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https://www.readbyqxmd.com/read/29028809/nasal-dna-methylation-differentiates-corticosteroid-treatment-response-in-pediatric-asthma-a-pilot-study
#1
Xue Zhang, Jocelyn M Biagini Myers, Veda K Yadagiri, Ashley Ulm, Xiaoting Chen, Matthew T Weirauch, Gurjit K Khurana Hershey, Hong Ji
BACKGROUND: Treatment response to systemic corticosteroid in asthmatic children is heterogeneous and may be mediated by epigenetic mechanism(s). We aim to identify DNA methylation (DNAm) changes responsive to steroid, and DNAm biomarkers that distinguish treatment response. MATERIALS AND METHODS: We followed 33 children (ages 5-18) presenting to the Emergency Department (ED) for asthma exacerbation. Based on whether they met discharge criteria in ≤24 hours, participants were grouped into good and poor responders to steroid treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28988914/dna-methylation-age-is-not-accelerated-in-brain-or-blood-of-subjects-with-schizophrenia
#2
Brandon C McKinney, Huang Lin, Ying Ding, David A Lewis, Robert A Sweet
Individuals with schizophrenia (SZ) exhibit multiple premature age-related phenotypes and die ~20years prematurely. The accelerated aging hypothesis of SZ has been advanced to explain these observations, it posits that SZ-associated factors accelerate the progressive biological changes associated with normal aging. Testing the hypothesis has been limited by the absence of robust, meaningful, and multi-tissue measures of biological age. Recently, a method was described in which DNA methylation (DNAm) levels at 353 genomic sites are used to produce "DNAm age", an estimate of biological age with advantages over existing measures...
October 5, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28977446/cell-type-deconvolution-from-dna-methylation-a-review-of-recent-applications
#3
Alexander J Titus, Rachel M Gallimore, Lucas A Salas, Brock C Christensen
Recent advances in cell-type deconvolution approaches are adding to our understanding of the biology underlying disease development and progression. DNA methylation (DNAm) can be used as a biomarker of cell types, and through deconvolution approaches, to infer underlying cell type proportions. Cell-type deconvolution algorithms have two main categories: reference-based and reference-free. Reference-based algorithms are supervised methods that determine the underlying composition of cell types within a sample by leveraging differentially methylated regions (DMRs) specific to cell type, identified from DNAm measures of purified cell populations...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28967789/exploring-genome-wide-dna-methylation-patterns-in-aicardi-syndrome
#4
Ignazio S Piras, Gabrielle Mills, Lorida Llaci, Marcus Naymik, Keri Ramsey, Newell Belnap, Chris D Balak, Wayne M Jepsen, Szabolcs Szelinger, Ashley L Siniard, Candace R Lewis, Madison LaFleur, Ryan F Richholt, Matt D De Both, Kristiina Avela, Sampathkumar Rangasamy, David W Craig, Vinodh Narayanan, Irma Järvelä, Matthew J Huentelman, Isabelle Schrauwen
AIM: To explore differential DNA methylation (DNAm) in Aicardi syndrome (AIC), a severe neurodevelopmental disorder with largely unknown etiology. PATIENTS & METHODS: We characterized DNAm in AIC female patients and parents using the Illumina 450 K array. Differential DNAm was assessed using the local outlier factor algorithm, and results were validated via qPCR in a larger set of AIC female patients, parents and unrelated young female controls. Functional epigenetic modules analysis was used to detect pathways integrating both genome-wide DNAm and RNA-seq data...
October 2, 2017: Epigenomics
https://www.readbyqxmd.com/read/28965790/dna-methylation-age-and-perceived-age-in-elderly-danish-twins
#5
Birgit Debrabant, Mette Soerensen, Lene Christiansen, Qihua Tan, Matt McGue, Kaare Christensen, Jacob Hjelmborg
Perceived age is an easily accessible biomarker of aging. Here, we studied its relation to DNA methylation age (DNAm age) as introduced in (Horvath, 2013) in 180 elderly Danish twins. We found perceived age and DNAm age to be associated with chronological age (P=0.04 resp. P=2.2e-10) when correcting for gender, but did not see an association between perceived age and DNAm age (P=0.44). Intrapair-analysis showed that the proportion of pairs where the twin with the highest perceived age also had the highest DNAm age was not different from 0...
September 28, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28951779/cd4-t-cells-and-natural-killer-cells-biomarkers-for-hepatic-fibrosis-in-human-immunodeficiency-virus-hepatitis-c-virus-coinfected-patients
#6
Natalia Laufer, Diego Ojeda, María Laura Polo, Ana Martinez, Héctor Pérez, Gabriela Turk, Pedro Cahn, Norberto Walter Zwirner, Jorge Quarleri
AIM: To characterize peripheral blood natural killer (NK) cells phenotypes by flow cytometry as potential biomarker of liver fibrosis in human immunodeficiency virus (HIV)/hepatitis C virus (HCV) coinfected patients. METHODS: Peripheral mononuclear cells from 24 HIV/HCV (HBV negative) coinfected and 5 HIV/HCV/HBV seronegative individuals were evaluated. HIV/HCV coinfected patients were divided in to groups: G1, patients with METAVIR F0-F2 and G2, patients with METAVIR F3-F4...
September 8, 2017: World Journal of Hepatology
https://www.readbyqxmd.com/read/28926142/primary-osteoporosis-is-not-reflected-by-disease-specific-dna-methylation-or-accelerated-epigenetic-age-in-blood
#7
Eduardo Fernandez-Rebollo, Monika Eipel, Lothar Seefried, Per Hoffmann, Klaus Strathmann, Franz Jakob, Wolfgang Wagner
Osteoporosis is an age-related metabolic bone disease. Hence, osteoporotic patients might suffer from molecular features of accelerated aging, which is generally reflected by specific age-associated DNA methylation (DNAm) changes. In this study, we analyzed genome wide DNAm profiles of peripheral blood from patients with manifest primary osteoporosis and non-osteoporotic controls. Statistical analysis did not reveal any individual CG dinucleotides (CpG sites) with significant aberrant DNAm in osteoporosis. Subsequently, we analyzed if age-associated DNAm patterns are increased in OP...
September 19, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28912426/deconvolution-of-dna-methylation-identifies-differentially-methylated-gene-regions-on-1p36-across-breast-cancer-subtypes
#8
Alexander J Titus, Gregory P Way, Kevin C Johnson, Brock C Christensen
Breast cancer is a complex disease consisting of four distinct molecular subtypes. DNA methylation-based (DNAm) studies in tumors are complicated further by disease heterogeneity. In the present study, we compared DNAm in breast tumors with normal-adjacent breast samples from The Cancer Genome Atlas (TCGA). We constructed models stratified by tumor stage and PAM50 molecular subtype and performed cell-type reference-free deconvolution to control for cellular heterogeneity. We identified nineteen differentially methylated gene regions (DMGRs) in early stage tumors across eleven genes (AGRN, C1orf170, FAM41C, FLJ39609, HES4, ISG15, KLHL17, NOC2L, PLEKHN1, SAMD11, WASH5P)...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28878806/measuring-animal-age-with-dna-methylation-from-humans-to-wild-animals
#9
REVIEW
Ricardo De Paoli-Iseppi, Bruce E Deagle, Clive R McMahon, Mark A Hindell, Joanne L Dickinson, Simon N Jarman
DNA methylation (DNAm) is a key mechanism for regulating gene expression in animals and levels are known to change with age. Recent studies have used DNAm changes as a biomarker to estimate chronological age in humans and these techniques are now also being applied to domestic and wild animals. Animal age is widely used to track ongoing changes in ecosystems, however chronological age information is often unavailable for wild animals. An ability to estimate age would lead to improved monitoring of (i) population trends and status and (ii) demographic properties such as age structure and reproductive performance...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28844970/role-of-dna-methylation-in-human-age-prediction
#10
REVIEW
Neelam Goel, Priya Karir, Vivek Kumar Garg
DNA methylation (DNAm) is a fundamental biochemical modification which occurs over the lifespan of an individual and it is a significant component in the aging process. Methylation level of CpG sites plays an important role in finding the age of a person. Different approaches were used to extract age-related CpG (AR-CpG) sites for developing age-prediction models because the level of methylation is directly related to age for some CpG sites. Several age prediction models have been developed over the past few years and most of these models were based on regression techniques...
August 24, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28841467/chronological-age-prediction-based-on-dna-methylation-massive-parallel-sequencing-and-random-forest-regression
#11
Jana Naue, Huub C J Hoefsloot, Olaf R F Mook, Laura Rijlaarsdam-Hoekstra, Marloes C H van der Zwalm, Peter Henneman, Ate D Kloosterman, Pernette J Verschure
The use of DNA methylation (DNAm) to obtain additional information in forensic investigations showed to be a promising and increasing field of interest. Prediction of the chronological age based on age-dependent changes in the DNAm of specific CpG sites within the genome is one such potential application. Here we present an age-prediction tool for whole blood based on massive parallel sequencing (MPS) and a random forest machine learning algorithm. MPS allows accurate DNAm determination of pre-selected markers and neighboring CpG-sites to identify the best age-predictive markers for the age-prediction tool...
August 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28796508/in-vivo-structure-activity-relationships-and-optimization-of-an-unnatural-base-pair-for-replication-in-a-semi-synthetic-organism
#12
Aaron W Feldman, Floyd E Romesberg
In an effort to expand the genetic alphabet and create semi-synthetic organisms (SSOs) that store and retrieve increased information, we have developed the unnatural base pairs (UBPs) dNaM and d5SICS or dTPT3 (dNaM-d5SICS and dNaM-dTPT3). The UBPs form based on hydrophobic and packing forces, as opposed to complementary hydrogen bonding, and while they are both retained within the in vivo environment of an Escherichia coli SSO, their development was based on structure-activity relationship (SAR) data generated in vitro...
August 23, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28770015/maternal-blood-contamination-of-collected-cord-blood-can-be-identified-using-dna-methylation-at-three-cpgs
#13
Alexander M Morin, Evan Gatev, Lisa M McEwen, Julia L MacIsaac, David T S Lin, Nastassja Koen, Darina Czamara, Katri Räikkönen, Heather J Zar, Karestan Koenen, Dan J Stein, Michael S Kobor, Meaghan J Jones
BACKGROUND: Cord blood is a commonly used tissue in environmental, genetic, and epigenetic population studies due to its ready availability and potential to inform on a sensitive period of human development. However, the introduction of maternal blood during labor or cross-contamination during sample collection may complicate downstream analyses. After discovering maternal contamination of cord blood in a cohort study of 150 neonates using Illumina 450K DNA methylation (DNAm) data, we used a combination of linear regression and random forest machine learning to create a DNAm-based screening method...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28765218/dengue-virus-infected-dendritic-cells-but-not-monocytes-activate-natural-killer-cells-through-a-contact-dependent-mechanism-involving-adhesion-molecules
#14
Vivian Vasconcelos Costa, Weijian Ye, Qingfeng Chen, Mauro Martins Teixeira, Peter Preiser, Eng Eong Ooi, Jianzhu Chen
Natural killer (NK) cells play a protective role against dengue virus (DENV) infection, but the cellular and molecular mechanisms are not fully understood. Using an optimized humanized mouse model, we show that human NK cells, through the secretion of gamma interferon (IFN-γ), are critical in the early defense against DENV infection. Depletion of NK cells or neutralization of IFN-γ leads to increased viremia and more severe thrombocytopenia and liver damage in humanized mice. In vitro studies using autologous human NK cells show that DENV-infected monocyte-derived dendritic cells (MDDCs), but not monocytes, activate NK cells in a contact-dependent manner, resulting in upregulation of CD69 and CD25 and secretion of IFN-γ...
August 1, 2017: MBio
https://www.readbyqxmd.com/read/28747766/dna-methylation-signatures-of-chronic-alcohol-dependence-in-purified-cd3-t-cells-of-patients-undergoing-alcohol-treatment
#15
Christof Brückmann, Sumaiya A Islam, Julia L MacIsaac, Alexander M Morin, Kathrin N Karle, Adriana Di Santo, Richard Wüst, Immanuel Lang, Anil Batra, Michael S Kobor, Vanessa Nieratschker
Several studies have shown an association of alcohol dependence with DNA methylation (DNAm), suggesting that environmentally-induced changes on epigenomic variation may play an important role in alcohol dependence. In the present study, we analysed genome-wide DNAm profiles of purified CD3(+) T-cells from pre- and post-treatment alcohol dependent patients, as well as closely matched healthy controls. We identified 59 differentially methylated CpG sites comparing patients prior to treatment with healthy controls and were able to confirm 8 of those sites in additional analyses for differentially methylated regions...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743252/quantification-of-tumour-evolution-and-heterogeneity-via-bayesian-epiallele-detection
#16
James E Barrett, Andrew Feber, Javier Herrero, Miljana Tanic, Gareth A Wilson, Charles Swanton, Stephan Beck
BACKGROUND: Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patterns along the genome - so-called 'epialleles' - offers greater insight into epigenetic dynamics than conventional analyses which examine DNAm marks individually. RESULTS: We have developed a Bayesian model to infer which epialleles are present in multiple regions of the same tumour...
July 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28736860/annual-research-review-dna-methylation-as-a-mediator-in-the-association-between-risk-exposure-and-child-and-adolescent-psychopathology
#17
REVIEW
Edward D Barker, Esther Walton, Charlotte A M Cecil
BACKGROUND: DNA methylation (DNAm) is a potential mechanism for propagating the effects of environmental exposures on child and adolescent mental health. In recent years, this field has experienced steady growth. METHODS: We provide a strategic review of the current child and adolescent literature to evaluate evidence for a mediating role of DNAm in the link between environmental risks and psychopathological outcomes, with a focus on internalising and externalising difficulties...
July 24, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28731985/accelerated-dna-methylation-age-associations-with-ptsd-and-mortality
#18
Erika J Wolf, Mark W Logue, Tawni B Stoop, Steven A Schichman, Annjanette Stone, Naomi Sadeh, Jasmeet P Hayes, Mark W Miller
OBJECTIVE: Recently-developed indices of cellular age based on DNA methylation (DNAm) data, referred to as DNAm age, are being used to study factors that influence the rate of aging and the health correlates of these metrics of the epigenetic clock. This study evaluated associations between trauma exposure, posttraumatic stress disorder (PTSD) symptoms, and accelerated versus decelerated DNAm age among military veterans. We also examined if accelerated DNAm age predicted mortality over the course of a 6...
July 20, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28680748/mycn-is-an-immunosuppressive-oncogene-dampening-the-expression-of-ligands-for-nk-cell-activating-receptors-in-human-high-risk-neuroblastoma
#19
Elisa Brandetti, Irene Veneziani, Ombretta Melaiu, Annalisa Pezzolo, Aurora Castellano, Renata Boldrini, Elisa Ferretti, Doriana Fruci, Lorenzo Moretta, Vito Pistoia, Franco Locatelli, Loredana Cifaldi
Neuroblastoma (NB) is the most common extracranial solid tumor occurring in childhood. Amplification of the MYCN oncogene is associated with poor prognosis. Downregulation on NB cells of ligands recognized by Natural Killer (NK) cell-activating receptors, involved in tumor cell recognition and lysis, may contribute to tumor progression and relapse. Here, we demonstrate that in human NB cell lines MYCN expression inversely correlates with that of ligands recognized by NKG2D and DNAM1 activating receptors in human NB cell lines...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28675549/visible-light-mediated-excited-state-relaxation-in-semi-synthetic-genetic-alphabet-d5sics-and-dnam
#20
Kalishankar Bhattacharyya, Ayan Datta
The excited state dynamics of an unnatural base pair (UBP) d5SICS/dNaM were investigated by accurate ab-initio calculations. Time-dependent density functional and high-level multireference calculations (MS-CASPT2) were performed to elucidate the excitation of this UBP and its excited state relaxation mechanism. After excitation to the bright state S2 (ππ*), it decays to the S1 state and then undergoes efficient intersystem crossing to the triplet manifold. The presence of sulfur atom in d5SICS leads to strong spin-orbit coupling (SOC) and a small energy gap that facilitates intersystem crossing from S1 (ns π*) to T2 (ππ*) followed by internal conversion to T1 state...
July 4, 2017: Chemistry: a European Journal
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