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Epigenome wide association

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https://www.readbyqxmd.com/read/28441426/identification-of-genes-associated-with-dissociation-of-cognitive-performance-and-neuropathological-burden-multistep-analysis-of-genetic-epigenetic-and-transcriptional-data
#1
Charles C White, Hyun-Sik Yang, Lei Yu, Lori B Chibnik, Robert J Dawe, Jingyun Yang, Hans-Ulrich Klein, Daniel Felsky, Alfredo Ramos-Miguel, Konstantinos Arfanakis, William G Honer, Reisa A Sperling, Julie A Schneider, David A Bennett, Philip L De Jager
INTRODUCTION: The molecular underpinnings of the dissociation of cognitive performance and neuropathological burden are poorly understood, and there are currently no known genetic or epigenetic determinants of the dissociation. METHODS AND FINDINGS: "Residual cognition" was quantified by regressing out the effects of cerebral pathologies and demographic characteristics on global cognitive performance proximate to death. To identify genes influencing residual cognition, we leveraged neuropathological, genetic, epigenetic, and transcriptional data available for deceased participants of the Religious Orders Study (n = 492) and the Rush Memory and Aging Project (n = 487)...
April 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28439531/genome-and-cd4-t-cell-methylome-wide-association-study-of-circulating-trimethylamine-n-oxide-in-the-genetics-of-lipid-lowering-drugs-and-diet-network-goldn
#2
Stella Aslibekyan, Marguerite R Irvin, Bertha A Hidalgo, Rodney T Perry, Elias J Jeyarajah, Erwin Garcia, Irina Shalaurova, Paul N Hopkins, Michael A Province, Hemant K Tiwari, Jose M Ordovas, Devin M Absher, Donna K Arnett
BACKGROUND: Trimethylamine-N-oxide (TMAO), an atherogenic metabolite species, has emerged as a possible new risk factor for cardiovascular disease. Animal studies have shown that circulating TMAO levels are regulated by genetic and environmental factors. However, large-scale human studies have failed to replicate the observed genetic associations, and epigenetic factors such as DNA methylation have never been examined in relation to TMAO levels. METHODS AND RESULTS: We used data from the family-based Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) to investigate the heritable determinants of plasma TMAO in humans...
June 2017: Journal of Nutrition & Intermediary Metabolism
https://www.readbyqxmd.com/read/28428977/19th-workshop-of-the-international-stroke-genetics-consortium-april-28-29-2016-boston-massachusetts-usa-2016-001-mri-defined-cerebrovascular-genomics-the-charge-consortium
#3
S Debette, Y Saba, D Vojinovic, X Jian, H Adams, G Chauhan, M Sargurupremraj, S Kaffashian, J Ding, J C Bis, P Nyquist, K Mather, C Van Duijn, L J Launer, M A Ikram, H Schmidt, W T Longstreth, M Fornage, S Seshadri
The CHARGE consortium is an investigator-initiated collaboration to facilitate meta-analyses of genome-wide association studies (GWAS) and genomic analyses based on next generation sequencing (NGS), among multiple large and well-phenotyped population-based cohort studies around the world (http://www.chargeconsortium.com). Within the neuro-CHARGE working group, we are presenting an update of ongoing genomic studies on MRI-markers of cerebrovascular disease. Large population-based studies have shown that the burden of cerebrovascular disease extends far beyond that of clinical stroke...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28421636/leveraging-cell-type-specific-regulatory-regions-to-detect-snps-associated-with-tissue-factor-pathway-inhibitor-plasma-levels
#4
Jessica Dennis, Alejandra Medina-Rivera, Vinh Truong, Lina Antounians, Nora Zwingerman, Giovana Carrasco, Lisa Strug, Phil Wells, David-Alexandre Trégouët, Pierre-Emmanuel Morange, Michael D Wilson, France Gagnon
Tissue factor pathway inhibitor (TFPI) regulates the formation of intravascular blood clots, which manifest clinically as ischemic heart disease, ischemic stroke, and venous thromboembolism (VTE). TFPI plasma levels are heritable, but the genetics underlying TFPI plasma level variability are poorly understood. Herein we report the first genome-wide association scan (GWAS) of TFPI plasma levels, conducted in 251 individuals from five extended French-Canadian Families ascertained on VTE. To improve discovery, we also applied a hypothesis-driven (HD) GWAS approach that prioritized single nucleotide polymorphisms (SNPs) in (1) hemostasis pathway genes, and (2) vascular endothelial cell (EC) regulatory regions, which are among the highest expressers of TFPI...
April 18, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28418867/early-detection-of-gastric-cancer-using-global-genome-wide-and-irf4-elmo1-clip4-and-msc-dna-methylation-in-endoscopic-biopsies
#5
Francesca Pirini, Sassan Noazin, Martha H Jahuira-Arias, Sebastian Rodriguez-Torres, Leah Friess, Christina Michailidi, Jaime Cok, Juan Combe, Gloria Vargas, William Prado, Ethan Soudry, Jimena Pérez, Tikki Yudin, Andrea Mancinelli, Helen Unger, Carmen Ili-Gangas, Priscilla Brebi-Mieville, Douglas E Berg, Masamichi Hayashi, David Sidransky, Robert H Gilman, Rafael Guerrero-Preston
Clinically useful molecular tools to triage gastric cancer patients are not currently available. We aimed to develop a molecular tool to predict gastric cancer risk in endoscopy-driven biopsies obtained from high-risk gastric cancer clinics in low resource settings.We discovered and validated a DNA methylation biomarker panel in endoscopic samples obtained from 362 patients seen between 2004 and 2009 in three high-risk gastric cancer clinics in Lima, Perú, and validated it in 306 samples from the Cancer Genome Atlas project ("TCGA")...
March 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28409176/systemic-analysis-of-osteoblast-specific-dna-methylation-marks-reveals-novel-epigenetic-basis-of-osteoblast-differentiation
#6
Fangtang Yu, Hui Shen, Hong-Wen Deng
DNA methylation is an important epigenetic modification that contributes to the lineage commitment and specific functions of different cell types. In this study, we compared ENCODE-generated genome-wide DNA methylation profiles of human osteoblast with 21 other types of human cells in order to identify osteoblast-specific methylation events. For most of the cell strains, data from two isogenic replicates were included, resulting in a total of 51 DNA methylation datasets. We identified 852 significant osteoblast-specific differentially methylated CpGs (DMCs) and 295 significant differentially methylated regions (DMRs)...
June 2017: Bone Reports
https://www.readbyqxmd.com/read/28394087/epigenome-wide-association-of-dna-methylation-in-whole-blood-with-bone-mineral-density
#7
John A Morris, Pei-Chien Tsai, Roby Joehanes, Jie Zheng, Katerina Trajanoska, Mette Soerensen, Vincenzo Forgetta, Juan Edgar Castillo-Fernandez, Morten Frost, Tim D Spector, Kaare Christensen, Lene Christiansen, Fernando Rivadeneira, Jonathan H Tobias, David M Evans, Douglas P Kiel, Yi-Hsiang Hsu, J Brent Richards, Jordana T Bell
Genetic and environmental determinants of skeletal phenotypes such as bone mineral density (BMD) may converge through the epigenome, providing a tool to better understand osteoporosis pathophysiology. As the epigenetics of BMD have been largely unexplored in humans, we performed an epigenome wide association study (EWAS) of BMD. We undertook a large-scale BMD EWAS using the Infinium HumanMethylation450 array to measure site-specific DNA methylation in up to 5,515 European descent individuals (NDiscovery  = 4,614, NValidation  = 901)...
April 10, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28391083/epigenome-wide-association-studies-for-cancer-biomarker-discovery-in-circulating-cell-free-dna-technical-advances-and-challenges
#8
REVIEW
Miljana Tanić, Stephan Beck
Since introducing the concept of epigenome-wide association studies (EWAS) in 2011, there has been a vast increase in the number of published EWAS studies in common diseases, including in cancer. These studies have increased our understanding of epigenetic events underlying carcinogenesis and have enabled the discovery of cancer-specific methylation biomarkers. In this mini-review, we have focused on the state of the art in EWAS applied to cell-free circulating DNA for epigenetic biomarker discovery in cancer and discussed associated technical advances and challenges, and our expectations for the future of the field...
February 16, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28387726/rethinking-the-epigenetic-framework-to-unravel-the-molecular-pathology-of-schizophrenia
#9
REVIEW
Ariel Cariaga-Martinez, Raúl Alelú-Paz
Schizophrenia is a complex mental disorder whose causes are still far from being known. Although researchers have focused on genetic or environmental contributions to the disease, we still lack a scientific framework that joins molecular and clinical findings. Epigenetic can explain how environmental variables may affect gene expression without modifying the DNA sequence. In fact, neuroepigenomics represents an effort to unify the research available on the molecular pathology of mental diseases, which has been carried out through several approaches ranging from interrogating single DNA methylation events and hydroxymethylation patterns, to epigenome-wide association studies, as well as studying post-translational modifications of histones, or nucleosomal positioning...
April 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28381277/unique-dna-methylation-signature-in-hpv-positive-head-and-neck-squamous-cell-carcinomas
#10
Davide Degli Esposti, Athena Sklias, Sheila C Lima, Stéphanie Beghelli-de la Forest Divonne, Vincent Cahais, Nora Fernandez-Jimenez, Marie-Pierre Cros, Szilvia Ecsedi, Cyrille Cuenin, Liacine Bouaoun, Graham Byrnes, Rosita Accardi, Anne Sudaka, Valérie Giordanengo, Hector Hernandez-Vargas, Luis Felipe Ribeiro Pinto, Ellen Van Obberghen-Schilling, Zdenko Herceg
BACKGROUND: Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermethylation in HPV(+) oropharyngeal cancers, but only few consistent target genes have been so far described, and the evidence of a functional impact on gene expression is still limited. METHODS: We performed global and stratified pooled analyses of epigenome-wide data in HNSCCs based on the Illumina HumanMethylation450 bead-array data in order to identify tissue-specific components and common viral epigenetic targets in HPV-associated tumours...
April 5, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28374850/genome-wide-association-analysis-for-chronic-venous-disease-identifies-efemp1-and-kcnh8-as-susceptibility-loci
#11
Eva Ellinghaus, David Ellinghaus, Petra Krusche, Aljoscha Greiner, Claudia Schreiber, Susanna Nikolaus, Christian Gieger, Konstantin Strauch, Wolfgang Lieb, Philip Rosenstiel, Norbert Frings, Andreas Fiebig, Stefan Schreiber, Andre Franke
Chronic venous disease (CVD) is a multifactorial condition representing one of the most common disorders among populations of Western countries. The heritability of about 17% suggests genetic risk factors in CVD etiology. However, so far the genetic causes are unknown. We undertook the hitherto first genome-wide association study (GWAS) for CVD, analyzing more than 1.93 M SNPs in 4,942 German individuals, followed by replication in two independent German data sets. The combined analysis of discovery and replication stages (2,269 cases and 7,765 controls) yielded robust associations within the two genes EFEMP1 and KCNH8 (rs17278665, rs727139 with P < 5 × 10(-8)), and suggestive association within gene SKAP2 (rs2030136 with P < 5 × 10(-7))...
April 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28369033/crispr-cas9-epigenome-editing-enables-high-throughput-screening-for-functional-regulatory-elements-in-the-human-genome
#12
Tyler S Klann, Joshua B Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B Hilton, Gregory E Crawford, Timothy E Reddy, Charles A Gersbach
Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context...
April 3, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28348007/genome-wide-analysis-of-dna-methylation-and-acute-coronary-syndrome
#13
Jun Li, Xiaoyan Zhu, Kuai Yu, Haijing Jiang, Yizhi Zhang, Siyun Deng, Longxian Cheng, Xuezhen Liu, Jia Zhong, Xiaomin Zhang, Mei'an He, Weihong Chen, Jing Yuan, Ming Gao, Yansen Bai, Xu Han, Bing Liu, Xiaoting Luo, Wenhua Mei, Xiaosheng He, Shunchang Sun, Liyun Zhang, Hesong Zeng, Huizhen Sun, Chuanyao Liu, Yanjun Guo, Bing Zhang, Zhihong Zhang, Jinyan Huang, An Pan, Yu Yuan, Francesca Angileri, Bingxia Ming, Fang Zheng, Qiutang Zeng, Xiaobo Mao, Yudong Peng, Yi Mao, Ping Ye, Qing K Wang, Lu Qi, Frank B Hu, Liming Liang, Tangchun Wu
Rationale: Acute coronary syndrome (ACS) is a leading cause of death worldwide. Immune functions play a vital role in ACS development, however, whether epigenetic modulation contributes to the regulation of blood immune cells in this disease has not been investigated. Objective: We conducted an epigenome-wide analysis with circulating immune cells to identify differentially methylated genes in ACS. Methods and Results: We examined genome-wide methylation of whole blood in 102 ACS patients and 101 controls using HumanMethylation450 array, and externally replicated significant discoveries in 100 patients and 102 controls...
March 27, 2017: Circulation Research
https://www.readbyqxmd.com/read/28346445/potential-energy-landscapes-identify-the-information-theoretic-nature-of-the-epigenome
#14
Garrett Jenkinson, Elisabet Pujadas, John Goutsias, Andrew P Feinberg
Epigenetics is the study of biochemical modifications carrying information independent of DNA sequence, which are heritable through cell division. In 1940, Waddington coined the term "epigenetic landscape" as a metaphor for pluripotency and differentiation, but methylation landscapes have not yet been rigorously computed. Using principles from statistical physics and information theory, we derive epigenetic energy landscapes from whole-genome bisulfite sequencing (WGBS) data that enable us to quantify methylation stochasticity genome-wide using Shannon's entropy, associating it with chromatin structure...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28346444/genetic-variants-associated-with-mosaic-y-chromosome-loss-highlight-cell-cycle-genes-and-overlap-with-cancer-susceptibility
#15
Daniel J Wright, Felix R Day, Nicola D Kerrison, Florian Zink, Alexia Cardona, Patrick Sulem, Deborah J Thompson, Svanhvit Sigurjonsdottir, Daniel F Gudbjartsson, Agnar Helgason, J Ross Chapman, Steve P Jackson, Claudia Langenberg, Nicholas J Wareham, Robert A Scott, Unnur Thorsteindottir, Ken K Ong, Kari Stefansson, John R B Perry
The Y chromosome is frequently lost in hematopoietic cells, which represents the most common somatic alteration in men. However, the mechanisms that regulate mosaic loss of chromosome Y (mLOY), and its clinical relevance, are unknown. We used genotype-array-intensity data and sequence reads from 85,542 men to identify 19 genomic regions (P < 5 × 10(-8)) that are associated with mLOY. Cumulatively, these loci also predicted X chromosome loss in women (n = 96,123; P = 4 × 10(-6)). Additional epigenome-wide methylation analyses using whole blood highlighted 36 differentially methylated sites associated with mLOY...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28345651/epigenome-mapping-highlights-chromatin-mediated-gene-regulation-in-the-protozoan-parasite-trichomonas-vaginalis
#16
Min-Ji Song, Mikyoung Kim, Yeeun Choi, Myung-Hee Yi, Juri Kim, Soon-Jung Park, Tai-Soon Yong, Hyoung-Pyo Kim
Trichomonas vaginalis is an extracellular flagellated protozoan parasite that causes trichomoniasis, one of the most common non-viral sexually transmitted diseases. To survive and to maintain infection, T. vaginalis adapts to a hostile host environment by regulating gene expression. However, the mechanisms of transcriptional regulation are poorly understood for this parasite. Histone modification has a marked effect on chromatin structure and directs the recruitment of transcriptional machinery, thereby regulating essential cellular processes...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28342734/integration-of-microbiome-and-epigenome-to-decipher-the-pathogenesis-of-autoimmune-diseases
#17
REVIEW
Beidi Chen, Luxi Sun, Xuan Zhang
The interaction between genetic predisposition and environmental factors are of great significance in the pathogenesis and development of autoimmune diseases (AIDs). The human mucosa is the most frequent site that interacts with the exterior environment, and commensal microbiota at the gut and other human mucosal cavities play a crucial role in the regulation of immune system. Growing evidence has shown that the compositional and functional changes of mucosal microbiota are closely related to AIDs. Gut dysbiosis not only influence the expression level of Toll-like receptors (TLRs) of antigen presenting cells, but also contribute to Th17/Treg imbalance...
March 23, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28325913/persistent-dna-methylation-changes-associated-with-prenatal-mercury-exposure-and-cognitive-performance-during-childhood
#18
Andres Cardenas, Sheryl L Rifas-Shiman, Golareh Agha, Marie-France Hivert, Augusto A Litonjua, Dawn L DeMeo, Xihong Lin, Chitra J Amarasiriwardena, Emily Oken, Matthew W Gillman, Andrea A Baccarelli
Prenatal exposure to mercury, a known neurotoxic metal, is associated with lower cognitive performance during childhood. Disruption of fetal epigenetic programming could explain mercury's neurodevelopmental effects. We screened for epigenome-wide methylation differences associated with maternal prenatal blood mercury levels in 321 cord blood DNA samples and examined the persistence of these alterations during early (n = 75; 2.9-4.9 years) and mid-childhood (n = 291; 6.7-10.5 years). Among males, prenatal mercury levels were associated with lower regional cord blood DNA methylation at the Paraoxonase 1 gene (PON1) that persisted in early childhood and was attenuated in mid-childhood blood...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28322586/the-neonatal-methylome-as-a-gatekeeper-in-the-trajectory-to-childhood-asthma
#19
Avery DeVries, Donata Vercelli
Asthma is a heterogeneous group of conditions that typically begin in early life and result in recurrent, reversible bronchial obstruction. The role played by epigenetic mechanisms in the pathogenesis of childhood asthma is understood only in part. Here we discuss asthma epigenetics within a developmental perspective based on our recent demonstration that the epigenetic trajectory to childhood asthma begins at birth. We next discuss how this trajectory may be affected by prenatal environmental exposures. Finally, we examine in vitro studies that model the impact of asthma-associated exposures on the epigenome...
March 21, 2017: Epigenomics
https://www.readbyqxmd.com/read/28322581/epigenetics-and-allergy-from-basic-mechanisms-to-clinical-applications
#20
Daniel P Potaczek, Hani Harb, Sven Michel, Bilal Alashkar Alhamwe, Harald Renz, Jörg Tost
Allergic diseases are on the rise in the Western world and well-known allergy-protecting and -driving factors such as microbial and dietary exposure, pollution and smoking mediate their influence through alterations of the epigenetic landscape. Here, we review key facts on the involvement of epigenetic modifications in allergic diseases and summarize and critically evaluate the lessons learned from epigenome-wide association studies. We show the potential of epigenetic changes for various clinical applications: as diagnostic tools, to assess tolerance following immunotherapy or possibly predict the success of therapy at an early time point...
March 21, 2017: Epigenomics
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