964 results match your criteria Epigenomics [Journal]


Corrigendum.

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Epigenomics 2019 Apr 11. Epub 2019 Apr 11.

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http://dx.doi.org/10.2217/epi-2017-0167cDOI Listing

Environmental factors influence the epigenetic signature of newborns from mothers with gestational diabetes.

Epigenomics 2019 Apr 10. Epub 2019 Apr 10.

Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Aim: To investigate the degree by which epigenetic signatures in children from mothers with gestational diabetes mellitus (GDM) are influenced by environmental factors.

Methods: We profiled the DNA methylation signature of blood from lean, obese and GDM mothers and their respective newborns.

Results: DNA methylation profiles of mothers showed high similarity across groups, while newborns from GDM mothers showed a marked distinct epigenetic profile compared with newborns of both lean and obese mothers. Read More

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http://dx.doi.org/10.2217/epi-2019-0055DOI Listing
April 2019
1 Read

Epigenetics in the development of diabetic cardiomyopathy.

Epigenomics 2019 Apr 21;11(5):469-472. Epub 2019 Mar 21.

Department of Pathology, Division of Molecular & Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

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http://dx.doi.org/10.2217/epi-2019-0027DOI Listing

Altered expression profile of circular RNAs in conjunctival melanoma.

Epigenomics 2019 Mar 20. Epub 2019 Mar 20.

Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, No. 12, Lane 833, Zhizaoju Road, Huangpu District, Shanghai 200001, China.

Aim: We aimed to explore the roles of circular RNA (circRNA) in conjunctival melanoma.

Materials & Methods: The altered circRNAs were identified by RNA sequencing. The function of one circRNA, circMTUS1, was explored by several experiments in conjunctival melanoma. Read More

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http://dx.doi.org/10.2217/epi-2019-0029DOI Listing
March 2019
1 Read

Genome-wide screening of altered m6A-tagged transcript profiles in the hippocampus after traumatic brain injury in mice.

Epigenomics 2019 Mar 18. Epub 2019 Mar 18.

Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China.

Aim: To systematically profile RNA m6A modification landscape after traumatic brain injury (TBI) in mice.

Materials & Methods: Expression of m6A-related genes was detected by quantitative real-time PCR (qPCR). Expression and location of METTL3, a key component of m6A methyltransferase complex, were determined by immunostaining. Read More

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http://dx.doi.org/10.2217/epi-2019-0002DOI Listing
March 2019
2 Reads

Genome-wide miRNA methylome analysis in oral cancer: possible biomarkers associated with patient survival.

Epigenomics 2019 Apr 15;11(5):473-487. Epub 2019 Mar 15.

Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand.

Aim: The methylome associated with miRNA loci was investigated in oral cancer to explore tobacco specific methylation and potential biomarkers for patient survival.

Methods: Methylome data was generated from 16 pairs of cancer-normal tissues by reduced representation bisulfite sequencing method. Differentially methylated regions were identified using the DMAP pipeline. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0078
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http://dx.doi.org/10.2217/epi-2018-0078DOI Listing
April 2019
7 Reads

DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype.

Epigenomics 2019 Apr 15;11(5):563-575. Epub 2019 Mar 15.

Departments of Pediatrics, Biochemistry & Oncology, Western University, London, ON, N6A 3K7, Canada.

Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS). Read More

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http://dx.doi.org/10.2217/epi-2018-0192DOI Listing
April 2019
3 Reads

DNA-methylation abundantly associates with fetal alcohol spectrum disorder and its subphenotypes.

Epigenomics 2019 Mar 15. Epub 2019 Mar 15.

Department of Anatomy, Embryology & Physiology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands.

Aim: Fetal alcohol spectrum disorder (FASD) involves prenatal growth delay, impaired facial and CNS development and causes severe clinical, social-economic burdens. Here, we aim to detect DNA-methylation aberrations associated with FASD and potential FASD diagnostic and prognostic biomarkers.

Patients & Methods:  The FASD diagnosis was established according to golden-standard protocols in a discovery and independent replication cohort. Read More

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http://dx.doi.org/10.2217/epi-2018-0221DOI Listing
March 2019
2 Reads

Clinicopathological, immune and molecular correlates of PD-L2 methylation in gastric adenocarcinomas.

Epigenomics 2019 Mar 1. Epub 2019 Mar 1.

Department of Otolaryngology, Head & Neck Surgery, University Hospital Bonn, Bonn, Germany.

Aim: We investigated the significance of PD-L2 DNA methylation in gastric adenocarcinomas.

Methods: We analyzed the methylation at different CpG sites within the PD-L2-encoding gene PDCD1LG2 with regard to correlations and associations with gene expression, clinicopathological parameters, molecular features and immune cell infiltrates in two publicly available cohorts (The Cancer Genome Atlas and Singapore cohorts) of a total of 594 gastric adenocarcinoma patients.

Results: PD-L2 methylation is significantly associated with transcriptional activity, survival, Epstein-Barr virus infection, PD-L2 gene amplification, CD8 T-cell infiltration, microsatellite instability and high mutational load (tumor mutational burden, hypermutation). Read More

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http://dx.doi.org/10.2217/epi-2018-0149DOI Listing
March 2019
2 Reads

Circular RNA profile of breast cancer brain metastasis: identification of potential biomarkers and therapeutic targets.

Epigenomics 2018 Dec;10(12):1619-1630

Jiangsu Key Laboratory of Molecule Imaging & Functional Imaging, Zhongda Hospital, Medical School, Southeast University, Nanjing, Jiangsu, PR China.

Aim: To explore the circular RNA (circRNA) profile of breast cancer brain metastasis (BCBM).

Materials & Methods: RNA-seq was performed to identify the circRNA expression profile of brain metastatic breast cancer cell line 231-BR, in comparison with its parental nonspecific metastatic cell line MDA-MB-231.

Results: A total of 215 upregulated and 191 downregulated circRNAs were identified. Read More

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http://dx.doi.org/10.2217/epi-2018-0090DOI Listing
December 2018

Histone H1, the forgotten histone.

Epigenomics 2019 Feb 22;11(4):363-366. Epub 2019 Feb 22.

Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.2217/epi-2019-0018DOI Listing
February 2019

Comprehensive data analysis for development of custom qRT-PCR miRNA assay for glioblastoma: a prevalidation study.

Epigenomics 2019 Feb 22;11(4):367-380. Epub 2019 Feb 22.

Department of Medical Biochemistry & Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt.

Aim: Glioblastoma (GB) is one notable example of miRNA-modulated neoplasms. Given its unique expression signature, proper miRNA profiling can help discriminate between GB and other types of brain tumors. The current work aimed to develop a more GB-specific and applicable custom designed quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) miRNA assay. Read More

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http://dx.doi.org/10.2217/epi-2018-0134DOI Listing
February 2019

Differentially expressed coding and noncoding RNAs in CoCl-induced cytotoxicity of C2C12 cells.

Epigenomics 2019 Feb 20;11(4):423-438. Epub 2019 Feb 20.

Guangzhou FitGene Biotechnology CO., LTD, Building D, 3 Ju Quan Road, Guangzhou 510663, PR China.

Aim: We aimed to explore potential regulators of coding and noncoding RNAs (ncRNAs) in Co(II) ion-induced myo cytotoxicity.

Materials & Methods: We confirmed the toxic effects of Co(II) on mouse skeletal C2C12 myotubes by CoCl, and performed the expression profiles of circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and mRNAs using microarray analysis. We constructed co-expression, competing endogenous RNA and cis/trans regulation networks for ncRNAs, and filtered 71 candidate circRNAs with coding potential. Read More

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http://dx.doi.org/10.2217/epi-2018-0087DOI Listing
February 2019
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Fine mapping and subphenotyping implicates ADRA1B gene variants in psoriasis susceptibility in a Chinese population.

Epigenomics 2019 Feb 20;11(4):455-467. Epub 2019 Feb 20.

HumanBiology, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA.

Aim: A genomic region on 5q33.3 lies between and encompasses the IL12B and PTTG1 genes, and contains many potential psoriasis causal variants. We aimed to further examine the influence of variants in and around this region. Read More

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http://dx.doi.org/10.2217/epi-2018-0131DOI Listing
February 2019

Circular RNA expression in exosomes derived from breast cancer cells and patients.

Epigenomics 2019 Feb 20;11(4):411-421. Epub 2019 Feb 20.

Center of Clinical Laboratory Science, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, PR China.

Aim: We aimed to explore the roles of circular RNAs (circRNAs) in breast cancer (BCa).

Materials & Methods: RNA was extracted from exosomes and BCa cells and analyzed using the RNA sequencing technique or microarray.

Results: Compared with controls, 1147 and 1195 circRNAs were dysregulated in exosomes from metastatic and localized BCa patients, respectively. Read More

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http://dx.doi.org/10.2217/epi-2018-0111DOI Listing
February 2019

GRIN2B promoter methylation deficits in early-onset schizophrenia and its association with cognitive function.

Epigenomics 2019 Feb 20;11(4):401-410. Epub 2019 Feb 20.

Biomolecular Sciences Research Centre, Sheffield Hallam University, UK.

Aim: We investigated GRIN1 and GRIN2B promoter methylation in first-episode schizophrenia patients compared with siblings and controls, testing for correlations between DNA methylation, cognitive performance and clinical variables.

Materials & Methods: Blood-derived DNA from all groups underwent bisulfite conversion and pyrosequencing to determine methylation at CpG sites within the GRIN1 and GRIN2B promoters and results were compared with the measure of global methylation LINE-1.

Results: We found hypomethylation among all CpGs analyzed within GRIN2B promoter in patients and greater LINE-1 methylation in patients and siblings. Read More

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http://dx.doi.org/10.2217/epi-2018-0127DOI Listing
February 2019

Core regulatory RNA molecules identified in articular cartilage stem/progenitor cells during osteoarthritis progression.

Epigenomics 2019 Feb 18. Epub 2019 Feb 18.

Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China.

Aim: To assess cartilage-derived-stem/progenitor cells (CSPCs) in osteoarthritis (OA) by employing mRNA-miRNA-circRNA-lncRNA network biology approach.

Methods: Differentially expressed (DE) RNAs in CSPCs from 2-/4-/8-month-old STR/Ort and CBA mice were identified to construct networks via RNA sequencing.

Results: Compared with age-matched CBA mice, 4-/8-month-old STR/Ort mice had cartilage lesions and their CSPCs exhibited lower proliferative and differentiation capacity (decreased CD44 and CD90), and identified 7082 DE RNAs in STR/Ort mice were associated with strain differences or OA progression. Read More

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http://dx.doi.org/10.2217/epi-2018-0212DOI Listing
February 2019
2 Reads

Metformin exerts antidepressant effects by regulated DNA hydroxymethylation.

Epigenomics 2019 Feb 13. Epub 2019 Feb 13.

Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China.

Aim: We aim to study the antidepressant mechanism of metformin.

Materials & Methods: Tail suspension test and forced swimming test were used to detect the depression-like behavior; the expressions of target protein were examined by western blot; the levels of target genes were tested by quantitative PCR; the content of α-ketoglutarate and 5hmC were detected by ELISA kit.

Results: We showed that metformin can improve the depression-like behavior in spatial restraint stress model; then we found that metformin through AMPK/Tet2 pathway increasing the expression of BDNF to antidepression. Read More

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http://dx.doi.org/10.2217/epi-2018-0187DOI Listing
February 2019

Whole-methylome analysis of circulating monocytes in acute diabetic Charcot foot reveals differentially methylated genes involved in the formation of osteoclasts.

Epigenomics 2019 Feb 1;11(3):281-296. Epub 2018 Nov 1.

Epigenetics Cardiovascular Laboratory, Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.

Aim: To assess whether DNA methylation of monocytes play a role in the development of acute diabetic Charcot foot (CF).

Patients & Methods: We studied the whole methylome (WM) of circulating monocytes in 18 patients with Type 2 diabetes (T2D) and acute CF, 18 T2D patients with equivalent neuropathy and 18 T2D patients without neuropathy, using the enhanced reduced representation bisulfite sequencing technique.

Results & Conclusion: WM analysis demonstrated that CF monocytes are differentially methylated compared with non-CF monocytes, in both CpG-site and gene-mapped analysis approaches. Read More

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http://dx.doi.org/10.2217/epi-2018-0144DOI Listing
February 2019
2 Reads

Epigenetic consequences of genome manipulations: caveats for human germline therapy and genetically modified organisms.

Authors:
Walter Doerfler

Epigenomics 2019 Feb;11(3):247-250

Institute for Clinical & Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, D-91054 Erlangen & Institute of Genetics, University of Cologne, D-50674 Cologne, Germany.

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http://dx.doi.org/10.2217/epi-2018-0201DOI Listing
February 2019

Welcome to the 11th volume of Epigenomics.

Authors:
Lucy Chard

Epigenomics 2019 Jan;11(1):1-4

Future Medicine, Future Science Group Ltd, London, UK.

Foreword by Lucy Chard Welcome to the 11th volume of Epigenomics. I would like to take this opportunity to wish all of our readers a Happy New Year. In this Foreword, I shall be taking a look back at some of the journal highlights of 2018. Read More

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http://dx.doi.org/10.2217/epi-2018-0198DOI Listing
January 2019
1 Read

Genome-wide methylotyping resolves breast cancer epigenetic heterogeneity and suggests novel therapeutic perspectives.

Epigenomics 2019 Feb 7. Epub 2019 Feb 7.

Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.

Aim: To provide a breast cancer (BC) methylotype classification by genome-wide CpG islands bisulfite DNA sequencing.

Materials & Methods: XmaI-reduced representation bisulfite sequencing DNA methylation sequencing method was used to profile DNA methylation of 110 BC samples and 6 normal breast samples. Intrinsic DNA methylation BC subtypes were elicited by unsupervised hierarchical cluster analysis, and cluster-specific differentially methylated genes were identified. Read More

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http://dx.doi.org/10.2217/epi-2018-0213DOI Listing
February 2019
1 Read

A two-gene methylation signature for the diagnosis of bladder cancer in urine.

Epigenomics 2019 Feb 1;11(3):337-347. Epub 2019 Feb 1.

Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands.

Aim: To analyze the potential of 14 cancer-associated genes, including six miRNAs, for bladder cancer (BC) diagnosis in urine.

Patients & Methods: DNA methylation levels of 14 genes were analyzed in urine of 72 BC patients and 75 healthy controls using quantitative methylation-specific PCR. Multivariate logistic regression analysis was used to determine an optimal marker panel. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0094
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http://dx.doi.org/10.2217/epi-2018-0094DOI Listing
February 2019
7 Reads

Comprehensive and combined omics analysis reveals factors of ischemia-reperfusion injury in liver transplantation.

Epigenomics 2019 Apr 31;11(5):527-542. Epub 2019 Jan 31.

Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China.

Aim: To explore molecular mechanisms underlying liver ischemia-reperfusion injury (IRI).

Materials & Methods: Four Gene Expression Omnibus datasets comprising liver transplantation data were collected for a comprehensive analysis. A proteomic analysis was performed and used for correlations analysis with transcriptomic. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0189
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http://dx.doi.org/10.2217/epi-2018-0189DOI Listing
April 2019
9 Reads

Tissue-specific epigenetics of atherosclerosis-related ANGPT and ANGPTL genes.

Epigenomics 2019 Feb 28;11(2):169-186. Epub 2019 Jan 28.

Center for Bioinformatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.

Aim: To understand tissue-specific regulation of angiopoietin/angiopoietin-like (ANGPT/ANGPTL) genes (especially the five genes embedded in introns of host genes) and their association with atherosclerosis.

Methods: Transcription and epigenomic databases from various normal tissues were examined in the vicinity of ANGPT1, ANGPT2, ANGPTL1, ANGPTL2, ANGPTL3, ANGPTL4 and ANGPTL8.

Results: We identified tissue-specific enhancer chromatin regions that are likely to regulate transcription of ANGPT/ANGPTL genes and were intragenic, intergenic or host gene-linked. Read More

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http://dx.doi.org/10.2217/epi-2018-0150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371847PMC
February 2019
1 Read

Frailty phenotype: a clinical marker of age acceleration in the older HIV-infected population.

Epigenomics 2019 Apr 24;11(5):501-509. Epub 2019 Jan 24.

Geriatrics Department, University Hospital Infanta Leonor, Madrid, Spain.

Aim: To evaluate the association between DNA methylation and frailty in the HIV-infected population and to investigate the usefulness of assessing frailty as a clinical marker to identify age acceleration.

Methods: Frailty was assessed according to Fried's frailty phenotype. DNA methylation was analyzed in 10 frail patients, and compared with 10 robust control patients, all with HIV. Read More

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http://dx.doi.org/10.2217/epi-2018-0130DOI Listing

The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene.

Epigenomics 2019 Feb 23;11(3):251-266. Epub 2019 Jan 23.

Laboratory of Mammalian Genetics, Centre for DNA Fingerprinting & Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad, India.

Aim: To investigate the regulatory potential of the Nnat second intron within the Nnat/Blcap micro-imprinted domain.

Materials & Methods: Mice with deletion of Nnat second intron at the endogenous Nnat/Blcap micro-imprinted domain were used to examine the effect of Nnat second intron on the transcriptional regulation of the Nnat and Blcap genes.

Results & Conclusion: Deletion of Nnat second intron affected Nnat expression in cis leading to the loss of Nnat expression from the active paternal allele. Read More

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http://dx.doi.org/10.2217/epi-2018-0060DOI Listing
February 2019

Role of histone acetylation in gastric cancer: implications of dietetic compounds and clinical perspectives.

Epigenomics 2019 Feb 23;11(3):349-362. Epub 2019 Jan 23.

Disciplina de Genética, Universidade Federal de São Paulo, SP, Brazil.

Histone modifications regulate the structural status of chromatin and thereby influence the transcriptional status of genes. These processes are controlled by the recruitment of different enzymes to a specific genomic site. Furthermore, obtaining an understanding of these mechanisms could help delineate alternative treatment and preventive strategies for cancer. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0081
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http://dx.doi.org/10.2217/epi-2018-0081DOI Listing
February 2019
16 Reads

Sex-specific histone modifications in mouse fetal and neonatal germ cells.

Epigenomics 2019 Apr 22;11(5):543-561. Epub 2019 Jan 22.

Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan.

Aims: Epigenetic signatures of germline cells are dynamically reprogrammed to induce appropriate differentiation, development and sex specification. We investigated sex-specific epigenetic changes in mouse fetal germ cells (FGCs) and neonatal germ cells.

Materials & Methods: Six histone marks in mouse E13. Read More

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http://dx.doi.org/10.2217/epi-2018-0193DOI Listing
April 2019
1 Read

Genome-wide profiling reveals novel microRNAs in hand-spinning-specific chrysotile exposure.

Epigenomics 2019 Apr 21;11(5):511-525. Epub 2019 Jan 21.

Department of Pneumoconiosis, Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, PR China.

Aim: We aimed to explore miRNA expression profiles in hand-spinning chrysotile exposed workers and their potential influencing factors.

Methods: miRNA array technique was applied to screen differentially expressed miRNAs between plasma samples from three exposed workers and three controls. Then, seven selected miRNAs were validated in 143 workers and 100 controls, and the potential influencing factors were revealed by multiple linear regression. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0143
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http://dx.doi.org/10.2217/epi-2018-0143DOI Listing
April 2019
13 Reads

Circular RNA circASS1 is downregulated in breast cancer cells MDA-MB-231 and suppressed invasion and migration.

Epigenomics 2019 Feb 18;11(2):199-213. Epub 2019 Jan 18.

Department of General Surgery, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China.

Aim: The study aimed to investigate the role of circular RNA circASS1 in breast cancer cells.

Materials & Methods: Circular RNAs microarray expression profile were analyzed in MCF-7, MDA-MB-231, and qRT-PCR and western blotting were used to quantify expression of circASS1 and its parental gene ASS1. Wound healing, migration and invasion assay were performed. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2017-0167
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http://dx.doi.org/10.2217/epi-2017-0167DOI Listing
February 2019
23 Reads

Evidence for DNA methylation mediating genetic liability to non-syndromic cleft lip/palate.

Epigenomics 2019 Feb 14;11(2):133-145. Epub 2019 Jan 14.

MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN, UK.

Aim: To determine if nonsyndromic cleft lip with or without cleft palate (nsCL/P) genetic risk variants influence liability to nsCL/P through gene regulation pathways, such as those involving DNA methylation.

Materials & Methods: nsCL/P genetic summary data and methylation data from four studies were used in conjunction with Mendelian randomization and joint likelihood mapping to investigate potential mediation of nsCL/P genetic variants.

Results & Conclusion: Evidence was found at VAX1 (10q25. Read More

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http://dx.doi.org/10.2217/epi-2018-0091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462847PMC
February 2019
2 Reads

Endometriosis-related ceRNA network to identify predictive biomarkers of endometrial receptivity.

Authors:
Xi Wang Qi Yu

Epigenomics 2019 Feb 14;11(2):147-167. Epub 2019 Jan 14.

Department of Obstetrics & Gynaecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.

Aim: As RNA, which plays a role in the regulation of endometrial receptivity, can be modulated via ceRNA mechanisms, we constructed a ceRNA network to explore potential RNA/ceRNA biomarkers indicating endometrial receptivity associated with endometriosis.

Materials & Methods: RNA sequencing was performed on eutopic endometrium from eight patients with and without endometriosis. Bioinformatics algorithms were used to predict ceRNA network and pathway analysis. Read More

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http://dx.doi.org/10.2217/epi-2018-0190DOI Listing
February 2019
2 Reads

Circulating miRNAs as mediators in cell-to-cell communication.

Epigenomics 2019 02 14;11(2):111-113. Epub 2019 Jan 14.

Institute of Molecular & Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625, Hannover, Germany.

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http://dx.doi.org/10.2217/epi-2018-0183DOI Listing
February 2019
1 Read

Measured maternal prepregnancy anthropometry and newborn DNA methylation.

Epigenomics 2019 Feb 8;11(2):187-198. Epub 2019 Jan 8.

Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, 6710B Rockledge Drive 7004, Bethesda, MD 20817, USA.

Aim: We examined maternal prepregnancy anthropometry and cord blood DNA methylation.

Methods: Associations between maternal measures (i.e. Read More

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http://dx.doi.org/10.2217/epi-2018-0099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371845PMC
February 2019
2 Reads

Expression profiles of exosomal miRNAs isolated from plasma of patients with desmoplastic small round cell tumor.

Epigenomics 2019 Apr 20;11(5):489-500. Epub 2018 Dec 20.

Department of Pediatric Hematology/Oncology, Bambino Gesù Children's Hospital, IRCCS, Piazza di Sant' Onofrio, 4, 00165 Rome, Italy.

Aim: Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive mesenchymal tumor, lacking biomarkers for diagnosis, treatment stratification and prognosis. We investigated the exosomal miRNA profile in plasma samples collected from DSRCT patients, evaluating their potential as circulating biomarkers for this tumor.

Patients & Methods: We isolated exosomes from plasma of three DSRCT adolescents and four age-matched healthy controls; expression of circulating miRNAs was quantified by qPCR. Read More

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http://dx.doi.org/10.2217/epi-2018-0179DOI Listing
April 2019
1 Read

Translation regulation in skin cancer from a tRNA point of view.

Epigenomics 2019 Feb 19;11(2):215-245. Epub 2018 Dec 19.

Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece.

Protein synthesis is a central and dynamic process, frequently deregulated in cancer through aberrant activation or expression of translation initiation factors and tRNAs. The discovery of tRNA-derived fragments, a new class of abundant and, in some cases stress-induced, small Noncoding RNAs has perplexed the epigenomics landscape and highlights the emerging regulatory role of tRNAs in translation and beyond. Skin is the biggest organ in human body, which maintains homeostasis of its multilayers through regulatory networks that induce translational reprogramming, and modulate tRNA transcription, modification and fragmentation, in response to various stress signals, like UV irradiation. Read More

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http://dx.doi.org/10.2217/epi-2018-0176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391632PMC
February 2019
1 Read

Integrated comparison of the miRNAome and mRNAome in muscles of dermatomyositis and polymyositis reveals common and specific miRNA-mRNAs.

Epigenomics 2019 Jan 7;11(1):23-33. Epub 2018 Dec 7.

Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.

Aim: Dermatomyositis (DM) and polymyositis (PM) are refractory systemic autoimmune diseases with unknown pathogenesis. miRNAs is an important epigenetic mechanism to regulate gene expression.

Methods: We performed whole miRNAs analysis, transcription analysis and the association between miRNAome and mRNAome. Read More

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http://dx.doi.org/10.2217/epi-2018-0064DOI Listing
January 2019
3 Reads

Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells.

Epigenomics 2019 Feb 11;11(4):439-453. Epub 2018 Dec 11.

Institute of Epigenetics & Epigenomics & College of Animal Science & Technology, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China.

Aim: To study the biological function of NSUN2 in regulating gene expression and cell proliferation.

Materials & Methods: The NSUN2 gene was knocked down in HEK293 cells via CRISPR/Cas9 system. mRNA m5C modification and gene expression were assessed using RNA-BisSeq and RNA-Seq. Read More

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http://dx.doi.org/10.2217/epi-2018-0169DOI Listing
February 2019
2 Reads

Identification and regulation pattern analysis of long noncoding RNAs in meibomian gland carcinoma.

Epigenomics 2019 Feb 7;11(4):381-400. Epub 2018 Dec 7.

Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China.

Aim: To identify long noncoding RNAs (lncRNAs) and to elucidate regulation patterns of lncRNAs in meibomian gland carcinoma (MGC).

Materials & Methods: We used RNA-Seq, gene ontology, ClueGO, Ingenuity Pathway Analysis and co-expression network analyses to profile the expression and regulation patterns of lncRNAs and mRNAs in MGC.

Results: We identified 500 lncRNAs and 326 mRNAs as differentially expressed. Read More

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http://dx.doi.org/10.2217/epi-2018-0182DOI Listing
February 2019
5 Reads

Methylation profiles of IL33 and CCL26 in bronchial epithelial cells are associated with asthma.

Epigenomics 2018 Dec 23;10(12):1555-1568. Epub 2018 Nov 23.

Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada.

Aim: This study aimed to characterize DNA methylation (DNA-me) in promoter region of IL33, IL1RL1 and CCL26 in asthma and their impacts on transcriptional activity in bronchial epithelial cells (BECs).

Patients & Methods: We performed bis-pyrosequencing, quantitative real-time PCR and sequencing in BECs from ten asthmatic and ten control individuals.

Results: We detected lower DNA-me levels of IL33 and CCL26 in asthmatic than control BECs. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0044
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http://dx.doi.org/10.2217/epi-2018-0044DOI Listing
December 2018
9 Reads

Epigenetic meta-analysis across three civilian cohorts identifies NRG1 and HGS as blood-based biomarkers for post-traumatic stress disorder.

Epigenomics 2018 Dec 20;10(12):1585-1601. Epub 2018 Nov 20.

Department of Psychiatry & Behavioral Sciences & Department of Obstetrics & Gynecology, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA 30322, USA.

Aim: Trauma exposure is a necessary, but not deterministic, contributor to post-traumatic stress disorder (PTSD). Epigenetic factors may distinguish between trauma-exposed individuals with versus without PTSD.

Materials & Methods: We conducted a meta-analysis of PTSD epigenome-wide association studies in trauma-exposed cohorts drawn from civilian contexts. Read More

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http://dx.doi.org/10.2217/epi-2018-0049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6331697PMC
December 2018
25 Reads

Circular RNA circRHOT1 is upregulated and promotes cell proliferation and invasion in pancreatic cancer.

Epigenomics 2019 Jan 16;11(1):53-63. Epub 2018 Nov 16.

Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China.

Aim: We aimed to identify the roles of circRHOT1 in pancreatic cancer.

Materials & Methods: The circRHOT1 was acquired from our previous study followed by quantitative real-time PCR and fluorescence in situ hybridization validation in pancreatic cancer. We used siRNA and shRNA to explore the function of circRHOT1 in pancreatic cancer cells. Read More

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http://dx.doi.org/10.2217/epi-2018-0051DOI Listing
January 2019
17 Reads

DNA methylation/hydroxymethylation regulate gene expression and alternative splicing during terminal granulopoiesis.

Epigenomics 2019 Jan 14;11(1):95-109. Epub 2018 Nov 14.

Gene & Stem Cell Therapy Program Centenary Institute, University of Sydney, Camperdown 2050, Australia.

Aim: To determine whether epigenetic modifications of DNA regulate gene expression and alternative splicing during terminal granulopoiesis.

Materials & Methods: Using whole genome bisulfite sequencing, reduced representation hydroxymethylation profiling and mRNA sequencing, we compare changes in DNA methylation, DNA hydroxymethylation, gene expression and alternative splicing in mouse promyelocytes and granulocytes.

Results & Conclusion: We show reduced DNA methylation at the promoters and enhancers of key granulopoiesis genes, indicating a regulatory role in the activation of lineage-specific genes during differentiation. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0050
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http://dx.doi.org/10.2217/epi-2018-0050DOI Listing
January 2019
6 Reads

The quantitative profiling of blood mSEPT9 determines the detection performance on colorectal tumors.

Epigenomics 2018 Dec 14;10(12):1569-1583. Epub 2018 Nov 14.

Department of Radiotherapy, the Chinese PLA 309th Hospital, Beijing, PR China.

Aim: To investigate the quantitative relationship between the positive detection rate (PDR) in colorectal tumor detection and the mSEPT9 level.

Materials & Methods: The level of blood mSEPT9 in various colorectal diseases was quantified by the Epi proColon 2.0 assay. Read More

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http://dx.doi.org/10.2217/epi-2017-0154DOI Listing
December 2018
3 Reads

Comprehensive analysis of miRNA-mRNA-lncRNA networks in severe asthma.

Epigenomics 2019 Feb 14;11(2):115-131. Epub 2018 Nov 14.

Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, 29 Xinlong Road, Changzhou 213003, PR China.

Aim: This study aimed to explore the molecular mechanism of severe asthma.

Materials & Methods: The shared and divergent differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs) in asthma and severe asthma were identified by RNA-sequencing. Severe asthma-specific and shared DEmiRNA-DEmRNA-DElncRNA interaction networks were performed. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0132
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http://dx.doi.org/10.2217/epi-2018-0132DOI Listing
February 2019
46 Reads

DNA hydroxymethylation changes in response to spinal cord damage in a multiple sclerosis mouse model.

Epigenomics 2019 Feb 14;11(3):323-335. Epub 2018 Nov 14.

Department of Orthopedics, Clinical Medical College, Yangzhou University, Yangzhou City, PR China.

Aim: Roles of DNA 5-hydroxymethylcytosine (5hmC) in myelin repair were investigated in an experimental autoimmune encephalomyelitis (EAE) mouse model via its regulation on BDNF.

Methods: DNA 5hmC level and its limiting enzymes were detected in EAE mice.

Results: Global 5hmC modification, Tet1 and Tet2 significantly decreased in the spinal cord tissues of EAE mice. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0162
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http://dx.doi.org/10.2217/epi-2018-0162DOI Listing
February 2019
16 Reads

DNA methylation profiling as a tool for testicular germ cell tumors subtyping.

Epigenomics 2018 Dec 12;10(12):1511-1523. Epub 2018 Nov 12.

Cancer Biology & Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.

Aim: Assess differential patterns of selected five genes' promoter methylation among testicular germ cell tumors (TGCT) subtypes.

Materials & Methods:  CRIPTO, HOXA9, MGMT, RASSF1A and SCGB3A1 promoter methylation levels were evaluated by quantitative methylation-specific PCR in 161 TGCT and 16 controls. Associations between clinicopathological parameters and promoter methylation levels were assessed, and receiver operating characteristics curve analysis was performed. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0034
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http://dx.doi.org/10.2217/epi-2018-0034DOI Listing
December 2018
39 Reads

Identification and integrated analysis of key differentially expressed circular RNAs in ER-positive subtype breast cancer.

Epigenomics 2019 Feb 12;11(3):297-321. Epub 2018 Nov 12.

Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China.

Aim: To systematically profile and characterize the circular RNA (circRNA) expression pattern in estrogen receptor (ER)-positive breast cancer (BC).

Materials & Methods: CircRNA expression profile was performed in ER-positive BC and adjacent nontumor tissues. The differentially expressed circRNAs (DECs) was analyzed by bioinformatics. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0147
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http://dx.doi.org/10.2217/epi-2018-0147DOI Listing
February 2019
6 Reads

Genome-wide epigenetic landscape of pig lincRNAs and their evolution during porcine domestication.

Epigenomics 2018 Dec 29;10(12):1603-1618. Epub 2018 Oct 29.

Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China.

Aim: We aimed to identify previously unreported long intergenic noncoding RNAs (lincRNAs) in the porcine liver, an important metabolic tissue, and further illustrate the epigenomic landscapes and the evolution of lincRNAs.

Materials & Methods: We used porcine omics data and comprehensively analyzed and identified lincRNAs and their methylation, expression and evolutionary patterns during pig domestication.

Results: LincRNAs exhibit highly methylated promoter and downstream regions, as well as lower expression levels and higher tissue specificity than protein-coding genes. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2017-0117
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http://dx.doi.org/10.2217/epi-2017-0117DOI Listing
December 2018
5 Reads