1
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Ni Q, Ge Z, Li Y, Shatkin G, Fu J, Bera K, Yang Y, Wang Y, Sen A, Wu Y, Vasconcelos ACN, Feinberg AP, Konstantopoulos K, Sun SX. Cytoskeletal activation of NHE1 regulates mechanosensitive cell volume adaptation and proliferation. bioRxiv 2024:2023.08.31.555808. [PMID: 37693593 PMCID: PMC10491192 DOI: 10.1101/2023.08.31.555808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Mammalian cells can rapidly respond to osmotic and hydrostatic pressure imbalances during an environmental change, generating large fluxes of water and ions that alter cell volume within minutes. While the role of ion pump and leak in cell volume regulation has been well-established, the potential contribution of the actomyosin cytoskeleton and its interplay with ion transporters is unclear. We discovered a cell volume regulation system that is controlled by cytoskeletal activation of ion transporters. After a hypotonic shock, normal-like cells (NIH-3T3, MCF-10A, and others) display a slow secondary volume increase (SVI) following the immediate regulatory volume decrease. We show that SVI is initiated by hypotonic stress induced Ca 2+ influx through stretch activated channel Piezo1, which subsequently triggers actomyosin remodeling. The actomyosin network further activates NHE1 through their synergistic linker ezrin, inducing SVI after the initial volume recovery. We find that SVI is absent in cancer cell lines such as HT1080 and MDA-MB-231, where volume regulation is dominated by intrinsic response of ion transporters. A similar cytoskeletal activation of NHE1 can also be achieved by mechanical stretching. On compliant substrates where cytoskeletal contractility is attenuated, SVI generation is abolished. Moreover, cytoskeletal activation of NHE1 during SVI triggers nuclear deformation, leading to a significant, immediate transcriptomic change in 3T3 cells, a phenomenon that is again absent in HT1080 cells. While hypotonic shock hinders ERK-dependent cell growth, cells deficient in SVI are unresponsive to such inhibitory effects. Overall, our findings reveal the critical role of Ca 2+ and actomyosin-mediated mechanosensation in the regulation of ion transport, cell volume, transcriptomics, and cell proliferation.
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Schrott R, Feinberg JI, Newschaffer CJ, Hertz-Picciotto I, Croen LA, Fallin MD, Volk HE, Ladd-Acosta C, Feinberg AP. Exposure to air pollution is associated with DNA methylation changes in sperm. Environ Epigenet 2024; 10:dvae003. [PMID: 38559770 PMCID: PMC10980975 DOI: 10.1093/eep/dvae003] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 04/04/2024]
Abstract
Exposure to air pollutants has been associated with adverse health outcomes in adults and children who were prenatally exposed. In addition to reducing exposure to air pollutants, it is important to identify their biologic targets in order to mitigate the health consequences of exposure. One molecular change associated with prenatal exposure to air pollutants is DNA methylation (DNAm), which has been associated with changes in placenta and cord blood tissues at birth. However, little is known about how air pollution exposure impacts the sperm epigenome, which could provide important insights into the mechanism of transmission to offspring. In the present study, we explored whether exposure to particulate matter less than 2.5 microns in diameter, particulate matter less than 10 microns in diameter, nitrogen dioxide (NO2), or ozone (O3) was associated with DNAm in sperm contributed by participants in the Early Autism Risk Longitudinal Investigation prospective pregnancy cohort. Air pollution exposure measurements were calculated as the average exposure for each pollutant measured within 4 weeks prior to the date of sample collection. Using array-based genome-scale methylation analyses, we identified 80, 96, 35, and 67 differentially methylated regions (DMRs) significantly associated with particulate matter less than 2.5 microns in diameter, particulate matter less than 10 microns in diameter, NO2, and O3, respectively. While no DMRs were associated with exposure to all four pollutants, we found that genes overlapping exposure-related DMRs had a shared enrichment for gene ontology biological processes related to neurodevelopment. Together, these data provide compelling support for the hypothesis that paternal exposure to air pollution impacts DNAm in sperm, particularly in regions implicated in neurodevelopment.
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Affiliation(s)
- Rose Schrott
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Craig J Newschaffer
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, State College, PA 16802, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, University of California, Davis, CA 95616, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - M Daniele Fallin
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Heather E Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Andrew P Feinberg
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Epigenetics, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Wulfridge P, Davidovich A, Salvador AC, Manno GC, Tryggvadottir R, Idrizi A, Huda MN, Bennett BJ, Adams LG, Hansen KD, Threadgill DW, Feinberg AP. Precision pharmacological reversal of strain-specific diet-induced metabolic syndrome in mice informed by epigenetic and transcriptional regulation. PLoS Genet 2023; 19:e1010997. [PMID: 37871105 PMCID: PMC10621921 DOI: 10.1371/journal.pgen.1010997] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/02/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Diet-related metabolic syndrome is the largest contributor to adverse health in the United States. However, the study of gene-environment interactions and their epigenomic and transcriptomic integration is complicated by the lack of environmental and genetic control in humans that is possible in mouse models. Here we exposed three mouse strains, C57BL/6J (BL6), A/J, and NOD/ShiLtJ (NOD), to a high-fat, high-carbohydrate diet, leading to varying degrees of metabolic syndrome. We then performed transcriptomic and genome-wide DNA methylation analyses for each strain and found overlapping but also highly divergent changes in gene expression and methylation upstream of the discordant metabolic phenotypes. Strain-specific pathway analysis of dietary effects revealed a dysregulation of cholesterol biosynthesis common to all three strains but distinct regulatory networks driving this dysregulation. This suggests a strategy for strain-specific targeted pharmacologic intervention of these upstream regulators informed by epigenetic and transcriptional regulation. As a pilot study, we administered the drug GW4064 to target one of these genotype-dependent networks, the farnesoid X receptor pathway, and found that GW4064 exerts strain-specific protection against dietary effects in BL6, as predicted by our transcriptomic analysis. Furthermore, GW4064 treatment induced inflammatory-related gene expression changes in NOD, indicating a strain-specific effect in its associated toxicities as well as its therapeutic efficacy. This pilot study demonstrates the potential efficacy of precision therapeutics for genotype-informed dietary metabolic intervention and a mouse platform for guiding this approach.
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Affiliation(s)
- Phillip Wulfridge
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Adam Davidovich
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Anna C. Salvador
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, Texas, United States of America
- Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
| | - Gabrielle C. Manno
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - M. Nazmul Huda
- Department of Nutrition, University of California, Davis, California, United States of America
- Obesity and Metabolism Research Unit, USDA, ARS, Western Human Nutrition Research Center, Davis, California, United States of America
| | - Brian J. Bennett
- Department of Nutrition, University of California, Davis, California, United States of America
- Obesity and Metabolism Research Unit, USDA, ARS, Western Human Nutrition Research Center, Davis, California, United States of America
| | - L. Garry Adams
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - David W. Threadgill
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, Texas, United States of America
- Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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4
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Lo EK, Mears BM, Maurer HC, Idrizi A, Hansen KD, Thompson ED, Hruban RH, Olive KP, Feinberg AP. Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis. Cancer Res 2023; 83:1905-1916. [PMID: 36989344 PMCID: PMC10239363 DOI: 10.1158/0008-5472.can-22-4052] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/29/2022] [Revised: 02/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is believed to arise from the accumulation of a series of somatic mutations and is also frequently associated with pancreatic intraepithelial neoplasia (PanIN) lesions. However, there is still debate as to whether the cell type-of-origin of PanINs and PDACs in humans is acinar or ductal. As cell type identity is maintained epigenetically, DNA methylation changes during pancreatic neoplasia can provide a compelling perspective to examine this question. Here, we performed laser-capture microdissection on surgically resected specimens from 18 patients to isolate, with high purity, DNA for whole-genome bisulfite sequencing from four relevant cell types: acini, nonneoplastic ducts, PanIN lesions, and PDAC lesions. Differentially methylated regions (DMR) were identified using two complementary analytical approaches: bsseq, which identifies any DMRs but is particularly useful for large block-like DMRs, and informME, which profiles the potential energy landscape across the genome and is particularly useful for identifying differential methylation entropy. Both global methylation profiles and block DMRs clearly implicated an acinar origin for PanINs. At the gene level, PanIN lesions exhibited an intermediate acinar-ductal phenotype resembling acinar-to-ductal metaplasia. In 97.6% of PanIN-specific DMRs, PanIN lesions had an intermediate methylation level between normal and PDAC, which suggests from an information theory perspective that PanIN lesions are epigenetically primed to progress to PDAC. Thus, epigenomic analysis complements histopathology to define molecular progression toward PDAC. The shared epigenetic lineage between PanIN and PDAC lesions could provide an opportunity for prevention by targeting aberrantly methylated progression-related genes. SIGNIFICANCE Analysis of DNA methylation landscapes provides insights into the cell-of-origin of PanIN lesions, clarifies the role of PanIN lesions as metaplastic precursors to human PDAC, and suggests potential targets for chemoprevention.
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Affiliation(s)
- Emily K.W. Lo
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian M. Mears
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - H. Carlo Maurer
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Elizabeth D. Thompson
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Baltimore, MD, USA
| | - Ralph H. Hruban
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Baltimore, MD, USA
| | - Kenneth P. Olive
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, MD, USA
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5
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Cuomo D, Nitcher M, Barba E, Feinberg AP, Rusyn I, Chiu WA, Threadgill DW. Refining risk estimates for lead in drinking water based on the impact of genetics and diet on blood lead levels using the Collaborative Cross mouse population. Toxicol Sci 2023:7181285. [PMID: 37243727 PMCID: PMC10375319 DOI: 10.1093/toxsci/kfad054] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
Blood lead (Pb) level (BLL) is a commonly used biomarker to evaluate associations with health effects. However, interventions to reduce the adverse effects of Pb require relating BLL to external exposure. Moreover, risk mitigation actions need to ensure protection of more susceptible individuals with a greater tendency to accumulate Pb. Because little data is available to quantify inter-individual variability in biokinetics of Pb, we investigated the influence of genetics and diet on BLL in the genetically diverse Collaborative Cross (CC) mouse population. Adult female mice from 49 CC strains received either a standard mouse chow or a chow mimicking the American diet while being provided water ad libitum with 1000 ppm Pb for 4 weeks. In both arms of the study, inter-strain variability was observed; however, in American diet-fed animals, the BLL was greater and more variable. Importantly, the degree of variation in BLL among strains on the American diet was greater (2.3) than the default variability estimate (1.6) used in setting the regulatory standards. Genetic analysis identified suggestive diet-associated haplotypes that were associated with variation in BLL, largely contributed by the PWK/PhJ strain. This study quantified the variation in BLL that is due to genetic background, diet, and their interactions, and observed that it may be greater than that assumed for current regulatory standards for Pb in drinking water. Moreover, this work highlights the need of characterizing inter-individual variation in BLL to ensure adequate public health interventions aimed at reducing human health risks from Pb.
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Affiliation(s)
- Danila Cuomo
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX, USA
| | - Megan Nitcher
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX, USA
| | - Estefania Barba
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Department of Biomedical Engineering, Department of Medicine, Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ivan Rusyn
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - Weihsueh A Chiu
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - David W Threadgill
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX, USA
- Department of Nutrition, Texas A&M University, College Station, TX, USA
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6
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Wulfridge P, Davidovich A, Salvador AC, Manno GC, Tryggvadottir R, Idrizi A, Huda MN, Bennett BJ, Adams LG, Hansen KD, Threadgill DW, Feinberg AP. Precision pharmacological reversal of genotype-specific diet-induced metabolic syndrome in mice informed by transcriptional regulation. bioRxiv 2023:2023.04.25.538156. [PMID: 37163127 PMCID: PMC10168252 DOI: 10.1101/2023.04.25.538156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Diet-related metabolic syndrome is the largest contributor to adverse health in the United States. However, the study of gene-environment interactions and their epigenomic and transcriptomic integration is complicated by the lack of environmental and genetic control in humans that is possible in mouse models. Here we exposed three mouse strains, C57BL/6J (BL6), A/J, and NOD/ShiLtJ (NOD), to a high-fat high-carbohydrate diet, leading to varying degrees of metabolic syndrome. We then performed transcriptomic and genomic DNA methylation analyses and found overlapping but also highly divergent changes in gene expression and methylation upstream of the discordant metabolic phenotypes. Strain-specific pathway analysis of dietary effects reveals a dysregulation of cholesterol biosynthesis common to all three strains but distinct regulatory networks driving this dysregulation. This suggests a strategy for strain-specific targeted pharmacologic intervention of these upstream regulators informed by transcriptional regulation. As a pilot study, we administered the drug GW4064 to target one of these genotype-dependent networks, the Farnesoid X receptor pathway, and found that GW4064 exerts genotype-specific protection against dietary effects in BL6, as predicted by our transcriptomic analysis, as well as increased inflammatory-related gene expression changes in NOD. This pilot study demonstrates the potential efficacy of precision therapeutics for genotype-informed dietary metabolic intervention, and a mouse platform for guiding this approach.
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7
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Feinberg JI, Schrott R, Ladd-Acosta C, Newschaffer CJ, Hertz-Picciotto I, Croen LA, Daniele Fallin M, Feinberg AP, Volk HE. Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort. Mol Psychiatry 2023:10.1038/s41380-023-02046-7. [PMID: 37100868 DOI: 10.1038/s41380-023-02046-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/28/2023]
Abstract
There is a need to consider paternal contributions to autism spectrum disorder (ASD) more strongly. Autism etiology is complex, and heritability is not explained by genetics alone. Understanding paternal gametic epigenetic contributions to autism could help fill this knowledge gap. In the present study, we explored whether paternal autistic traits, and the sperm epigenome, were associated with autistic traits in children at 36 months enrolled in the Early Autism Risk Longitudinal Investigation (EARLI) cohort. EARLI is a pregnancy cohort that recruited and enrolled pregnant women in the first half of pregnancy who already had a child with ASD. After maternal enrollment, EARLI fathers were approached and asked to provide a semen specimen. Participants were included in the present study if they had genotyping, sperm methylation data, and Social Responsiveness Scale (SRS) score data available. Using the CHARM array, we performed genome-scale methylation analyses on DNA from semen samples contributed by EARLI fathers. The SRS-a 65-item questionnaire measuring social communication deficits on a quantitative scale-was used to evaluate autistic traits in EARLI fathers (n = 45) and children (n = 31). We identified 94 significant child SRS-associated differentially methylated regions (DMRs), and 14 significant paternal SRS-associated DMRs (fwer p < 0.05). Many child SRS-associated DMRs were annotated to genes implicated in ASD and neurodevelopment. Six DMRs overlapped across the two outcomes (fwer p < 0.1), and, 16 DMRs overlapped with previous child autistic trait findings at 12 months of age (fwer p < 0.05). Child SRS-associated DMRs contained CpG sites independently found to be differentially methylated in postmortem brains of individuals with and without autism. These findings suggest paternal germline methylation is associated with autistic traits in 3-year-old offspring. These prospective results for autism-associated traits, in a cohort with a family history of ASD, highlight the potential importance of sperm epigenetic mechanisms in autism.
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Affiliation(s)
- Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rose Schrott
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Craig J Newschaffer
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, State College, PA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, University of California, Davis, CA, USA
| | - Lisa A Croen
- Autism Research Program, Division of Research, Kaiser Permanente, Oakland, CA, USA
| | - M Daniele Fallin
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Andrew P Feinberg
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Center for Epigenetics, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Heather E Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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8
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Abstract
The concept of an epigenetic landscape describing potential cellular fates arising from pluripotent cells, first advanced by Conrad Waddington, has evolved in light of experiments showing nondeterministic outcomes of regulatory processes and mathematical methods for quantifying stochasticity. In this Review, we discuss modern approaches to epigenetic and gene regulation landscapes and the associated ideas of entropy and attractor states, illustrating how their definitions are both more precise and relevant to understanding cancer etiology and the plasticity of cancerous states. We address the interplay between different types of regulatory landscapes and how their changes underlie cancer progression. We also consider the roles of cellular aging and intrinsic and extrinsic stimuli in modulating cellular states and how landscape alterations can be quantitatively mapped onto phenotypic outcomes and thereby used in therapy development.
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University Schools of Medicine, Biomedical Engineering, and Public Health, Baltimore, MD 21205, USA
| | - Andre Levchenko
- Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
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9
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Gao RD, Maeda M, Tallon C, Feinberg AP, Slusher BS, Tsukamoto T. Effects of 6-Aminonicotinic Acid Esters on the Reprogrammed Epigenetic State of Distant Metastatic Pancreatic Carcinoma. ACS Med Chem Lett 2022; 13:1892-1897. [DOI: 10.1021/acsmedchemlett.2c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Run-Duo Gao
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Masahiro Maeda
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Carolyn Tallon
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, United States
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Barbara S. Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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10
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Bera K, Kiepas A, Godet I, Li Y, Mehta P, Ifemembi B, Paul CD, Sen A, Serra SA, Stoletov K, Tao J, Shatkin G, Lee SJ, Zhang Y, Boen A, Mistriotis P, Gilkes DM, Lewis JD, Fan CM, Feinberg AP, Valverde MA, Sun SX, Konstantopoulos K. Extracellular fluid viscosity enhances cell migration and cancer dissemination. Nature 2022; 611:365-373. [PMID: 36323783 PMCID: PMC9646524 DOI: 10.1038/s41586-022-05394-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
Abstract
Cells respond to physical stimuli, such as stiffness1, fluid shear stress2 and hydraulic pressure3,4. Extracellular fluid viscosity is a key physical cue that varies under physiological and pathological conditions, such as cancer5. However, its influence on cancer biology and the mechanism by which cells sense and respond to changes in viscosity are unknown. Here we demonstrate that elevated viscosity counterintuitively increases the motility of various cell types on two-dimensional surfaces and in confinement, and increases cell dissemination from three-dimensional tumour spheroids. Increased mechanical loading imposed by elevated viscosity induces an actin-related protein 2/3 (ARP2/3)-complex-dependent dense actin network, which enhances Na+/H+ exchanger 1 (NHE1) polarization through its actin-binding partner ezrin. NHE1 promotes cell swelling and increased membrane tension, which, in turn, activates transient receptor potential cation vanilloid 4 (TRPV4) and mediates calcium influx, leading to increased RHOA-dependent cell contractility. The coordinated action of actin remodelling/dynamics, NHE1-mediated swelling and RHOA-based contractility facilitates enhanced motility at elevated viscosities. Breast cancer cells pre-exposed to elevated viscosity acquire TRPV4-dependent mechanical memory through transcriptional control of the Hippo pathway, leading to increased migration in zebrafish, extravasation in chick embryos and lung colonization in mice. Cumulatively, extracellular viscosity is a physical cue that regulates both short- and long-term cellular processes with pathophysiological relevance to cancer biology.
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Affiliation(s)
- Kaustav Bera
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA
| | - Alexander Kiepas
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA
| | - Inês Godet
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Yizeng Li
- grid.264260.40000 0001 2164 4508Department of Biomedical Engineering, Binghamton University, SUNY, Binghamton, NY USA
| | - Pranav Mehta
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA
| | - Brent Ifemembi
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA
| | - Colin D. Paul
- grid.48336.3a0000 0004 1936 8075Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Anindya Sen
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA
| | - Selma A. Serra
- grid.5612.00000 0001 2172 2676Laboratory of Molecular Physiology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Konstantin Stoletov
- grid.17089.370000 0001 2190 316XDepartment of Oncology, University of Alberta, Edmonton, Alberta Canada
| | - Jiaxiang Tao
- grid.443927.f0000 0004 0411 0530Department of Embryology, Carnegie Institution for Science, Baltimore, MD USA
| | - Gabriel Shatkin
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD USA
| | - Se Jong Lee
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA
| | - Yuqi Zhang
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA
| | - Adrianna Boen
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA
| | - Panagiotis Mistriotis
- grid.252546.20000 0001 2297 8753Department of Chemical Engineering, Auburn University, Auburn, AL USA
| | - Daniele M. Gilkes
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - John D. Lewis
- grid.17089.370000 0001 2190 316XDepartment of Oncology, University of Alberta, Edmonton, Alberta Canada
| | - Chen-Ming Fan
- grid.443927.f0000 0004 0411 0530Department of Embryology, Carnegie Institution for Science, Baltimore, MD USA
| | - Andrew P. Feinberg
- grid.21107.350000 0001 2171 9311Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Miguel A. Valverde
- grid.5612.00000 0001 2172 2676Laboratory of Molecular Physiology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sean X. Sun
- grid.21107.350000 0001 2171 9311Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD USA
| | - Konstantinos Konstantopoulos
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA. .,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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11
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Bakulski KM, Dou JF, Feinberg JI, Aung MT, Ladd-Acosta C, Volk HE, Newschaffer CJ, Croen LA, Hertz-Picciotto I, Levy SE, Landa R, Feinberg AP, Fallin MD. Autism-Associated DNA Methylation at Birth From Multiple Tissues Is Enriched for Autism Genes in the Early Autism Risk Longitudinal Investigation. Front Mol Neurosci 2021; 14:775390. [PMID: 34899183 PMCID: PMC8655859 DOI: 10.3389/fnmol.2021.775390] [Citation(s) in RCA: 15] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Pregnancy measures of DNA methylation, an epigenetic mark, may be associated with autism spectrum disorder (ASD) development in children. Few ASD studies have considered prospective designs with DNA methylation measured in multiple tissues and tested overlap with ASD genetic risk loci. Objectives: To estimate associations between DNA methylation in maternal blood, cord blood, and placenta and later diagnosis of ASD, and to evaluate enrichment of ASD-associated DNA methylation for known ASD-associated genes. Methods: In the Early Autism Risk Longitudinal Investigation (EARLI), an ASD-enriched risk birth cohort, genome-scale maternal blood (early n = 140 and late n = 75 pregnancy), infant cord blood (n = 133), and placenta (maternal n = 106 and fetal n = 107 compartments) DNA methylation was assessed on the Illumina 450k HumanMethylation array and compared to ASD diagnosis at 36 months of age. Differences in site-specific and global methylation were tested with ASD, as well as enrichment of single site associations for ASD risk genes (n = 881) from the Simons Foundation Autism Research Initiative (SFARI) database. Results: No individual DNA methylation site was associated with ASD at genome-wide significance, however, individual DNA methylation sites nominally associated with ASD (P < 0.05) in each tissue were highly enriched for SFARI genes (cord blood P = 7.9 × 10-29, maternal blood early pregnancy P = 6.1 × 10-27, maternal blood late pregnancy P = 2.8 × 10-16, maternal placenta P = 5.6 × 10-15, fetal placenta P = 1.3 × 10-20). DNA methylation sites nominally associated with ASD across all five tissues overlapped at 144 (29.5%) SFARI genes. Conclusion: DNA methylation sites nominally associated with later ASD diagnosis in multiple tissues were enriched for ASD risk genes. Our multi-tissue study demonstrates the utility of examining DNA methylation prior to ASD diagnosis.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Max T Aung
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, United States
| | - Lisa A Croen
- Kaiser Permanente Division of Research, Oakland, CA, United States
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
| | - Susan E Levy
- Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Rebecca Landa
- Kennedy Krieger Institute Center for Autism and Related Disorders, Baltimore, MD, United States
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret D Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
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12
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Abante J, Kambhampati S, Feinberg AP, Goutsias J. Estimating DNA methylation potential energy landscapes from nanopore sequencing data. Sci Rep 2021; 11:21619. [PMID: 34732768 PMCID: PMC8566571 DOI: 10.1038/s41598-021-00781-x] [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: 07/20/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
High-throughput third-generation nanopore sequencing devices have enormous potential for simultaneously observing epigenetic modifications in human cells over large regions of the genome. However, signals generated by these devices are subject to considerable noise that can lead to unsatisfactory detection performance and hamper downstream analysis. Here we develop a statistical method, CpelNano, for the quantification and analysis of 5mC methylation landscapes using nanopore data. CpelNano takes into account nanopore noise by means of a hidden Markov model (HMM) in which the true but unknown (“hidden”) methylation state is modeled through an Ising probability distribution that is consistent with methylation means and pairwise correlations, whereas nanopore current signals constitute the observed state. It then estimates the associated methylation potential energy function by employing the expectation-maximization (EM) algorithm and performs differential methylation analysis via permutation-based hypothesis testing. Using simulations and analysis of published data obtained from three human cell lines (GM12878, MCF-10A, and MDA-MB-231), we show that CpelNano can faithfully estimate DNA methylation potential energy landscapes, substantially improving current methods and leading to a powerful tool for the modeling and analysis of epigenetic landscapes using nanopore sequencing data.
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Affiliation(s)
- Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Sandeep Kambhampati
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew P Feinberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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13
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Abstract
Single-cell omics is transforming our understanding of cell biology and disease, yet the systems-level analysis and interpretation of single-cell data faces many challenges. In this Perspective, we describe the impact that fundamental concepts from statistical mechanics, notably entropy, stochastic processes and critical phenomena, are having on single-cell data analysis. We further advocate the need for more bottom-up modelling of single-cell data and to embrace a statistical mechanics analysis paradigm to help attain a deeper understanding of single-cell systems biology.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,UCL Cancer Institute, University College London, London, UK.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Koldobskiy MA, Jenkinson G, Abante J, Rodriguez DiBlasi VA, Zhou W, Pujadas E, Idrizi A, Tryggvadottir R, Callahan C, Bonifant CL, Rabin KR, Brown PA, Ji H, Goutsias J, Feinberg AP. Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nat Biomed Eng 2021; 5:360-376. [PMID: 33859388 PMCID: PMC8370714 DOI: 10.1038/s41551-021-00703-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/18/2021] [Indexed: 02/02/2023]
Abstract
In cancer, linking epigenetic alterations to drivers of transformation has been difficult, in part because DNA methylation analyses must capture epigenetic variability, which is central to tumour heterogeneity and tumour plasticity. Here, by conducting a comprehensive analysis, based on information theory, of differences in methylation stochasticity in samples from patients with paediatric acute lymphoblastic leukaemia (ALL), we show that ALL epigenomes are stochastic and marked by increased methylation entropy at specific regulatory regions and genes. By integrating DNA methylation and single-cell gene-expression data, we arrived at a relationship between methylation entropy and gene-expression variability, and found that epigenetic changes in ALL converge on a shared set of genes that overlap with genetic drivers involved in chromosomal translocations across the disease spectrum. Our findings suggest that an epigenetically driven gene-regulation network, with UHRF1 (ubiquitin-like with PHD and RING finger domains 1) as a central node, links genetic drivers and epigenetic mediators in ALL.
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Affiliation(s)
- Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garrett Jenkinson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Varenka A Rodriguez DiBlasi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim, Ridgefield, CT, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elisabet Pujadas
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Challice L Bonifant
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen R Rabin
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Patrick A Brown
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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15
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Abstract
In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases.
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Affiliation(s)
- J Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Y Fang
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - A P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - J Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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16
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Koldobskiy MA, Abante J, Jenkinson G, Pujadas E, Tetens A, Zhao F, Tryggvadottir R, Idrizi A, Reinisch A, Majeti R, Goutsias J, Feinberg AP. A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML. Epigenetics 2020; 15:841-858. [PMID: 32114880 DOI: 10.1080/15592294.2020.1734149] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Translocations of the KMT2A (MLL) gene define a biologically distinct and clinically aggressive subtype of acute myeloid leukaemia (AML), marked by a characteristic gene expression profile and few cooperating mutations. Although dysregulation of the epigenetic landscape in this leukaemia is particularly interesting given the low mutation frequency, its comprehensive analysis using whole genome bisulphite sequencing (WGBS) has not been previously performed. Here we investigated epigenetic dysregulation in nine MLL-rearranged (MLL-r) AML samples by comparing them to six normal myeloid controls, using a computational method that encapsulates mean DNA methylation measurements along with analyses of methylation stochasticity. We discovered a dramatically altered epigenetic profile in MLL-r AML, associated with genome-wide hypomethylation and a markedly increased DNA methylation entropy reflecting an increasingly disordered epigenome. Methylation discordance mapped to key genes and regulatory elements that included bivalent promoters and active enhancers. Genes associated with significant changes in methylation stochasticity recapitulated known MLL-r AML expression signatures, suggesting a role for the altered epigenetic landscape in the transcriptional programme initiated by MLL translocations. Accordingly, we established statistically significant associations between discordances in methylation stochasticity and gene expression in MLL-r AML, thus providing a link between the altered epigenetic landscape and the phenotype.
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Affiliation(s)
- Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University , Baltimore, MD, USA
| | - Garrett Jenkinson
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Whitaker Biomedical Engineering Institute, Johns Hopkins University , Baltimore, MD, USA.,Department of Health Science Research, Mayo Clinic , Rochester, MN, USA
| | - Elisabet Pujadas
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai , New York, NY, USA
| | - Ashley Tetens
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Feifei Zhao
- Department of Medicine, Division of Hematology, Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, CA, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Andreas Reinisch
- Department of Medicine, Division of Hematology, Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, CA, USA.,Division of Hematology, Medical University of Graz , Graz, Austria
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, CA, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University , Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine , Baltimore, MD, USA
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17
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Chan RF, Shabalin AA, Montano C, Hannon E, Hultman CM, Fallin MD, Feinberg AP, Mill J, van den Oord EJCG, Aberg KA. Independent Methylome-Wide Association Studies of Schizophrenia Detect Consistent Case-Control Differences. Schizophr Bull 2020; 46:319-327. [PMID: 31165892 PMCID: PMC7442362 DOI: 10.1093/schbul/sbz056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Methylome-wide association studies (MWASs) are promising complements to sequence variation studies. We used existing sequencing-based methylation data, which assayed the majority of all 28 million CpGs in the human genome, to perform an MWAS for schizophrenia in blood, while controlling for cell-type heterogeneity with a recently generated platform-specific reference panel. Next, we compared the MWAS results with findings from 3 existing large-scale array-based schizophrenia methylation studies in blood that assayed up to ~450 000 CpGs. Our MWAS identified 22 highly significant loci (P < 5 × 10-8) and 852 suggestively significant loci (P < 1 × 10-5). The top finding (P = 5.62 × 10-11, q = 0.001) was located in MFN2, which encodes mitofusin-2 that regulates Ca2+ transfer from the endoplasmic reticulum to mitochondria in cooperation with DISC1. The second-most significant site (P = 1.38 × 10-9, q = 0.013) was located in ALDH1A2, which encodes an enzyme for astrocyte-derived retinoic acid-a key neuronal morphogen with relevance for schizophrenia. Although the most significant MWAS findings were not assayed on the arrays, we observed significant enrichment of overlapping findings with 2 of the 3 array datasets (P = 0.0315, 0.0045, 0.1946). Overrepresentation analysis of Gene Ontology terms for the genes in the significant overlaps suggested high similarity in the biological functions detected by the different datasets. Top terms were related to immune and/or stress responses, cell adhesion and motility, and a broad range of processes essential for neurodevelopment.
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Affiliation(s)
- Robin F Chan
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | | | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Margaret D Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Andrew P Feinberg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
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18
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Wulfridge P, Langmead B, Feinberg AP, Hansen KD. Analyzing whole genome bisulfite sequencing data from highly divergent genotypes. Nucleic Acids Res 2019; 47:e117. [PMID: 31392989 PMCID: PMC6821270 DOI: 10.1093/nar/gkz674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 11/07/2018] [Revised: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 11/13/2022] Open
Abstract
In the study of DNA methylation, genetic variation between species, strains or individuals can result in CpG sites that are exclusive to a subset of samples, and insertions and deletions can rearrange the spatial distribution of CpGs. How to account for this variation in an analysis of the interplay between sequence variation and DNA methylation is not well understood, especially when the number of CpG differences between samples is large. Here, we use whole-genome bisulfite sequencing data on two highly divergent mouse strains to study this problem. We show that alignment to personal genomes is necessary for valid methylation quantification. We introduce a method for including strain-specific CpGs in differential analysis, and show that this increases power. We apply our method to a human normal-cancer dataset, and show this improves accuracy and power, illustrating the broad applicability of our approach. Our method uses smoothing to impute methylation levels at strain-specific sites, thereby allowing strain-specific CpGs to contribute to the analysis, while accounting for differences in the spatial occurrences of CpGs. Our results have implications for joint analysis of genetic variation and DNA methylation using bisulfite-converted DNA, and unlocks the use of personal genomes for addressing this question.
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Affiliation(s)
- Phillip Wulfridge
- Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA.,Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA.,Department of Biomedical Engineering, Whiting School of Engineering, 3400 N. Charles St, Baltimore, MD 21218, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, MD 21205, USA
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
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19
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Wilton R, Li X, Feinberg AP, Szalay AS. Arioc: GPU-accelerated alignment of short bisulfite-treated reads. Bioinformatics 2019; 34:2673-2675. [PMID: 29554207 DOI: 10.1093/bioinformatics/bty167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/14/2018] [Indexed: 01/25/2023] Open
Abstract
Motivation The alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can be mitigated by appropriate algorithmic and software-engineering improvements. One strategy is to modify the read-alignment algorithms by integrating the logic related to BS-seq alignment, with the goal of making the software implementation amenable to optimizations that lead to higher speed and greater sensitivity than might otherwise be attainable. Results We evaluated this strategy using Arioc, a short-read aligner that uses GPU (general-purpose graphics processing unit) hardware to accelerate computationally-expensive programming logic. We integrated the BS-seq computational logic into both GPU and CPU code throughout the Arioc implementation. We then carried out a read-by-read comparison of Arioc's reported alignments with the alignments reported by well-known CPU-based BS-seq read aligners. With simulated reads, Arioc's accuracy is equal to or better than the other read aligners we evaluated. With human sequencing reads, Arioc's throughput is at least 10 times faster than existing BS-seq aligners across a wide range of sensitivity settings. Availability and implementation The Arioc software is available for download at https://github.com/RWilton/Arioc. It is released under a BSD open-source license. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Richard Wilton
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Li
- School of Medicine, Sun Yat-sen University, Guangdong, China
| | - Andrew P Feinberg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins Whitehead School of Engineering, Baltimore, MD, USA
| | - Alexander S Szalay
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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20
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Agha G, Mendelson MM, Ward-Caviness CK, Joehanes R, Huan T, Gondalia R, Salfati E, Brody JA, Fiorito G, Bressler J, Chen BH, Ligthart S, Guarrera S, Colicino E, Just AC, Wahl S, Gieger C, Vandiver AR, Tanaka T, Hernandez DG, Pilling LC, Singleton AB, Sacerdote C, Krogh V, Panico S, Tumino R, Li Y, Zhang G, Stewart JD, Floyd JS, Wiggins KL, Rotter JI, Multhaup M, Bakulski K, Horvath S, Tsao PS, Absher DM, Vokonas P, Hirschhorn J, Fallin MD, Liu C, Bandinelli S, Boerwinkle E, Dehghan A, Schwartz JD, Psaty BM, Feinberg AP, Hou L, Ferrucci L, Sotoodehnia N, Matullo G, Peters A, Fornage M, Assimes TL, Whitsel EA, Levy D, Baccarelli AA. Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease. Circulation 2019; 140:645-657. [PMID: 31424985 PMCID: PMC6812683 DOI: 10.1161/circulationaha.118.039357] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND DNA methylation is implicated in coronary heart disease (CHD), but current evidence is based on small, cross-sectional studies. We examined blood DNA methylation in relation to incident CHD across multiple prospective cohorts. METHODS Nine population-based cohorts from the United States and Europe profiled epigenome-wide blood leukocyte DNA methylation using the Illumina Infinium 450k microarray, and prospectively ascertained CHD events including coronary insufficiency/unstable angina, recognized myocardial infarction, coronary revascularization, and coronary death. Cohorts conducted race-specific analyses adjusted for age, sex, smoking, education, body mass index, blood cell type proportions, and technical variables. We conducted fixed-effect meta-analyses across cohorts. RESULTS Among 11 461 individuals (mean age 64 years, 67% women, 35% African American) free of CHD at baseline, 1895 developed CHD during a mean follow-up of 11.2 years. Methylation levels at 52 CpG (cytosine-phosphate-guanine) sites were associated with incident CHD or myocardial infarction (false discovery rate<0.05). These CpGs map to genes with key roles in calcium regulation (ATP2B2, CASR, GUCA1B, HPCAL1), and genes identified in genome- and epigenome-wide studies of serum calcium (CASR), serum calcium-related risk of CHD (CASR), coronary artery calcified plaque (PTPRN2), and kidney function (CDH23, HPCAL1), among others. Mendelian randomization analyses supported a causal effect of DNA methylation on incident CHD; these CpGs map to active regulatory regions proximal to long non-coding RNA transcripts. CONCLUSION Methylation of blood-derived DNA is associated with risk of future CHD across diverse populations and may serve as an informative tool for gaining further insight on the development of CHD.
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Affiliation(s)
- Golareh Agha
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, NY, NY 10032, USA
| | - Michael M. Mendelson
- Population Sciences Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA; Framingham Heart Study, Framingham, MA 01702, USA; Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Cavin K. Ward-Caviness
- National Health and Environmental Effects Research Laboratory, Environmental Public Health Division, Chapel Hill NC 27514, USA; Institute of Epidemiology II, Helmholtz Institute, Ingolstaedter Landstrasse 1, Neuherberg, Germany 85764
| | - Roby Joehanes
- National Heart, Lung and Blood Institute, Bethesda, MD 20824-0105, USA; Hebrew SeniorLife, Harvard Medical School, Boston, MA 02115, USA
| | - TianXiao Huan
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Rahul Gondalia
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Elias Salfati
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Giovanni Fiorito
- Italian Institute for Genomic Medicine (IIGM/HuGeF) and Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Brian H. Chen
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21250, USA
| | - Symen Ligthart
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine (IIGM/HuGeF) and Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allan C. Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simone Wahl
- Research Unit Molecualr Epidemiology, Helmholtz Zentrum München, 1 InglastaedterLandstrasse 1 85764, München, Germany
| | - Christian Gieger
- Research Unit Molecualr Epidemiology, Helmholtz Zentrum München, 1 InglastaedterLandstrasse 1 85764, München, Germany
| | - Amy R. Vandiver
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21250, USA
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luke C. Pilling
- Epidemiology and Public Health Group, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital and Center for Cancer Prevention (CPO), Turin, Italy
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Rosario Tumino
- Cancer Registry And Histopathology Department, “Civic- M.P. Arezzo2 Hospital, Asp Ragusa, Italy
| | - Yun Li
- Department of Genetics, Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Guosheng Zhang
- Curriculum in Bioinformatics and Computational Biology, and Department of Genetics, and Department of Statistics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - James D. Stewart
- Carolina Population Center and Department of Epidemiology, University of North Carolina at Chapel Hill, NC 27514, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Michael Multhaup
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kelly Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Steven Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Philip S. Tsao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Pantel Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Joel Hirschhorn
- Department of Medicine, Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA; Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | | | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, MRC–PHE Centre for Environment & Health, School of 346 Public Health, Imperial College London, UK
| | - Joel D. Schwartz
- Department of Epidemiology, and Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA 98195, USA; Kaier Permanente Washington Health Research Institute, Seattle, WA 98195, USA
| | - Andrew P. Feinberg
- Departments of Medicine, Biomedical Engineering and Mental Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University , Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Luigi Ferrucci
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nona Sotoodehnia
- Division of Cardiology, Departments of Medicine and Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Giuseppe Matullo
- Italian Institute for Genomic Medicine (IIGM/HuGeF) and Department of Medical Sciences, University of Turin, Turin, Italy
| | - Annette Peters
- Helmholtz Zentrum München, Institute of Epidemiology, Neuherberg, Germany; German Research Center for Cardiovascular Disease (DzHK e.V. - partner site Munich), Munich, Germany; Ludwig-Maximilians University, Institute for Biometry, Medical Information Science and Epidemiology, Munich, Germany
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine McGovern Medical School, and Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Themistocles L. Assimes
- Department of Medicine (Cardiovascular Medicine), and Department of Health Research & Policy, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric A. Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, and Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, NY, NY 10032, USA
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21
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Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science 2019; 364:364/6436/eaau8650. [PMID: 30975860 DOI: 10.1126/science.aau8650] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
To understand the health impact of long-duration spaceflight, one identical twin astronaut was monitored before, during, and after a 1-year mission onboard the International Space Station; his twin served as a genetically matched ground control. Longitudinal assessments identified spaceflight-specific changes, including decreased body mass, telomere elongation, genome instability, carotid artery distension and increased intima-media thickness, altered ocular structure, transcriptional and metabolic changes, DNA methylation changes in immune and oxidative stress-related pathways, gastrointestinal microbiota alterations, and some cognitive decline postflight. Although average telomere length, global gene expression, and microbiome changes returned to near preflight levels within 6 months after return to Earth, increased numbers of short telomeres were observed and expression of some genes was still disrupted. These multiomic, molecular, physiological, and behavioral datasets provide a valuable roadmap of the putative health risks for future human spaceflight.
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Affiliation(s)
- Francine E Garrett-Bakelman
- Weill Cornell Medicine, New York, NY, USA.,University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Ruben C Gur
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ling Lin
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Jad Nasrini
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Lynn Taylor
- Colorado State University, Fort Collins, CO, USA
| | | | | | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sara Ahadi
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Aditya Ambati
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Songjie Chen
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Marisa Covington
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | - Brian E Crucian
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | - David F Dinges
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | - Ryan P Hillary
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Peng Jiang
- Northwestern University, Evanston, IL, USA
| | | | | | | | | | | | | | | | - Tyler M Moore
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Hemal H Patel
- University of California, San Diego, La Jolla, CA, USA
| | | | - Varsha Rao
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rintaro Saito
- University of California, San Diego, La Jolla, CA, USA
| | - Denis N Salins
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Michael B Stenger
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | | | | | | | - Jing Zhang
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | - John B Charles
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
| | - Craig E Kundrot
- Space Life and Physical Sciences Division, NASA Headquarters, Washington, DC, USA.
| | - Graham B I Scott
- National Space Biomedical Research Institute, Baylor College of Medicine, Houston, TX, USA.
| | | | - Mathias Basner
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | | | | | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA. .,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | | | - Brinda K Rana
- University of California, San Diego, La Jolla, CA, USA.
| | - Scott M Smith
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
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22
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Ladd-Acosta C, Feinberg JI, Brown SC, Lurmann FW, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Feinberg AP, Fallin MD, Volk HE. Epigenetic marks of prenatal air pollution exposure found in multiple tissues relevant for child health. Environ Int 2019; 126:363-376. [PMID: 30826615 PMCID: PMC6446941 DOI: 10.1016/j.envint.2019.02.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 10/04/2018] [Revised: 01/05/2019] [Accepted: 02/10/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Prenatal air pollution exposure has been linked to many adverse health conditions in the offspring. However, little is known about the mechanisms underlying these associations. Epigenetics may be one plausible biologic link. Here, we sought to identify site-specific and global DNA methylation (DNAm) changes, in developmentally relevant tissues, associated with prenatal exposure to nitrogen dioxide (NO2) and ozone (O3). Additionally, we assessed whether sex-specific changes in methylation exist and whether DNAm changes are consistently observed across tissues. METHODS Genome-scale DNAm measurements were obtained using the Infinium HumanMethylation450k platform for 133 placenta and 175 cord blood specimens from Early Autism Risk Longitudinal Investigation (EARLI) neonates. Ambient NO2 and O3 exposure levels were based on prenatal address locations of EARLI mothers and the Environmental Protection Agency's AirNOW monitoring network using inverse distance weighting. We computed sample-level aggregate methylation measures for each of 5 types of genomic regions including genome-wide, open sea, shelf, shore, and island regions. Linear regression was performed for each genomic region; per-sample aggregate methylation measures were modeled as a function of quantitative exposure level with covariate adjustment. In addition, bumphunting was performed to identify differentially methylated regions (DMRs) associated with prenatal O3 and NO2 exposures in each tissue and by sex, with adjustment for technical and biological sources of variation. RESULTS We identified global and locus-specific changes in DNA methylation related to prenatal exposure to NO2 and O3 in 2 developmentally relevant tissues. Neonates with increased prenatal O3 exposure had lower aggregate levels of DNAm at CpGs located in open sea and shelf regions of the genome. We identified 6 DMRs associated with prenatal NO2 exposure, including 3 sex-specific. An additional 3 sex-specific DMRs were associated with prenatal O3 exposure levels. DMRs initially detected in cord blood samples (n = 4) showed consistent exposure-related changes in DNAm in placenta. However, the DMRs initially detected in placenta (n = 5) did not show DNAm differences in cord blood and, thus, they appear to be tissue-specific. CONCLUSIONS We observed global, locus, and sex-specific methylation changes associated with prenatal NO2 and O3 exposures. Our findings support DNAm is a biologic target of prenatal air pollutant exposures and highlight epigenetic involvement in sex-specific differential susceptibility to environmental exposure effects in 2 developmentally relevant tissues.
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Affiliation(s)
- Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Shannon C Brown
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Lisa A Croen
- Autism Research Program, Division of Research, Kaiser Permanente, Oakland, CA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, University of California, Davis, CA, USA
| | - Craig J Newschaffer
- A.J. Drexel Autism Institute and Department of Epidemiology and Biostatistics, Drexel University School of Public Health, Philadelphia, PA, USA
| | - Andrew P Feinberg
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Heather E Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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23
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Küpers LK, Monnereau C, Sharp GC, Yousefi P, Salas LA, Ghantous A, Page CM, Reese SE, Wilcox AJ, Czamara D, Starling AP, Novoloaca A, Lent S, Roy R, Hoyo C, Breton CV, Allard C, Just AC, Bakulski KM, Holloway JW, Everson TM, Xu CJ, Huang RC, van der Plaat DA, Wielscher M, Merid SK, Ullemar V, Rezwan FI, Lahti J, van Dongen J, Langie SAS, Richardson TG, Magnus MC, Nohr EA, Xu Z, Duijts L, Zhao S, Zhang W, Plusquin M, DeMeo DL, Solomon O, Heimovaara JH, Jima DD, Gao L, Bustamante M, Perron P, Wright RO, Hertz-Picciotto I, Zhang H, Karagas MR, Gehring U, Marsit CJ, Beilin LJ, Vonk JM, Jarvelin MR, Bergström A, Örtqvist AK, Ewart S, Villa PM, Moore SE, Willemsen G, Standaert ARL, Håberg SE, Sørensen TIA, Taylor JA, Räikkönen K, Yang IV, Kechris K, Nawrot TS, Silver MJ, Gong YY, Richiardi L, Kogevinas M, Litonjua AA, Eskenazi B, Huen K, Mbarek H, Maguire RL, Dwyer T, Vrijheid M, Bouchard L, Baccarelli AA, Croen LA, Karmaus W, Anderson D, de Vries M, Sebert S, Kere J, Karlsson R, Arshad SH, Hämäläinen E, Routledge MN, Boomsma DI, Feinberg AP, Newschaffer CJ, Govarts E, Moisse M, Fallin MD, Melén E, Prentice AM, Kajantie E, Almqvist C, Oken E, Dabelea D, Boezen HM, Melton PE, Wright RJ, Koppelman GH, Trevisi L, Hivert MF, Sunyer J, Munthe-Kaas MC, Murphy SK, Corpeleijn E, Wiemels J, Holland N, Herceg Z, Binder EB, Davey Smith G, Jaddoe VWV, Lie RT, Nystad W, London SJ, Lawlor DA, Relton CL, Snieder H, Felix JF. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nat Commun 2019; 10:1893. [PMID: 31015461 PMCID: PMC6478731 DOI: 10.1038/s41467-019-09671-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/18/2019] [Indexed: 12/16/2022] Open
Abstract
Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (PBonferroni < 1.06 x 10-7). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10-74) and BMI in pregnancy (3/914, p = 1.13x10-3), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.
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Affiliation(s)
- Leanne K Küpers
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
- Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Claire Monnereau
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Paul Yousefi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatisitcs and Epidemology, Oslo University Hospital, Oslo, Norway
| | - Sarah E Reese
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ritu Roy
- HDF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Computational Biology and Informatics, UCSF, San Francisco, CA, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Catherine Allard
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Todd M Everson
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Jari Lahti
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jenny van Dongen
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sabine A S Langie
- VITO - Health, Mol, Belgium
- Theoretical Physics, Faculty of Sciences, Hasselt University, Hasselt, Belgium
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Zongli Xu
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- MRC/PHE Centre for Environment and Health School of Public Health Imperial College London, St Mary's Campus, Norfolk Place, London, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Olivia Solomon
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Joosje H Heimovaara
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mariona Bustamante
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Patrice Perron
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC, Canada
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC, Canada
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis MIND Institute, Sacramento, CA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
| | | | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Anne K Örtqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Pia M Villa
- Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- Department of Women and Children's Health, King's College London, London, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ivana V Yang
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Yun Yun Gong
- School of Food Sciences and Nutrition, University of Leeds, Leeds, UK
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin, Turin, Italy
- AOU Citta della Salute e della Sceinza, CPO Piemonte, Turin, Italy
| | - Manolis Kogevinas
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brenda Eskenazi
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Community and Family Medicine, Duke University Medical Center, Raleigh, NC, USA
| | - Terence Dwyer
- The George Institute for Global Health, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Martine Vrijheid
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- ECOGENE-21 Biocluster, Chicoutimi Hospital, Saguenay, QC, Canada
| | - Andrea A Baccarelli
- Laboratory of Precision Environmental Biosciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department for Genomics of Common Diseases, School of Public Health, Imperial College London, London, UK
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Esa Hämäläinen
- HUSLAB and the Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | | | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | | | | | - Matthieu Moisse
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Stockholm, Sweden
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Hospital for Children and Adolescents, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, and Department of Pediatrics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Phillip E Melton
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
| | - Rosalind J Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Letizia Trevisi
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Marie-France Hivert
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC, Canada
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jordi Sunyer
- ISGlobal, Bacelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Joseph Wiemels
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Altanta, GA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rolv T Lie
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Wenche Nystad
- Department for Non-Communicable Diseases, Norwegian Institute for Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Service, Research Triangle Park, Durham, NC, USA
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Jenkinson G, Abante J, Koldobskiy MA, Feinberg AP, Goutsias J. Ranking genomic features using an information-theoretic measure of epigenetic discordance. BMC Bioinformatics 2019; 20:175. [PMID: 30961526 PMCID: PMC6454630 DOI: 10.1186/s12859-019-2777-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/14/2018] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background Establishment and maintenance of DNA methylation throughout the genome is an important epigenetic mechanism that regulates gene expression whose disruption has been implicated in human diseases like cancer. It is therefore crucial to know which genes, or other genomic features of interest, exhibit significant discordance in DNA methylation between two phenotypes. We have previously proposed an approach for ranking genes based on methylation discordance within their promoter regions, determined by centering a window of fixed size at their transcription start sites. However, we cannot use this method to identify statistically significant genomic features and handle features of variable length and with missing data. Results We present a new approach for computing the statistical significance of methylation discordance within genomic features of interest in single and multiple test/reference studies. We base the proposed method on a well-articulated hypothesis testing problem that produces p- and q-values for each genomic feature, which we then use to identify and rank features based on the statistical significance of their epigenetic dysregulation. We employ the information-theoretic concept of mutual information to derive a novel test statistic, which we can evaluate by computing Jensen-Shannon distances between the probability distributions of methylation in a test and a reference sample. We design the proposed methodology to simultaneously handle biological, statistical, and technical variability in the data, as well as variable feature lengths and missing data, thus enabling its wide-spread use on any list of genomic features. This is accomplished by estimating, from reference data, the null distribution of the test statistic as a function of feature length using generalized additive regression models. Differential assessment, using normal/cancer data from healthy fetal tissue and pediatric high-grade glioma patients, illustrates the potential of our approach to greatly facilitate the exploratory phases of clinically and biologically relevant methylation studies. Conclusions The proposed approach provides the first computational tool for statistically testing and ranking genomic features of interest based on observed DNA methylation discordance in comparative studies that accounts, in a rigorous manner, for biological, statistical, and technical variability in methylation data, as well as for variability in feature length and for missing data. Electronic supplementary material The online version of this article (10.1186/s12859-019-2777-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Garrett Jenkinson
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Currently with Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
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Rizzardi LF, Hickey PF, Rodriguez DiBlasi V, Tryggvadóttir R, Callahan CM, Idrizi A, Hansen KD, Feinberg AP. Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. Nat Neurosci 2019; 22:307-316. [PMID: 30643296 PMCID: PMC6348048 DOI: 10.1038/s41593-018-0297-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [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: 05/07/2018] [Accepted: 11/13/2018] [Indexed: 12/21/2022]
Abstract
Epigenetic modifications confer stable transcriptional patterns in the brain and both normal and abnormal brain function involve specialized brain regions. We examined DNA methylation by whole genome bisulfite sequencing in neuronal and non-neuronal populations from four brain regions (anterior cingulate gyrus, hippocampus, prefrontal cortex, and nucleus accumbens) as well as chromatin accessibility in the latter two. We find pronounced differences in CpG and non-CpG differentially methylated regions (CG- and CH-DMRs) only in neuronal cells across regions. While neuronal CH-DMRs were highly associated with differential gene expression, CG-DMRs were consistent with chromatin accessibility and enriched for regulatory regions. These CG-DMRs comprise ~12 Mb of the genome that is highly enriched for genomic regions associated with heritability of neuropsychiatric traits including addictive behavior, schizophrenia, and neuroticism, suggesting a mechanistic link between pathology and differential neuron-specific epigenetic regulation in distinct brain regions.
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Affiliation(s)
- Lindsay F Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter F Hickey
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Varenka Rodriguez DiBlasi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rakel Tryggvadóttir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin M Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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26
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Vanaja KG, Timp W, Feinberg AP, Levchenko A. A Loss of Epigenetic Control Can Promote Cell Death through Reversing the Balance of Pathways in a Signaling Network. Mol Cell 2018; 72:60-70.e3. [PMID: 30244832 DOI: 10.1016/j.molcel.2018.08.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 07/18/2017] [Revised: 06/04/2018] [Accepted: 08/15/2018] [Indexed: 12/31/2022]
Abstract
Epigenetic control of regulatory networks is only partially understood. Expression of Insulin-like growth factor-II (IGF2) is controlled by genomic imprinting, mediated by silencing of the maternal allele. Loss of imprinting of IGF2 (LOI) is linked to intestinal and colorectal cancers, causally in murine models and epidemiologically in humans. However, the molecular underpinnings of the LOI phenotype are not clear. Surprisingly, in LOI cells, we find a reversal of the relative activities of two canonical signaling pathways triggered by IGF2, causing further rebalancing between pro- and anti-apoptotic signaling. A predictive mathematical model shows that this network rebalancing quantitatively accounts for the effect of receptor tyrosine kinase inhibition in both WT and LOI cells. This mechanism also quantitatively explains both the stable LOI phenotype and the therapeutic window for selective killing of LOI cells, and thus prevention of epigenetically controlled cancers. These findings suggest a framework for understanding epigenetically modified cell signaling.
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Affiliation(s)
- Kiran G Vanaja
- Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, MD 21205, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, MD 21205, USA
| | - Andrew P Feinberg
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Andre Levchenko
- Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, MD 21205, USA.
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27
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Andrews SV, Sheppard B, Windham GC, Schieve LA, Schendel DE, Croen LA, Chopra P, Alisch RS, Newschaffer CJ, Warren ST, Feinberg AP, Fallin MD, Ladd-Acosta C. Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. Mol Autism 2018; 9:40. [PMID: 29988321 PMCID: PMC6022498 DOI: 10.1186/s13229-018-0224-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [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: 03/08/2018] [Accepted: 06/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies. Methods DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample. Findings In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12 × 10− 7. Seven CpGs showed differences at p < 1 × 10− 5 and 48 at 1 × 10− 4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpG hits, which was consistent across EWAS and meQTL discovery p value thresholds. Conclusions No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the seven sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan V Andrews
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Brooke Sheppard
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Gayle C Windham
- 3California Department of Public Health, Environmental Health Investigations Branch, 850 Marina Bay Parkway, Richmond, CA 94804 USA
| | - Laura A Schieve
- 4National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, MS E-86, 1600 Clifton Road, Atlanta, GA 30333 USA
| | - Diana E Schendel
- 5Deparment of Public Health, Section of Epidemiology, Aarhus University, Aarhus, Denmark.,6Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,7Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Lisa A Croen
- 8Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA 94612 USA
| | - Pankaj Chopra
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Reid S Alisch
- 10Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd, Madison, WI 53719 USA
| | - Craig J Newschaffer
- 11Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market Street Suite 560, Philadelphia, PA 19104 USA
| | - Stephen T Warren
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,13Department of Biochemistry, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,14Department of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Andrew P Feinberg
- 15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,16Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA
| | - M Daniele Fallin
- 2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA.,15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,17Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH850, Baltimore, MD 21205 USA
| | - Christine Ladd-Acosta
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
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28
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Affiliation(s)
- Andrew P Feinberg
- From the Department of Medicine, Johns Hopkins University School of Medicine, the Department of Biomedical Engineering, Whiting School of Engineering, and the Department of Mental Health, Johns Hopkins Bloomberg School of Public Health - all in Baltimore
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29
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Abstract
BACKGROUND DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior. However, the performance of most currently available methods for methylation analysis is hampered by their inability to directly account for statistical dependencies between neighboring methylation sites, thus ignoring significant information available in WGBS reads. RESULTS We present a powerful information-theoretic approach for genome-wide modeling and analysis of WGBS data based on the 1D Ising model of statistical physics. This approach takes into account correlations in methylation by utilizing a joint probability model that encapsulates all information available in WGBS methylation reads and produces accurate results even when applied on single WGBS samples with low coverage. Using the Shannon entropy, our approach provides a rigorous quantification of methylation stochasticity in individual WGBS samples genome-wide. Furthermore, it utilizes the Jensen-Shannon distance to evaluate differences in methylation distributions between a test and a reference sample. Differential performance assessment using simulated and real human lung normal/cancer data demonstrate a clear superiority of our approach over DSS, a recently proposed method for WGBS data analysis. Critically, these results demonstrate that marginal methods become statistically invalid when correlations are present in the data. CONCLUSIONS This contribution demonstrates clear benefits and the necessity of modeling joint probability distributions of methylation using the 1D Ising model of statistical physics and of quantifying methylation stochasticity using concepts from information theory. By employing this methodology, substantial improvement of DNA methylation analysis can be achieved by effectively taking into account the massive amount of statistical information available in WGBS data, which is largely ignored by existing methods.
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Affiliation(s)
- Garrett Jenkinson
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
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30
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Andrews SV, Ellis SE, Bakulski KM, Sheppard B, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Feinberg AP, Arking DE, Ladd-Acosta C, Fallin MD. Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. Nat Commun 2017; 8:1011. [PMID: 29066808 PMCID: PMC5654961 DOI: 10.1038/s41467-017-00868-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/28/2017] [Indexed: 01/07/2023] Open
Abstract
Integration of emerging epigenetic information with autism spectrum disorder (ASD) genetic results may elucidate functional insights not possible via either type of information in isolation. Here we use the genotype and DNA methylation (DNAm) data from cord blood and peripheral blood to identify SNPs associated with DNA methylation (meQTL lists). Additionally, we use publicly available fetal brain and lung meQTL lists to assess enrichment of ASD GWAS results for tissue-specific meQTLs. ASD-associated SNPs are enriched for fetal brain (OR = 3.55; P < 0.001) and peripheral blood meQTLs (OR = 1.58; P < 0.001). The CpG targets of ASD meQTLs across cord, blood, and brain tissues are enriched for immune-related pathways, consistent with other expression and DNAm results in ASD, and reveal pathways not implicated by genetic findings. This joint analysis of genotype and DNAm demonstrates the potential of both brain and blood-based DNAm for insights into ASD and psychiatric phenotypes more broadly. “There have been a number of recent epigenetic studies on autism spectrum disorder. Here, the authors integrate genetic and epigenetic data from cord and peripheral blood and also from brain tissues to show the potential of blood-based epigenetic data to provide insights into psychiatric disorders.”
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Affiliation(s)
- Shan V Andrews
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Shannon E Ellis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Brooke Sheppard
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis, 4610 X St, Sacramento, CA, 95817, USA.,MIND Institute, University of California Davis, 2825 50th St, Sacramento, CA, 95817, USA
| | - Craig J Newschaffer
- AJ Drexel Autism Institute, Drexel University, 3020 Market St #560, Philadelphia, PA, 19104, USA.,Department of Epidemiology and Biostatistics, Drexel University Dornsife School of Public Health, 3125 Market St, Philadelphia, PA, 19104, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA.,Department of Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Dan E Arking
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA. .,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA. .,Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA.
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA. .,Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA. .,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Baltimore, MD, 21205, USA.
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31
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Meng W, Zhu Z, Jiang X, Too CL, Uebe S, Jagodic M, Kockum I, Murad S, Ferrucci L, Alfredsson L, Zou H, Klareskog L, Feinberg AP, Ekström TJ, Padyukov L, Liu Y. DNA methylation mediates genotype and smoking interaction in the development of anti-citrullinated peptide antibody-positive rheumatoid arthritis. Arthritis Res Ther 2017; 19:71. [PMID: 28356135 PMCID: PMC5372280 DOI: 10.1186/s13075-017-1276-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple factors, including interactions between genetic and environmental risks, are important in susceptibility to rheumatoid arthritis (RA). However, the underlying mechanism is not fully understood. This study was undertaken to evaluate whether DNA methylation can mediate the interaction between genotype and smoking in the development of anti-citrullinated peptide antibody (ACPA)-positive RA. METHODS We investigated the gene-smoking interactions in DNA methylation using 393 individuals from the Epidemiological Investigation of Rheumatoid Arthritis (EIRA). The interaction between rs6933349 and smoking in the risk of developing ACPA-positive RA was further evaluated in a larger portion of the EIRA (1119 controls and 944 ACPA-positive patients with RA), and in the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA) (1556 controls and 792 ACPA-positive patients with RA). Finally, mediation analysis was performed to investigate whether DNA methylation of cg21325723 mediates this gene-environment interaction on the risk of developing of ACPA-positive RA. RESULTS We identified and replicated one significant gene-environment interaction between rs6933349 and smoking in DNA methylation of cg21325723. This gene-smoking interaction is a novel interaction in the risk of developing ACPA-positive in both Caucasian (multiplicative P value = 0.056; additive P value = 0.016) and Asian populations (multiplicative P value = 0.035; additive P value = 0.00027), and it is mediated through DNA methylation of cg21325723. CONCLUSIONS We showed that DNA methylation of cg21325723 can mediate the gene-environment interaction between rs6933349 and smoking, impacting the risk of developing ACPA-positive RA, thus being a potential regulator that integrates both internal genetic and external environmental risk factors.
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Affiliation(s)
- Weida Meng
- Department of Biochemistry and Molecular Biology, The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University, West Building 13, 130 Dong An Road, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, China
| | - Zaihua Zhu
- Division of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xia Jiang
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chun Lai Too
- Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia.,Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shahnaz Murad
- Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
| | - Luigi Ferrucci
- Instramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Hejian Zou
- Division of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Andrew P Feinberg
- Center for Epigenetics and Departments of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tomas J Ekström
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
| | - Yun Liu
- Department of Biochemistry and Molecular Biology, The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University, West Building 13, 130 Dong An Road, Shanghai, China. .,State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, China.
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32
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Ligthart S, Marzi C, Aslibekyan S, Mendelson MM, Conneely KN, Tanaka T, Colicino E, Waite LL, Joehanes R, Guan W, Brody JA, Elks C, Marioni R, Jhun MA, Agha G, Bressler J, Ward-Caviness CK, Chen BH, Huan T, Bakulski K, Salfati EL, Fiorito G, Wahl S, Schramm K, Sha J, Hernandez DG, Just AC, Smith JA, Sotoodehnia N, Pilling LC, Pankow JS, Tsao PS, Liu C, Zhao W, Guarrera S, Michopoulos VJ, Smith AK, Peters MJ, Melzer D, Vokonas P, Fornage M, Prokisch H, Bis JC, Chu AY, Herder C, Grallert H, Yao C, Shah S, McRae AF, Lin H, Horvath S, Fallin D, Hofman A, Wareham NJ, Wiggins KL, Feinberg AP, Starr JM, Visscher PM, Murabito JM, Kardia SLR, Absher DM, Binder EB, Singleton AB, Bandinelli S, Peters A, Waldenberger M, Matullo G, Schwartz JD, Demerath EW, Uitterlinden AG, van Meurs JBJ, Franco OH, Chen YDI, Levy D, Turner ST, Deary IJ, Ressler KJ, Dupuis J, Ferrucci L, Ong KK, Assimes TL, Boerwinkle E, Koenig W, Arnett DK, Baccarelli AA, Benjamin EJ, Dehghan A. DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases. Genome Biol 2016; 17:255. [PMID: 27955697 PMCID: PMC5151130 DOI: 10.1186/s13059-016-1119-5] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [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: 10/07/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is associated with chronic low-grade inflammation may reveal novel pathways or therapeutic targets for inflammation. RESULTS We performed a meta-analysis of epigenome-wide association studies (EWAS) of serum C-reactive protein (CRP), which is a sensitive marker of low-grade inflammation, in a large European population (n = 8863) and trans-ethnic replication in African Americans (n = 4111). We found differential methylation at 218 CpG sites to be associated with CRP (P < 1.15 × 10-7) in the discovery panel of European ancestry and replicated (P < 2.29 × 10-4) 58 CpG sites (45 unique loci) among African Americans. To further characterize the molecular and clinical relevance of the findings, we examined the association with gene expression, genetic sequence variants, and clinical outcomes. DNA methylation at nine (16%) CpG sites was associated with whole blood gene expression in cis (P < 8.47 × 10-5), ten (17%) CpG sites were associated with a nearby genetic variant (P < 2.50 × 10-3), and 51 (88%) were also associated with at least one related cardiometabolic entity (P < 9.58 × 10-5). An additive weighted score of replicated CpG sites accounted for up to 6% inter-individual variation (R2) of age-adjusted and sex-adjusted CRP, independent of known CRP-related genetic variants. CONCLUSION We have completed an EWAS of chronic low-grade inflammation and identified many novel genetic loci underlying inflammation that may serve as targets for the development of novel therapeutic interventions for inflammation.
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Affiliation(s)
- Symen Ligthart
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carola Marzi
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherber, Germany.,German Center for Diabetes Research (DZD e.V.), Partner Munich, Germany
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael M Mendelson
- Boston University School of Medicine, Boston, MA, USA.,Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Elena Colicino
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lindsay L Waite
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Roby Joehanes
- Hebrew SeniorLife, Harvard Medical School, Boston, MA, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Cathy Elks
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Riccardo Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Min A Jhun
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Golareh Agha
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Cavin K Ward-Caviness
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherber, Germany
| | - Brian H Chen
- Longitudinal Studies Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kelly Bakulski
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elias L Salfati
- Department of Medicine - Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Giovanni Fiorito
- Human Genetics Foundation, Torino, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | | | - Simone Wahl
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherber, Germany.,German Center for Diabetes Research (DZD e.V.), Partner Munich, Germany
| | - Katharina Schramm
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, München, Germany
| | - Jin Sha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Allan C Just
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter Medical School, RILD Building Level 3 Research, Exeter, UK
| | - James S Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Phil S Tsao
- Stanford University School of Medicine, Palo Alto, CA, USA.,VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Chunyu Liu
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Simonetta Guarrera
- Human Genetics Foundation, Torino, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Vasiliki J Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Marjolein J Peters
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David Melzer
- Epidemiology and Public Health, University of Exeter Medical School, RILD Building Level 3 Research, Exeter, UK
| | - Pantel Vokonas
- VA Boston Healthcare System and Boston University Schools of Public Health and Medicine, Jamaica Plain, Boston, MA, USA
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, München, Germany
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Audrey Y Chu
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christian Herder
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Center for Diabetes Research (DZD e.V.), München-Neuherberg, Germany
| | - Harald Grallert
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherber, Germany.,German Center for Diabetes Research (DZD e.V.), Partner Munich, Germany
| | - Chen Yao
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonia Shah
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Allan F McRae
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Honghuang Lin
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Steve Horvath
- UCLA, Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Daniele Fallin
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Peter M Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elisabeth B Binder
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA.,Max-Planck Institute of Psychiatry, Munich, Germany
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | | | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherber, Germany
| | - Melanie Waldenberger
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherber, Germany
| | - Giuseppe Matullo
- Human Genetics Foundation, Torino, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Joel D Schwartz
- Department of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ellen W Demerath
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yii-Der Ida Chen
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Daniel Levy
- Boston University School of Medicine, Boston, MA, USA.,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA.,Division of Depression & Anxiety Disorders, McLean Hospital, Belmont, MA, USA.,Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Wolfgang Koenig
- Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, Ulm, Germany.,Deutsches Herzzentrum München, Technische Universität München, Munich, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Donna K Arnett
- University of Kentucky, College of Public Health, Lexington, KY, USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Emelia J Benjamin
- Boston University School of Medicine, Boston, MA, USA.,Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.,Boston University and the NHLBI's Framingham Heart Study, Boston, MA, USA
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands. .,Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
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Gomez-Cabrero D, Almgren M, Sjöholm LK, Hensvold AH, Ringh MV, Tryggvadottir R, Kere J, Scheynius A, Acevedo N, Reinius L, Taub MA, Montano C, Aryee MJ, Feinberg JI, Feinberg AP, Tegnér J, Klareskog L, Catrina AI, Ekström TJ. High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis. Genome Med 2016; 8:124. [PMID: 27876072 PMCID: PMC5120506 DOI: 10.1186/s13073-016-0374-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 10/04/2016] [Accepted: 10/20/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Twin studies are powerful models to elucidate epigenetic modifications resulting from gene-environment interactions. Yet, commonly a limited number of clinical twin samples are available, leading to an underpowered situation afflicted with false positives and hampered by low sensitivity. We investigated genome-wide DNA methylation data from two small sets of monozygotic twins representing different phases during the progression of rheumatoid arthritis (RA) to find novel genes for further research. METHODS We implemented a robust statistical methodology aimed at investigating a small number of samples to identify differential methylation utilizing the comprehensive CHARM platform with whole blood cell DNA from two sets of twin pairs discordant either for ACPA (antibodies to citrullinated protein antigens)-positive RA versus ACPA-negative healthy or for ACPA-positive healthy (a pre-RA stage) versus ACPA-negative healthy. To deconvolute cell type-dependent differential methylation, we assayed the methylation patterns of sorted cells and used computational algorithms to resolve the relative contributions of different cell types and used them as covariates. RESULTS To identify methylation biomarkers, five healthy twin pairs discordant for ACPAs were profiled, revealing a single differentially methylated region (DMR). Seven twin pairs discordant for ACPA-positive RA revealed six significant DMRs. After deconvolution of cell type proportions, profiling of the healthy ACPA discordant twin-set revealed 17 genome-wide significant DMRs. When methylation profiles of ACPA-positive RA twin pairs were adjusted for cell type, the analysis disclosed one significant DMR, associated with the EXOSC1 gene. Additionally, the results from our methodology suggest a temporal connection of the protocadherine beta-14 gene to ACPA-positivity with clinical RA. CONCLUSIONS Our biostatistical methodology, optimized for a low-sample twin design, revealed non-genetically linked genes associated with two distinct phases of RA. Functional evidence is still lacking but the results reinforce further study of epigenetic modifications influencing the progression of RA. Our study design and methodology may prove generally useful in twin studies.
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Affiliation(s)
- David Gomez-Cabrero
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Unit of Computational Medicine, Stockholm, Sweden.,Bioinformatic Infrastructure for Life Sciences, Stockholm, Sweden.,Mucosal and Salivary Biology Division, King's College London Dental Institute, London, UK
| | - Malin Almgren
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA
| | - Louise K Sjöholm
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Aase H Hensvold
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Unit of Rheumatology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Mikael V Ringh
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Juha Kere
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Nathalie Acevedo
- Translational Immunology Unit, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lovisa Reinius
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Margaret A Taub
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Carolina Montano
- Medical Scientist Training Program, and Predoctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin J Aryee
- Departments of Pathology, Massachusetts General Hospital, Charlestown, MA, USA.,Harvard Medical School, Boston, MD, USA.,Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jason I Feinberg
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.,Departments of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.,Departments of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Jesper Tegnér
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Unit of Computational Medicine, Stockholm, Sweden
| | - Lars Klareskog
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Unit of Rheumatology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Anca I Catrina
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Unit of Rheumatology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Tomas J Ekström
- Center for Molecular Medicine at Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden. .,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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34
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McIntyre ABR, Rizzardi L, Yu AM, Alexander N, Rosen GL, Botkin DJ, Stahl SE, John KK, Castro-Wallace SL, McGrath K, Burton AS, Feinberg AP, Mason CE. Nanopore sequencing in microgravity. NPJ Microgravity 2016; 2:16035. [PMID: 28725742 PMCID: PMC5515536 DOI: 10.1038/npjmgrav.2016.35] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 01/25/2016] [Revised: 06/24/2016] [Accepted: 08/07/2016] [Indexed: 11/23/2022] Open
Abstract
Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close monitoring of crew health, but spaceflight places stringent restrictions on the mass and volume of instruments, crew operation time, and instrument functionality. The recent emergence of portable, nanopore-based tools with streamlined sample preparation protocols finally enables DNA sequencing on missions in microgravity. As a first step toward sequencing in space and aboard the International Space Station (ISS), we tested the Oxford Nanopore Technologies MinION during a parabolic flight to understand the effects of variable gravity on the instrument and data. In a successful proof-of-principle experiment, we found that the instrument generated DNA reads over the course of the flight, including the first ever sequenced in microgravity, and additional reads measured after the flight concluded its parabolas. Here we detail modifications to the sample-loading procedures to facilitate nanopore sequencing aboard the ISS and in other microgravity environments. We also evaluate existing analysis methods and outline two new approaches, the first based on a wave-fingerprint method and the second on entropy signal mapping. Computationally light analysis methods offer the potential for in situ species identification, but are limited by the error profiles (stays, skips, and mismatches) of older nanopore data. Higher accuracies attainable with modified sample processing methods and the latest version of flow cells will further enable the use of nanopore sequencers for diagnostics and research in space.
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Affiliation(s)
- Alexa B R McIntyre
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Lindsay Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Angela M Yu
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Gail L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | | | | | - Kristen K John
- Exploration Integration and Science Directorate, Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX, USA.,NASA Postdoctoral Program, NASA Johnson Space Center, Houston, TX, USA
| | - Sarah L Castro-Wallace
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX, USA
| | - Ken McGrath
- Australian Genome Research Facility, Gehrmann Labs, University of Queensland, St Lucia, QLD, Australia
| | - Aaron S Burton
- Exploration Integration and Science Directorate, Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute (BMRI), New York, NY, USA
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35
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Rizzardi LF, Kunz H, Rubins K, Chouker A, Quiriarte H, Sams C, Crucian BE, Feinberg AP. Evaluation of techniques for performing cellular isolation and preservation during microgravity conditions. NPJ Microgravity 2016; 2:16025. [PMID: 28725735 PMCID: PMC5515526 DOI: 10.1038/npjmgrav.2016.25] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 02/04/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 11/27/2022] Open
Abstract
Genomic and epigenomic studies require the precise transfer of microliter volumes among different types of tubes in order to purify DNA, RNA, or protein from biological samples and subsequently perform analyses of DNA methylation, RNA expression, and chromatin modifications on a genome-wide scale. Epigenomic and transcriptional analyses of human blood cells, for example, require separation of purified cell types to avoid confounding contributions of altered cellular proportions, and long-term preservation of these cells requires their isolation and transfer into appropriate freezing media. There are currently no protocols for these cellular isolation procedures on the International Space Station (ISS). Currently human blood samples are either frozen as mixed cell populations (within the CPT collection tubes) with poor yield of viable cells required for cell-type isolations, or returned under ambient conditions, which requires timing with Soyuz missions. Here we evaluate the feasibility of translating terrestrial cell purification techniques to the ISS. Our evaluations were performed in microgravity conditions during parabolic atmospheric flight. The pipetting of open liquids in microgravity was evaluated using analog-blood fluids and several types of pipette hardware. The best-performing pipettors were used to evaluate the pipetting steps required for peripheral blood mononuclear cell (PBMC) isolation following terrestrial density-gradient centrifugation. Evaluation of actual blood products was performed for both the overlay of diluted blood, and the transfer of isolated PBMCs. We also validated magnetic purification of cells. We found that positive-displacement pipettors avoided air bubbles, and the tips allowed the strong surface tension of water, glycerol, and blood to maintain a patent meniscus and withstand robust pipetting in microgravity. These procedures will greatly increase the breadth of research that can be performed on board the ISS, and allow improvised experimentation by astronauts on extraterrestrial missions.
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Affiliation(s)
- Lindsay F Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hawley Kunz
- Science, Technology and Engineering Group, Wyle, Houston, TX, USA
| | - Kathleen Rubins
- Astronaut Office, NASA Johnson Space Center, Houston, TX, USA
| | - Alexander Chouker
- Department of Anesthesiology, Hospital of the Ludwig-Maximilians-University, Munich, Germany
| | | | - Clarence Sams
- Space and Clinical Operations Division, NASA Johnson Space Center, Houston, TX, USA
| | - Brian E Crucian
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Departments of Medicine, Biomedical Engineering, and Mental Health, Johns Hopkins University Schools of Medicine, Engineering, and Public Health, Baltimore, MD, USA
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36
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Montano C, Taub MA, Jaffe A, Briem E, Feinberg JI, Trygvadottir R, Idrizi A, Runarsson A, Berndsen B, Gur RC, Moore TM, Perry RT, Fugman D, Sabunciyan S, Yolken RH, Hyde TM, Kleinman JE, Sobell JL, Pato CN, Pato MT, Go RC, Nimgaonkar V, Weinberger DR, Braff D, Gur RE, Fallin MD, Feinberg AP. Association of DNA Methylation Differences With Schizophrenia in an Epigenome-Wide Association Study. JAMA Psychiatry 2016; 73:506-14. [PMID: 27074206 PMCID: PMC6353566 DOI: 10.1001/jamapsychiatry.2016.0144] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE DNA methylation may play an important role in schizophrenia (SZ), either directly as a mechanism of pathogenesis or as a biomarker of risk. OBJECTIVE To scan genome-wide DNA methylation data to identify differentially methylated CpGs between SZ cases and controls. DESIGN, SETTING, AND PARTICIPANTS Epigenome-wide association study begun in 2008 using DNA methylation levels of 456 513 CpG loci measured on the Infinium HumanMethylation450 array (Illumina) in a consortium of case-control studies for initial discovery and in an independent replication set. Primary analyses used general linear regression, adjusting for age, sex, race/ethnicity, smoking, batch, and cell type heterogeneity. The discovery set contained 689 SZ cases and 645 controls (n = 1334), from 3 multisite consortia: the Consortium on the Genetics of Endophenotypes in Schizophrenia, the Project among African-Americans To Explore Risks for Schizophrenia, and the Multiplex Multigenerational Family Study of Schizophrenia. The replication set contained 247 SZ cases and 250 controls (n = 497) from the Genomic Psychiatry Cohort. MAIN OUTCOMES AND MEASURES Identification of differentially methylated positions across the genome in SZ cases compared with controls. RESULTS Of the 689 case participants in the discovery set, 477 (69%) were men and 258 (37%) were non-African American; of the 645 controls, 273 (42%) were men and 419 (65%) were non-African American. In our replication set, cases/controls were 76% male and 100% non-African American. We identified SZ-associated methylation differences at 923 CpGs in the discovery set (false discovery rate, <0.2). Of these, 625 showed changes in the same direction including 172 with P < .05 in the replication set. Some replicated differentially methylated positions are located in a top-ranked SZ region from genome-wide association study analyses. CONCLUSIONS AND RELEVANCE This analysis identified 172 replicated new associations with SZ after careful correction for cell type heterogeneity and other potential confounders. The overlap with previous genome-wide association study data can provide potential insights into the functional relevance of genetic signals for SZ.
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Affiliation(s)
- Carolina Montano
- Medical Scientist Training Program and Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Margaret A. Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andrew Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Eirikur Briem
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jason I. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rakel Trygvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Arni Runarsson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Birna Berndsen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ruben C. Gur
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tyler M. Moore
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rodney T. Perry
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | - Doug Fugman
- Rutgers University Cell and DNA Repository, Piscataway, New Jersey
| | - Sarven Sabunciyan
- Stanley Division of Developmental Neurovirology, Johns Hopkins, School of Medicine, Baltimore, Maryland
| | - Robert H. Yolken
- Stanley Division of Developmental Neurovirology, Johns Hopkins, School of Medicine, Baltimore, Maryland
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Janet L. Sobell
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Carlos N. Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Michele T. Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Rodney C. Go
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - David Braff
- Department of Psychiatry, University of California San Diego School of Medicine, La Jolla,VISN22, Mental Illness Research, Education, and Clinical Center, VA Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Raquel E. Gur
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Margaret Daniele Fallin
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland,Departments of Medicine and Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, Maryland
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37
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Joubert BR, Felix JF, Yousefi P, Bakulski KM, Just AC, Breton C, Reese SE, Markunas CA, Richmond RC, Xu CJ, Küpers LK, Oh SS, Hoyo C, Gruzieva O, Söderhäll C, Salas LA, Baïz N, Zhang H, Lepeule J, Ruiz C, Ligthart S, Wang T, Taylor JA, Duijts L, Sharp GC, Jankipersadsing SA, Nilsen RM, Vaez A, Fallin MD, Hu D, Litonjua AA, Fuemmeler BF, Huen K, Kere J, Kull I, Munthe-Kaas MC, Gehring U, Bustamante M, Saurel-Coubizolles MJ, Quraishi BM, Ren J, Tost J, Gonzalez JR, Peters MJ, Håberg SE, Xu Z, van Meurs JB, Gaunt TR, Kerkhof M, Corpeleijn E, Feinberg AP, Eng C, Baccarelli AA, Benjamin Neelon SE, Bradman A, Merid SK, Bergström A, Herceg Z, Hernandez-Vargas H, Brunekreef B, Pinart M, Heude B, Ewart S, Yao J, Lemonnier N, Franco OH, Wu MC, Hofman A, McArdle W, Van der Vlies P, Falahi F, Gillman MW, Barcellos LF, Kumar A, Wickman M, Guerra S, Charles MA, Holloway J, Auffray C, Tiemeier HW, Smith GD, Postma D, Hivert MF, Eskenazi B, Vrijheid M, Arshad H, Antó JM, Dehghan A, Karmaus W, Annesi-Maesano I, Sunyer J, Ghantous A, Pershagen G, Holland N, Murphy SK, DeMeo DL, Burchard EG, Ladd-Acosta C, Snieder H, Nystad W, Koppelman GH, Relton CL, Jaddoe VWV, Wilcox A, Melén E, London SJ. DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis. Am J Hum Genet 2016; 98:680-96. [PMID: 27040690 PMCID: PMC4833289 DOI: 10.1016/j.ajhg.2016.02.019] [Citation(s) in RCA: 556] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/20/2016] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The mechanisms are largely unknown, but epigenetics most likely plays a role. We formed the Pregnancy And Childhood Epigenetics (PACE) consortium and meta-analyzed, across 13 cohorts (n = 6,685), the association between maternal smoking in pregnancy and newborn blood DNA methylation at over 450,000 CpG sites (CpGs) by using the Illumina 450K BeadChip. Over 6,000 CpGs were differentially methylated in relation to maternal smoking at genome-wide statistical significance (false discovery rate, 5%), including 2,965 CpGs corresponding to 2,017 genes not previously related to smoking and methylation in either newborns or adults. Several genes are relevant to diseases that can be caused by maternal smoking (e.g., orofacial clefts and asthma) or adult smoking (e.g., certain cancers). A number of differentially methylated CpGs were associated with gene expression. We observed enrichment in pathways and processes critical to development. In older children (5 cohorts, n = 3,187), 100% of CpGs gave at least nominal levels of significance, far more than expected by chance (p value < 2.2 × 10(-16)). Results were robust to different normalization methods used across studies and cell type adjustment. In this large scale meta-analysis of methylation data, we identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.
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Affiliation(s)
- Bonnie R Joubert
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - Paul Yousefi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Kelly M Bakulski
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Allan C Just
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carrie Breton
- University of Southern California, Los Angeles, CA 90032, USA
| | - Sarah E Reese
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Christina A Markunas
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Cheng-Jian Xu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Leanne K Küpers
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Cathrine Hoyo
- Department of Biological Sciences and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695-7633, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Lucas A Salas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Nour Baïz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Saint-Antoine Medical School, F75012 Paris, France
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Johanna Lepeule
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Institut Albert Bonniot, Institut National de la Santé et de le Recherche Médicale, University of Grenoble Alpes, Centre Hospitalier Universitaire de Grenoble, F-38000 Grenoble, France
| | - Carlos Ruiz
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Symen Ligthart
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Tianyuan Wang
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jack A Taylor
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Liesbeth Duijts
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands; Division of Neonatology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands; Division of Respiratory Medicine, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Soesma A Jankipersadsing
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Roy M Nilsen
- Department of Global Public Health and Primary Care, University of Bergen, Bergen 5018, Norway
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; School of Medicine, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - M Daniele Fallin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bernard F Fuemmeler
- Department of Community and Family Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Karen Huen
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Inger Kull
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | | | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, the Netherlands
| | - Mariona Bustamante
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Center for Genomic Regulation (CRG), Barcelona 08003, Spain
| | | | - Bilal M Quraishi
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Jie Ren
- University of Southern California, Los Angeles, CA 90032, USA
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, 91000 Evry, France
| | - Juan R Gonzalez
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Marjolein J Peters
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Siri E Håberg
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo 0403, Norway
| | - Zongli Xu
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Joyce B van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Marjan Kerkhof
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Andrew P Feinberg
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Asa Bradman
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3508 TD, the Netherlands
| | - Mariona Pinart
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Barbara Heude
- INSERM, UMR 1153, Early Origin of the Child's Health And Development (ORCHAD) Team, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Université Paris Descartes, 94807 Villejuif, France
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jin Yao
- University of Southern California, Los Angeles, CA 90032, USA
| | - Nathanaël Lemonnier
- Centre National de la Recherche Scientifique-École Normale Supérieure de Lyon-Université Claude Bernard (Lyon 1), Université de Lyon, European Institute for Systems Biology and Medicine 69007 Lyon, France
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Michael C Wu
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Pieter Van der Vlies
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Fahimeh Falahi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Matthew W Gillman
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Lisa F Barcellos
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Department of Public Health Epidemiology, Unit of Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, Basel 4051, Switzerland; University of Basel, Basel 4001, Switzerland
| | - Magnus Wickman
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Sachs' Children's Hospital and Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm 171 77, Sweden
| | - Stefano Guerra
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain
| | - Marie-Aline Charles
- INSERM, UMR 1153, Early Origin of the Child's Health And Development (ORCHAD) Team, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Université Paris Descartes, 94807 Villejuif, France
| | - John Holloway
- Faculty of Medicine, Clinical & Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK; Faculty of Medicine, Human Development & Health, University of Southampton, Southampton SO16 6YD, UK
| | - Charles Auffray
- Centre National de la Recherche Scientifique-École Normale Supérieure de Lyon-Université Claude Bernard (Lyon 1), Université de Lyon, European Institute for Systems Biology and Medicine 69007 Lyon, France
| | - Henning W Tiemeier
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Dirkje Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Marie-France Hivert
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Martine Vrijheid
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Hasan Arshad
- Faculty of Medicine, Clinical & Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Josep M Antó
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Isabella Annesi-Maesano
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Saint-Antoine Medical School, F75012 Paris, France
| | - Jordi Sunyer
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Nina Holland
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Susan K Murphy
- Departments of Obstetrics and Gynecology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Christine Ladd-Acosta
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Wenche Nystad
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo 0403, Norway
| | - Gerard H Koppelman
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - Allen Wilcox
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Sachs' Children's Hospital and Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm 171 77, Sweden
| | - Stephanie J London
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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Bakulski KM, Feinberg JI, Andrews SV, Yang J, Brown S, L McKenney S, Witter F, Walston J, Feinberg AP, Fallin MD. DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Epigenetics 2016; 11:354-62. [PMID: 27019159 DOI: 10.1080/15592294.2016.1161875] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Epigenome-wide association studies of disease widely use DNA methylation measured in blood as a surrogate tissue. Cell proportions can vary between people and confound associations of exposure or outcome. An adequate reference panel for estimating cell proportions from adult whole blood for DNA methylation studies is available, but an analogous cord blood cell reference panel is not yet available. Cord blood has unique cell types and the epigenetic signatures of standard cell types may not be consistent throughout the life course. Using magnetic bead sorting, we isolated cord blood cell types (nucleated red blood cells, granulocytes, monocytes, natural killer cells, B cells, CD4(+)T cells, and CD8(+)T cells) from 17 live births at Johns Hopkins Hospital. We confirmed enrichment of the cell types using fluorescence assisted cell sorting and ran DNA from the separated cell types on the Illumina Infinium HumanMethylation450 BeadChip array. After filtering, the final analysis was on 104 samples at 429,794 probes. We compared cell type specific signatures in cord to each other and methylation at 49.2% of CpG sites on the array differed by cell type (F-test P < 10(-8)). Differences between nucleated red blood cells and the remainder of the cell types were most pronounced (36.9% of CpG sites at P < 10(-8)) and 99.5% of these sites were hypomethylated relative to the other cell types. We also compared the mean-centered sorted cord profiles to the available adult reference panel and observed high correlation between the overlapping cell types for granulocytes and monocytes (both r=0.74), and poor correlation for CD8(+)T cells and NK cells (both r=0.08). We further provide an algorithm for estimating cell proportions in cord blood using the newly developed cord reference panel, which estimates biologically plausible cell proportions in whole cord blood samples.
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Affiliation(s)
- Kelly M Bakulski
- a Department of Epidemiology , Johns Hopkins University Bloomberg School of Public Health , Baltimore , Maryland , USA.,b Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA.,c Department of Epidemiology , University of Michigan School of Public Health , Ann Arbor , Michigan , USA
| | - Jason I Feinberg
- b Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA.,d Department of Mental Health , Johns Hopkins University Bloomberg School of Public Health , Baltimore , Maryland , USA
| | - Shan V Andrews
- a Department of Epidemiology , Johns Hopkins University Bloomberg School of Public Health , Baltimore , Maryland , USA
| | - Jack Yang
- e Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Shannon Brown
- a Department of Epidemiology , Johns Hopkins University Bloomberg School of Public Health , Baltimore , Maryland , USA.,f Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health , Baltimore , Maryland , USA
| | - Stephanie L McKenney
- g Division of Neonatology, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Frank Witter
- h Division of Gynecology and Obstetrics, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA.,i Department of International Health , Johns Hopkins University Bloomberg School of Public Health , Baltimore , Maryland , USA
| | - Jeremy Walston
- e Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA
| | - Andrew P Feinberg
- b Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA.,d Department of Mental Health , Johns Hopkins University Bloomberg School of Public Health , Baltimore , Maryland , USA
| | - M Daniele Fallin
- b Center for Epigenetics, Johns Hopkins University School of Medicine , Baltimore , Maryland , USA.,d Department of Mental Health , Johns Hopkins University Bloomberg School of Public Health , Baltimore , Maryland , USA.,f Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health , Baltimore , Maryland , USA
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39
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Abstract
This year is the tenth anniversary of the publication in this journal of a model suggesting the existence of 'tumour progenitor genes'. These genes are epigenetically disrupted at the earliest stages of malignancies, even before mutations, and thus cause altered differentiation throughout tumour evolution. The past decade of discovery in cancer epigenetics has revealed a number of similarities between cancer genes and stem cell reprogramming genes, widespread mutations in epigenetic regulators, and the part played by chromatin structure in cellular plasticity in both development and cancer. In the light of these discoveries, we suggest here a framework for cancer epigenetics involving three types of genes: 'epigenetic mediators', corresponding to the tumour progenitor genes suggested earlier; 'epigenetic modifiers' of the mediators, which are frequently mutated in cancer; and 'epigenetic modulators' upstream of the modifiers, which are responsive to changes in the cellular environment and often linked to the nuclear architecture. We suggest that this classification is helpful in framing new diagnostic and therapeutic approaches to cancer.
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe Street, Rangos 570, Baltimore, Maryland 21205, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe Street, Rangos 570, Baltimore, Maryland 21205, USA
| | - Anita Göndör
- Department of Microbiology, Tumour and Cell Biology, Nobels väg 16, Karolinska Institutet, S-171 77 Stockholm, Sweden
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40
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Ladd-Acosta C, Shu C, Lee BK, Gidaya N, Singer A, Schieve LA, Schendel DE, Jones N, Daniels JL, Windham GC, Newschaffer CJ, Croen LA, Feinberg AP, Daniele Fallin M. Presence of an epigenetic signature of prenatal cigarette smoke exposure in childhood. Environ Res 2016; 144:139-148. [PMID: 26610292 PMCID: PMC4915563 DOI: 10.1016/j.envres.2015.11.014] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [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: 09/24/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 05/20/2023]
Abstract
Prenatal exposure to tobacco smoke has lifelong health consequences. Epigenetic signatures such as differences in DNA methylation (DNAm) may be a biomarker of exposure and, further, might have functional significance for how in utero tobacco exposure may influence disease risk. Differences in infant DNAm associated with maternal smoking during pregnancy have been identified. Here we assessed whether these infant DNAm patterns are detectible in early childhood, whether they are specific to smoking, and whether childhood DNAm can classify prenatal smoke exposure status. Using the Infinium 450K array, we measured methylation at 26 CpG loci that were previously associated with prenatal smoking in infant cord blood from 572 children, aged 3-5, with differing prenatal exposure to cigarette smoke in the Study to Explore Early Development (SEED). Striking concordance was found between the pattern of prenatal smoking associated DNAm among preschool aged children in SEED and those observed at birth in other studies. These DNAm changes appear to be tobacco-specific. Support vector machine classification models and 10-fold cross-validation were applied to show classification accuracy for childhood DNAm at these 26 sites as a biomarker of prenatal smoking exposure. Classification models showed prenatal exposure to smoking can be assigned with 81% accuracy using childhood DNAm patterns at these 26 loci. These findings support the potential for blood-derived DNAm measurements to serve as biomarkers for prenatal exposure.
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Affiliation(s)
- Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Chang Shu
- Department of Mental Health, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Brian K Lee
- Drexel University School of Public Health, Philadelphia, PA, USA
| | - Nicole Gidaya
- Drexel University School of Public Health, Philadelphia, PA, USA
| | - Alison Singer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Laura A Schieve
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Diana E Schendel
- Department of Public Health, Institute of Epidemiology and Social Medicine, Department of Economics and Business, National Centre for Register-based Research, Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus University, Aarhus, Denmark
| | - Nicole Jones
- Biomedical Research Informatics Core, Michigan State University, East Lansing, MI, USA
| | - Julie L Daniels
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Gayle C Windham
- Division of Environmental and Occupational Disease Control, California Department of Public Health, Richmond, CA, USA
| | - Craig J Newschaffer
- Drexel University School of Public Health, Philadelphia, PA, USA; The A.J. Drexel Autism Institute, Drexel University School of Public Health, Philadelphia, PA, USA
| | - Lisa A Croen
- Kaiser Permanente Northern California Division of Research, Oakland, CA, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Institute for Basic Biomedical Science, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins School of Public Health, Baltimore, MD, USA.
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41
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Vandiver AR, Idrizi A, Rizzardi L, Feinberg AP, Hansen KD. DNA methylation is stable during replication and cell cycle arrest. Sci Rep 2015; 5:17911. [PMID: 26648411 PMCID: PMC4673417 DOI: 10.1038/srep17911] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 08/14/2015] [Accepted: 11/09/2015] [Indexed: 01/15/2023] Open
Abstract
DNA methylation is an epigenetic modification with important functions in development. Large-scale loss of DNA methylation is a hallmark of cancer. Recent work has identified large genomic blocks of hypomethylation associated with cancer, EBV transformation and replicative senescence, all of which change the proportion of actively proliferating cells within the population measured. We asked if replication or cell-cycle arrest affects the global levels of methylation or leads to hypomethylated blocks as observed in other settings. We used fluorescence activated cell sorting to isolate primary dermal fibroblasts in G0, G1 and G2 based on DNA content and Ki67 staining. We additionally examined G0 cells arrested by contact inhibition for one week to determine the effects of extended arrest. We analyzed genome wide DNA methylation from sorted cells using whole genome bisulfite sequencing. This analysis demonstrated no global changes or large-scale hypomethylated blocks in any of the examined cell cycle phases, indicating that global levels of methylation are stable with replication and arrest.
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Affiliation(s)
- Amy R Vandiver
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Lindsay Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine.,Department of Medicine, Johns Hopkins University School of Medicine
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
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42
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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43
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Abstract
In this issue of Cell Stem Cell, Savić et al. (2014) and Kim et al. (2014) provide insight into how global heterochromatin condensation and LIN28 sequestration in embryonic stem cells are independent mechanisms regulating pluripotency in the oft-overlooked nucleolus.
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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44
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Bakulski KM, Lee H, Feinberg JI, Wells EM, Brown S, Herbstman JB, Witter FR, Halden RU, Caldwell K, Mortensen ME, Jaffe AE, Moye J, Caulfield LE, Pan Y, Goldman LR, Feinberg AP, Fallin MD. Prenatal mercury concentration is associated with changes in DNA methylation at TCEANC2 in newborns. Int J Epidemiol 2015; 44:1249-62. [PMID: 25906783 DOI: 10.1093/ije/dyv032] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Human exposure to the widespread environmental contaminant mercury is a known risk factor for common diseases such as cancer, cardiovascular disease and neurological disorders through poorly characterized mechanisms. Evidence suggests mercury exposure may alter DNA methylation levels, but to date, the effects in early life on a genome-wide scale have not been investigated. METHODS A study sample of 141 newborns was recruited in Baltimore, MD, USA and total mercury and methylmercury were measured in cord blood samples. We quantified genome-wide DNA methylation data using CHARM 2.0, an array-based method, and used region-finding analyses to identify concentration-associated differentially methylated regions (DMRs). To test for replication of these identified DMRs in the pilot, or Vanguard, phase of the National Children's Study (NCS), we compared bisulfite-pyrosequenced DNA at candidate regions from 85 whole cord blood samples with matched first trimester maternal mercury concentration measures. RESULTS Total mercury concentration was associated with methylation at DMRs inside ANGPT2 and near PRPF18 genes [false discovery rate (FDR) < 0.05], as well as DMRs near FOXD2 and within TCEANC2 (FDR< 0.1) genes. Methylmercury concentration was associated with an overlapping DMR within TCEANC2 (FDR< 0.05). In NCS replication analyses, methylation levels at three of four cytosine-guanine DNA dinucleotides (CpG sites) within the TCEANC2 DMR were associated with total mercury concentration (P < 0.05), and this association was diminished after adjusting for estimated cell proportions. CONCLUSIONS Evidence for an association between mercury and DNA methylation at the TCEANC2 region was found, which may represent a mercury-associated shift in cord blood cell composition or a change in methylation within blood cell types. Further confirmatory studies are needed.
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Affiliation(s)
- Kelly M Bakulski
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - HwaJin Lee
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jason I Feinberg
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ellen M Wells
- Purdue University, School of Health Sciences, West Lafayette, Indiana, USA
| | - Shannon Brown
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Julie B Herbstman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA, Columbia University Mailman School of Public Health, New York City, New York, USA
| | - Frank R Witter
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rolf U Halden
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, Arizona State University, Fulton School of Engineering, Tempe, Arizona, USA
| | - Kathleen Caldwell
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mary Ellen Mortensen
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew E Jaffe
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - John Moye
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA and
| | - Laura E Caulfield
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yi Pan
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lynn R Goldman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA, George Washington University School of Public Health, Washington D.C., USA
| | - Andrew P Feinberg
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - M Daniele Fallin
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,
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Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, Chien AL, Wang TS, Leung SG, Kang S, Feinberg AP. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol 2015; 16:80. [PMID: 25886480 PMCID: PMC4423110 DOI: 10.1186/s13059-015-0644-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [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: 12/08/2014] [Accepted: 03/23/2015] [Indexed: 01/09/2023] Open
Abstract
Background Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging and/or chronic sun exposure in humans. Results We compare epidermis and dermis of both sun-protected and sun-exposed skin derived from younger subjects (under 35 years old) and older subjects (over 60 years old), using the Infinium HumanMethylation450 array and whole genome bisulfite sequencing. We observe large blocks of the genome that are hypomethylated in older, sun-exposed epidermal samples, with the degree of hypomethylation associated with clinical measures of photo-aging. We replicate these findings using whole genome bisulfite sequencing, comparing epidermis from an additional set of younger and older subjects. These blocks largely overlap known hypomethylated blocks in colon cancer and we observe that these same regions are similarly hypomethylated in squamous cell carcinoma samples. Conclusions These data implicate large scale epigenomic change in mediating the effects of environmental damage with photo-aging. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0644-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amy R Vandiver
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA.
| | - Rafael A Irizarry
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA. .,Dana-Farber Cancer Institute, CLSB 11007, 450 Brookline Ave, Boston, MA, 02215, USA.
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA. .,Department of Biostatistics and Institute for Genetic Medicine, Johns Hopkins University School of Medicine, 615N. Wolfe St, E3527, Baltimore, MD, 21205, USA.
| | - Luis A Garza
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Arni Runarsson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA.
| | - Xin Li
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA.
| | - Anna L Chien
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Timothy S Wang
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Sherry G Leung
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Sewon Kang
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA. .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Feinberg JI, Bakulski KM, Jaffe AE, Tryggvadottir R, Brown SC, Goldman LR, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Fallin MD, Feinberg AP. Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort. Int J Epidemiol 2015; 44:1199-210. [PMID: 25878217 DOI: 10.1093/ije/dyv028] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Epigenetic mechanisms such as altered DNA methylation have been suggested to play a role in autism, beginning with the classical association of Prader-Willi syndrome, an imprinting disorder, with autistic features. OBJECTIVES Here we tested for the relationship of paternal sperm DNA methylation with autism risk in offspring, examining an enriched-risk cohort of fathers of autistic children. METHODS We examined genome-wide DNA methylation (DNAm) in paternal semen biosamples obtained from an autism spectrum disorder (ASD) enriched-risk pregnancy cohort, the Early Autism Risk Longitudinal Investigation (EARLI) cohort, to estimate associations between sperm DNAm and prospective ASD development, using a 12-month ASD symptoms assessment, the Autism Observation Scale for Infants (AOSI). We analysed methylation data from 44 sperm samples run on the CHARM 3.0 array, which contains over 4 million probes (over 7 million CpG sites), including 30 samples also run on the Illumina Infinium HumanMethylation450 (450K) BeadChip platform (∼485 000 CpG sites). We also examined associated regions in an independent sample of post-mortem human brain ASD and control samples for which Illumina 450K DNA methylation data were available. RESULTS Using region-based statistical approaches, we identified 193 differentially methylated regions (DMRs) in paternal sperm with a family-wise empirical P-value [family-wise error rate (FWER)] <0.05 associated with performance on the Autism Observational Scale for Infants (AOSI) at 12 months of age in offspring. The DMRs clustered near genes involved in developmental processes, including many genes in the SNORD family, within the Prader-Willi syndrome gene cluster. These results were consistent among the 75 probes on the Illumina 450K array that cover AOSI-associated DMRs from CHARM. Further, 18 of 75 (24%) 450K array probes showed consistent differences in the cerebellums of autistic individuals compared with controls. CONCLUSIONS These data suggest that epigenetic differences in paternal sperm may contribute to autism risk in offspring, and provide evidence that directionally consistent, potentially related epigenetic mechanisms may be operating in the cerebellum of individuals with autism.
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Affiliation(s)
- Jason I Feinberg
- Johns Hopkins Bloomberg School of Public Health, Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Center for Epigenetics
| | - Kelly M Bakulski
- Johns Hopkins Bloomberg School of Public Health, Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Center for Epigenetics, Johns Hopkins Bloomberg School of Public Health, Epidemiology
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Bloomberg School of Public Health, Mental Health and
| | | | - Shannon C Brown
- Johns Hopkins Bloomberg School of Public Health, Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Epidemiology
| | - Lynn R Goldman
- George Washington University, Milken Institute School of Public Health, Johns Hopkins Bloomberg School of Public Health
| | - Lisa A Croen
- Kaiser Permanente, Division of Research, Autism Research Program
| | | | - Craig J Newschaffer
- Drexel University, A.J. Drexel Autism Institute, Drexel University School of Public Health, Epidemiology and Biostatistics
| | - M Daniele Fallin
- Johns Hopkins Bloomberg School of Public Health, Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Mental Health and
| | - Andrew P Feinberg
- Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Medicine
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47
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Marioni RE, Shah S, McRae AF, Chen BH, Colicino E, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, Martin NG, Montgomery GW, Feinberg AP, Fallin MD, Multhaup ML, Jaffe AE, Joehanes R, Schwartz J, Just AC, Lunetta KL, Murabito JM, Starr JM, Horvath S, Baccarelli AA, Levy D, Visscher PM, Wray NR, Deary IJ. DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol 2015; 16:25. [PMID: 25633388 PMCID: PMC4350614 DOI: 10.1186/s13059-015-0584-6] [Citation(s) in RCA: 716] [Impact Index Per Article: 79.6] [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: 07/10/2014] [Accepted: 01/12/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA methylation levels change with age. Recent studies have identified biomarkers of chronological age based on DNA methylation levels. It is not yet known whether DNA methylation age captures aspects of biological age. RESULTS Here we test whether differences between people's chronological ages and estimated ages, DNA methylation age, predict all-cause mortality in later life. The difference between DNA methylation age and chronological age (Δage) was calculated in four longitudinal cohorts of older people. Meta-analysis of proportional hazards models from the four cohorts was used to determine the association between Δage and mortality. A 5-year higher Δage is associated with a 21% higher mortality risk, adjusting for age and sex. After further adjustments for childhood IQ, education, social class, hypertension, diabetes, cardiovascular disease, and APOE e4 status, there is a 16% increased mortality risk for those with a 5-year higher Δage. A pedigree-based heritability analysis of Δage was conducted in a separate cohort. The heritability of Δage was 0.43. CONCLUSIONS DNA methylation-derived measures of accelerated aging are heritable traits that predict mortality independently of health status, lifestyle factors, and known genetic factors.
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Affiliation(s)
- Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. .,Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK. .,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Sonia Shah
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, QLD, Australia. .,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Allan F McRae
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, QLD, Australia. .,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Brian H Chen
- The NHLBI's Framingham Heart Study, Framingham, MA, 01702, USA. .,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, 01702, USA.
| | - Elena Colicino
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. .,Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Jude Gibson
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Anjali K Henders
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, 4029, QLD, Australia.
| | - Paul Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| | - Simon R Cox
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. .,Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| | - Alison Pattie
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| | - Janie Corley
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| | - Lee Murphy
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, 4029, QLD, Australia.
| | - Grant W Montgomery
- Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, 4029, QLD, Australia.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Departments of Medicine, Molecular Biology/Genetics, Oncology, and Biostatistics, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
| | - M Daniele Fallin
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Michael L Multhaup
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Andrew E Jaffe
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA. .,Lieber Institute for Brain Development, Baltimore, MD, 21205, USA.
| | - Roby Joehanes
- The NHLBI's Framingham Heart Study, Framingham, MA, 01702, USA. .,Harvard Medical School, Boston, MA, 02115, USA. .,Hebrew Senior Life, Boston, MA, 02131, USA.
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA.
| | - Allan C Just
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Kathryn L Lunetta
- The NHLBI's Framingham Heart Study, Framingham, MA, 01702, USA. .,Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.
| | - Joanne M Murabito
- The NHLBI's Framingham Heart Study, Framingham, MA, 01702, USA. .,Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. .,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| | - Steve Horvath
- Human Genetics, Gonda Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095-7088, USA. .,Biostatistics, School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA.
| | - Daniel Levy
- The NHLBI's Framingham Heart Study, Framingham, MA, 01702, USA. .,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, 01702, USA.
| | - Peter M Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. .,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, QLD, Australia. .,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Naomi R Wray
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. .,Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
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Multhaup ML, Seldin MM, Jaffe AE, Lei X, Kirchner H, Mondal P, Li Y, Rodriguez V, Drong A, Hussain M, Lindgren C, McCarthy M, Näslund E, Zierath JR, Wong GW, Feinberg AP. Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metab 2015; 21:138-49. [PMID: 25565211 PMCID: PMC4340475 DOI: 10.1016/j.cmet.2014.12.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 11/24/2014] [Accepted: 12/16/2014] [Indexed: 12/27/2022]
Abstract
Using a functional approach to investigate the epigenetics of type 2 diabetes (T2D), we combine three lines of evidence-diet-induced epigenetic dysregulation in mouse, epigenetic conservation in humans, and T2D clinical risk evidence-to identify genes implicated in T2D pathogenesis through epigenetic mechanisms related to obesity. Beginning with dietary manipulation of genetically homogeneous mice, we identify differentially DNA-methylated genomic regions. We then replicate these results in adipose samples from lean and obese patients pre- and post-Roux-en-Y gastric bypass, identifying regions where both the location and direction of methylation change are conserved. These regions overlap with 27 genetic T2D risk loci, only one of which was deemed significant by GWAS alone. Functional analysis of genes associated with these regions revealed four genes with roles in insulin resistance, demonstrating the potential general utility of this approach for complementing conventional human genetic studies by integrating cross-species epigenomics and clinical genetic risk.
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Affiliation(s)
- Michael L Multhaup
- Department of Medicine, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Marcus M Seldin
- Department of Physiology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Xia Lei
- Department of Physiology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Henriette Kirchner
- Department of Molecular Medicine and Surgery Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Prosenjit Mondal
- Department of Pediatrics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Yuanyuan Li
- Department of Pediatrics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Varenka Rodriguez
- Department of Medicine, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Alexander Drong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Mehboob Hussain
- Department of Pediatrics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Cecilia Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Mark McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford OX3 7LI, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Old Road, Headington, Oxford OX3 7LI, UK
| | - Erik Näslund
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, 182 88 Stockholm, Sweden
| | - Juleen R Zierath
- Department of Molecular Medicine and Surgery Karolinska Institutet, 171 77 Stockholm, Sweden
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrew P Feinberg
- Department of Medicine, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA.
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49
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Schlaeger TM, Daheron L, Brickler TR, Entwisle S, Chan K, Cianci A, DeVine A, Ettenger A, Fitzgerald K, Godfrey M, Gupta D, McPherson J, Malwadkar P, Gupta M, Bell B, Doi A, Jung N, Li X, Lynes MS, Brookes E, Cherry ABC, Demirbas D, Tsankov AM, Zon LI, Rubin LL, Feinberg AP, Meissner A, Cowan CA, Daley GQ. A comparison of non-integrating reprogramming methods. Nat Biotechnol 2014; 33:58-63. [PMID: 25437882 DOI: 10.1038/nbt.3070] [Citation(s) in RCA: 346] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/14/2014] [Indexed: 01/06/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) are useful in disease modeling and drug discovery, and they promise to provide a new generation of cell-based therapeutics. To date there has been no systematic evaluation of the most widely used techniques for generating integration-free hiPSCs. Here we compare Sendai-viral (SeV), episomal (Epi) and mRNA transfection mRNA methods using a number of criteria. All methods generated high-quality hiPSCs, but significant differences existed in aneuploidy rates, reprogramming efficiency, reliability and workload. We discuss the advantages and shortcomings of each approach, and present and review the results of a survey of a large number of human reprogramming laboratories on their independent experiences and preferences. Our analysis provides a valuable resource to inform the use of specific reprogramming methods for different laboratories and different applications, including clinical translation.
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Affiliation(s)
- Thorsten M Schlaeger
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | | | | | | | - Karrie Chan
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Amelia Cianci
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexander DeVine
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Andrew Ettenger
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kelly Fitzgerald
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michelle Godfrey
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Dipti Gupta
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jade McPherson
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Prerana Malwadkar
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Manav Gupta
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Blair Bell
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Akiko Doi
- 1] Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Namyoung Jung
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xin Li
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Emily Brookes
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anne B C Cherry
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Didem Demirbas
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alexander M Tsankov
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - Leonard I Zon
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Lee L Rubin
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Andrew P Feinberg
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexander Meissner
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - Chad A Cowan
- 1] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA. [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [4] Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - George Q Daley
- 1] Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [3] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts, USA
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Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med 2014; 6:61. [PMID: 25191524 PMCID: PMC4154522 DOI: 10.1186/s13073-014-0061-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [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: 06/12/2014] [Accepted: 08/12/2014] [Indexed: 01/30/2023] Open
Abstract
Background One of the most provocative recent observations in cancer epigenetics is the discovery of large hypomethylated blocks, including single copy genes, in colorectal cancer, that correspond in location to heterochromatic LOCKs (large organized chromatin lysine-modifications) and LADs (lamin-associated domains). Methods Here we performed a comprehensive genome-scale analysis of 10 breast, 28 colon, nine lung, 38 thyroid, 18 pancreas cancers, and five pancreas neuroendocrine tumors as well as matched normal tissue from most of these cases, as well as 51 premalignant lesions. We used a new statistical approach that allows the identification of large hypomethylated blocks on the Illumina HumanMethylation450 BeadChip platform. Results We find that hypomethylated blocks are a universal feature of common solid human cancer, and that they occur at the earliest stage of premalignant tumors and progress through clinical stages of thyroid and colon cancer development. We also find that the disrupted CpG islands widely reported previously, including hypermethylated island bodies and hypomethylated shores, are enriched in hypomethylated blocks, with flattening of the methylation signal within and flanking the islands. Finally, we found that genes showing higher between individual gene expression variability are enriched within these hypomethylated blocks. Conclusion Thus hypomethylated blocks appear to be a universal defining epigenetic alteration in human cancer, at least for common solid tumors. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0061-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Winston Timp
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Hector Corrada Bravo
- Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, MD USA
| | - Oliver G McDonald
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Michael Goggins
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Chris Umbricht
- Departments of Surgery and Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Martha Zeiger
- Departments of Surgery and Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rafael A Irizarry
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD USA ; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA ; Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health, Boston, MA USA
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