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Methylomics

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https://www.readbyqxmd.com/read/28106943/a-pilot-investigation-of-the-impact-of-smoking-cessation-on-biological-age
#1
Man-Kit Lei, Steven R H Beach, Meeshanthini V Dogan, Robert A Philibert
BACKGROUND AND OBJECTIVES: Smoking is known to increase biological age. However, whether this process is reversible through smoking cessation is not known. In this pilot study, we attempt to determine whether smoking cessation reduces biological age. METHODS: We conducted regression analyses of methylation data from 22 subjects, as they entered and exited inpatient substance use treatment, to determine change in biological age, as indicated by the deviation of their methylomic age from chronological age across two time points...
January 20, 2017: American Journal on Addictions
https://www.readbyqxmd.com/read/28101231/the-biological-significance-of-methylome-differences-in-human-papilloma-virus-associated-head-and-neck-cancer
#2
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/28100422/osteoarthritis-year-in-review-2016-genetics-genomics-and-epigenetics
#3
REVIEW
J B J van Meurs
The purpose of this narrative review is to provide an overview of last year's publications in the field of genetics, genomics and epigenetics in the osteoarthritis (OA) field. Major themes arising from a Pubmed search on (epi)genetics in OA were identified. In addition, general developments in the fast evolving field of (epi)genetics are reviewed and relevance for the OA field is summarized. In the last 5 years, a number of genome-wide association studies have identified a modest number of genetic loci associated to OA...
December 22, 2016: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28094813/a-methylome-wide-mqtl-analysis-reveals-associations-of-methylation-sites-with-gad1-and-hdac3-snps-and-a-general-psychiatric-risk-score
#4
D M Ciuculete, A E Boström, S Voisin, H Philipps, O E Titova, M Bandstein, L Nikontovic, M J Williams, J Mwinyi, H B Schiöth
Genome-wide association studies have identified a number of single-nucleotide polymorphisms (SNPs) that are associated with psychiatric diseases. Increasing body of evidence suggests a complex connection of SNPs and the transcriptional and epigenetic regulation of gene expression, which is poorly understood. In the current study, we investigated the interplay between genetic risk variants, shifts in methylation and mRNA levels in whole blood from 223 adolescents distinguished by a risk for developing psychiatric disorders...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28093925/hypermethylation-of-antisense-long-noncoding-rnas-in-acute-lymphoblastic-leukemia
#5
Gerald Arthur, Md Almamun, Kristen Taylor
AIM: Long noncoding RNAs serve critical regulatory functions highly specific for a tissue and its developmental stage. Antisense long ncRNA (AS-lncRNA) methylation changes in acute lymphoblastic leukemia (ALL) versus normal pre-B-cell lymphoblasts were evaluated to identify potential differential methylation in this group of genes. MATERIALS & METHODS: The methylome of ALL and normal lymphoblasts was examined by the methylated CpG island recovery assay followed by NGS...
January 17, 2017: Epigenomics
https://www.readbyqxmd.com/read/28088687/whole-genome-dna-methylation-profiling-identifies-epigenetic-signatures-of-uterine-carcinosarcoma
#6
Jing Li, Xiaoyun Xing, Daofeng Li, Bo Zhang, David G Mutch, Ian S Hagemann, Ting Wang
Uterine carcinosarcoma (UCS) is a form of endometrial cancer simultaneously exhibiting carcinomatous and sarcomatous elements, but the underlying molecular and epigenetic basis of this disease is poorly understood. We generated complete DNA methylomes for both the carcinomatous and the sarcomatous components of three UCS samples separated by laser capture microdissection and compared DNA methylomes of UCS with those of normal endometrium as well as methylomes derived from endometrioid carcinoma, serous endometrial carcinoma, and endometrial stromal sarcoma...
January 12, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28074437/aberrant-endometrial-dna-methylome-of-homeobox-a10-and-catechol-o-methyltransferase-in-endometriosis
#7
Fei Ji, Xinhua Yang, Yan He, Hui Wang, Aixingzi Aili, Yan Ding
PURPOSE: Differential methylation of both HOXA10 and catechol-O-methyltransferase (COMT) has been reported in different endometrium disorders, and the two genes are linked through the estrogen pathway. The current study investigates the DNA methylation of HOXA10 and COMT in ectopic and eutopic endometrial tissues and its correlation with and the occurrence of endometriosis in women from Xinjiang province in China. METHODS: In the current study, 120 patients with endometriosis were recruited from our hospital between January 2011 and June 2014...
January 10, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28074387/epigenetic-sampling-effects-nephrectomy-modifies-the-clear-cell-renal-cell-cancer-methylome
#8
Christophe Van Neste, Alexander Laird, Fiach O'Mahony, Wim Van Criekinge, Dieter Deforce, Filip Van Nieuwerburgh, Thomas Powles, David J Harrison, Grant D Stewart, Tim De Meyer
PURPOSE: Currently, it is unclear to what extent sampling procedures affect the epigenome. Here, this phenomenon was evaluated by studying the impact of artery ligation on DNA methylation in clear cell renal cancer. METHODS: DNA methylation profiles between vascularised tumour biopsy samples and devascularised nephrectomy samples from two individuals were compared. The relevance of significantly altered methylation profiles was validated in an independent clinical trial cohort...
January 10, 2017: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/28069692/genes-involved-in-development-and-differentiation-are-commonly-methylated-in-cancers-derived-from-multiple-organs-a-single-institutional-methylome-analysis-using-1007-tissue-specimens
#9
Kentaro Ohara, Eri Arai, Yoriko Takahashi, Nanako Ito, Ayako Shibuya, Koji Tsuta, Ryoji Kushima, Hitoshi Tsuda, Hidenori Ojima, Hiroyuki Fujimoto, Shun-Ichi Watanabe, Hitoshi Katai, Takayuki Kinoshita, Tatsuhiro Shibata, Takashi Kohno, Yae Kanai
The aim of this study was to clarify the significance of DNA methylation alterations shared by cancers derived from multiple organs. We analyzed single-institutional methylome data by single-CpG-resolution Infinium assay for 1,007 samples of non-cancerous tissue (N) and corresponding cancerous tissue (T) obtained from lung, stomach, kidney, breast and liver. Principal component analysis revealed that N samples of each organ showed distinct DNA methylation profiles, DNA methylation profiles of N samples of each organ being inherited by the corresponding T samples and DNA methylation profiles of T samples being more similar to those of N samples in the same organ than those of T samples in other organs...
January 9, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28067867/germline-brca2-mutations-drive-prostate-cancers-with-distinct-evolutionary-trajectories
#10
Renea A Taylor, Michael Fraser, Julie Livingstone, Shadrielle Melijah G Espiritu, Heather Thorne, Vincent Huang, Winnie Lo, Yu-Jia Shiah, Takafumi N Yamaguchi, Ania Sliwinski, Sheri Horsburgh, Alice Meng, Lawrence E Heisler, Nancy Yu, Fouad Yousif, Melissa Papargiris, Mitchell G Lawrence, Lee Timms, Declan G Murphy, Mark Frydenberg, Julia F Hopkins, Damien Bolton, David Clouston, John D McPherson, Theodorus van der Kwast, Paul C Boutros, Gail P Risbridger, Robert G Bristow
Germline mutations in the BRCA2 tumour suppressor are associated with both an increased lifetime risk of developing prostate cancer (PCa) and increased risk of aggressive disease. To understand this aggression, here we profile the genomes and methylomes of localized PCa from 14 carriers of deleterious germline BRCA2 mutations (BRCA2-mutant PCa). We show that BRCA2-mutant PCa harbour increased genomic instability and a mutational profile that more closely resembles metastastic than localized disease. BRCA2-mutant PCa shows genomic and epigenomic dysregulation of the MED12L/MED12 axis, which is frequently dysregulated in metastatic castration-resistant prostate cancer (mCRPC)...
January 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28067321/methylome-wide-association-study-of-atrial-fibrillation-in-framingham-heart-study
#11
Honghuang Lin, Xiaoyan Yin, Zhijun Xie, Kathryn L Lunetta, Steven A Lubitz, Martin G Larson, Darae Ko, Jared W Magnani, Michael M Mendelson, Chunyu Liu, David D McManus, Daniel Levy, Patrick T Ellinor, Emelia J Benjamin
Atrial fibrillation (AF) is the most common cardiac arrhythmia, but little is known about the molecular mechanisms associated with AF arrhythmogenesis. DNA methylation is an important epigenetic mechanism that regulates gene expression and downstream biological processes. We hypothesize that DNA methylation might play an important role in the susceptibility to develop AF. A total of 2,639 participants from the Offspring Cohort of Framingham Heart Study were enrolled in the current study. These participants included 183 participants with prevalent AF and 220 with incident AF during up to 9 years follow up...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28052964/whole-genome-bisulfite-sequencing-of-human-pancreatic-islets-reveals-novel-differentially-methylated-regions-in-type-2-diabetes-pathogenesis
#12
Petr Volkov, Karl Bacos, Jones K Ofori, Jonathan Lou S Esguerra, Lena Eliasson, Tina Rönn, Charlotte Ling
Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology...
January 4, 2017: Diabetes
https://www.readbyqxmd.com/read/28052017/rhcg-and-tcaf1-promoter-hypermethylation-predicts-biochemical-recurrence-in-prostate-cancer-patients-treated-by-radical-prostatectomy
#13
Siri H Strand, Michal Switnicki, Mia Moller, Christa Haldrup, Tine M Storebjerg, Jakob Hedegaard, Iver Nordentoft, Soren Hoyer, Michael Borre, Jakob S Pedersen, Peter J Wild, Jong Y Park, Torben F Orntoft, Karina D Sorensen
PURPOSE: The lack of biomarkers that can distinguish aggressive from indolent prostate cancer has caused substantial overtreatment of clinically insignificant disease. Here, by genome-wide DNA methylome profiling, we sought to identify new biomarkers to improve the accuracy of prostate cancer diagnosis and prognosis. EXPERIMENTAL DESIGN: Eight novel candidate markers, COL4A6, CYBA, TCAF1 (FAM115A), HLF, LINC01341 (LOC149134), LRRC4, PROM1, and RHCG, were selected from Illumina Infinium HumanMethylation450 BeadChip analysis of 21 tumor (T) and 21 non-malignant (NM) prostate specimens...
December 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/28045465/methylomic-profiling-of-cortex-samples-from-completed-suicide-cases-implicates-a-role-for-psors1c3-in-major-depression-and-suicide
#14
T M Murphy, B Crawford, E L Dempster, E Hannon, J Burrage, G Turecki, Z Kaminsky, J Mill
Major depressive disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesised that regulatory genomic processes are involved in the pathology of both MDD and suicidality. In this study, genome-wide patterns of DNA methylation were assessed in depressed suicide completers (n=20) and compared with non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25))...
January 3, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28045116/comparative-analysis-of-dna-methylome-and-transcriptome-of-skeletal-muscle-in-lean-obese-and-mini-type-pigs
#15
Yalan Yang, Guoming Liang, Guanglin Niu, Yuanyuan Zhang, Rong Zhou, Yanfang Wang, Yulian Mu, Zhonglin Tang, Kui Li
DNA methylation plays a pivotal role in biological processes by affecting gene expression. However, how DNA methylation mediates phenotype difference of skeletal muscle between lean-, obese-, and mini-type pigs remains unclear. We systematically carried out comparative analysis of skeletal muscle by integrating analysis of genome-wide DNA methylation, mRNA, lncRNA and miRNA profiles in three different pig breeds (obese-type Tongcheng, lean-type Landrace, and mini-type Wuzhishan pigs). We found that the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress and muscle development...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28044062/opening-up-the-dna-methylome-of-dementia
#16
R Delgado-Morales, M Esteller
Dementia is a complex clinical condition characterized by several cognitive impairments that interfere with patient independence in executing everyday tasks. Various neurodegenerative disorders have dementia in common among their clinical manifestations. In addition, these diseases, such as Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies and frontotemporal dementia, share molecular alterations at the neuropathological level. In recent years, the field of neuroepigenetics has expanded massively and it is now clear that epigenetic processes, such as DNA methylation, are mechanisms involved in both normal and pathological brain function...
January 3, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28040747/statistical-method-evaluation-for-differentially-methylated-cpgs-in-base-resolution-next-generation-dna-sequencing-data
#17
Yun Zhang, Saurabh Baheti, Zhifu Sun
High-throughput bisulfite methylation sequencing such as reduced representation bisulfite sequencing (RRBS), Agilent SureSelect Human Methyl-Seq (Methyl-seq) or whole-genome bisulfite sequencing is commonly used for base resolution methylome research. These data are represented either by the ratio of methylated cytosine versus total coverage at a CpG site or numbers of methylated and unmethylated cytosines. Multiple statistical methods can be used to detect differentially methylated CpGs (DMCs) between conditions, and these methods are often the base for the next step of differentially methylated region identification...
December 31, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28038456/dna-methylation-landscape-of-hepatoblastomas-reveals-arrest-at-early-stages-of-liver-differentiation-and-cancer-related-alterations
#18
Mariana Maschietto, Tatiane Cristina Rodrigues, André Yoshiaki Kashiwabara, Érica Sara Souza de Araujo, Talita Ferreira Marques Aguiar, Cecilia Maria Lima da Costa, Isabela Werneck da Cunha, Luciana Dos Reis Vasques, Monica Cypriano, Helena Brentani, Silvia Regina Caminada de Toledo, Peter Lees Pearson, Dirce Maria Carraro, Carla Rosenberg, Ana Cristina Victorino Krepischi
Hepatoblastomas are uncommon embryonal liver tumors accounting for approximately 80% of childhood hepatic cancer. We hypothesized that epigenetic changes, including DNA methylation, could be relevant to hepatoblastoma onset. The methylomes of eight matched hepatoblastomas and non-tumoral liver tissues were characterized, and data were validated in an independent group (11 hepatoblastomas). In comparison to differentiated livers, hepatoblastomas exhibited a widespread and non-stochastic pattern of global low-level hypomethylation...
December 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/28035030/came-identification-of-chromatin-accessibility-from-nucleosome-occupancy-and-methylome-sequencing
#19
Yongjun Piao, Seong Keon Lee, Eun-Joon Lee, Keith D Robertson, Huidong Shi, Keun Ho Ryu, Jeong-Hyeon Choi
MOTIVATION: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules...
December 29, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28032673/dental-pulp-stem-cells-model-early-life-and-imprinted-dna-methylation-patterns
#20
Keith Dunaway, Sarita Goorha, Lauren Matelski, Nora Urraca, Pamela J Lein, Ian Korf, Lawrence T Reiter, Janine M LaSalle
Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30%-40% of the genome in oocytes, preimplantation embryos, and placenta...
December 29, 2016: Stem Cells
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