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Epigenetic methylation signature

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https://www.readbyqxmd.com/read/27891302/epidemiology-of-sj%C3%A3-gren-s-syndrome-from-an-oral-perspective
#1
REVIEW
Anne Isine Bolstad, Kathrine Skarstein
Oral symptoms are among the most distressing manifestations for patients with Sjögren's syndrome (SS). The feeling of dry mouth is unpleasant, and hyposalivation may contribute to difficulty in speaking, chewing and swallowing and reduced quality of life. Reduced salivary flow increases the risk for dental caries and problems with prosthetic replacement. It seems that SS is not as frequently occurring as previously anticipated. Population-based prevalence studies on primary SS in Europe, conducted on large background populations and in accordance with the AECG criteria, reported of a prevalence of 1-9 cases per 10,000 people...
2016: Current Oral Health Reports
https://www.readbyqxmd.com/read/27890672/epigenetics-of-cell-fate-reprogramming-and-its-implications-for-neurological-disorders-modelling
#2
REVIEW
Maciej Grzybek, Aleksandra Golonko, Marta Walczak, Pawel Lisowski
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies...
November 23, 2016: Neurobiology of Disease
https://www.readbyqxmd.com/read/27881521/is-famine-exposure-during-developmental-life-in-rural-bangladesh-associated-with-a-metabolic-and-epigenetic-signature-in-young-adulthood-a-historical-cohort-study
#3
S Finer, M S Iqbal, R Lowe, B W Ogunkolade, S Pervin, C Mathews, M Smart, D S Alam, G A Hitman
OBJECTIVES: Famine exposure in utero can 'programme' an individual towards type 2 diabetes and obesity in later life. We sought to identify, (1) whether Bangladeshis exposed to famine during developmental life are programmed towards diabetes and obesity, (2) whether this programming was specific to gestational or postnatal exposure windows and (3) whether epigenetic differences were associated with famine exposure. DESIGN: A historical cohort study was performed as part of a wider cross-sectional survey...
November 23, 2016: BMJ Open
https://www.readbyqxmd.com/read/27877174/dna-methyltransferase-inhibitor-promotes-human-cd4-cd25-h-foxp3-regulatory-t-lymphocyte-induction-under-suboptimal-tcr-stimulation
#4
Chun-Hao Lu, Cheng-Jang Wu, Cheng-Chi Chan, Duc T Nguyen, Kuo-Ray Lin, Syh-Jae Lin, Li-Chen Chen, Jeffrey Jong-Yong Yen, Ming-Ling Kuo
The "master transcription factor" FOXP3 regulates the differentiation, homeostasis, and suppressor function of CD4(+) regulatory T (Treg) cells, which are critical in maintaining immune tolerance. Epigenetic regulation of FOXP3 expression has been demonstrated to be important to Treg cell development, but the induction of human Treg cells through epigenetic modification has not been clearly described. We report that the combination of the DNA methyltransferase inhibitor 5-azacytidine (5-Aza) and suboptimal T cell receptor (TCR) stimulation promoted CD4(+)CD25(h)FOXP3(+) T cell induction from human CD4(+)CD25(-) T cells...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27874289/epigenetic-changes-as-prognostic-predictors-in-endometrial-carcinomas
#5
Sanja A Farkas, Bengt G Sorbe, Torbjörn K Nilsson
Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively)...
November 22, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27866807/genome-wide-analysis-of-the-nucleus-accumbens-identifies-dna-methylation-signals-differentiating-low-binge-from-heavy-alcohol-drinking
#6
Rita Cervera-Juanes, Larry J Wilhelm, Byung Park, Kathleen A Grant, Betsy Ferguson
Alcohol use disorders encompass a range of drinking levels and behaviors, including low, binge and heavy drinking. In this regard, investigating the neural state of individuals who chronically self-administer lower doses of alcohol may provide insight into mechanisms that prevent the escalation of alcohol use. DNA methylation is one of the epigenetic mechanisms that stabilizes adaptations in gene expression and has been associated with alcohol use. Thus, we investigated DNA methylation, gene expression and the predicted neural effects in the nucleus accumbens core (NAcc) of male rhesus macaques categorized as "low" or "binge" drinkers, compared to "alcohol-naïve" and "heavy" drinkers based on drinking patterns during a 12 month alcohol self-administration protocol...
November 10, 2016: Alcohol
https://www.readbyqxmd.com/read/27863519/tet-dependent-regulation-of-retrotransposable-elements-in-mouse-embryonic-stem-cells
#7
Lorenzo de la Rica, Özgen Deniz, Kevin C L Cheng, Christopher D Todd, Cristina Cruz, Jonathan Houseley, Miguel R Branco
BACKGROUND: Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable elements (TEs), which make up nearly half of the mouse and human genomes. Epigenetic mechanisms controlling TEs have the potential to affect their mobility and to drive the co-adoption of TEs for the benefit of the host. RESULTS: We performed a detailed investigation of the role of TET enzymes in the regulation of TEs in mouse embryonic stem cells (ESCs)...
November 18, 2016: Genome Biology
https://www.readbyqxmd.com/read/27855638/alteration-of-histone-h3k4-methylation-in-glomerular-podocytes-associated-with-proteinuria-in-patients-with-membranous-nephropathy
#8
Takayuki Fujino, Naoyuki Hasebe
BACKGROUND: Histone H3K4 trimethylation (H3K4 me3) is found in active euchromatic regions and plays an important role in podocyte function in which actin filaments are abundant in the foot processes. The pathogenesis of membranous nephropathy (MN), the most prevalent cause of primary nephrotic syndrome in the middle-aged and elderly, is podocyte dysfunction. METHODS: We investigated the role of H3K4 me3 in podocyte dysfunction in nephrotic syndrome using cultured podocytes and a mouse proteinuria model induced by LPS...
November 17, 2016: BMC Nephrology
https://www.readbyqxmd.com/read/27853465/epigenetic-dna-methylation-profiling-with-msre-a-quantitative-ngs-approach-using-a-parkinson-s-disease-test-case
#9
Adam G Marsh, Matthew T Cottrell, Morton F Goldman
Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27851915/epigenomic-profiling-of-human-cd4-t-cells-supports-a-linear-differentiation-model-and-highlights-molecular-regulators-of-memory-development
#10
Pawel Durek, Karl Nordström, Gilles Gasparoni, Abdulrahman Salhab, Christopher Kressler, Melanie de Almeida, Kevin Bassler, Thomas Ulas, Florian Schmidt, Jieyi Xiong, Petar Glažar, Filippos Klironomos, Anupam Sinha, Sarah Kinkley, Xinyi Yang, Laura Arrigoni, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Lars Feuerbach, Oliver Gorka, Peter Ebert, Fabian Müller, Na Li, Stefan Frischbutter, Stephan Schlickeiser, Carla Cendon, Sebastian Fröhler, Bärbel Felder, Nina Gasparoni, Charles D Imbusch, Barbara Hutter, Gideon Zipprich, Yvonne Tauchmann, Simon Reinke, Georgi Wassilew, Ute Hoffmann, Andreas S Richter, Lina Sieverling, Hyun-Dong Chang, Uta Syrbe, Ulrich Kalus, Jürgen Eils, Benedikt Brors, Thomas Manke, Jürgen Ruland, Thomas Lengauer, Nikolaus Rajewsky, Wei Chen, Jun Dong, Birgit Sawitzki, Ho-Ryun Chung, Philip Rosenstiel, Marcel H Schulz, Joachim L Schultze, Andreas Radbruch, Jörn Walter, Alf Hamann, Julia K Polansky
The impact of epigenetics on the differentiation of memory T (Tmem) cells is poorly defined. We generated deep epigenomes comprising genome-wide profiles of DNA methylation, histone modifications, DNA accessibility, and coding and non-coding RNA expression in naive, central-, effector-, and terminally differentiated CD45RA(+) CD4(+) Tmem cells from blood and CD69(+) Tmem cells from bone marrow (BM-Tmem). We observed a progressive and proliferation-associated global loss of DNA methylation in heterochromatic parts of the genome during Tmem cell differentiation...
November 15, 2016: Immunity
https://www.readbyqxmd.com/read/27849614/epipolymorphisms-associated-with-the-clinical-outcome-of-autoimmune-arthritis-affect-cd4-t-cell-activation-pathways
#11
Roberto Spreafico, Maura Rossetti, John W Whitaker, Wei Wang, Daniel J Lovell, Salvatore Albani
Multifactorial diseases, including autoimmune juvenile idiopathic arthritis (JIA), result from a complex interplay between genetics and environment. Epigenetic mechanisms are believed to integrate such gene-environment interactions, fine-tuning gene expression, and possibly contributing to immune system dysregulation. Although anti-TNF therapy has strongly increased JIA remission rates, it is not curative and up to 80% of patients flare upon treatment withdrawal. Thus, a crucial unmet medical and scientific need is to understand the immunological mechanisms associated with remission or flare to inform clinical decisions...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27846393/decoding-the-dna-methylome-of-mantle-cell-lymphoma-in-the-light-of-the-entire-b-cell-lineage
#12
Ana C Queirós, Renée Beekman, Roser Vilarrasa-Blasi, Martí Duran-Ferrer, Guillem Clot, Angelika Merkel, Emanuele Raineri, Nuria Russiñol, Giancarlo Castellano, Sílvia Beà, Alba Navarro, Marta Kulis, Núria Verdaguer-Dot, Pedro Jares, Anna Enjuanes, María José Calasanz, Anke Bergmann, Inga Vater, Itziar Salaverría, Harmen J G van de Werken, Wyndham H Wilson, Avik Datta, Paul Flicek, Romina Royo, Joost Martens, Eva Giné, Armando Lopez-Guillermo, Hendrik G Stunnenberg, Wolfram Klapper, Christiane Pott, Simon Heath, Ivo G Gut, Reiner Siebert, Elías Campo, José I Martín-Subero
We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11...
November 14, 2016: Cancer Cell
https://www.readbyqxmd.com/read/27843151/a-dna-methylation-biomarker-of-alcohol-consumption
#13
C Liu, R E Marioni, Å K Hedman, L Pfeiffer, P-C Tsai, L M Reynolds, A C Just, Q Duan, C G Boer, T Tanaka, C E Elks, S Aslibekyan, J A Brody, B Kühnel, C Herder, L M Almli, D Zhi, Y Wang, T Huan, C Yao, M M Mendelson, R Joehanes, L Liang, S-A Love, W Guan, S Shah, A F McRae, A Kretschmer, H Prokisch, K Strauch, A Peters, P M Visscher, N R Wray, X Guo, K L Wiggins, A K Smith, E B Binder, K J Ressler, M R Irvin, D M Absher, D Hernandez, L Ferrucci, S Bandinelli, K Lohman, J Ding, L Trevisi, S Gustafsson, J H Sandling, L Stolk, A G Uitterlinden, I Yet, J E Castillo-Fernandez, T D Spector, J D Schwartz, P Vokonas, L Lind, Y Li, M Fornage, D K Arnett, N J Wareham, N Sotoodehnia, K K Ong, J B J van Meurs, K N Conneely, A A Baccarelli, I J Deary, J T Bell, K E North, Y Liu, M Waldenberger, S J London, E Ingelsson, D Levy
The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal=13 317; 54% women; mean age across cohorts 42-76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples...
November 15, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27842508/global-dna-methylation-profiling-uncovers-distinct-methylation-patterns-of-protocadherin-alpha4-in-metastatic-and-non-metastatic-rhabdomyosarcoma
#14
L Tombolan, E Poli, P Martini, A Zin, C Millino, B Pacchioni, B Celegato, G Bisogno, C Romualdi, A Rosolen, G Lanfranchi
BACKGROUND: Rhabdomyosarcoma (RMS), which can be classified as embryonal RMS (ERMS) and alveolar RMS (ARMS), represents the most frequent soft tissue sarcoma in the pediatric population; the latter shows greater aggressiveness and metastatic potential with respect to the former. Epigenetic alterations in cancer include DNA methylation changes and histone modifications that influence overall gene expression patterns. Different tumor subtypes are characterized by distinct methylation signatures that could facilitate early disease detection and greater prognostic accuracy...
November 14, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27836463/understanding-epigenetic-architecture-of-suicide-neurobiology-a-critical-perspective
#15
REVIEW
Bhaskar Roy, Yogesh Dwivedi
Current understanding of environmental cross-talk with genetic makeup is found to be mediated through an epigenetic interface which is associated with prominent reversible and heritable changes at gene expression level. Recent emergence of epigenetic modulation in shaping the genetic information has become a key regulatory factor in answering the underlying complexities associated with several mental disorders. A comprehensive understanding of the pertinent changes in the epigenetic makeup of suicide phenotype exhibits a characteristic signature with the possibility of using it as a biomarker to help predict the risk factors associated with suicide...
November 9, 2016: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/27833618/depletion-of-key-meiotic-genes-and-transcriptome-wide-abiotic-stress-reprogramming-mark-early-preparatory-events-ahead-of-apomeiotic-transition
#16
Jubin N Shah, Olga Kirioukhova, Pallavi Pawar, Muhammad Tayyab, Juan L Mateo, Amal J Johnston
Molecular dissection of apomixis - an asexual reproductive mode - is anticipated to solve the enigma of loss of meiotic sex, and to help fixing elite agronomic traits. The Brassicaceae genus Boechera comprises of both sexual and apomictic species, permitting comparative analyses of meiotic circumvention (apomeiosis) and parthenogenesis. Whereas previous studies reported local transcriptome changes during these events, it remained unclear whether global changes associated with hybridization, polyploidy and environmental adaptation that arose during evolution of Boechera might serve as (epi)genetic regulators of early development prior apomictic initiation...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27833093/molecular-alterations-in-bone-marrow-mesenchymal-stromal-cells-derived-from-acute-myeloid-leukemia-patients
#17
E K von der Heide, M Neumann, S Vosberg, A R James, M P Schroeder, J O Tanchez, K Isaakidis, C Schlee, M Luther, K Jöhrens, I Anagnostopoulos, L H Mochmann, D Nowak, W-K Hofmann, P A Greif, C D Baldus
The contribution of molecular alterations in bone marrow mesenchymal stromal cells (BM-MSC) to the pathogenesis of acute myeloid leukemia (AML) is poorly understood. Thus, we assessed genome wide genetic, transcriptional and epigenetic alterations in BM-MSC derived from AML patients (AML BM-MSC). Whole exome sequencing (WES) of AML BM-MSC samples from 21 patients revealed a non-specific pattern of genetic alterations in the stromal compartment. The only mutation present in AML BM-MSC at serial time points of diagnosis, complete remission and relapse was a mutation in the PLEC gene encoding for cytoskeleton key player Plectin in one AML patient...
November 11, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27832427/dna-methylation-changes-in-response-to-active-smoking-exposure-are-associated-with-leukocyte-telomere-length-among-older-adults
#18
Xu Gao, Ute Mons, Yan Zhang, Lutz Philipp Breitling, Hermann Brenner
Telomere length (TL) is associated with an increased risk of aging-related diseases. As a preventable environmental hazard of morbidity and mortality, smoking has been reported to promote TL attrition by producing a variety of oxidants and free radicals. Since DNA methylation has been demonstrated to play an important role in the pathways of smoking and smoking-induced diseases, this study aimed to address whether the smoking-associated DNA methylation changes could be associated with accelerated TL shortening...
November 10, 2016: European Journal of Epidemiology
https://www.readbyqxmd.com/read/27826848/rewriting-dna-methylation-signatures-at-will-the-curable-genome-within-reach
#19
Sabine Stolzenburg, Désirée Goubert, Marianne G Rots
Epigenetic regulation of gene expression is vital for the maintenance of genome integrity and cell phenotype. In addition, many different diseases have underlying epigenetic mutations, and understanding their role and function may unravel new insights for diagnosis, treatment, and even prevention of diseases. It was an important breakthrough when epigenetic alterations could be gene-specifically manipulated using epigenetic regulatory proteins in an approach termed epigenetic editing. Epigenetic editors can be designed for virtually any gene by targeting effector domains to a preferred sequence, where they write or erase the desired epigenetic modification...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27824951/epigenetic-signatures-at-aqp3-and-socs3-engage-in-low-grade-inflammation-across-different-tissues
#20
Carola Marzi, Lesca M Holdt, Giovanni Fiorito, Pei-Chien Tsai, Anja Kretschmer, Simone Wahl, Simonetta Guarrera, Daniel Teupser, Tim D Spector, Licia Iacoviello, Carlotta Sacerdote, Konstantin Strauch, Serene Lee, Wolfgang E Thasler, Annette Peters, Barbara Thorand, Petra Wolf, Holger Prokisch, Rosario Tumino, Christian Gieger, Vittorio Krogh, Salvatore Panico, Jordana T Bell, Giuseppe Matullo, Melanie Waldenberger, Harald Grallert, Wolfgang Koenig
BACKGROUND: Elevated levels of C-reactive protein (CRP, determined by a high-sensitivity assay) indicate low-grade inflammation which is implicated in many age-related disorders. Epigenetic studies on CRP might discover molecular mechanisms underlying CRP regulation. We aimed to identify DNA methylation sites related to CRP concentrations in cells and tissues regulating low-grade inflammation. RESULTS: Genome-wide DNA methylation was measured in peripheral blood in 1,741 participants of the KORA F4 study using Illumina HumanMethylation450 BeadChip arrays...
2016: PloS One
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