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Methylation enrichment

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https://www.readbyqxmd.com/read/28823044/diagnostic-implications-of-tert-promoter-mutation-status-in-diffuse-gliomas-in-a-routine-clinical-setting
#1
Ekkehard Hewer, Nadine Prebil, Sabina Berezowska, Marielena Gutt-Will, Philippe Schucht, Matthias S Dettmer, Erik Vassella
IDH (isocitrate dehydrogenase) gene mutations are present in most diffuse low-grade gliomas and define the clinico-pathological core of the respective morphologically defined entities. Conversely, according to the 2016 WHO classification, the majority of glioblastomas belong to the IDH-wildtype category, which is defined by exclusion. TERT (telomerase reverse transcriptase gene) promoter mutations have been suggested as a molecular marker for primary glioblastomas. We analyzed molecular, histopathological, and clinical profiles of a series of 110 consecutive diffuse gliomas (WHO grades II-IV) diagnosed at our institution, in which TERT promoter mutation analysis had been performed as part of diagnostic work-up...
August 19, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28822057/short-term-exposure-to-enriched-environment-in-adult-rats-restores-mk-801-induced-cognitive-deficits-and-gabaergic-interneuron-immunoreactivity-loss
#2
Ane Murueta-Goyena, Naiara Ortuzar, Pascual Gargiulo, José Vicente Lafuente, Harkaitz Bengoetxea
Perinatal injections of N-methyl-D-aspartate (NMDA) receptor antagonist in rodents emulate some cognitive impairments and neurochemical alterations, such as decreased GABAergic (gamma aminobutyric acid) interneuron immunoreactivity, also found in schizophrenia. These features are pervasive, and developing neuroprotective or neurorestorative strategies is of special interest. In this work, we aimed to investigate if a short exposure to enriched environment (EE) in early adulthood (P55-P73) was an effective strategy to improve cognitive dysfunction and to restore interneuron expression in medial prefrontal cortex (mPFC) and hippocampus (HPC)...
August 18, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28820292/p53-binding-sites-in-normal-and-cancer-cells-are-characterized-by-distinct-chromatin-context
#3
Feifei Bao, Peter R LoVerso, Jeffrey N Fisk, Victor B Zhurkin, Feng Cui
The tumor suppressor protein p53 interacts with DNA in a sequence-dependent manner. Thousands of p53 binding sites have been mapped genome-wide in normal and cancer cells. However, the way p53 selectively binds its cognate sites in different types of cells is not fully understood. Here, we performed a comprehensive analysis of 25 published p53 cistromes and identified 3,551 and 6,039 'high-confidence' binding sites in normal and cancer cells, respectively. Our analysis revealed two distinct epigenetic features underlying p53-DNA interactions in vivo...
August 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28818737/genome-wide-dna-methylation-profiling-of-articular-cartilage-reveals-significant-epigenetic-alterations-in-kashin-beck-disease-and-osteoarthritis
#4
Wenyu Wang, Yan Yu, Jingcan Hao, Yan Wen, Jing Han, Weikun Hou, Ruiyu Liu, Bo Zhao, Awen He, Ping Li, Qianrui Fan, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Xiong Guo, Feng Zhang
OBJECTIVE: To determine genome-wide DNA methylation profiles of knee cartilage from patients with Kashin-Beck disease (KBD) and osteoarthritis (OA). METHOD: Knee cartilage was collected from 14 grade III KBD patients, 5 primary OA patients and 13 healthy subjects. The genome-wide methylation profiles of 5 KBD cartilage, 5 OA cartilage and 5 normal cartilage were determined by Illumina HumanMethylation450 array. Illumina Methylation Analyzer package was employed for identifying differentially methylated CpG sites...
August 14, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28815391/the-role-of-epigenetics-in-type-1-diabetes
#5
REVIEW
Samuel T Jerram, Mary N Dang, R David Leslie
PURPOSE OF REVIEW: Epigenetics is defined as mitotically heritable changes in gene expression that do not directly alter the DNA sequence. By implication, such epigenetic changes are non-genetically determined, although they can be affected by inherited genetic variation. Extensive evidence indicates that autoimmune diseases including type 1 diabetes are determined by the interaction of genetic and non-genetic factors. Much is known of the genetic causes of these diseases, but the non-genetic effects are less clear-cut...
August 16, 2017: Current Diabetes Reports
https://www.readbyqxmd.com/read/28814741/twin-birth-changes-dna-methylation-of-subsequent-siblings
#6
Shuai Li, Eunae Kim, Ee Ming Wong, Ji-Hoon Eric Joo, Tuong L Nguyen, Jennifer Stone, Yun-Mi Song, Louisa B Flander, Richard Saffery, Graham G Giles, Melissa C Southey, Joohon Sung, John L Hopper
We asked if twin birth influences the DNA methylation of subsequent siblings. We measured whole blood methylation using the HumanMethylation450 array for siblings from two twin and family studies in Australia and Korea. We compared the means and correlations in methylation between pairs of siblings born before a twin birth (BT siblings), born on either side of a twin birth (B/AT pairs) and born after a twin birth (AT siblings). For the genome-wide average DNA methylation, the correlation for AT pairs (rAT) was larger than the correlation for BT pairs (rBT) in both studies, and from the meta-analysis, rAT = 0...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811843/transcriptomics-and-methylomics-in-chronic-periodontitis-with-tobacco-use-a-pilot-study
#7
Young-Dan Cho, Pil-Jong Kim, Hong-Gee Kim, Yang-Jo Seol, Yong-Moo Lee, Young Ku, In-Chul Rhyu, Hyun-Mo Ryoo
BACKGROUND: Accumulating evidence suggests that tobacco smoking affects the susceptibility to and severity of chronic periodontitis. Epigenetics may explain the role of smoking in the development and progress of periodontal disease. In this study, we performed transcriptomic and methylomic analyses of non-periodontitis and periodontitis-affected gingival tissues according to smoking status. METHODS: Human gingival tissues were obtained from 20 patients, including non-smokers with and without periodontitis (n = 5 per group) and smokers with and without periodontitis (n = 5 per group)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28811741/consistency-and-variability-of-dna-methylation-in-women-during-puberty-young-adulthood-and-pregnancy
#8
Su Chen, Nandini Mukherjee, Vimala Devi Janjanam, S Hasan Arshad, Ramesh J Kurukulaaratchy, John W Holloway, Hongmei Zhang, Wilfried Karmaus
Prior DNA methylation (DNA-m) analyses have identified cytosine-phosphate-guanine (CpG) sites, which show either a significant change or consistency during lifetime. However, the proportion of CpGs that are neither significantly different nor consistent over time (indifferent CpGs) is unknown. We investigated the methylation dynamics, both longitudinal changes and consistency, in women from preadolescence to late pregnancy using DNA-m of peripheral blood cells. Consistency of cell type-adjusted DNA-m between paired individuals was assessed by regressing CpGs of subsequent age on the prior, stability by intraclass correlation coefficients (>0...
2017: Genetics & Epigenetics
https://www.readbyqxmd.com/read/28810598/differentially-methylated-regions-in-patients-with-rheumatic-heart-disease-and-secondary-pulmonary-arterial-hypertension
#9
Dawei Zheng, Xiaoying Chen, Ni Li, Lebo Sun, Qingyun Zhou, Huoshun Shi, Guodong Xu, Jing Liu, Limin Xu, Shiwei Duan, Guofeng Shao
The aim of the present study was to identify differentially methylated regions (DMRs) in patients with rheumatic heart disease and secondary pulmonary arterial hypertension (RHD-PAH). A genome-wide DNA methylation assay was performed between 6 patients with RHD-PAH and 6 healthy controls using an Illumina Infinium HumanMethylation450 BeadChip kit. The Limma software package was subsequently used to identify significant DMRs. A total of 40 hypome-thylated and 64 hypermethylated CpG sites were identified between the RHD-PAH group and the control group...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28808395/hepatoprotective-effect-of-gallotannin-enriched-extract-isolated-from-gall-on-hydrogen-peroxide-induced-cytotoxicity-in-hepg2-cells
#10
Jun Go, Ji Eun Kim, Eun Kyoung Koh, Sung Hwa Song, Hyun Gu Kang, Young Hee Lee, Han Do Kim, Jin Tae Hong, Dae Youn Hwang
BACKGROUND: Gall (Galla Rhois [GR]) is known to have antibacterial, anti-inflammatory, antimetastatic, and anti-invasion activities and exert hepatoprotective effects. However, the hepatoprotective effects of gallotannin-enriched GR (GEGR) and their mechanisms have not yet been investigated. OBJECTIVE: The potential protective effect of GEGR against hepatotoxicity induced by hydrogen peroxide (H2O2) was investigated. MATERIALS AND METHODS: Changes in cell viability, apoptosis protein expression, and reactive oxygen species (ROS) generation were determined in HepG2 cells that were pretreated with four different concentrations of GEGR (6...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28808306/phf20-positively-regulates-osteoblast-differentiation-via-increasing-the-expression-and-activation-of-runx2-with-enrichment-of-h3k4me3
#11
Jin-Woo Yang, Byung-Chul Jeong, Jongsun Park, Jeong-Tae Koh
Plant homeodomain finger protein 20 (PHF20), a methyl lysine effector protein, is a component MOF-NSL lysine acetyltranferase complex. Global deletion of PHF20 has shown spinal bone defects and reduced skeletal formation. However, the molecular basis of PHF20 involved in skeletal development has not been elucidated yet. The objective of this study was to determine the role of PHF20 in osteoblast differentiation and mineralization. Expression of PHF20 was gradually increased during osteoblast differentiation...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808137/regulatory-rnps-a-novel-class-of-ribonucleoproteins-that-potentially-contribute-to-ribosome-heterogeneity
#12
Aaron R Poole, Ian Vicino, Hironori Adachi, Yi-Tao Yu, Michael D Hebert
Many ribonucleoproteins (RNPs), which are comprised of non-coding RNA and associated proteins, are involved in essential cellular processes such as translation and pre-mRNA splicing. One class of RNP is the small Cajal body-specific RNP (scaRNP), which contributes to the biogenesis of small nuclear RNPs (snRNPs) that are central components of the spliceosome. Three scaRNAs are internally processed, generating stable nucleolus-enriched RNAs of unknown function. Here we provide data that these RNAs become part of RNPs we term regulatory RNPs (regRNPs)...
August 14, 2017: Biology Open
https://www.readbyqxmd.com/read/28795405/genomewide-dna-methylation-analysis-in-combat-veterans-reveals-a-novel-locus-for-ptsd
#13
D Mehta, D Bruenig, T Carrillo-Roa, B Lawford, W Harvey, C P Morris, A K Smith, E B Binder, R McD Young, J Voisey
OBJECTIVE: Epigenetic modifications such as DNA methylation may play a key role in the aetiology and serve as biomarkers for post-traumatic stress disorder (PTSD). We performed a genomewide analysis to identify genes whose DNA methylation levels are associated with PTSD. METHOD: A total of 211 individuals comprising Australian male Vietnam War veterans (n = 96) and males from a general population belonging to the Grady Trauma Project (n = 115) were included. Genomewide DNA methylation was performed from peripheral blood using the Illumina arrays...
August 9, 2017: Acta Psychiatrica Scandinavica
https://www.readbyqxmd.com/read/28794688/aberrantly-methylated-differentially-expressed-genes-and-pathways-in-colorectal-cancer
#14
Jingwei Liu, Hao Li, Liping Sun, Zhenning Wang, Chengzhong Xing, Yuan Yuan
BACKGROUND: Methylation plays an important role in the etiology and pathogenesis of colorectal cancer (CRC). This study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) and pathways in CRC by comprehensive bioinformatics analysis. METHODS: Data of gene expression microarrays (GSE68468, GSE44076) and gene methylation microarrays (GSE29490, GSE17648) were downloaded from GEO database. Aberrantly methylated-DEGs were obtained by GEO2R. Functional and enrichment analyses of selected genes were performed using DAVID database...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28793334/spheroid-growth-in-ovarian-cancer-alters-transcriptome-responses-for-stress-pathways-and-epigenetic-responses
#15
Trillitye Paullin, Chase Powell, Christopher Menzie, Robert Hill, Feng Cheng, Christopher J Martyniuk, Sandy D Westerheide
Ovarian cancer is the most lethal gynecological cancer, with over 200,000 women diagnosed each year and over half of those cases leading to death. These poor statistics are related to a lack of early symptoms and inadequate screening techniques. This results in the cancer going undetected until later stages when the tumor has metastasized through a process that requires the epithelial to mesenchymal transition (EMT). In lieu of traditional monolayer cell culture, EMT and cancer progression in general is best characterized through the use of 3D spheroid models...
2017: PloS One
https://www.readbyqxmd.com/read/28793267/epigenomic-landscapes-of-hesc-derived-neural-rosettes-modeling-neural-tube-formation-and-diseases
#16
Cristina Valensisi, Colin Andrus, Sam Buckberry, Naresh Doni Jayavelu, Riikka J Lund, Ryan Lister, R David Hawkins
We currently lack a comprehensive understanding of the mechanisms underlying neural tube formation and their contributions to neural tube defects (NTDs). Developing a model to study such a complex morphogenetic process, especially one that models human-specific aspects, is critical. Three-dimensional, human embryonic stem cell (hESC)-derived neural rosettes (NRs) provide a powerful resource for in vitro modeling of human neural tube formation. Epigenomic maps reveal enhancer elements unique to NRs relative to 2D systems...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28783567/assessment-of-chlorella-vulgaris-and-indigenous-microalgae-biomass-with-treated-wastewater-as-growth-culture-medium
#17
Luis C Fernández-Linares, Claudia Guerrero Barajas, Enrique Durán Páramo, Jesús A Badillo Corona
The aim of the present work was to evaluate the feasibility of microalgae cultivation using secondary treated domestic wastewater. Two Chlorella vulgaris strains (CICESE and UTEX) and an indigenous consortium, were cultivated on treated wastewater enriched with and without the fertilizer Bayfolan®. Biomass production for C. vulgaris UTEX, CICESE and the indigenous consortium grown in treated wastewater was 1.167±0.057, 1.575±0.434 and 1.125±0.250g/L, with a total lipid content of 25.70±1.24, 23.35±3.01and 20...
July 27, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28783101/analysis-of-argonaute-4-associated-long-non-coding-rna-in-arabidopsis-thaliana-sheds-novel-insights-into-gene-regulation-through-rna-directed-dna-methylation
#18
Phil Chi Khang Au, Elizabeth S Dennis, Ming-Bo Wang
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28778066/inhibition-of-lsd1-epigenetically-attenuates-oral-cancer-growth-and-metastasis
#19
Saqer F Alsaqer, Mustafa M Tashkandi, Vinay K Kartha, Ya-Ting Yang, Yazeed Alkheriji, Andrew Salama, Xaralabos Varelas, Maria Kukuruzinska, Stefano Monti, Manish V Bais
Lysine-specific demethylase 1 (LSD1) is a nuclear histone demethylase and a member of the amine oxidase (AO) family. LSD1 is a flavin-containing AO that specifically catalyzes the demethylation of mono- and di-methylated histone H3 lysine 4 through an FAD-dependent oxidative reaction. LSD1 is inappropriately upregulated in lung, liver, brain and esophageal cancers, where it promotes cancer initiation, progression, and metastasis. However, unlike other lysine-specific demethylases, the role and specific targets of LSD1 in oral squamous cell carcinoma (OSCC) pathogenesis remain unknown...
July 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28777307/epigenomics-of-major-depressive-disorders-and-schizophrenia-early-life-decides
#20
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
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