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Xing-Bo Mo, Shu-Feng Lei, Yong-Hong Zhang, Huan Zhang
AIM: To investigate the effects of m6 A-single nucleotide polymorphisms (SNPs) on coronary artery disease (CAD). METHODS: We examined the association of m6 A-SNPs with CAD in about 185,000 cases and controls and further performed eQTL and differential expression analyses to support the identified m6 A-SNPs. RESULTS: Among the 4390 m6 A-SNPs detected, 304 seemed to be associated with CAD (p < 0.05). SNP rs12286 was significantly associated with CAD at genome-wide level (p = 4...
September 17, 2018: Epigenomics
Huili Li, Lee Niswander
No abstract text is available yet for this article.
September 14, 2018: Epigenomics
Shanliang Zhong, Jinyan Wang, Junchen Hou, Qian Zhang, Hanzi Xu, Jiahua Hu, Jianhua Zhao, Jifeng Feng
AIM: We aimed to explore the roles of circRNAs in gastric cancer. MATERIALS & METHODS: The dysregulated circRNAs and miRNAs were identified using data from Gene Expression Omnibus. The roles of specifically selected circRNAs were explored. Survival analysis was performed using data from the Cancer Genome Atlas. RESULTS: We identified 68 dysregulated circRNAs and 51 dysregulated miRNAs. We found that hsa_circ_0000993 inhibited migration, invasion and proliferation of gastric cancer cells and could act as a miRNA sponge for miR-214-5p but did not modulate expression of its parental gene, ATL2...
September 14, 2018: Epigenomics
Noriko Katoh, Keiji Kuroda, Junko Tomikawa, Hiroko Ogata-Kawata, Rie Ozaki, Asako Ochiai, Mari Kitade, Satoru Takeda, Kazuhiko Nakabayashi, Kenichiro Hata
AIM: Decidualization is essential for embryo implantation and placental development. We aimed to obtain transcriptome and epigenome profiles for primary endometrial stromal cells (ESCs) and in vitro decidualized cells. MATERIALS & METHODS: ESCs isolated from human endometrial tissues remained untreated (D0), or decidualized for 4 days (D4) and 8 days (D8) in the presence of 8-bromo-cAMP and progesterone. RESULTS: Among the epigenetic modifications examined (DNA methylation, H3K27ac, H3K9me3 and H3K27me3), the H3K27ac patterns changed most dramatically, with a moderate correlation with gene expression changes, upon decidualization...
September 13, 2018: Epigenomics
Chenchen Yang, Theresa Ryan Stueve, Chunli Yan, Suhn K Rhie, Daniel J Mullen, Jiao Luo, Beiyun Zhou, Zea Borok, Crystal N Marconett, Ite A Offringa
AIM: To identify functional lung adenocarcinoma (LUAD) risk SNPs. MATERIALS & METHODS: Eighteen validated LUAD risk SNPs (p ≤ 5 × 10-8 ) and 930 SNPs in high linkage disequilibrium (r2  > 0.5) were integrated with epigenomic information from primary human alveolar epithelial cells. Enhancer-associated SNPs likely affecting transcription factor-binding sites were predicted. Three SNPs were functionally investigated using luciferase assays, expression quantitative trait loci and cancer-specific expression...
September 13, 2018: Epigenomics
Yuhua Feng, Meizuo Zhong, Shan Zeng, Leyuan Wang, Ping Liu, Xiangyu Xiao, Yiping Liu
AIM: To analyze the expression profiles, clinicopathological features and chemotherapeutic efficacies of exosome-derived miRNAs in diffuse large B-cell lymphoma (DLBCL). MATERIALS & METHODS: Next-generation sequencing technique was performed to identify miRNA profiles in exosomes from parental and chemoresistant DLBCL cells. The results were validated by quantitative real-time PCR, and further analyzed by bioinformatics and statistical methods. RESULTS: We identified 37 significantly upregulated and 17 downregulated miRNAs...
September 13, 2018: Epigenomics
Lin Ye, Tingxiu Xiang, Yu Fan, Dongsheng Zhang, Lili Li, Chong Zhang, Xiaoqian He, Qin Xiang, Qian Tao, Guosheng Ren
AIM: To study the epigenetic alternations and biological functions of ZFP82 in esophageal squamous cell carcinoma. MATERIALS & METHODS: Analysis of ZFP82 expression was carried out by quantitative real-time PCR. Cell function was tested by MTS cell proliferation assay, transwell assay and flow cytometry. Gene mechanisms were studied by Reverse Transcription-Polymerase Chain Reaction (RT-PCR), quantitative real-time PCR, luciferase reporter assay and Western blot...
September 13, 2018: Epigenomics
Justo L Bermejo, Guanmengqian Huang, Mehdi Manoochehri, Karen G Mesa, Matthias Schick, Rosa G Silos, Yon-Dschun Ko, Thomas Brüning, Hiltrud Brauch, Wing-Yee Lo, Jörg D Hoheisel, Ute Hamann
AIM: To identify DNA methylation biomarkers in peripheral blood samples from triple-negative breast cancer (TNBC) patients. MATERIALS & METHODS: We conducted an epigenome-wide association study (EWAS): the most promising markers were identified in 233 TNBC case-control pairs (discovery set) and subsequently validated in an independent validation set (57 TNBC patients and 124 controls). RESULTS: cg06588802 (LINC00299/ID2) showed a higher methylation in TNBC patients compared with controls (discovery set: 3% increase, p-value = 0...
September 13, 2018: Epigenomics
Zhu Kun-Peng, Ma Xiao-Long, Zhang Lei, Zhang Chun-Lin, Hu Jian-Ping, Zhan Tai-Cheng
AIM: To identify circular RNAs (circRNAs) related to osteosarcoma (OS) chemoresistance. MATERIALS & METHODS: CircRNA expression profile was performed in three paired human chemoresistant and chemosensitive OS cell lines by next-generation sequencing. Quantitative real-time-PCR (qRT-PCR) was used to confirm next-generation sequencing data. Bioinformatics analysis was conducted to predict their functions. RESULTS: Eighty circRNAs were dysregulated in the chemoresistant OS cells compared with the control, after validated by qRT-PCR...
September 7, 2018: Epigenomics
Iben Daugaard, Dianna Hussmann, Louise Kristensen, Thomas Kristensen, Tina E Kjeldsen, Charlotte G Nyvold, Thomas S Larsen, Michael B Møller, Lise Lotte Hansen, Tomasz K Wojdacz
AIM: We investigated whether DNA methylation regulates expression of LPL and PI3K complex genes in chronic lymphocytic leukemia (CLL) and evaluated the prognostic significance of LPL promoter methylation in CLL patients. Patients & methods: Methylation of LPL promoter was assessed in 112 patients using methylation-sensitive high-resolution melting (MS-HRM). RESULTS: Patients with a fully or heterogeneously methylated LPL promoter had significantly longer median time to treatment (p < 0...
September 5, 2018: Epigenomics
Ding Peng, Guangzhe Ge, Zhengzheng Xu, Qin Ma, Yue Shi, Yuanyuan Zhou, Yanqing Gong, Gengyan Xiong, Cuijian Zhang, Shiming He, Zhisong He, Xuesong Li, Weimin Ci, Liqun Zhou
AIM: We intended to construct DNA methylation-based models for the diagnosis and prognosis of three common urological cancers including prostate adenocarcinoma, renal clear cell carcinoma and bladder urothelial carcinoma. MATERIALS & METHODS:  Total 450K methylation array data from the cancer genome atlas and gene expression omnibus datasets were downloaded. Moderated t-statistics and least absolute shrinkage and selection operator method were used to build diagnosis and prognosis models...
September 5, 2018: Epigenomics
Ji-Xi Liu, Wen Li, Jing-Tao Li, Fang Liu, Lei Zhou
AIM: We aim to identify the key long noncoding RNAs (lncRNAs) in early-stage colon adenocarcinoma (COAD). PATIENTS & METHODS: Compared with colonic intraepithelial neoplasia, differentially expressed lncRNAs (DElncRNAs) in early-stage COAD were obtained by RNA-sequencing. Our previous work has obtained the differentially expressed mRNAs and miRNAs (DEmRNAs and DEmiRNAs) in early-stage COAD. DEmiRNA-DElncRNA-DEmRNA interaction analysis and functional annotation were performed...
September 5, 2018: Epigenomics
Aaron J Stevens, Julia J Rucklidge, Kathryn A Darling, Matthew Jf Eggleston, John F Pearson, Martin A Kennedy
Exposure times and dosage required for dietary components to modify DNA methylation patterns are largely unknown. AIM: This exploratory research represents the first genome-wide analysis of DNA methylation changes during a randomized-controlled-trial (RCT) for dietary supplementation with broad spectrum vitamins, minerals and amino acids in humans. METHODS: Genome-wide changes in methylation from paired, peripheral blood samples were assessed using the Infinium Methylation EPIC 850 K array...
September 5, 2018: Epigenomics
He-da Zhang, Lin-Hong Jiang, Jun-Chen Hou, Si-Ying Zhou, Shan-Liang Zhong, Ling-Ping Zhu, Dan-Dan Wang, Su-Jin Yang, Yun-Jie He, Chang-Fei Mao, Yong Yang, Jin-Yan Wang, Qian Zhang, Han-Zi Xu, Dan-Dan Yu, Jian-Hua Zhao, Jin-Hai Tang, Zhen-Ling Ji
AIM: To study the role of hsa_circ_0072995 in regulating the invasion and migration of breast cancer cells. MATERIALS & METHODS: Hsa_circ_0072995 expression was confirmed by quantitative real-time PCR; evaluating the migration and invasion of breast cancer cells through transwell assay; predicating circRNA/microRNAs interaction using the miRanda and RNAhybrid software; identifying the relationship between hsa_circ_0072995 and miR-30c-2-3p by luciferase activity assay; detecting the location of hsa_circ_0072995 by Fluorescence in situ hybridization assay...
September 5, 2018: Epigenomics
Okyaz Eminaga, Jochen Fries, Susanne Neiß, Michaela Heitmann, Fabian Wötzel, Axel Heidenreich, Christiane Bruns, Hakan Alakus, Ute Warnecke-Eberz
AIM: To show the association between the expression level of hsa-miR-210 (miR-210) and tumor progression in prostate cancer (PCa). METHODS: Quantitative PCR was performed to measure miR-210 on 55 subjects with different tumor stages; our results were then validated using three external datasets. ANOVA and Tukey's post hoc analysis were performed for comparative analyses between different tumor stages. Using the transcriptome data from The Cancer Genome Atlas for CaP, the gene expression analyses were performed on experimentally validated target genes of miR-210 identified in Tarbase and miRWalk datasets...
August 15, 2018: Epigenomics
Jue Yang, Hui Song, Li Chen, Kun Cao, Yongqiang Zhang, Yanmei Li, Xiaojiang Hao
AIM: The potential functions and underlying mechanism of microfibrillar-associated proteins (MFAPs) are explored in human cancers. MATERIALS & METHODS: Here, we examined the expression profiles, prognostic values, epigenetic and genetic alterations of MFAPs in human cancers from public omics repository. RESULTS: Among MFAPs family, MFAP4 was frequently downregulated in the most human cancers and high mRNA expression of MFAP4 significantly correlated with better overall survival in breast cancer...
August 9, 2018: Epigenomics
Andrea Stoccoro, Lorena Mosca, Vittoria Carnicelli, Ugo Cavallari, Christian Lunetta, Alessandro Marocchi, Lucia Migliore, Fabio Coppedè
AIM: To investigate mitochondrial DNA (mtDNA) copy number and D-loop region methylation in carriers of SOD1, TARDBP, FUS and C9orf72 mutations. METHODS: Investigations were performed in blood DNA from 114 individuals, including amyotrophic lateral sclerosis (ALS) patients, presymptomatic carriers and noncarrier family members. RESULTS: Increased mtDNA copy number (p = 0.0001) was observed in ALS patients, and particularly in those with SOD1 or C9orf72 mutations...
August 8, 2018: Epigenomics
Fabio Coppedè, Andrea Stoccoro, Alessandro Lazzarotti, Roberto Spisni, Lucia Migliore
AIM: To investigate GHSR and GHRL methylation in 73 pairs of colorectal cancer (CRC) tissues and healthy adjacent mucosa. METHODS: Methylation was assessed with methylation-sensitive high-resolution melting. RESULTS: GHSR was significantly hypermethylated in CRC tissues than in healthy mucosa (p < 1 × 10-5 ), but no significant changes of GHRL methylation were observed. GHSR hypermethylation was already detectable at the adenoma stage and maintained in later stages independently of age, gender, anatomical location, histological grading, MLH1 deficiency, as well as of major polymorphisms in folate-pathway genes, yielding an area under the curve of 0...
July 2, 2018: Epigenomics
Yaoshu Teng, Yuandong Li, Zhihong Lin, Yueqiu Gao, Xiaolin Cao, Xiangyu Lou, Fengchun Lin, Yong Li
AIM: To analyze the expression profile, diagnostic and clinicopathological significances of miRNAs in  sinonasal inverted papilloma (SNIP). MATERIALS & METHODS: The expression profile of miRNAs was analyzed using a miRNA microarray approach. The potential functions and clinical significances of specific miRNAs were further analyzed by bioinformatics and statistical methods. RESULTS: The microarray assay identified 37 significantly upregulated and 21 downregulated miRNAs in SNIP...
June 28, 2018: Epigenomics
Sarah-Jayne Mackin, Karla M O'Neill, Colum P Walsh
AIM: 5-aza-2'deoxycytidine (Aza) is used to treat myelodysplastic syndrome and is in trials for other cancers. It acts chiefly as a hypomethylating agent inhibiting DNMT1. A lack of understanding of off-target effects in normal cells hinders wider usage. MATERIALS & METHODS: We compared treatment of the same normosomic, nontransformed fibroblast cell line with Aza and SMARTpool siRNA against DNMT1. Methylation and transcription were assayed using Illumina 450k and HT12 arrays...
August 2018: Epigenomics
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