451
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Pubertal development in healthy children is mirrored by DNA methylation patterns in peripheral blood. Sci Rep 2016; 6:28657. [PMID: 27349168 PMCID: PMC4923870 DOI: 10.1038/srep28657] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/07/2016] [Indexed: 12/21/2022] Open
Abstract
Puberty marks numerous physiological processes which are initiated by central activation of the hypothalamic–pituitary–gonadal axis, followed by development of secondary sexual characteristics. To a large extent, pubertal timing is heritable, but current knowledge of genetic polymorphisms only explains few months in the large inter-individual variation in the timing of puberty. We have analysed longitudinal genome-wide changes in DNA methylation in peripheral blood samples (n = 102) obtained from 51 healthy children before and after pubertal onset. We show that changes in single methylation sites are tightly associated with physiological pubertal transition and altered reproductive hormone levels. These methylation sites cluster in and around genes enriched for biological functions related to pubertal development. Importantly, we identified that methylation of the genomic region containing the promoter of TRIP6 was co-ordinately regulated as a function of pubertal development. In accordance, immunohistochemistry identified TRIP6 in adult, but not pre-pubertal, testicular Leydig cells and circulating TRIP6 levels doubled during puberty. Using elastic net prediction models, methylation patterns predicted pubertal development more accurately than chronological age. We demonstrate for the first time that pubertal attainment of secondary sexual characteristics is mirrored by changes in DNA methylation patterns in peripheral blood. Thus, modulations of the epigenome seem involved in regulation of the individual pubertal timing.
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452
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Liu J, Siegmund KD. An evaluation of processing methods for HumanMethylation450 BeadChip data. BMC Genomics 2016; 17:469. [PMID: 27334613 PMCID: PMC4918139 DOI: 10.1186/s12864-016-2819-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 06/08/2016] [Indexed: 12/13/2022] Open
Abstract
Background Illumina’s HumanMethylation450 arrays provide the most cost-effective means of high-throughput DNA methylation analysis. As with other types of microarray platforms, technical artifacts are a concern, including background fluorescence, dye-bias from the use of two color channels, bias caused by type I/II probe design, and batch effects. Several approaches and pipelines have been developed, either targeting a single issue or designed to address multiple biases through a combination of methods. We evaluate the effect of combining separate approaches to improve signal processing. Results In this study nine processing methods, including both within- and between- array methods, are applied and compared in four datasets. For technical replicates, we found both within- and between-array methods did a comparable job in reducing variance across replicates. For evaluating biological differences, within-array processing always improved differential DNA methylation signal detection over no processing, and always benefitted from performing background correction first. Combinations of within-array procedures were always among the best performing methods, with a slight advantage appearing for the between-array method Funnorm when batch effects explained more variation in the data than the methylation alterations between cases and controls. However, when this occurred, RUVm, a new batch correction method noticeably improved reproducibility of differential methylation results over any of the signal-processing methods alone. Conclusions The comparisons in our study provide valuable insights in preprocessing HumanMethylation450 BeadChip data. We found the within-array combination of Noob + BMIQ always improved signal sensitivity, and when combined with the RUVm batch-correction method, outperformed all other approaches in performing differential DNA methylation analysis. The effect of the data processing method, in any given data set, was a function of both the signal and noise. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2819-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Liu
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Kimberly D Siegmund
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, USA. .,Department of Preventive Medicine, USC Keck School of Medicine, 2001 N. Soto Street, Suite 202 W, Los Angeles, CA, 90089, USA.
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453
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Chen DP, Lin YC, Fann CSJ. Methods for identifying differentially methylated regions for sequence- and array-based data. Brief Funct Genomics 2016; 15:485-490. [PMID: 27323952 DOI: 10.1093/bfgp/elw018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms, and participates in the pathogenic processes of many diseases. Differentially methylated regions (DMRs) in the genome have been reported and implicated in a number of different diseases, tissues and cell types, and are associated with gene expression levels. Therefore, identification of DMRs is one of the most critical and fundamental issues in dissecting the disease etiologies. Based on bisulfite conversion, advances in sequence- and array-based technologies have helped investigators study genome-wide DNA methylation. Many methods have been developed to detect DMRs, and they have revolutionized our understanding of DNA methylation and provided new insights into its role in diverse biological functions. According to data and region types, we discuss various methods in detecting DMRs, their utility and limitations comprehensively. We recommend using a few of the methods in the same data and region type to detect DMRs because they could be complementary to one another.
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454
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Maksimovic J, Phipson B, Oshlack A. A cross-package Bioconductor workflow for analysing methylation array data. F1000Res 2016; 5:1281. [PMID: 27347385 DOI: 10.12688/f1000research.8839.2] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 01/30/2023] Open
Abstract
Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation arrays are by far the most common way to interrogate methylation across the human genome. This paper provides a Bioconductor workflow using multiple packages for the analysis of methylation array data. Specifically, we demonstrate the steps involved in a typical differential methylation analysis pipeline including: quality control, filtering, normalization, data exploration and statistical testing for probe-wise differential methylation. We further outline other analyses such as differential methylation of regions, differential variability analysis, estimating cell type composition and gene ontology testing. Finally, we provide some examples of how to visualise methylation array data.
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Affiliation(s)
- Jovana Maksimovic
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Belinda Phipson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia.,School of BioSciences, University of Melbourne, Melbourne, Australia.,School of Physics, University of Melbourne, Melbourne, Australia
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455
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Maksimovic J, Phipson B, Oshlack A. A cross-package Bioconductor workflow for analysing methylation array data. F1000Res 2016; 5:1281. [PMID: 27347385 DOI: 10.12688/f1000research.8839.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 01/01/2023] Open
Abstract
Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation arrays are by far the most common way to interrogate methylation across the human genome. This paper provides a Bioconductor workflow using multiple packages for the analysis of methylation array data. Specifically, we demonstrate the steps involved in a typical differential methylation analysis pipeline including: quality control, filtering, normalization, data exploration and statistical testing for probe-wise differential methylation. We further outline other analyses such as differential methylation of regions, differential variability analysis, estimating cell type composition and gene ontology testing. Finally, we provide some examples of how to visualise methylation array data.
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Affiliation(s)
- Jovana Maksimovic
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Belinda Phipson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia.,School of BioSciences, University of Melbourne, Melbourne, Australia.,School of Physics, University of Melbourne, Melbourne, Australia
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456
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Maksimovic J, Phipson B, Oshlack A. A cross-package Bioconductor workflow for analysing methylation array data. F1000Res 2016; 5:1281. [PMID: 27347385 PMCID: PMC4916993 DOI: 10.12688/f1000research.8839.3] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/03/2017] [Indexed: 12/22/2022] Open
Abstract
Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation arrays are by far the most common way to interrogate methylation across the human genome. This paper provides a Bioconductor workflow using multiple packages for the analysis of methylation array data. Specifically, we demonstrate the steps involved in a typical differential methylation analysis pipeline including: quality control, filtering, normalization, data exploration and statistical testing for probe-wise differential methylation. We further outline other analyses such as differential methylation of regions, differential variability analysis, estimating cell type composition and gene ontology testing. Finally, we provide some examples of how to visualise methylation array data.
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Affiliation(s)
- Jovana Maksimovic
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Belinda Phipson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia.,School of BioSciences, University of Melbourne, Melbourne, Australia.,School of Physics, University of Melbourne, Melbourne, Australia
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457
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Urdinguio RG, Torró MI, Bayón GF, Álvarez-Pitti J, Fernández AF, Redon P, Fraga MF, Lurbe E. Longitudinal study of DNA methylation during the first 5 years of life. J Transl Med 2016; 14:160. [PMID: 27259700 PMCID: PMC4891837 DOI: 10.1186/s12967-016-0913-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/18/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early life epigenetic programming influences adult health outcomes. Moreover, DNA methylation levels have been found to change more rapidly during the first years of life. Our aim was the identification and characterization of the CpG sites that are modified with time during the first years of life. We hypothesize that these DNA methylation changes would lead to the detection of genes that might be epigenetically modulated by environmental factors during early childhood and which, if disturbed, might contribute to susceptibility to diseases later in life. METHODS The study of the DNA methylation pattern of 485577 CpG sites was performed on 30 blood samples from 15 subjects, collected both at birth and at 5 years old, using Illumina(®) Infinium 450 k array. To identify differentially methylated CpG (dmCpG) sites, the methylation status of each probe was examined using linear models and the Empirical Bayes Moderated t test implemented in the limma package of R/Bioconductor. Surogate variable analysis was used to account for batch effects. RESULTS DNA methylation levels significantly changed from birth to 5 years of age in 6641 CpG sites. Of these, 36.79 % were hypermethylated and were associated with genes related mainly to developmental ontology terms, while 63.21 % were hypomethylated probes and associated with genes related to immune function. CONCLUSIONS Our results suggest that DNA methylation alterations with age during the first years of life might play a significant role in development and the regulation of leukocyte-specific functions. This supports the idea that blood leukocytes experience genome remodeling related to their interaction with environmental factors, underlining the importance of environmental exposures during the first years of life and suggesting that new strategies should be take into consideration for disease prevention.
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Affiliation(s)
- Rocio G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain.,Nanomaterials and Nanotechnology Research Center (CINN)-Spanish Council for Scientific Research (CSIC), (CINN-CSIC), Avenida de la Vega 4-6, 33940, El Entrego, Spain
| | - María Isabel Torró
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain.,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Gustavo F Bayón
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Julio Álvarez-Pitti
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain.,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Pau Redon
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain.,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain. .,Nanomaterials and Nanotechnology Research Center (CINN)-Spanish Council for Scientific Research (CSIC), (CINN-CSIC), Avenida de la Vega 4-6, 33940, El Entrego, Spain.
| | - Empar Lurbe
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain. .,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain.
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458
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Pervjakova N, Kasela S, Morris AP, Kals M, Metspalu A, Lindgren CM, Salumets A, Mägi R. Imprinted genes and imprinting control regions show predominant intermediate methylation in adult somatic tissues. Epigenomics 2016; 8:789-99. [PMID: 27004446 PMCID: PMC5066126 DOI: 10.2217/epi.16.8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/03/2016] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting is an epigenetic feature characterized by parent-specific monoallelic gene expression. The aim of this study was to compare the DNA methylation status of imprinted genes and imprinting control regions (ICRs), harboring differentially methylated regions (DMRs) in a comprehensive panel of 18 somatic tissues. The germline DMRs analyzed were divided into ubiquitously imprinted and placenta-specific DMRs, which show identical and different methylation imprints in adult somatic and placental tissues, respectively. We showed that imprinted genes and ICR DMRs maintain methylation patterns characterized by intermediate methylation levels in somatic tissues, which are pronounced in a specific region of the promoter area, located 200-1500 bp from the transcription start site. This intermediate methylation is concordant with gene expression from a single unmethylated allele and silencing of a reciprocal parental allele through DNA methylation. The only exceptions were seen for ICR DMRs of placenta-specific imprinted genes, which showed low levels of methylation, suggesting that these genes escape parent-specific epigenetic regulation in somatic tissues.
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Affiliation(s)
- Natalia Pervjakova
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- National Institute for Health & Welfare, University of Helsinki, Helsinki FI-00271, Finland
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Silva Kasela
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu 50409, Estonia
| | - Andres Metspalu
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Big Data Institute, University of Oxford, Oxford, OX3 7BN, UK
- Broad Institute of the Massachusetts Institute of Technology & Harvard University, Cambridge, MA 02142, USA
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu 50410, Estonia
- Department of Obstetrics & Gynecology, University of Tartu, Tartu 51014, Estonia
- Institute of Bio- & Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
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459
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Wang F, Zhang N, Wang J, Wu H, Zheng X. Tumor purity and differential methylation in cancer epigenomics. Brief Funct Genomics 2016; 15:408-419. [PMID: 27199459 DOI: 10.1093/bfgp/elw016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is an epigenetic modification of DNA molecule that plays a vital role in gene expression regulation. It is not only involved in many basic biological processes, but also considered an important factor for tumorigenesis and other human diseases. Study of DNA methylation has been an active field in cancer epigenomics research. With the advances of high-throughput technologies and the accumulation of enormous amount of data, method development for analyzing these data has gained tremendous interests in the fields of computational biology and bioinformatics. In this review, we systematically summarize the recent developments of computational methods and software tools in high-throughput methylation data analysis with focus on two aspects: differential methylation analysis and tumor purity estimation in cancer studies.
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460
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Curtius K, Wong CJ, Hazelton WD, Kaz AM, Chak A, Willis JE, Grady WM, Luebeck EG. A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus. PLoS Comput Biol 2016; 12:e1004919. [PMID: 27168458 PMCID: PMC4864310 DOI: 10.1371/journal.pcbi.1004919] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/15/2016] [Indexed: 02/07/2023] Open
Abstract
Biomarkers that drift differentially with age between normal and premalignant tissues, such as Barrett’s esophagus (BE), have the potential to improve the assessment of a patient’s cancer risk by providing quantitative information about how long a patient has lived with the precursor (i.e., dwell time). In the case of BE, which is a metaplastic precursor to esophageal adenocarcinoma (EAC), such biomarkers would be particularly useful because EAC risk may change with BE dwell time and it is generally not known how long a patient has lived with BE when a patient is first diagnosed with this condition. In this study we first describe a statistical analysis of DNA methylation data (both cross-sectional and longitudinal) derived from tissue samples from 50 BE patients to identify and validate a set of 67 CpG dinucleotides in 51 CpG islands that undergo age-related methylomic drift. Next, we describe how this information can be used to estimate a patient’s BE dwell time. We introduce a Bayesian model that incorporates longitudinal methylomic drift rates, patient age, and methylation data from individually paired BE and normal squamous tissue samples to estimate patient-specific BE onset times. Our application of the model to 30 sporadic BE patients’ methylomic profiles first exposes a wide heterogeneity in patient-specific BE onset times. Furthermore, independent application of this method to a cohort of 22 familial BE (FBE) patients reveals significantly earlier mean BE onset times. Our analysis supports the conjecture that differential methylomic drift occurs in BE (relative to normal squamous tissue) and hence allows quantitative estimation of the time that a BE patient has lived with BE. Barrett’s Esophagus (BE) is a metaplastic precursor to esophageal adenocarcinoma (EAC). When a patient is diagnosed with BE, it is generally not known how long he/she has had this condition because BE is asymptomatic. While the question of how long a premalignant tissue or lesion has been resident in an organ (dwell time) may not be of importance for cases where curative interventions are readily available (such as adenomas in the colon), for BE, curative interventions are either costly or carry patient risks. Knowledge of a precursor’s dwell time may therefore be advantageous in determining the cancer risk due to the stepwise accumulation of critical mutations in the precursor. In this study, we create a molecular clock model that infers patient-specific BE onsets from DNA methylation data. We show that there is considerable variation in the predicted BE onset times which translates, using mathematical modeling of EAC, into large variation in individual EAC risks. We make the case that, notwithstanding other known risk factors such as chronological age, gender, reflux status, etc., knowledge of biological tissue age can provide valuable patient-specific risk information when a patient is first diagnosed with BE.
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Affiliation(s)
- Kit Curtius
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (KC); (EGL)
| | - Chao-Jen Wong
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - William D. Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrew M. Kaz
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Gastroenterology Section, VA Puget Sound Health Care System, Seattle, Washington, United States of America
| | - Amitabh Chak
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Joseph E. Willis
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - William M. Grady
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - E. Georg Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (KC); (EGL)
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461
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Clifford RL, Jones MJ, MacIsaac JL, McEwen LM, Goodman SJ, Mostafavi S, Kobor MS, Carlsten C. Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation. J Allergy Clin Immunol 2016; 139:112-121. [PMID: 27321436 DOI: 10.1016/j.jaci.2016.03.046] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/15/2016] [Accepted: 03/22/2016] [Indexed: 01/24/2023]
Abstract
BACKGROUND Allergic disease affects 30% to 40% of the world's population, and its development is determined by the interplay between environmental and inherited factors. Air pollution, primarily consisting of diesel exhaust emissions, has increased at a similar rate to allergic disease. Exposure to diesel exhaust may play a role in the development and progression of allergic disease, in particular allergic respiratory disease. One potential mechanism underlying the connection between air pollution and increased allergic disease incidence is DNA methylation, an epigenetic process with the capacity to integrate gene-environment interactions. OBJECTIVE We sought to investigate the effect of allergen and diesel exhaust exposure on bronchial epithelial DNA methylation. METHODS We performed a randomized crossover-controlled exposure study to allergen and diesel exhaust in humans, and measured single-site (CpG) resolution global DNA methylation in bronchial epithelial cells. RESULTS Exposure to allergen alone, diesel exhaust alone, or allergen and diesel exhaust together (coexposure) led to significant changes in 7 CpG sites at 48 hours. However, when the same lung was exposed to allergen and diesel exhaust but separated by approximately 4 weeks, significant changes in more than 500 sites were observed. Furthermore, sites of differential methylation differed depending on which exposure was experienced first. Functional analysis of differentially methylated CpG sites found genes involved in transcription factor activity, protein metabolism, cell adhesion, and vascular development, among others. CONCLUSIONS These findings suggest that specific exposures can prime the lung for changes in DNA methylation induced by a subsequent insult.
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Affiliation(s)
- Rachel L Clifford
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa M McEwen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah J Goodman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara Mostafavi
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada; Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Canadian Institute for Advanced Research, Toronto, Ontario, Canada; Human Early Learning Partnership, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chris Carlsten
- Air Pollution Exposure Laboratory, Chan-Yeung Centre for Occupational and Environmental Lung Disease, Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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462
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Niu L, Xu Z, Taylor JA. RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. Bioinformatics 2016; 32:2659-63. [PMID: 27153672 DOI: 10.1093/bioinformatics/btw285] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/28/2016] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes-Infinium I (type I) and Infinium II (type II)-in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis. RESULTS Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ. AVAILABILITY We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html). CONTACT niulg@ucmail.uc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Liang Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | | | - Jack A Taylor
- Epidemiology Branch Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
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463
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Shui IM, Wong CJ, Zhao S, Kolb S, Ebot EM, Geybels MS, Rubicz R, Wright JL, Lin DW, Klotzle B, Bibikova M, Fan JB, Ostrander EA, Feng Z, Stanford JL. Prostate tumor DNA methylation is associated with cigarette smoking and adverse prostate cancer outcomes. Cancer 2016; 122:2168-77. [PMID: 27142338 DOI: 10.1002/cncr.30045] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 11/11/2022]
Abstract
BACKGROUND DNA methylation has been hypothesized as a mechanism for explaining the association between smoking and adverse prostate cancer (PCa) outcomes. This study was aimed at assessing whether smoking is associated with prostate tumor DNA methylation and whether these alterations may explain in part the association of smoking with PCa recurrence and mortality. METHODS A total of 523 men had radical prostatectomy as their primary treatment, detailed smoking history data, long-term follow-up for PCa outcomes, and tumor tissue profiled for DNA methylation. Ninety percent of the men also had matched tumor gene expression data. A methylome-wide analysis was conducted to identify differentially methylated regions (DMRs) by smoking status. To select potential functionally relevant DMRs, their correlation with the messenger RNA (mRNA) expression of corresponding genes was evaluated. Finally, a smoking-related methylation score based on the top-ranked DMRs was created to assess its association with PCa outcomes. RESULTS Forty DMRs were associated with smoking status, and 10 of these were strongly correlated with mRNA expression (aldehyde oxidase 1 [AOX1], claudin 5 [CLDN5], early B-cell factor 1 [EBF1], homeobox A7 [HOXA7], lectin galactoside-binding soluble 3 [LGALS3], microtubule-associated protein τ [MAPT], protocadherin γ A [PCDHGA]/protocadherin γ B [PCDHGB], paraoxonase 3 [PON3], synaptonemal complex protein 2 like [SYCP2L], and zinc finger and SCAN domain containing 12 [ZSCAN12]). Men who were in the highest tertile for the smoking-methylation score derived from these DMRs had a higher risk of recurrence (odds ratio [OR], 2.29; 95% confidence interval [CI], 1.42-3.72) and lethal disease (OR, 4.21; 95% CI, 1.65-11.78) in comparison with men in the lower 2 tertiles. CONCLUSIONS This integrative molecular epidemiology study supports the hypothesis that smoking-associated tumor DNA methylation changes may explain at least part of the association between smoking and adverse PCa outcomes. Future studies are warranted to confirm these findings and understand the implications for improving patient outcomes. Cancer 2016;122:2168-77. © 2016 American Cancer Society.
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Affiliation(s)
- Irene M Shui
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Chao-Jen Wong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Rohina Rubicz
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jonathan L Wright
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Urology, University of Washington School of Medicine, Seattle, Washington
| | - Daniel W Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Urology, University of Washington School of Medicine, Seattle, Washington
| | | | | | | | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ziding Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
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464
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Ivanov M, Kals M, Lauschke V, Barragan I, Ewels P, Käller M, Axelsson T, Lehtiö J, Milani L, Ingelman-Sundberg M. Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression. Nucleic Acids Res 2016; 44:6756-69. [PMID: 27131363 PMCID: PMC5001587 DOI: 10.1093/nar/gkw316] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 04/13/2016] [Indexed: 01/31/2023] Open
Abstract
To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.
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Affiliation(s)
- Maxim Ivanov
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia Institute of Mathematics and Statistics, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Volker Lauschke
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Isabel Barragan
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Von Eulers väg 8 IV, 17177 Stockholm, Sweden
| | - Philip Ewels
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Max Käller
- Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Tomas Axelsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - Janne Lehtiö
- Science for Life Laboratory, Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, 17121 Stockholm, Sweden
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
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465
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Wright ML, Dozmorov MG, Wolen AR, Jackson-Cook C, Starkweather AR, Lyon DE, York TP. Establishing an analytic pipeline for genome-wide DNA methylation. Clin Epigenetics 2016; 8:45. [PMID: 27127542 PMCID: PMC4848848 DOI: 10.1186/s13148-016-0212-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
The need for research investigating DNA methylation (DNAm) in clinical studies has increased, leading to the evolution of new analytic methods to improve accuracy and reproducibility of the interpretation of results from these studies. The purpose of this article is to provide clinical researchers with a summary of the major data processing steps routinely applied in clinical studies investigating genome-wide DNAm using the Illumina HumanMethylation 450K BeadChip. In most studies, the primary goal of employing DNAm analysis is to identify differential methylation at CpG sites among phenotypic groups. Experimental design considerations are crucial at the onset to minimize bias from factors related to sample processing and avoid confounding experimental variables with non-biological batch effects. Although there are currently no de facto standard methods for analyzing these data, we review the major steps in processing DNAm data recommended by several research studies. We describe several variations available for clinical researchers to process, analyze, and interpret DNAm data. These insights are applicable to most types of genome-wide DNAm array platforms and will be applicable for the next generation of DNAm array technologies (e.g., the 850K array). Selection of the DNAm analytic pipeline followed by investigators should be guided by the research question and supported by recently published methods.
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Affiliation(s)
| | - Mikhail G. Dozmorov
- />Department of Biostatistics, Virginia Commonwealth University, Richmond, VA USA
| | - Aaron R. Wolen
- />Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA USA
| | - Colleen Jackson-Cook
- />Departments of Pathology and Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA USA
| | | | - Debra E. Lyon
- />College of Nursing, University of Florida, Gainesville, FL USA
| | - Timothy P. York
- />Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA USA
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466
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van den Dungen MW, Murk AJ, Kok DE, Steegenga WT. Comprehensive DNA Methylation and Gene Expression Profiling in Differentiating Human Adipocytes. J Cell Biochem 2016; 117:2707-2718. [PMID: 27061314 DOI: 10.1002/jcb.25568] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/05/2016] [Indexed: 01/09/2023]
Abstract
Insight into the processes controlling adipogenesis is important in the battle against the obesity epidemic and its related disorders. The transcriptional regulatory cascade involved in adipocyte differentiation has been extensively studied, however, the mechanisms driving the transcription activation are still poorly understood. In this study, we explored the involvement of DNA methylation in transcriptional regulation during adipocyte differentiation of primary human mesenchymal stem cells (hMSCs). Genome-wide changes in DNA methylation were measured using the Illumina 450K BeadChip. In addition, expression of 84 adipogenic genes was determined, of which 43 genes showed significant expression changes during the differentiation process. Among these 43 differentially expressed genes, differentially methylated regions (DMRs) were detected in only three genes. By comparing genome-wide DNA methylation profiles in undifferentiated and differentiated adipocytes 793 significant DMRs were detected. Pathway analysis revealed the adipogenesis pathway as the most statistically significant, although only a small number of genes were differentially methylated. Genome-wide DNA methylation changes for single probes were most often located in intergenic regions, and underrepresented close to the transcription start site. In conclusion, DNA methylation remained relatively stable during adipocyte differentiation, implying that changes in DNA methylation are not the underlying mechanism regulating gene expression during adipocyte differentiation. J. Cell. Biochem. 117: 2707-2718, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Myrthe W van den Dungen
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.,Division of Human Nutrition, Wageningen University, P.O. Box 8129, 6700 EV, Wageningen, The Netherlands
| | - Albertinka J Murk
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.,Marine Animal Ecology Group, Wageningen University, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Dieuwertje E Kok
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Wilma T Steegenga
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.
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467
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Plant D, Webster A, Nair N, Oliver J, Smith SL, Eyre S, Hyrich KL, Wilson AG, Morgan AW, Isaacs JD, Worthington J, Barton A. Differential Methylation as a Biomarker of Response to Etanercept in Patients With Rheumatoid Arthritis. Arthritis Rheumatol 2016; 68:1353-60. [PMID: 26814849 PMCID: PMC4914881 DOI: 10.1002/art.39590] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/07/2016] [Indexed: 01/03/2023]
Abstract
Objective Biologic drug therapies represent a huge advance in the treatment of rheumatoid arthritis (RA). However, very good disease control is achieved in only 30% of patients, making identification of biomarkers of response a research priority. We undertook this study to test our hypothesis that differential DNA methylation patterns may provide biomarkers predictive of response to tumor necrosis factor inhibitor (TNFi) therapy in patients with RA. Methods An epigenome‐wide association study was performed on pretreatment whole blood DNA from patients with RA. Patients who displayed good response (n = 36) or no response (n = 36) to etanercept therapy at 3 months were selected. Differentially methylated positions were identified using linear regression. Variance of methylation at differentially methylated positions was assessed for correlation with cis‐acting single‐nucleotide polymorphisms (SNPs). A replication experiment for prioritized SNPs was performed in an independent cohort of 1,204 RA patients. Results Five positions that were differentially methylated between responder groups were identified, with a false discovery rate of <5%. The top 2 differentially methylated positions mapped to exon 7 of the LRPAP1 gene on chromosome 4 (cg04857395, P = 1.39 × 10−8 and cg26401028, P = 1.69 × 10−8). The A allele of the SNP rs3468 was correlated with higher levels of methylation for both of the top 2 differentially methylated positions (P = 2.63 × 10−7 and P = 1.05 × 10−6, respectively). Furthermore, the A allele of rs3468 was correlated with European League Against Rheumatism nonresponse in the discovery cohort (P = 0.03; n = 56) and in the independent replication cohort (P = 0.003; n = 1,204). Conclusion We identify DNA methylation as a potential biomarker of response to TNFi therapy, and we report the association between response and the LRPAP1 gene, which encodes a chaperone of low‐density lipoprotein receptor–related protein 1. Additional replication experiments in independent sample collections are now needed.
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Affiliation(s)
- Darren Plant
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, and Central Manchester NHS Trust, Manchester, UK
| | - Amy Webster
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Nisha Nair
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - James Oliver
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Samantha L Smith
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Steven Eyre
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Kimme L Hyrich
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Anthony G Wilson
- University College Dublin School of Medicine and Medical Science, and Conway Institute, Dublin, Ireland
| | - Ann W Morgan
- NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - John D Isaacs
- NIHR Newcastle Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, and Newcastle-Upon-Tyne NHS Foundation Trust, Newcastle-Upon-Tyne, UK
| | - Jane Worthington
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, and Central Manchester NHS Trust, and Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Anne Barton
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, and Central Manchester NHS Trust, and Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
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468
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Abstract
Aberrant DNA methylation is considered to be one of the most common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNA methylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide DNA methylation, and the available cancer-associated methylation databases. Additionally, we focus on the computational methods for preprocessing, analyzing and interpreting the cancer methylome data. It not only discusses the challenges of the differentially methylated region calling and the prediction model construction but also highlights the biomarker investigation for cancer diagnosis, prognosis and response to treatment. Finally, some emerging challenges in the computational analysis of cancer methylome data are summarized.
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469
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Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. Nat Methods 2016; 13:443-5. [PMID: 27018579 DOI: 10.1038/nmeth.3809] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/12/2016] [Indexed: 02/08/2023]
Abstract
In epigenome-wide association studies (EWAS), different methylation profiles of distinct cell types may lead to false discoveries. We introduce ReFACTor, a method based on principal component analysis (PCA) and designed for the correction of cell type heterogeneity in EWAS. ReFACTor does not require knowledge of cell counts, and it provides improved estimates of cell type composition, resulting in improved power and control for false positives in EWAS. Corresponding software is available at http://www.cs.tau.ac.il/~heran/cozygene/software/refactor.html.
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470
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Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G. Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells. Epigenetics Chromatin 2016; 9:12. [PMID: 27014370 PMCID: PMC4806452 DOI: 10.1186/s13072-016-0060-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/08/2016] [Indexed: 11/30/2022] Open
Abstract
Background Fragile X syndrome (FXS) is caused by CGG expansion over 200 repeats at the 5′ UTR of the FMR1 gene and subsequent DNA methylation of both the expanded sequence and the CpGs of the promoter region. This epigenetic change causes transcriptional silencing of the gene. We have previously demonstrated that 5-aza-2-deoxycytidine (5-azadC) treatment of FXS lymphoblastoid cell lines reactivates the FMR1 gene, concomitant with CpG sites demethylation, increased acetylation of histones H3 and H4 and methylation of lysine 4 on histone 3. Results In order to check the specificity of the 5-azadC-induced DNA demethylation, now we performed bisulphite sequencing of the entire methylation boundary upstream the FMR1 promoter region, which is preserved in control wild-type cells. We did not observe any modification of the methylation boundary after treatment. Furthermore, methylation analysis by MS-MLPA of PWS/AS and BWS/SRS loci demonstrated that 5-azadC treatment has no demethylating effect on these regions. Genome-wide methylation analysis through Infinium 450K (Illumina) showed no significant enrichment of specific GO terms in differentially methylated regions after 5-azadC treatment. We also observed that reactivation of FMR1 transcription lasts up to a month after a 7-day treatment and that maximum levels of transcription are reached at 10–15 days after last administration of 5-azadC. Conclusions Taken together, these data demonstrate that the demethylating effect of 5-azadC on genomic DNA is not random, but rather restricted to specific regions, if not exclusively to the FMR1 promoter. Moreover, we showed that 5-azadC has a long-lasting reactivating effect on the mutant FMR1 gene. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0060-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisabetta Tabolacci
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Giorgia Mancano
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Stella Lanni
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Federica Palumbo
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Martina Goracci
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Fabrizio Ferrè
- Department of Biology, Centre for Molecular Bioinformatics (CBM), University of Rome Tor Vergata, Rome, Italy
| | - Manuela Helmer-Citterich
- Department of Biology, Centre for Molecular Bioinformatics (CBM), University of Rome Tor Vergata, Rome, Italy
| | - Giovanni Neri
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
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471
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Wang T, Guan W, Lin J, Boutaoui N, Canino G, Luo J, Celedón JC, Chen W. A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data. Epigenetics 2016; 10:662-9. [PMID: 26036609 PMCID: PMC4623491 DOI: 10.1080/15592294.2015.1057384] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
DNA methylation plays an important role in disease etiology. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a widely used platform in large-scale epidemiologic studies. This platform can efficiently and simultaneously measure methylation levels at ∼480,000 CpG sites in the human genome in multiple study samples. Due to the intrinsic chip design of 2 types of chemistry probes, data normalization or preprocessing is a critical step to consider before data analysis. To date, numerous methods and pipelines have been developed for this purpose, and some studies have been conducted to evaluate different methods. However, validation studies have often been limited to a small number of CpG sites to reduce the variability in technical replicates. In this study, we measured methylation on a set of samples using both whole-genome bisulfite sequencing (WGBS) and 450K chips. We used WGBS data as a gold standard of true methylation states in cells to compare the performances of 8 normalization methods for 450K data on a genome-wide scale. Analyses on our dataset indicate that the most effective methods are peak-based correction (PBC) and quantile normalization plus β-mixture quantile normalization (QN.BMIQ). To our knowledge, this is the first study to systematically compare existing normalization methods for Illumina 450K data using novel WGBS data. Our results provide a benchmark reference for the analysis of DNA methylation chip data, particularly in white blood cells.
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Affiliation(s)
- Ting Wang
- a Division of Pulmonary Medicine; Allergy and Immunology; Department of Pediatrics; Children's Hospital of Pittsburgh of UPMC; University of Pittsburgh ; Pittsburgh , PA , USA
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472
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Brække Norheim K, Imgenberg-Kreuz J, Jonsdottir K, Janssen EAM, Syvänen AC, Sandling JK, Nordmark G, Omdal R. Epigenome-wide DNA methylation patterns associated with fatigue in primary Sjögren's syndrome. Rheumatology (Oxford) 2016; 55:1074-82. [PMID: 26966136 DOI: 10.1093/rheumatology/kew008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Chronic fatigue is a common, disabling and poorly understood phenomenon. Recent studies indicate that epigenetic mechanisms may be involved in the expression of fatigue, a prominent feature of primary SS (pSS). The aim of this study was to investigate whether DNA methylation profiles of whole blood are associated with fatigue in patients with pSS. METHODS Forty-eight pSS patients with high (n = 24) or low (n = 24) fatigue as measured by a visual analogue scale were included. Genome-wide DNA methylation was investigated using the Illumina HumanMethylation450 BeadChip array. After quality control, a total of 383 358 Cytosine-phosphate-Guanine (CpG) sites remained for further analysis. Age, sex and differential cell count estimates were included as covariates in the association model. A false discovery rate-corrected P < 0.05 was considered significant, and a cut-off of 3% average difference in methylation levels between high- and low-fatigue patients was applied. RESULTS A total of 251 differentially methylated CpG sites were associated with fatigue. The CpG site with the most pronounced hypomethylation in pSS high fatigue annotated to the SBF2-antisense RNA1 gene. The most distinct hypermethylation was observed at a CpG site annotated to the lymphotoxin alpha gene. Functional pathway analysis of genes with differently methylated CpG sites in subjects with high vs low fatigue revealed enrichment in several pathways associated with innate and adaptive immunity. CONCLUSION Some genes involved in regulation of the immune system and in inflammation are differently methylated in pSS patients with high vs low fatigue. These findings point to functional networks that may underlie fatigue. Epigenetic changes could constitute a fatigue-regulating mechanism in pSS.
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Affiliation(s)
- Katrine Brække Norheim
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Juliana Imgenberg-Kreuz
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Kristin Jonsdottir
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
| | - Emiel A M Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
| | - Ann-Christine Syvänen
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Gunnel Nordmark
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
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473
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Koestler DC, Jones MJ, Usset J, Christensen BC, Butler RA, Kobor MS, Wiencke JK, Kelsey KT. Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC Bioinformatics 2016; 17:120. [PMID: 26956433 PMCID: PMC4782368 DOI: 10.1186/s12859-016-0943-7] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/09/2016] [Indexed: 12/16/2022] Open
Abstract
Background Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA methylation for deconvoluting the cellular mixture of heterogenous biospecimens offer a promising solution, however the performance of such methods depends entirely on the library of methylation markers being used for deconvolution. Here, we introduce a novel algorithm for Identifying Optimal Libraries (IDOL) that dynamically scans a candidate set of cell-specific methylation markers to find libraries that optimize the accuracy of cell fraction estimates obtained from cell mixture deconvolution. Results Application of IDOL to training set consisting of samples with both whole-blood DNA methylation data (Illumina HumanMethylation450 BeadArray (HM450)) and flow cytometry measurements of cell composition revealed an optimized library comprised of 300 CpG sites. When compared existing libraries, the library identified by IDOL demonstrated significantly better overall discrimination of the entire immune cell landscape (p = 0.038), and resulted in improved discrimination of 14 out of the 15 pairs of leukocyte subtypes. Estimates of cell composition across the samples in the training set using the IDOL library were highly correlated with their respective flow cytometry measurements, with all cell-specific R2>0.99 and root mean square errors (RMSEs) ranging from [0.97 % to 1.33 %] across leukocyte subtypes. Independent validation of the optimized IDOL library using two additional HM450 data sets showed similarly strong prediction performance, with all cell-specific R2>0.90 and RMSE<4.00 %. In simulation studies, adjustments for cell composition using the IDOL library resulted in uniformly lower false positive rates compared to competing libraries, while also demonstrating an improved capacity to explain epigenome-wide variation in DNA methylation within two large publicly available HM450 data sets. Conclusions Despite consisting of half as many CpGs compared to existing libraries for whole blood mixture deconvolution, the optimized IDOL library identified herein resulted in outstanding prediction performance across all considered data sets and demonstrated potential to improve the operating characteristics of EWAS involving adjustments for cell distribution. In addition to providing the EWAS community with an optimized library for whole blood mixture deconvolution, our work establishes a systematic and generalizable framework for the assembly of libraries that improve the accuracy of cell mixture deconvolution. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0943-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, 66160, KS, USA.
| | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, The University of British Columbia, 950 West 28th Ave., Vancouver, V5Z 4H4, BC, Canada.
| | - Joseph Usset
- Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, 66160, KS, USA.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr., Lebanon, 03756, NH, USA. .,Department of Pharmacology and Toxicology, Dartmouth College, 1 Rope Ferry Rd., Hanover, 03755, NH, USA. .,Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr., Lebanon, 03756, NH, USA.
| | - Rondi A Butler
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St., Providence, 02912, RI, USA.
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, The University of British Columbia, 950 West 28th Ave., Vancouver, V5Z 4H4, BC, Canada.
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, 505 Parnassus Ave., San Francisco, 94143, CA, USA.
| | - Karl T Kelsey
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St., Providence, 02912, RI, USA. .,Department of Epidemiology, Brown University, 121 South Main St., Providence, 02912, RI, USA.
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474
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De Souza RAG, Islam SA, McEwen LM, Mathelier A, Hill A, Mah SM, Wasserman WW, Kobor MS, Leavitt BR. DNA methylation profiling in human Huntington's disease brain. Hum Mol Genet 2016; 25:2013-2030. [PMID: 26953320 DOI: 10.1093/hmg/ddw076] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
Despite extensive progress in Huntington's disease (HD) research, very little is known about the association of epigenetic variation and HD pathogenesis in human brain tissues. Moreover, its contribution to the tissue-specific transcriptional regulation of the huntingtin gene (HTT), in which HTT expression levels are highest in brain and testes, is currently unknown. To investigate the role of DNA methylation in HD pathogenesis and tissue-specific expression of HTT, we utilized the Illumina HumanMethylation450K BeadChip array to measure DNA methylation in a cohort of age-matched HD and control human cortex and liver tissues. In cortex samples, we found minimal evidence of HD-associated DNA methylation at probed sites after correction for cell heterogeneity but did observe an association with the age of disease onset. In contrast, comparison of matched cortex and liver samples revealed tissue-specific DNA methylation of the HTT gene region at 38 sites (FDR < 0.05). Importantly, we identified a novel differentially methylated binding site in the HTT proximal promoter for the transcription factor CTCF. This CTCF site displayed increased occupancy in cortex, where HTT expression is higher, compared with the liver. Additionally, CTCF silencing reduced the activity of an HTT promoter-reporter construct, suggesting that CTCF plays a role in regulating HTT promoter function. Overall, although we were unable to detect HD-associated DNA methylation alterations at queried sites, we found that DNA methylation may be correlated to the age of disease onset in cortex tissues. Moreover, our data suggest that DNA methylation may, in part, contribute to tissue-specific HTT transcription through differential CTCF occupancy.
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Affiliation(s)
- Rebecca A G De Souza
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Sumaiya A Islam
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Lisa M McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Austin Hill
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Sarah M Mah
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
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475
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Gross JA, Lefebvre F, Lutz PE, Bacot F, Vincent D, Bourque G, Turecki G. Variations in 5-methylcytosine and 5-hydroxymethylcytosine among human brain, blood, and saliva using oxBS and the Infinium MethylationEPIC array. Biol Methods Protoc 2016; 1:1-8. [PMID: 32328532 PMCID: PMC7164292 DOI: 10.1093/biomethods/bpw002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/20/2022] Open
Abstract
Investigating 5-methylcytosine (5mC) has led to many hypotheses regarding molecular mechanism underlying human diseases and disorders. Many of these studies, however, utilize bisulfite conversion alone, which cannot distinguish 5mC from its recently discovered oxidative product, 5-hydroxymethylcytosine (5hmC). Furthermore, previous array-based technologies do not have the necessary probes to adequately investigate both modifications simultaneously. In this manuscript, we used technical replicates of DNA from human brain, human blood, and human saliva, in combination with oxidative bisulfite conversion and Illumina's Infinium MethylationEPIC array, to analyze 5mC and 5hmC at more than 650 000 and 450 000 relevant loci, respectively, in the human genome. We show the presence of loci with detectable 5mC and 5hmC to be equally distributed across chromosomes and genomic features, while also being present in genomic regions with transcriptional regulatory properties. We also describe 2528 5hmC sites common across tissue types that show a strong association with immune-related functions. Lastly, in human brain, we show that 5hmC accounts for one-third of the total signal from bisulfite-converted data. As such, not only do our results confirm the efficacy and sensitivity of pairing oxidative bisulfite conversion and the EPIC array to detect 5mC and 5hmC in all three tissue types, but they also highlight the importance of dissociating 5hmC from 5mC in future studies related to cytosine modifications.
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Affiliation(s)
- Jeffrey A. Gross
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - François Lefebvre
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Pierre-Eric Lutz
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - François Bacot
- McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Daniel Vincent
- McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
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476
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Sensitivity Analysis of the MGMT-STP27 Model and Impact of Genetic and Epigenetic Context to Predict the MGMT Methylation Status in Gliomas and Other Tumors. J Mol Diagn 2016; 18:350-361. [PMID: 26927331 DOI: 10.1016/j.jmoldx.2015.11.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/12/2015] [Accepted: 11/24/2015] [Indexed: 11/24/2022] Open
Abstract
The methylation status of the O(6)-methylguanine-DNA methyltransferase (MGMT) gene is an important predictive biomarker for benefit from alkylating agent therapy in glioblastoma. Our model MGMT-STP27 allows prediction of the methylation status of the MGMT promoter using data from the Illumina's Human Methylation BeadChips (HM-27K and HM-450K) that is publically available for many cancer data sets. Here, we investigate the impact of the context of genetic and epigenetic alterations and tumor type on the classification and report on technical aspects, such as robustness of cutoff definition and preprocessing of the data. The association between gene copy number variation, predicted MGMT methylation, and MGMT expression revealed a gene dosage effect on MGMT expression in lower grade glioma (World Health Organization grade II/III) that in contrast to glioblastoma usually carry two copies of chromosome 10 on which MGMT resides (10q26.3). This implies some MGMT expression, potentially conferring residual repair function blunting the therapeutic effect of alkylating agents. A sensitivity analyses corroborated the performance of the original cutoff for various optimization criteria and for most data preprocessing methods. Finally, we propose an R package mgmtstp27 that allows prediction of the methylation status of the MGMT promoter and calculation of appropriate confidence and/or prediction intervals. Overall, MGMT-STP27 is a robust model for MGMT classification that is independent of tumor type and is adapted for single sample prediction.
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477
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Price EM, Peñaherrera MS, Portales-Casamar E, Pavlidis P, Van Allen MI, McFadden DE, Robinson WP. Profiling placental and fetal DNA methylation in human neural tube defects. Epigenetics Chromatin 2016; 9:6. [PMID: 26889207 PMCID: PMC4756451 DOI: 10.1186/s13072-016-0054-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/25/2016] [Indexed: 12/16/2022] Open
Abstract
Background The incidence of neural tube defects (NTDs) declined by about 40 % in Canada with the introduction of a national folic acid (FA) fortification program. Despite the fact that few Canadians currently exhibit folate deficiency, NTDs are still the second most common congenital abnormality. FA fortification may have aided in reducing the incidence of NTDs by overcoming abnormal one carbon metabolism cycling, the process which provides one carbon units for methylation of DNA. We considered that NTDs persisting in a folate-replete population may also occur in the context of FA-independent compromised one carbon metabolism, and that this might manifest as abnormal DNA methylation (DNAm). Second trimester human placental chorionic villi, kidney, spinal cord, brain, and muscle were collected from 19 control, 22 spina bifida, and 15 anencephalic fetuses in British Columbia, Canada. DNA was extracted, assessed for methylenetetrahydrofolate reductase (MTHFR) genotype and for genome-wide DNAm using repetitive elements, in addition to the Illumina Infinium HumanMethylation450 (450k) array. Results No difference in repetitive element DNAm was noted between NTD status groups. Using a false discovery rate <0.05 and average group difference in DNAm ≥0.05, differentially methylated array sites were identified only in (1) the comparison of anencephaly to controls in chorionic villi (n = 4 sites) and (2) the comparison of spina bifida to controls in kidney (n = 3342 sites). Conclusions We suggest that the distinctive DNAm of spina bifida kidneys may be consequent to the neural tube defect or reflective of a common etiology for abnormal neural tube and renal development. Though there were some small shifts in DNAm in the other tested tissues, our data do not support the long-standing hypothesis of generalized altered genome-wide DNAm in NTDs. This finding may be related to the fact that most Canadians are not folate deficient, but it importantly opens the field to the investigation of other epigenetic and non-epigenetic mechanisms in the etiology of NTDs. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0054-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Magda Price
- Child and Family Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 UK ; Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK ; Dept of Obstetrics and Gynaecology, University of British Columbia, C420-4500 Oak St, Vancouver, BC V6H 3N1 UK
| | - Maria S Peñaherrera
- Child and Family Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 UK ; Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK
| | | | - Paul Pavlidis
- Centre for High-Throughput Biology, University of British Columbia, 2185 East Mall, Vancouver, V6T 1Z4 UK ; Dept of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC V6T 2A1 UK
| | - Margot I Van Allen
- Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK
| | - Deborah E McFadden
- Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK ; Dept of Pathology and Laboratory Medicine, Rm G227-2211, Wesbrook Mall, Vancouver, BC V6T 2B5 UK
| | - Wendy P Robinson
- Child and Family Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 UK ; Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK
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478
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Nicodemus-Johnson J, Naughton KA, Sudi J, Hogarth K, Naurekas ET, Nicolae DL, Sperling AI, Solway J, White SR, Ober C. Genome-Wide Methylation Study Identifies an IL-13-induced Epigenetic Signature in Asthmatic Airways. Am J Respir Crit Care Med 2016; 193:376-85. [PMID: 26474238 PMCID: PMC4803084 DOI: 10.1164/rccm.201506-1243oc] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/15/2015] [Indexed: 01/12/2023] Open
Abstract
RATIONALE Epigenetic changes to airway cells have been proposed as important modulators of the effects of environmental exposures on airway diseases, yet no study to date has shown epigenetic responses to exposures in the airway that correlate with disease state. The type 2 cytokine IL-13 is a key mediator of allergic airway diseases, such as asthma, and is up-regulated in response to many asthma-promoting exposures. OBJECTIVES To directly study the epigenetic response of airway epithelial cells (AECs) to IL-13 and test whether IL-13-induced epigenetic changes differ between individuals with and without asthma. METHODS Genome-wide DNA methylation and gene expression patterns were studied in 58 IL-13-treated and untreated primary AEC cultures and validated in freshly isolated cells of subjects with and without asthma using the Illumina Human Methylation 450K and HumanHT-12 BeadChips. IL-13-mediated comethylation modules were identified and correlated with clinical phenotypes using weighted gene coexpression network analysis. MEASUREMENTS AND MAIN RESULTS IL-13 altered global DNA methylation patterns in cultured AECs and were significantly enriched near genes associated with asthma. Importantly, a significant proportion of this IL-13 epigenetic signature was validated in freshly isolated AECs from subjects with asthma and clustered into two distinct modules, with module 1 correlated with asthma severity and lung function and module 2 with eosinophilia. CONCLUSIONS These results suggest that a single exposure of IL-13 may selectively induce long-lasting DNA methylation changes in asthmatic airways that alter specific AEC pathways and contribute to asthma phenotypes.
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Affiliation(s)
| | | | | | | | | | - Dan L. Nicolae
- Department of Human Genetics
- Section of Genetic Medicine, Department of Medicine, and
- Department of Statistics, University of Chicago, Chicago, Illinois
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479
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Imgenberg-Kreuz J, Sandling JK, Almlöf JC, Nordlund J, Signér L, Norheim KB, Omdal R, Rönnblom L, Eloranta ML, Syvänen AC, Nordmark G. Genome-wide DNA methylation analysis in multiple tissues in primary Sjögren's syndrome reveals regulatory effects at interferon-induced genes. Ann Rheum Dis 2016; 75:2029-2036. [PMID: 26857698 PMCID: PMC5099203 DOI: 10.1136/annrheumdis-2015-208659] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/16/2016] [Indexed: 01/08/2023]
Abstract
Objectives Increasing evidence suggests an epigenetic contribution to the pathogenesis of autoimmune diseases, including primary Sjögren's Syndrome (pSS). The aim of this study was to investigate the role of DNA methylation in pSS by analysing multiple tissues from patients and controls. Methods Genome-wide DNA methylation profiles were generated using HumanMethylation450K BeadChips for whole blood, CD19+ B cells and minor salivary gland biopsies. Gene expression was analysed in CD19+ B cells by RNA-sequencing. Analysis of genetic regulatory effects on DNA methylation at known pSS risk loci was performed. Results We identified prominent hypomethylation of interferon (IFN)-regulated genes in whole blood and CD19+ B cells, including at the genes MX1, IFI44L and PARP9, replicating previous reports in pSS, as well as identifying a large number of novel associations. Enrichment for genomic overlap with histone marks for enhancer and promoter regions was observed. We showed for the first time that hypomethylation of IFN-regulated genes in pSS B cells was associated with their increased expression. In minor salivary gland biopsies we observed hypomethylation of the IFN-induced gene OAS2. Pathway and disease analysis resulted in enrichment of antigen presentation, IFN signalling and lymphoproliferative disorders. Evidence for genetic control of methylation levels at known pSS risk loci was observed. Conclusions Our study highlights the role of epigenetic regulation of IFN-induced genes in pSS where replication is needed for novel findings. The association with altered gene expression suggests a functional mechanism for differentially methylated CpG sites in pSS aetiology.
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Affiliation(s)
- Juliana Imgenberg-Kreuz
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jonas Carlsson Almlöf
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Linnea Signér
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Katrine Braekke Norheim
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Lars Rönnblom
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Gunnel Nordmark
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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480
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Christiansen L, Lenart A, Tan Q, Vaupel JW, Aviv A, McGue M, Christensen K. DNA methylation age is associated with mortality in a longitudinal Danish twin study. Aging Cell 2016; 15:149-54. [PMID: 26594032 PMCID: PMC4717264 DOI: 10.1111/acel.12421] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2015] [Indexed: 12/15/2022] Open
Abstract
An epigenetic profile defining the DNA methylation age (DNAm age) of an individual has been suggested to be a biomarker of aging, and thus possibly providing a tool for assessment of health and mortality. In this study, we estimated the DNAm age of 378 Danish twins, age 30–82 years, and furthermore included a 10‐year longitudinal study of the 86 oldest‐old twins (mean age of 86.1 at follow‐up), which subsequently were followed for mortality for 8 years. We found that the DNAm age is highly correlated with chronological age across all age groups (r = 0.97), but that the rate of change of DNAm age decreases with age. The results may in part be explained by selective mortality of those with a high DNAm age. This hypothesis was supported by a classical survival analysis showing a 35% (4–77%) increased mortality risk for each 5‐year increase in the DNAm age vs. chronological age. Furthermore, the intrapair twin analysis revealed a more‐than‐double mortality risk for the DNAm oldest twin compared to the co‐twin and a ‘dose–response pattern’ with the odds of dying first increasing 3.2 (1.05–10.1) times per 5‐year DNAm age difference within twin pairs, thus showing a stronger association of DNAm age with mortality in the oldest‐old when controlling for familial factors. In conclusion, our results support that DNAm age qualifies as a biomarker of aging.
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Affiliation(s)
- Lene Christiansen
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
| | - Adam Lenart
- Max Planck Odense Center on the Biodemography of Aging Institute of Public Health University of Southern Denmark Odense Denmark
| | - Qihua Tan
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
- Department of Clinical Genetics Odense University Hospital Odense Denmark
| | - James W. Vaupel
- Max Planck Odense Center on the Biodemography of Aging Institute of Public Health University of Southern Denmark Odense Denmark
- Max Planck Institute for Demographic Research Rostock Germany
| | - Abraham Aviv
- The Center for Human Development and Aging New Jersey Medical School University of Medicine and Dentistry of New Jersey Newark NJ USA
| | - Matt McGue
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
- Department of Psychology University of Minnesota Minneapolis MN USA
| | - Kaare Christensen
- The Danish Aging Research Center, and The Danish twin Registry Institute of Public Health University of Southern Denmark Odense Denmark
- Department of Clinical Genetics Odense University Hospital Odense Denmark
- Department of Clinical Biochemistry and Pharmacology Odense University Hospital Odense Denmark
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481
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Chen M, Baumbach J, Vandin F, Röttger R, Barbosa E, Dong M, Frost M, Christiansen L, Tan Q. Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs. Ann Hum Genet 2016; 80:81-7. [DOI: 10.1111/ahg.12146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Mubo Chen
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
- Department of Electrical and Computer Engineering, Faculty of Science and Technology; University of Macau; Macau China
| | - Jan Baumbach
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Fabio Vandin
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
- Department of Information Engineering; University of Padova; Padova Italy
| | - Richard Röttger
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Eudes Barbosa
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Mingchui Dong
- Department of Electrical and Computer Engineering, Faculty of Science and Technology; University of Macau; Macau China
| | - Morten Frost
- Department of Endocrinology; Odense University Hospital; Odense Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health; University of Southern Denmark; Odense Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health; University of Southern Denmark; Odense Denmark
- Unit of Human Genetics, Department of Clinical Research; University of Southern Denmark; Odense Denmark
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482
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Butcher LM, Ito M, Brimpari M, Morris TJ, Soares FAC, Ährlund-Richter L, Carey N, Vallier L, Ferguson-Smith AC, Beck S. Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells. Nat Commun 2016; 7:10458. [PMID: 26822956 PMCID: PMC4740175 DOI: 10.1038/ncomms10458] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/11/2015] [Indexed: 01/07/2023] Open
Abstract
Non-CG methylation is an unexplored epigenetic hallmark of pluripotent stem cells. Here we report that a reduction in non-CG methylation is associated with impaired differentiation capacity into endodermal lineages. Genome-wide analysis of 2,670 non-CG sites in a discovery cohort of 25 phenotyped human induced pluripotent stem cell (hiPSC) lines revealed unidirectional loss (Δβ=13%, P<7.4 × 10(-4)) of non-CG methylation that correctly identifies endodermal differentiation capacity in 23 out of 25 (92%) hiPSC lines. Translation into a simplified assay of only nine non-CG sites maintains predictive power in the discovery cohort (Δβ=23%, P<9.1 × 10(-6)) and correctly identifies endodermal differentiation capacity in nine out of ten pluripotent stem cell lines in an independent replication cohort consisting of hiPSCs reprogrammed from different cell types and different delivery systems, as well as human embryonic stem cell (hESC) lines. This finding infers non-CG methylation at these sites as a biomarker when assessing endodermal differentiation capacity as a readout.
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Affiliation(s)
- Lee M Butcher
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Mitsuteru Ito
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Minodora Brimpari
- Anne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Tiffany J Morris
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Cambridge Epigenetix, Jonas Webb Building, Babraham Campus, Cambridge CB22 3AT, UK
| | - Filipa A C Soares
- Anne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Lars Ährlund-Richter
- Division of Paediatric Oncology, Department of Women's and Children's Health, Karolinska Institutet,171 76 Stockholm, Sweden
| | - Nessa Carey
- PraxisUnico, The Jeffreys Building, St John's Innovation Park, Cambridge CB4 0DE, UK
| | - Ludovic Vallier
- Anne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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483
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Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, Gilad Y. Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PLoS Genet 2016; 12:e1005793. [PMID: 26812582 PMCID: PMC4727884 DOI: 10.1371/journal.pgen.1005793] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/17/2015] [Indexed: 02/06/2023] Open
Abstract
The advent of induced pluripotent stem cells (iPSCs) revolutionized human genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues. This technology can have immense implications for regenerative medicine, but iPSCs also represent a paradigm shift in the study of complex human phenotypes, including gene regulation and disease. Yet, an unresolved caveat of the iPSC model system is the extent to which reprogrammed iPSCs retain residual phenotypes from their precursor somatic cells. To directly address this issue, we used an effective study design to compare regulatory phenotypes between iPSCs derived from two types of commonly used somatic precursor cells. We find a remarkably small number of differences in DNA methylation and gene expression levels between iPSCs derived from different somatic precursors. Instead, we demonstrate genetic variation is associated with the majority of identifiable variation in DNA methylation and gene expression levels. We show that the cell type of origin only minimally affects gene expression levels and DNA methylation in iPSCs, and that genetic variation is the main driver of regulatory differences between iPSCs of different donors. Our findings suggest that studies using iPSCs should focus on additional individuals rather than clones from the same individual. Induced pluripotent stem cells (iPSCs) are a new and powerful cell type that provides scientists the ability to model complex human diseases in vitro. These cells can be cryopreserved and later expanded, providing a renewable source of cells from the same individual. iPSCs can be made from a variety of somatic cells in the body and many labs have created them from blood and skin cells. We asked whether the cell type of origin impacts methylation and gene expression patterns in the reprogrammed iPSCs. Our findings indicate that there are remarkably few regulatory remnants of the cell type of origin in the iPSCs. In other words, most of the variation between iPSCs can be attributed to individual genetics. Our findings suggest that studies using iPSCs should focus on obtaining additional individuals rather than additional clones from the same individual. We caution that our current findings are limited to iPSCs and further studies are needed to address the question of somatic memory in differentiated cell types.
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Affiliation(s)
- Courtney K. Burrows
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Nicholas E. Banovich
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Bryan J. Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Kristen Patterson
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Irene Gallego Romero
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan K. Pritchard
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
- Departments of Genetics and Biology, Stanford University, Stanford, California, United States of America
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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484
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Shiwa Y, Hachiya T, Furukawa R, Ohmomo H, Ono K, Kudo H, Hata J, Hozawa A, Iwasaki M, Matsuda K, Minegishi N, Satoh M, Tanno K, Yamaji T, Wakai K, Hitomi J, Kiyohara Y, Kubo M, Tanaka H, Tsugane S, Yamamoto M, Sobue K, Shimizu A. Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols. PLoS One 2016; 11:e0147519. [PMID: 26799745 PMCID: PMC4723336 DOI: 10.1371/journal.pone.0147519] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 01/05/2016] [Indexed: 11/25/2022] Open
Abstract
Differences in DNA collection protocols may be a potential confounder in epigenome-wide association studies (EWAS) using a large number of blood specimens from multiple biobanks and/or cohorts. Here we show that pre-analytical procedures involved in DNA collection can induce systematic bias in the DNA methylation profiles of blood cells that can be adjusted by cell-type composition variables. In Experiment 1, whole blood from 16 volunteers was collected to examine the effect of a 24 h storage period at 4°C on DNA methylation profiles as measured using the Infinium HumanMethylation450 BeadChip array. Our statistical analysis showed that the P-value distribution of more than 450,000 CpG sites was similar to the theoretical distribution (in quantile-quantile plot, λ = 1.03) when comparing two control replicates, which was remarkably deviated from the theoretical distribution (λ = 1.50) when comparing control and storage conditions. We then considered cell-type composition as a possible cause of the observed bias in DNA methylation profiles and found that the bias associated with the cold storage condition was largely decreased (λadjusted = 1.14) by taking into account a cell-type composition variable. As such, we compared four respective sample collection protocols used in large-scale Japanese biobanks or cohorts as well as two control replicates. Systematic biases in DNA methylation profiles were observed between control and three of four protocols without adjustment of cell-type composition (λ = 1.12–1.45) and no remarkable biases were seen after adjusting for cell-type composition in all four protocols (λadjusted = 1.00–1.17). These results revealed important implications for comparing DNA methylation profiles between blood specimens from different sources and may lead to discovery of disease-associated DNA methylation markers and the development of DNA methylation profile-based predictive risk models.
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Affiliation(s)
- Yuh Shiwa
- Division of Biobank and Data Management, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Tsuyoshi Hachiya
- Division of Biobank and Data Management, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Ryohei Furukawa
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Kanako Ono
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Hisaaki Kudo
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
| | - Jun Hata
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812–8582, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812–8582, Japan
| | - Atsushi Hozawa
- Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045, Japan
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Minegishi
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
| | - Mamoru Satoh
- Division of Biobank and Data Management, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Community Medical Supports and Health Record Informatics, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Science, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Kozo Tanno
- Department of Hygiene and Preventive Medicine, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466–8550, Japan
| | - Jiro Hitomi
- Deputy Executive Director, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Department of Anatomy, School of Medicine, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Yutaka Kiyohara
- Department of Environmental Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812–8582, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Genomic Medicine, RIKEN, Yokohama, Japan
| | - Hideo Tanaka
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2–1, Aoba-ku, Sendai 980–8575, Japan
| | - Kenji Sobue
- Executive Director, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Department of Neuroscience, Institute for Biomedical Science, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- * E-mail:
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485
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Hanna CW, Peñaherrera MS, Saadeh H, Andrews S, McFadden DE, Kelsey G, Robinson WP. Pervasive polymorphic imprinted methylation in the human placenta. Genome Res 2016; 26:756-67. [PMID: 26769960 PMCID: PMC4889973 DOI: 10.1101/gr.196139.115] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/07/2016] [Indexed: 01/19/2023]
Abstract
The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilization. There are a large number of germline DMRs that have not yet been associated with imprinting, and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs in the human placenta and investigated the dynamics of these imprinted DMRs during development in somatic and extraembryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 134 human tissue samples, publicly available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. Forty-three known and 101 novel imprinted DMRs were identified in the human placenta by comparing methylation between diandric and digynic triploid conceptions in addition to female and male gametes. Seventy-two novel DMRs showed a pattern consistent with placental-specific imprinting, and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation between placental samples. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Maria S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Deborah E McFadden
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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486
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Díaz-Pérez FI, Hiden U, Gauster M, Lang I, Konya V, Heinemann A, Lögl J, Saffery R, Desoye G, Cvitic S. Post-transcriptional down regulation of ICAM-1 in feto-placental endothelium in GDM. Cell Adh Migr 2016; 10:18-27. [PMID: 26761204 DOI: 10.1080/19336918.2015.1127467] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Maternal gestational diabetes (GDM) is associated with hyperglycaemia and hyperinsulinemia in the fetal circulation which consequently may induce endothelial dysfunction in the feto-placental vasculature. In fact, feto-placental vasculature reveals various morphological changes in response to GDM. The cell adhesion molecules (CAMs) ICAM-1, VCAM-1 and E-selectin promote attachment and trans-endothelial migration of leukocytes, and are up regulated in inflammation and endothelial dysfunction. Thus, we hypothesized that the GDM environment upregulates ICAM-1, VCAM-1 and E-selectin in the feto-placental endothelium. We isolated primary feto-placental endothelial cells (fpEC) after normal (n=18) and GDM pregnancy (n=11) and analyzed mRNA (RT-qPCR) and protein expression (Immunoblot) of ICAM-1, VCAM-1 and E-selectin. While other CAMs were unchanged on mRNA and protein levels, ICAM-1 protein was decreased by GDM. Further analysis revealed also a decrease in the release of soluble ICAM-1 (sICAM-1), whose levels correlated negatively with maternal BMI. We conclude that this reduction of ICAM-1 protein species is the result of post-translational regulation, since ICAM-1 mRNA expression was unchanged. In fact, miRNAs targeting ICAM-1 were upregulated in GDM fpEC. Immunohistochemistry showed weaker ICAM-1 staining in the placental endothelium after GDM pregnancies, and demonstrated ICAM-1 binding partners CD11a and CD18 expressed on leukocytes in fetal circulation and on placental tissue macrophages. This study identified reduction of ICAM-1 protein in fpEC in GDM pregnancy, which was regulated post-transcriptionally. Low ICAM-1 protein production may represent a protective, placenta-specific mechanism to avoid leukocyte transmigration into the placenta in response to GDM.
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Affiliation(s)
| | - Ursula Hiden
- a Department of Obstetrics and Gynecology , Medical University of Graz , Austria
| | - Martin Gauster
- b Institute of Cell Biology, Histology and Embryology, Medical University of Graz , Austria
| | - Ingrid Lang
- b Institute of Cell Biology, Histology and Embryology, Medical University of Graz , Austria
| | - Viktoria Konya
- c Institute of Experimental and Clinical Pharmacology, Medical University of Graz , Austria
| | - Akos Heinemann
- c Institute of Experimental and Clinical Pharmacology, Medical University of Graz , Austria
| | - Jelena Lögl
- a Department of Obstetrics and Gynecology , Medical University of Graz , Austria
| | - Richard Saffery
- d Cancer and Disease Epigenetics, Murdoch Children's Research Institute , Parkville , Victoria , Australia.,e Department of Pediatrics , University of Melbourne , Victoria , Australia
| | - Gernot Desoye
- a Department of Obstetrics and Gynecology , Medical University of Graz , Austria
| | - Silvija Cvitic
- a Department of Obstetrics and Gynecology , Medical University of Graz , Austria
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487
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Kirchner H, Sinha I, Gao H, Ruby MA, Schönke M, Lindvall JM, Barrès R, Krook A, Näslund E, Dahlman-Wright K, Zierath JR. Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients. Mol Metab 2016; 5:171-183. [PMID: 26977391 PMCID: PMC4770265 DOI: 10.1016/j.molmet.2015.12.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 12/23/2015] [Accepted: 12/27/2015] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Epigenetic modifications contribute to the etiology of type 2 diabetes. METHOD We performed genome-wide methylome and transcriptome analysis in liver from severely obese men with or without type 2 diabetes and non-obese men to discover aberrant pathways underlying the development of insulin resistance. Results were validated by pyrosequencing. RESULT We identified hypomethylation of genes involved in hepatic glycolysis and insulin resistance, concomitant with increased mRNA expression and protein levels. Pyrosequencing revealed the CpG-site within ATF-motifs was hypomethylated in four of these genes in liver of severely obese non-diabetic and type 2 diabetic patients, suggesting epigenetic regulation of transcription by altered ATF-DNA binding. CONCLUSION Severely obese non-diabetic and type 2 diabetic patients have distinct alterations in the hepatic methylome and transcriptome, with hypomethylation of several genes controlling glucose metabolism within the ATF-motif regulatory site. Obesity appears to shift the epigenetic program of the liver towards increased glycolysis and lipogenesis, which may exacerbate the development of insulin resistance.
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Affiliation(s)
- Henriette Kirchner
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Indranil Sinha
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Hui Gao
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maxwell A Ruby
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Milena Schönke
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jessica M Lindvall
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Romain Barrès
- Section of Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Anna Krook
- Section of Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Näslund
- Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Karin Dahlman-Wright
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Juleen R Zierath
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Section of Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Section of Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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488
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Webster AP, Smith SL, Worthington J, Barton A, Plant D. Cryopreservation of cells does not substantially alter the DNA methylome of CD3+CD4+ T cells. Scand J Rheumatol 2015; 45:329-30. [PMID: 26690697 DOI: 10.3109/03009742.2015.1115896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- A P Webster
- a Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, University of Manchester , Manchester , UK
| | - S L Smith
- a Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, University of Manchester , Manchester , UK
| | - J Worthington
- a Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, University of Manchester , Manchester , UK.,b NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences , Manchester , UK
| | - A Barton
- a Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, University of Manchester , Manchester , UK.,b NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences , Manchester , UK
| | - D Plant
- b NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences , Manchester , UK
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489
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Wong Doo N, Makalic E, Joo JE, Vajdic CM, Schmidt DF, Wong EM, Jung CH, Severi G, Park DJ, Chung J, Baglietto L, Prince HM, Seymour JF, Tam C, Hopper JL, English DR, Milne RL, Harrison SJ, Southey MC, Giles GG. Global measures of peripheral blood-derived DNA methylation as a risk factor in the development of mature B-cell neoplasms. Epigenomics 2015; 8:55-66. [PMID: 26679037 DOI: 10.2217/epi.15.97] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AIM To examine whether peripheral blood methylation is associated with risk of developing mature B-cell neoplasms (MBCNs). MATERIALS & METHODS We conducted a case-control study nested within a large prospective cohort. Peripheral blood was collected from healthy participants. Cases of MBCN were identified by linkage to cancer registries. Methylation was measured using the Infinium(®) HumanMethylation450. RESULTS During a median of 10.6-year follow-up, 438 MBCN cases were evaluated. Global hypomethylation was associated with increased risk of MBCN (odds ratio: 2.27, [95% CI: 1.59-3.25]). Within high CpG promoter regions, hypermethylation was associated with increased risk (odds ratio: 1.76 [95% CI: 1.25-2.48]). Promoter hypermethylation was observed in HOXA9 and CDH1 genes. CONCLUSION Aberrant global DNA methylation is detectable in peripheral blood collected years before diagnosis and is associated with increased risk of MBCN, suggesting changes to DNA methylation are an early event in MBCN development.
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Affiliation(s)
- Nicole Wong Doo
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Concord General & Repatriation Hospital, NSW, Australia
| | - Enes Makalic
- Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - JiHoon E Joo
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Ee Ming Wong
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Chol-Hee Jung
- VLSCI Life Sciences Computation Centre, The University of Melbourne, Victoria, Australia
| | | | - Daniel J Park
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Jessica Chung
- VLSCI Life Sciences Computation Centre, The University of Melbourne, Victoria, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Henry Miles Prince
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - John F Seymour
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Constantine Tam
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
| | - Simon J Harrison
- Department of Haematology, Peter MacCallum Cancer Centre, Victoria, Australia
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Australia.,Centre for Epidemiology & Biostatistics, The University of Melbourne, Victoria, Australia
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490
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Fasanelli F, Baglietto L, Ponzi E, Guida F, Campanella G, Johansson M, Grankvist K, Johansson M, Assumma MB, Naccarati A, Chadeau-Hyam M, Ala U, Faltus C, Kaaks R, Risch A, De Stavola B, Hodge A, Giles GG, Southey MC, Relton CL, Haycock PC, Lund E, Polidoro S, Sandanger TM, Severi G, Vineis P. Hypomethylation of smoking-related genes is associated with future lung cancer in four prospective cohorts. Nat Commun 2015; 6:10192. [PMID: 26667048 PMCID: PMC4682166 DOI: 10.1038/ncomms10192] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 11/16/2015] [Indexed: 01/10/2023] Open
Abstract
DNA hypomethylation in certain genes is associated with tobacco exposure but it is unknown whether these methylation changes translate into increased lung cancer risk. In an epigenome-wide study of DNA from pre-diagnostic blood samples from 132 case-control pairs in the NOWAC cohort, we observe that the most significant associations with lung cancer risk are for cg05575921 in AHRR (OR for 1 s.d.=0.37, 95% CI: 0.31-0.54, P-value=3.3 × 10(-11)) and cg03636183 in F2RL3 (OR for 1 s.d.=0.40, 95% CI: 0.31-0.56, P-value=3.9 × 10(-10)), previously shown to be strongly hypomethylated in smokers. These associations remain significant after adjustment for smoking and are confirmed in additional 664 case-control pairs tightly matched for smoking from the MCCS, NSHDS and EPIC HD cohorts. The replication and mediation analyses suggest that residual confounding is unlikely to explain the observed associations and that hypomethylation of these CpG sites may mediate the effect of tobacco on lung cancer risk.
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Affiliation(s)
- Francesca Fasanelli
- Molecular end Epidemiology Unit, HuGeF, Human Genetics Foundation, Torino 10126, Italy
- Unit of Cancer Epidemiology, Citta' della Salute e della Scienza Hospital-University of Turin, Center for Cancer Prevention, Via Santena 7, Torino 10126, Italy
| | - Laura Baglietto
- Inserm (Institut National de la Santé et de la Recherche Médicale), Centre for Research in Epidemiology and Population Health, U1018, Team 9, 114 rue Edouard Vaillant, Villejuif 94805, France
- Paris-South University, Villejuif 91450, France
- Department of Genetic Epidemiology, Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne, Victoria 3004, Australia
- School of Population and Global Health, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Erica Ponzi
- Molecular end Epidemiology Unit, HuGeF, Human Genetics Foundation, Torino 10126, Italy
| | - Florence Guida
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Gianluca Campanella
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Mattias Johansson
- Genetic Epidemiology Division, International Agency for Research on Cancer, Lyon 69008, France
- Department of Biobank Research, Umeå University, Umeå SE—90187, Sweden
| | - Kjell Grankvist
- Department of Biobank Research, Umeå University, Umeå SE—90187, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Umeå University, Umeå SE—90187, Sweden
| | | | - Alessio Naccarati
- Molecular end Epidemiology Unit, HuGeF, Human Genetics Foundation, Torino 10126, Italy
| | - Marc Chadeau-Hyam
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Ugo Ala
- Department of Molecular Biotechnology and Health Sciences, Università di Torino, Torino 10126, Italy
| | - Christian Faltus
- Division of Epigenomics and Cancer Risk Factors, DKFZ—German Cancer Research Center, Heidelberg 69121, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, DKFZ—German Cancer Research Center, Heidelberg 69121, Germany
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, DKFZ—German Cancer Research Center, Heidelberg 69121, Germany
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany
- Division of Cancer Research and Epigenetics, Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria
| | - Bianca De Stavola
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Allison Hodge
- Department of Genetic Epidemiology, Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne, Victoria 3004, Australia
| | - Graham G. Giles
- Department of Genetic Epidemiology, Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne, Victoria 3004, Australia
- School of Population and Global Health, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Philip C. Haycock
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Eiliv Lund
- Department of Community Medicine UiT–The Arctic University of Norway, Tromso 9019, Norway
| | - Silvia Polidoro
- Molecular end Epidemiology Unit, HuGeF, Human Genetics Foundation, Torino 10126, Italy
| | - Torkjel M. Sandanger
- Department of Community Medicine UiT–The Arctic University of Norway, Tromso 9019, Norway
| | - Gianluca Severi
- Molecular end Epidemiology Unit, HuGeF, Human Genetics Foundation, Torino 10126, Italy
- Inserm (Institut National de la Santé et de la Recherche Médicale), Centre for Research in Epidemiology and Population Health, U1018, Team 9, 114 rue Edouard Vaillant, Villejuif 94805, France
- Paris-South University, Villejuif 91450, France
- Department of Genetic Epidemiology, Cancer Epidemiology Centre, Cancer Council of Victoria, Melbourne, Victoria 3004, Australia
- School of Population and Global Health, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Paolo Vineis
- Molecular end Epidemiology Unit, HuGeF, Human Genetics Foundation, Torino 10126, Italy
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
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491
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Geybels MS, Alumkal JJ, Luedeke M, Rinckleb A, Zhao S, Shui IM, Bibikova M, Klotzle B, van den Brandt PA, Ostrander EA, Fan JB, Feng Z, Maier C, Stanford JL. Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors. Clin Epigenetics 2015; 7:128. [PMID: 26692910 PMCID: PMC4676897 DOI: 10.1186/s13148-015-0161-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/03/2015] [Indexed: 12/17/2022] Open
Abstract
Background About half of all prostate cancers harbor the TMPRSS2:ERG (T2E) gene fusion. While T2E-positive and T2E-negative tumors represent specific molecular subtypes of prostate cancer (PCa), previous studies have not yet comprehensively investigated how these tumor subtypes differ at the epigenetic level. We therefore investigated epigenome-wide DNA methylation profiles of PCa stratified by T2E status. Results The study included 496 patients with clinically localized PCa who had a radical prostatectomy as primary treatment for PCa. Fluorescence in situ hybridization (FISH) “break-apart” assays were used to determine tumor T2E-fusion status, which showed that 266 patients (53.6 %) had T2E-positive PCa. The study showed global DNA methylation differences between tumor subtypes. A large number of differentially methylated CpG sites were identified (false-discovery rate [FDR] Q-value <0.00001; n = 27,876) and DNA methylation profiles accurately distinguished between tumor T2E subgroups. A number of top-ranked differentially methylated CpGs in genes (FDR Q-values ≤1.53E−29) were identified: C3orf14, CACNA1D, GREM1, KLK10, NT5C, PDE4D, RAB40C, SEPT9, and TRIB2, several of which had a corresponding alteration in mRNA expression. These genes may have various roles in the pathogenesis of PCa, and the calcium-channel gene CACNA1D is a known ERG-target. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. Conclusions This study identified substantial differences in DNA methylation profiles of T2E-positive and T2E-negative tumors, thereby providing further evidence that different underlying oncogenic pathways characterize these molecular subtypes. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0161-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Joshi J Alumkal
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR USA
| | - Manuel Luedeke
- Institute of Human Genetics and Department of Urology, Faculty of Medicine, University of Ulm, Ulm, Germany
| | - Antje Rinckleb
- Institute of Human Genetics and Department of Urology, Faculty of Medicine, University of Ulm, Ulm, Germany
| | - Shanshan Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NC Research Triangle Park, USA
| | - Irene M Shui
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | | | - Piet A van den Brandt
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD USA
| | - Jian-Bing Fan
- Illumina, Inc., San Diego, CA USA ; Present Address: AnchorDx Corp., Guangzhou, 510300 People's Republic of China
| | | | - Christiane Maier
- Institute of Human Genetics and Department of Urology, Faculty of Medicine, University of Ulm, Ulm, Germany
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA USA
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492
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Soriano-Tárraga C, Jiménez-Conde J, Giralt-Steinhauer E, Mola-Caminal M, Vivanco-Hidalgo RM, Ois A, Rodríguez-Campello A, Cuadrado-Godia E, Sayols-Baixeras S, Elosua R, Roquer J. Epigenome-wide association study identifies TXNIP gene associated with type 2 diabetes mellitus and sustained hyperglycemia. Hum Mol Genet 2015; 25:609-19. [PMID: 26643952 DOI: 10.1093/hmg/ddv493] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/26/2015] [Indexed: 12/17/2022] Open
Abstract
Type 2 diabetes mellitus (DM) is an established risk factor for a wide range of vascular diseases, including ischemic stroke (IS). Glycated hemoglobin A1c (HbA1c), a marker for average blood glucose levels over the previous 12 weeks, is used as a measure of glycemic control and also as a diagnostic criterion for diabetes (HbA1c levels ≥ 6.5%). Epigenetic mechanisms, such as DNA methylation, may be associated with aging processes and with modulation of the risk of various pathologies, such as DM. Specifically, DNA methylation could be one of the mechanisms mediating the relation between DM and environmental exposures. Our goal was to identify new CpG methylation sites associated with DM. We performed a genome-wide methylation study in whole-blood DNA from an IS patient cohorts. Illumina HumanMethylation450 BeadChip array was used to measure DNA methylation in CpG sites. All statistical analyses were adjusted for sex, age, hyperlipidemia, body mass index (BMI), smoking habit and cell count. Findings were replicated in two independent cohorts, an IS cohort and a population-based cohort, using the same array. In the discovery phase (N = 355), we identified a CpG site, cg19693031 (located in the TXNIP gene) that was associated with DM (P = 1.17 × 10(-12)); this CpG was replicated in two independent cohorts (N = 167 and N = 645). Methylation of TXNIP was inversely and intensely associated with HbA1c levels (P = 7.3 × 10(-16)), specifically related to diabetic patients with poor control of glucose levels. We identified an association between the TXNIP gene and DM through epigenetic mechanisms, related to sustained hyperglycemia levels (HbA1c ≥ 7%).
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Affiliation(s)
- Carolina Soriano-Tárraga
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Jiménez-Conde
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain,
| | - Eva Giralt-Steinhauer
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Marina Mola-Caminal
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Rosa M Vivanco-Hidalgo
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Angel Ois
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana Rodríguez-Campello
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Elisa Cuadrado-Godia
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain and Universitat Pompeu Fabra, Barcelona, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain and
| | - Jaume Roquer
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
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493
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Laufer BI, Kapalanga J, Castellani CA, Diehl EJ, Yan L, Singh SM. Associative DNA methylation changes in children with prenatal alcohol exposure. Epigenomics 2015; 7:1259-74. [DOI: 10.2217/epi.15.60] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aim: Prenatal alcohol exposure (PAE) can cause fetal alcohol spectrum disorders (FASD). Previously, we assessed PAE in brain tissue from mouse models, however whether these changes are present in humans remains unknown. Materials & methods: In this report, we show some identical changes in DNA methylation in the buccal swabs of six children with FASD using the 450K array. Results: The changes occur in genes related to protocadherins, glutamatergic synapses, and hippo signaling. The results were found to be similar in another heterogeneous replication group of six FASD children. Conclusion: The replicated results suggest that children born with FASD have unique DNA methylation defects that can be influenced by sex and medication exposure. Ultimately, with future clinical development, assessment of DNA methylation from buccal swabs can provide a novel strategy for the diagnosis of FASD.
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Affiliation(s)
- Benjamin I Laufer
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Joachim Kapalanga
- Department of Pediatrics, The University of Western Ontario, London, ON, Canada
| | - Christina A Castellani
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Eric J Diehl
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | | | - Shiva M Singh
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
- Department of Pediatrics, The University of Western Ontario, London, ON, Canada
- Program in Neuroscience, The University of Western Ontario, London, ON, Canada
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494
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Geybels MS, Zhao S, Wong CJ, Bibikova M, Klotzle B, Wu M, Ostrander EA, Fan JB, Feng Z, Stanford JL. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue. Prostate 2015; 75:1941-50. [PMID: 26383847 PMCID: PMC4928710 DOI: 10.1002/pros.23093] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/31/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Aberrant DNA methylation may promote prostate carcinogenesis. We investigated epigenome-wide DNA methylation profiles in prostate cancer (PCa) compared to adjacent benign tissue to identify differentially methylated CpG sites. METHODS The study included paired PCa and adjacent benign tissue samples from 20 radical prostatectomy patients. Epigenetic profiling was done using the Infinium HumanMethylation450 BeadChip. Linear models that accounted for the paired study design and False Discovery Rate Q-values were used to evaluate differential CpG methylation. mRNA expression levels of the genes with the most differentially methylated CpG sites were analyzed. RESULTS In total, 2,040 differentially methylated CpG sites were identified in PCa versus adjacent benign tissue (Q-value < 0.001), the majority of which were hypermethylated (n = 1,946; 95%). DNA methylation profiles accurately distinguished between PCa and benign tissue samples. Twenty-seven top-ranked hypermethylated CpGs had a mean methylation difference of at least 40% between tissue types, which included 25 CpGs in 17 genes. Furthermore, for 10 genes over 50% of promoter region CpGs were hypermethylated in PCa versus benign tissue. The top-ranked differentially methylated genes included three genes that were associated with both promoter hypermethylation and reduced gene expression: SCGB3A1, HIF3A, and AOX1. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. CONCLUSIONS This study of PCa versus adjacent benign tissue showed many differentially methylated CpGs and regions in and outside gene promoter regions, which may potentially be used for the development of future epigenetic-based diagnostic tests or as therapeutic targets.
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Affiliation(s)
- Milan S. Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Shanshan Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- National Institute of Environmental Health Sciences, Biostatistics & Computational Biology Branch, North Carolina
| | - Chao-Jen Wong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Michael Wu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | | | | | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
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495
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Fagny M, Patin E, MacIsaac JL, Rotival M, Flutre T, Jones MJ, Siddle KJ, Quach H, Harmant C, McEwen LM, Froment A, Heyer E, Gessain A, Betsem E, Mouguiama-Daouda P, Hombert JM, Perry GH, Barreiro LB, Kobor MS, Quintana-Murci L. The epigenomic landscape of African rainforest hunter-gatherers and farmers. Nat Commun 2015; 6:10047. [PMID: 26616214 PMCID: PMC4674682 DOI: 10.1038/ncomms10047] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/28/2015] [Indexed: 12/23/2022] Open
Abstract
The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time. Genetic and environmental factors affect genome-wide patterns of epigenetic variation. Here, the authors show that while current habitat and historical lifestyle impact the methylome of rainforest hunter-gatherers and sedentary farmers, the biological functions affected and the degree of genetic control differ.
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Affiliation(s)
- Maud Fagny
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.,Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.,Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris 75015, France
| | - Etienne Patin
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.,Centre National de la Recherche Scientifique, URA3012, Paris 75015, France
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4
| | - Maxime Rotival
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.,Centre National de la Recherche Scientifique, URA3012, Paris 75015, France
| | | | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4
| | - Katherine J Siddle
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.,Centre National de la Recherche Scientifique, URA3012, Paris 75015, France
| | - Hélène Quach
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.,Centre National de la Recherche Scientifique, URA3012, Paris 75015, France
| | - Christine Harmant
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.,Centre National de la Recherche Scientifique, URA3012, Paris 75015, France
| | - Lisa M McEwen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4
| | - Alain Froment
- IRD-MNHN, Sorbonne Universités, UMR208, Paris 75005, France
| | - Evelyne Heyer
- CNRS, MNHN, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Université, UMR7206, Paris 75005, France
| | - Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Paris 75015, France
| | - Edouard Betsem
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Paris 75015, France.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, BP1364 Yaoundé, Cameroon
| | - Patrick Mouguiama-Daouda
- Laboratoire Langue, Culture et Cognition (LCC), Université Omar Bongo, BP 13131 Libreville, Gabon
| | | | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Luis B Barreiro
- Université de Montréal, Centre de Recherche CHU Sainte-Justine, Montréal, Canada H3T 1C5
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4
| | - Lluis Quintana-Murci
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.,Centre National de la Recherche Scientifique, URA3012, Paris 75015, France
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496
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Daca-Roszak P, Pfeifer A, Żebracka-Gala J, Rusinek D, Szybińska A, Jarząb B, Witt M, Ziętkiewicz E. Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies. BMC Genomics 2015; 16:1003. [PMID: 26607064 PMCID: PMC4659175 DOI: 10.1186/s12864-015-2202-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 11/11/2015] [Indexed: 01/22/2023] Open
Abstract
Background Infinium HumanMethylation 450 BeadChip Arrays by Illumina (Illumina HM450K) are among the most popular CpG microarray platforms widely used in biological and medical research. Several recent studies highlighted the potentially confounding impact of the genomic variation on the results of methylation studies performed using Illumina’s Infinium methylation probes. However, the complexity of SNPs impact on the methylation level measurements (β values) has not been comprehensively described. Results In our comparative study of European and Asian populations performed using Illumina HM450K, we found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. Characteristic tri-modal or bi-modal patterns of β values distribution among individual samples were observed for CpGs with SNPs in the first and second position, respectively. To better understand how SNPs affect methylation readouts, we investigated their impact in the context of SNP position and type, and of the Illumina probe type (Infinium I or II). Conclusions Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes. In addition, it provides important practical clues for discriminating between differences due to the methylation status and to the genomic polymorphisms, based on the inspection of methylation readouts in individual samples. This approach is of special importance when Illumina Infinium assay is used for any comparative population studies, whether related to cancer, disease, ethnicity where SNP frequencies differentiate the studied groups.
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Affiliation(s)
| | - Aleksandra Pfeifer
- Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | - Jadwiga Żebracka-Gala
- Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | - Dagmara Rusinek
- Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | | | - Barbara Jarząb
- Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland. .,International Institute of Molecular and Cell Biology, Warsaw, Poland.
| | - Ewa Ziętkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.
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497
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Kok DEG, Dhonukshe-Rutten RAM, Lute C, Heil SG, Uitterlinden AG, van der Velde N, van Meurs JBJ, van Schoor NM, Hooiveld GJEJ, de Groot LCPGM, Kampman E, Steegenga WT. The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects. Clin Epigenetics 2015; 7:121. [PMID: 26568774 PMCID: PMC4644301 DOI: 10.1186/s13148-015-0154-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/04/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Folate and its synthetic form folic acid function as donor of one-carbon units and have been, together with other B-vitamins, implicated in programming of epigenetic processes such as DNA methylation during early development. To what extent regulation of DNA methylation can be altered via B-vitamins later in life, and how this relates to health and disease, is not exactly known. The aim of this study was to identify effects of long-term supplementation with folic acid and vitamin B12 on genome-wide DNA methylation in elderly subjects. This project was part of a randomized, placebo-controlled trial on effects of supplemental intake of folic acid and vitamin B12 on bone fracture incidence (B-vitamins for the PRevention Of Osteoporotic Fractures (B-PROOF) study). Participants with mildly elevated homocysteine levels, aged 65-75 years, were randomly assigned to take 400 μg folic acid and 500 μg vitamin B12 per day or a placebo during an intervention period of 2 years. DNA was isolated from buffy coats, collected before and after intervention, and genome-wide DNA methylation was determined in 87 participants (n = 44 folic acid/vitamin B12, n = 43 placebo) using the Infinium HumanMethylation450 BeadChip. RESULTS After intervention with folic acid and vitamin B12, 162 (versus 14 in the placebo group) of the 431,312 positions were differentially methylated as compared to baseline. Comparisons of the DNA methylation changes in the participants receiving folic acid and vitamin B12 versus placebo revealed one single differentially methylated position (cg19380919) with a borderline statistical significance. However, based on the analyses of differentially methylated regions (DMRs) consisting of multiple positions, we identified 6 regions that differed statistically significantly between the intervention and placebo group. Pronounced changes were found for regions in the DIRAS3, ARMC8, and NODAL genes, implicated in carcinogenesis and early embryonic development. Furthermore, serum levels of folate and vitamin B12 or plasma homocysteine were related to DNA methylation of 173, 425, and 11 regions, respectively. Interestingly, for several members of the developmental HOX genes, DNA methylation was related to serum levels of folate. CONCLUSIONS Long-term supplementation with folic acid and vitamin B12 in elderly subjects resulted in effects on DNA methylation of several genes, among which genes implicated in developmental processes.
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Affiliation(s)
- Dieuwertje E G Kok
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | | | - Carolien Lute
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Sandra G Heil
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Genetic Laboratory Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands ; Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nathalie van der Velde
- Genetic Laboratory Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands ; Department of Internal Medicine, Section of Geriatrics, Academic Medical Center, Amsterdam, The Netherlands
| | - Joyce B J van Meurs
- Genetic Laboratory Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Natasja M van Schoor
- Department of Epidemiology and Biostatistics, EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Guido J E J Hooiveld
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Lisette C P G M de Groot
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Ellen Kampman
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Wilma T Steegenga
- Division of Human Nutrition, Wageningen University, PO Box 8129, 6700 EV Wageningen, The Netherlands
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498
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DNA Methylation Changes in the IGF1R Gene in Birth Weight Discordant Adult Monozygotic Twins. Twin Res Hum Genet 2015; 18:635-46. [DOI: 10.1017/thg.2015.76] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Low birth weight (LBW) can have an impact on health outcomes in later life, especially in relation to pre-disposition to metabolic disease. Several studies suggest that LBW resulting from restricted intrauterine growth leaves a footprint on DNA methylation in utero, and this influence likely persists into adulthood. To investigate this further, we performed epigenome-wide association analyses of blood DNA methylation using Infinium HumanMethylation450 BeadChip profiles in 71 adult monozygotic (MZ) twin pairs who were extremely discordant for birth weight. A signal mapping to the IGF1R gene (cg12562232, p = 2.62 × 10−8), was significantly associated with birth weight discordance at a genome-wide false-discovery rate (FDR) of 0.05. We pursued replication in three additional independent datasets of birth weight discordant MZ pairs and observed the same direction of association, but the results were not significant. However, a meta-analysis across the four independent samples, in total 216 birth-weight discordant MZ twin pairs, showed a significant positive association between birth weight and DNA methylation differences at IGF1R (random-effects meta-analysis p = .04), and the effect was particularly pronounced in older twins (random-effects meta-analysis p = .008, 98 older birth-weight discordant MZ twin pairs). The results suggest that severe intra-uterine growth differences (birth weight discordance >20%) are associated with methylation changes in the IGF1R gene in adulthood, independent of genetic effects.
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499
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Glossop JR, Emes RD, Nixon NB, Packham JC, Fryer AA, Mattey DL, Farrell WE. Genome-wide profiling in treatment-naive early rheumatoid arthritis reveals DNA methylome changes in T and B lymphocytes. Epigenomics 2015; 8:209-24. [PMID: 26556652 DOI: 10.2217/epi.15.103] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AIM Although aberrant DNA methylation has been described in rheumatoid arthritis (RA), no studies have interrogated this epigenetic modification in early disease. Following recent investigations of T and B lymphocytes in established disease, we now characterize in these cell populations genome-wide DNA methylation in treatment-naive patients with early RA. PATIENTS & METHODS HumanMethylation450 BeadChips were used to examine genome-wide DNA methylation in lymphocyte populations from 23 early RA patients and 11 healthy individuals. RESULTS Approximately 2000 CpGs in each cell type were differentially methylated in early RA. Clustering analysis identified a novel methylation signature in each cell type (150 sites in T lymphocytes, 113 sites in B lymphocytes) that clustered all patients separately from controls. A subset of sites differentially methylated in early RA displayed similar changes in established disease. CONCLUSION Treatment-naive early RA patients display novel disease-specific DNA methylation aberrations, supporting a potential role for these changes in the development of RA.
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Affiliation(s)
- John R Glossop
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK.,Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Richard D Emes
- School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK.,Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Nicola B Nixon
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Jon C Packham
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Anthony A Fryer
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Derek L Mattey
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK.,Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - William E Farrell
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
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500
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Genetic and Environmental Causes of Variation in the Difference Between Biological Age Based on DNA Methylation and Chronological Age for Middle-Aged Women. Twin Res Hum Genet 2015; 18:720-6. [PMID: 26527295 DOI: 10.1017/thg.2015.75] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The disease- and mortality-related difference between biological age based on DNA methylation and chronological age (Δage) has been found to have approximately 40% heritability by assuming that the familial correlation is only explained by additive genetic factors. We calculated two different Δage measures for 132 middle-aged female twin pairs (66 monozygotic and 66 dizygotic twin pairs) and their 215 sisters using DNA methylation data measured by the Infinium HumanMethylation450 BeadChip arrays. For each Δage measure, and their combined measure, we estimated the familial correlation for MZ, DZ and sibling pairs using the multivariate normal model for pedigree analysis. We also pooled our estimates with those from a former study to estimate weighted average correlations. For both Δage measures, there was familial correlation that varied across different types of relatives. No evidence of a difference was found between the MZ and DZ pair correlations, or between the DZ and sibling pair correlations. The only difference was between the MZ and sibling pair correlations (p < .01), and there was marginal evidence that the MZ pair correlation was greater than twice the sibling pair correlation (p < .08). For weighted average correlation, there was evidence that the MZ pair correlation was greater than the DZ pair correlation (p < .03), and marginally greater than twice the sibling pair correlation (p < .08). The varied familial correlation of Δage is not explained by additive genetic factors alone, implying the existence of shared non-genetic factors explaining variation in Δage for middle-aged women.
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