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https://www.readbyqxmd.com/read/29315717/impact-of-cigarette-smoking-on-sperm-dna-methylation-and-its-effect-on-sperm-parameters
#1
Y Alkhaled, M Laqqan, S Tierling, C Lo Porto, H Amor, M E Hammadeh
DNA methylation is an epigenetic modification of the genome. The purpose of this study was to determine the influence of cigarette-smoking on sperm DNA methylation from a genomewide survey of sperm samples and to ascertain its effect on sperm parameters. Twenty-eight sperm DNA samples (from 14 fertile smokers as a case study and 14 proven fertile nonsmokers as controls) were subjected to Infinium 450K BeadChip arrays to identify the changes in the DNA methylation level between the two groups. Then, deep bisulphite sequencing was used to validate five CpGs on 78 samples...
January 9, 2018: Andrologia
https://www.readbyqxmd.com/read/29258561/a-pilot-investigation-on-dna-methylation-modifications-associated-with-complex-posttraumatic-symptoms-in-elderly-traumatized-in-childhood
#2
Zoya Marinova, Andreas Maercker, Edna Grünblatt, Tomasz K Wojdacz, Susanne Walitza
OBJECTIVE: Complex posttraumatic stress disorder (CPTSD) is a newly proposed diagnosis in the International Classification of Diseases-version 11, which is currently intensively investigated. Childhood trauma is regarded as main source of CPTSD symptoms, even in later life. Induction of DNA methylation changes by childhood trauma may contribute to its long-lasting adverse health consequences. The current study analyzed the correlation of genome-wide DNA methylation profiles with complex posttraumatic sequelae in buccal epithelial cells from 31 elderly former indentured child laborers (Verdingkinder) using the Infinium Illumina 450k Human DNA methylation chip...
December 19, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29231988/methylation-based-estimated-biological-age-and-cardiovascular-disease
#3
Lars Lind, Erik Ingelsson, Johan Sundström, Agneta Siegbahn, Erik Lampa
BACKGROUND: DNA methylation changes over life at specific sites in the genome, which can be used to estimate "biological age". The aim of this population-based longitudinal cohort study was to investigate the association between estimated biological age and incident cardiovascular disease (CVD). MATERIALS AND METHODS: Based on formulas published by Hannum et al and Horvath et al, "biological age" was calculated using data from the Illumina 450k Bead Methylation chip in 832 participants free from cardiovascular disease in the Prospective Study of the Vasculature in Uppsala Seniors (PIVUS) study (50% women, all aged 70 years at the examination)...
December 12, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29230837/alterations-in-dna-methylation-patterns-and-gene-expression-in-spermatozoa-of-subfertile-males
#4
M Laqqan, M E Hammadeh
This study was designed to evaluate the DNA methylation patterns and gene expression in spermatozoa from subfertile males. Thirty samples were subjected to 450K arrays as a screening study to evaluate the variation in sperm DNA methylation levels between cases and controls groups, and then three CpG sites (cg07227024, cg05813498 and cg23081194) have the highest difference in methylation levels and located within ALS2CR12, GAA and UBE2G2 genes respectively; these were selected for further analysis using deep bisulphite sequencing and qPCR in 136 samples (64 proven fertile males "controls" and 72 subfertile males "cases")...
December 12, 2017: Andrologia
https://www.readbyqxmd.com/read/29224151/a-guide-to-illumina-beadchip-data-analysis
#5
Michael C Wu, Pei-Fen Kuan
The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29197076/dna-methylation-based-biological-aging-and-cancer-risk-and-survival-pooled-analysis-of-seven-prospective-studies
#6
Pierre-Antoine Dugué, Julie K Bassett, JiHoon E Joo, Chol-Hee Jung, Ee Ming Wong, Margarita Moreno-Betancur, Daniel Schmidt, Enes Makalic, Shuai Li, Gianluca Severi, Allison M Hodge, Daniel D Buchanan, Dallas R English, John L Hopper, Melissa C Southey, Graham G Giles, Roger L Milne
The association between aging and cancer is complex. Recent studies have developed measures of biological aging based on DNA methylation and called them 'age acceleration'. We aimed to assess associations of age acceleration with risk of and survival from seven common cancers. Seven case-control studies of DNA methylation and colorectal, gastric, kidney, lung, prostate and urothelial cancer, and B-cell lymphoma, nested in the Melbourne Collaborative Cohort Study were conducted. Cancer cases, vital status and cause of death were ascertained through linkage with cancer and death registries...
December 2, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29168084/bioinformatic-analysis-of-gene-expression-and-methylation-regulation-in-glioblastoma
#7
Wen Wang, Zheng Zhao, Fan Wu, Haoyuan Wang, Jiangfei Wang, Qing Lan, Jizong Zhao
Different gene expression and methylation profiles are identified in glioblastoma (GBM). To screen the differentially expressed genes affected by DNA methylation modification and further investigate their prognostic values for GBMs. We included The Cancer Genome Atlas (TCGA) RNA sequencing (676) and DNA methylation (Illumina Human Methylation 450K; 657) databases to detect the gene expression and methylation profiles. Chinese Glioma Genome Atlas (CGGA) RNA sequencing database and TCGA DNA methylation (Illumina Human Methylation 27K; 283) was included for validation...
November 22, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29164275/dna-methylation-markers-associated-with-type-2-diabetes-fasting-glucose-and-hba1c-levels-a-systematic-review-and-replication-in-a-case-control-sample-of-the-lifelines-study
#8
Eliza Walaszczyk, Mirjam Luijten, Annemieke M W Spijkerman, Marc J Bonder, Helen L Lutgers, Harold Snieder, Bruce H R Wolffenbuttel, Jana V van Vliet-Ostaptchouk
AIMS/HYPOTHESIS: Epigenetic mechanisms may play an important role in the aetiology of type 2 diabetes. Recent epigenome-wide association studies (EWASs) identified several DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA1c levels. Here we present a systematic review of these studies and attempt to replicate the CpG sites (CpGs) with the most significant associations from these EWASs in a case-control sample of the Lifelines study. METHODS: We performed a systematic literature search in PubMed and EMBASE for EWASs to test the association between DNA methylation and type 2 diabetes and/or glycaemic traits and reviewed the search results...
November 21, 2017: Diabetologia
https://www.readbyqxmd.com/read/29162648/biological-age-of-the-endometrium-using-dna-methylation
#9
Mia S Olesen, Anna Starnawska, Jonas Bybjerg-Grauholm, Alexandra P Bielfeld, Inge E Agerholm, Axel Forman, Michael T Overgaard, Mette Nyegaard
Age has a detrimental effect on reproduction and as an increasing number of women postpone motherhood, it is imperative to assess biological age in terms of fertility prognosis and optimizing fertility treatment individually. Horvath's epigenetic clock is a mathematical algorithm that calculates the biological age of human cells, tissues or organs based on DNA methylation levels. The clock however, was previously shown to be highly inaccurate for the human endometrium, most likely because of the hormonal responsive nature of this tissue...
November 21, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/29159506/a-longitudinal-study-of-dna-methylation-as-a-potential-mediator-of-age-related-diabetes-risk
#10
Crystal D Grant, Nadereh Jafari, Lifang Hou, Yun Li, James D Stewart, Guosheng Zhang, Archana Lamichhane, JoAnn E Manson, Andrea A Baccarelli, Eric A Whitsel, Karen N Conneely
DNA methylation (DNAm) has been found to show robust and widespread age-related changes across the genome. DNAm profiles from whole blood can be used to predict human aging rates with great accuracy. We sought to test whether DNAm-based predictions of age are related to phenotypes associated with type 2 diabetes (T2D), with the goal of identifying risk factors potentially mediated by DNAm. Our participants were 43 women enrolled in the Women's Health Initiative. We obtained methylation data via the Illumina 450K Methylation array on whole blood samples from participants at three timepoints, covering on average 16 years per participant...
November 20, 2017: GeroScience
https://www.readbyqxmd.com/read/29099283/lowly-methylated-region-analysis-identifies-ebf1-as-a-potential-epigenetic-modifier-in-breast-cancer
#11
Nora Fernandez-Jimenez, Athena Sklias, Szilvia Ecsedi, Vincent Cahais, Davide Degli-Esposti, Antonin Jay, Pierre Benoit Ancey, Hae Dong Woo, Hector Hernandez-Vargas, Zdenko Herceg
Breast cancer (BC) encompasses heterogeneous pathologies with different subtypes exhibiting distinct molecular changes, including those related to DNA methylation. However, the role of these changes in mediating BC heterogeneity is poorly understood. Lowly methylated regions (LMRs), non-CpG island loci that usually contain transcription factor (TF) binding sites, have been suggested to act as regulatory elements that define cellular identity. In this study, we aimed to identify the key subtype-specific TFs that may lead to LMR generation and shape the BC methylome and transcription program...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29084233/genetically-defined-elevated-homocysteine-levels-do-not-result-in-widespread-changes-of-dna-methylation-in-leukocytes
#12
Pooja R Mandaviya, Roby Joehanes, Dylan Aïssi, Brigitte Kühnel, Riccardo E Marioni, Vinh Truong, Lisette Stolk, Marian Beekman, Marc Jan Bonder, Lude Franke, Christian Gieger, Tianxiao Huan, M Arfan Ikram, Sonja Kunze, Liming Liang, Jan Lindemans, Chunyu Liu, Allan F McRae, Michael M Mendelson, Martina Müller-Nurasyid, Annette Peters, P Eline Slagboom, John M Starr, David-Alexandre Trégouët, André G Uitterlinden, Marleen M J van Greevenbroek, Diana van Heemst, Maarten van Iterson, Philip S Wells, Chen Yao, Ian J Deary, France Gagnon, Bastiaan T Heijmans, Daniel Levy, Pierre-Emmanuel Morange, Melanie Waldenberger, Sandra G Heil, Joyce B J van Meurs
BACKGROUND: DNA methylation is affected by the activities of the key enzymes and intermediate metabolites of the one-carbon pathway, one of which involves homocysteine. We investigated the effect of the well-known genetic variant associated with mildly elevated homocysteine: MTHFR 677C>T independently and in combination with other homocysteine-associated variants, on genome-wide leukocyte DNA-methylation. METHODS: Methylation levels were assessed using Illumina 450k arrays on 9,894 individuals of European ancestry from 12 cohort studies...
2017: PloS One
https://www.readbyqxmd.com/read/29072328/aberrations-in-sperm-dna-methylation-patterns-of-males-suffering-from-reduced-fecundity
#13
M Laqqan, M E Hammadeh
The purpose of this study was to evaluate the aberrations in sperm DNA methylation patterns of males suffering from reduced fecundity. A total of 108 males (65 males suffering from reduced fecundity as cases and 43 proven fertile males as a control) were included in the study. Thirty samples were subjected to 450K arrays as a screening phase, and then, three CpG sites located in the following genes: TYRO3, CGβ and FAM189A1 were selected to validate on 78 samples using deep bisulphite sequencing. A significant difference in the methylation level was found between cases and controls at all CpGs in TYRO3 gene-related amplicon (CpG1, p ≤ ...
October 26, 2017: Andrologia
https://www.readbyqxmd.com/read/29049890/dna-methylation-signatures-in-peripheral-blood-mononuclear-cells-from-a-lifestyle-intervention-for-women-at-midlife-a-pilot-rct
#14
Lisa M McEwen, Evan G Gatev, Meaghan J Jones, Julia L MacIsaac, Megan M McAllister, Rebecca E Goulding, Kenneth M Madden, Martin G Dawes, Michael S Kobor, Maureen C Ashe
OBJECTIVES: Physical activity confers many health benefits, but the underlying mechanisms require further exploration. In this pilot randomized controlled trial we tested the association between longitudinal measures of DNA methylation and changes in objective measures including physical activity, weight loss, and C-reactive protein levels in community-dwelling women aged 55 to 70 years. METHODS: We assessed DNA methylation from 20 healthy post-menopausal women (55-70 years of age), who did not have a mobility disability and allocated them to a group-based intervention, Everyday Activity Supports You (EASY), or a control group (monthly group-based health-related education sessions)...
October 19, 2017: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/29047347/the-dynamics-of-smoking-related-disturbed-methylation-a-two-time-point-study-of-methylation-change-in-smokers-non-smokers-and-former-smokers
#15
Rory Wilson, Simone Wahl, Liliane Pfeiffer, Cavin K Ward-Caviness, Sonja Kunze, Anja Kretschmer, Eva Reischl, Annette Peters, Christian Gieger, Melanie Waldenberger
BACKGROUND: The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using observations for individuals at multiple time-points. Here, through the use of the Illumina 450K BeadChip and data collected at two time-points separated by approximately 7 years, we investigate changes in methylation over time associated with quitting smoking or remaining a former smoker, and those associated with continued smoking...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29034560/estimation-of-a-significance-threshold-for-epigenome-wide-association-studies
#16
Ayden Saffari, Matt J Silver, Patrizia Zavattari, Loredana Moi, Amedeo Columbano, Emma L Meaburn, Frank Dudbridge
Epigenome-wide association studies (EWAS) are designed to characterise population-level epigenetic differences across the genome and link them to disease. Most commonly, they assess DNA-methylation status at cytosine-guanine dinucleotide (CpG) sites, using platforms such as the Illumina 450k array that profile a subset of CpGs genome wide. An important challenge in the context of EWAS is determining a significance threshold for declaring a CpG site as differentially methylated, taking multiple testing into account...
October 15, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28981624/array-probe-density-and-pathobiological-relevant-cpg-calling-bias-in-human-disease-and-physiological-dna-methylation-profiling
#17
Guillermo A Silva-Martínez, Silvio Zaina, Gertrud Lund
The HumanMethylation450 BeadChip array (450K; Infinium) is a widely used tool in epigenomics. A recognized concern in the 450K platform is the potential effect of the number of probes/gene (PG) on ranking differentially methylated (DM) CpGs (DM-CpGs) before testing for enrichment of gene ontology categories. We previously showed in a fatty acid (FA)-induced DNA methylation profiling study that when DM-CpGs are ranked by the number of called DM-CpGs-to-PG ratio, the 150 top-ranking gene list is enriched in pathways that overlap with the corresponding Affymetrix array-based expression data...
August 3, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28961746/champ-updated-methylation-analysis-pipeline-for-illumina-beadchips
#18
Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E Teschendorff
Summary: The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage compared to the older 450K array. Here we present a significantly updated and improved version of the Bioconductor package ChAMP, which can be used to analyze EPIC and 450k data. Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis, and a series of interactive graphical user interfaces...
August 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28957329/uncovering-the-dna-methylation-landscape-in-key-regulatory-regions-within-the-fads-cluster
#19
Elaheh Rahbar, Hannah C Ainsworth, Timothy D Howard, Gregory A Hawkins, Ingo Ruczinski, Rasika Mathias, Michael C Seeds, Susan Sergeant, James E Hixson, David M Herrington, Carl D Langefeld, Floyd H Chilton
Genetic variants near and within the fatty acid desaturase (FADS) cluster are associated with polyunsaturated fatty acid (PUFA) biosynthesis, levels of several disease biomarkers and risk of human disease. However, determining the functional mechanisms by which these genetic variants impact PUFA levels remains a challenge. Utilizing an Illumina 450K array, we previously reported strong allele-specific methylation (ASM) associations (p = 2.69×10-29) between a single nucleotide polymorphism (SNP) rs174537 and DNA methylation of CpG sites located in the putative enhancer region between FADS1 and FADS2, in human liver tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28947923/an-epigenome-wide-association-study-in-whole-blood-of-measures-of-adiposity-among-ghanaians-the-rodam-study
#20
Karlijn A C Meeks, Peter Henneman, Andrea Venema, Tom Burr, Cecilia Galbete, Ina Danquah, Matthias B Schulze, Frank P Mockenhaupt, Ellis Owusu-Dabo, Charles N Rotimi, Juliet Addo, Liam Smeeth, Silver Bahendeka, Joachim Spranger, Marcel M A M Mannens, Mohammad H Zafarmand, Charles Agyemang, Adebowale Adeyemo
BACKGROUND: Epigenome-wide association studies (EWAS) have identified DNA methylation loci involved in adiposity. However, EWAS on adiposity in sub-Saharan Africans are lacking despite the high burden of adiposity among African populations. We undertook an EWAS for anthropometric indices of adiposity among Ghanaians aiming to identify DNA methylation loci that are significantly associated. METHODS: The Illumina 450k DNA methylation array was used to profile DNA methylation in whole blood samples of 547 Ghanaians from the Research on Obesity and Diabetes among African Migrants (RODAM) study...
2017: Clinical Epigenetics
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