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Cencen Li, Cheng Zou, Yong Cui, Yuhua Fu, Chengchi Fang, Yao Li, Jingxuan Li, Wen Wang, Hui Xiang, Changchun Li
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...
October 29, 2018: Epigenomics
Hui Song, Jue Yang, Yongqiang Zhang, Jianjiang Zhou, Yanmei Li, Xiaojiang Hao
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...
October 26, 2018: Epigenomics
Nicole R Bush, Rachel D Edgar, Mina Park, Julia L MacIsaac, Lisa M McEwen, Nancy E Adler, Marilyn J Essex, Michael S Kobor, W Thomas Boyce
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...
October 23, 2018: Epigenomics
Sadegh Fattahi, Monireh Golpour, Fatemeh Amjadi-Moheb, Marzieh Sharifi-Pasandi, Parastesh Khodadadi, Maryam Pilehchian-Langroudi, Gholam Hossein Ashrafi, Haleh Akhavan-Niaki
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. In this review, we discussed key factors or mechanisms such as SNPs, infections and genetic modifications that trigger DNMTs level modification in gastric cancer, and their potential roles in cancer progression...
October 16, 2018: Epigenomics
Gaëlle Judes, Lucas Dubois, Khaldoun Rifaï, Mouhamed Idrissou, Florence Mishellany, Amaury Pajon, Sophie Besse, Marine Daures, Françoise Degoul, Yves-Jean Bignon, Frédérique Penault-Llorca, Dominique Bernard-Gallon
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...
October 16, 2018: Epigenomics
Xiaohui Sun, Yiping Tian, Qianqian Zheng, Ruizhi Zheng, Aifen Lin, Tianhui Chen, Yimin Zhu, Maode Lai
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. A model for discriminating CRC based on methylation levels was established using least absolute shrinkage and selection operator regression...
October 16, 2018: Epigenomics
Sylvia E Badon, Alyson J Littman, Kwun Chuen Gary Chan, Mahlet G Tadesse, Patricia L Stapleton, Theo K Bammler, Tanya K Sorensen, Michelle A Williams, Daniel A Enquobahrie
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 = 0.137, 95% CI: 0.004-0.270) and higher circulating miR-146b-5p (β = 0.084, 95% CI: 0...
October 16, 2018: Epigenomics
Han-Wei Lin, Chi-Feng Fu, Ming-Cheng Chang, Tzu-Pin Lu, Hsiu-Ping Lin, Ying-Cheng Chiang, Chi-An Chen, Wen-Fang Cheng
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. RESULTS: The presence of two or more methylated genes was significant in recurrence (hazard ratio [HR]: 1.91 [1.33-2.76]; p = 0.002) and death (HR: 1...
October 16, 2018: Epigenomics
Hernán Guillermo Hernández, Adrián Gabriel Sandoval-Hernández, Pablo Garrido-Gil, José Luis Labandeira-Garcia, María Victoria Zelaya, Gustavo F Bayon, Agustín F Fernández, Mario F Fraga, Gonzalo Arboleda, Humberto Arboleda
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...
October 16, 2018: Epigenomics
Duncan Ayers
No abstract text is available yet for this article.
October 16, 2018: Epigenomics
He-da Zhang, Lin-Hong Jiang, Jun-Chen Hou, Shan-Liang Zhong, Ling-Ping Zhu, Dan-Dan Wang, Si-Ying Zhou, Su-Jin Yang, Jin-Yan Wang, Qian Zhang, Han-Zi Xu, Jian-Hua Zhao, Zhen-Ling Ji, Jin-Hai Tang
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. Exosomes could promote the short- and long-distance exchanges of genetic information by acting as mediators of cell-to-cell communication. In addition, exosomes participate in drug resistance of tumor cells by genetic exchange between cells...
October 12, 2018: Epigenomics
Ramya Potabattula, Marcus Dittrich, Julia Böck, Larissa Haertle, Tobias Müller, Thomas Hahn, Martin Schorsch, Nady El Hajj, Thomas Haaf
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...
September 21, 2018: Epigenomics
Rebecca L Mather, Yuzhuo Wang, Francesco Crea
No abstract text is available yet for this article.
September 21, 2018: Epigenomics
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
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
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