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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
#1
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/28068175/cpg-methylation-signature-predicts-recurrence-in-early-stage-hepatocellular-carcinoma-results-from-a-multicenter-study
#2
Jiliang Qiu, Baogang Peng, Yunqiang Tang, Yeben Qian, Pi Guo, Mengfeng Li, Junhang Luo, Bin Chen, Hui Tang, Canliang Lu, Muyan Cai, Zunfu Ke, Wei He, Yun Zheng, Dan Xie, Binkui Li, Yunfei Yuan
Purpose Early-stage hepatocellular carcinoma (E-HCC) is being diagnosed increasingly, and in one half of diagnosed patients, recurrence will develop. Thus, it is urgent to identify recurrence-related markers. We investigated the effectiveness of CpG methylation in predicting recurrence for patients with E-HCCs. Patients and Methods In total, 576 patients with E-HCC from four independent centers were sorted by three phases. In the discovery phase, 66 tumor samples were analyzed using the Illumina Methylation 450k Beadchip...
January 9, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28035024/preprocessing-normalization-and-integration-of-the-illumina-humanmethylationepic-array-with-minfi
#3
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen
: The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC ('EPIC') array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 ('450k') and EPIC platforms. We introduce the single-sample Noob (ssNoob) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28011750/epigenetic-effects-of-carbon-nanotubes-in-human-monocytic-cells
#4
Deniz Öner, Matthieu Moisse, Manosij Ghosh, Radu C Duca, Katrien Poels, Katrien Luyts, Eveline Putzeys, Stevan M Cokic, Kirsten Van Landuyt, Jeroen Vanoirbeek, Diether Lambrechts, Lode Godderis, Peter H M Hoet
Carbon nanotubes (CNTs) are fibrous carbon-based nanomaterials with a potential to cause carcinogenesis in humans. Alterations in DNA methylation on cytosine-phosphate-guanidine (CpG) sites are potential markers of exposure-induced carcinogenesis. This study examined cytotoxicity, genotoxicity and DNA methylation alterations on human monocytic cells (THP-1) after incubation with single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs). Higher cytotoxicity and genotoxicity were observed after incubation with SWCNTs than incubation with MWCNTs...
January 2017: Mutagenesis
https://www.readbyqxmd.com/read/28011059/epigenome-wide-analysis-links-smad3-methylation-at-birth-to-asthma-in-children-of-asthmatic-mothers
#5
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/27982729/differential-dna-methylation-and-pm2-5-species-in-a-450k-epigenome-wide-association-study
#6
Lingzhen Dai, Amar Mehta, Irina Mordukhovich, Allan C Just, Jincheng Shen, Lifang Hou, Petros Koutrakis, David Sparrow, Pantel S Vokonas, Andrea A Baccarelli, Joel D Schwartz
Although there is growing evidence that exposure to ambient particulate matter is associated with global DNA methylation and gene-specific methylation, little is known regarding epigenome-wide changes in DNA methylation in relation to particles and, especially, particle components. Using the Illumina Infinium HumanMethylation450 BeadChip, we examined the relationship between one-year moving averages of PM2.5 species (Al, Ca, Cu, Fe, K, Na, Ni, S, Si, V, and Zn) and DNA methylation at 484,613 CpG probes in a longitudinal cohort that included 646 subjects...
December 16, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27942592/dna-methylation-in-lung-cells-is-associated-with-asthma-endotypes-and-genetic-risk
#7
Jessie Nicodemus-Johnson, Rachel A Myers, Noburu J Sakabe, Debora R Sobreira, Douglas K Hogarth, Edward T Naureckas, Anne I Sperling, Julian Solway, Steven R White, Marcelo A Nobrega, Dan L Nicolae, Yoav Gilad, Carole Ober
The epigenome provides a substrate through which environmental exposures can exert their effects on gene expression and disease risk, but the relative importance of epigenetic variation on human disease onset and progression is poorly characterized. Asthma is a heterogeneous disease of the airways, for which both onset and clinical course result from interactions between host genotype and environmental exposures, yet little is known about the molecular mechanisms for these interactions. We assessed genome-wide DNA methylation using the Infinium Human Methylation 450K Bead Chip and characterized the transcriptome by RNA sequencing in primary airway epithelial cells from 74 asthmatic and 41 nonasthmatic adults...
December 8, 2016: JCI Insight
https://www.readbyqxmd.com/read/27935972/distinct-epigenetic-effects-of-tobacco-smoking-in-whole-blood-and-among-leukocyte-subtypes
#8
Dan Su, Xuting Wang, Michelle R Campbell, Devin K Porter, Gary S Pittman, Brian D Bennett, Ma Wan, Neal A Englert, Christopher L Crowl, Ryan N Gimple, Kelly N Adamski, Zhiqing Huang, Susan K Murphy, Douglas A Bell
Tobacco smoke exposure dramatically alters DNA methylation in blood cells and may mediate smoking-associated complex diseases through effects on immune cell function. However, knowledge of smoking effects in specific leukocyte subtypes is limited. To better characterize smoking-associated methylation changes in whole blood and leukocyte subtypes, we used Illumina 450K arrays and Reduced Representation Bisulfite Sequencing (RRBS) to assess genome-wide DNA methylation. Differential methylation analysis in whole blood DNA from 172 smokers and 81 nonsmokers revealed 738 CpGs, including 616 previously unreported CpGs, genome-wide significantly associated with current smoking (p <1...
2016: PloS One
https://www.readbyqxmd.com/read/27933755/maternal-pre-pregnancy-bmi-downregulates-neonatal-cord-blood-lep-methylation
#9
R Kadakia, Y Zheng, Z Zhang, W Zhang, L Hou, J L Josefson
BACKGROUND: Neonatal adiposity has many determinants and may be a risk factor for future obesity. Epigenetic regulation of metabolically important genes is a potential contributor. OBJECTIVES: The objective of the study is to determine whether methylation changes in the LEP gene in cord blood DNA are impacted by the maternal environment or affect neonatal adiposity measures. METHODS: A cross-sectional study of 114 full-term neonates born to healthy mothers with normal glucose tolerance was performed...
December 8, 2016: Pediatric Obesity
https://www.readbyqxmd.com/read/27922636/dna-methylation-and-substance-use-risk-a-prospective-genome-wide-study-spanning-gestation-to-adolescence
#10
C A M Cecil, E Walton, R G Smith, E Viding, E J McCrory, C L Relton, M Suderman, J-B Pingault, W McArdle, T R Gaunt, J Mill, E D Barker
Epigenetic processes have been implicated in addiction; yet, it remains unclear whether these represent a risk factor and/or a consequence of substance use. Here, we believe we conducted the first genome-wide, longitudinal study to investigate whether DNA methylation patterns in early life prospectively associate with substance use in adolescence. The sample comprised of 244 youth (51% female) from the Avon Longitudinal Study of Parents and Children (ALSPAC), with repeated assessments of DNA methylation (Illumina 450k array; cord blood at birth, whole blood at age 7) and substance use (tobacco, alcohol and cannabis use; age 14-18)...
December 6, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27911095/epigenetic-alterations-in-blood-mirror-age-associated-dna-methylation-and-gene-expression-changes-in-human-liver
#11
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
#12
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 1166 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...
February 1, 2017: Cancer Letters
https://www.readbyqxmd.com/read/27893424/accumulated-promoter-methylation-as-a-potential-biomarker-for-esophageal-cancer
#13
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
#14
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
#15
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
#16
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
#17
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
#18
Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach
MOTIVATION: Epigenome-wide association studies (EWAS) generate big epidemiological datasets. 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
#19
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
#20
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
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