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https://www.readbyqxmd.com/read/29099283/lowly-methylated-region-analysis-identifies-ebf1-as-a-potential-epigenetic-modifier-in-breast-cancer
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28938489/prognostic-classifier-based-on-genome-wide-dna-methylation-profiling-in-well-differentiated-thyroid-tumors
#11
Mariana Bisarro Dos Reis, Mateus Camargo Barros-Filho, Fábio Albuquerque Marchi, Caroline Moraes Beltrami, Hellen Kuasne, Clóvis Antônio Lopes Pinto, Srikant Ambatipudi, Zdenko Herceg, Luiz Paulo Kowalski, Silvia Regina Rogatto
Context: Even though the majority of well-differentiated thyroid carcinoma (WDTC) is indolent, a number of cases display an aggressive behavior. Cumulative evidence suggests that the deregulation of DNA methylation has the potential to point out molecular markers associated with worse prognosis. Objective: To identify a prognostic epigenetic signature in thyroid cancer. Design: Genome-wide DNA methylation assays (450k platform, Illumina) were performed in a cohort of 50 nonneoplastic thyroid tissues (NTs), 17 benign thyroid lesions (BTLs), and 74 thyroid carcinomas (60 papillary, 8 follicular, 2 Hürthle cell, 1 poorly differentiated, and 3 anaplastic)...
November 1, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28930171/comprehensive-evaluation-of-tff3-promoter-hypomethylation-and-molecular-biomarker-potential-for-prostate-cancer-diagnosis-and-prognosis
#12
Maibritt Nørgaard, Christa Haldrup, Tine Maj Storebjerg, Else Marie Vestergaard, Peter J Wild, Søren Høyer, Michael Borre, Torben Falck Ørntoft, Karina Dalsgaard Sørensen
Overdiagnosis and overtreatment of clinically insignificant tumors remains a major problem in prostate cancer (PC) due to suboptimal diagnostic and prognostic tools. Thus, novel biomarkers are urgently needed. In this study, we investigated the biomarker potential of Trefoil factor 3 (TFF3) promoter methylation and RNA expression levels for PC. Initially, by quantitative methylation specific PCR (qMSP) analysis of a large radical prostatectomy (RP) cohort (n = 292), we found that the TFF3 promoter was significantly hypomethylated in PC compared to non-malignant (NM) prostate tissue samples (p < 0...
September 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28903418/histone-modification-alteration-coordinated-with-acquisition-of-promoter-dna-methylation-during-epstein-barr-virus-infection
#13
Sayaka Funata, Keisuke Matsusaka, Ryota Yamanaka, Shogo Yamamoto, Atsushi Okabe, Masaki Fukuyo, Hiroyuki Aburatani, Masashi Fukayama, Atsushi Kaneda
Aberrant DNA hypermethylation is a major epigenetic mechanism to inactivate tumor suppressor genes in cancer. Epstein-Barr virus positive gastric cancer is the most frequently hypermethylated tumor among human malignancies. Herein, we performed comprehensive analysis of epigenomic alteration during EBV infection, by Infinium HumanMethylation 450K BeadChip for DNA methylation and ChIP-sequencing for histone modification alteration during EBV infection into gastric cancer cell line MKN7. Among 7,775 genes with increased DNA methylation in promoter regions, roughly half were "DNA methylation-sensitive" genes, which acquired DNA methylation in the whole promoter regions and thus were repressed...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28889075/epigenetic-clock-analysis-in-long-term-meditators
#14
Raphaëlle Chaix, Maria Jesús Alvarez-López, Maud Fagny, Laure Lemee, Béatrice Regnault, Richard J Davidson, Antoine Lutz, Perla Kaliman
In this paper, we examined whether meditation practice influences the epigenetic clock, a strong and reproducible biomarker of biological aging, which is accelerated by cumulative lifetime stress and with age-related chronic diseases. Using the Illumina 450K array platform, we analyzed the DNA methylome from blood cells of long-term meditators and meditation-naïve controls to estimate their Intrinsic Epigenetic Age Acceleration (IEAA), using Horvath's calculator. IEAA was similar in both groups. However, controls showed a different IEAA trajectory with aging than meditators: older controls (age≥52) had significantly higher IEAAs compared with younger controls (age <52), while meditators were protected from this epigenetic aging effect...
August 31, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28841467/chronological-age-prediction-based-on-dna-methylation-massive-parallel-sequencing-and-random-forest-regression
#15
Jana Naue, Huub C J Hoefsloot, Olaf R F Mook, Laura Rijlaarsdam-Hoekstra, Marloes C H van der Zwalm, Peter Henneman, Ate D Kloosterman, Pernette J Verschure
The use of DNA methylation (DNAm) to obtain additional information in forensic investigations showed to be a promising and increasing field of interest. Prediction of the chronological age based on age-dependent changes in the DNAm of specific CpG sites within the genome is one such potential application. Here we present an age-prediction tool for whole blood based on massive parallel sequencing (MPS) and a random forest machine learning algorithm. MPS allows accurate DNAm determination of pre-selected markers and neighboring CpG-sites to identify the best age-predictive markers for the age-prediction tool...
August 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28837395/nightshift-work-chronotype-and-genome-wide-dna-methylation-in-blood
#16
Charleen D Adams, Kristina M Jordahl, Wade Copeland, Dana K Mirick, Xiaoling Song, Cassandra L Sather, Karl Kelsey, Andres Houseman, Scott Davis, Timothy Randolph, Parveen Bhatti
Molecular mechanisms underlying the negative health effects of shift work are poorly understood, which remains a barrier to developing intervention strategies to protect the long-term health of shift workers. We evaluated genome-wide differences in DNA methylation (measured in blood) between 111 actively employed female nightshift and 86 actively employed female dayshift workers from the Seattle metropolitan area. We also explored the effect of chronotype (i.e., measure of preference for activity earlier or later in the day) on DNA methylation among 110 of the female nightshift workers and an additional group of 131 male nightshift workers...
August 24, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28809127/the-correlation-of-methylation-levels-measured-using-illumina-450k-and-epic-beadchips-in-blood-samples
#17
Mark W Logue, Alicia K Smith, Erika J Wolf, Hannah Maniates, Annjanette Stone, Steven A Schichman, Regina E McGlinchey, William Milberg, Mark W Miller
AIM: We examined concordance of methylation levels across the Illumina Infinium HumanMethylation450 BeadChip and the Infinium MethylationEPIC BeadChip. METHODS: We computed the correlation for 145 whole blood DNA samples at each of the 422,524 CpG sites measured by both chips. RESULTS: The correlation at some sites was high (up to r = 0.95), but many sites had low correlation (55% had r < 0.20). The low correspondence between 450K and EPIC measured methylation values at many loci was largely due to the low variability in methylation values for the majority of the CpG sites in blood...
November 2017: Epigenomics
https://www.readbyqxmd.com/read/28797927/molecular-dynamics-study-of-unfolding-of-lysozyme-in-water-and-its-mixtures-with-dimethyl-sulfoxide
#18
Igor A Sedov, Timur I Magsumov
All-atom explicit solvent molecular dynamics was used to study the process of unfolding of hen egg white lysozyme in water and mixtures of water with dimethyl sulfoxide at different compositions. We have determined the kinetic parameters of unfolding at a constant temperature 450K. For each run, the time of disruption of the tertiary structure of lysozyme tu was defined as the moment when a certain structural criterion computed from the trajectory reaches its critical value. A good agreement is observed between the results obtained using several different criteria...
August 1, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28770015/maternal-blood-contamination-of-collected-cord-blood-can-be-identified-using-dna-methylation-at-three-cpgs
#19
Alexander M Morin, Evan Gatev, Lisa M McEwen, Julia L MacIsaac, David T S Lin, Nastassja Koen, Darina Czamara, Katri Räikkönen, Heather J Zar, Karestan Koenen, Dan J Stein, Michael S Kobor, Meaghan J Jones
BACKGROUND: Cord blood is a commonly used tissue in environmental, genetic, and epigenetic population studies due to its ready availability and potential to inform on a sensitive period of human development. However, the introduction of maternal blood during labor or cross-contamination during sample collection may complicate downstream analyses. After discovering maternal contamination of cord blood in a cohort study of 150 neonates using Illumina 450K DNA methylation (DNAm) data, we used a combination of linear regression and random forest machine learning to create a DNAm-based screening method...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28756535/foxa1-hypermethylation-link-between-parity-and-er-negative-breast-cancer-in-african-american-women
#20
Allyson C Espinal, Matthew F Buas, Dan Wang, David Ting-Yuan Cheng, Lara Sucheston-Campbell, Qiang Hu, Li Yan, Rochelle Payne-Ondracek, Eduardo Cortes, Li Tang, Zhihong Gong, Gary Zirpoli, Thaer Khoury, Song Yao, Angela Omilian, Kitaw Demissie, Elisa V Bandera, Song Liu, Christine B Ambrosone, Michael J Higgins
BACKGROUND: Reproductive factors, particularly parity, have differential effects on breast cancer risk according to estrogen receptor (ER) status, especially among African American (AA) women. One mechanism could be through DNA methylation, leading to altered expression levels of genes important in cell fate decisions. METHODS: Using the Illumina 450K BeadChip, we compared DNA methylation levels in paraffin-archived tumor samples from 383 AA and 350 European American (EA) women in the Women's Circle of Health Study (WCHS)...
November 2017: Breast Cancer Research and Treatment
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