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Hoang TT, Lee Y, McCartney DL, Kersten ETG, Page CM, Hulls PM, Lee M, Walker RM, Breeze CE, Bennett BD, Burkholder AB, Ward J, Brantsæter AL, Caspersen IH, Motsinger-Reif AA, Richards M, White JD, Zhao S, Richmond RC, Magnus MC, Koppelman GH, Evans KL, Marioni RE, Håberg SE, London SJ. Comprehensive evaluation of smoking exposures and their interactions on DNA methylation. EBioMedicine 2024; 100:104956. [PMID: 38199042 PMCID: PMC10825325 DOI: 10.1016/j.ebiom.2023.104956] [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: 07/07/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Smoking impacts DNA methylation, but data are lacking on smoking-related differential methylation by sex or dietary intake, recent smoking cessation (<1 year), persistence of differential methylation from in utero smoking exposure, and effects of environmental tobacco smoke (ETS). METHODS We meta-analysed data from up to 15,014 adults across 5 cohorts with DNA methylation measured in blood using Illumina's EPIC array for current smoking (2560 exposed), quit < 1 year (500 exposed), in utero (286 exposed), and ETS exposure (676 exposed). We also evaluated the interaction of current smoking with sex or diet (fibre, folate, and vitamin C). FINDINGS Using false discovery rate (FDR < 0.05), 65,857 CpGs were differentially methylated in relation to current smoking, 4025 with recent quitting, 594 with in utero exposure, and 6 with ETS. Most current smoking CpGs attenuated within a year of quitting. CpGs related to in utero exposure in adults were enriched for those previously observed in newborns. Differential methylation by current smoking at 4-71 CpGs may be modified by sex or dietary intake. Nearly half (35-50%) of differentially methylated CpGs on the 450 K array were associated with blood gene expression. Current smoking and in utero smoking CpGs implicated 3049 and 1067 druggable targets, including chemotherapy drugs. INTERPRETATION Many smoking-related methylation sites were identified with Illumina's EPIC array. Most signals revert to levels observed in never smokers within a year of cessation. Many in utero smoking CpGs persist into adulthood. Smoking-related druggable targets may provide insights into cancer treatment response and shared mechanisms across smoking-related diseases. FUNDING Intramural Research Program of the National Institutes of Health, Norwegian Ministry of Health and Care Services and the Ministry of Education and Research, Chief Scientist Office of the Scottish Government Health Directorates and the Scottish Funding Council, Medical Research Council UK and the Wellcome Trust.
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Affiliation(s)
- Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA; Department of Pediatrics, Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Cancer and Hematology Center, Texas Children's Hospital, Houston, TX, USA
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Elin T G Kersten
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Dept. of Pediatric Pulmonology and Pediatric Allergy, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Physical Health and Ageing, Division for Physical and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Paige M Hulls
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK
| | - Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; School of Psychology, University of Exeter, Perry Road, Exeter, UK
| | - Charles E Breeze
- UCL Cancer Institute, University College London, Paul O'Gorman Building, London, UK; Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Brian D Bennett
- Department of Health and Human Services, Integrative Bioinformatics Support Group, National Institutes of Health, Research Triangle Park, NC, USA
| | - Adam B Burkholder
- Department of Health and Human Services, Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - James Ward
- Department of Health and Human Services, Integrative Bioinformatics Support Group, National Institutes of Health, Research Triangle Park, NC, USA
| | - Anne Lise Brantsæter
- Department of Food Safety, Division of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ida H Caspersen
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alison A Motsinger-Reif
- Department of Health and Human Services, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | | | - Julie D White
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA; GenOmics and Translational Research Center, Analytics Practice Area, RTI International, Research Triangle Park, NC, USA
| | - Shanshan Zhao
- Department of Health and Human Services, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Rebecca C Richmond
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Dept. of Pediatric Pulmonology and Pediatric Allergy, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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Karlow JA, Pehrsson EC, Xing X, Watson M, Devarakonda S, Govindan R, Wang T. Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:991-1013. [PMID: 37742993 PMCID: PMC10928376 DOI: 10.1016/j.gpb.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 02/11/2023] [Accepted: 03/14/2023] [Indexed: 09/26/2023]
Abstract
Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence cancer progression and treatment outcome. To determine the potential contribution of DNAmethylation alterations to tumor phenotype in non-small cell lung cancer (NSCLC) in both smoker and never-smoker patients, we performed genome-wide profiling of DNA methylation in 17 primary NSCLC tumors and 10 matched normal lung samples using the complementary assays, methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation sensitive restriction enzyme sequencing (MRE-seq). We reported recurrent methylation changes in the promoters of several genes, many previously implicated in cancer, including FAM83A and SEPT9 (hypomethylation), as well as PCDH7, NKX2-1, and SOX17 (hypermethylation). Although many methylation changes between tumors and their paired normal samples were shared across patients, several were specific to a particular smoking status. For example, never-smokers displayed a greater proportion of hypomethylated differentially methylated regions (hypoDMRs) and a greater number of recurrently hypomethylated promoters, including those of ASPSCR1, TOP2A, DPP9, and USP39, all previously linked to cancer. Changes outside of promoters were also widespread and often recurrent, particularly methylation loss over repetitive elements, highly enriched for ERV1 subfamilies. Recurrent hypoDMRs were enriched for several transcription factor binding motifs, often for genes involved in signaling and cell proliferation. For example, 71% of recurrent promoter hypoDMRs contained a motif for NKX2-1. Finally, the majority of DMRs were located within an active chromatin state in tissues profiled using the Roadmap Epigenomics data, suggesting that methylation changes may contribute to altered regulatory programs through the adaptation of cell type-specific expression programs.
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Affiliation(s)
- Jennifer A Karlow
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mark Watson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Siddhartha Devarakonda
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
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3
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Noble AJ, Purcell RV, Adams AT, Lam YK, Ring PM, Anderson JR, Osborne AJ. A Final Frontier in Environment-Genome Interactions? Integrated, Multi-Omic Approaches to Predictions of Non-Communicable Disease Risk. Front Genet 2022; 13:831866. [PMID: 35211161 PMCID: PMC8861380 DOI: 10.3389/fgene.2022.831866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/19/2022] [Indexed: 12/26/2022] Open
Abstract
Epidemiological and associative research from humans and animals identifies correlations between the environment and health impacts. The environment—health inter-relationship is effected through an individual’s underlying genetic variation and mediated by mechanisms that include the changes to gene regulation that are associated with the diversity of phenotypes we exhibit. However, the causal relationships have yet to be established, in part because the associations are reduced to individual interactions and the combinatorial effects are rarely studied. This problem is exacerbated by the fact that our genomes are highly dynamic; they integrate information across multiple levels (from linear sequence, to structural organisation, to temporal variation) each of which is open to and responds to environmental influence. To unravel the complexities of the genomic basis of human disease, and in particular non-communicable diseases that are also influenced by the environment (e.g., obesity, type II diabetes, cancer, multiple sclerosis, some neurodegenerative diseases, inflammatory bowel disease, rheumatoid arthritis) it is imperative that we fully integrate multiple layers of genomic data. Here we review current progress in integrated genomic data analysis, and discuss cases where data integration would lead to significant advances in our ability to predict how the environment may impact on our health. We also outline limitations which should form the basis of future research questions. In so doing, this review will lay the foundations for future research into the impact of the environment on our health.
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Affiliation(s)
- Alexandra J Noble
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Rachel V Purcell
- Department of Surgery, University of Otago Christchurch, Christchurch, New Zealand
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Ying K Lam
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Paulina M Ring
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jessica R Anderson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy J Osborne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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Ohmomo H, Harada S, Komaki S, Ono K, Sutoh Y, Otomo R, Umekage S, Hachiya T, Katanoda K, Takebayashi T, Shimizu A. DNA Methylation Abnormalities and Altered Whole Transcriptome Profiles after Switching from Combustible Tobacco Smoking to Heated Tobacco Products. Cancer Epidemiol Biomarkers Prev 2022; 31:269-279. [PMID: 34728466 PMCID: PMC9398167 DOI: 10.1158/1055-9965.epi-21-0444] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/29/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The use of heated tobacco products (HTP) has increased exponentially in Japan since 2016; however, their effects on health remain a major concern. METHODS Tsuruoka Metabolome Cohort Study participants (n = 11,002) were grouped on the basis of their smoking habits as never smokers (NS), past smokers (PS), combustible tobacco smokers (CS), and HTP users for <2 years. Peripheral blood mononuclear cells were collected from 52 participants per group matched to HTP users using propensity scores, and DNA and RNA were purified from the samples. DNA methylation (DNAm) analysis of the 17 smoking-associated DNAm biomarker genes (such as AHRR, F2RL3, LRRN3, and GPR15), as well as whole transcriptome analysis, was performed. RESULTS Ten of the 17 genes were significantly hypomethylated in CS and HTP users compared with NS, among which AHRR, F2RL3, and RARA showed intermediate characteristics between CS and NS; nonetheless, AHRR expression was significantly higher in CS than in the other three groups. Conversely, LRRN3 and GPR15 were more hypomethylated in HTP users than in NS, and GPR15 expression was markedly upregulated in all the groups when compared with that in NS. CONCLUSIONS HTP users (switched from CS <2 years) display abnormal DNAm and transcriptome profiles, albeit to a lesser extent than the CS. However, because the molecular genetic effects of long-term HTP use are still unknown, long-term molecular epidemiologic studies are needed. IMPACT This study provides new insights into the molecular genetic effects on DNAm and transcriptome profiles in HTP users who switched from CS.
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Affiliation(s)
- Hideki Ohmomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Shohei Komaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Kanako Ono
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Yoichi Sutoh
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Ryo Otomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - So Umekage
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| | - Kota Katanoda
- Division of Cancer Statistics Integration, National Cancer Center Research Institute, Chuo, Tokyo, Japan
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan.,Corresponding Author: Atsushi Shimizu, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate 028-3694, Japan. Phone: 81-19-651-5110, ext. 5473; E-mail:
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5
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Jiang W, Wu H, Yu X, Wang Y, Gu W, Wei W, Li B, Jiang X, Wang Y, Hou W, Dong Q, Yan X, Li Y, Sun C, Han T. Third-hand smoke exposure is associated with abnormal serum melatonin level via hypomethylation of CYP1A2 promoter: Evidence from human and animal studies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116669. [PMID: 33652180 DOI: 10.1016/j.envpol.2021.116669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/08/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to examine whether and how third-hand smoke (THS) exposure would influence serum melatonin level. 1083 participants with or without exposure to THS were enrolled. Serum ROS, SOD, GSH-Px, and melatonin were measured by ELISA. Methylation microarrays detection and WGCNA were performed to identify hub methylated-sites. The methylation levels of hub-sites were validated in addtional samples. Moreover, mice were exposed to THS for 6 months mimicking exposure of human and the serum, liver, and pineal were collected. Oxidative stress-related indicators in serum, pineal, and liver were measured by ELISA. The expressions of mRNA and protein and methylation levels of hub-gene discovered in human data were further explored by RT-PCR, western-blot, and TBS. The results showed the participants exposed to THS had lower melatonin-level. 820 differentially methylated sites associated with THS were identified. And the hub-site located on the CYP1A2 promoter was identified, which mediated the association between THS and decreased melatonin-level. Decreased peak of serum melatonin, increased ROS and reduced SOD and GSH-Px in pineal and liver, and elevated CYP1A2 expression in liver was also found in the THS-exposed mice. Hypo-methylation of 7 CPG sites on the CYP1A2 promoter was identified, which accelerated the catabolism of melatonin. Overall, THS exposure is associated with abnormal melatonin catabolism through hypo-methylation of CYP1A2-promoter.
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Affiliation(s)
- Wenbo Jiang
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Huanyu Wu
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Xinyang Yu
- Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Wenbo Gu
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Wei Wei
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Bai Li
- University of Ottawa, Ottawa K1N 6N5, Canada
| | - XiTao Jiang
- IT and Environment, College of Engineering, Charles Darwin University, Darwin, Northern Territory 0810, Australia
| | - Yue Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Wanying Hou
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Qiuying Dong
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Xuemin Yan
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Ying Li
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Changhao Sun
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China
| | - Tianshu Han
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, P. R. China.
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Sun Y, Zhang Y, Ren S, Li X, Yang P, Zhu J, Lin L, Wang Z, Jia Y. Low expression of RGL4 is associated with a poor prognosis and immune infiltration in lung adenocarcinoma patients. Int Immunopharmacol 2020; 83:106454. [PMID: 32259700 DOI: 10.1016/j.intimp.2020.106454] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/22/2023]
Abstract
Lung adenocarcinoma (LUAD) is a frequently diagnosed histologic subtype with increasing morbidity and mortality. RalGDS-Like 4 (RGL4) has not been reported to be associated with cancer risk, prognosis, immunotherapy or any other treatments. We perform a bioinformatics analysis on data downloaded from the Cancer Genome Atlas (TCGA)-LUAD, and we find that low expression of RGL4 is accompanied by worse outcomes and prognosis in LUAD patients. As a promising predictor, the potential influence and mechanisms of RGL4 on overall survival are worth exploring. Moreover, RGL4 expression is significantly associated with a variety of tumor-infiltrating immune cells (TIICs), particularly memory B cells, CD8+T cells and neutrophils. Subsequently, we evaluated the most notable KEGG pathways, including glycolysis gluconeogenesis, the P53 signaling pathway, RNA degradation, and the B cell receptor signaling pathway, among others. Our findings provide evidence that the decreased expression of RGL4 is significantly associated with poor prognosis and immune cell infiltration in patients with LUAD and highlight the use of RGL4 as a novel predictive biomarker for the prognosis of LUAD and other cancers. RGL4 may also be used in combination with immune checkpoints to identify the benefits of immunotherapy. Subjects: Bioinformatics, Genomics, Oncology, Thoracic surgery.
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Affiliation(s)
- Yidan Sun
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China; Department of Oncology, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Ying Zhang
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Shiqi Ren
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, PR China; Department of Medicine, Nantong University Xinling College, Nantong, Jiangsu 226001, PR China
| | - Xiaojiang Li
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Peiying Yang
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Jinli Zhu
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Lisen Lin
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China
| | - Ziheng Wang
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, PR China.
| | - Yingjie Jia
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, PR China.
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7
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Battram T, Richmond RC, Baglietto L, Haycock PC, Perduca V, Bojesen SE, Gaunt TR, Hemani G, Guida F, Carreras-Torres R, Hung R, Amos CI, Freeman JR, Sandanger TM, Nøst TH, Nordestgaard BG, Teschendorff AE, Polidoro S, Vineis P, Severi G, Hodge AM, Giles GG, Grankvist K, Johansson MB, Johansson M, Davey Smith G, Relton CL. Appraising the causal relevance of DNA methylation for risk of lung cancer. Int J Epidemiol 2019; 48:1493-1504. [PMID: 31549173 PMCID: PMC6857764 DOI: 10.1093/ije/dyz190] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DNA methylation changes in peripheral blood have recently been identified in relation to lung cancer risk. Some of these changes have been suggested to mediate part of the effect of smoking on lung cancer. However, limitations with conventional mediation analyses mean that the causal nature of these methylation changes has yet to be fully elucidated. METHODS We first performed a meta-analysis of four epigenome-wide association studies (EWAS) of lung cancer (918 cases, 918 controls). Next, we conducted a two-sample Mendelian randomization analysis, using genetic instruments for methylation at CpG sites identified in the EWAS meta-analysis, and 29 863 cases and 55 586 controls from the TRICL-ILCCO lung cancer consortium, to appraise the possible causal role of methylation at these sites on lung cancer. RESULTS Sixteen CpG sites were identified from the EWAS meta-analysis [false discovery rate (FDR) < 0.05], for 14 of which we could identify genetic instruments. Mendelian randomization provided little evidence that DNA methylation in peripheral blood at the 14 CpG sites plays a causal role in lung cancer development (FDR > 0.05), including for cg05575921-AHRR where methylation is strongly associated with both smoke exposure and lung cancer risk. CONCLUSIONS The results contrast with previous observational and mediation analysis, which have made strong claims regarding the causal role of DNA methylation. Thus, previous suggestions of a mediating role of methylation at sites identified in peripheral blood, such as cg05575921-AHRR, could be unfounded. However, this study does not preclude the possibility that differential DNA methylation at other sites is causally involved in lung cancer development, especially within lung tissue.
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Affiliation(s)
- Thomas Battram
- MRC Integrative Epidemiology Unit
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées, Université Paris Descartes, Paris, France
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Florence Guida
- Genetic Epidemiology Division, International Agency for Research on Cancer, Lyon, France
| | - Robert Carreras-Torres
- Genetic Epidemiology Division, International Agency for Research on Cancer, Lyon, France
| | - Rayjean Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Joshua R Freeman
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA
| | - Torkjel M Sandanger
- Department of Community Medicine,Arctic University of Norway, Tromso, Norway
| | - Therese H Nøst
- Department of Community Medicine,Arctic University of Norway, Tromso, Norway
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andrew E Teschendorff
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, CAS–Max Planck Gesellschaft (MPG) Partner Institute for Computational Biology, Shanghai, China
| | - Silvia Polidoro
- Molecular and Genetic Epidemiology Unit, Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Paolo Vineis
- Molecular and Genetic Epidemiology Unit, Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Gianluca Severi
- CESP (Inserm U1018), Facultés de Médicine Université Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, 94805, Villejuif, France
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population & Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Allison M Hodge
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population & Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population & Global Health, University of Melbourne, Melbourne, VIC, Australia
| | | | | | - Mattias Johansson
- Genetic Epidemiology Division, International Agency for Research on Cancer, Lyon, France
| | - George Davey Smith
- MRC Integrative Epidemiology Unit
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit
- Population Health Sciences, University of Bristol, Bristol, UK
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8
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Ha S, Zhou H, Gautam M, Song Y, Wang C. Reduced ribosomal RNA expression and unchanged ribosomal DNA promoter methylation in oral squamous cell carcinoma. Mol Genet Genomic Med 2019; 7:e00783. [PMID: 31169368 PMCID: PMC6625366 DOI: 10.1002/mgg3.783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/07/2019] [Accepted: 05/17/2019] [Indexed: 12/31/2022] Open
Abstract
Background Ribosomal RNA (rRNA) consists of four non‐coding RNAs, the 28S, 5.8S, 18S, and 5S rRNA. Abnormal expression of rRNA has been found in multiple tumors, and the methylation of rDNA promoter may affect rRNA expression as an epigenetic regulatory mechanism. Oral squamous cell carcinoma (OSCC) is a kind of aggressive tumors which occurs in multiple sites in oral cavity. rRNA expression and the methylation of rDNA promoter in modulating rRNA expression in OSCC maintain unclear. This study aims to investigate the rRNA expression, the methylation status within rDNA promoter, and the underlying mechanism of methylation in regulating rRNA expression in OSCC. Methods Twelve primary OSCC and matched normal tissue samples were collected from patients with OSCC. Quantitative real‐time PCR was used to evaluate the rRNA level. HpaII/MspI digestion and bisulfite sequencing were used to investigate the methylation status of rDNA promoter. Results Ribosomal RNA levels were suppressed in OSCC as compared with matched normal tissues. HpaII/MspI digestion and bisulfite sequencing showed no significant differences for the methylation of rDNA promoter between the tumor and matched normal tissues. Conclusion The methylation in rDNA promoter could not explain for the suppressed rRNA expression in OSCC tissues.
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Affiliation(s)
- Shanshan Ha
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mayank Gautam
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yaling Song
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Changning Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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9
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Freudenheim JL, Shields PG, Song MA, Smiraglia D. DNA Methylation and Smoking: Implications for Understanding Effects of Electronic Cigarettes. CURR EPIDEMIOL REP 2019. [DOI: 10.1007/s40471-019-00191-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Li X, Qin M, Huang J, Ma J, Hu X. Clinical significance of miRNA‑1 and its potential target gene network in lung squamous cell carcinoma. Mol Med Rep 2019; 19:5063-5078. [PMID: 31059033 PMCID: PMC6522896 DOI: 10.3892/mmr.2019.10171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 09/21/2019] [Indexed: 11/25/2022] Open
Abstract
Previous studies demonstrated that miRNA-1 (miR-1) is downregulated in certain human cancer and serves a crucial role in the progression of cancer. However, there are only a few previous studies examining the association between miR-1 and lung squamous cell carcinoma (LUSC) and the regulatory mechanism of miR-1 in LUSC remains unclear. Therefore, the present study investigated the clinical significance and determined the potential molecular mechanism of miR-1 in LUSC. The expression of miR-1 and its clinical significance in LUSC was examined by conducting a meta-analysis of 12 studies using Stata 14, MetaDiSc1.4 and SPSS version 23. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the potential target genes of miR-1 gathered from Gene Expression Omnibus and ArrayExpress. Meta-analysis demonstrated that miR-1 was significantly downregulated in LUSC [standardized mean difference: −1.44; 95% confidence interval (CI): −2.08, −0.81], and the area under the curve was 0.9096 (Q*=0.8416) with sensitivity of 0.71 (95% CI: 0.66, 0.76) and specificity of 0.88 (95% CI: 0.86, 0.90). The pooled positive likelihood ratio and negative likelihood ratio were 4.93 (95% CI: 2.54, 9.55) and 0.24 (95% CI: 0.10, 0.54), respectively. Bioinformatics analysis demonstrated that miR-1 may be involved in the progression of LUSC via the ‘cell cycle’, ‘p53 signaling pathway’, ‘Fanconi anemia pathway’, ‘homologous recombination’, ‘glycine, serine and threonine metabolism’ and ‘oocyte meiosis’. In summary, miR-1 was significantly downregulated in LUSC, suggesting a novel and promising non-invasive biomarker for diagnosing LUSC, and miR-1 was involved in LUSC progression via a number of significant pathways.
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Affiliation(s)
- Xiaojiao Li
- Department of Positron Emission Tomography‑Computed Tomography, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Meijiao Qin
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jiacheng Huang
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiaohua Hu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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11
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Fragou D, Pakkidi E, Aschner M, Samanidou V, Kovatsi L. Smoking and DNA methylation: Correlation of methylation with smoking behavior and association with diseases and fetus development following prenatal exposure. Food Chem Toxicol 2019; 129:312-327. [PMID: 31063835 DOI: 10.1016/j.fct.2019.04.059] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Among epigenetic mechanisms, DNA methylation has been widely studied with respect to many environmental factors. Smoking is a common factor which affects both global and gene-specific DNA methylation. It is supported that smoking directly affects DNA methylation, and these effects contribute to the development and progression of various diseases, such as cancer, lung and cardiovascular diseases and male infertility. In addition, prenatal smoking influences the normal development of the fetus via DNA methylation changes. The DNA methylation profile and its smoking-induced alterations helps to distinguish current from former smokers and non-smokers and can be used to predict the risk for the development of a disease. This review summarizes the DNA methylation changes induced by smoking, their correlation with smoking behavior and their association with various diseases and fetus development.
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Affiliation(s)
- Domniki Fragou
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece
| | - Eleni Pakkidi
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Michael Aschner
- Departments of Molecular Pharmacology, Neuroscience, and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Victoria Samanidou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece.
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12
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Active and secondhand smoke exposure throughout life and DNA methylation in breast tumors. Cancer Causes Control 2019; 30:53-62. [PMID: 30617699 DOI: 10.1007/s10552-018-1102-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
Abstract
PURPOSE Tobacco smoke exposure has been associated with altered DNA methylation. However, there is a paucity of information regarding tobacco smoke exposure and DNA methylation of breast tumors. METHODS We conducted a case-only analysis using breast tumor tissue from 493 postmenopausal and 225 premenopausal cases in the Western New York Exposures and Breast Cancer (WEB) study. Methylation of nine genes (SFN, SCGB3A1, RARB, GSTP1, CDKN2A, CCND2, BRCA1, FHIT, and SYK) was measured with pyrosequencing. Participants reported their secondhand smoke (SHS) and active smoking exposure for seven time periods. Unconditional logistic regression was used to estimate odds ratios (OR) of having methylation higher than the median. RESULTS SHS exposure was associated with tumor DNA methylation among postmenopausal but not premenopausal women. Active smoking at certain ages was associated with increased methylation of GSTP1, FHIT, and CDKN2A and decreased methylation of SCGB3A1 and BRCA1 among both pre- and postmenopausal women. CONCLUSION Exposure to tobacco smoke may contribute to breast carcinogenesis via alterations in DNA methylation. Further studies in a larger panel of genes are warranted.
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13
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Epigenetic signatures of starting and stopping smoking. EBioMedicine 2018; 37:214-220. [PMID: 30389506 PMCID: PMC6286188 DOI: 10.1016/j.ebiom.2018.10.051] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 01/28/2023] Open
Abstract
Background Multiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well–established. Here, we assess DNA methylation patterns from peripheral blood samples in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers. Methods Dimensionality reduction was applied to DNA methylation data at 90 previously identified smoking–associated CpG sites for over 4900 individuals in the Generation Scotland cohort. K–means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day). Findings Two clusters were specified, corresponding to never smokers (97·5% of whom were assigned to Cluster 1) and current smokers (81·1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to the smoker–enriched cluster varied between 5 and 9 years in heavier smokers and between 15 and 19 years in lighter smokers. Low–dose former smokers were more likely to be assigned to the never smoker–enriched cluster in the first year following cessation. In contrast, a period of at least two years was required before the majority of former high–dose smokers were assigned to the never smoker–enriched cluster. Interpretation Our findings suggest that smoking–associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation–based signatures of smoking status be predictive of smoking–related health outcomes, our findings may provide an additional criterion on which to stratify risk.
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14
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Tsai PC, Glastonbury CA, Eliot MN, Bollepalli S, Yet I, Castillo-Fernandez JE, Carnero-Montoro E, Hardiman T, Martin TC, Vickers A, Mangino M, Ward K, Pietiläinen KH, Deloukas P, Spector TD, Viñuela A, Loucks EB, Ollikainen M, Kelsey KT, Small KS, Bell JT. Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health. Clin Epigenetics 2018; 10:126. [PMID: 30342560 PMCID: PMC6196025 DOI: 10.1186/s13148-018-0558-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/03/2018] [Indexed: 12/14/2022] Open
Abstract
Background Tobacco smoking is a risk factor for multiple diseases, including cardiovascular disease and diabetes. Many smoking-associated signals have been detected in the blood methylome, but the extent to which these changes are widespread to metabolically relevant tissues, and impact gene expression or metabolic health, remains unclear. Methods We investigated smoking-associated DNA methylation and gene expression variation in adipose tissue biopsies from 542 healthy female twins. Replication, tissue specificity, and longitudinal stability of the smoking-associated effects were explored in additional adipose, blood, skin, and lung samples. We characterized the impact of adipose tissue smoking methylation and expression signals on metabolic disease risk phenotypes, including visceral fat. Results We identified 42 smoking-methylation and 42 smoking-expression signals, where five genes (AHRR, CYP1A1, CYP1B1, CYTL1, F2RL3) were both hypo-methylated and upregulated in current smokers. CYP1A1 gene expression achieved 95% prediction performance of current smoking status. We validated and replicated a proportion of the signals in additional primary tissue samples, identifying tissue-shared effects. Smoking leaves systemic imprints on DNA methylation after smoking cessation, with stronger but shorter-lived effects on gene expression. Metabolic disease risk traits such as visceral fat and android-to-gynoid ratio showed association with methylation at smoking markers with functional impacts on expression, such as CYP1A1, and at tissue-shared smoking signals, such as NOTCH1. At smoking-signals, BHLHE40 and AHRR DNA methylation and gene expression levels in current smokers were predictive of future gain in visceral fat upon smoking cessation. Conclusions Our results provide the first comprehensive characterization of coordinated DNA methylation and gene expression markers of smoking in adipose tissue. The findings relate to human metabolic health and give insights into understanding the widespread health consequence of smoking outside of the lung. Electronic supplementary material The online version of this article (10.1186/s13148-018-0558-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK. .,Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan. .,Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Craig A Glastonbury
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7LF, UK
| | - Melissa N Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM) and Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Idil Yet
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | | | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Pfizer - University of Granada - Andalusian Government Center for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Thomas Hardiman
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Division of Cancer Studies, King's College London, London, SE1 9RT, UK
| | - Tiphaine C Martin
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
| | - Alice Vickers
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, SE1 9RT, UK
| | - Kirsten Ward
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Kirsi H Pietiläinen
- Research Programs Unit, Diabetes and Obesity, Obesity Research Unit, University of Helsinki, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Department of Genetic Medicine and Development, University of Geneva Medical School, 1211, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland.,Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Eric B Loucks
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM) and Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, 02912, USA.,Department of Laboratory Medicine & Pathology, Brown University, Providence, RI, 02912, USA
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
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15
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Murphy SE, Park SL, Balbo S, Haiman CA, Hatsukami DK, Patel Y, Peterson LA, Stepanov I, Stram DO, Tretyakova N, Hecht SS, Le Marchand L. Tobacco biomarkers and genetic/epigenetic analysis to investigate ethnic/racial differences in lung cancer risk among smokers. NPJ Precis Oncol 2018; 2:17. [PMID: 30155522 PMCID: PMC6105591 DOI: 10.1038/s41698-018-0057-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
The Multiethnic Cohort Study has demonstrated that African Americans and Native Hawaiians have a higher risk for lung cancer due to cigarette smoking than Whites while Latinos and Japanese Americans have a lower risk. These findings are consistent with other epidemiologic studies in the literature. In this review, we summarize tobacco carcinogen and toxicant biomarker studies and genetic analyses which partially explain these differences. As determined by measurement of total nicotine equivalents in urine, which account for about 85% of the nicotine dose, African Americans take up greater amounts of nicotine than Whites per cigarette while Japanese Americans take up less. There are corresponding differences in the uptake of tobacco smoke carcinogens such as tobacco-specific nitrosamines, polycyclic aromatic hydrocarbons, 1,3-butadiene, and other toxic volatiles. The lower nicotine uptake of Japanese Americans is clearly linked to the preponderance of low activity forms of the primary nicotine metabolizing enzyme CYP2A6 in this ethnic group, leading to more unchanged nicotine in the body and thus lower smoking intensity. But the relatively high risk of Native Hawaiians and the low risk of Latino smokers for lung cancer are not explained by these factors. The possible role of epigenetics in modifying lung cancer risk among smokers is also discussed here. The results of these published studies may lead to a better understanding of susceptibility factors for lung cancer in cigarette smokers thus potentially identifying biomarkers that can detect those individuals at highest risk so that preventive approaches can be initiated at an early stage of the lung cancer development process.
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Affiliation(s)
- Sharon E. Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Sungshim Lani Park
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Christopher A. Haiman
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | | | - Yesha Patel
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | - Lisa A. Peterson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Irina Stepanov
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Daniel O. Stram
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | - Natalia Tretyakova
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Loïc Le Marchand
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI 96813 USA
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16
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Kennedy EM, Goehring GN, Nichols MH, Robins C, Mehta D, Klengel T, Eskin E, Smith AK, Conneely KN. An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells. BMC Genomics 2018; 19:476. [PMID: 29914364 PMCID: PMC6006777 DOI: 10.1186/s12864-018-4842-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/30/2018] [Indexed: 01/06/2023] Open
Abstract
Background Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. Results We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), > 50% are distal (> 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P < 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60–70% of occurrences and are enriched for annotated gene promoters and enhancers (P < 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control. Conclusions This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-4842-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth M Kennedy
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA. .,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - George N Goehring
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael H Nichols
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.,Department of Biology, Emory University, Atlanta, GA, USA
| | - Chloe Robins
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.,Population Biology, Ecology and Evolution Program, Emory University, Atlanta, GA, USA
| | - Divya Mehta
- School of Psychology and Counseling, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia
| | - Torsten Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Alicia K Smith
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.,Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen N Conneely
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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17
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Al-Obaide MAI, Ibrahim BA, Al-Humaish S, Abdel-Salam ASG. Genomic and Bioinformatics Approaches for Analysis of Genes Associated With Cancer Risks Following Exposure to Tobacco Smoking. Front Public Health 2018; 6:84. [PMID: 29616208 PMCID: PMC5869936 DOI: 10.3389/fpubh.2018.00084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/05/2018] [Indexed: 01/03/2023] Open
Abstract
Cancer is a significant health problem in the Middle East and global population. It is well established that there is a direct link between tobacco smoking and cancer, which will continue to pose a significant threat to human health. The impact of long-term exposure to tobacco smoke on the risk of cancer encouraged the study of biomarkers for vulnerable individuals to tobacco smoking, especially children, who are more susceptible than adults to the action of environmental carcinogens. The carcinogens in tobacco smoke condensate induce DNA damage and play a significant role in determining the health and well-being of smokers, non-smoker, and primarily children. Cancer is a result of genomic and epigenomic malfunctions that lead to an initial premalignant condition. Although premalignancy genetic cascade is a much-delayed process, it will end with adverse health consequences. In addition to the DNA damage and mutations, tobacco smoke can cause changes in the DNA methylation and gene expression associated with cancer. The genetic events hint on the possible use of genomic–epigenomic changes in genes related to cancer, in predicting cancer risks associated with exposure to tobacco smoking. Bioinformatics provides indispensable tools to identify the cascade of expressed genes in active smokers and non-smokers and could assist the development of a framework to manage this cascade of events linked with the evolvement of disease including cancer. The aim of this mini review is to cognize the essential genomic processes and health risks associated with tobacco smoking and the implications of bioinformatics in cancer prediction, prevention, and intervention.
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Affiliation(s)
- Mohammed A I Al-Obaide
- Department of Biomedical Science, School of Pharmacy, Texas Tech University Health Science Center, Amarillo, TX, United States
| | | | | | - Abdel-Salam G Abdel-Salam
- Department of Mathematics, Statistics and Physics, College of Arts and Sciences, Qatar University, Doha, Qatar
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18
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Association of Smoking, Alcohol Use, and Betel Quid Chewing with Epigenetic Aberrations in Cancers. Int J Mol Sci 2017; 18:ijms18061210. [PMID: 28587272 PMCID: PMC5486033 DOI: 10.3390/ijms18061210] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/16/2022] Open
Abstract
Numerous environmental factors such as diet, alcohol use, stress, and environmental chemicals are known to elicit epigenetic changes, leading to increased rates of cancers and other diseases. The incidence of head and neck cancer, one of the most common cancers in Taiwanese males, is increasing: oral cancer and nasopharyngeal carcinoma are ranked fourth and tenth respectively, among the top ten cancers in this group, and a major cause of cancer-related deaths in Taiwanese males. Previous studies have identified smoking, alcohol use, and betel quid chewing as the three major causes of head and neck cancers; these three social habits are commonly observed in Taiwanese males, resulting in an increasing morbidity rate of head and neck cancers in this population. In this literature review, we discuss the association between specific components of betel quid, alcohol, and tobacco, and the occurrence of head and neck cancers, lung cancer, gastrointestinal cancers, and urethral cancer. We focus on regulatory mechanisms at the epigenetic level and their oncogenic effects. The review further discusses the application of FDA-approved epigenetic drugs as therapeutic strategies against cancer.
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Fish TJ, Benninghoff AD. DNA methylation in lung tissues of mouse offspring exposed in utero to polycyclic aromatic hydrocarbons. Food Chem Toxicol 2017; 109:703-713. [PMID: 28476633 DOI: 10.1016/j.fct.2017.04.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/29/2017] [Accepted: 04/29/2017] [Indexed: 12/19/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) comprise an important class of environmental pollutants that are known to cause lung cancer in animals and are suspected lung carcinogens in humans. Moreover, evidence from cell-based studies points to PAHs as modulators of the epigenome. The objective of this work was to assess patterns of genome-wide DNA methylation in lung tissues of adult offspring initiated in utero with the transplacental PAH carcinogens dibenzo [def,p]chrysene (DBC) or benzo [a]pyrene (BaP). Genome-wide methylation patterns for normal (not exposed), normal adjacent and lung tumor tissues obtained from adult offspring were determined using methylated DNA immunoprecipitation (MeDIP) with the NimbleGen mouse DNA methylation CpG island array. Lung tumor incidence in 45-week old mice initiated with BaP was 32%, much lower than that of the DBC-exposed offspring at 96%. Also, male offspring appeared more susceptible to BaP as compared to females. Distinct patterns of DNA methylation were associated with non-exposed, normal adjacent and adenocarcinoma lung tissues, as determined by principal components, hierarchical clustering and gene ontology analyses. From these methylation profiles, a set of genes of interest was identified that includes potential important targets for epigenetic modification during the process of lung tumorigenesis in animals exposed to environmental PAHs.
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Affiliation(s)
- Trevor J Fish
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA; School of Veterinary Medicine, Utah State University, Logan, UT 84322, USA.
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Tang Y, Jiang S, Gu Y, Li W, Mo Z, Huang Y, Li T, Hu Y. Promoter DNA methylation analysis reveals a combined diagnosis of CpG-based biomarker for prostate cancer. Oncotarget 2017; 8:58199-58209. [PMID: 28938548 PMCID: PMC5601644 DOI: 10.18632/oncotarget.16437] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/28/2017] [Indexed: 01/08/2023] Open
Abstract
Background Prostate cancer (PCa) is the most common tumor in elderly men. However, the specificity and sensitivity of serum prostate-specific antigen levels in PCa diagnosis are controversial. This study aims to reveal a novel diagnosis biomarker in PCa. Materials and Methods The differential methylated CpG sites between 423 primary PCa and 39 adjacent samples from The Cancer Genome Atlas (TCGA) on Illumina HumanMethylation 450 platform were analyzed. The diagnostic methylation markers were mined using the Prediction Analysis of Microarrays package in Bioconductor. Then, the Gene Expression Omnibus data was used for verification. Pyrosequencing was applied to improve methylation levels of five CpGs (cg06363129, cg08843517, cg05385513, cg07220448 and cg11417025). Results The area under curve of receiver operating characteristic of eight diagnostic methylation CpGs (cg06363129, cg08843517, cg03576469, cg05385513, cg07220448, cg11417025, cg20883831, and cg23824801) in TCGA data ranged from 0.910 to 0.939. Except for cg20883831 and cg23824801, the correlations between methylation levels of six other sites and their expressions in patients were significant (r > 0.5 and P < 0.001). The methylation level of cg06363129 was significantly different between the groups of Gleason Score (GS) = 7 and GS ≥ 8 (P < 0.05). Pyrosequencing in our samples confirmed that four diagnostic methylation sites (cg06363129, cg08843517, cg05385513, and cg11417025) had high diagnostic efficacy. Conclusions The combined diagnosis of four methylation CpGs sites (cg06363129, cg08843517, cg05385513, and cg11417025) in the gene promoter has high tissue specificity and diagnostic efficacy for PCa. Results revealed a novel potential biomarker for prostate cancer diagnosis.
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Affiliation(s)
- Yuanyuan Tang
- Guangxi Reproductive Medical Research Center, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Shusuan Jiang
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yinmin Gu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Weidong Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Zengnan Mo
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yuanjie Huang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Tianyu Li
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yanling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi 530021, China
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