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Li JL, Jain N, Tamayo LI, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL. The association of cigarette smoking with DNA methylation and gene expression in human tissue samples. Am J Hum Genet 2024; 111:636-653. [PMID: 38490207 PMCID: PMC11023923 DOI: 10.1016/j.ajhg.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Cigarette smoking adversely affects many aspects of human health, and epigenetic responses to smoking may reflect mechanisms that mediate or defend against these effects. Prior studies of smoking and DNA methylation (DNAm), typically measured in leukocytes, have identified numerous smoking-associated regions (e.g., AHRR). To identify smoking-associated DNAm features in typically inaccessible tissues, we generated array-based DNAm data for 916 tissue samples from the GTEx (Genotype-Tissue Expression) project representing 9 tissue types (lung, colon, ovary, prostate, blood, breast, testis, kidney, and muscle). We identified 6,350 smoking-associated CpGs in lung tissue (n = 212) and 2,735 in colon tissue (n = 210), most not reported previously. For all 7 other tissue types (sample sizes 38-153), no clear associations were observed (false discovery rate 0.05), but some tissues showed enrichment for smoking-associated CpGs reported previously. For 1,646 loci (in lung) and 22 (in colon), smoking was associated with both DNAm and local gene expression. For loci detected in both lung and colon (e.g., AHRR, CYP1B1, CYP1A1), top CpGs often differed between tissues, but similar clusters of hyper- or hypomethylated CpGs were observed, with hypomethylation at regulatory elements corresponding to increased expression. For lung tissue, 17 hallmark gene sets were enriched for smoking-associated CpGs, including xenobiotic- and cancer-related gene sets. At least four smoking-associated regions in lung were impacted by lung methylation quantitative trait loci (QTLs) that co-localize with genome-wide association study (GWAS) signals for lung function (FEV1/FVC), suggesting epigenetic alterations can mediate the effects of smoking on lung health. Our multi-tissue approach has identified smoking-associated regions in disease-relevant tissues, including effects that are shared across tissue types.
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Affiliation(s)
- James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Niyati Jain
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lizeth I Tamayo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, University of Chicago, Chicago, IL 60637, USA.
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Qin Q, Zhou Y, Guo J, Chen Q, Tang W, Li Y, You J, Li Q. Conserved methylation signatures associate with the tumor immune microenvironment and immunotherapy response. Genome Med 2024; 16:47. [PMID: 38566132 PMCID: PMC10985907 DOI: 10.1186/s13073-024-01318-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Aberrant DNA methylation is a major characteristic of cancer genomes. It remains unclear which biological processes determine epigenetic reprogramming and how these processes influence the variants in the cancer methylome, which can further impact cancer phenotypes. METHODS We performed pairwise permutations of 381,900 loci in 569 paired DNA methylation profiles of cancer tissue and matched normal tissue from The Cancer Genome Atlas (TCGA) and defined conserved differentially methylated positions (DMPs) based on the resulting null distribution. Then, we derived independent methylation signatures from 2,465 cancer-only methylation profiles from the TCGA and 241 cell line-based methylation profiles from the Genomics of Drug Sensitivity in Cancer (GDSC) cohort using nonnegative matrix factorization (NMF). We correlated DNA methylation signatures with various clinical and biological features, including age, survival, cancer stage, tumor immune microenvironment factors, and immunotherapy response. We inferred the determinant genes of these methylation signatures by integrating genomic and transcriptomic data and evaluated the impact of these signatures on cancer phenotypes in independent bulk and single-cell RNA/methylome cohorts. RESULTS We identified 7,364 differentially methylated positions (2,969 Hyper-DMPs and 4,395 Hypo-DMPs) in nine cancer types from the TCGA. We subsequently retrieved three highly conserved, independent methylation signatures (Hyper-MS1, Hypo-MS1, and Hypo-MS4) from cancer tissues and cell lines based on these Hyper and Hypo-DMPs. Our data suggested that Hypo-MS4 activity predicts poor survival and is associated with immunotherapy response and distant tumor metastasis, and Hypo-MS4 activity is related to TP53 mutation and FOXA1 binding specificity. In addition, we demonstrated a correlation between the activities of Hypo-MS4 in cancer cells and the fractions of regulatory CD4 + T cells with the expression levels of immunological genes in the tumor immune microenvironment. CONCLUSIONS Our findings demonstrated that the methylation signatures of distinct biological processes are associated with immune activity in the cancer microenvironment and predict immunotherapy response.
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Affiliation(s)
- Qingqing Qin
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Ying Zhou
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jintao Guo
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Qinwei Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
| | - Weiwei Tang
- Department of Medical Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University and Institute of Hematology, Xiamen University, Xiamen, 361003, China
- Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, The School of Clinical Medicine of Fujian, Medical University, Xiamen, 361003, China
| | - Yuchen Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jun You
- Department of Gastrointestinal Oncology Surgery, The First Affiliated Hospital of Xiamen University, Cancer Center, Xiamen, 361003, China
| | - Qiyuan Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China.
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China.
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China.
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Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P. Pan-cancer proteogenomics characterization of tumor immunity. Cell 2024; 187:1255-1277.e27. [PMID: 38359819 PMCID: PMC10988632 DOI: 10.1016/j.cell.2024.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/29/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024]
Abstract
Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Francesca Pia Caruso
- BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy; Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", Naples, Italy
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua M Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John Erol Evangelista
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaoyu Song
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Berk Turhan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David A Lewis
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Rossana Lazcano Segura
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Harsh Batra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Ying Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Maciej Wiznerowicz
- Department of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland; Department of Oncology, Heliodor Swiecicki Clinical Hospital, 60-203 Poznań, Poland
| | - Tania J González-Robles
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Antonio Iavarone
- Department of Neurological Surgery, Department of Biochemistry, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sara J C Gosline
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Alexey I Nesvizhskii
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marcin Cieslik
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & Environmental Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA; Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Domingo-Relloso A, Joehanes R, Rodriguez-Hernandez Z, Lahousse L, Haack K, Fallin MD, Herreros-Martinez M, Umans JG, Best LG, Huan T, Liu C, Ma J, Yao C, Jerolon A, Bermudez JD, Cole SA, Rhoades DA, Levy D, Navas-Acien A, Tellez-Plaza M. Smoking, blood DNA methylation sites and lung cancer risk. Environ Pollut 2023; 334:122153. [PMID: 37442331 PMCID: PMC10528956 DOI: 10.1016/j.envpol.2023.122153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Altered DNA methylation (DNAm) might be a biological intermediary in the pathway from smoking to lung cancer. In this study, we investigated the contribution of differential blood DNAm to explain the association between smoking and lung cancer incidence. Blood DNAm was measured in 2321 Strong Heart Study (SHS) participants. Incident lung cancer was assessed as time to event diagnoses. We conducted mediation analysis, including validation with DNAm and paired gene expression data from the Framingham Heart Study (FHS). In the SHS, current versus never smoking and pack-years single-mediator models showed, respectively, 29 and 21 differentially methylated positions (DMPs) for lung cancer with statistically significant mediated effects (14 of 20 available, and five of 14 available, positions, replicated, respectively, in FHS). In FHS, replicated DMPs showed gene expression downregulation largely in trans, and were related to biological pathways in cancer. The multimediator model identified that DMPs annotated to the genes AHRR and IER3 jointly explained a substantial proportion of lung cancer. Thus, the association of smoking with lung cancer was partly explained by differences in baseline blood DNAm at few relevant sites. Experimental studies are needed to confirm the biological role of identified eQTMs and to evaluate potential implications for early detection and control of lung cancer.
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Affiliation(s)
- Arce Domingo-Relloso
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain; Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA; Department of Statistics and Operations Research, University of Valencia, Spain.
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, And Blood Institute, National Institutes of Health, Bethesda, MD, USA; Framingham Heart Study, Framingham, MA, USA
| | - Zulema Rodriguez-Hernandez
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Lies Lahousse
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University, Baltimore, USA; Department of Epidemiology, Johns Hopkins University, Baltimore, USA
| | | | - Jason G Umans
- MedStar Health Research Institute, Washington DC, USA; Georgetown-Howard Universities Center for Clinical and Translational Science, Washington DC, USA
| | - Lyle G Best
- Missouri Breaks Industries and Research Inc., Eagle Butte, SD, USA
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, MA, USA; University of Massachusetts Medical School, Worcester, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, MA, USA; Boston University School of Public Health, Boston, MA, USA
| | - Jiantao Ma
- Framingham Heart Study, Framingham, MA, USA; Tufts University Friedman School of Nutrition Science and Policy, Boston, MA, USA
| | - Chen Yao
- Framingham Heart Study, Framingham, MA, USA; Bristol Myers Squibb, Cambridge, MA, USA
| | - Allan Jerolon
- Université Paris Cité, CNRS, MAP5, F-75006, Paris, France
| | - Jose D Bermudez
- Department of Statistics and Operations Research, University of Valencia, Spain
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Dorothy A Rhoades
- Stephenson Cancer Center, University of Oklahoma Health Sciences Department of Medicine, Oklahoma City, OK, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, And Blood Institute, National Institutes of Health, Bethesda, MD, USA; Framingham Heart Study, Framingham, MA, USA
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Maria Tellez-Plaza
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
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5
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Sato A, Ishigami A. Effects of heated tobacco product aerosol extracts on DNA methylation and gene transcription in lung epithelial cells. Toxicol Appl Pharmacol 2023; 475:116637. [PMID: 37499768 DOI: 10.1016/j.taap.2023.116637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
AIMS Smoking causes DNA methylation (DNAm) alterations that lead to lung cancer development. Although the use of heated tobacco products (HTPs) has recently increased, their impact on health remains unclear. This study aimed to evaluate the effects of HTPs on DNAm and gene transcription in human lung epithelial cells in vitro. MAIN METHODS Human lung adenocarcinoma (A549) cells with type II alveolar epithelial characteristics were treated with aerosol extracts of two HTPs or a smoke extract of combustible reference cigarette (RC). Global 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels were quantified using dot blot analysis. Furthermore, reduced representation of bisulfite sequencing, DNA microarray, and quantitative PCR analyses were performed to determine CpG methylation and gene transcription changes induced by HTP and RC. KEY FINDINGS Global 5-mC and 5-hmC levels were decreased by the RC extract but not the HTP extracts. However, an HTP extract altered the CpG methylation pattern, and Gene Ontology enrichment analysis of the differentially methylated regions of the RC and HTP groups showed a similar pattern. The HTP extract affected gene expression, albeit to a lesser extent than the RC extract. In particular, the HTP extract markedly affected the mRNA expression and promoter methylation of cytochrome P450 family 1 subfamily A member 1 (CYP1A1), which is associated with carcinogenic risk. SIGNIFICANCE The study results suggest that HTPs as well as conventional combustible cigarettes can alter CpG methylation and gene transcription in lung epithelial cells.
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Affiliation(s)
- Ayami Sato
- Molecular Regulation of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo 173-0015, Japan
| | - Akihito Ishigami
- Molecular Regulation of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo 173-0015, Japan.
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Morin A, Thompson EE, Helling BA, Shorey-Kendrick LE, Faber P, Gebretsadik T, Bacharier LB, Kattan M, O'Connor GT, Rivera-Spoljaric K, Wood RA, Barnes KC, Mathias RA, Altman MC, Hansen K, McEvoy CT, Spindel ER, Hartert T, Jackson DJ, Gern JE, McKennan CG, Ober C. A functional genomics pipeline to identify high-value asthma and allergy CpGs in the human methylome. J Allergy Clin Immunol 2023; 151:1609-1621. [PMID: 36754293 PMCID: PMC10859971 DOI: 10.1016/j.jaci.2022.12.828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/24/2022] [Accepted: 12/20/2022] [Indexed: 02/09/2023]
Abstract
BACKGROUND DNA methylation of cytosines at cytosine-phosphate-guanine (CpG) dinucleotides (CpGs) is a widespread epigenetic mark, but genome-wide variation has been relatively unexplored due to the limited representation of variable CpGs on commercial high-throughput arrays. OBJECTIVES To explore this hidden portion of the epigenome, this study combined whole-genome bisulfite sequencing with in silico evidence of gene regulatory regions to design a custom array of high-value CpGs. This study focused on airway epithelial cells from children with and without allergic asthma because these cells mediate the effects of inhaled microbes, pollution, and allergens on asthma and allergic disease risk. METHODS This study identified differentially methylated regions from whole-genome bisulfite sequencing in nasal epithelial cell DNA from a total of 39 children with and without allergic asthma of both European and African ancestries. This study selected CpGs from differentially methylated regions, previous allergy or asthma epigenome-wide association studies (EWAS), or genome-wide association study loci, and overlapped them with functional annotations for inclusion on a custom Asthma&Allergy array. This study used both the custom and EPIC arrays to perform EWAS of allergic sensitization (AS) in nasal epithelial cell DNA from children in the URECA (Urban Environment and Childhood Asthma) birth cohort and using the custom array in the INSPIRE [Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure] birth cohort. Each CpG on the arrays was assigned to its nearest gene and its promotor capture Hi-C interacting gene and performed expression quantitative trait methylation (eQTM) studies for both sets of genes. RESULTS Custom array CpGs were enriched for intermediate methylation levels compared to EPIC CpGs. Intermediate methylation CpGs were further enriched among those associated with AS and for eQTMs on both arrays. CONCLUSIONS This study revealed signature features of high-value CpGs and evidence for epigenetic regulation of genes at AS EWAS loci that are robust to race/ethnicity, ascertainment, age, and geography.
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Affiliation(s)
- Andréanne Morin
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Emma E Thompson
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | | | - Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Ore
| | - Pieter Faber
- Genomics Core, University of Chicago, Chicago, Ill
| | - Tebeb Gebretsadik
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn
| | - Leonard B Bacharier
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn
| | - Meyer Kattan
- Department of Pediatrics, Columbia University Medical Center, New York, NY
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Mass
| | | | - Robert A Wood
- Department of Pediatrics, Johns Hopkins University, Baltimore, Md
| | | | | | - Matthew C Altman
- Systems Immunology Division, Benaroya Research Institute Systems, Seattle, Wash; Department of Medicine, University of Washington, Seattle, Wash
| | - Kasper Hansen
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Md
| | - Cindy T McEvoy
- Department of Pediatrics, Oregon Health and Science University, Portland, Ore
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Ore
| | - Tina Hartert
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Chris G McKennan
- Department of Statistics, University of Pittsburgh, Pittsburgh, Pa.
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill.
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7
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Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
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Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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8
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Li P, Liu S, Du L, Mohseni G, Zhang Y, Wang C. Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer. Clin Epigenetics 2022; 14:118. [PMID: 36153611 PMCID: PMC9509651 DOI: 10.1186/s13148-022-01337-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is quite poor. Although low-dose computed tomography (LDCT) is a routine clinical examination for early detection of LC, the false-positive rate is over 90%. As one of the intensely studied epigenetic modifications, DNA methylation plays a key role in various diseases, including cancer and other diseases. Hypermethylation in tumor suppressor genes or hypomethylation in oncogenes is an important event in tumorigenesis. Remarkably, DNA methylation usually occurs in the very early stage of malignant tumors. Thus, DNA methylation analysis may provide some useful information about the early detection of LC. In recent years, liquid biopsy has developed rapidly. Liquid biopsy can detect and monitor both primary and metastatic malignant tumors and can reflect tumor heterogeneity. Moreover, it is a minimally invasive procedure, and it causes less pain for patients. This review summarized various liquid biopsies based on DNA methylation for LC. At first, we briefly discussed some emerging technologies for DNA methylation analysis. Subsequently, we outlined cell-free DNA (cfDNA), sputum, bronchoalveolar lavage fluid, bronchial aspirates, and bronchial washings DNA methylation-based liquid biopsy for the early detection of LC. Finally, the prognostic value of DNA methylation in cfDNA and sputum and the diagnostic value of other DNA methylation-based liquid biopsies for LC were also analyzed.
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9
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Munawar Z, Ahmad F, Awadh Alanazi S, Nisar KS, Khalid M, Anwar M, Murtaza K. Predicting the prevalence of lung cancer using feature transformation techniques. Egyptian Informatics Journal 2022. [DOI: 10.1016/j.eij.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Sohrabi SS, Rashidipour M, Sohrabi SM, Hadizadeh M, Shams MH, Mohammadi M. Genome-wide evaluation of transcriptomic responses of human tissues to smoke: A systems biology study. Gene X 2022; 820:146114. [PMID: 35077830 DOI: 10.1016/j.gene.2021.146114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
The harmful compounds in various sources of smoke threaten human health. So far, many studies have investigated the effects of compounds of smoke on transcriptome changes in different human tissues. However, no study has been conducted on the effects of these compounds on transcriptome changes in different human tissues simultaneously. Hence, the present study was conducted to identify smoke-related genes (SRGs) and their response mechanisms to smoke in various human cells and tissues using systems biology based methods. A total of 6,484 SRGs were identified in the studied tissues, among which 4,095 SRGs were up-regulated and 2,389 SRGs were down-regulated. Totally, 459 SRGs were smoke-related transcription factors (SRTFs). Gene regulatory network analysis showed that the studied cells and tissues have different gene regulation and responses to compounds of smoke. The comparison of different tissues revealed no common SRG among the all studied tissues. However, the CYP1B1 gene was common among seven cells and tissues, and had the same expression trend. Network analysis showed that the CYP1B1 is a hub gene among SRGs in various cells and tissues. To the best of our knowledge, for the first time, our results showed that compounds of smoke induce and increase the expression of CYP1B1 key gene in all target and non-target tissues of human. Moreover, despite the specific characteristics of CYP1B1 gene and its identical expression trend in target and non-target tissues, it can be used as a biomarker for diagnosis and prognosis.
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Affiliation(s)
- Seyed Sajad Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, Iran; Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Marzieh Rashidipour
- Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; Nutritional Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Morteza Hadizadeh
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad-Hossein Shams
- Department of Immunology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohsen Mohammadi
- Razi Herbal Medicines Research Center and Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran
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11
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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12
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Huang X, Wu B, Zhang F, Chen F, Zhang Y, Guo H, Zhang H. Epigenetic Biomarkers Screening of Non-Coding RNA and DNA Methylation Based on Peripheral Blood Monocytes in Smokers. Front Genet 2022; 13:766553. [PMID: 35233217 PMCID: PMC8882369 DOI: 10.3389/fgene.2022.766553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
This study aims to use bioinformatics methods to determine the epigenetic changes in microRNA expression and DNA methylation caused by cigarette smoking. The data of mRNA, miRNA expression, and methylation microarray were obtained from the GEO database to filter differentially expressed genes (DEGs), differentially expressed miRNAs (DEMs), and methylated CpG probes (DMPs) through the limma package. The R clusterProfile package was used for functional annotation and enrichment analysis. The protein-protein interaction (PPI) network was constructed by the String database and visualized in Cytoscape software. Starbase database was employed to predict lncRNA and CirRNA based on the sequence of miRNA, and to establish a regulatory network of ceRNA. By overlapping DEG and DEM, 107 down-miRNA-targeted up-regulated genes and 65 up-miRNA-target down-regulated genes were obtained, which were mainly enriched in autophagy signaling pathways and protein ubiquitination pathways, respectively. In addition, 324 genes with low methylation and high expression and 204 genes with high methylation and low expression were respectively related to the degeneration of the nervous system and the function of the cardiovascular system. Interestingly, 43 genes were up-regulated under the dual regulation of reduced miRNA and hypomethylation, while 14 genes were down-regulated under the dual regulation of increased miRNA and hypermethylation. Ten chemicals have been identified as putative therapeutic agents for pathological conditions caused by smoking. In addition, among these genes, HSPA4, GRB2, PRKCA, and BCL2L1 could play a fundamental role in related diseases caused by smoking and may be used as the biomarkers for precise diagnosis and targets for future therapies of smoking-related diseases.
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Affiliation(s)
- Xiaowei Huang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bian Wu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Fangxue Zhang
- Knee Surgery Department of the Institute of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Peking University, Beijing, China
| | - Fancheng Chen
- Department of Orthopaedics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huizhi Guo
- The First Institute of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongtao Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Hongtao Zhang,
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13
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Johnson C, Mullen DJ, Selamat SA, Campan M, Offringa IA, Marconett CN. The Sulfotransferase SULT1C2 Is Epigenetically Activated and Transcriptionally Induced by Tobacco Exposure and Is Associated with Patient Outcome in Lung Adenocarcinoma. Int J Environ Res Public Health 2021; 19:416. [PMID: 35010676 PMCID: PMC8744592 DOI: 10.3390/ijerph19010416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 01/03/2023]
Abstract
Lung cancer is the leading cause of cancer-related death. Tobacco exposure is associated with 80-90% of lung cancer cases. The SULT1C2 sulfotransferase modifies xenobiotic compounds to enhance secretion but can also render these compounds carcinogenic. To determine if SULT1C2 contributes to tobacco-related carcinogenesis in the lung, we analyzed the expression and epigenetic state of SULT1C2 in human lung adenocarcinoma (LUAD) samples and in LUAD cell lines exposed to cigarette smoke condensate (CSC). SULT1C2 expression was significantly positively correlated to overall LUAD patient survival in smokers, was elevated in LUAD tumors compared to adjacent non-tumor lung, and was significantly correlated with levels of patient exposure to tobacco smoke. SULT1C2 promoter DNA methylation was inversely correlated with expression in LUAD, and hypomethylation of the SULT1C2 promoter was observed in Asian patients, as compared to Caucasians. In vitro analysis of LUAD cell lines indicates that CSC stimulates expression of SULT1C2 in a dose-dependent and cell-line-specific manner. In vitro methylation of the SULT1C2 promoter significantly decreased transcriptional activity of a reporter plasmid, and SULT1C2 expression was activated by the DNA demethylating agent 5-Aza-2'-deoxycytidine in a cell line in which the SULT1C2 promoter was hypermethylated. An aryl hydrocarbon receptor (AHR) binding site was detected spanning critical methylation sites upstream of SULT1C2. CSC exposure significantly increased AHR binding to this predicted binding site in the SULT1C2 promoter in multiple lung cell lines. Our data suggest that CSC exposure leads to activation of the AHR transcription factor, increased binding to the SULT1C2 promoter, and upregulation of SULT1C2 expression and that this process is inhibited by DNA methylation at the SULT1C2 locus. Additionally, our results suggest that the level of SULT1C2 promoter methylation and gene expression in normal lung varies depending on the race of the patient, which could in part reflect the molecular mechanisms of racial disparities seen in lung cellular responses to cigarette smoke exposure.
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Affiliation(s)
- Candace Johnson
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Daniel J. Mullen
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Suhaida A. Selamat
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Mihaela Campan
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Ite A. Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
| | - Crystal N. Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA; (C.J.); (D.J.M.); (S.A.S.); (M.C.); (I.A.O.)
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9520, USA
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14
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Cui Y, Luo C, Luo L, Yu Z. High-Dimensional Mediation Analysis Based on Additive Hazards Model for Survival Data. Front Genet 2021; 12:771932. [PMID: 35003213 PMCID: PMC8734376 DOI: 10.3389/fgene.2021.771932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Mediation analysis has been extensively used to identify potential pathways between exposure and outcome. However, the analytical methods of high-dimensional mediation analysis for survival data are still yet to be promoted, especially for non-Cox model approaches. We propose a procedure including "two-step" variable selection and indirect effect estimation for the additive hazards model with high-dimensional mediators. We first apply sure independence screening and smoothly clipped absolute deviation regularization to select mediators. Then we use the Sobel test and the BH method for indirect effect hypothesis testing. Simulation results demonstrate its good performance with a higher true-positive rate and accuracy, as well as a lower false-positive rate. We apply the proposed procedure to analyze DNA methylation markers mediating smoking and survival time of lung cancer patients in a TCGA (The Cancer Genome Atlas) cohort study. The real data application identifies four mediate CpGs, three of which are newly found.
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Affiliation(s)
- Yidan Cui
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Chengwen Luo
- Public Laboratory, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Linghao Luo
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Camiña N, Penning TM. Genetic and epigenetic regulation of the NRF2-KEAP1 pathway in human lung cancer. Br J Cancer 2021; 126:1244-1252. [PMID: 34845361 DOI: 10.1038/s41416-021-01642-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 10/23/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
Electrophilic and oxidative stress is caused when homeostatic mechanisms are disrupted. A major defense mechanism involves the activation of the nuclear factor erythroid 2-related factor 2 (NRF2) transcription factor encoded by the NFE2L2 gene, which can accelerate the detoxification of electrophilic carcinogens and prevent cancer and on the other hand in certain exposure contexts may exacerbate the carcinogenic process. NRF2-target genes activated under these conditions can be used as biomarkers of stress signalling, while activation of NRF2 can also reveal the epigenetic mechanisms that modulate NFE2L2 expression. Epigenetic mechanisms that regulate NFE2L2 and the gene for its adaptor protein KEAP1 include DNA methylation, histone modifications and microRNA. Understanding the activation of the NRF2-KEAP1 signalling pathway in human lung cancer, its epigenetic regulation and its role in oncogenesis is the subject of this review.
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Affiliation(s)
- Nuria Camiña
- Department of Systems Pharmacology & Translational Therapeutics, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Trevor M Penning
- Department of Systems Pharmacology & Translational Therapeutics, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Keshawarz A, Joehanes R, Guan W, Huan T, DeMeo DL, Grove ML, Fornage M, Levy D, O'Connor G. Longitudinal change in blood DNA epigenetic signature after smoking cessation. Epigenetics 2021; 17:1098-1109. [PMID: 34570667 DOI: 10.1080/15592294.2021.1985301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cigarette smoking is associated with epigenetic changes that may be reversible following smoking cessation. Whole blood DNA methylation was evaluated in Framingham Heart Study Offspring (n = 169) and Third Generation (n = 30) cohort participants at two study visits 6 years apart and in Atherosclerosis Risk in Communities (ARIC) study (n = 222) participants at two study visits 20 years apart. Changes in DNA methylation (delta β values) at 483,565 cytosine-phosphate-guanine (CpG) sites and differentially methylated regions (DMRs) were compared between participants who were current, former, or never smokers at both visits (current-current, former-former, never-never, respectively), versus those who quit in the interim (current-former). Interim quitters had more hypermethylation at four CpGs annotated to AHRR, one CpG annotated to F2RL3, and one intergenic CpG (cg21566642) compared with current-current smokers (FDR < 0.02 for all), and two significant DMRs were identified. While there were no significant differentially methylated CpGs in the comparison of interim quitters and former-former smokers, 106 DMRs overlapping with small nucleolar RNA were identified. As compared with all non-smokers, current-current smokers additionally had more hypermethylation at two CpG sites annotated to HIVEP3 and TMEM126A, respectively, and another intergenic CpG (cg14339116). Gene transcripts associated with smoking cessation were implicated in immune responses, cell homoeostasis, and apoptosis. Smoking cessation is associated with early reversion of blood DNA methylation changes at CpG sites annotated to AHRR and F2RL3 towards those of never smokers. Associated gene expression suggests a role of longitudinal smoking-related DNA methylation changes in immune response processes.
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Affiliation(s)
- Amena Keshawarz
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.,Framingham Heart Study, Framingham, MA, USA
| | - Roby Joehanes
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.,Framingham Heart Study, Framingham, MA, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, MA, USA.,Department of Ophthalmology and Visual Sciences, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Myriam Fornage
- McGovern Medical School and Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - George O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, USA
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17
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Zeng P, Shao Z, Zhou X. Statistical methods for mediation analysis in the era of high-throughput genomics: Current successes and future challenges. Comput Struct Biotechnol J 2021; 19:3209-3224. [PMID: 34141140 PMCID: PMC8187160 DOI: 10.1016/j.csbj.2021.05.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mediation analysis investigates the intermediate mechanism through which an exposure exerts its influence on the outcome of interest. Mediation analysis is becoming increasingly popular in high-throughput genomics studies where a common goal is to identify molecular-level traits, such as gene expression or methylation, which actively mediate the genetic or environmental effects on the outcome. Mediation analysis in genomics studies is particularly challenging, however, thanks to the large number of potential mediators measured in these studies as well as the composite null nature of the mediation effect hypothesis. Indeed, while the standard univariate and multivariate mediation methods have been well-established for analyzing one or multiple mediators, they are not well-suited for genomics studies with a large number of mediators and often yield conservative p-values and limited power. Consequently, over the past few years many new high-dimensional mediation methods have been developed for analyzing the large number of potential mediators collected in high-throughput genomics studies. In this work, we present a thorough review of these important recent methodological advances in high-dimensional mediation analysis. Specifically, we describe in detail more than ten high-dimensional mediation methods, focusing on their motivations, basic modeling ideas, specific modeling assumptions, practical successes, methodological limitations, as well as future directions. We hope our review will serve as a useful guidance for statisticians and computational biologists who develop methods of high-dimensional mediation analysis as well as for analysts who apply mediation methods to high-throughput genomics studies.
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Affiliation(s)
- Ping Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
- Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Zhonghe Shao
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor 48109, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor 48109, MI, USA
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18
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Hu X, Tian K. [A Review of Epigenetic Modifications Regulate MicroRNA Expression in Lung Cancer]. Zhongguo Fei Ai Za Zhi 2021; 23:582-588. [PMID: 32702792 PMCID: PMC7406441 DOI: 10.3779/j.issn.1009-3419.2020.102.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
肺癌是全世界癌症引起死亡中较常见的一种。近年来,参与肺癌发病的分子机制被逐步揭开,但是其发生发展的确切机制并未完全阐明。其中微小RNAs(microRNAs, miRNAs)是一种短小并且广泛存在于植物、病毒及人类等各种生物中的内源性单链的非编码RNA。miRNAs在正常肺组织中发挥着多种功能,它参与细胞生长、代谢、增殖和分化等众多生物学过程。而miRNAs的异常表达与肺肿瘤的发生、发展、侵袭、转移相关。因此,miRNAs可被视为一种新的生物标志物。与编码蛋白质的基因类似,miRNA的表达和功能受多种因素以及表观遗传网络(包括DNA甲基化和组蛋白修饰机制)的调控。此外,miRNAs本身也能调控那些表观遗传修饰的关键酶来影响表观修饰。miRNA与表观基因学之间的相互联系将有助于我们研发以miRNA为导向的肺癌诊断、治疗和预后的方案。
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Affiliation(s)
- Xilin Hu
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China
| | - Kaihua Tian
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China
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19
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Reddy KD, Lan A, Boudewijn IM, Rathnayake SNH, Koppelman GH, Oliver BG, van den Berge M, Faiz A. Current-Smoking alters Gene Expression and DNA Methylation in the Nasal Epithelium of Asthmatics. Am J Respir Cell Mol Biol 2021; 65:366-377. [PMID: 33989148 DOI: 10.1165/rcmb.2020-0553oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Current-smoking contributes to worsened asthma prognosis, more severe symptoms and limits the beneficial effects of corticosteroids. As the nasal epithelium can reflect smoking-induced changes in the lower airways, it is a relevant source to investigate changes in gene expression and DNA methylation. This study explores gene expression and DNA methylation changes in current and ex-smokers with asthma. Matched gene expression and epigenome-wide DNA methylation samples collected from nasal brushings of 55 patients enrolled in a clinical trial investigation of current and ex-smoker asthma patients were analysed. Differential gene expression and DNA methylation analyses were conducted comparing current- vs ex-smokers. Expression quantitative trait methylation (eQTM) analysis was completed to explore smoking relevant genes by CpG sites that differ between current and ex-smokers. To investigate the relevance of the smoking-associated DNA methylation changes for the lower airways, significant CpG sites were explored in bronchial biopsies from patients who had stopped smoking. 809 genes and 18,814 CpG sites were differentially associated with current-smoking in the nose. The cis-eQTM analysis uncovered 171 CpG sites whose methylation status associated with smoking-related gene expression, including AHRR, ALDH3A1, CYP1A1 and CYP1B1. Methylation status of CpG sites altered by current-smoking reversed with one-year smoking cessation. We confirm current-smoking alters epigenetic patterns and affects gene expression in the nasal epithelium of asthma patients, which is partially reversible in bronhcial biopsies after smoking cessation. We demonstrate the ability to discern molecular changes in the nasal epithelium, presenting this as a tool in future investigations into disease-relevant effects of tobacco smoke.
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Affiliation(s)
- Karosham D Reddy
- Woolcock Institute of Medical Research, 104349, Cell Biology, Glebe, New South Wales, Australia.,University of Technology Sydney, 1994, School of Life Sciences, Ultimo, New South Wales, Australia;
| | - Andy Lan
- University of Groningen, 3647, Department of Pulmonary Diseases, Groningen, Netherlands.,University of Groningen, 3647, GRIAC Research Institute, Groningen, Netherlands
| | - Ilse M Boudewijn
- University of Groningen, 3647, Department of Pulmonary Diseases, Groningen, Netherlands.,University of Groningen, 3647, GRIAC Research Insitute, Groningen, Netherlands
| | - Senani N H Rathnayake
- University of Technology Sydney, 1994, Respiratory Bioinformatics and Molecular Biology (RBMB) group,, Sydney, New South Wales, Australia
| | - Gerard H Koppelman
- University of Groningen, 3647, University Medical Center Groningen, Department of Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, Netherlands.,University of Groningen, 3647, University Medical Center Groningen, GRIAC research institute, Groningen, Netherlands
| | - Brian G Oliver
- Woolcock Institute of Medical Research, 104349, Glebe, New South Wales, Australia.,University of Technology Sydney, 1994, School of Medical and Molecular Biosciences, Sydney, New South Wales, Australia
| | - Maarten van den Berge
- University of Groningen, 3647, University Medical Center, Department of Pulmonary Diseases, Groningen, Netherlands.,University Medical Center Göttingen, 84922, Groningen Research Institute for Asthma and COPD (GRIAC), Gottingen, Germany
| | - Alen Faiz
- University of Technology Sydney, 1994, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, New South Wales, Australia
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20
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Lee SB, Park YS, Sung JS, Lee JW, Kim B, Kim YH. Tumor Suppressor miR-584-5p Inhibits Migration and Invasion in Smoking Related Non-Small Cell Lung Cancer Cells by Targeting YKT6. Cancers (Basel) 2021; 13:1159. [PMID: 33800298 DOI: 10.3390/cancers13051159] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Cigarette smoke is a major carcinogen that causes lung cancer and induces DNA methylation. DNA methylation regulates the expression of microRNA (miRNAs), which are important regulators of cancer biology. However, the association between smoking and miRNAs has not been fully elucidated in smoking-related lung carcinogenesis. In this study, we found that miR-584-5p expression was downregulated with cancer progression using a lung carcinogenesis model cell line. Moreover, we demonstrated that miR-584-5p is downregulated by the methylation of its promoter region and that it suppresses migration and invasion by targeting YKT6 in smoking-related non-small cell lung cancer (NSCLC) cells. Our results provide a better understanding of the underlying changes in miRNA expression in smoking-related lung carcinogenesis and suggest that miR-584-5p is a potential molecular biomarker for smoking-related NSCLC. Abstract Cigarette smoke (CS) affects the expression of microRNAs (miRNAs), which are important regulators of gene expression by inducing DNA methylation. However, the effects of smoking on miRNA expression have not been fully elucidated in smoking-related lung carcinogenesis. Therefore, in this study, to investigate the change of miRNA expression pattern and to identify tumor suppressor miRNAs by smoking in lung carcinogenesis, we used lung carcinogenesis model cell lines that, derived from a murine xenograft model with human bronchial epithelial cells (BEAS-2B), exposed CS or not. The microarray analysis revealed that miR-584-5p expression was downregulated with cancer progression in lung carcinogenesis model cell lines. We confirmed by pyrosequencing that the methylation level of the miR-584-5p promoter increased with cancer progression. In vitro and in vivo experiments showed that miR-584-5p suppressed migration and invasion in non-small cell lung cancer (NSCLC) cells by targeting YKT6. Furthermore, we showed that high level of YKT6 was associated with a poor survival rate in NSCLC patients with a history of smoking. These results suggest that miR-584-5p acts as a tumor suppressor and is a potential molecular biomarker for smoking-related NSCLC.
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21
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Campbell KA, Colacino JA, Park SK, Bakulski KM. Cell Types in Environmental Epigenetic Studies: Biological and Epidemiological Frameworks. Curr Environ Health Rep 2021; 7:185-197. [PMID: 32794033 DOI: 10.1007/s40572-020-00287-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW This article introduces the roles of perinatal DNA methylation in human health and disease, highlights the challenges of tissue and cellular heterogeneity to studying DNA methylation, summarizes approaches to overcome these challenges, and offers recommendations in conducting research in environmental epigenetics. RECENT FINDINGS Epigenetic modifications are essential for human development and are labile to environmental influences, especially during gestation. Epigenetic dysregulation is also a hallmark of multiple diseases. Environmental epigenetic studies routinely measure DNA methylation in readily available tissues. However, tissues and cell types exhibit specific epigenetic patterning and heterogeneity between samples complicates epigenetic studies. Failure to account for cell-type heterogeneity limits identification of biological mechanisms and biases study results. Tissue-level epigenetic measures represent a convolution of epigenetic signals from individual cell types. Tissue-specific epigenetics is an evolving field and the use of disease-affected target, surrogate, or multiple tissues has inherent trade-offs and affects inference. Likewise, experimental and bioinformatic approaches to accommodate cell-type heterogeneity have varying assumptions and inherent trade-offs that affect inference. The relationships between exposure, disease, tissue-level DNA methylation, cell type-specific DNA methylation, and cell-type heterogeneity must be carefully considered in study design and analysis. Causal diagrams can inform study design and analytic strategies. Properly addressing cell-type heterogeneity limits sources of potential bias, avoids misinterpretation of study results, and allows investigators to distinguish shifts in cell-type proportions from direct changes to cellular epigenetic programming, both of which provide insights into environmental disease etiology and aid development of novel methods for prevention and treatment.
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Affiliation(s)
- Kyle A Campbell
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Sung Kyun Park
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
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22
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Grieshober L, Graw S, Barnett MJ, Thornquist MD, Goodman GE, Chen C, Koestler DC, Marsit CJ, Doherty JA. AHRR methylation in heavy smokers: associations with smoking, lung cancer risk, and lung cancer mortality. BMC Cancer 2020; 20:905. [PMID: 32962699 PMCID: PMC7510160 DOI: 10.1186/s12885-020-07407-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A low level of methylation at cg05575921 in the aryl-hydrocarbon receptor repressor (AHRR) gene is robustly associated with smoking, and some studies have observed associations between cg05575921 methylation and increased lung cancer risk and mortality. To prospectively examine whether decreased methylation at cg05575921 may identify high risk subpopulations for lung cancer screening among heavy smokers, and mortality in cases, we evaluated associations between cg05575921 methylation and lung cancer risk and mortality, by histotype, in heavy smokers. METHODS The β-Carotene and Retinol Efficacy Trial (CARET) included enrollees ages 45-69 with ≥ 20 pack-year smoking histories and/or occupational asbestos exposure. A subset of CARET participants had cg05575921 methylation available from HumanMethylationEPIC assays of blood collected on average 4.3 years prior to lung cancer diagnosis in cases. Cg05575921 methylation β-values were treated continuously for a 10% methylation decrease and as quintiles, where quintile 1 (Q1, referent) represents high methylation and Q5, low methylation. We used conditional logistic regression models to examine lung cancer risk overall and by histotype in a nested case-control study including 316 lung cancer cases (diagnosed through 2005) and 316 lung cancer-free controls matched on age (±5 years), sex, race/ethnicity, enrollment year, current/former smoking, asbestos exposure, and follow-up time. Mortality analyses included 372 lung cancer cases diagnosed between 1985 and 2013 with available methylation data. We used Cox proportional hazards models to examine mortality overall and by histotype. RESULTS Decreased cg05575921 methylation was strongly associated with smoking, even in our population of heavy smokers. We did not observe associations between decreased pre-diagnosis cg05575921 methylation and increased lung cancer risk, overall or by histotype. We observed linear increasing trends for lung cancer-specific mortality across decreasing cg05575921 methylation quintiles for adenocarcinoma and small cell carcinoma (P-trends = 0.01 and 0.04, respectively). CONCLUSIONS In our study of heavy smokers, decreased cg05575921 methylation was strongly associated with smoking but not increased lung cancer risk. The observed association between cg05575921 methylation and increased mortality in adenocarcinoma and small cell histotypes requires further examination. Our results do not support using decreased cg05575921 methylation as a biomarker for lung cancer screening risk stratification.
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Affiliation(s)
- Laurie Grieshober
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Room 4746, Salt Lake City, UT, 84112, USA.
| | - Stefan Graw
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Matt J Barnett
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark D Thornquist
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gary E Goodman
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA.,Department of Otolaryngology: Head and Neck Surgery, School of Medicine, University of Washington, Seattle, WA, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jennifer A Doherty
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Room 4746, Salt Lake City, UT, 84112, USA.,Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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23
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Mishra P, Hänninen I, Raitoharju E, Marttila S, Mishra B, Mononen N, Kähönen M, Hurme M, Raitakari O, Törönen P, Holm L, Lehtimäki T. Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study. Biosci Rep 2020; 40:BSR20200596. [PMID: 32583859 PMCID: PMC7340865 DOI: 10.1042/bsr20200596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
Smoking as a major risk factor for morbidity affects numerous regulatory systems of the human body including DNA methylation. Most of the previous studies with genome-wide methylation data are based on conventional association analysis and earliest threshold-based gene set analysis that lacks sensitivity to be able to reveal all the relevant effects of smoking. The aim of the present study was to investigate the impact of active smoking on DNA methylation at three biological levels: 5'-C-phosphate-G-3' (CpG) sites, genes and functionally related genes (gene sets). Gene set analysis was done with mGSZ, a modern threshold-free method previously developed by us that utilizes all the genes in the experiment and their differential methylation scores. Application of such method in DNA methylation study is novel. Epigenome-wide methylation levels were profiled from Young Finns Study (YFS) participants' whole blood from 2011 follow-up using Illumina Infinium HumanMethylation450 BeadChips. We identified three novel smoking related CpG sites and replicated 57 of the previously identified ones. We found that smoking is associated with hypomethylation in shore (genomic regions 0-2 kilobases from CpG island). We identified smoking related methylation changes in 13 gene sets with false discovery rate (FDR) ≤ 0.05, among which is olfactory receptor activity, the flagship novel finding of the present study. Overall, we extended the current knowledge by identifying: (i) three novel smoking related CpG sites, (ii) similar effects as aging on average methylation in shore, and (iii) a novel finding that olfactory receptor activity pathway responds to tobacco smoke and toxin exposure through epigenetic mechanisms.
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Affiliation(s)
- Pashupati P. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Ismo Hänninen
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Saara Marttila
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere University, Tampere, Finland
| | - Binisha H. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Mikko Hurme
- Gerontology Research Center (GEREC), Tampere University, Tampere, Finland
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Petri Törönen
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland
| | - Liisa Holm
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
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24
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Zhu T, Brown AP, Ji H. The Emerging Role of Ten-Eleven Translocation 1 in Epigenetic Responses to Environmental Exposures. Epigenet Insights 2020; 13:2516865720910155. [PMID: 32166220 PMCID: PMC7054729 DOI: 10.1177/2516865720910155] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
Mounting evidence from epidemiological studies and animal models has linked exposures to environmental factors to changes in epigenetic markers, especially in DNA methylation. These epigenetic changes may lead to dysregulation of molecular processes and functions and mediate the impact of environmental exposures in complex diseases. However, detailed molecular events that result in epigenetic changes following exposures remain unclear. Here, we review the emerging evidence supporting a critical role of ten-eleven translocation 1 (TET1) in mediating these processes. Targeting TET1 and its associated pathways may have therapeutic potential in alleviating negative impacts of environmental exposures, preventing and treating exposure-related diseases.
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Affiliation(s)
- Tao Zhu
- California National Primate Research
Center, University of California, Davis, Davis, CA, USA
| | - Anthony P Brown
- California National Primate Research
Center, University of California, Davis, Davis, CA, USA
| | - Hong Ji
- California National Primate Research
Center, University of California, Davis, Davis, CA, USA
- Department of Anatomy, Physiology &
Cell Biology, School of Veterinary Medicine, University of California, Davis, CA,
USA
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25
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Abstract
An estimated 70-90% of all cancers are linked to exposure to environmental risk factors. In parallel, the number of stem cells in a tissue has been shown to be a strong predictor of risk of developing cancer in that tissue. Tumors themselves are characterized by an acquisition of "stem cell" characteristics, and a growing body of evidence points to tumors themselves being sustained and propagated by a stem cell-like population. Here, we review our understanding of the interplay between environmental exposures, stem cell biology, and cancer. We provide an overview of the role of stem cells in development, tissue homeostasis, and wound repair. We discuss the pathways and mechanisms governing stem cell plasticity and regulation of the stem cell state, and describe experimental methods for assessment of stem cells. We then review the current understanding of how environmental exposures impact stem cell function relevant to carcinogenesis and cancer prevention, with a focus on environmental and occupational exposures to chemical, physical, and biological hazards. We also highlight key areas for future research in this area, including defining whether the biological basis for cancer disparities is related to effects of complex exposure mixtures on stem cell biology.
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Affiliation(s)
- Tasha Thong
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Chanese A Forté
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Evan M Hill
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
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26
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Abstract
BACKGROUND Lung cancer remains the most common cause of cancer-related death, with a 5-year survival rate of only 18%. In recent years, the development of targeted pharmacological agents and immunotherapies has substantially increased the survival of a subset of patients. However, most patients lack such efficacious therapy and are, thus, treated with classical chemotherapy with poor clinical outcomes. Therefore, novel therapeutic strategies are urgently needed. In recent years, the development of epigenetic assays and their application to cancer research have highlighted the relevance of epigenetic regulation in the initiation, development, progression and treatment of lung cancer. CONCLUSIONS A variety of epigenetic modifications do occur at different steps of lung cancer development, some of which are key to tumor progression. The rise of cutting-edge technologies such as single cell epigenomics is, and will continue to be, crucial for uncovering epigenetic events at a single cell resolution, leading to a better understanding of the biology underlying lung cancer development and to the design of novel therapeutic options. This approach has already led to the development of strategies involving single agents or combined agents targeting epigenetic modifiers, currently in clinical trials. Here, we will discuss the epigenetics of every step of lung cancer development, as well as the translation of these findings into clinical applications.
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Affiliation(s)
| | - Sonia Molina-Pinelo
- Unidad Clínica de Oncología Médica, Radioterapia y Radiofísica, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Avda. Manuel Siurot s/n, 41013, Seville, Spain. .,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
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27
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Affiliation(s)
- Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Srikant Ambatipudi
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
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28
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Affiliation(s)
- Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
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