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Jacob K Kresovich, Peter H Gann, Serap Erdal, Hua Y Chen, Maria Argos, Garth H Rauscher
AIM: We examined methylation patterns with aggressive tumor phenotypes and investigated demographic, socioeconomic and reproductive predictors of gene methylation. MATERIALS & METHODS: Pyrosequencing quantified methylation of BRCA1, EGFR, GSTM2, RASSF1, TFF1 and Sat 2. We used quantile regression models to calculate adjusted median methylation values by estrogen and progesterone receptor (ER/PR) status. Bivariate associations between participant characteristics and methylation were examined...
March 12, 2018: Epigenomics
Yunfeng Huang, Qin Hui, Douglas I Walker, Karan Uppal, Jack Goldberg, Dean P Jones, Viola Vaccarino, Yan V Sun
AIM: We conducted a joint metabolomic-epigenomic study to identify patterns of epigenetic associations with smoking-related metabolites. PATIENTS & METHODS: We performed an untargeted metabolome-wide association study of smoking and epigenome-wide association studies of smoking-related metabolites among 180 male twins. We examined the patterns of epigenetic association linked to smoking-related metabolites using hierarchical clustering. RESULTS: Among 12 annotated smoking-related metabolites identified from a metabolome-wide association study, we observed significant hypomethylation associated with increased level of N-acetylpyrrolidine, cotinine, 5-hydroxycotinine and nicotine and hypermethylation associated with increased level of 8-oxoguanine...
March 12, 2018: Epigenomics
Guochao Li, Dong Wang, Wencui Ma, Ke An, Zongzhi Liu, Xinyu Wang, Caiyun Yang, Fengxia Du, Xiao Han, Shuang Chang, Hui Yu, Zilong Zhang, Zitong Zhao, Yan Zhang, Junyun Wang, Yingli Sun
AIM: Cancer stem cells (CSCs) drive triple-negative breast cancer recurrence via their properties of self-renewal, invasiveness and radio/chemotherapy resistance. This study examined how CSCs might sustain these properties. MATERIALS & METHODS: Transcriptomes, DNA methylomes and histone modifications were compared between CSCs and non-CSCs. RESULTS: Transcriptome analysis revealed several pathways that were activated in CSCs, whereas cell cycle regulation pathways were inhibited...
February 26, 2018: Epigenomics
Chuan Jiao, Chunling Zhang, Rujia Dai, Yan Xia, Kangli Wang, Gina Giase, Chao Chen, Chunyu Liu
AIM: We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. MATERIALS & METHODS: Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods. RESULTS: We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset...
February 22, 2018: Epigenomics
Jian Zhang, Yujie Yuan, Zhewei Wei, Jianwei Ren, Xun Hou, Dongjie Yang, Sirong Cai, Chuangqi Chen, Min Tan, George Gong Chen, Kaiming Wu, Yulong He
AIM: Our study investigated the significance of the crosstalk between long noncoding RNAs (lncRNAs) and mRNAs in gastric cancer (GC). METHODS: lncRNA and mRNA expression profiling data in 671 GC tumors and 77 nontumorous gastric tissues were retrieved from the gene expression omnibus database: GSE54129, GSE13911, GSE19826, GSE79973, GSE15459 and GSE66229. Differentially expressed analysis, RNA coexpression network construction, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted in this study...
February 6, 2018: Epigenomics
Barry M Lester, Carmen J Marsit
As the 'third brain' the placenta links the developing fetal brain and the maternal brain enabling study of epigenetic process in placental genes that affect infant neurodevelopment. We described the characteristics and findings of the 17 studies on epigenetic processes in placental genes and human infant neurobehavior. Studies showed consistent findings in the same cohort of term healthy infants across epigenetic processes (DNA methylation, genome wide, gene and miRNA expression) genomic region (single and multiple genes, imprinted genes and miRNAs) using candidate gene and genome wide approaches and across biobehavioral systems (neurobehavior, cry acoustics and neuroendocrine)...
January 30, 2018: Epigenomics
Cheng Xu, Jiamei Liu, Weifeng Yang, Yayun Shu, Zhipeng Wei, Weiwei Zheng, Xin Feng, Fengfeng Zhou
AIM: Transcriptomic and methylomic patterns represent two major OMIC data sources impacted by both inheritable genetic information and environmental factors, and have been widely used as disease diagnosis and prognosis biomarkers. MATERIALS & METHODS: Modern transcriptomic and methylomic profiling technologies detect the status of tens of thousands or even millions of probing residues in the human genome, and introduce a major computational challenge for the existing feature selection algorithms...
January 19, 2018: Epigenomics
Naoko Iida, Yoshihiro Okuda, Osamu Ogasawara, Satoshi Yamashita, Hideyuki Takeshima, Toshikazu Ushijima
AIM: Bioinformatics analysis for Illumina Infinium Human DNA methylation BeadArray is essential, but still remains difficult task for many experimental researchers. We here aimed to develop a browser-accessible bioinformatics tool for analyzing the BeadArray data. MATERIALS & METHODS: The tool was established as an analytical pipeline using R, Perl and Python programming languages. RESULTS: We introduced a method that groups neighboring probes into a genomic block, which facilitated efficient identification of densely methylated/unmethylated regions...
January 18, 2018: Epigenomics
Jing Zhou, Xia Liu, Changhe Wang, Changzhong Li
AIM: This study was intended to identify the metastasis-related miRNAs and target genes in cervical squamous cell carcinoma. MATERIALS & METHODS: The mRNA and miRNA next-generation sequencing data were downloaded. Differential expression analysis was carried out, followed by target gene prediction of differentially expressed miRNAs. The biological function of differentially expressed genes was performed. Validation was carried out by survival analysis and qRT-PCR...
January 18, 2018: Epigenomics
Babu Swathy, Koramannil R Saradalekshmi, Indu V Nair, Chandrasekharan Nair, Moinak Banerjee
AIM: The present study intends to evaluate whether antipsychotic drugs can modulate the host epigenome and if so whether drug-induced epigenetic modulation can explain the heterogeneity in drug response. METHODS: Present study was conducted in in vitro cells and significance of these in vitro observations was further evaluated in a clinical setting, between drug responsive and nonresponsive schizophrenia patients. A number of DNA modifications were assessed at global level using 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine followed by evaluating the expression of epigenetic modifier genes and their crosstalk with miRNAs...
January 18, 2018: Epigenomics
Maturada Patchsung, Sirapat Settayanon, Monnat Pongpanich, Dharm Mutirangura, Pornrutsami Jintarith, Apiwat Mutirangura
Global DNA hypomethylation promoting genomic instability leads to cancer and deterioration of human health with age. AIM: To invent a biotechnology that can reprogram this process. METHODS: We used Alu siRNA to direct Alu interspersed repetitive sequences methylation in human cells. We evaluated the correlation between DNA damage and Alu methylation levels. RESULTS: We observed an inverse correlation between Alu element methylation and endogenous DNA damage in white blood cells...
January 16, 2018: Epigenomics
Licong Shen, Yu Zhang, Wenjun Zhou, Zheng Peng, Xiaxia Hong, Yi Zhang
AIM: Circular RNAs (circRNAs) with miRNA response elements (MREs) could function as competing endogenous RNA (ceRNA) in regulating gene expression. This study was carried out to identify the expression profile and role of circRNAs in endometriosis. MATERIALS & METHODS: Microarray assay was performed in four paired ovarian endometriomas and eutopic endometrium, followed by quantitative real-time RT-PCR in 24 paired samples. Bioinformatical algorithms were used to predict MREs, as well as ceRNA and KEGG pathway analysis...
January 16, 2018: Epigenomics
Phuc-Loi Luu, Daniela Gerovska, Hans R Schöler, Marcos J Araúzo-Bravo
AIM: Disclosing the mechanisms that regulate reprogramming memory. MATERIALS & METHODS: We established computational procedure to find DNA methylation somatic memory sites (SMSs) at single CpGs and integrated them with genomics, epigenomics, transcriptomics and imprinting information. RESULTS & CONCLUSION: Reprogramming memory persists at late passages in low methylated regions. Contrarily to hypomethylated, hypermethylated SMSs occur at evolutionary conserved sites overlapping active transcription loci in dynamic chromatin regions...
January 16, 2018: Epigenomics
Priyadarshini Kachroo, Silke Szymczak, Femke-Anouska Heinsen, Michael Forster, Jörn Bethune, Georg Hemmrich-Stanisak, Lewis Baker, Martin Schrappe, Martin Stanulla, Andre Franke
AIM: To determine whether methylation differences between mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes can be associated with differential gene expression and remission. MATERIALS & METHODS: Five (extremely rare) TCF3-HLF versus five (very similar) TCF3-PBX1 patients were sampled before and after remission and analyzed using reduced representation bisulfite sequencing and RNA-sequencing. RESULTS: We identified 7000 differentially methylated CpG sites between subtypes, of which 78% had lower methylation levels in TCF3-HLF...
January 15, 2018: Epigenomics
Hanzi Xu, Zhen Gong, Yang Shen, Yichen Fang, Shanliang Zhong
AIM: We aimed to explore the roles of circular RNAs (circRNAs) in extracellular vesicles (EVs) isolated from serum of patients with endometrial cancer. MATERIALS & METHODS: EVs were isolated from serum samples of three patients with stage III adenocarcinoma aged 50-60 years and three matched healthy controls. RNA was extracted from the EVs and analyzed using RNA-seq technique. RESULTS: We got 209 upregulated circRNAs and 66 downregulated circRNAs...
January 15, 2018: Epigenomics
Brandon L Pearson, Dan Ehninger
No abstract text is available yet for this article.
January 15, 2018: Epigenomics
Zhengdao Mao, Yujia Shi, Qi Cao, Yi Chen, Yun Sun, Zhiguang Liu, Qian Zhang, Mao Huang
AIM: This study was intended to evaluate transcriptional regulation of gene expression signatures in combined allergic rhinitis and asthma syndrome (CARAS). MATERIALS & METHODS: The blood samples of three patients with CARAS, three patients with allergic rhinitis and three normal controls were obtained. The cuffdiff, miRDeep2 and DEGseq were used to quantify the expression of genes and miRNAs, respectively. And p-value < 0.01 and false discovery rate < 0...
January 15, 2018: Epigenomics
Chengchi Fang, Cheng Zou, Yuhua Fu, Jingxuan Li, Yao Li, Yunlong Ma, Shuhong Zhao, Changchun Li
AIM: This study aims to couple DNA methylation changes and evolution of retrogenes. MATERIALS & METHODS: A new two-step strategy was developed to screen retrogenes. Further, reduced representation bisulfite sequencing and RNA-seq data of eight tissues were used to analyze retrogenes. RESULTS: A total of 964 retrocopies were identified and new retrocopies were available for the synthesis of glycans and lipids corresponding to pig phenotypic traits...
January 15, 2018: Epigenomics
Stefanie Weber, Astghik Hakobyan, Hovakim Zakaryan, Walter Doerfler
AIM: Sequence-specific CpG methylation of eukaryotic promoters is an important epigenetic signal for long-term gene silencing. We have now studied the methylation status of African swine fever virus (ASFV) DNA at various times after infection of Vero cells in culture. METHODS & RESULTS: ASFV DNA was detectable throughout the infection cycle and was found unmethylated in productively infected Vero cells as documented by bisulfite sequencing of 13 viral DNA segments...
January 12, 2018: Epigenomics
Vijayachitra Modhukur, Tatjana Iljasenko, Tauno Metsalu, Kaie Lokk, Triin Laisk-Podar, Jaak Vilo
AIM: To develop a web tool for survival analysis based on CpG methylation patterns. MATERIALS & METHODS: We utilized methylome data from 'The Cancer Genome Atlas' and used the Cox proportional-hazards model to develop an interactive web interface for survival analysis. RESULTS: MethSurv enables survival analysis for a CpG located in or around the proximity of a query gene. For further mining, cluster analysis for a query gene to associate methylation patterns with clinical characteristics and browsing of top biomarkers for each cancer type are provided...
December 21, 2017: Epigenomics
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