keyword
MENU ▼
Read by QxMD icon Read
search

Epigenome wide association

keyword
https://www.readbyqxmd.com/read/28802249/high-resolution-mapping-of-chromatin-conformation-in-cardiac-myocytes-reveals-structural-remodeling-of-the-epigenome-in-heart-failure
#1
Manuel Rosa-Garrido, Douglas J Chapski, Anthony D Schmitt, Todd H Kimball, Elaheh Karbassi, Emma Monte, Enrique Balderas, Matteo Pellegrini, Tsai-Ting Shih, Elizabeth Soehalim, David A Liem, Peipei Ping, Niels J Galjart, Shuxun Ren, Yibin Wang, Bing Ren, Thomas M Vondriska
Background -Cardiovascular disease is associated with epigenomic changes in the heart, however the endogenous structure of cardiac myocyte chromatin has never been determined. Methods -To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype...
August 11, 2017: Circulation
https://www.readbyqxmd.com/read/28791728/smoking-is-associated-with-hypermethylation-of-the-apc-1a-promoter-in-colorectal-cancer-the-colocare-study
#2
Timothy M Barrow, Hagen Klett, Reka Toth, Jürgen Böhm, Biljana Gigic, Nina Habermann, Dominique Scherer, Petra Schrotz-King, Stephanie Skender, Clare Abbenhardt-Martin, Lin Zielske, Martin Schneider, Alexis Ulrich, Peter Schirmacher, Esther Herpel, Hermann Brenner, Hauke Busch, Melanie Boerries, Cornelia M Ulrich, Karin B Michels
Smoking tobacco is a known risk factor for the development of colorectal cancer, and for mortality associated with the disease. Smoking has been reported to be associated with changes in DNA methylation in blood and in lung tumour tissues, although there has been scant investigation of how epigenetic factors may be implicated in the increased risk of developing colorectal cancer. To identify epigenetic changes associated with smoking behaviours, we performed epigenome-wide analysis of DNA methylation in colorectal tumours from 36 never smokers, 47 former smokers and 13 active smokers, and adjacent mucosa from 49 never smokers, 64 former smokers and 18 active smokers...
August 9, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28777307/epigenomics-of-major-depressive-disorders-and-schizophrenia-early-life-decides
#3
REVIEW
Anke Hoffmann, Vincenza Sportelli, Michael Ziller, Dietmar Spengler
Brain development is guided by the interactions between the genetic blueprint and the environment. Epigenetic mechanisms, especially DNA methylation, can mediate these interactions and may also trigger long-lasting adaptations in developmental programs that increase the risk of major depressive disorders (MDD) and schizophrenia (SCZ). Early life adversity is a major risk factor for MDD/SCZ and can trigger persistent genome-wide changes in DNA methylation at genes important to early, but also to mature, brain function, including neural proliferation, differentiation, and synaptic plasticity, among others...
August 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28756210/the-role-of-epigenomic-alterations-in-furan-induced-hepatobiliary-pathologies
#4
Aline de Conti, Frederick A Beland, Igor P Pogribny
Furan, a volatile heterocyclic organic chemical found in a wide spectrum of common human foods, is a liver toxicant and carcinogen in mice and rats. The carcinogenic effects of furan have been attributed to genotoxic and non-genotoxic mechanisms. Among the broad range of non-genotoxic alterations induced by furan, epigenetic alterations are of special interest because of their connection to all other non-genotoxic events. This review summarizes current evidence of alterations for epigenetic mechanisms, including cytosine DNA methylation, histone modifications, and microRNA expression, caused by furan exposure and highlights the role of these aberrations in furan-associated hepatobiliary pathologies...
July 26, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28754147/design-and-implementation-of-a-custom-next-generation-sequencing-panel-for-selected-vitamin-d-associated-genes
#5
Katherine Angela Benson, Sourabh Chand, Alexander Peter Maxwell, Laura Jane Smyth, Jill Kilner, Richard Borrows, Amy Jayne McKnight
BACKGROUND: Biologically active vitamin D has an important regulatory role within the genome. It binds the vitamin D receptor (VDR) in order to control the expression of a wide range of genes as well as interacting with the epigenome to modify chromatin and methylation status. Vitamin D deficiency is associated with several human diseases including end-stage renal disease. METHODS: This article describes the design and testing of a custom, targeted next generation sequencing (NGS) panel for selected vitamin D associated genes...
July 28, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28753427/a-genetic-variant-associated-with-five-vascular-diseases-is-a-distal-regulator-of-endothelin-1-gene-expression
#6
Rajat M Gupta, Joseph Hadaya, Aditi Trehan, Seyedeh M Zekavat, Carolina Roselli, Derek Klarin, Connor A Emdin, Catharina R E Hilvering, Valerio Bianchi, Christian Mueller, Amit V Khera, Russell J H Ryan, Jesse M Engreitz, Robbyn Issner, Noam Shoresh, Charles B Epstein, Wouter de Laat, Jonathan D Brown, Renate B Schnabel, Bradley E Bernstein, Sekar Kathiresan
Genome-wide association studies (GWASs) implicate the PHACTR1 locus (6p24) in risk for five vascular diseases, including coronary artery disease, migraine headache, cervical artery dissection, fibromuscular dysplasia, and hypertension. Through genetic fine mapping, we prioritized rs9349379, a common SNP in the third intron of the PHACTR1 gene, as the putative causal variant. Epigenomic data from human tissue revealed an enhancer signature at rs9349379 exclusively in aorta, suggesting a regulatory function for this SNP in the vasculature...
July 27, 2017: Cell
https://www.readbyqxmd.com/read/28749184/is-cellular-heterogeneity-merely-a-confounder-to-be-removed-from-epigenome-wide-association-studies
#7
Joanna D Holbrook, Rae-Chi Huang, Sheila J Barton, Richard Saffery, Karen A Lillycrop
Excitement about DNA methylation biomarkers has been tempered by a growing appreciation of the complex causal relations with cell fate. Intersample differences in DNA methylation can be partitioned into those that are independent of cellular heterogeneity and those that are caused by differential mixtures of cell types. Generally, the field has assumed that the former are more likely to be causative of disease. The latter has been considered a likely consequence of disease and a confounder to be removed. We argue that the conceptual separation of these signals is artificial and not necessarily informative about causation...
July 27, 2017: Epigenomics
https://www.readbyqxmd.com/read/28747766/dna-methylation-signatures-of-chronic-alcohol-dependence-in-purified-cd3-t-cells-of-patients-undergoing-alcohol-treatment
#8
Christof Brückmann, Sumaiya A Islam, Julia L MacIsaac, Alexander M Morin, Kathrin N Karle, Adriana Di Santo, Richard Wüst, Immanuel Lang, Anil Batra, Michael S Kobor, Vanessa Nieratschker
Several studies have shown an association of alcohol dependence with DNA methylation (DNAm), suggesting that environmentally-induced changes on epigenomic variation may play an important role in alcohol dependence. In the present study, we analysed genome-wide DNAm profiles of purified CD3(+) T-cells from pre- and post-treatment alcohol dependent patients, as well as closely matched healthy controls. We identified 59 differentially methylated CpG sites comparing patients prior to treatment with healthy controls and were able to confirm 8 of those sites in additional analyses for differentially methylated regions...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28722770/asbestos-associated-genome-wide-dna-methylation-changes-in-lung-cancer
#9
Eeva Kettunen, Hector Hernandez-Vargas, Marie-Pierre Cros, Geoffroy Durand, Florence Le Calvez-Kelm, Kristina Stuopelyte, Sonata Jarmalaite, Kaisa Salmenkivi, Sisko Anttila, Henrik Wolff, Zdenko Herceg, Kirsti Husgafvel-Pursiainen
Previous studies have revealed a robust association between exposure to asbestos and human lung cancer. Accumulating evidence has highlighted the role of epigenome deregulation in the mechanism of carcinogen-induced malignancies. We examined the impact of asbestos on DNA methylation. Our genome-wide studies (using Illumina HumanMethylation450K BeadChip) of lung cancer tissue and paired normal lung from 28 asbestos-exposed or non-exposed patients, mostly smokers, revealed distinctive DNA methylation changes...
July 19, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28714605/epigenetic-alterations-and-prenatal-maternal-depression
#10
REVIEW
Zsofia Nemoda, Moshe Szyf
Major depressive disorder of the mother affects 6 to 17% of pregnancies worldwide and can lead to negative outcomes, such as preterm delivery and later mental health problems of the child. It has been proposed that developmental programming has long-lasting effects in the offspring that might be mediated by epigenetic mechanisms, such as DNA methylation. Altered stress regulation or impaired immunological function of the mother can potentially affect DNA methylation processes of the fetus, changing gene expression levels in utero...
July 17, 2017: Birth defects research
https://www.readbyqxmd.com/read/28709969/role-of-epigenome-in-tumorigenesis-and-drug-resistance
#11
Qidong Hu, Gyeong Hun Baeg
The last few decades have witnessed a tremendous advancement in understanding the genetic basis of major human diseases such as cancer. Intriguingly, there is also an evergrowing body of evidence that suggest the critical role of epigenetic regulation in pathogenesis. In contrast to genetic mechanisms often associated with changes in DNA sequence, epigenetics generally refers to the regulation of gene expression featuring alterations in histone modification, DNA methylation, chromatin conformation and noncoding RNAs, with the first two categories being the best-characterized so far...
July 11, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28693600/normal-breast-tissue-dna-methylation-differences-at-regulatory-elements-are-associated-with-the-cancer-risk-factor-age
#12
Kevin C Johnson, E Andres Houseman, Jessica E King, Brock C Christensen
BACKGROUND: The underlying biological mechanisms through which epidemiologically defined breast cancer risk factors contribute to disease risk remain poorly understood. Identification of the molecular changes associated with cancer risk factors in normal tissues may aid in determining the earliest events of carcinogenesis and informing cancer prevention strategies. METHODS: Here we investigated the impact cancer risk factors have on the normal breast epigenome by analyzing DNA methylation genome-wide (Infinium 450 K array) in cancer-free women from the Susan G...
July 10, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28691784/epigenome-wide-association-of-ptsd-from-heterogeneous-cohorts-with-a-common-multi-site-analysis-pipeline
#13
Andrew Ratanatharathorn, Marco P Boks, Adam X Maihofer, Allison E Aiello, Ananda B Amstadter, Allison E Ashley-Koch, Dewleen G Baker, Jean C Beckham, Evelyn Bromet, Michelle Dennis, Melanie E Garrett, Elbert Geuze, Guia Guffanti, Michael A Hauser, Varun Kilaru, Nathan A Kimbrel, Karestan C Koenen, Pei-Fen Kuan, Mark W Logue, Benjamin J Luft, Mark W Miller, Colter Mitchell, Nicole R Nugent, Kerry J Ressler, Bart P F Rutten, Murray B Stein, Eric Vermetten, Christiaan H Vinkers, Nagy A Youssef, Monica Uddin, Caroline M Nievergelt, Alicia K Smith
Compelling evidence suggests that epigenetic mechanisms such as DNA methylation play a role in stress regulation and in the etiologic basis of stress related disorders such as Post traumatic Stress Disorder (PTSD). Here we describe the purpose and methods of an international consortium that was developed to study the role of epigenetics in PTSD. Inspired by the approach used in the Psychiatric Genomics Consortium, we brought together investigators representing seven cohorts with a collective sample size of N = 1147 that included detailed information on trauma exposure, PTSD symptoms, and genome-wide DNA methylation data...
July 10, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28679169/differential-dna-methylation-and-gene-expression-in-reciprocal-hybrids-between-solanum-lycopersicum-and-s-pimpinellifolium
#14
Muhammad Ammar Raza, Ningning Yu, Dan Wang, Liwen Cao, Susheng Gan, Liping Chen
Wide hybridization is a common and efficient breeding strategy for enhancing crop yield and quality. An interesting phenomenon is that the reciprocal hybrids usually show different phenotypes, and its underlying mechanism is not well understood. Here, we reported our comparative analysis of the DNA methylation patterns in Solanum lycopersicum, Solanum pimpinellifolium and their reciprocal hybrids by methylated DNA immunoprecipitation sequencing. The reciprocal hybrids had lower levels of DNA methylation in CpG islands and LTR retroelements when compared with those of their parents...
June 29, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28678539/histone-3-modifications-and-blood-pressure-in-the-beijing-truck-driver-air-pollution-study
#15
Jacob K Kresovich, Zhou Zhang, Fang Fang, Yinan Zheng, Marco Sanchez-Guerra, Brian T Joyce, Jia Zhong, Yana Chervona, Sheng Wang, Dou Chang, John P McCracken, Anaite Díaz, Matteo Bonzini, Michele Carugno, Petros Koutrakis, Choong-Min Kang, Shurui Bian, Tao Gao, Hyang-Min Byun, Joel Schwartz, Andrea A Baccarelli, Lifang Hou
CONTEXT: Histone modifications regulate gene expression; dysregulation has been linked with cardiovascular diseases. Associations between histone modification levels and blood pressure in humans are unclear. OBJECTIVE: We examine the relationship between global histone concentrations and various markers of blood pressure. MATERIALS AND METHODS: Using the Beijing Truck Driver Air Pollution Study, we investigated global peripheral white blood cell histone modifications (H3K9ac, H3K9me3, H3K27me3, and H3K36me3) associations with pre- and post-work measurements of systolic (SBP) and diastolic (DBP) blood pressure, mean arterial pressure (MAP), and pulse pressure (PP) using multivariable mixed-effect models...
September 2017: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/28667419/regulation-of-dna-methylation-on-eef1d-and-rpl8-expression-in-cattle
#16
Xuan Liu, Jie Yang, Qin Zhang, Li Jiang
Dynamic changes to the epigenome play a critical role in a variety of biology processes and complex traits. Many important candidate genes have been identified through our previous genome wide association study (GWAS) on milk production traits in dairy cattle. However, the underlying mechanism of candidate genes have not yet been clearly understood. In this study, we analyzed the methylation variation of the candidate genes, EEF1D and RPL8, which were identified to be strongly associated with milk production traits in dairy cattle in our previous studies, and its effect on protein and mRNA expression...
June 30, 2017: Genetica
https://www.readbyqxmd.com/read/28654093/an-epigenome-wide-dna-methylation-study-of-ptsd-and-depression-in-world-trade-center-responders
#17
P-F Kuan, M A Waszczuk, R Kotov, C J Marsit, G Guffanti, A Gonzalez, X Yang, K Koenen, E Bromet, B J Luft
Previous epigenome-wide association studies (EWAS) of posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) have been inconsistent. This may be due to small sample sizes, and measurement and tissue differences. The current two EWA analyses of 473 World Trade Center responders are the largest to date for both PTSD and MDD. These analyses investigated DNA methylation patterns and biological pathways influenced by differentially methylated genes associated with each disorder. Methylation was profiled on blood samples using Illumina 450 K Beadchip...
June 27, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28645023/maternal-serum-pfoa-concentration-and-dna-methylation-in-cord-blood-a-pilot-study
#18
Samantha L Kingsley, Karl T Kelsey, Rondi Butler, Aimin Chen, Melissa N Eliot, Megan E Romano, Andres Houseman, Devin C Koestler, Bruce P Lanphear, Kimberly Yolton, Joseph M Braun
Perfluorooctanoic acid (PFOA), a perfluoroalkyl substance, is commonly detected in the serum of pregnant women and may impact fetal development via epigenetic re-programming. In a pilot study, we explored associations between serum PFOA concentrations during pregnancy and offspring peripheral leukocyte DNA methylation at delivery in women with high (n = 22, range: 12-26ng/mL) and low (n = 22, range: 1.1-3.1ng/mL) PFOA concentrations. After adjusting for cell type, child sex, and income, we did not find differences in CpG methylation in the two exposure groups that reached epigenome-wide significance...
October 2017: Environmental Research
https://www.readbyqxmd.com/read/28640705/genomic-analysis-of-childhood-brain-tumors-methods-for-genome-wide-discovery-and-precision-medicine-become-mainstream
#19
Stephen C Mack, Paul A Northcott
Recent breakthroughs in next-generation sequencing technology and complementary genomic platforms have transformed our capacity to interrogate the molecular landscapes of human cancers, including childhood brain tumors. Numerous high-throughput genomic studies have been reported for the major histologic brain tumor entities diagnosed in children, including interrogations at the level of the genome, epigenome, and transcriptome, many of which have yielded essential new insights into disease biology. The nature of these discoveries has been largely platform dependent, exemplifying the usefulness of applying different genomic and computational strategies, or integrative approaches, to address specific biologic and/or clinical questions...
July 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28637314/dna-methylation-signatures-and-coagulation-factors-in-the-peripheral-blood-leucocytes-of-epithelial-ovarian-cancer
#20
Lian Li, Hong Zheng, Yubei Huang, Caiyun Huang, Shuang Zhang, Jing Tian, Pei Li, Anil K Sood, Wei Zhang, Kexin Chen
Solid tumors are increasingly recognized as a systemic disease that is manifested by changes in DNA, RNA, proteins, and metabolites in the blood. Whereas many studies have reported gene mutation events in the circulation, few studies have focused on epigenetic DNA methylation markers. To identify DNA methylation biomarkers in peripheral blood for ovarian cancer, we performed a two-stage epigenome-wide association study. In the discovery stage, we measured genome wide DNA methylation for 485,000 CpG sites in peripheral blood in 24 epithelial ovarian cancer cases and 24 age-matched healthy controls...
June 16, 2017: Carcinogenesis
keyword
keyword
83888
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"