952 results match your criteria Epigenomics [Journal]


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

Epigenomics 2019 Feb 20. 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

Fine mapping and subphenotyping implicates ADRA1B gene variants in psoriasis susceptibility in a Chinese population.

Epigenomics 2019 Feb 20. 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. 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. 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

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
1 Read

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

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

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
2 Reads

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

Epigenomics 2019 Jan 31. 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
January 2019
2 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

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

Epigenomics 2019 Jan 24. 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
January 2019

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
8 Reads

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

Epigenomics 2019 Jan 22. 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
January 2019
1 Read

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

Epigenomics 2019 01 21. Epub 2019 Jan 21.

Department of Pneumoconiosis, Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 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
January 2019
9 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
10 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
February 2019
1 Read

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
1 Read

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

Epigenomics 2018 12 20. 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
December 2018
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
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
2 Reads

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

Epigenomics 2018 Dec 11. Epub 2018 Dec 11.

Institute of Epigenetics & Epigenomics & College of Animal Science & Technology, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu 225009, 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
December 2018
1 Read

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

Epigenomics 2018 Dec 7. 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
December 2018
4 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 Nov 20. 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
November 2018
20 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
12 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 Nov 14. 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
November 2018
2 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
29 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
9 Reads

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

Epigenomics 2018 Nov 12. 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
November 2018
21 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
5 Reads

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

Epigenomics 2018 Oct 29. 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
October 2018
4 Reads

Integrated analysis of pseudogene RP11-564D11.3 expression and its potential roles in hepatocellular carcinoma.

Epigenomics 2019 Feb 26;11(3):267-280. Epub 2018 Oct 26.

The State Key Laboratory of Functions & Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China.

Aim: We aim to identify differentially expressed pseudogenes and investigate their functional roles in carcinogenesis.

Materials & Methods: Here, we identify dysregulated pseudogenes, analyze their prognostic values and investigate their potential functions through pseudogene-miRNA-mRNA network from public -omics repositories.

Results: We identified 16 frequently upregulated pseudogenes among which high expression levels of RP11-564D11. Read More

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http://dx.doi.org/10.2217/epi-2018-0152DOI Listing
February 2019
1 Read

The biological embedding of early-life socioeconomic status and family adversity in children's genome-wide DNA methylation.

Epigenomics 2018 Nov 23;10(11):1445-1461. Epub 2018 Oct 23.

Department of Psychiatry, Center for Health & Community, Weill Neuroscience Institute, University of California, San Francisco, 3333 California Street, Suite 465, San Francisco, CA 94118, USA.

Aim: To examine variation in child DNA methylation to assess its potential as a pathway for effects of childhood social adversity on health across the life course.

Materials & Methods: In a diverse, prospective community sample of 178 kindergarten children, associations between three types of social experience and DNA methylation within buccal epithelial cells later in childhood were examined.

Results: Family income, parental education and family psychosocial adversity each associated with increased or decreased DNA methylation (488, 354 and 102 sites, respectively) within a unique set of genomic CpG sites. Read More

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http://dx.doi.org/10.2217/epi-2018-0042DOI Listing
November 2018
1 Read

DNA methyltransferases and gastric cancer: insight into targeted therapy.

Epigenomics 2018 Nov 16;10(11):1477-1497. Epub 2018 Oct 16.

Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, 4717647745, Babol, Iran.

Gastric cancer is a major health problem worldwide occupying most frequent causes of cancer-related mortality. In addition to genetic modifications, epigenetic alterations catalyzed by DNA methyltransferases (DNMTs) are a well-characterized epigenetic hallmark in gastric cancer. The reversible nature of epigenetic alterations and central role of DNA methylation in diverse biological processes provides an opportunity for using DNMT inhibitors to enhance the efficacy of chemotherapeutics. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0096
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http://dx.doi.org/10.2217/epi-2018-0096DOI Listing
November 2018
17 Reads

TIP60: an actor in acetylation of H3K4 and tumor development in breast cancer.

Epigenomics 2018 Nov 16;10(11):1415-1430. Epub 2018 Oct 16.

Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 Place Henri-Dunant, 63001, Clermont-Ferrand, France.

Aim: The acetyltransferase TIP60 is reported to be downregulated in several cancers, in particular breast cancer, but the molecular mechanisms resulting from its alteration are still unclear.

Materials & Methods: In breast tumors, H3K4ac enrichment and its link with TIP60 were evaluated by chromatin immunoprecipitation-qPCR and re-chromatin immunoprecipitation techniques. To assess the biological roles of TIP60 in breast cancer, two cell lines of breast cancer, MDA-MB-231 (ER-) and MCF-7 (ER+) were transfected with shRNA specifically targeting TIP60 and injected to athymic Balb-c mice. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0004
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http://dx.doi.org/10.2217/epi-2018-0004DOI Listing
November 2018
7 Reads

A novel discriminating colorectal cancer model for differentiating normal and tumor tissues.

Epigenomics 2018 Nov 16;10(11):1463-1475. Epub 2018 Oct 16.

Key Laboratory of Disease Proteomics of Zhejiang Province & Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, PR China.

Aim: To construct a model discriminating colorectal cancer (CRC) based on differential DNA methylation.

Materials & Methods: The CRC-related methylation-modulated genes were retrieved from literature. The methylation levels of CpG sites in the promoter regions and the first exons of candidate genes were verified in The Cancer Genome Atlas data. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0063
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http://dx.doi.org/10.2217/epi-2018-0063DOI Listing
November 2018
8 Reads

Physical activity and epigenetic biomarkers in maternal blood during pregnancy.

Epigenomics 2018 Nov 16;10(11):1383-1395. Epub 2018 Oct 16.

Department of Epidemiology, University of Washington, Seattle, WA 98185, USA.

Aim: Investigate associations of leisure time physical activity (LTPA) with DNA methylation and miRNAs during pregnancy. Patients & methods: LTPA, candidate DNA methylation and circulating miRNAs were measured (average 15 weeks gestation) in pregnant women (n = 92).

Results: Each additional hour of prepregnancy LTPA duration was associated with hypermethylation in C1orf212 (β = 0. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2017-0169
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http://dx.doi.org/10.2217/epi-2017-0169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275564PMC
November 2018
17 Reads

CDH1, DLEC1 and SFRP5 methylation panel as a prognostic marker for advanced epithelial ovarian cancer.

Epigenomics 2018 Nov 16;10(11):1397-1413. Epub 2018 Oct 16.

Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei 10055, Taiwan.

Aim: To investigate the CDH1, DLEC1 and SFRP5 gene methylation panel for advanced epithelial ovarian carcinoma (EOC).

Materials & Methods: One hundred and seventy-seven advanced EOC specimens were evaluated by methylation-specific PCR. We also used The Cancer Genome Atlas dataset to evaluate the panel. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0035
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http://dx.doi.org/10.2217/epi-2018-0035DOI Listing
November 2018
5 Reads

Alzheimer's disease DNA methylome of pyramidal layers in frontal cortex: laser-assisted microdissection study.

Epigenomics 2018 Nov 16;10(11):1365-1382. Epub 2018 Oct 16.

Grupo de Neurociencias y muerte Celular, Facultad de Medicina e instituto de Genética, Universidad Nacional de Colombia, Colombia.

Objective: To study DNA methylation patterns of cortical pyramidal layers susceptible to late-onset Alzheimer's disease (LOAD) neurodegeneration.

Methods: Laser-assisted microdissection to select pyramidal layers' cells in frontal cortex of 32 human brains (18 LOAD) and Infinium DNA Methylation 450K analysis were performed to find differential methylated positions and regions, in addition to the corresponding gene set functional enrichment analyses.

Results: Differential hypermethylation in several genomic regions and genes mainly in HOXA3, GSTP1, CXXC1-3 and BIN1. Read More

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http://dx.doi.org/10.2217/epi-2017-0160DOI Listing
November 2018
2 Reads

Noncoding RNAs and their epitranscriptomic influences in cancer.

Authors:
Duncan Ayers

Epigenomics 2018 Nov 16;10(11):1361-1363. Epub 2018 Oct 16.

Centre for Molecular Medicine & Biobanking, University of Malta, Msida, Malta.

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https://www.futuremedicine.com/doi/10.2217/epi-2018-0119
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http://dx.doi.org/10.2217/epi-2018-0119DOI Listing
November 2018
9 Reads

Exosome: a novel mediator in drug resistance of cancer cells.

Epigenomics 2018 Nov 12;10(11):1499-1509. Epub 2018 Oct 12.

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

Exosomes are small membrane vesicles with a diameter of 40-100 nm, which are released into the intracellular environment. Exosomes could influence the genetic and epigenetic changes of receptor cells by promoting the horizontal transfer of various proteins or RNAs, especially miRNAs. Moreover, exosomes also play an important role in tumor microenvironment. Read More

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https://www.futuremedicine.com/doi/10.2217/epi-2017-0151
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http://dx.doi.org/10.2217/epi-2017-0151DOI Listing
November 2018
4 Reads

Allele-specific methylation of imprinted genes in fetal cord blood is influenced by cis-acting genetic variants and parental factors.

Epigenomics 2018 Oct 21;10(10):1315-1326. Epub 2018 Sep 21.

Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.

Aim: To examine the effects of genetic variation, parental age and BMI on parental allele-specific methylation of imprinted genes in fetal cord blood samples.

Methodology: We have developed SNP genotyping and deep bisulphite sequencing assays for six imprinted genes to determine parental allele-specific methylation patterns in diploid somatic tissues.

Results: Multivariate linear regression analyses revealed a negative correlation of paternal age with paternal MEG3 allele methylation in fetal cord blood. Read More

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http://dx.doi.org/10.2217/epi-2018-0059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240887PMC
October 2018
2 Reads

Getting to the marrow of trained immunity.

Epigenomics 2018 09;10(9):1151-1154

Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.2217/epi-2018-0098DOI Listing
September 2018
1 Read