It impedes the ability to develop inclusive models, screen comprehensively for effective compounds, pre-clinically test new drugs, and optimize precision medicine. It thereby hinders the development of therapies that can increase the survival of minority and underserved patients. The noted lack of cell lines from underrepresented groups should constitute a call to action to establish additional cell lines and ensure adequate representation of all population groups in this critical pre-clinical research resource.
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Affiliation(s)
- Christopher Leon
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | | | - Aaron M. Neely
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jonathan Castillo
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Michele Ramos Correa
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Diego A. Velarde
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Minxiao Yang
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Pablo E. Puente
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Diana I. Romero
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, United States
| | - Bing Ren
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, United States
| | - Wenxuan Chai
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, United States
| | - Matthew Gladstone
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Nazarius S. Lamango
- College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL, United States
| | - Yong Huang
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, United States
| | - Ite A. Offringa
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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Chen LS, Baker TB, Ramsey A, Amos CI, Bierut LJ. Genomic medicine to reduce tobacco and related disorders: Translation to precision prevention and treatment. ADDICTION NEUROSCIENCE 2023; 7:100083. [PMID: 37602286 PMCID: PMC10434839 DOI: 10.1016/j.addicn.2023.100083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Genomic medicine can enhance prevention and treatment. First, we propose that advances in genomics have the potential to enhance assessment of disease risk, improve prognostic predictions, and guide treatment development and application. Clinical implementation of polygenic risk scores (PRSs) has emerged as an area of active research. The pathway from genomic discovery to implementation is an iterative process. Second, we provide examples on how genomic medicine has the potential to solve problems in prevention and treatment using two examples: Lung cancer screening and evidence-based tobacco treatment are both under-utilized and great opportunities for genomic interventions. Third, we discuss the translational process for developing genomic interventions from evidence to implementation by presenting a model to evaluate genomic evidence for clinical implementation, mechanisms of genomic interventions, and patient desire for genomic interventions. Fourth, we present potential challenges in genomic interventions including a great need for evidence in all diverse populations, little evidence on treatment algorithms, challenges in accommodating a dynamic evidence base, and implementation challenges in real world clinical settings. Finally, we conclude that research to identify genomic markers that are associated with smoking cessation success and the efficacy of smoking cessation treatments is needed to empower people of all diverse ancestry. Importantly, genomic data can be used to help identify patients with elevated risk for nicotine addiction, difficulty quitting smoking, favorable response to specific pharmacotherapy, and tobacco-related health problems.
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Affiliation(s)
- Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
| | - Timothy B. Baker
- Center for Tobacco Research and Intervention, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Alex Ramsey
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
| | - Christopher I. Amos
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, United States
- Department of Medicine, Baylor College of Medicine, Institute for Clinical and Translational Research, Houston, TX, United States
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
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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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Parlato LA, Welch R, Ong IM, Long J, Cai Q, Steinwandel MD, Blot WJ, Zheng W, Warren Andersen S. Genome-wide association study (GWAS) of circulating vitamin D outcomes among individuals of African ancestry. Am J Clin Nutr 2023; 117:308-316. [PMID: 36811574 PMCID: PMC10196601 DOI: 10.1016/j.ajcnut.2022.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/01/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Vitamin D deficiency is more common among African-ancestry individuals and may be associated with adverse health outcomes. Vitamin D binding protein (VDBP) regulates concentrations of biologically active vitamin D. OBJECTIVE We conducted genome-wide association study (GWAS) of VDBP and 25-hydroxyvitamin D among African-ancestry individuals. METHODS Data were collected from 2,602 African American adults from the Southern Community Cohort Study (SCCS) and 6,934 African- or Caribbean-ancestry adults from the UK Biobank. Serum VDBP concentrations were available only in the SCCS and were measured by using the Polyclonal Human VDBP ELISA kit. Serum 25-hydroxyvitamin D concentrations for both study samples were measured by using Diasorin Liason, a chemiluminescent immunoassay. Participants were genotyped for single nucleotide polymorphisms (SNPs) with genome-wide coverage by using Illumina or Affymetrix platforms. Fine-mapping analysis was performed by using forward stepwise linear regression models including all variants with P value < 5 × 10-8 and within 250 kbps of a lead SNP. RESULTS We identified 4 loci notably associated with VDBP concentrations in the SCCS population: rs7041 (per allele β = 0.61 μg/mL, SE = 0.05, P = 1.4 × 10-48) and rs842998 (per allele β = 0.39 μg/mL, SE = 0.03, P = 4.0 × 10-31) in GC, rs8427873 (per allele β = 0.31 μg/mL, SE = 0.04, P = 3.0 × 10-14) near GC and rs11731496 (per allele β = 0.21 μg/mL, SE = 0.03, P = 3.6 × 10-11) in between GC and NPFFR2. In conditional analyses, which included the above-mentioned SNPs, only rs7041 remained notable (P = 4.1 × 10-21). SNP rs4588 in GC was the only GWAS-identified SNP associated with 25-hydroxyvitamin D concentration. Among UK Biobank participants: per allele β = -0.11 μg/mL, SE = 0.01, P = 1.5 × 10-13; in the SCCS: per allele β = -0.12 μg/mL, SE = 0.06, P = 2.8 × 10-02). rs7041 and rs4588 are functional SNPs that influence the binding affinity of VDBP to 25-hydroxyvitamin D. CONCLUSIONS Our results were in line with previous studies conducted in European-ancestry populations, showing that GC, the gene that directly encodes for VDBP, would be important for VDBP and 25-hydroxyvitamin D concentrations. The current study extends our knowledge of the genetics of vitamin D in diverse populations.
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Affiliation(s)
- Lisa A Parlato
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Rene Welch
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, Madison, WI, USA; Department of Obstetrics and Gynecology, UW-Health Hospital, University of Wisconsin-Madison, Madison, WI, USA
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, Madison, WI, USA; Department of Obstetrics and Gynecology, UW-Health Hospital, University of Wisconsin-Madison, Madison, WI, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mark D Steinwandel
- International Epidemiology Field Station, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA; International Epidemiology Field Station, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shaneda Warren Andersen
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, Madison, WI, USA; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
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James BA, Williams JL, Nemesure B. A systematic review of genetic ancestry as a risk factor for incidence of non-small cell lung cancer in the US. Front Genet 2023; 14:1141058. [PMID: 37082203 PMCID: PMC10110850 DOI: 10.3389/fgene.2023.1141058] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023] Open
Abstract
Background: Non-Small Cell Lung Cancer (NSCLC), the leading cause of cancer-related death in the United States, is the most diagnosed form of lung cancer. While lung cancer incidence has steadily declined over the last decade, disparities in incidence and mortality rates persist among African American (AA), Caucasian American (CA), and Hispanic American (HA) populations. Researchers continue to explore how genetic ancestry may influence differential outcomes in lung cancer risk and development. The purpose of this evaluation is to highlight experimental research that investigates the differential impact of genetic mutations and ancestry on NSCLC incidence. Methods: This systematic review was conducted using PubMed and Google Scholar search engines. The following key search terms were used to select articles published between 2011 and 2022: "African/European/Latin American Ancestry NSCLC"; "Racial Disparities NSCLC"; "Genetic Mutations NSCLC"; "NSCLC Biomarkers"; "African Americans/Hispanic Americans/Caucasian Americans NSCLC incidence." Systematic reviews, meta-analyses, and studies outside of the US were excluded. A total of 195 articles were initially identified and after excluding 156 which did not meet eligibility criteria, 38 were included in this investigation. Results: Studies included in this analysis focused on racial/ethnic disparities in the following common genetic mutations observed in NSCLC: KRAS, EGFR, TP53, PIK3CA, ALK Translocations, ROS-1 Rearrangements, STK11, MET, and BRAF. Results across studies varied with respect to absolute differential expression. No significant differences in frequencies of specific genetic mutational profiles were noted between racial/ethnic groups. However, for HAs, lower mutational frequencies in KRAS and STK11 genes were observed. In genetic ancestry level analyses, multiple studies suggest that African ancestry is associated with a higher frequency of EGFR mutations. Conversely, Latin ancestry is associated with TP53 mutations. At the genomic level, several novel predisposing variants associated with African ancestry and increased risk of NSCLC were discovered. Family history among all racial/ethnic groups was also considered a risk factor for NSCLC. Conclusion: Results from racially and ethnically diverse studies can elucidate driving factors that may increase susceptibility and subsequent lung cancer risk across different racial/ethnic groups. Identification of biomarkers that can be used as diagnostic, prognostic, and therapeutic tools may help improve lung cancer survival among high-risk populations.
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Shi Q, Zhang XX, Shi XQ, Chen Y, Sun C. Identification of rs2736099 as a novel cis-regulatory variation for TERT and implications for tumorigenesis and cell proliferation. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04372-9. [PMID: 36131156 DOI: 10.1007/s00432-022-04372-9] [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: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Lung cancer is a malignant tumor with obvious genetic predisposition. Association studies have proposed that rs2853677, a SNP localizing at intron region of TERT (telomerase reverse transcriptase), is significantly associated with TERT expression, telomere length and eventually lung cancer risk. However, functional genomics work indicates that rs2853677 is not with the ability to alter gene expression. All these facts make us hypothesize that some other genetic variation(s) are in linkage disequilibrium (LD) with rs2853677 and influence TERT expression. METHODS LD pattern in rs2853677 nearby region was analyzed based on 1000 genomes data for three representative populations in the world and functional genomics research was performed for this locus. RESULTS Only one SNP, rs2736099, is in strong LD with rs2853677 in East Asian. Dual-luciferase reporter assay verifies that rs2736099 can regulate gene expression and should be the causal SNP for this disease. Through chromosome conformation capture assay, it is disclosed that the enhancer surrounding rs2736099 can interact with TERT promoter. Through chromatin immunoprecipitation, the transcription factor SP1 (Sp1 transcription factor) is recognized for the chromatin segment spanning rs2736099. CONCLUSIONS Our results provide the missing piece between genetic variation at this locus and lung cancer risk, which is also applied to tumorigenesis in other tissues and cell proliferation.
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Affiliation(s)
- Qiang Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
| | - Xin-Xin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
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Bai Y, Zheng J, Cheng L, Liu Q, Zhao G, Li J, Gu Y, Xu W, Wang M, Wei Q, Zhang R. Potentially functional genetic variants of VAV2 and PSMA4 in the immune-activation pathway and non-small cell lung cancer survival. J Gene Med 2022; 24:e3447. [PMID: 36039727 DOI: 10.1002/jgm.3447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/27/2022] [Accepted: 08/12/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Lung cancer ranks the highest mortality among cancers, represented by a low 5-year survival rate. The function of the immune system has a profound influence on the development and progression of lung cancer. Thus genetic variants of the immune-related genes may serve as potential predictors of non-small cell lung cancer (NSCLC) survival. METHODS In the present study, we conducted a two-stage survival analysis in 1,531 NSCLC patients and assessed the associations between genetic variants in the immune-activation gene-set and overall survival (OS) of NSCLC. The validated variants were further subjected to functional annotation and in vitro experiments. RESULTS We identified 25 SNPs spanning 6 loci associated with NSCLC OS after multiple-testing corrections in all datasets, in which two variants, PSMA4 rs12901682 A>C and VAV2 rs12002767 C>T were shown to potentially affect lung cancer OS by cis-regulating the expression of the corresponding genes [(HR (95% CI) = 0.76 (0.65-0.89) and 1.36 (1.12-1.65), P=4.29E-04 and 0.002, respectively)]. CONCLUSION Our findings provide new insights into the role of genetic variants in the immune-activation pathway genes in lung cancer progression.
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Affiliation(s)
- Yushun Bai
- School of Public Health|Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China
| | - Ji Zheng
- School of Public Health|Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
| | - Lei Cheng
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Liu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
| | - Genming Zhao
- School of Public Health|Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
| | - Jingrao Li
- School of Public Health|Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
| | - Yanzi Gu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
| | - Wanghong Xu
- School of Public Health|Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
| | - Mengyun Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Ruoxin Zhang
- School of Public Health|Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
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13
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Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlov I, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, Amos CI. Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. Nat Genet 2022; 54:1167-1177. [PMID: 35915169 PMCID: PMC9373844 DOI: 10.1038/s41588-022-01115-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/27/2022] [Indexed: 02/03/2023]
Abstract
To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.
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Affiliation(s)
- Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 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, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 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
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | - Wen Zhou
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ann Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | - Christine Lusk
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | | | | | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yanhong Liu
- 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
| | - Xihao Li
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 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
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 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
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Susan Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - James C Willey
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Ming You
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX, USA
| | | | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephan Lam
- Department of Integrative Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Stig Bojeson
- Department of Clinical Biochemistry, Herlev Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Thomas Muley
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - David C Christiani
- Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, KY, USA
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sanjay Shete
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Departments of Epidemiology and Community and Family Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - 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, FL, USA
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alpa Patel
- American Cancer Society, Atlanta, GA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Margaret Spitz
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xihong Lin
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 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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14
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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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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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Lin X, Peng M, Chen Q, Yuan M, Chen R, Deng H, Deng J, Liu O, Weng Y, Chen M, Zhou C. Identification of the Unique Clinical and Genetic Features of Chinese Lung Cancer Patients With EGFR Germline Mutations in a Large-Scale Retrospective Study. Front Oncol 2021; 11:774156. [PMID: 34869019 PMCID: PMC8637204 DOI: 10.3389/fonc.2021.774156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/23/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Epidemiological surveys have suggested that lung cancer has inherited susceptibility and shows familial aggregation. However, the distribution and prevalence of epidermal growth factor receptor (EGFR) germline variants and their roles in lung cancer genetic predisposition in Chinese population remain to be elucidated. METHODS In this study, EGFR germline and somatic variants were retrospectively reviewed from the next-generation sequencing results of 31,906 patients with lung cancer. Clinical information was also collected for patients with confirmed EGFR germline mutations. RESULTS A total of 22 germline EGFR variants were identified in 64 patients with lung cancer, accounting for 0.2% of the total cases studied. Five patients were diagnosed as multiple primary carcinomas. Family history was documented in 31.3% (20/64) of patients, 55% of which were diagnosed as lung cancer. G863D was the most frequent EGFR germline mutation, followed by P848L, D1014N, and K757R. Somatic EGFR-sensitive mutations were identified in 51.6% of patients with germline EGFR mutations. The proportion of L858R mutation, exon 19 deletion, and rare sensitive mutation was 50%, 17.6%, and 32.4%, respectively. D1014N and T790M mutations were common in young patients. The family members of patients with P848L, R776H, V769M, and V774M mutations were more commonly diagnosed with cancers. A total of 19 patients were confirmed to have received EGFR tyrosine kinase inhibitors (TKIs), but the response to EGFR-TKIs differed among patients with different EGFR mutations. CONCLUSION Chinese patients with lung cancer harbored unique and dispersive EGFR germline mutations and showed unique clinical and genetic characteristics, with varied response patterns to EGFR-TKI treatment.
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Affiliation(s)
- Xinqing Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Muyun Peng
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Quanfang Chen
- Department of Respiratory Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Mingming Yuan
- Medical Department, Geneplus-Beijing, Beijing, China
| | - Rongrong Chen
- Medical Department, Geneplus-Beijing, Beijing, China
| | - Haiyi Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaxi Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ouqi Liu
- Department of Respiratory and Critical Medicine, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Yuqing Weng
- Department of Respiratory and Critical Medicine, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, China
| | - Mingjiu Chen
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chengzhi Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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17
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Bergen AW, McMahan CS, McGee S, Ervin CM, Tindle HA, Le Marchand L, Murphy SE, Stram DO, Patel YM, Park SL, Baurley JW. Multiethnic Prediction of Nicotine Biomarkers and Association With Nicotine Dependence. Nicotine Tob Res 2021; 23:2162-2169. [PMID: 34313775 PMCID: PMC8757310 DOI: 10.1093/ntr/ntab124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/11/2021] [Indexed: 01/16/2023]
Abstract
INTRODUCTION The nicotine metabolite ratio and nicotine equivalents are measures of metabolism rate and intake. Genome-wide prediction of these nicotine biomarkers in multiethnic samples will enable tobacco-related biomarker, behavioral, and exposure research in studies without measured biomarkers. AIMS AND METHODS We screened genetic variants genome-wide using marginal scans and applied statistical learning algorithms on top-ranked genetic variants, age, ethnicity and sex, and, in additional modeling, cigarettes per day (CPD), (in additional modeling) to build prediction models for the urinary nicotine metabolite ratio (uNMR) and creatinine-standardized total nicotine equivalents (TNE) in 2239 current cigarette smokers in five ethnic groups. We predicted these nicotine biomarkers using model ensembles and evaluated external validity using dependence measures in 1864 treatment-seeking smokers in two ethnic groups. RESULTS The genomic regions with the most selected and included variants for measured biomarkers were chr19q13.2 (uNMR, without and with CPD) and chr15q25.1 and chr10q25.3 (TNE, without and with CPD). We observed ensemble correlations between measured and predicted biomarker values for the uNMR and TNE without (with CPD) of 0.67 (0.68) and 0.65 (0.72) in the training sample. We observed inconsistency in penalized regression models of TNE (with CPD) with fewer variants at chr15q25.1 selected and included. In treatment-seeking smokers, predicted uNMR (without CPD) was significantly associated with CPD and predicted TNE (without CPD) with CPD, time-to-first-cigarette, and Fagerström total score. CONCLUSIONS Nicotine metabolites, genome-wide data, and statistical learning approaches developed novel robust predictive models for urinary nicotine biomarkers in multiple ethnic groups. Predicted biomarker associations helped define genetically influenced components of nicotine dependence. IMPLICATIONS We demonstrate development of robust models and multiethnic prediction of the uNMR and TNE using statistical and machine learning approaches. Variants included in trained models for nicotine biomarkers include top-ranked variants in multiethnic genome-wide studies of smoking behavior, nicotine metabolites, and related disease. Association of the two predicted nicotine biomarkers with Fagerström Test for Nicotine Dependence items supports models of nicotine biomarkers as predictors of physical dependence and nicotine exposure. Predicted nicotine biomarkers may facilitate tobacco-related disease and treatment research in samples with genomic data and limited nicotine metabolite or tobacco exposure data.
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Affiliation(s)
- Andrew W Bergen
- Oregon Research Institute, Eugene, OR, USA
- BioRealm, LLC, Walnut, CA, USA
| | - Christopher S McMahan
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, USA
| | | | | | - Hilary A Tindle
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, USA
| | - Loïc Le Marchand
- Cancer Epidemiology and University of Hawaii Cancer Center, University of Hawai’i, Honolulu, HI, USA
| | - Sharon E Murphy
- Biochemistry, Molecular Biology, and Biophysics and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yesha M Patel
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sungshim L Park
- Cancer Epidemiology and University of Hawaii Cancer Center, University of Hawai’i, Honolulu, HI, USA
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18
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Xiao J, Wang Y, Wang Z, Zhang Y, Li Y, Xu C, Xiao M, Wang H, Guo S, Jin L, Wang J, Bao Y, Shang Y, Wu J. The relevance analysis of GSTP1 rs1695 and lung cancer in the Chinese Han population. Int J Biol Markers 2021; 36:48-54. [PMID: 34596453 DOI: 10.1177/17246008211039236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND This study explored the relevance between rs1695 and susceptibility to the lung cancer in the Chinese Han population. Stratification analysis was conducted on the basis of age, gender, smoking status, tumor-related family history, and pathological type to observe relations between rs1695 and susceptibility to lung cancer in the subgroups. METHODS A case-control study was performed with 974 lung cancer patients who were pathologically diagnosed and 1005 healthy cases based on physical examination to analyze the association between rs1695 and the risk of lung cancer. RESULTS The frequencies of the AA, GA, and GG genotypes of rs1695 were 68.4%, 28.7%, and 2.9% in cases and 64.8%, 30.8%, and 4.2% in controls, respectively. After adjustment for age, gender, smoking status, and family history, it appears that the rs1695 G allele decreases the risk of lung cancer (OR = 0.811, 95% CI 0.684-0.961, P = 0.016). Moreover, compared with the AA genotype, the GA + GG genotype decreased lung cancer susceptibility (OR = 0.808, 95% CI 0.663-0.985, P = 0.035) and the GG genotype (OR = 0.591, 95% CI 0.347-0.988, P = 0.048). In a stratified analysis, the risk of lung cancer in the G allele carriers decreased among the males, patients without a tumor-related family history, and patients with lung adenocarcinoma, especially in smokers. CONCLUSION The polymorphism of locus rs1695 is related to the risk of lung cancer and is expected to be a target for the prediction of lung cancer.
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Affiliation(s)
- Jiang Xiao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yulu Wang
- Department of Emergency, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Zhimin Wang
- Shanghai-MOST key Laboratory of Heath and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Yao Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yutao Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chang Xu
- Clinical College of Xiangnan University, Chenzhou, China
| | - Man Xiao
- Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Haijian Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yang Bao
- Department of Cardiothoracic Surgery, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Yan Shang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, China.,Department of General Practice, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Junjie Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
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19
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McGuire D, Jiang Y, Liu M, Weissenkampen JD, Eckert S, Yang L, Chen F, Berg A, Vrieze S, Jiang B, Li Q, Liu DJ. Model-based assessment of replicability for genome-wide association meta-analysis. Nat Commun 2021; 12:1964. [PMID: 33785739 PMCID: PMC8009871 DOI: 10.1038/s41467-021-21226-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/07/2021] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association meta-analysis (GWAMA) is an effective approach to enlarge sample sizes and empower the discovery of novel associations between genotype and phenotype. Independent replication has been used as a gold-standard for validating genetic associations. However, as current GWAMA often seeks to aggregate all available datasets, it becomes impossible to find a large enough independent dataset to replicate new discoveries. Here we introduce a method, MAMBA (Meta-Analysis Model-based Assessment of replicability), for assessing the "posterior-probability-of-replicability" for identified associations by leveraging the strength and consistency of association signals between contributing studies. We demonstrate using simulations that MAMBA is more powerful and robust than existing methods, and produces more accurate genetic effects estimates. We apply MAMBA to a large-scale meta-analysis of addiction phenotypes with 1.2 million individuals. In addition to accurately identifying replicable common variant associations, MAMBA also pinpoints novel replicable rare variant associations from imputation-based GWAMA and hence greatly expands the set of analyzable variants.
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Affiliation(s)
- Daniel McGuire
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Yu Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - J Dylan Weissenkampen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Scott Eckert
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Lina Yang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | | | - Arthur Berg
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
| | - Qunhua Li
- Department of Statistics, Penn State University, University Park, PA, USA.
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
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20
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Zhang J, Zhang L, Luo J, Ge T, Fan P, Sun L, Hou L, Li J, Yu H, Wu C, Zhu Y, Wu C, Jiang G, Troncone G, Malhotra J, Okuda K, Santarpia M, Zamarchi R, Goto T, Cardona AF, Xu J, Chen Q, Zhang Z, Zhang P. Comprehensive genomic profiling of combined small cell lung cancer. Transl Lung Cancer Res 2021; 10:636-650. [PMID: 33718010 PMCID: PMC7947408 DOI: 10.21037/tlcr-20-1099] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Combined small cell lung cancer (CSCLC) is an uncommon and heterogeneous subtype of small cell lung cancer (SCLC). However, there is limited data concerning the different molecular changes and clinical features in CSCLC compared to pure SCLC. Methods The clinical and pathological characteristics of pure SCLC and CSCLC patients were analyzed. Immunohistochemistry and microdissection were performed to isolate the CSCLC components. Further molecular analysis was carried out by next-generation sequencing (NGS) in 12 CSCLC and 30 pure SCLC. Results There were no significant differences in clinical features between CSCLC and pure SCLC. Overall survival (OS) of CSCLC patients was worse than pure SCLC (P=0.005). NGS results indicated that TP53 and RB1 were the most frequently mutated genes in both CSCLC (83.33% and 66.67%) and pure SCLC (80.00% and 63.33%) groups. However, less than 10% common mutations were found in both CSCLC and pure SCLC. When analyzing the data of SCLC and non-small cell lung cancer (NSCLC) components of CSCLC, more than 50% common mutations, and identical genes with mutations were detected. Moreover, there were also common biological processes and signaling pathways identified in CSCLC and pure SCLC, in addition to SCLC and NSCLC components. Conclusions There were no significant differences in terms of clinical features between CSCLC and pure SCLC. However, the prognosis for CSCLC was worse than pure SCLC. NGS analysis suggested that CSCLC components might derive from the same pluripotent single clone with common initial molecular alterations and subsequent acquisitions of other genetic mutations.
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Affiliation(s)
- Jing Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liping Zhang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Luo
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tao Ge
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Pengyu Fan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liangdong Sun
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junqiang Li
- D1Med, Building 6, No. 28 Xiangle Road, Jiading District, Shanghai, China
| | - Huansha Yu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunxiao Wu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yuming Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Jyoti Malhotra
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Katsuhiro Okuda
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Rita Zamarchi
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Taichiro Goto
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Andrés F Cardona
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia.,Foundation for Clinical and Applied Cancer Research-FICMAC, Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-G), El Bosque University, Bogotá, Colombia
| | - Jianfang Xu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiankun Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhonghong Zhang
- Respiration Department II, the First Affiliated Hospital of Shihezi University Medical College, Xinjiang, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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21
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Morgunova A, Pokhvisneva I, Nolvi S, Entringer S, Wadhwa P, Gilmore J, Styner M, Buss C, Sassi RB, Hall GBC, O'Donnell KJ, Meaney MJ, Silveira PP, Flores CA. DCC gene network in the prefrontal cortex is associated with total brain volume in childhood. J Psychiatry Neurosci 2021; 46:E154-E163. [PMID: 33206040 PMCID: PMC7955849 DOI: 10.1503/jpn.200081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Genetic variation in the guidance cue DCC gene is linked to psychopathologies involving dysfunction in the prefrontal cortex. We created an expression-based polygenic risk score (ePRS) based on the DCC coexpression gene network in the prefrontal cortex, hypothesizing that it would be associated with individual differences in total brain volume. METHODS We filtered single nucleotide polymorphisms (SNPs) from genes coexpressed with DCC in the prefrontal cortex obtained from an adult postmortem donors database (BrainEAC) for genes enriched in children 1.5 to 11 years old (BrainSpan). The SNPs were weighted by their effect size in predicting gene expression in the prefrontal cortex, multiplied by their allele number based on an individual's genotype data, and then summarized into an ePRS. We evaluated associations between the DCC ePRS and total brain volume in children in 2 community-based cohorts: the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) and University of California, Irvine (UCI) projects. For comparison, we calculated a conventional PRS based on a genome-wide association study of total brain volume. RESULTS Higher ePRS was associated with higher total brain volume in children 8 to 10 years old (β = 0.212, p = 0.043; n = 88). The conventional PRS at several different thresholds did not predict total brain volume in this cohort. A replication analysis in an independent cohort of newborns from the UCI study showed an association between the ePRS and newborn total brain volume (β = 0.101, p = 0.048; n = 80). The genes included in the ePRS demonstrated high levels of coexpression throughout the lifespan and are primarily involved in regulating cellular function. LIMITATIONS The relatively small sample size and age differences between the main and replication cohorts were limitations. CONCLUSION Our findings suggest that the DCC coexpression network in the prefrontal cortex is critically involved in whole brain development during the first decade of life. Genes comprising the ePRS are involved in gene translation control and cell adhesion, and their expression in the prefrontal cortex at different stages of life provides a snapshot of their dynamic recruitment.
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Affiliation(s)
- Alice Morgunova
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Irina Pokhvisneva
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Saara Nolvi
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Sonja Entringer
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Pathik Wadhwa
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - John Gilmore
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Martin Styner
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Claudia Buss
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Roberto Britto Sassi
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Geoffrey B C Hall
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Kieran J O'Donnell
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Michael J Meaney
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Patricia P Silveira
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
| | - Cecilia A Flores
- From the Integrated Program in Neuroscience (IPN), McGill University, Montréal, Que., Canada (Morgunova); the Department of Psychiatry, Faculty of Medicine, McGill University, Montréal, Que., Canada (O'Donnell, Meaney, Silveira, Flores); the Department of Neurology and Neurosurgery, McGill University, Montréal, Que., Canada (Flores); the Douglas Research Centre, Montréal, Que., Canada (Morgunova, Flores, Silveira); the Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Centre, McGill University, Montréal, Que., Canada (Pokhvisneva, O'Donnell, Meaney, Silveira); the Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ont., Canada (O'Donnell, Meaney); the Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR; Meaney); the Department of Medical Psychology Charité Universitätsmedizin, Berlin, Germany (Nolvi, Buss); the FinnBrain Birth Cohort Study, Department of Clinical Medicine, University of Turku, Turku, Finland (Nolvi); the Development, Health and Disease Research Program, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, USA (Entringer, Wadhwa); the Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Berlin, Germany (Entringer); the Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Epidemiology, School of Medicine, University of California, Irvine, CA, USA (Wadhwa); the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Gilmore, Styner); the Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA (Styner); the Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ont., Canada (Sassi); and the Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ont., Canada (Hall)
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Küster MM, Schneider MA, Richter AM, Richtmann S, Winter H, Kriegsmann M, Pullamsetti SS, Stiewe T, Savai R, Muley T, Dammann RH. Epigenetic Inactivation of the Tumor Suppressor IRX1 Occurs Frequently in Lung Adenocarcinoma and Its Silencing Is Associated with Impaired Prognosis. Cancers (Basel) 2020; 12:E3528. [PMID: 33256112 PMCID: PMC7760495 DOI: 10.3390/cancers12123528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Iroquois homeobox (IRX) encodes members of homeodomain containing genes which are involved in development and differentiation. Since it has been reported that the IRX1 gene is localized in a lung cancer susceptibility locus, the epigenetic regulation and function of IRX1 was investigated in lung carcinogenesis. We observed frequent hypermethylation of the IRX1 promoter in non-small cell lung cancer (NSCLC) compared to small cell lung cancer (SCLC). Aberrant IRX1 methylation was significantly correlated with reduced IRX1 expression. In normal lung samples, the IRX1 promoter showed lower median DNA methylation levels (<10%) compared to primary adenocarcinoma (ADC, 22%) and squamous cell carcinoma (SQCC, 14%). A significant hypermethylation and downregulation of IRX1 was detected in ADC and SQCC compared to matching normal lung samples (p < 0.0001). Low IRX1 expression was significantly correlated with impaired prognosis of ADC patients (p = 0.001). Reduced survival probability was also associated with higher IRX1 promoter methylation (p = 0.02). Inhibition of DNA methyltransferase (DNMT) activity reactivated IRX1 expression in human lung cancer cell lines. Induced DNMT3A and EZH2 expression was correlated with downregulation of IRX1. On the cellular level, IRX1 exhibits nuclear localization and expression of IRX1 induced fragmented nuclei in cancer cells. Localization of IRX1 and induction of aberrant nuclei were dependent on the presence of the homeobox of IRX1. By data mining, we showed that IRX1 is negatively correlated with oncogenic pathways and IRX1 expression induces the proapoptotic regulator BAX. In conclusion, we report that IRX1 expression is significantly associated with improved survival probability of ADC patients. IRX1 hypermethylation may serve as molecular biomarker for ADC diagnosis and prognosis. Our data suggest that IRX1 acts as an epigenetically regulated tumor suppressor in the pathogenesis of lung cancer.
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Affiliation(s)
- Miriam M. Küster
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Marc A. Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Antje M. Richter
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
| | - Sarah Richtmann
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Hauke Winter
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Surgery, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Mark Kriegsmann
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Pathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Soni S. Pullamsetti
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thorsten Stiewe
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, 35032 Marburg, Germany
| | - Rajkumar Savai
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany; (M.A.S.); (S.R.); (T.M.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
| | - Reinhard H. Dammann
- Faculty of Biology, Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany; (M.M.K.); (A.M.R.)
- Marburg Lung Center (UGMLC) and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Universities of Giessen, 35392 Giessen, Germany; (H.W.); (M.K.); (S.S.P.); (T.S.); (R.S.)
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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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Watza D, Lusk CM, Dyson G, Purrington KS, Wenzlaff AS, Neslund-Dudas C, Soubani AO, Gadgeel SM, Schwartz AG. COPD-dependent effects of genetic variation in key inflammation pathway genes on lung cancer risk. Int J Cancer 2020; 147:747-756. [PMID: 31709530 PMCID: PMC7211135 DOI: 10.1002/ijc.32780] [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: 04/23/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWAS) have identified several loci contributing to lung cancer and COPD risk independently; however, inflammation-related pathways likely harbor additional lung cancer risk-associated variants in biologically relevant immune genes that differ dependent on COPD. We selected single nucleotide polymorphisms (SNPs) proximal to 2,069 genes within 48 immune pathways. We modeled the contribution of these variants to lung cancer risk in a discovery sample of 1,932 lung cancer cases and controls stratified by COPD status and validation sample of 953 cases and controls also stratified by COPD. There were 43 validated SNPs in those with COPD and 60 SNPs in those without COPD associated with lung cancer risk. Furthermore, 29 of 43 and 28 of 60 SNPs demonstrated a statistically significant interaction with COPD in the pooled sample. These variants demonstrated tissue-dependent effects on proximal gene expression, enhanced network connectivity and resided together in specific immune pathways. These results reveal that key inflammatory related genes and pathways, not found in prior GWAS, impact lung cancer risk in a COPD-dependent manner. Genetic variation identified in our study supplements prior lung cancer GWAS and serves as a foundation to further interrogate risk relationships in smoking and COPD populations.
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Affiliation(s)
- Donovan Watza
- Department of Oncology Wayne State University School of Medicine, Detroit, MI 48201, USA
- Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Christine M. Lusk
- Department of Oncology Wayne State University School of Medicine, Detroit, MI 48201, USA
- Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Gregory Dyson
- Department of Oncology Wayne State University School of Medicine, Detroit, MI 48201, USA
- Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Kristen S. Purrington
- Department of Oncology Wayne State University School of Medicine, Detroit, MI 48201, USA
- Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Angela S. Wenzlaff
- Department of Oncology Wayne State University School of Medicine, Detroit, MI 48201, USA
- Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Christine Neslund-Dudas
- Department of Public Health Sciences, Henry Ford Health System and Henry Ford Cancer Institute, Detroit, MI 48202, USA
| | - Ayman O. Soubani
- Karmanos Cancer Institute, Detroit, MI 48201, USA
- Department of Internal Medicine, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Shirish M. Gadgeel
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ann G. Schwartz
- Department of Oncology Wayne State University School of Medicine, Detroit, MI 48201, USA
- Karmanos Cancer Institute, Detroit, MI 48201, USA
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Vosberg DE, Leyton M, Flores C. The Netrin-1/DCC guidance system: dopamine pathway maturation and psychiatric disorders emerging in adolescence. Mol Psychiatry 2020; 25:297-307. [PMID: 31659271 PMCID: PMC6974431 DOI: 10.1038/s41380-019-0561-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 02/02/2023]
Abstract
Axon guidance molecules direct growing axons toward their targets, assembling the intricate wiring of the nervous system. One of these molecules, Netrin-1, and its receptor, DCC (deleted in colorectal cancer), has profound effects, in laboratory animals, on the adolescent expansion of mesocorticolimbic pathways, particularly dopamine. Now, a rapidly growing literature suggests that (1) these same alterations could occur in humans, and (2) genetic variants in Netrin-1 and DCC are associated with depression, schizophrenia, and substance use. Together, these findings provide compelling evidence that Netrin-1 and DCC influence mesocorticolimbic-related psychopathological states that emerge during adolescence.
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Affiliation(s)
- Daniel E Vosberg
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Integrated Program in Neuroscience (IPN), McGill University, Montreal, QC, Canada
- Population Neuroscience and Developmental Neuroimaging, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | - Marco Leyton
- Department of Psychiatry, McGill University, Montreal, QC, Canada.
- Integrated Program in Neuroscience (IPN), McGill University, Montreal, QC, Canada.
- Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
| | - Cecilia Flores
- Department of Psychiatry, McGill University, Montreal, QC, Canada.
- Integrated Program in Neuroscience (IPN), McGill University, Montreal, QC, Canada.
- Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
- Douglas Mental Health University Institute, Montreal, QC, Canada.
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26
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Wei X, Wang C, Feng H, Li B, Jiang P, Yang J, Zhu D, Zhang S, Jin T, Meng Y. Effects of ALOX5, IL6R and SFTPD gene polymorphisms on the risk of lung cancer: A case-control study in China. Int Immunopharmacol 2020; 79:106155. [PMID: 31918059 DOI: 10.1016/j.intimp.2019.106155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 01/26/2023]
Abstract
BACKGROUND ALOX5, IL6R and SFTPD are all immune related genes that may be involved in the development of lung cancer. We sought to explore the effect of polymorphisms of these genes on the risk of lung cancer. METHODS Six single nucleotide polymorphisms (SNPs) were genotyped using a MassARRAY platform in a case-control cohort including 550 patients with lung cancer and 550 healthy controls. RESULTS The rs4845626-T and rs4329505-C alleles were associated with a decreased risk of lung cancer (p < 0.001), while the rs745986-G and rs2245121-A alleles were correlated with an increased risk of lung cancer (p < 0.01). The rs4845626-GT/GG and rs4329505-TC genotypes were protective against lung cancer (p < 0.001). However, the rs745986-AG and rs2245121-AG/AA genotypes were associated with an increased risk of lung cancer (p < 0.01). Stratification analysis showed that the rs4845626 and rs4329505 polymorphisms of IL6R were associated with a reduced risk of lung cancer in both smokers and nonsmokers (p < 0.05). However, rs892690, rs745986 and rs2115819 of ALOX5 were associated with an increased risk of disease in nonsmokers, while rs2245121 of SFTPD was correlated with a higher risk of disease in smokers (p < 0.05). CONCLUSION Our results provide candidate SNPs for early screening for lung cancer and new clues for further study of the pathogenesis of the disease.
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Affiliation(s)
- Xiaoping Wei
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China.
| | - Chen Wang
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Haiming Feng
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Bing Li
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Peng Jiang
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Jianbao Yang
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Duojie Zhu
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Shaobo Zhang
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Tao Jin
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
| | - Yuqi Meng
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
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Aldrich MC, Mercaldo SF, Sandler KL, Blot WJ, Grogan EL, Blume JD. Evaluation of USPSTF Lung Cancer Screening Guidelines Among African American Adult Smokers. JAMA Oncol 2019; 5:1318-1324. [PMID: 31246249 DOI: 10.1001/jamaoncol.2019.1402] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance The United States Preventive Services Task Force (USPSTF) recommends low-dose computed tomography screening for lung cancer. However, USPSTF screening guidelines were derived from a study population including only 4% African American smokers, and racial differences in smoking patterns were not considered. Objective To evaluate the diagnostic accuracy of USPSTF lung cancer screening eligibility criteria in a predominantly African American and low-income cohort. Design, Setting, and Participants The Southern Community Cohort Study prospectively enrolled adults visiting community health centers across 12 southern US states from March 25, 2002, through September 24, 2009, and followed up for cancer incidence through December 31, 2014. Participants included African American and white current and former smokers aged 40 through 79 years. Statistical analysis was performed from May 11, 2016, to December 6, 2018. Exposures Self-reported race, age, and smoking history. Cumulative exposure smoking histories encompassed most recent follow-up questionnaires. Main Outcomes and Measures Incident lung cancer cases assessed for eligibility for lung cancer screening using USPSTF criteria. Results Among 48 364 ever smokers, 32 463 (67%) were African American and 15 901 (33%) were white, with 1269 incident lung cancers identified. Among all 48 364 Southern Community Cohort Study participants, 5654 of 32 463 African American smokers (17%) were eligible for USPSTF screening compared with 4992 of 15 901 white smokers (31%) (P < .001). Among persons diagnosed with lung cancer, a significantly lower percentage of African American smokers (255 of 791; 32%) was eligible for screening compared with white smokers (270 of 478; 56%) (P < .001). The lower percentage of eligible lung cancer cases in African American smokers was primarily associated with fewer smoking pack-years among African American vs white smokers (median pack-years: 25.8 [interquartile range, 16.9-42.0] vs 48.0 [interquartile range, 30.2-70.5]; P < .001). Racial disparity was observed in the sensitivity and specificity of USPSTF guidelines between African American and white smokers for all ages. Lowering the smoking pack-year eligibility criteria to a minimum 20-pack-year history was associated with an increased percentage of screening eligibility of African American smokers and with equitable performance of sensitivity and specificity compared with white smokers across all ages (for a 55-year-old current African American smoker, sensitivity increased from 32.2% to 49.0% vs 56.5% for a 55-year-old white current smoker; specificity decreased from 83.0% to 71.6% vs 69.4%; P < .001). Conclusions and Relevance Current USPSTF lung cancer screening guidelines may be too conservative for African American smokers. The findings suggest that race-specific adjustment of pack-year criteria in lung cancer screening guidelines would result in more equitable screening for African American smokers at high risk for lung cancer.
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Affiliation(s)
- Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sarah F Mercaldo
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Radiology, Massachusetts General Hospital, Boston
| | - Kim L Sandler
- Department of Radiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eric L Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeffrey D Blume
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
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Mitchell KA, Shah E, Bowman ED, Zingone A, Nichols N, Pine SR, Kittles RA, Ryan BM. Relationship between West African ancestry with lung cancer risk and survival in African Americans. Cancer Causes Control 2019; 30:1259-1268. [PMID: 31468279 DOI: 10.1007/s10552-019-01212-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 07/30/2019] [Indexed: 01/12/2023]
Abstract
PURPOSE African Americans, especially men, have a higher incidence of lung cancer compared with all other racial and ethnic groups in the US. Self-reported race is frequently used in genomic research studies to capture an individual's race or ethnicity. However, it is clear from studies of genetic admixture that human genetic variation does not segregate into the same biologically discrete categories as socially defined categories of race. Previous studies have suggested that the degree of West African ancestry among African Americans can contribute to cancer risk in this population, though few studies have addressed this question in lung cancer. METHODS Using a genetic ancestry panel of 100 SNPs, we estimated West African, European, and Native American ancestry in 1,407 self-described African Americans and 2,413 European Americans. RESULTS We found that increasing West African ancestry was associated with increased risk of lung cancer among African American men (ORQ5 vs Q1 = 2.55 (1.45-4.48), p = 0.001), while no association was observed in African American women (ORQ5 vs Q1 = 0.90 (0.51-1.59), p = 0.56). This relationship diminished following adjustment for income and education. CONCLUSIONS Genetic ancestry is not a major contributor to lung cancer risk or survival disparities.
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Affiliation(s)
- Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ebony Shah
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Noah Nichols
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Sharon R Pine
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
| | - Rick A Kittles
- Division of Health Equities, Department of Populations Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA. .,Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, Building 37, Room 3060C, Bethesda, MD, 20892, USA.
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29
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Zeybek A, Öz N, Kalemci S, Edgünlü T, Kızıltuğ MT, Tosun K, Tunç M, Tekin L, Erdal ME. Diagnostic Value of MiR-125b as a Potential Biomarker for Stage I Lung Adenocarcinoma. Curr Mol Med 2019; 19:216-227. [DOI: 10.2174/1566524019666190314113800] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/31/2022]
Abstract
Background:We aimed at exploring biological functions of differentially expressed miRNAs during carcinogenesis, to identify miRNAs dysegulations involved in DNA repair mechanisms, and to evaluate potential of miRNAs as prognostic and diagnostic biomarkers for early lung adenocarcinomas (LAC).Methods:We obtained 21 LAC and paired adjacent normal formalin-fixed, paraffinembedded lung tissues from patients who underwent curative resection for stage I LAC. We compared expression levels of eight miRNAs involved in the DNA repair mechanism between LAC and adjacent tissues.Results:Expressions of Hsa-miR-9-5p, hsa-miR-24-3p, hsa-miR-125a-3p, hsa-miR- 125b-5p, hsa-miR-155-5p, and hsa-let-7a-5p were significantly up-regulated in stage I LAC tissues compared with those in the adjacent tissues. In addition, expressions of hsa-mir-9-5p, hsa-mir-24-3p, hsa-mir-125a-3p, hsa-mir-125b-5p, and hsa-mir-155-5p were significantly up-regulated in stage Ia LAC tissues, whereas expressions of hsa-mir- 125a-3p and hsa-mir-125b-5p were significantly up-regulated in stage Ib LAC tissues. Receiver operating characteristic (ROC) analysis revealed that AUROC of hsa-mir-125b- 5p was 0.875 (P < 0.001).Conclusion:Expression of hsa-mir-125b-5p could be used to distinguish LAC from adjacent tissues. Our result suggests that hsa-mir125b-5p can be a prognostic and diagnostic biomarker for LAC.
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Affiliation(s)
- Arife Zeybek
- Department of Thoracic Surgery, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey
| | - Necdet Öz
- Department of Thoracic Surgery, Private Medstar Antalya Hospital, Antalya, Turkey
| | | | - Tuba Edgünlü
- Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey
| | | | - Kürşad Tosun
- Science School, Siena College, Newyork, NY, United States
| | - Mustafa Tunç
- Department of Medical Pathology, Private Antalya Pathology Center, Antalya, Turkey
| | - Leyla Tekin
- Department of Medical Pathology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey
| | - Mehmet Emin Erdal
- Department of Medical Biology, School of Medicine, Mersin University, Mersin, Turkey
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Estrogen receptor 1 gene variants and estradiol activities in alcohol dependence. Prog Neuropsychopharmacol Biol Psychiatry 2019; 92:301-307. [PMID: 30677468 DOI: 10.1016/j.pnpbp.2019.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/29/2018] [Accepted: 01/20/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Alcohol use disorders inflict a great individual and societal burden. Although sex hormone effects have been implicated in alcohol dependence, research has mostly neglected estrogen activities and female alcohol-dependent patients. Here, we investigated associations of estrogen receptor 1 (ESR1) genetics and serum estradiol activities with aspects of alcohol dependence. METHOD Serum estradiol activities of early-abstinent alcohol-dependent in-patients (n[♂] = 113, n[♀] = 87) were followed for at median 5 days and compared with healthy controls (n[♂] = 133, n[♀] = 107). All participants were genotyped for five ESR1 single nucleotide polymorphisms (rs6902771, rs11155819, rs6557171, rs2982683, rs2982712). RESULTS Bioavailable estradiol levels decreased during withdrawal treatment (P[♂] < .001, P[♀] = .011). Male patients with an increase of bioavailable estradiol during withdrawal showed fewer days to (P = .033) and more alcohol-related readmissions (P < .05) during the 12-month follow-up. Higher estradiol and estradiol-to-testosterone activities were significantly related to liver, muscle, and cell count damage in male patients. Estradiol-to-testosterone activities in female patients were lower compared to female controls (total P = .013, bioavailable P = .009). Moreover, the ESR1 genotypes jointly separated alcohol-dependent patients from controls (P = .037). CONCLUSION Our findings support the role of ESR1 genetics in alcohol dependence and show for the first time that estradiol activities may sex-specifically predict alcohol-related sequelae and outcome following in-patient withdrawal treatment.
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Bhat GR, Bhat A, Verma S, Sethi I, Shah R, Sharma V, Dar KA, Abrol D, Kaneez S, Kaul S, Ganju R, Kumar R. Association of newly identified genetic variant rs2853677 of TERT with non-small cell lung cancer and leukemia in population of Jammu and Kashmir, India. BMC Cancer 2019; 19:493. [PMID: 31126249 PMCID: PMC6533689 DOI: 10.1186/s12885-019-5685-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 05/08/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Telomere genetics has recently been emerged as an important field in molecular oncology. Various genome-wide association studies in different population groups have revealed that polymorphisms in Telomere maintenance gene (TERT) gene located on 5p15.33 is associated with susceptibility to leukemia and lung cancer risk. However, association of TERT with leukemia and lung cancer risk in north Indian population groups is still unknown. This study observed the association between genetic variant rs2853677 of TERT and leukemia and lung cancer in the state of Jammu and Kashmir, India. METHODS A total of 781 subjects, out of which 381 cases (203 leukemic patients and 178 non-small cell lung cancer patients NSCLC) and 400 healthy controls were recruited for the study. Genetic variant rs2853677of TERT was detected using the real-time and Taqman Chemistry. Hardy-Weinberg Equilibrium was assessed using the chi square test. The allele and genotype- specific risks were estimated as odds ratio with 95% confidence interval. RESULTS We observed that variant rs2853677 was strongly associated with lung cancer and leukemia risk with an odds ratio (OR) =1.8 (1.03-3.2 at 95% CI); p value (adjusted) = 0.03; odds ratio (OR) =2.9 (1.4-5.5.at 95% CI); p value (adjusted) = 0.002, respectively. CONCLUSION The results of this study suggested that rs2853677 of TERT signifies association in multiple cancers and suggests that it can become potential marker for diagnosis of non-small cell lung cancer and leukemia. The study will provide an insight in understanding the genetic etiology and highlights the role of telomere-associated pathways in non-small cell lung cancer and leukemia. However, it would be quite interesting to explore the contribution of this variant in other cancers as well.
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Affiliation(s)
- Gh Rasool Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Amrita Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Sonali Verma
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Itty Sethi
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ruchi Shah
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Khursheed A Dar
- Chest Disease Hospital, Government Medical College, Srinagar, India
| | - Deepak Abrol
- Department of Radiotherapy, Government Medical College, Jammu, India
| | - Subiya Kaneez
- Department of Radiotherapy, Government Medical College, Srinagar, India
| | - Sandeep Kaul
- Department of surgical Oncology, Shri Mata Vaishno Devi Narayana Super speciality hospital, kata, India
| | - Ramesh Ganju
- Department of Pathology, College of Medicine, The OHIO State University, Columbus, USA
| | - Rakesh Kumar
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
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Jones CC, Bradford Y, Amos CI, Blot WJ, Chanock SJ, Harris CC, Schwartz AG, Spitz MR, Wiencke JK, Wrensch MR, Wu X, Aldrich MC. Cross-Cancer Pleiotropic Associations with Lung Cancer Risk in African Americans. Cancer Epidemiol Biomarkers Prev 2019; 28:715-723. [PMID: 30894353 PMCID: PMC6449205 DOI: 10.1158/1055-9965.epi-18-0935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/02/2018] [Accepted: 12/31/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Identifying genetic variants with pleiotropic associations across multiple cancers can reveal shared biologic pathways. Prior pleiotropic studies have primarily focused on European-descent individuals. Yet population-specific genetic variation can occur, and potential pleiotropic associations among diverse racial/ethnic populations could be missed. We examined cross-cancer pleiotropic associations with lung cancer risk in African Americans. METHODS We conducted a pleiotropic analysis among 1,410 African American lung cancer cases and 2,843 controls. We examined 36,958 variants previously associated (or in linkage disequilibrium) with cancer in prior genome-wide association studies. Logistic regression analyses were conducted, adjusting for age, sex, global ancestry, study site, and smoking status. RESULTS We identified three novel genomic regions significantly associated (FDR-corrected P <0.10) with lung cancer risk (rs336958 on 5q14.3, rs7186207 on 16q22.2, and rs11658063 on 17q12). On chromosome16q22.2, rs7186207 was significantly associated with reduced risk [OR = 0.43; 95% confidence interval (CI), 0.73-0.89], and functional annotation using GTEx showed rs7186207 modifies DHODH gene expression. The minor allele at rs336958 on 5q14.3 was associated with increased lung cancer risk (OR = 1.47; 95% CI, 1.22-1.78), whereas the minor allele at rs11658063 on 17q12 was associated with reduced risk (OR = 0.80; 95% CI, 0.72-0.90). CONCLUSIONS We identified novel associations on chromosomes 5q14.3, 16q22.2, and 17q12, which contain HNF1B, DHODH, and HAPLN1 genes, respectively. SNPs within these regions have been previously associated with multiple cancers. This is the first study to examine cross-cancer pleiotropic associations for lung cancer in African Americans. IMPACT Our findings demonstrate novel cross-cancer pleiotropic associations with lung cancer risk in African Americans.
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Affiliation(s)
- Carissa C Jones
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuki Bradford
- School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | | | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Margaret R Spitz
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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Ryan BM. Lung cancer health disparities. Carcinogenesis 2019; 39:741-751. [PMID: 29547922 DOI: 10.1093/carcin/bgy047] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/13/2018] [Indexed: 12/16/2022] Open
Abstract
Compared with all other racial and ethnic groups in the United States, African Americans are disproportionally affected by lung cancer, both in terms of incidence and survival. It is likely that smoking, as the main etiological factor associated with lung cancer, contributes to these disparities, but the precise mechanism is still unclear. This paper seeks to explore the history of lung cancer disparities and review to the literature regarding the various factors that contribute to them.
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Affiliation(s)
- Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Mitchell KA, Zingone A, Toulabi L, Boeckelman J, Ryan BM. Comparative Transcriptome Profiling Reveals Coding and Noncoding RNA Differences in NSCLC from African Americans and European Americans. Clin Cancer Res 2018; 23:7412-7425. [PMID: 29196495 DOI: 10.1158/1078-0432.ccr-17-0527] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/26/2017] [Accepted: 09/08/2017] [Indexed: 12/19/2022]
Abstract
Purpose: To determine whether racial differences in gene and miRNA expression translates to differences in lung tumor biology with clinical relevance in African Americans (AAs) and European Americans (EAs).Experimental Design: The NCI-Maryland Case Control Study includes seven Baltimore City hospitals and is overrepresented with AA patients (∼40%). Patients that underwent curative NSCLC surgery between 1998 and 2014 were enrolled. Comparative molecular profiling used mRNA (n = 22 AAs and 19 EAs) and miRNA (n = 42 AAs and 55 EAs) expression arrays to track differences in paired fresh frozen normal tissues and lung tumor specimens from AAs and EAs. Pathway enrichment, predicted drug response, tumor microenvironment infiltration, cancer immunotherapy antigen profiling, and miRNA target enrichment were assessed.Results: AA-enriched differential gene expression was characterized by stem cell and invasion pathways. Differential gene expression in lung tumors from EAs was primarily characterized by cell proliferation pathways. Population-specific gene expression was partly driven by population-specific miRNA expression profiles. Drug susceptibility predictions revealed a strong inverse correlation between AA resistance and EA sensitivity to the same panel of drugs. Statistically significant differences in M1 and M2 macrophage infiltration were observed in AAs (P < 0.05); however, PD-L1, PD-L2 expression was similar between both.Conclusions: Comparative transcriptomic profiling revealed clear differences in lung tumor biology between AAs and EAs. Increased participation by AAs in lung cancer clinical trials are needed to integrate, and leverage, transcriptomic differences with other clinical information to maximize therapeutic benefit in both AAs and EAs. Clin Cancer Res; 23(23); 7412-25. ©2017 AACR.
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Affiliation(s)
- Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Leila Toulabi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jacob Boeckelman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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Li C, Wang X, Li Y, Zhang X, Sun M, Liu S, Sun L, Shi L, Yao Y. Genetic polymorphisms in the TERT gene and susceptibility to non-small cell lung cancer in a Chinese Han population. Cancer Manag Res 2018; 10:1487-1495. [PMID: 29928145 PMCID: PMC6001840 DOI: 10.2147/cmar.s166235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background Recent studies have revealed that the TERT gene plays crucial roles in cancer initiation and development. Genome-wide analysis studies and case-control studies have demonstrated that polymorphisms in the TERT gene are associated with various cancers. Materials and methods In the current study, we analyzed the associations of eight single nucleotide polymorphisms (SNPs) in the TERT gene with non-small cell lung cancer (NSCLC) in a Chinese Han population. A total of 467 NSCLC patients and 526 healthy individuals were recruited for SNP genotyping using a TaqMan assay. Results Our results revealed that the allelic frequencies of rs2853677 and rs2853691 were significantly different between the NSCLC and control groups (P=0.004 and 0.001, respectively). Moreover, the T allele of rs2853677 and the A allele of rs2853691 might be the protective factors against NSCLC (OR=0.766; 95%CI: 0.639–0.918 and OR=0.714; 95%CI: 0.584–0.875, respectively). Additionally, stratified association analysis of the eight SNPs with the different pathological NSCLC stages (I+II and III+IV) and different pathological types (adenocarcinoma and squamous cell carcinoma) revealed that none of the SNPs were significantly different between patients with different pathological stages and pathological types. Conclusion Our results indicated that rs2853677 and rs2853691 in the TERT gene might be associated with NSCLC in this Chinese Han population.
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Affiliation(s)
- Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Xiaona Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Yingfu Li
- Department of Geriatrics, The No.1 Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Xinwen Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Mingbo Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Le Sun
- Kunming Medical University, Kunming 650032, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
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O’Brien TD, Jia P, Aldrich MC, Zhao Z. Lung Cancer: One Disease or Many. Hum Hered 2018; 83:65-70. [PMID: 29864749 PMCID: PMC6261707 DOI: 10.1159/000488942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/03/2018] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE Lung cancer is classified as a single entity comprised of multiple histological subtypes. But how similar are these subtypes on a genetic level? This paper aims to address this question through a concise overview of germline and somatic differences between small cell lung cancer, lung adenocarcinoma, and lung squamous cell carcinoma. METHODS We reveal the weak overlap found between these 3 lung cancer subtypes using published data from one of the largest germline genetic studies on lung cancer to date and somatic mutation data from Catalogue of Somatic Mutations in Cancer (COSMIC). RESULTS These data indicate that these 3 subtypes share very little with each other at the genetic level. At the germline SNP level, only 24 independent SNPs from 2 chromosomes were shared across all 3 subtypes. We also demonstrate that only 30 unique cancer-specific mutations overlap the 3 subtypes from COSMIC, and that this is fewer than overlapping mutations chosen at random. Finally, we show that only 3 somatic mutational signatures are shared between these 3 subtypes. CONCLUSION This paper highlights that these 3 lung cancer subtypes may be distinct diseases at the genetic level. In the era of precision medicine, we feel that these genomic differences will be of utmost importance in the choice of lung cancer therapy in the future.
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Affiliation(s)
- Timothy D. O’Brien
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Li Z, Pu Z, Fan J, Li N, Zhu M, Zhang J, Wang Y, Geng L, Cheng Y, Ma H, Jin G, Dai J, Hu Z, Shen H. Fine mapping in TERT-CLPTM1L region identified three independent lung cancer susceptibility signals: A large-scale multi-ethnic population study. Mol Carcinog 2018; 57:1289-1299. [PMID: 29809284 DOI: 10.1002/mc.22843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022]
Abstract
Genome-wide association studies (GWAS) and fine mapping studies have identified multiple lung cancer susceptibility variants in TERT-CLPTM1L region. However, it is still unclear about the relationship between these risk variants and the independent lung cancer risk signals in this region. Therefore, we evaluated the independent susceptibility signals for lung cancer and explored the potential functional variants in this region. Sequential conditional analysis was used to detect the independent susceptibility loci based on four lung cancer GWAS datasets with 12 843 lung cases and 12 639 controls. Comprehensively functional annotations were performed for each independent signal. Three independent susceptibility signals were identified in multi-ethnic population. For the first signal, rs2736100 showed the most significant association with lung cancer risk (C > A, OR = 0.82, 95%CI: 0.79-0.85, P = 1.98 × 10-25 ). Rs36019446 was the top-ranked site (A > G, OR = 0.88, 95%CI: 0.84-0.92, P = 1.74 × 10-9 ) in the second signal. For the third signal, rs326048 was the leading SNP (A > G, OR = 0.91, 95%CI: 0.87-0.95, P = 1.38 × 10-5 ). The following subgroup analysis found the same three loci among Asian population. Further, we compared the difference between various subgroup populations. Functional annotations revealed that rs2736100, rs27996 (r2 = 0.85 with rs36019446) and rs326049 (r2 = 0.73 with rs326048) could be potential functional variants in these three risk signals, respectively. In conclusion, although multiple variants have been found associated with lung cancer risk in TERT-CLPTM1L region, our findings indicated that there are three independent lung cancer susceptibility signals in this region.
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Affiliation(s)
- Zhihua Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhening Pu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingyi Fan
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ni Li
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiahui Zhang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuzhuo Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Liguo Geng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yang Cheng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
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O'Brien TD, Jia P, Caporaso NE, Landi MT, Zhao Z. Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels. Genome Med 2018; 10:16. [PMID: 29486777 PMCID: PMC5828003 DOI: 10.1186/s13073-018-0522-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/13/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). These subtypes are mainly classified by physiological and pathological characteristics, although there is increasing evidence of genetic and molecular differences as well. Although some work has been done at the somatic level to explore the genetic and biological differences among subtypes, little work has been done that interrogates these differences at the germline level to characterize the unique and shared susceptibility genes for each subtype. METHODS We used single-nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) of European samples to interrogate the similarity of the subtypes at the SNP, gene, pathway, and regulatory levels. We expanded these genotyped SNPs to include all SNPs in linkage disequilibrium (LD) using data from the 1000 Genomes Project. We mapped these SNPs to several lung tissue expression quantitative trait loci (eQTL) and enhancer datasets to identify regulatory SNPs and their target genes. We used these genes to perform a biological pathway analysis for each subtype. RESULTS We identified 8295, 8734, and 8361 SNPs with moderate association signals for LUAD, LUSC, and SCLC, respectively. Those SNPs had p < 1 × 10- 3 in the original GWAS or were within LD (r2 > 0.8, Europeans) to the genotyped SNPs. We identified 215, 320, and 172 disease-associated genes for LUAD, LUSC, and SCLC, respectively. Only five genes (CHRNA5, IDH3A, PSMA4, RP11-650 L12.2, and TBC1D2B) overlapped all subtypes. Furthermore, we observed only two pathways from the Kyoto Encyclopedia of Genes and Genomes shared by all subtypes. At the regulatory level, only three eQTL target genes and two enhancer target genes overlapped between all subtypes. CONCLUSIONS Our results suggest that the three lung cancer subtypes do not share much genetic signal at the SNP, gene, pathway, or regulatory level, which differs from the common subtype classification based upon histology. However, three (CHRNA5, IDH3A, and PSMA4) of the five genes shared between the subtypes are well-known lung cancer genes that may act as general lung cancer genes regardless of subtype.
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Affiliation(s)
- Timothy D O'Brien
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Zhongming Zhao
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA. .,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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Ye G, Tan N, Meng C, Li J, Jing L, Yan M, Jin T, Chen F. Genetic variations in TERC and TERT genes are associated with lung cancer risk in a Chinese Han population. Oncotarget 2017; 8:110145-110152. [PMID: 29299136 PMCID: PMC5746371 DOI: 10.18632/oncotarget.22329] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/05/2017] [Indexed: 11/29/2022] Open
Abstract
The study was aimed to explore whether the TERT and TERC polymorphisms are associated with the lung cancer risk. Five TERC and TERT polymorphisms were genotyped from 554 lung cancer patients and 603 healthy controls. We used χ2 test, genetic model, linkage disequilibrium (LD) and haplotype analyses to evaluate the association between the polymorphisms and lung cancer risk. We found that the allele “C” of rs10936599 (TERC) and the allele “T” of rs10069690 (TERT) were associated with increased risk of lung cancer (OR = 1.32, 95% CI: 1.12-1.55, P = 0.001; OR = 1.41, 95% CI: 1.14-1.76, P = 0.002, respectively). The genotype of “CC” of rs10936599, genotype “CT” of rs10069690 and genotype “GG and “AG” of rs2853677 were also associated with increased the risk of lung cancer. In addition, rs10936599 under the dominant, recessive and log-additive models; rs10069690 under the dominant, overdominant and log-additive models; rs2853677 under the dominant and log-additive models were found to be associated with increased lung cancer risk. The SNP rs2242652 was found to be associated with an increased lung cancer risk under the dominant and overdominant models without adjustment. The haplotype “TA” of TERT was also associated with an increased risk of lung cancer. Our study indicated that rs10936599 (TERC) and rs10069690, rs2242652 and rs2853677 in TERT and haplotype “TA” of TERT were revealed as risk factors of lung cancer in a Chinese Han population. However, it required to verify our result and investigate the function genetic variants and mechanism of lung cancer.
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Affiliation(s)
- Gang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P. R. China
| | - Nan Tan
- Department of Cadre's Ward, Xi'an No.1 Hospital, Xi'an, Shaanxi 710002, China
| | - Chenyang Meng
- Graduate School of Inner Mongolia Medical University, Hohhot, Inner Mongolia 010050, China
| | - Jingjie Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Li Jing
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Mengdan Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.,Xi'an Tianqin Precision Medical Institute, Xi'an, Shaanxi 710075, China
| | - Fulin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
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Pinto R, Assis J, Nogueira A, Pereira C, Pereira D, Medeiros R. Rethinking ovarian cancer genomics: where genome-wide association studies stand? Pharmacogenomics 2017; 18:1611-1625. [DOI: 10.2217/pgs-2017-0108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) allow the finding of genetic variants associated with several traits. Regarding ovarian cancer (OC), 15 GWAS have been conducted since 2009, with the discovery of 49 SNPs associated with disease susceptibility and 46 with impact in the clinical outcome of patients (p < 5.00 × 10-2). Among them, 14 variants reached the genome-wide significance (p < 5.00 × 10−8). Despite the results obtained, they should be validated in independent sets. So far, five validation studies have been conducted which could confirm the association of 12 OC susceptibility SNPs. Consequently, post-GWAS studies are crucial unravel the biological plausibility of GWAS’ findings and the allelic spectrum of OC.
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Affiliation(s)
- Ricardo Pinto
- Molecular Oncology & Viral Pathology Group-Research Center, Portuguese Institute of Oncology, Edifício Laboratórios. 4° piso, Rua Dr. António Bernardino de Almeida, 4200–4072, Porto, Portugal
- ICBAS, Abel Salazar Institute for the Biomedical Sciences, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Joana Assis
- Molecular Oncology & Viral Pathology Group-Research Center, Portuguese Institute of Oncology, Edifício Laboratórios. 4° piso, Rua Dr. António Bernardino de Almeida, 4200–4072, Porto, Portugal
- FMUP, Faculty of Medicine, Porto University, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Augusto Nogueira
- Molecular Oncology & Viral Pathology Group-Research Center, Portuguese Institute of Oncology, Edifício Laboratórios. 4° piso, Rua Dr. António Bernardino de Almeida, 4200–4072, Porto, Portugal
- FMUP, Faculty of Medicine, Porto University, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Carina Pereira
- Molecular Oncology & Viral Pathology Group-Research Center, Portuguese Institute of Oncology, Edifício Laboratórios. 4° piso, Rua Dr. António Bernardino de Almeida, 4200–4072, Porto, Portugal
- CINTESIS, Center for Health technology and Services Research, Faculty of Medicine, Porto University, Rua Dr. Plácido da Costa, 4200-450, Porto, Portugal
| | - Deolinda Pereira
- Oncology Department, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology & Viral Pathology Group-Research Center, Portuguese Institute of Oncology, Edifício Laboratórios. 4° piso, Rua Dr. António Bernardino de Almeida, 4200–4072, Porto, Portugal
- Research Department, Portuguese League AgainstCancer (NRNorte), Estrada Interior da Circunvalação, 6657, 4200-172, Porto, Portugal
- CEBIMED, Faculty of Health Sciences, FernandoPessoa University, Praça 9 de Abril, 349, 4249-004, Porto, Portugal
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Schuit E, Panagiotou OA, Munafò MR, Bennett DA, Bergen AW, David SP. Pharmacotherapy for smoking cessation: effects by subgroup defined by genetically informed biomarkers. Cochrane Database Syst Rev 2017; 9:CD011823. [PMID: 28884473 PMCID: PMC6483659 DOI: 10.1002/14651858.cd011823.pub2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Smoking cessation therapies are not effective for all smokers, and researchers are interested in identifying those subgroups of individuals (e.g. based on genotype) who respond best to specific treatments. OBJECTIVES To assess whether quit rates vary by genetically informed biomarkers within pharmacotherapy treatment arms and as compared with placebo. To assess the effects of pharmacotherapies for smoking cessation in subgroups of smokers defined by genotype for identified genome-wide significant polymorphisms. SEARCH METHODS We searched the Cochrane Tobacco Addiction Group specialised register, clinical trial registries, and genetics databases for trials of pharmacotherapies for smoking cessation from inception until 16 August 2016. SELECTION CRITERIA We included randomised controlled trials (RCTs) that recruited adult smokers and reported pharmacogenomic analyses from trials of smoking cessation pharmacotherapies versus controls. Eligible trials included those with data on a priori genome-wide significant (P < 5 × 10-8) single-nucleotide polymorphisms (SNPs), replicated non-SNPs, and/or the nicotine metabolite ratio (NMR), hereafter collectively described as biomarkers. DATA COLLECTION AND ANALYSIS We used standard methodological procedures expected by Cochrane. The primary outcome was smoking abstinence at six months after treatment. The secondary outcome was abstinence at end of treatment (EOT). We conducted two types of meta-analyses- one in which we assessed smoking cessation of active treatment versus placebo within genotype groups, and another in which we compared smoking cessation across genotype groups within treatment arms. We carried out analyses separately in non-Hispanic whites (NHWs) and non-Hispanic blacks (NHBs). We assessed heterogeneity between genotype groups using T², I², and Cochrane Q statistics. MAIN RESULTS Analyses included 18 trials including 9017 participants, of whom 6924 were NHW and 2093 NHB participants. Data were available for the following biomarkers: nine SNPs (rs1051730 (CHRNA3); rs16969968, rs588765, and rs2036527 (CHRNA5); rs3733829 and rs7937 (in EGLN2, near CYP2A6); rs1329650 and rs1028936 (LOC100188947); and rs215605 (PDE1C)), two variable number tandem repeats (VNTRs; DRD4 and SLC6A4), and the NMR. Included data produced a total of 40 active versus placebo comparisons, 16 active versus active comparisons, and 64 between-genotype comparisons within treatment arms.For those meta-analyses showing statistically significant heterogeneity between genotype groups, we found the quality of evidence (GRADE) to be generally moderate. We downgraded quality most often because of imprecision or risk of bias due to potential selection bias in genotyping trial participants. Comparisons of relative treatment effects by genotypeFor six-month abstinence, we found statistically significant heterogeneity between genotypes (rs16969968) for nicotine replacement therapy (NRT) versus placebo at six months for NHB participants (P = 0.03; n = 2 trials), but not for other biomarkers or treatment comparisons. Six-month abstinence was increased in the active NRT group as compared to placebo among participants with a GG genotype (risk ratio (RR) 1.47, 95% confidence interval (CI) 1.07 to 2.03), but not in the combined group of participants with a GA or AA genotype (RR 0.43, 95% CI 0.15 to 1.26; ratio of risk ratios (RRR) GG vs GA or AA of 3.51, 95% CI 1.19 to 10.3). Comparisons of treatment effects between genotype groups within pharmacotherapy randomisation armsFor those receiving active NRT, treatment was more effective in achieving six-month abstinence among individuals with a slow NMR than among those with a normal NMR among NHW and NHB combined participants (normal NMR vs slow NMR: RR 0.54, 95% CI 0.37 to 0.78; n = 2 trials). We found no such differences in treatment effects between genotypes at six months for any of the other biomarkers among individuals who received pharmacotherapy or placebo. AUTHORS' CONCLUSIONS We did not identify widespread differential treatment effects of pharmacotherapy based on genotype. Some genotype groups within certain ethnic groups may benefit more from NRT or may benefit less from the combination of bupropion with NRT. The reader should interpret these results with caution because none of the statistically significant meta-analyses included more than two trials per genotype comparison, many confidence intervals were wide, and the quality of this evidence (GRADE) was generally moderate. Although we found evidence of superior NRT efficacy for NMR slow versus normal metabolisers, because of the lack of heterogeneity between NMR groups, we cannot conclude that NRT is more effective for slow metabolisers. Access to additional data from multiple trials is needed, particularly for comparisons of different pharmacotherapies.
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Affiliation(s)
- Ewoud Schuit
- Stanford UniversityMeta‐Research Innovation Center at Stanford (METRICS)StanfordCAUSA
- University Medical Center UtrechtCochrane NetherlandsUtrechtNetherlands
- University Medical Center UtrechtJulius Center for Health Sciences and Primary CareUtrechtNetherlands
| | - Orestis A. Panagiotou
- School of Public Health, Brown UniversityDepartment of Health Services, Policy & Practice121 S. Main StreetProvidenceRIUSA02903
| | - Marcus R Munafò
- University of BristolSchool of Experimental Psychology and MRC Integrative Epidemiology Unit8 Woodland RoadBristolUKBS8 1TN
| | - Derrick A Bennett
- University of OxfordClinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population HealthRichard Doll BuildingOld Road CampusOxfordUKOX3 7LF
| | | | - Sean P David
- Stanford UniversityDivision of Primary Care and Population Health, Department of MedicineStanfordCaliforniaUSA94304‐5559
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Liu C, Cui H, Gu D, Zhang M, Fang Y, Chen S, Tang M, Zhang B, Chen H. Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies. Lung Cancer 2017; 113:18-29. [PMID: 29110844 DOI: 10.1016/j.lungcan.2017.08.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023]
Abstract
A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.
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Affiliation(s)
- Caiyang Liu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China
| | - Huijie Cui
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Dongqing Gu
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Min Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yanfei Fang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Siyu Chen
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Mingshuang Tang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China.
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Yu H, Frank C, Hemminki A, Sundquist K, Hemminki K. Other cancers in lung cancer families are overwhelmingly smoking-related cancers. ERJ Open Res 2017; 3:00006-2017. [PMID: 28670582 PMCID: PMC5486776 DOI: 10.1183/23120541.00006-2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/16/2017] [Indexed: 11/21/2022] Open
Abstract
Familial risks of lung cancer are well-established, but whether lung cancer clusters with other discordant cancers is less certain, particularly beyond smoking-related sites, which may provide evidence on genetic contributions to lung cancer aetiology. We used a novel approach to search for familial associations in the Swedish Family-Cancer Database. This involved assessment of familial relative risk for cancer X in families with increasing numbers of lung cancer patients and, conversely, relative risks for lung cancer in families with increasing numbers of patients with cancers X. However, we lacked information on smoking. The total number of lung cancers in the database was 125 563. We applied stringent statistical criteria and found that seven discordant cancers were associated with lung cancer among family members, and six of these were known to be connected with smoking: oesophageal, upper aerodigestive tract, liver, cervical, kidney and urinary bladder cancers. A further novel finding was that cancer of unknown primary also associated with lung cancer. We also factored in histological evidence and found that anal and connective tissue cancers could be associated with lung cancer for reasons other than smoking. For endometrial and prostate cancers, suggestive negative associations with lung cancer were found. Although we lacked information on smoking it is prudent to conclude that practically all observed discordant associations of lung cancer were with cancers for which smoking is a risk factor. Among family members of lung cancer patients, 7 other cancers were found, all of which were smoking relatedhttp://ow.ly/ZLnt30csVfZ
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Affiliation(s)
- Hongyao Yu
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Frank
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Akseli Hemminki
- Cancer Gene Therapy Group, Faculty of Medicine, University of Helsinki, Finland.,Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | | | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
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Park SL, Cheng I, Haiman CA. Genome-Wide Association Studies of Cancer in Diverse Populations. Cancer Epidemiol Biomarkers Prev 2017. [PMID: 28637795 DOI: 10.1158/1055-9965.epi-17-0169] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) of cancer have identified more than 700 risk loci, of which approximately 80% were first discovered in European ancestry populations, approximately 15% in East Asians, 3% in multiethnic scans, and less than 1% in African and Latin American populations. These percentages closely mirror the distribution of samples included in the discovery phase of cancer GWAS to date (84% European, 11% East Asian, 4% African, and 1% Latin American ancestry). GWAS in non-European ancestry populations have provided insight into ancestry-specific variation in cancer and have pointed to regions of susceptibility that are of particular importance in certain populations. Uncovering and characterizing cancer risk loci in diverse populations is critical for understanding underlying biological mechanisms and developing future genetic risk prediction models in non-European ancestry populations. New GWAS and continued collaborations will be required to eliminate population inequalities in the number of studies, sample sizes, and variant content on GWAS arrays, and to better align genetic research in cancer to the global distribution of race/ethnicity Cancer Epidemiol Biomarkers Prev; 27(4); 405-17. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Sungshim L Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California.,Stanford Cancer Institute, Palo Alto, California
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
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