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https://www.readbyqxmd.com/read/28298607/human-herpesvirus-6b-induces-hypomethylation-on-chromosome-17p13-3-correlating-with-increased-gene-expression-and-virus-integration
#1
Elin Engdahl, Nicky Dunn, Pitt Niehusmann, Sarah Wideman, Peter Wipfler, Albert J Becker, Tomas J Ekström, Malin Almgren, Anna Fogdell-Hahn
Human herpesvirus 6B (HHV-6B) is a neurotropic beta-herpesvirus that achieves latency by integrating its genome into host cell chromosomes. Several viruses can induce epigenetic modifications in their host cells, but no study has investigated the epigenetic modifications induced by HHV-6B. This study analyzed methylation with Illumina 450K array comparing HHV-6B infected and uninfected Molt-3 T cells three days post infection. Bisulfite pyrosequencing was used to validate Illumina results and investigate methylation over time in vitro Expression of genes was investigated using qPCR, and virus integration was investigated with PCR...
March 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28284085/detection-of-turner-syndrome-using-x-chromosome-inactivation-specific-differentially-methylated-cpg-sites-a-pilot-study
#2
Qiang Zhang, Xiaohong Guo, Tian Tian, Teng Wang, Qiaoli Li, Lei Wang, Yun Liu, Qinghe Xing, Lin He, Xinzhi Zhao
BACKGROUND: Early diagnosis of Turner syndrome (TS) may improve preventive measures and treatment. X-chromosome inactivation specific differentially methylated CpG sites (XIDMSs) that are high methylated in inactive X chromosomes (Xi) and unmethylated in active X chromosomes (Xa) may be potential makers for TS detection. METHODS: The candidate XIDMSs were screened from 9 male and 12 female DNA samples with normal karyotypes using the Illumina 450k array and validated by bisulfite sequencing PCR and pyrosequencing assay...
March 8, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28271161/dna-methylation-profiling-reveals-the-presence-of-population-specific-signatures-correlating-with-phenotypic-characteristics
#3
Anil K Giri, Soham Bharadwaj, Priyanka Banerjee, Shraddha Chakraborty, Vaisak Parekatt, Donaka Rajashekar, Abhishek Tomar, Aarthi Ravindran, Analabha Basu, Nikhil Tandon, Dwaipayan Bharadwaj
Phenotypic characteristics are known to vary substantially among different ethnicities around the globe. These variations are mediated by number of stochastic events and cannot be attributed to genetic architecture alone. DNA methylation is a well-established mechanism that sculpts our epigenome influencing phenotypic variation including disease manifestation. Since DNA methylation is an important determinant for health issues of a population, it demands a thorough investigation of the natural differences in genome wide DNA methylation patterns across different ethnic groups...
March 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28270869/epigenome-wide-discovery-and-evaluation-of-leukocyte-dna-methylation-markers-for-the-detection-of-colorectal-cancer-in-a-screening-setting
#4
Jonathan Alexander Heiss, Hermann Brenner
BACKGROUND: Colorectal cancer (CRC) is the third most common cancer worldwide. If detected at an early stage, prognosis is good. Despite increasing evidence for the benefits of implemented screening programs, such as screening colonoscopy, compliance is rather low. Hence there is demand for non-invasive tests for the early detection of CRC with high acceptance in population-wide screening. The objective of this study was to identify and evaluate leukocyte DNA methylation patterns as a potential biomarker for early detection of CRC...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28259012/dna-methylome-analysis-identifies-accelerated-epigenetic-ageing-associated-with-postmenopausal-breast-cancer-susceptibility
#5
Srikant Ambatipudi, Steve Horvath, Flavie Perrier, Cyrille Cuenin, Hector Hernandez-Vargas, Florence Le Calvez-Kelm, Geoffroy Durand, Graham Byrnes, Pietro Ferrari, Liacine Bouaoun, Athena Sklias, Véronique Chajes, Kim Overvad, Gianluca Severi, Laura Baglietto, Françoise Clavel-Chapelon, Rudolf Kaaks, Myrto Barrdahl, Heiner Boeing, Antonia Trichopoulou, Pagona Lagiou, Androniki Naska, Giovanna Masala, Claudia Agnoli, Silvia Polidoro, Rosario Tumino, Salvatore Panico, Martijn Dollé, Petra H M Peeters, N Charlotte Onland-Moret, Torkjel M Sandanger, Therese H Nøst, Elisabete Weiderpass, J Ramón Quirós, Antonio Agudo, Miguel Rodriguez-Barranco, José María Huerta Castaño, Aurelio Barricarte, Ander Matheu Fernández, Ruth C Travis, Paolo Vineis, David C Muller, Elio Riboli, Marc Gunter, Isabelle Romieu, Zdenko Herceg
AIM OF THE STUDY: A vast majority of human malignancies are associated with ageing, and age is a strong predictor of cancer risk. Recently, DNA methylation-based marker of ageing, known as 'epigenetic clock', has been linked with cancer risk factors. This study aimed to evaluate whether the epigenetic clock is associated with breast cancer risk susceptibility and to identify potential epigenetics-based biomarkers for risk stratification. METHODS: Here, we profiled DNA methylation changes in a nested case-control study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (n = 960) using the Illumina HumanMethylation 450K BeadChip arrays and used the Horvath age estimation method to calculate epigenetic age for these samples...
February 28, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28255110/methylome-wide-association-study-of-whole-blood-dna-in-the-norfolk-island-isolate-identifies-robust-loci-associated-with-age
#6
Miles C Benton, Heidi G Sutherland, Donia Macartney-Coxson, Larisa M Haupt, Rodney A Lea, Lyn R Griffiths
Epigenetic regulation of various genomic functions, including gene expression, provide mechanisms whereby an organism can dynamically respond to changes in its environment and modify gene expression accordingly. One epigenetic mechanism implicated in human aging and age-related disorders is DNA methylation. Isolated populations such as Norfolk Island (NI) should be advantageous for the identification of epigenetic factors related to aging due to reduced genetic and environmental variation. Here we conducted a methylome-wide association study of age using whole blood DNA in 24 healthy female individuals from the NI genetic isolate (aged 24-47 years)...
February 28, 2017: Aging
https://www.readbyqxmd.com/read/28254385/dna-methylation-based-forensic-age-prediction-using-artificial-neural-networks-and-next-generation-sequencing
#7
Athina Vidaki, David Ballard, Anastasia Aliferi, Thomas H Miller, Leon P Barron, Denise Syndercombe Court
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person's lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2-90 years) analysed with Illumina's genome-wide methylation platforms (27K/450K)...
February 26, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28242323/arsenic-exposure-from-drinking-water-is-associated-with-decreased-gene-expression-and-increased-dna-methylation-in-peripheral-blood
#8
Syeda Shegufta Ameer, Karin Engström, Mohammad Bakhtiar Hossain, Gabriela Concha, Marie Vahter, Karin Broberg
BACKGROUND: Exposure to inorganic arsenic increases the risk of cancer and non-malignant diseases. Inefficient arsenic metabolism is a marker for susceptibility to arsenic toxicity. Arsenic may alter gene expression, possibly by altering DNA methylation. OBJECTIVES: To elucidate the associations between arsenic exposure, gene expression, and DNA methylation in peripheral blood, and the modifying effects of arsenic metabolism. METHODS: The study participants, women from the Andes, Argentina, were exposed to arsenic via drinking water...
February 24, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28221163/controlling-the-growth-of-bi-110-and-bi-111-films-on-an-insulating-substrate
#9
Maciej Jankowski, Daniel Kamiński, Kurt Vergeer, Marta Mirolo, Francesco Carla, Guus Rijnders, Tjeerd R J Bollmann
We demonstrate the controlled growth of Bi(110) and Bi(111) films on an α-Al2O3(0001) substrate by surface x-ray diffraction and x-ray reflectivity using synchrotron radiation. At temperatures as low as 40 K, unanticipated pseudo-cubic Bi(110) films are grown with thicknesses ranging from a few to tens of nanometers. The roughness at the film-vacuum as well as the film-substrate interface, can be reduced by mild heating, where a crystallographic orientation transition of Bi(110) towards Bi(111) is observed at 400 K...
April 18, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28184257/an-empirically-driven-data-reduction-method-on-the-human-450k-methylation-array-to-remove-tissue-specific-non-variable-cpgs
#10
Rachel D Edgar, Meaghan J Jones, Wendy P Robinson, Michael S Kobor
BACKGROUND: Population based epigenetic association studies of disease and exposures are becoming more common with the availability of economical genome-wide technologies for interrogation of the methylome, such as the Illumina 450K Human Methylation Array (450K). Often, the expected small number of differentially methylated cytosine-guanine pairs (CpGs) in studies of the human methylome presents a statistical challenge, as the large number of CpGs measured on the 450K necessitates careful multiple test correction...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28184256/immunomethylomic-approach-to-explore-the-blood-neutrophil-lymphocyte-ratio-nlr-in-glioma-survival
#11
John K Wiencke, Devin C Koestler, Lucas A Salas, Joseph L Wiemels, Ritu P Roy, Helen M Hansen, Terri Rice, Lucie S McCoy, Paige M Bracci, Annette M Molinaro, Karl T Kelsey, Margaret R Wrensch, Brock C Christensen
BACKGROUND: Differentially methylated regions (DMRs) within DNA isolated from whole blood can be used to estimate the proportions of circulating leukocyte subtypes. We use the term "immunomethylomics" to describe the application of these immune lineage DMRs to studying leukocyte profiles. Here, we applied this approach to peripheral blood DNA from 72 glioma patients with molecularly defined brain tumors, representing common patient groups with defined characteristic survival times and risk factors...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28165855/genome-wide-dna-methylation-associations-with-spontaneous-preterm-birth-in-us-blacks-findings-in-maternal-and-cord-blood-samples
#12
Xiumei Hong, Ben Sherwood, Christine Ladd-Acosta, Shouneng Peng, Hongkai Ji, Ke Hao, Irina Burd, Tami R Bartell, Guoying Wang, Hui-Ju Tsai, Xin Liu, Yuelong Ji, Anastacia Wahl, Deanna Caruso, Aviva Lee-Parritz, Barry Zuckerman, Xiaobin Wang
Preterm birth (PTB) affects one in six U.S. Black babies. Epigenetics is believed to play a role in PTB; however, only a limited number of epigenetic studies of PTB have been reported, most of which have focused on cord blood DNA methylation (DNAm) and/or were conducted in white populations. Here we conducted, by far, the largest epigenome-wide DNAm analysis in 300 Black women who delivered early spontaneous preterm (sPTB, n = 150) or full-term babies (n = 150) and replicated the findings in an independent set of Black mother-newborn pairs from the Boston Birth Cohort...
February 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28149326/genome-wide-methylation-data-mirror-ancestry-information
#13
Elior Rahmani, Liat Shenhav, Regev Schweiger, Paul Yousefi, Karen Huen, Brenda Eskenazi, Celeste Eng, Scott Huntsman, Donglei Hu, Joshua Galanter, Sam S Oh, Melanie Waldenberger, Konstantin Strauch, Harald Grallert, Thomas Meitinger, Christian Gieger, Nina Holland, Esteban G Burchard, Noah Zaitlen, Eran Halperin
BACKGROUND: Genetic data are known to harbor information about human demographics, and genotyping data are commonly used for capturing ancestry information by leveraging genome-wide differences between populations. In contrast, it is not clear to what extent population structure is captured by whole-genome DNA methylation data. RESULTS: We demonstrate, using three large-cohort 450K methylation array data sets, that ancestry information signal is mirrored in genome-wide DNA methylation data and that it can be further isolated more effectively by leveraging the correlation structure of CpGs with cis-located SNPs...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28130639/global-epigenetic-profiling-identifies-methylation-subgroups-associated-with-recurrence-free-survival-in-meningioma
#14
Adriana Olar, Khalida M Wani, Charmaine D Wilson, Gelareh Zadeh, Franco DeMonte, David T W Jones, Stefan M Pfister, Erik P Sulman, Kenneth D Aldape
Meningioma is the most common primary brain tumor and carries a substantial risk of local recurrence. Methylation profiles of meningioma and their clinical implications are not well understood. We hypothesized that aggressive meningiomas have unique DNA methylation patterns that could be used to better stratify patient management. Samples (n = 140) were profiled using the Illumina HumanMethylation450BeadChip. Unsupervised modeling on a training set (n = 89) identified 2 molecular methylation subgroups of meningioma (MM) with significantly different recurrence-free survival (RFS) times between the groups: a prognostically unfavorable subgroup (MM-UNFAV) and a prognostically favorable subgroup (MM-FAV)...
March 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28125717/epigenetic-alterations-affecting-transcription-factors-and-signaling-pathways-in-stromal-cells-of-endometriosis
#15
Iveta Yotova, Emily Hsu, Catherine Do, Aulona Gaba, Matthias Sczabolcs, Sabine Dekan, Lukas Kenner, Rene Wenzl, Benjamin Tycko
Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains...
2017: PloS One
https://www.readbyqxmd.com/read/28118602/a-methodological-study-of-genome-wide-dna-methylation-analyses-using-matched-archival-formalin-fixed-paraffin-embedded-and-fresh-frozen-breast-tumors
#16
Allyson C Espinal, Dan Wang, Li Yan, Song Liu, Li Tang, Qiang Hu, Carl D Morrison, Christine B Ambrosone, Michael J Higgins, Lara E Sucheston-Campbell
BACKGROUND: DNA from archival formalin-fixed and paraffin embedded (FFPE) tissue is an invaluable resource for genome-wide methylation studies although concerns about poor quality may limit its use. In this study, we compared DNA methylation profiles of breast tumors using DNA from fresh-frozen (FF) tissues and three types of matched FFPE samples. RESULTS: For 9/10 patients, correlation and unsupervised clustering analysis revealed that the FF and FFPE samples were consistently correlated with each other and clustered into distinct subgroups...
January 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28101231/the-biological-significance-of-methylome-differences-in-human-papilloma-virus-associated-head-and-neck-cancer
#17
Maria J Worsham, Kang Mei Chen, Indrani Datta, Josena K Stephen, Dhananjay Chitale, Alexandra Gothard, George Divine
In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA)...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28098396/effects-of-chronic-cobalt-and-chromium-exposure-after-metal-on-metal-hip-resurfacing-an-epigenome-wide-association-pilot-study
#18
Julia Steinberg, Karan M Shah, Alison Gartland, Eleftheria Zeggini, Jeremy 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/28074068/a-cpg-island-methylator-phenotype-in-acute-myeloid-leukemia-independent-of-idh-mutations-and-associated-with-a-favorable-outcome
#19
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 with 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 data revealed a CGI methylator phenotype independent of IDH1/2 mutations we term AML-CGI methylator phenotype (CIMP) (A-CIMP(+))...
January 31, 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
#20
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...
March 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
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