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Epigenetic methylation signature

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https://www.readbyqxmd.com/read/29157945/food-allergy-a-review-and-update-on-epidemiology-pathogenesis-diagnosis-prevention-and-management
#1
Scott H Sicherer, Hugh A Sampson
This review provides general information to serve as a primer for those embarking on understanding food allergy and also details advances and updates in epidemiology, pathogenesis, diagnosis and treatment that have occurred over the four years since our last comprehensive review. Although firm prevalence data are lacking, there is a strong impression that food allergy has increased, and rates as high as ∼10% have been documented. Genetic, epigenetic and environmental risk factors are being increasingly elucidated, opening the potential for improved prevention and treatment strategies targeted to those at risk...
November 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29141958/dna-methylation-defines-regional-identity-of-human-intestinal-epithelial-organoids-and-undergoes-dynamic-changes-during-development
#2
Judith Kraiczy, Komal M Nayak, Kate J Howell, Alexander Ross, Jessica Forbester, Camilla Salvestrini, Roxana Mustata, Sally Perkins, Amanda Andersson-Rolf, Esther Leenen, Anke Liebert, Ludovic Vallier, Philip C Rosenstiel, Oliver Stegle, Gordon Dougan, Robert Heuschkel, Bon-Kyoung Koo, Matthias Zilbauer
OBJECTIVE: Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited. DESIGN: We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology...
November 15, 2017: Gut
https://www.readbyqxmd.com/read/29133016/dynamic-transcriptional-control-of-macrophage-mirna-signature-via-inflammation-responsive-enhancers-revealed-using-a-combination-of-next-generation-sequencing-based-approaches
#3
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29109980/the-abundance-of-metabolites-related-to-protein-methylation-correlates-with-the-metastatic-capacity-of-human-melanoma-xenografts
#4
Xiaolei Shi, Alpaslan Tasdogan, Fang Huang, Zeping Hu, Sean J Morrison, Ralph J DeBerardinis
Metabolic reprogramming is a major factor in transformation, and particular metabolic phenotypes correlate with oncogenotype, tumor progression, and metastasis. By profiling metabolites in 17 patient-derived xenograft melanoma models, we identified durable metabolomic signatures that correlate with biological features of the tumors. BRAF mutant tumors had metabolomic and metabolic flux features of enhanced glycolysis compared to BRAF wild-type tumors. Tumors that metastasized efficiently from their primary sites had elevated levels of metabolites related to protein methylation, including trimethyllysine (TML)...
November 2017: Science Advances
https://www.readbyqxmd.com/read/29109526/genome-wide-genetic-and-epigenetic-analyses-of-pancreatic-acinar-cell-carcinomas-reveal-aberrations-in-genome-stability
#5
Cornelia Jäkel, Frank Bergmann, Reka Toth, Yassen Assenov, Daniel van der Duin, Oliver Strobel, Thomas Hank, Günter Klöppel, Craig Dorrell, Markus Grompe, Joshua Moss, Yuval Dor, Peter Schirmacher, Christoph Plass, Odilia Popanda, Peter Schmezer
Pancreatic acinar cell carcinoma (ACC) is an aggressive exocrine tumor with largely unknown biology. Here, to identify potential targets for personalized treatment, we perform integrative genome-wide and epigenome-wide analyses. The results show frequently aberrant DNA methylation, abundant chromosomal amplifications and deletions, and mutational signatures suggesting defective DNA repair. In contrast to pancreatic ductal adenocarcinoma, no recurrent point mutations are detected. The tumor suppressors ID3, ARID1A, APC, and CDKN2A are frequently impaired also on the protein level and thus potentially affect ACC tumorigenesis...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29098673/biochemical-diagnosis-in-substance-and-non-substance-addiction
#6
Wenwen Shen, Huifeng Liu, Xiaohu Xie, Haixiong Liu, Wenhua Zhou
An optimal biochemical marker for addiction would be some easily traced molecules in body specimens, which indicates indulgent addictive behaviors, or susceptibility to certain addictive stimuli. In this chapter, we discussed existing literature about possible biomarkers, and classified them into three categories: origin forms and metabolites of substances, markers from biochemical responses to certain addiction, and genetic and epigenetic biomarkers suggesting susceptibility to addiction. In every category, we examined studies concerning certain type of addiction one by one, with focuses mainly on opiates, psychostimulants, and pathological gambling...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29097680/epigenome-wide-association-studies-identify-dna-methylation-associated-with-kidney-function
#7
Audrey Y Chu, Adrienne Tin, Pascal Schlosser, Yi-An Ko, Chengxiang Qiu, Chen Yao, Roby Joehanes, Morgan E Grams, Liming Liang, Caroline A Gluck, Chunyu Liu, Josef Coresh, Shih-Jen Hwang, Daniel Levy, Eric Boerwinkle, James S Pankow, Qiong Yang, Myriam Fornage, Caroline S Fox, Katalin Susztak, Anna Köttgen
Chronic kidney disease (CKD) is defined by reduced estimated glomerular filtration rate (eGFR). Previous genetic studies have implicated regulatory mechanisms contributing to CKD. Here we present epigenome-wide association studies of eGFR and CKD using whole-blood DNA methylation of 2264 ARIC Study and 2595 Framingham Heart Study participants to identify epigenetic signatures of kidney function. Of 19 CpG sites significantly associated (P < 1e-07) with eGFR/CKD and replicated, five also associate with renal fibrosis in biopsies from CKD patients and show concordant DNA methylation changes in kidney cortex...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29095713/bicuspid-aortic-valve-associated-aortopathy-update-on-biomarkers
#8
Ashna K Maredia, Steven C Greenway, Subodh Verma, Paul W M Fedak
PURPOSE OF REVIEW: Bicuspid aortic valve (BAV)-associated aortopathy is common and its progression for individual patients is difficult to predict. The present review aims to identify recent developments using biomarkers for the determination of risk and progression of disease in patients with BAV aortopathy. RECENT FINDINGS: Novel rare genetic variants and epigenetic methylation signatures affecting non-cytosine phosphate guanine (non-CpG) and CpG sites, nicotinamide phosphoribosyltransferase and Sod expression may lead to improved prediction of the aortopathy phenotype...
October 31, 2017: Current Opinion in Cardiology
https://www.readbyqxmd.com/read/29093522/genome-wide-discovery-of-long-intergenic-noncoding-rnas-and-their-epigenetic-signatures-in-the-rat
#9
Aimin Li, Zhong-Yin Zhou, Xinhong Hei, Newton O Otecko, Junying Zhang, Yajun Liu, Hongfang Zhou, Zhiqiang Zhao, Lei Wang
Long intergenic noncoding RNAs (lincRNAs) play a crucial role in many biological processes. The rat is an important model organism in biomedical research. Recent studies have detected rat lincRNA genes from several samples. However, identification of rat lincRNAs using large-scale RNA-seq datasets remains unreported. Herein, using more than 100 billion RNA-seq reads from 59 publications together with RefSeq and UniGene annotated RNAs, we report 39,154 lincRNA transcripts encoded by 19,162 lincRNA genes in the rat...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29089052/epigenetic-control-of-epilepsy-target-genes-contributes-to-a-cellular-memory-of-epileptogenesis-in-cultured-rat-hippocampal-neurons
#10
K Kiese, J Jablonski, J Hackenbracht, J K Wrosch, T W Groemer, J Kornhuber, I Blümcke, K Kobow
Hypersynchronous neuronal excitation manifests clinically as seizure (ictogenesis), and may recur spontaneously and repetitively after a variable latency period (epileptogenesis). Despite tremendous research efforts to describe molecular pathways and signatures of epileptogenesis, molecular pathomechanisms leading to chronic epilepsy remain to be clarified. We hypothesized that epigenetic modifications may form the basis for a cellular memory of epileptogenesis, and used a primary neuronal cell culture model of the rat hippocampus to study the translation of massive neuronal excitation into persisting changes of epigenetic signatures and pro-epileptogenic target gene expression...
October 31, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/29079368/p14-methylation-an-epigenetic-signature-of-salivary-gland-mucoepidermoid-carcinoma-in-the-serbian-population
#11
Nadja Nikolic, Jelena Carkic, Ivana Ilic Dimitrijevic, Najib Eljabo, Milena Radunovic, Boban Anicic, Nasta Tanic, Markus Falk, Jelena Milasin
OBJECTIVE: To investigate the prevalence of p16(INK4 a), p14(ARF), tumor protein p53 (TP53), and human telomerase reverse transcriptase (hTERT) promoter hypermethylation in mucoepidermoid carcinomas (MECs) and search for a possible association between methylation status and clinicopathological parameters. STUDY DESIGN: DNA extracted from 35 formalin-fixed and paraffin-embedded MEC samples and 10 normal salivary gland (NSG) tissue samples was analyzed for the presence of promoter hypermethylation using methylation-specific polymerase chain reaction testing...
September 28, 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/29076965/mutational-and-epigenetic-signatures-in-cancer-tissue-linked-to-environmental-exposures-and-lifestyle
#12
Vittorio Perduca, Hanane Omichessan, Laura Baglietto, Gianluca Severi
PURPOSE OF REVIEW: In this article, we describe how recent advances in the study of mutational and epigenetic signatures in tumours provide new opportunities to understand the role of the environment and lifestyle in cancer development. RECENT FINDINGS: Cancer-related mutational events have been investigated for decades but only recently the wide availability of genomic sequences and epigenomic data from thousands of cancer genomes has made it possible to identify numerous distinct mutational and epigenetic signatures through the application of advanced mathematical models...
October 25, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29074395/epigenetics-of-malignant-melanoma
#13
REVIEW
Bruce Moran, Romina Silva, Antoinette S Perry, William M Gallagher
Patients with malignant melanoma generally have a good prognosis if the disease presents prior to metastasis. Due to progress with targeted and immunotherapies, the median survival of metastatic melanoma patients is now over 2 years. The disease is characterised by one of the highest somatic mutation rates observed amongst cancer types, with a specific mutational signature based on UV radiation damage evident. Highly prevalent mutations, such as the BRAF(V600E), in the MAPK cascade indicate truncal involvement of this pathway in the earliest stage of melanoma...
October 23, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29066912/identification-of-key-pathways-and-genes-with-aberrant-methylation-in-prostate-cancer-using-bioinformatics-analysis
#14
Anshika N Singh, Neeti Sharma
Prostate cancer (PCa), a multifocal clinically heterogeneous disease, is the most commonly diagnosed non-cutaneous neoplasm in men worldwide. The epigenome of PCa is a typical representation of catastrophic model of epigenetic alterations during tumorigenesis and its progression. Alterations in methylation patterns in tumor suppressors, cell cycle, oncogenes and metabolism-related genes are the most commonly observed epigenetic alterations in PCa. In this study, we have developed a computational strategy to identify methylated biomarker signature panels as potential targets of PCa by screening >160 genes reported to be epigenetically dysregulated, and shortlisted 26 differentially methylated genes (DMGs) that significantly contribute to oncogenesis...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29066321/macrophage-polarization-and-allergic-asthma
#15
REVIEW
Arjun Saradna, Danh C Do, Shruthi Kumar, Qing-Ling Fu, Peisong Gao
Allergic asthma is associated with airway inflammation and airway hyperresponsiveness. Macrophage polarization has been shown to have a profound impact on asthma pathogenesis. On exposure to local microenvironments, recruited macrophages can be polarized into either classically activated (or M1) or alternatively activated (or M2) phenotypes. Macrophage polarization has been heavily associated with development of asthma. The process of regulation of macrophage polarization involves an intricate interplay between various cytokines, chemokines, transcriptional factors, and immune-regulatory cells...
October 7, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/29057612/rapid-response-to-changing-environments-during-biological-invasions-dna-methylation-perspectives
#16
Xuena Huang, Shiguo Li, Ping Ni, Yangchun Gao, Bei Jiang, Zunchun Zhou, Aibin Zhan
Dissecting complex interactions between species and their environments has long been a research hotspot in the fields of ecology and evolutionary biology. The well-recognized Darwinian evolution has well explained long-term adaptation scenarios; however, "rapid" processes of biological responses to environmental changes remain largely unexplored, particularly moleculare mechanisms such as DNA methylation that have recently been proposed to play crucial roles in rapid environmental adaptation. Invasive species, which have capacities to successfully survive rapidly changing environments during biological invasions, provide great opportunities to study molecular mechanisms of rapid environemental adaptation...
October 23, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29056289/genomic-and-epigenetic-characterization-for-the-comparison-of-synchronous-bilateral-tongue-squamous-cell-carcinomas-a-case-report
#17
Ilda P Ribeiro, Leonor Barroso, Francisco Marques, André Santos, Francisco Caramelo, Maria J Julião, Joana B Melo, Isabel M Carreira
The tongue is the most common and aggressive site for tumors in the oral cavity. These tumors are usually located in the lateral border of the tongue and are often related to the use of tobacco and alcohol. Clinical management of these tumors is predominantly based on anatomic location and TNM classification. The identification of molecular signatures with ability to explain the different outcomes observed in these patients is of paramount importance to guide and help their management. CASE PRESENTATION: we herein describe an 88-year-old woman diagnosed with synchronous bilateral tongue carcinoma...
October 4, 2017: Current Problems in Cancer
https://www.readbyqxmd.com/read/29049890/dna-methylation-signatures-in-peripheral-blood-mononuclear-cells-from-a-lifestyle-intervention-for-women-at-midlife-a-pilot-rct
#18
Lisa M McEwen, Evan G Gatev, Meaghan J Jones, Julia L MacIsaac, Megan M McAllister, Rebecca E Goulding, Kenneth M Madden, Martin G Dawes, Michael S Kobor, Maureen C Ashe
OBJECTIVES: Physical activity confers many health benefits, but the underlying mechanisms require further exploration. In this pilot randomized controlled trial we tested the association between longitudinal measures of DNA methylation and changes in objective measures including physical activity, weight loss, and C-reactive protein levels in community-dwelling women aged 55 to 70 years. METHODS: We assessed DNA methylation from 20 healthy post-menopausal women (55-70 years of age), who did not have a mobility disability and allocated them to a group-based intervention, Everyday Activity Supports You (EASY), or a control group (monthly group-based health-related education sessions)...
October 19, 2017: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/29028941/dysregulation-of-cortical-neuron-dna-methylation-profile-in-autism-spectrum-disorder
#19
Stefano Nardone, Dev Sharan Sams, Antonino Zito, Eli Reuveni, Evan Elliott
Autism Spectrum Disorder (ASD) is a complex neuropsychiatric syndrome whose etiology includes genetic and environmental components. Since epigenetic marks are sensitive to environmental insult, they may be involved in the development of ASD. Initial brain studies have suggested a dysregulation of epigenetic marks in ASD. However, due to cellular heterogeneity in the brain, these studies have not determined if there is a true change in the neuronal epigenetic signature. Here, we report a genome-wide methylation study on fluorescence-activated cell sorting-sorted neuronal nuclei from the frontal cortex of 16 male ASD and 15 male control subjects...
December 1, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/29027401/identification-of-dna-methylation-associated-gene-signatures-in-endometrial-cancer-via-integrated-analysis-of-dna-methylation-and-gene-expression-systematically
#20
Chuandi Men, Hongjuan Chai, Xumin Song, Yue Li, Huawen Du, Qing Ren
OBJECTIVE: Endometrial cancer (EC) is a common gynecologic cancer worldwide. However, the pathogenesis of EC has not been epigenetically elucidated. Here, this study aims to describe the DNA methylation profile and identify favorable gene signatures highly associated with aberrant DNA methylation changes in EC. METHODS: The data regarding DNA methylation and gene expression were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially methylated CpG sites (DMCs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs) were identified, and the relationship between the 2 omics was further analyzed...
November 2017: Journal of Gynecologic Oncology
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