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Epigenome wide association

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https://www.readbyqxmd.com/read/29777237/dna-methylation-variant-b-vitamins-intake-and-longitudinal-change-in-body-mass-index
#1
Xiang Li, Tiange Wang, Min Zhao, Tao Huang, Dianjianyi Sun, Liyuan Han, Hoirun Nisa, Xiaoyun Shang, Yoriko Heianza, Lu Qi
BACKGROUND: Growing evidence has implicated DNA methylation (DNAm) in the regulation of body adiposity; a recent epigenome-wide association study (EWAS) identified a genetic variant determining DNAm at the SREBF1 gene that affected body mass index (BMI). OBJECTIVE: In the present study, we tested interactions between DNAm variant rs752579 and methylation metabolism-related B-vitamins (folate, vitamin B2 , vitamin B6 , and vitamin B12 ) on longitudinal change in BMI in the Women's Health Initiative Memory Study (WHIMS)...
May 17, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29773832/distinct-epigenetic-landscapes-underlie-the-pathobiology-of-pancreatic-cancer-subtypes
#2
Gwen Lomberk, Yuna Blum, Rémy Nicolle, Asha Nair, Krutika Satish Gaonkar, Laetitia Marisa, Angela Mathison, Zhifu Sun, Huihuang Yan, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Tamas Ordog, Jeong-Heon Lee, Gavin Oliver, Eric Klee, Vincent Moutardier, Odile Gayet, Benjamin Bian, Pauline Duconseil, Marine Gilabert, Martin Bigonnet, Stephane Garcia, Olivier Turrini, Jean-Robert Delpero, Marc Giovannini, Philippe Grandval, Mohamed Gasmi, Veronique Secq, Aurélien De Reyniès, Nelson Dusetti, Juan Iovanna, Raul Urrutia
Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29771388/gwas4d-multidimensional-analysis-of-context-specific-regulatory-variant-for-human-complex-diseases-and-traits
#3
Dandan Huang, Xianfu Yi, Shijie Zhang, Zhanye Zheng, Panwen Wang, Chenghao Xuan, Pak Chung Sham, Junwen Wang, Mulin Jun Li
Genome-wide association studies have generated over thousands of susceptibility loci for many human complex traits, and yet for most of these associations the true causal variants remain unknown. Tissue/cell type-specific prediction and prioritization of non-coding regulatory variants will facilitate the identification of causal variants and underlying pathogenic mechanisms for particular complex diseases and traits. By leveraging recent large-scale functional genomics/epigenomics data, we develop an intuitive web server, GWAS4D (http://mulinlab...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29762666/discovery-and-validation-of-methylation-biomarkers-for-ulcerative-colitis-associated-neoplasia
#4
Andrew D Beggs, Jonathan James, Germaine Caldwell, Toby Prout, Mark P Dilworth, Phillipe Taniere, Tariq Iqbal, Dion G Morton, Glenn Matthews
Background and aims: Ulcerative colitis (UC) is associated with a higher background risk of dysplasia and/or neoplasia due to chronic inflammation. There exist few biomarkers for identification of patients with dysplasia, and targeted biopsies in this group of patients are inaccurate in reliably identifying dysplasia. We aimed to examine the epigenome of UC dysplasia and to identify and validate potential biomarkers. Methods: Colonic samples from patients with UC-associated dysplasia or neoplasia underwent epigenome-wide analysis on the Illumina 450K methylation array...
May 14, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29762635/an-epigenome-wide-association-study-ewas-of-obesity-related-traits
#5
Klodian Dhana, Kim V E Braun, Jana Nano, Trudy Voortman, Ellen W Demerath, Weihua Guan, Myriam Fornage, Joyce B J van Meurs, Andre G Uitterlinden, Albert Hofman, Oscar H Franco, Abbas Dehghan
We conducted an epigenome-wide association study on obesity-related traits. We used data from two prospective, population-based cohort studies: the Rotterdam Study (RS) (2006-2013) and the Atherosclerosis Risk in Communities (ARIC) Study (1990-1992). We used RS (n = 1,454) as the discovery panel and ARIC (n = 2,097) as replication panel. Linear mixed-effect models were used to assess the cross-sectional association between genome-wide DNA methylation in leukocytes with body mass index (BMI) and waist circumference (WC) adjusting for sex, age, smoking, leukocyte proportions, array number and position on array...
May 14, 2018: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29754148/age-prediction-of-children-and-adolescents-aged-6-17-years-an-epigenome-wide-analysis-of-dna-methylation
#6
Chunxiao Li, Wenjing Gao, Ying Gao, Canqing Yu, Jun Lv, Ruoran Lv, Jiali Duan, Ying Sun, Xianghui Guo, Weihua Cao, Liming Li
The DNA methylation age, a good reflection of human aging process, has been used to predict chronological age of adults and newborns. However, the prediction model for children and adolescents was absent. In this study, we aimed to generate a prediction model of chronological age for children and adolescents aged 6-17 years by using age-specific DNA methylation patterns from 180 Chinese twin individuals. We identified 6,350 age-related CpGs from the epigenome-wide association analysis (N=179). 116 known age-related sites in children were confirmed...
May 12, 2018: Aging
https://www.readbyqxmd.com/read/29752424/placenta-dna-methylation-adaptation-to-maternal-glycemic-response-in-pregnancy
#7
Andres Cardenas, Valerie Gagné-Ouellet, Catherine Allard, Diane Brisson, Patrice Perron, Luigi Bouchard, Marie-France Hivert
Maternal hyperglycemia during pregnancy is associated with excess fetal growth and adverse perinatal and developmental outcomes. Placental epigenetic maladaptation may underlie these associations. We performed an epigenome-wide association study (>850,000 CpG sites) of term placentas and prenatal maternal glycemic response 2-hour post oral glucose challenge at 24-30 weeks of gestation among 448 mother-infant pairs. Maternal 2-hour glycemia post-load was strongly associated with lower DNA methylation of 4 CpGs (FDR q<0...
May 11, 2018: Diabetes
https://www.readbyqxmd.com/read/29741735/widespread-epigenomic-transcriptomic-and-proteomic-differences-between-hip-osteophytic-and-articular-chondrocytes-in-osteoarthritis
#8
Julia Steinberg, Roger A Brooks, Lorraine Southam, Sahir Bhatnagar, Theodoros I Roumeliotis, Konstantinos Hatzikotoulas, Eleni Zengini, J Mark Wilkinson, Jyoti S Choudhary, Andrew W McCaskie, Eleftheria Zeggini
Objectives: To identify molecular differences between chondrocytes from osteophytic and articular cartilage tissue from OA patients. Methods: We investigated genes and pathways by combining genome-wide DNA methylation, RNA sequencing and quantitative proteomics in isolated primary chondrocytes from the cartilaginous layer of osteophytes and matched areas of low- and high-grade articular cartilage across nine patients with OA undergoing hip replacement surgery. Results: Chondrocytes from osteophytic cartilage showed widespread differences to low-grade articular cartilage chondrocytes...
May 8, 2018: Rheumatology
https://www.readbyqxmd.com/read/29741584/translating-gwas-in-rheumatic-disease-approaches-to-establishing-mechanism-and-function-for-genetic-associations-with-ankylosing-spondylitis
#9
Julie A Osgood, Julian C Knight
Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants. Fine mapping using methods leveraging Bayesian approaches are outlined...
May 5, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29740313/epigenome-wide-association-study-of-soluble-tumor-necrosis-factor-receptor-2-levels-in-the-framingham-heart-study
#10
Michael M Mendelson, Roby Johannes, Chunyu Liu, Tianxiao Huan, Chen Yao, Xiao Miao, Joanne M Murabito, Josée Dupuis, Daniel Levy, Emelia J Benjamin, Honghuang Lin
Background: Transmembrane tumor necrosis factor (TNF) receptors are involved in inflammatory, apoptotic, and proliferative processes. In the bloodstream, soluble TNF receptor II (sTNFR2) can modify the inflammatory response of immune cells and is predictive of cardiovascular disease risk. We hypothesize that sTNFR2 is associated with epigenetic modifications of circulating leukocytes, which may relate to the pathophysiology underlying atherogenic risk. Methods: We conducted an epigenome-wide association study of sTNFR2 levels in the Framingham Heart Study Offspring cohort (examination 8; 2005-2008)...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29740122/differential-activity-of-transcribed-enhancers-in-the-prefrontal-cortex-of-537-cases-with-schizophrenia-and-controls
#11
Mads E Hauberg, John F Fullard, Lingxue Zhu, Ariella T Cohain, Claudia Giambartolomei, Ruth Misir, Sarah Reach, Jessica S Johnson, Minghui Wang, Manuel Mattheisen, Anders Dupont Børglum, Bin Zhang, Solveig K Sieberts, Mette A Peters, Enrico Domenici, Eric E Schadt, Bernie Devlin, Pamela Sklar, Kathryn Roeder, Panos Roussos
Transcription at enhancers is a widespread phenomenon which produces so-called enhancer RNA (eRNA) and occurs in an activity-dependent manner. However, the role of eRNA and its utility in exploring disease-associated changes in enhancer function, and the downstream coding transcripts that they regulate, is not well established. We used transcriptomic and epigenomic data to interrogate the relationship of eRNA transcription to disease status and how genetic variants alter enhancer transcriptional activity in the human brain...
May 8, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29736028/pm20d1-is-a-quantitative-trait-locus-associated-with-alzheimer-s-disease
#12
Jose V Sanchez-Mut, Holger Heyn, Bianca A Silva, Lucie Dixsaut, Paula Garcia-Esparcia, Enrique Vidal, Sergi Sayols, Liliane Glauser, Ana Monteagudo-Sánchez, Jordi Perez-Tur, Isidre Ferrer, David Monk, Bernard Schneider, Manel Esteller, Johannes Gräff
The chances to develop Alzheimer's disease (AD) result from a combination of genetic and non-genetic risk factors 1 , the latter likely being mediated by epigenetic mechanisms 2 . In the past, genome-wide association studies (GWAS) have identified an important number of risk loci associated with AD pathology 3 , but a causal relationship remains difficult to establish. In contrast, locus-specific or epigenome-wide association studies (EWAS) have revealed site-specific epigenetic alterations, which provide mechanistic insights for a particular risk gene but often lack the statistical power of GWAS 4 ...
May 7, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29724186/genome-wide-expert-annotation-of-the-epigenetic-machinery-of-the-plant-parasitic-nematodes-meloidogyne-spp-with-a-focus-on-the-asexually-reproducing-species
#13
Loris Pratx, Corinne Rancurel, Martine Da Rocha, Etienne G J Danchin, Philippe Castagnone-Sereno, Pierre Abad, Laetitia Perfus-Barbeoch
BACKGROUND: The renewed interest in epigenetics has led to the understanding that both the environment and individual lifestyle can directly interact with the epigenome to influence its dynamics. Epigenetic phenomena are mediated by DNA methylation, stable chromatin modifications and non-coding RNA-associated gene silencing involving specific proteins called epigenetic factors. Multiple organisms, ranging from plants to yeast and mammals, have been used as model systems to study epigenetics...
May 3, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29717273/identification-of-an-episignature-of-human-colorectal-cancer-associated-with-obesity-by-genome-wide-dna-methylation-analysis
#14
Ana B Crujeiras, Sonsoles Morcillo, Angel Diaz-Lagares, Juan Sandoval, Daniel Castellano-Castillo, Esperanza Torres, David Hervas, Sebastian Moran, Manel Esteller, Manuel Macias-Gonzalez, Felipe F Casanueva, Francisco J Tinahones
BACKGROUND: Obesity was established as a relevant modifiable risk factor in the onset and progression of colorectal cancer (CRC). This relationship could be mediated by an epigenetic regulation. OBJECTIVES: The current work aimed to explore the effects of excess body weight on the DNA methylation profile of CRC using a genome-wide DNA methylation approach and to identify an epigenetic signature of obesity-related CRC. METHODS: Fifty-six CRC-diagnosed patients (50 years) were included in the study and categorized according to their body mass index (BMI) as non-obese (BMI ≤ 25 kg/m2 ) or overweight/obese (BMI > 25 kg/m2 )...
May 1, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29713043/epigenome-wide-association-study-of-adiposity-and-future-risk-of-obesity-related-diseases
#15
Gianluca Campanella, Marc J Gunter, Silvia Polidoro, Vittorio Krogh, Domenico Palli, Salvatore Panico, Carlotta Sacerdote, Rosario Tumino, Giovanni Fiorito, Simonetta Guarrera, Licia Iacoviello, Ingvar A Bergdahl, Beatrice Melin, Per Lenner, Theo M C M de Kok, Panagiotis Georgiadis, Jos C S Kleinjans, Soterios A Kyrtopoulos, H Bas Bueno-de-Mesquita, Karen A Lillycrop, Anne M May, N Charlotte Onland-Moret, Robert Murray, Elio Riboli, Monique Verschuren, Eiliv Lund, Nicolle Mode, Torkjel M Sandanger, Valentina Fiano, Morena Trevisan, Giuseppe Matullo, Philippe Froguel, Paul Elliott, Paolo Vineis, Marc Chadeau-Hyam
BACKGROUND: Obesity is an established risk factor for several common chronic diseases such as breast and colorectal cancer, metabolic and cardiovascular diseases; however, the biological basis for these relationships is not fully understood. To explore the association of obesity with these conditions, we investigated peripheral blood leucocyte (PBL) DNA methylation markers for adiposity and their contribution to risk of incident breast and colorectal cancer and myocardial infarction. METHODS: DNA methylation profiles (Illumina Infinium® HumanMethylation450 BeadChip) from 1941 individuals from four population-based European cohorts were analysed in relation to body mass index, waist circumference, waist-hip and waist-height ratio within a meta-analytical framework...
May 1, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29712937/galactic-cosmic-radiation-induces-persistent-epigenome-alterations-relevant-to-human-lung-cancer
#16
E M Kennedy, D R Powell, Z Li, J S K Bell, B G Barwick, H Feng, M R McCrary, B Dwivedi, J Kowalski, W S Dynan, K N Conneely, P M Vertino
Human deep space and planetary travel is limited by uncertainties regarding the health risks associated with exposure to galactic cosmic radiation (GCR), and in particular the high linear energy transfer (LET), heavy ion component. Here we assessed the impact of two high-LET ions 56 Fe and 28 Si, and low-LET X rays on genome-wide methylation patterns in human bronchial epithelial cells. We found that all three radiation types induced rapid and stable changes in DNA methylation but at distinct subsets of CpG sites affecting different chromatin compartments...
April 30, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29707254/parenting-stress-and-dna-methylation-among-african-americans-in-the-intergen-study
#17
Michelle L Wright, Yunfeng Huang, Qin Hui, Kevin Newhall, Cindy Crusto, Yan V Sun, Jacquelyn Y Taylor
Introduction: General life stress has been associated with altered DNA methylation in individuals of African Ancestry, although the relationship between parenting stress and DNA methylation has not been described. The purpose of this study was to examine the relationship between maternal parenting stress and DNA methylation among African Ancestry mother-child dyads. Methods: We evaluated epigenome-wide DNA methylation relative to parenting stress in 74 mother-child dyads using linear mixed models...
December 2017: Journal of Clinical and Translational Science
https://www.readbyqxmd.com/read/29706346/an-osteoporosis-risk-snp-at-1p36-12-acts-as-an-allele-specific-enhancer-to-modulate-linc00339-expression-via-long-range-loop-formation
#18
Xiao-Feng Chen, Dong-Li Zhu, Man Yang, Wei-Xin Hu, Yuan-Yuan Duan, Bing-Jie Lu, Yu Rong, Shan-Shan Dong, Ruo-Han Hao, Jia-Bin Chen, Yi-Xiao Chen, Shi Yao, Hlaing Nwe Thynn, Yan Guo, Tie-Lin Yang
Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (∼360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region...
April 14, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29695247/impact-on-birth-weight-of-maternal-smoking-throughout-pregnancy-mediated-by-dna-methylation
#19
Stephanie H Witt, Josef Frank, Maria Gilles, Maren Lang, Jens Treutlein, Fabian Streit, Isabell A C Wolf, Verena Peus, Barbara Scharnholz, Tabea S Send, Stefanie Heilmann-Heimbach, Sugirthan Sivalingam, Helene Dukal, Jana Strohmaier, Marc Sütterlin, Janine Arloth, Manfred Laucht, Markus M Nöthen, Michael Deuschle, Marcella Rietschel
BACKGROUND: Cigarette smoking has severe adverse health consequences in adults and in the offspring of mothers who smoke during pregnancy. One of the most widely reported effects of smoking during pregnancy is reduced birth weight which is in turn associated with chronic disease in adulthood. Epigenome-wide association studies have revealed that smokers show a characteristic "smoking methylation pattern", and recent authors have proposed that DNA methylation mediates the impact of maternal smoking on birth weight...
April 25, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29692868/epigenome-wide-association-study-of-total-serum-immunoglobulin-e-in-children-a-life-course-approach
#20
Cheng Peng, Andres Cardenas, Sheryl L Rifas-Shiman, Marie-France Hivert, Diane R Gold, Thomas A Platts-Mills, Xihong Lin, Emily Oken, Andrea A Baccarelli, Augusto A Litonjua, Dawn L DeMeo
Background: IgE-mediated sensitization may be epigenetically programmed in utero, but early childhood environment may further alter complex traits and disease phenotypes through epigenetic plasticity. However, the epigenomic footprint underpinning IgE-mediated type-I hypersensitivity has not been well-understood, especially under a longitudinal early-childhood life-course framework. Methods: We used epigenome-wide DNA methylation (IlluminaHumanMethylation450 BeadChip) in cord blood and mid-childhood peripheral blood to investigate pre- and post-natal methylation marks associated with mid-childhood (age 6...
2018: Clinical Epigenetics
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