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Epigenome wide association

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https://www.readbyqxmd.com/read/28098396/the-effects-of-chronic-cobalt-and-chromium-exposure-after-metal-on-metal-hip-resurfacing-an-epigenome-wide-association-pilot-study
#1
Julia Steinberg, Karan M Shah, Alison Gartland, Eleftheria Zeggini, J Mark Wilkinson
Metal-on-metal (MOM) hip resurfacing has recently been a popular prosthesis choice for the treatment of symptomatic arthritis, but results in the release of cobalt and chromium ions into the circulation that can be associated with adverse clinical effects. The mechanism underlying these effects remains unclear. While chromosomal aneuploidy and translocations are associated with this exposure, the presence of subtle structural epigenetic modifications in patients with MOM joint-replacements remains unexplored...
January 18, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28096648/identification-of-genetic-and-epigenetic-variants-associated-with-breast-cancer-prognosis-by-integrative-bioinformatics-analysis
#2
Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K Patra, Ramana V Davuluri
INTRODUCTION: Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28093418/cell-specific-epigenome-wide-dna-methylation-profile-in-long-term-cultured-minor-salivary-gland-epithelial-cells-from-patients-with-sj%C3%A3-gren-s-syndrome
#3
Amandine Charras, Orsia D Konsta, Christelle Le Dantec, Cristina Bagacean, Efstathia K Kapsogeorgou, Athanasios G Tzioufas, Jacques-Olivier Pers, Anne Bordron, Yves Renaudineau
OBJECTIVES: The aetiology of primary Sjögren's syndrome (pSS), also referred to as autoimmune epithelitis, is incompletely understood but includes an epigenetic contribution. Accordingly, the aim of this study was to investigate DNA methylation in salivary gland epithelial cells (SGEC), and to compare results with those publicly available from pSS B and T cells. METHODS: Long-term cultured SGEC were selected to conduct an epigenome-wide association study (EWAS) in patients with pSS with comparison to controls using the HumanMethylation 450 K array from Illumina...
January 16, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28081217/collective-genetic-interaction-effects-and-the-role-of-antigen-presenting-cells-in-autoimmune-diseases
#4
Hyung Jun Woo, Chenggang Yu, Jaques Reifman
Autoimmune diseases occur when immune cells fail to develop or lose their tolerance toward self and destroy body's own tissues. Both insufficient negative selection of self-reactive T cells and impaired development of regulatory T cells preventing effector cell activation are believed to contribute to autoimmunity. Genetic predispositions center around the major histocompatibility complex (MHC) class II loci involved in antigen presentation, the key determinant of CD4+ T cell activation. Recent studies suggested that variants in the MHC region also exhibit significant non-additive interaction effects...
2017: PloS One
https://www.readbyqxmd.com/read/28075199/an-epigenome-wide-association-analysis-of-cardiac-autonomic-responses-among-a-population-of-welders
#5
Jinming Zhang, Zhonghua Liu, Peter E Umukoro, Jennifer M Cavallari, Shona C Fang, Marc G Weisskopf, Xihong Lin, Murray A Mittleman, David C Christiani
DNA methylation is one of the potential epigenetic mechanisms associated with various adverse cardiovascular effects; however, its association with cardiac autonomic dysfunction, in particular, is unknown. In the current study, we aimed to identify epigenetic variants associated with alterations in cardiac autonomic responses. Cardiac autonomic responses were measured with two novel markers: acceleration capacity (AC) and deceleration capacity (DC). We examined DNA methylation levels at more than 472,506 CpG probes through the Illumina Infinium HumanMethylation450 BeadChip assay...
January 11, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28074068/a-cpg-island-methylator-phenotype-in-acute-myeloid-leukemia-independent-of-idh-mutations-and-associated-with-a-favorable-outcome
#6
A D Kelly, H Kroeger, J Yamazaki, R Taby, F Neumann, S Yu, J T Lee, B Patel, Y Li, R He, S Liang, Y Lu, M Cesaroni, S A Pierce, S M Kornblau, C E Bueso-Ramos, F Ravandi, H M Kantarjian, J Jelinek, J-Pj Issa
Genetic changes are infrequent in acute myeloid leukemia (AML) compared to other malignancies and often involve epigenetic regulators, suggesting that an altered epigenome may underlie AML biology and outcomes. In 96 AML cases including 65 pilot samples selected for cured/not-cured, we found higher CpG island (CGI) promoter methylation in cured patients. Expanded genome-wide digital restriction enzyme analysis of methylation (DREAM) data revealed a CGI methylator phenotype independent of IDH1/2 mutations we term AML-CIMP (A-CIMP(+))...
January 11, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28070760/the-generation-r-study-design-and-cohort-update-2017
#7
Marjolein N Kooijman, Claudia J Kruithof, Cornelia M van Duijn, Liesbeth Duijts, Oscar H Franco, Marinus H van IJzendoorn, Johan C de Jongste, Caroline C W Klaver, Aad van der Lugt, Johan P Mackenbach, Henriëtte A Moll, Robin P Peeters, Hein Raat, Edmond H H M Rings, Fernando Rivadeneira, Marc P van der Schroeff, Eric A P Steegers, Henning Tiemeier, André G Uitterlinden, Frank C Verhulst, Eppo Wolvius, Janine F Felix, Vincent W V Jaddoe
The Generation R Study is a population-based prospective cohort study from fetal life until adulthood. The study is designed to identify early environmental and genetic causes and causal pathways leading to normal and abnormal growth, development and health from fetal life, childhood and young adulthood. This multidisciplinary study focuses on several health outcomes including behaviour and cognition, body composition, eye development, growth, hearing, heart and vascular development, infectious disease and immunity, oral health and facial growth, respiratory health, allergy and skin disorders of children and their parents...
December 2016: European Journal of Epidemiology
https://www.readbyqxmd.com/read/28069425/an-epigenome-wide-association-study-of-total-serum-immunoglobulin-e-in-hispanic-children
#8
Wei Chen, Ting Wang, Maria Pino-Yanes, Erick Forno, Liming Liang, Qi Yan, Donglei Hu, Daniel E Weeks, Andrea Baccarelli, Edna Acosta-Perez, Celeste Eng, Yueh-Ying Han, Nadia Boutaoui, Catherine Laprise, Gwyneth A Davies, Julian M Hopkin, Miriam F Moffatt, William O C M Cookson, Glorisa Canino, Esteban G Burchard, Juan C Celedón
BACKGROUND: Total immunoglobulin E (IgE) is a therapeutic target in allergic diseases. DNA methylation in white blood cells (WBCs) was associated with total IgE in an epigenome-wide association study (EWAS) of Caucasians. Whether DNA methylation of eosinophils explains those findings is insufficiently understood. METHODS: We tested for association between genome-wide DNA methylation in WBCs and total IgE in two studies of Hispanic children: the Puerto Rico Genetics of Asthma and Lifestyle Study (PR-GOAL, n = 306) and the Genes-environments and Admixture in Latino Americans (GALA II, n = 573)...
January 6, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28062490/dna-methylation-and-high-density-lipoprotein-functionality-the-regicor-study
#9
Sergi Sayols-Baixeras, Alvaro Hernáez, Issac Subirana, Carla Lluis-Ganella, Daniel Muñoz, Montserrat Fitó, Jaume Marrugat, Roberto Elosua
OBJECTIVE: The function of high-density lipoproteins (HDLs) may better reflect their atheroprotective role, compared with HDL-cholesterol levels. The association between DNA methylation and HDL function has not yet been established. APPROACH AND RESULTS: We designed an epigenome-wide association study including 645 individuals from the REGICOR study. We determined DNA methylation from peripheral blood cells using the HumanMethylation450 array. We analyzed HDL functionality by determining HDL cholesterol efflux capacity and HDL inflammatory index...
January 5, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28057210/epigenetic-changes-in-chronic-inflammatory-diseases
#10
O Fogel, C Richard-Miceli, J Tost
The number of people diagnosed with chronic inflammatory diseases has increased noteworthy in the last 40 years. Spondyloarthritis (SpA), inflammatory bowel diseases (IBD), and psoriasis are the most frequent chronic inflammatory diseases, resulting from a combination of genetic predisposition and environmental factors. Epigenetic modifications include DNA methylation, histone modifications, and small and long noncoding RNAs. They are influenced by environmental exposure, life-style, and aging and have recently been shown to be altered in many complex diseases including inflammatory diseases...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28056824/the-emerging-landscape-of-dynamic-dna-methylation-in-early-childhood
#11
Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, Ulrike Gehring, Soesma A Jankipersadsing, Pieter van der Vlies, Cleo C van Diemen, Bianca van Rijkom, Jocelyne Just, Inger Kull, Juha Kere, Josep Maria Antó, Jean Bousquet, Alexandra Zhernakova, Cisca Wijmenga, Isabella Annesi-Maesano, Jordi Sunyer, Erik Melén, Yang Li, Dirkje S Postma, Gerard H Koppelman
BACKGROUND: DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood. RESULTS: By analysing 538 paired DNA blood samples from children at birth and at 4-5 years old and 726 paired samples from children at 4 and 8 years old from four European birth cohorts using the Illumina Infinium Human Methylation 450 k chip, we have identified 14,150 consistent age-differential methylation sites (a-DMSs) at epigenome-wide significance of p < 1...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28052262/neil3-dependent-regulation-of-cardiac-fibroblast-proliferation-prevents-myocardial-rupture
#12
Maria B Olsen, Gunn A Hildrestrand, Katja Scheffler, Leif Erik Vinge, Katrine Alfsnes, Vuk Palibrk, Junbai Wang, Christine G Neurauter, Luisa Luna, Jostein Johansen, Jonas D S Øgaard, Ingrid K Ohm, Geir Slupphaug, Anna Kuśnierczyk, Arnt E Fiane, Sverre-Henning Brorson, Lili Zhang, Lars Gullestad, William E Louch, Per Ole Iversen, Ingunn Østlie, Arne Klungland, Geir Christensen, Ivar Sjaastad, Pål Sætrom, Arne Yndestad, Pål Aukrust, Magnar Bjørås, Alexandra V Finsen
Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme NEIL3 was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 after MI in mice, especially in a fibroblast-enriched cell fraction...
January 3, 2017: Cell Reports
https://www.readbyqxmd.com/read/28049437/relic-a-novel-dye-bias-correction-method-for-illumina-methylation-beadchip
#13
Zongli Xu, Sabine A S Langie, Patrick De Boever, Jack A Taylor, Liang Niu
BACKGROUND: The Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in epigenome-wide association studies. Both arrays use two fluorescent dyes (Cy3-green/Cy5-red) to measure methylation level at CpG sites. However, performance difference between dyes can result in biased estimates of methylation levels. RESULTS: Here we describe a novel method, called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28045116/comparative-analysis-of-dna-methylome-and-transcriptome-of-skeletal-muscle-in-lean-obese-and-mini-type-pigs
#14
Yalan Yang, Guoming Liang, Guanglin Niu, Yuanyuan Zhang, Rong Zhou, Yanfang Wang, Yulian Mu, Zhonglin Tang, Kui Li
DNA methylation plays a pivotal role in biological processes by affecting gene expression. However, how DNA methylation mediates phenotype difference of skeletal muscle between lean-, obese-, and mini-type pigs remains unclear. We systematically carried out comparative analysis of skeletal muscle by integrating analysis of genome-wide DNA methylation, mRNA, lncRNA and miRNA profiles in three different pig breeds (obese-type Tongcheng, lean-type Landrace, and mini-type Wuzhishan pigs). We found that the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress and muscle development...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28032437/birth-weight-discordance-dna-methylation-and-cortical-morphology-of-adolescent-monozygotic-twins
#15
Kevin F Casey, Melissa L Levesque, Moshe Szyf, Elmira Ismaylova, Marie-Pier Verner, Matthew Suderman, Frank Vitaro, Mara Brendgen, Ginette Dionne, Michel Boivin, Richard E Tremblay, Linda Booij
BACKGROUND: Several studies have shown that the in utero environment, which can be indexed by birth weight (BW), is associated with cortical morphology in adolescence and adulthood. Work in monozygotic (MZ) twins suggests that this association is driven by non-shared environmental factors. This correlation could be the result of in utero impacts on DNA methylation. The aim of the present study with MZ twins is to replicate the association between discordance in BW and brain morphology and test whether discordance in DNA methylation mediates this relationship...
December 29, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/28011458/insulin-and-glucose-alter-death-associated-protein-kinase-3-dapk3-dna-methylation-in-human-skeletal-muscle
#16
Jonathan M Mudry, David G Lassiter, Carolina Nylén, Sonia García-Calzón, Erik Näslund, Anna Krook, Juleen R Zierath
DNA methylation is altered by environmental factors. We hypothesized DNA methylation is altered in skeletal muscle in response to either insulin or glucose exposure. We performed a genome-wide DNA methylation analysis in muscle from healthy men before and after insulin exposure. DNA methylation of selected genes was determined in muscle from healthy and type 2 diabetic men before and after a glucose tolerance test. Insulin altered DNA methylation in the 3'UTR of the calcium pump ATP2A3 gene. Insulin increased DNA methylation in the gene body of DAPK3, a gene involved in cell proliferation, apoptosis and autophagy...
December 23, 2016: Diabetes
https://www.readbyqxmd.com/read/28011059/epigenome-wide-analysis-links-smad3-methylation-at-birth-to-asthma-in-children-of-asthmatic-mothers
#17
Avery DeVries, Gabriela Wlasiuk, Susan J Miller, Anthony Bosco, Debra A Stern, I Carla Lohman, Janet Rothers, Anya C Jones, Jessie Nicodemus-Johnson, Monica M Vasquez, John A Curtin, Angela Simpson, Adnan Custovic, Daniel J Jackson, James E Gern, Robert F Lemanske, Stefano Guerra, Anne L Wright, Carole Ober, Marilyn Halonen, Donata Vercelli
BACKGROUND: The timing and mechanisms of asthma inception remain imprecisely defined. Although epigenetic mechanisms likely contribute to asthma pathogenesis, little is known about their role in asthma inception. OBJECTIVE: To assess whether the trajectory to asthma begins already at birth and epigenetic mechanisms, specifically DNA methylation, contribute to asthma inception. METHODS: We used Methylated CpG Island Recovery Assay (MIRA)-chip to survey DNA methylation in cord blood mononuclear cells (CBMC) from 36 children (18 non-asthmatic, 18 asthmatic by age 9) from the Infant Immune Study (IIS), an unselected birth cohort closely monitored for asthma for a decade...
December 20, 2016: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28002404/epigenome-wide-association-study-of-body-mass-index-and-the-adverse-outcomes-of-adiposity
#18
Simone Wahl, Alexander Drong, Benjamin Lehne, Marie Loh, William R Scott, Sonja Kunze, Pei-Chien Tsai, Janina S Ried, Weihua Zhang, Youwen Yang, Sili Tan, Giovanni Fiorito, Lude Franke, Simonetta Guarrera, Silva Kasela, Jennifer Kriebel, Rebecca C Richmond, Marco Adamo, Uzma Afzal, Mika Ala-Korpela, Benedetta Albetti, Ole Ammerpohl, Jane F Apperley, Marian Beekman, Pier Alberto Bertazzi, S Lucas Black, Christine Blancher, Marc-Jan Bonder, Mario Brosch, Maren Carstensen-Kirberg, Anton J M de Craen, Simon de Lusignan, Abbas Dehghan, Mohamed Elkalaawy, Krista Fischer, Oscar H Franco, Tom R Gaunt, Jochen Hampe, Majid Hashemi, Aaron Isaacs, Andrew Jenkinson, Sujeet Jha, Norihiro Kato, Vittorio Krogh, Michael Laffan, Christa Meisinger, Thomas Meitinger, Zuan Yu Mok, Valeria Motta, Hong Kiat Ng, Zacharoula Nikolakopoulou, Georgios Nteliopoulos, Salvatore Panico, Natalia Pervjakova, Holger Prokisch, Wolfgang Rathmann, Michael Roden, Federica Rota, Michelle Ann Rozario, Johanna K Sandling, Clemens Schafmayer, Katharina Schramm, Reiner Siebert, P Eline Slagboom, Pasi Soininen, Lisette Stolk, Konstantin Strauch, E-Shyong Tai, Letizia Tarantini, Barbara Thorand, Ettje F Tigchelaar, Rosario Tumino, Andre G Uitterlinden, Cornelia van Duijn, Joyce B J van Meurs, Paolo Vineis, Ananda Rajitha Wickremasinghe, Cisca Wijmenga, Tsun-Po Yang, Wei Yuan, Alexandra Zhernakova, Rachel L Batterham, George Davey Smith, Panos Deloukas, Bastiaan T Heijmans, Christian Herder, Albert Hofman, Cecilia M Lindgren, Lili Milani, Pim van der Harst, Annette Peters, Thomas Illig, Caroline L Relton, Melanie Waldenberger, Marjo-Riitta Järvelin, Valentina Bollati, Richie Soong, Tim D Spector, James Scott, Mark I McCarthy, Paul Elliott, Jordana T Bell, Giuseppe Matullo, Christian Gieger, Jaspal S Kooner, Harald Grallert, John C Chambers
Approximately 1.5 billion people worldwide are overweight or affected by obesity, and are at risk of developing type 2 diabetes, cardiovascular disease and related metabolic and inflammatory disturbances. Although the mechanisms linking adiposity to associated clinical conditions are poorly understood, recent studies suggest that adiposity may influence DNA methylation, a key regulator of gene expression and molecular phenotype. Here we use epigenome-wide association to show that body mass index (BMI; a key measure of adiposity) is associated with widespread changes in DNA methylation (187 genetic loci with P < 1 × 10(-7), range P = 9...
December 21, 2016: Nature
https://www.readbyqxmd.com/read/27998510/stress-burnout-and-depression-a-systematic-review-on-dna-methylation-mechanisms
#19
REVIEW
Jelena Bakusic, Wilmar Schaufeli, Stephan Claes, Lode Godderis
Despite that burnout presents a serious burden for modern society, there are no diagnostic criteria. Additional difficulty is the differential diagnosis with depression. Consequently, there is a need to dispose of a burnout biomarker. Epigenetic studies suggest that DNA methylation is a possible mediator linking individual response to stress and psychopathology and could be considered as a potential biomarker of stress-related mental disorders. Thus, the aim of this review is to provide an overview of DNA methylation mechanisms in stress, burnout and depression...
January 2017: Journal of Psychosomatic Research
https://www.readbyqxmd.com/read/27984638/dawning-of-the-age-of-genomics-for-platelet-granule-disorders-improving-insight-diagnosis-and-management
#20
REVIEW
Tadbir K Bariana, Willem H Ouwehand, Jose A Guerrero, Keith Gomez
Inherited disorders of platelet granules are clinically heterogeneous and their prevalence is underestimated because most patients do not undergo a complete diagnostic work-up. The lack of a genetic diagnosis limits the ability to tailor management, screen family members, aid with family planning, predict clinical progression and detect serious consequences, such as myelofibrosis, lung fibrosis and malignancy, in a timely manner. This is set to change with the introduction of high throughput sequencing (HTS) as a routine clinical diagnostic test...
December 16, 2016: British Journal of Haematology
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