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https://www.readbyqxmd.com/read/27911095/epigenetic-alterations-in-blood-mirror-age-associated-dna-methylation-and-gene-expression-changes-in-human-liver
#1
Madhusudhan Bysani, Alexander Perfilyev, Vanessa D de Mello, Tina Rönn, Emma Nilsson, Jussi Pihlajamäki, Charlotte Ling
AIM: To study the impact of aging on DNA methylation and mRNA expression in human liver. EXPERIMENTAL PROCEDURES: We analysed genome-wide DNA methylation and gene expression in human liver samples using Illumina 450K and HumanHT12 expression BeadChip arrays. RESULTS: DNA methylation analysis of ∼455,000 CpG sites in human liver revealed that age was significantly associated with altered DNA methylation of 20,396 CpG sites. Comparison of liver methylation data with published methylation data in other tissues showed that vast majority of the age-associated significant CpG sites overlapped between liver and blood, whereas a smaller overlap was found between liver and pancreatic islets or adipose tissue, respectively...
December 2, 2016: Epigenomics
https://www.readbyqxmd.com/read/27894957/dna-methylation-profiling-identifies-ptrf-cavin-1-as-a-novel-tumor-suppressor-in-ewing-sarcoma-when-co-expressed-with-caveolin-1
#2
Juan Huertas-Martínez, Franck Court, Santiago Rello-Varona, David Herrero-Martín, Olga Almacellas-Rabaiget, Miguel Sáinz-Jaspeado, Silvia Garcia-Monclús, Laura Lagares-Tena, Raquel Buj, Lourdes Hontecillas-Prieto, Ana Sastre, Daniel Azorin, Xavier Sanjuan, Roser López-Alemany, Sebastian Moran, Josep Roma, Soledad Gallego, Jaume Mora, Xavier García Del Muro, Paloma H Giangrande, Miquel A Peinado, Javier Alonso, Enrique de Alava, Dave Monk, Manel Esteller, Oscar M Tirado
Epigenetic modifications have been shown to be important in developmental tumors as Ewing sarcoma. We profiled the DNA methylation status of 15 primary tumors, 7 cell lines, 10 healthy tissues and 4 human mesenchymal stem cells lines samples using the Infinium Human Methylation 450k. Differential methylation analysis between Ewing sarcoma and reference samples revealed 1,166 hypermethylated and 864 hypomethylated CpG sites (Bonferroni p<0.05, δ-β-value with absolute difference of >0.20) corresponding to 392 and 470 genes respectively...
November 25, 2016: Cancer Letters
https://www.readbyqxmd.com/read/27893424/accumulated-promoter-methylation-as-a-potential-biomarker-for-esophageal-cancer
#3
Xianzhen Peng, Hengchuan Xue, Lingshuang Lü, Peiyi Shi, Jianping Wang, Jianming Wang
We performed a two-stage molecular epidemiological study to explore DNA methylation profiles for potential biomarkers of esophageal squamous cell carcinoma (ESCC) in a Chinese population. Infinium Methylation 450K BeadChip was used to identify genes with differentially methylated CpG sites. Sixteen candidate genes were validated by sequencing 1160 CpG sites in their promoter regions using the Illumina MiSeq platform. When excluding sites with negative changes, 10 genes (BNIP3, BRCA1, CCND1, CDKN2A, HTATIP2, ITGAV, NFKB1, PIK3R1, PRDM16 and PTX3) showed significantly different methylation levels among cancer lesions, remote normal-appearing tissues, and healthy controls...
November 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27891191/birth-weight-for-gestational-age-is-associated-with-dna-methylation-at-birth-and-in-childhood
#4
Golareh Agha, Hanine Hajj, Sheryl L Rifas-Shiman, Allan C Just, Marie-France Hivert, Heather H Burris, Xihong Lin, Augusto A Litonjua, Emily Oken, Dawn L DeMeo, Matthew W Gillman, Andrea A Baccarelli
BACKGROUND: Both higher and lower fetal growth are associated with cardio-metabolic health later in life, suggesting that prenatal developmental programming determines long-term cardiovascular disease risk. Epigenetic mechanisms, which orchestrate fetal growth and development, may offer insight on the early programming of health and disease. We investigated whether birth weight-for-gestational is associated with DNA methylation at birth and mid-childhood, measured via the Infinium 450K array...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27888796/altered-dna-methylation-in-neonates-born-large-for-gestational-age-is-associated-with-cardiometabolic-risk-in-children
#5
Xian-Hua Lin, Dan-Dan Wu, Ling Gao, Jun-Yu Zhang, Hai-Tao Pan, Hui Wang, Cheng Li, Ping Zhang, Meng-Xi Guo, Yan-Ting Wu, Ya-Jing Tan, Li Jin, Yu-Qian Xiang, Ju-Xue Li, Jian-Zhong Sheng, He-Feng Huang
BACKGROUND: Infants being born Large-for-gestational-age (LGA) are prone to developing cardiometabolic disease. However, the underlying mechanisms remain unclear. RESULTS: Clinical investigation showed that children born LGA had significantly higher serum level of total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-c), and insulin, ratio of TC/high-density lipoprotein-cholesterol (HDL-c) compared to children born appropriate for gestational age (AGA)...
November 18, 2016: Oncotarget
https://www.readbyqxmd.com/read/27875981/a-statistical-model-for-the-analysis-of-beta-values-in-dna-methylation-studies
#6
Leonie Weinhold, Simone Wahl, Sonali Pechlivanis, Per Hoffmann, Matthias Schmid
BACKGROUND: The analysis of DNA methylation is a key component in the development of personalized treatment approaches. A common way to measure DNA methylation is the calculation of beta values, which are bounded variables of the form M/(M+U) that are generated by Illumina's 450k BeadChip array. The statistical analysis of beta values is considered to be challenging, as traditional methods for the analysis of bounded variables, such as M-value regression and beta regression, are based on regularity assumptions that are often too strong to adequately describe the distribution of beta values...
November 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27871469/placental-telomere-length-decline-with-gestational-age-differs-by-sex-and-tert-dnmt1-and-dnmt3a-dna-methylation
#7
Samantha L Wilson, Yao Liu, Wendy P Robinson
INTRODUCTION: Telomere length (TL) has been suggested to be influenced by inherited genetic and epigenetic variation, hormonal effects, oxidative stress and age. However, the dynamics of TL during in utero development have not been well explored. This study investigates the relationship between placental TL and sex, gestational age (GA), and DNA methylation (DNAm). Placental TL is further evaluated in pregnancies complicated by preeclampsia (PE) and intrauterine growth restriction (IUGR), conditions hypothesized to lead to decreased placental TL due to increased oxidative stress...
December 2016: Placenta
https://www.readbyqxmd.com/read/27794558/efficient-detection-of-differentially-methylated-regions-using-dimmer
#8
Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach
MOTIVATION: Epigenome-wide association studies (EWAS) generate big epidemiological data sets. They aim for detecting differentially methylated DNA regions that are likely to influence transcriptional gene activity and, thus, the regulation of metabolic processes. The by far most widely used technology is the Illumina Methylation BeadChip, which measures the methylation levels of 450 (850) thousand cytosines, in the CpG dinucleotide context in a set of patients compared to a control group...
October 29, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27746755/epigenetics-in-schizophrenia-a-pilot-study-of-global-dna-methylation-in-different-brain-regions-associated-with-higher-cognitive-functions
#9
Raúl Alelú-Paz, Francisco J Carmona, José V Sanchez-Mut, Ariel Cariaga-Martínez, Ana González-Corpas, Nadia Ashour, Maria J Orea, Ana Escanilla, Alfonso Monje, Carmen Guerrero Márquez, Jerónimo Saiz-Ruiz, Manel Esteller, Santiago Ropero
Attempts to discover genes that are involved in the pathogenesis of major psychiatric disorders have been frustrating and often fruitless. Concern is building about the need to understand the complex ways in which nature and nurture interact to produce mental illness. We analyze the epigenome in several brain regions from schizophrenic patients with severe cognitive impairment using high-resolution (450K) DNA methylation array. We identified 139 differentially methylated CpG sites included in known and novel candidate genes sequences as well as in and intergenic sequences which functions remain unknown...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27723282/rheumatoid-arthritis-na%C3%A3-ve-t-cells-share-hypermethylation-sites-with-synoviocytes
#10
Brooke Rhead, Calliope Holingue, Michael Cole, Xiaorong Shao, Hong L Quach, Diana Quach, Khooshbu Shah, Elizabeth Sinclair, John Graf, Thomas Link, Ruby Harrison, Elior Rahmani, Eran Halperin, Wei Wang, Gary S Firestein, Lisa F Barcellos, Lindsey A Criswell
Objectives Our study aimed to determine whether differentially methylated CpGs in synovium-derived fibroblast-like synoviocytes (FLS) of rheumatoid arthritis (RA) patients were also differentially methylated in peripheral blood samples. Methods We measured 371 genome-wide DNA methylation profiles from 63 RA cases and 31 controls, in CD14+ monocytes, CD19+ B cells, CD4+ memory T cells and CD4+ naïve T cells, using Illumina HumanMethylation450 (450k) BeadChips. Results We found that of 5,532 hypermethylated FLS candidate CpGs, 1,056 were hypermethylated in CD4+ naïve T cells of RA cases compared to controls...
October 9, 2016: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27709425/epigenome-wide-dna-methylation-analysis-in-siblings-and-monozygotic-twins-discordant-for-sporadic-parkinson-s-disease-revealed-different-epigenetic-patterns-in-peripheral-blood-mononuclear-cells
#11
Oliver Kaut, Ina Schmitt, Jörg Tost, Florence Busato, Yi Liu, Per Hofmann, Stephanie H Witt, Marcella Rietschel, Holger Fröhlich, Ullrich Wüllner
Numerous studies have elucidated the genetics of Parkinson's disease; however, the aetiology of the majority of sporadic cases has not yet been resolved. We hypothesized that epigenetic variations could be associated with PD and evaluated the DNA methylation pattern in PD patients compared to brothers or twins without PD. The methylation of DNA from peripheral blood mononuclear cells of 62 discordant siblings including 24 monozygotic twins was characterized with Illumina DNA Methylation 450K bead arrays and subsequently validated in two independent cohorts: 221 PD vs...
October 6, 2016: Neurogenetics
https://www.readbyqxmd.com/read/27692602/spermatozoa-from-infertile-patients-exhibit-differences-of-dna-methylation-associated-with-spermatogenesis-related-processes-an-array-based-analysis
#12
Cristina Camprubí, Albert Salas-Huetos, Riccardo Aiese-Cigliano, Anna Godo, Maria-Carme Pons, Giancarlo Castellano, Mark Grossmann, Walter Sanseverino, José I Martin-Subero, Nicolás Garrido, Joan Blanco
The influence of aberrant sperm DNA methylation on the reproductive capacity of couples has been postulated as a cause of infertility. This study compared the DNA methylation of spermatozoa of 19 fertile donors and 42 infertile patients using the Illumina 450K array. Clustering analysis of methylation data arranged fertile and infertile patients into two groups. Bivariate clustering analysis identified a differential distribution of samples according to the characteristics of seminogram and age, suggesting a possible link between these parameters and specific methylation profiles...
September 15, 2016: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/27687885/characterizing-the-hypomethylated-dna-methylation-profile-of-nucleated-red-blood-cells-from-cord-blood
#13
Olivia M de Goede, Pascal M Lavoie, Wendy P Robinson
AIM: To provide insight into fetal nucleated red blood cell (nRBC) development using genome-wide DNA methylation (DNAm) profiling. MATERIALS & METHODS: The DNAm profile (Illumina 450K array) of cord blood (n = 7) derived nRBCs was compared with B cells, CD4 and CD8 T cells, natural killer cells, granulocytes, monocytes and placenta (n = 5). RESULTS: nRBCs and placenta had similarly low array-wide DNAm compared with white blood cells, but their patterns of hypomethylation differed at biologically relevant subsets of the array...
September 30, 2016: Epigenomics
https://www.readbyqxmd.com/read/27687697/widespread-dna-hypomethylation-and-differential-gene-expression-in-turner-syndrome
#14
Christian Trolle, Morten Muhlig Nielsen, Anne Skakkebæk, Philippe Lamy, Søren Vang, Jakob Hedegaard, Iver Nordentoft, Torben Falck Ørntoft, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Adults with 45,X monosomy (Turner syndrome) reflect a surviving minority since more than 99% of fetuses with 45,X monosomy die in utero. In adulthood 45,X monosomy is associated with increased morbidity and mortality, although strikingly heterogeneous with some individuals left untouched while others suffer from cardiovascular disease, autoimmune disease and infertility. The present study investigates the leukocyte DNAmethylation profile by using the 450K-Illumina Infinium assay and the leukocyte RNA-expression profile in 45,X monosomy compared with karyotypically normal female and male controls...
September 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27663594/platinum-based-chemotherapy-induces-methylation-changes-in-blood-dna-associated-with-overall-survival-in-ovarian-cancer-patients
#15
James M Flanagan, Angela Wilson, Chail Koo, Nahal Masrour, John Gallon, Erick Loomis, Kirsty Flower, Charlotte Wilhelm-Benartzi, Alexander Hergovich, Paula Cunnea, Hani Gabra, Elena I Braicu, Jalid Sehouli, Silvia Darb-Esfahani, Adriaan Vanderstichele, Ignace Vergote, Caroline Kreuzinger, Dan Cacsire Castillo-Tong, Gijsbertha Ba Wisman, Els M J J Berns, Nadeem Siddiqui, James Paul, Robert Brown
PURPOSE: DNA damage repair can lead to epigenetic changes. DNA mismatch repair proteins bind to platinum DNA adducts and at sites of DNA damage can recruit the DNA methylating enzyme DNMT1, resulting in aberrant methylation. We hypothesised that DNA damage repair during platinum-based chemotherapy may cause aberrant DNA methylation in normal tissues of patients such as blood. EXPERIMENTAL DESIGN: We used Illumina 450k methylation arrays and bisulphite pyrosequencing to investigate methylation at presentation and relapse in blood DNA from ovarian cancer patients enrolled in the SCOTROC1 trial (n=247) and in a cohort of ovarian tumour DNA samples collected at first relapse (n=46)...
September 23, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27651444/epigenetic-signatures-of-cigarette-smoking
#16
Roby Joehanes, Allan C Just, Riccardo E Marioni, Luke C Pilling, Lindsay M Reynolds, Pooja R Mandaviya, Weihua Guan, Tao Xu, Cathy E Elks, Stella Aslibekyan, Hortensia Moreno-Macias, Jennifer A Smith, Jennifer A Brody, Radhika Dhingra, Paul Yousefi, James S Pankow, Sonja Kunze, Sonia Shah, Allan F McRae, Kurt Lohman, Jin Sha, Devin M Absher, Luigi Ferrucci, Wei Zhao, Ellen W Demerath, Jan Bressler, Megan L Grove, Tianxiao Huan, Chunyu Liu, Michael M Mendelson, Chen Yao, Douglas P Kiel, Annette Peters, Rui Wang-Sattler, Peter M Visscher, Naomi R Wray, John M Starr, Jingzhong Ding, Carlos J Rodriguez, Nicholas J Wareham, Marguerite R Irvin, Degui Zhi, Myrto Barrdahl, Paolo Vineis, Srikant Ambatipudi, André G Uitterlinden, Albert Hofman, Joel Schwartz, Elena Colicino, Lifang Hou, Pantel S Vokonas, Dena G Hernandez, Andrew B Singleton, Stefania Bandinelli, Stephen T Turner, Erin B Ware, Alicia K Smith, Torsten Klengel, Elisabeth B Binder, Bruce M Psaty, Kent D Taylor, Sina A Gharib, Brenton R Swenson, Liming Liang, Dawn L DeMeo, George T O'Connor, Zdenko Herceg, Kerry J Ressler, Karen N Conneely, Nona Sotoodehnia, Sharon L R Kardia, David Melzer, Andrea A Baccarelli, Joyce B J van Meurs, Isabelle Romieu, Donna K Arnett, Ken K Ong, Yongmei Liu, Melanie Waldenberger, Ian J Deary, Myriam Fornage, Daniel Levy, Stephanie J London
BACKGROUND: -DNA methylation leaves a long-term signature of smoking exposure and is one potential mechanism by which tobacco exposure predisposes to adverse health outcomes, such as cancers, osteoporosis, lung, and cardiovascular disorders. METHODS AND RESULTS: -To comprehensively determine the association between cigarette smoking and DNA methylation, we conducted a meta-analysis of genome-wide DNA methylation assessed using the Illumina BeadChip 450K array on 15,907 blood derived DNA samples from participants in 16 cohorts (including 2,433 current, 6,518 former, and 6,956 never smokers)...
September 20, 2016: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/27643535/aberrant-methylation-of-protocadherin-17-and-its-prognostic-value-in-pediatric-acute-lymphoblastic-leukemia
#17
Thanh Nha Uyen, Kazuo Sakashita, Lika'a Fasih Y Al-Kzayer, Yozo Nakazawa, Takashi Kurata, Kenichi Koike
BACKGROUND: The outcome of approximately 20% of patients with acute lymphoblastic leukemia (ALL) remains poor because of disease recurrence. We examined whether DNA methylation of cadherin superfamily genes is a useful biomarker for ALL relapse. PROCEDURE: We used Infinium Methylation 450K Arrays to assess genome-wide DNA methylation status. The methylation status of each individual gene was then determined by a combination of bisulfite restriction analysis and genome bisulfite sequencing...
September 19, 2016: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/27621875/global-dna-methylation-and-pten-hypermethylation-alterations-in-lung-tissues-from-human-silicosis
#18
Xianan Zhang, Xiaowei Jia, Liangying Mei, Min Zheng, Chen Yu, Meng Ye
BACKGROUND: Silicosis is a respiratory disease caused by long-term silica dust exposure. Our previous study has demonstrated that silica mediates the activation of phosphatidylinositol 3-kinase (PI3K)/phosphatase and tensin homolog deleted on chromosome 10 (PTEN)/serine or threonine kinase (AKT)/mitogen-activated protein kinases (MAPK)/AP-1 pathway in human embryo lung fibroblasts (HELFs). The purpose of this study is to identify genome-wide aberrant DNA methylation profiling in lung tissues from silicosis patients...
August 2016: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/27592479/blood-dna-methylation-markers-in-potentially-identified-chinese-patients-with-hepatocellular-carcinoma
#19
Zongying Liu, Haixiu Yan, Jinshu Zhang
To determine whether blood DNA methylation is associated with hepatocellular carcinoma (HCC) for Chinese patients, we used genome-wide DNA methylation detection to access the blood samples of Chinese patients by Illumina Human methylation 450K arrays. Sixty potentially gene locis which had different methylated levels significantly among tumor and adjacent normal tissues would be tested in this study. A previous study was conducted in China communities and followed with 7 years. The DNA from white blood cells (WBC) from 192 patients with HCC and 215 matched controls were assayed in this study...
July 2016: Pakistan Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27585642/genome-wide-dna-methylation-patterns-in-cd4-t-cells-from-chinese-han-patients-with-rheumatoid-arthritis
#20
Shicheng Guo, Qi Zhu, Ting Jiang, Rongsheng Wang, Yi Shen, Xiao Zhu, Yan Wang, Fengmin Bai, Qin Ding, Xiaodong Zhou, Guangjie Chen, Dong Yi He
INTRODUCTION: Rheumatoid arthritis (RA) is an autoimmune disease that causes chronic inflammation of the joints. Recent evidence indicated the epigenetic changes may contribute to the pathogenesis of RA. METHOD: To understand the extent and nature of dysregulated DNA methylation in RA CD4T cells, we performed a genome-wide DNA methylation study in CD4 + T cells in 12 RA patients compared to 12 matched normal healthy controls. Cytosine methylation status was quantified with Illumina methylation 450K microarray...
September 1, 2016: Modern Rheumatology
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