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Eri Arai, Fumihito Miura, Yasushi Totoki, Satoshi Yamashita, Ying Tian, Masahiro Gotoh, Hidenori Ojima, Hiroyuki Nakagawa, Yoriko Takahashi, Hiromi Nakamura, Natsuko Hama, Mamoru Kato, Hiroshi Kimura, Yutaka Suzuki, Takashi Ito, Tatsuhiro Shibata, Yae Kanai
AIM: The aim of this study was to reveal the epigenome landscape of human normal hepatocytes. MATERIALS & METHODS: Cells purified from partial hepatectomy specimens of Japanese patients were subjected to whole-genome bisulfite sequencing using postbisulfite adaptor tagging, chromatin immunoprecipitation sequencing, RNA sequencing and whole-genome sequencing. RESULTS: CHG and CHH methylations were inversely associated with gene expression...
July 4, 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
Jose R Hernandez Mora, Chiharu Tayama, Marta Sánchez-Delgado, Ana Monteagudo-Sánchez, Kenichiro Hata, Tsutomu Ogata, Jose Medrano, Maria E Poo-Llanillo, Carlos Simón, Sebastian Moran, Manel Esteller, Jair Tenorio, Pablo Lapunzina, Masayo Kagami, David Monk, Kazuhiko Nakabayashi
AIM: This study aimed to establish a catalog of probes corresponding to imprinted differentially methylated regions (DMRs) on the Infinium HumanMethylationEPIC BeadChip. MATERIALS & METHODS: Reciprocal uniparental diploidies with low normal biparental mosaic contribution, together with normal diploid controls, were subjected to EPIC BeadChip hybridization. The methylation profiles were assessed for imprinted differential methylation. Top candidates were validated using locus-specific PCR-based assays...
July 2, 2018: Epigenomics
Juan Gómez, Rebeca Lorca, Julián R Reguero, María Martín, César Morís, Belén Alonso, Sara Iglesias, Beatriz Díaz-Molina, Pablo Avanzas, Eliecer Coto
AIM: The long noncoding RNA H19 and its host micro RNA miR-675 have been found deregulated in cardiac hypertrophy and heart failure tissues. Our aim was to investigate whether the H19 gene variants were associated with the risk of hypertrophic cardiomyopathy (HCM). PATIENTS & METHODS: We genotyped two H19 tag single nucleotide polymorphisms in 405 HCM patients and 550 controls, and sequenced this gene in 100 patients. RESULTS: The rs2107425 C was significantly increased in sarcomere no-mutation patients (n = 225; p = 0...
July 2, 2018: Epigenomics
Gwen Tindula, Susan K Murphy, Carole Grenier, Zhiqing Huang, Karen Huen, Maria Escudero-Fung, Asa Bradman, Brenda Eskenazi, Cathrine Hoyo, Nina Holland
AIM: Imprinted genes exhibit expression in a parent-of-origin-dependent manner and are critical for child development. Recent limited evidence suggests that prenatal exposure to phthalates, ubiquitous endocrine disruptors, can affect their epigenetic dysregulation. MATERIALS & METHODS: We quantified DNA methylation of nine imprinted gene differentially methylated regions by pyrosequencing in 296 cord blood DNA samples in a Mexican-American cohort. Fetal exposure was estimated by phthalate metabolite concentrations in maternal urine samples during pregnancy...
June 29, 2018: Epigenomics
Wenhua Lv, Mengying Zhang, Jiang Zhu, Min Zhang, Ce Ci, Shipeng Shang, Yanjun Wei, Hui Liu, Xin Li, Yan Zhang
AIM: To discover CpG island methylator phenotype (CIMP) as a predictor for cancer drug-response mechanism. MATERIALS & METHODS: CIMP classification of 966 cancer cell lines was determined according to identified copy number alteration and differential methylation by DNA methylation profiles. CIMP-related drugs were analyzed by analysis of variance. Tissue-cell-drug networks were developed to predict drug response of individual samples. RESULTS & CONCLUSION: One hundred and thirty-six copy number gain and 142 copy number loss cell lines were classified into CIMP-high and CIMP-low groups, meanwhile 9 and 24 CIMP-associated drugs were identified, respectively...
June 29, 2018: Epigenomics
Yuk Jing Loke, Evelyne Muggli, Linh Nguyen, Joanne Ryan, Richard Saffery, Elizabeth J Elliott, Jane Halliday, Jeffrey M Craig
AIM: Epigenetic changes, in particular in the placenta, may mediate the effects of prenatal alcohol exposure (PAE) on children's health. We examined the relationship between PAE patterns, based on dose and timing, and placental global DNA methylation. METHODS: Using linear regression analysis, we examined the association between different PAE categories and placental global DNA methylation (n = 187), using the proxy measure of Alu-interspersed repeats. RESULTS: Following adjustment for important covariates, we found no evidence of an association between PAE and placental global DNA methylation overall...
June 29, 2018: Epigenomics
Dashzeveg Bayarsaihan
No abstract text is available yet for this article.
June 29, 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
Nabil Hajji, Daniel J García-Domínguez, Lourdes Hontecillas-Prieto, Kevin O'Neill, Enrique de Álava, Nelofer Syed
One of the major obstacles to the development of effective new cancer treatments and the main factor for the increasing number of clinical trial failures appears to be the paucity of accurate, reproducible and robust drug resistance testing methods. Most research assessing the resistance of cancers to chemotherapy has concentrated on genetic-based molecular mechanisms, while the role of epigenetics in drug resistance has been generally overlooked. This is rather surprising given that an increasing body of evidence pointing to the fact that epigenetic mechanism alterations appear to play a pivotal role in cancer initiation, progression and development of chemoresistance...
June 22, 2018: Epigenomics
Pawel Karpinski, Arpad V Patai, Wojciech Hap, Wojciech Kielan, Izabela Laczmanska, Maria Malgorzata Sasiadek
AIM: We aimed to assess to what extent CpG island methylator phenotype (CIMP) contributes to cancer subtypes obtained by multilevel omic data analysis. MATERIALS & METHODS: 16 The Cancer Genome Atlas datasets encompassing three data layers in 4688 tumor samples were analyzed. We identified cancer integrative subtypes (ISs) by the use of similarity network fusion and consensus clustering. CIMP high (CIMP-H) associated ISs were profiled by gene sets and transcriptional regulators enrichment analysis...
June 13, 2018: Epigenomics
Jennifer Pasquier, Vimal Ramachandran, Moh'd Rasheed Abu-Qaoud, Binitha Thomas, Manasi J Benurwar, Omar Chidiac, Jessica Hoarau-Véchot, Amal Robay, Khalid Fakhro, Robert A Menzies, Amin Jayyousi, Mahmoud Zirie, Jassim Al Suwaidi, Rayaz A Malik, Talal K Talal, Seyed Hani Najafi-Shoushtari, Arash Rafii, Charbel Abi Khalil
AIM: Charcot foot (CF) is a rare complication of Type 2 diabetes (T2D). MATERIALS & METHODS: We assessed circulating miRNAs in 17 patients with T2D and acute CF (G1), 17 patients with T2D (G2) and equivalent neuropathy and 17 patients with T2D without neuropathy (G3) using the high-throughput miRNA expression profiling. RESULTS: 51 significantly deregulated miRNAs were identified in G1 versus G2, 37 in G1 versus G3 and 64 in G2 versus G3...
June 5, 2018: Epigenomics
Ye Liu, Zhongqi Chen, Kun Xu, Zhengxia Wang, Chaojie Wu, Zhixiao Sun, Ningfei Ji, Mao Huang, Mingshun Zhang
AIM: To explore the miRNAs profile of CD4+ T lymphocytes in asthma via next generation sequencing. METHODS: In the murine model of acute asthma, spleen CD4+ T lymphocytes were sorted, in which small RNAs were extracted and sequenced. Novel miRNAs were measured with real time quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: A total of 127 miRNAs were found to exhibit at least twofold change. In the 262 predicted novel miRNAs, 14 novel miRNAs were measured in qRT-PCR in the sorted CD4+ T cells or in the differentiated Th1/Th2 cells and novel miR-11 (xxx-m0228-3p) was significantly decreased in the sorted CD4+ T cells from the murine model of asthma and in the Th2 cells...
May 8, 2018: Epigenomics
Shijie C Zheng, Amy P Webster, Danyue Dong, Andy Feber, David G Graham, Roisin Sullivan, Sarah Jevons, Laurence B Lovat, Stephan Beck, Martin Widschwendter, Andrew E Teschendorff
AIM: An outstanding challenge in epigenome studies is the estimation of cell-type proportions in complex epithelial tissues. MATERIALS & METHODS: Here, we construct and validate a DNA methylation reference and algorithm for complex tissues that contain epithelial, immune and nonimmune stromal cells. RESULTS: Using this reference, we show that easily accessible tissues such as saliva, buccal and cervix exhibit substantial variation in immune cell (IC) contamination...
April 25, 2018: Epigenomics
Jiaojiao Hu, Qi Han, Yan Gu, Jinlong Ma, Mary McGrath, Fengchang Qiao, Baoan Chen, Chunhua Song, Zheng Ge
AIM: The roles of circular RNA PVT1 (circPVT1) are explored in the patients with acute lymphoblastic leukemia (ALL). METHODS: The circPVT1 level was detected by qRT-PCR and western blot. The apoptotic cells were examined by the annexin V assay in lentiviral shRNA knockdown cells. RESULTS: circPVT1 was highly expressed in ALL compared with normal bone marrow samples. circPVT1 expression was also significantly higher in ALL cell lines. circPVT1 knockdown inhibited cell proliferation and induced cell apoptosis through suppression of its neighbor gene c-Myc, and antiapoptotic Bcl-2 protein expression...
April 25, 2018: Epigenomics
Wei Chen, Ling Zhang, Changhua Shi, Guanhua Ren, Qi Kong, Chuan Qin
AIM: This study aims to explore the similarity and difference of hippocampal miRNAomes between humans and mice. MATERIALS & METHODS: A systematic comparison of the miRNAomes between healthy human and mouse hippocampi was performed using high-throughput sequencing followed by bioinformatic analyses. RESULTS: A novel miRNA termed novel-21-5p and a human-specific miR-656-3p were identified in human hippocampi, which were expressed ubiquitously and predicted to be associated with neural activities...
June 2018: Epigenomics
Sagi Snir, Matteo Pellegrini
AIM: DNA methylation has proven to be a remarkably accurate biomarker for human age, allowing the prediction of chronological age to within a couple of years. Recently, we proposed that the Universal PaceMaker (UPM), a flexible paradigm for modeling evolution, could be applied to epigenetic aging. Nevertheless, application to real data was restricted to small datasets for technical limitations. MATERIALS & METHODS: We partition the set of variables into to two subsets and optimize the likelihood function on each set separately...
June 2018: Epigenomics
Brandon L Pearson, Leonie P Posselt, Kristin S Henzel, Dan Ehninger
AIM: Epigenetic analyses of sperm require pure samples devoid of diploid cell contamination. We sought to determine the efficacy of somatic cell lysis buffer (SCLB) treatment to purify mouse epididymis sperm samples. MATERIALS & METHODS: Sperm cell concentration, sperm purity, small RNA contents and sperm and somatic marker gene expression was compared in SCLB-treated sperm samples and two different control conditions. RESULTS: The SCLB condition as well as the control condition mimicking the additional pelleting and re-suspension steps resulted in substantial cell loss without evidence of enhanced purification of sperm cells as compared with epididymis-derived sperm samples that were not manipulated further...
June 2018: Epigenomics
Lydia Hopp, Henry Löffler-Wirth, Jörg Galle, Hans Binder
AIM: We present here a novel method that enables unraveling the interplay between gene expression and DNA methylation in complex diseases such as cancer. MATERIALS & METHODS: The method is based on self-organizing maps and allows for analysis of data landscapes from 'governed by methylation' to 'governed by expression'. RESULTS: We identified regulatory modules of coexpressed and comethylated genes in high-grade gliomas: two modes are governed by genes hypermethylated and underexpressed in IDH-mutated cases, while two other modes reflect immune and stromal signatures in the classical and mesenchymal subtypes...
June 2018: Epigenomics
Jacob K Kresovich, Brian T Joyce, Tao Gao, Yinan Zheng, Zhou Zhang, Christopher J Achenbach, Robert L Murphy, Allan C Just, Jincheng Shen, Hushan Yang, Pantel Vokonas, Joel Schwartz, Andrea A Baccarelli, Lifang Hou
AIM: Previous studies suggest telomere shortening represses PGC1A and PGC1B expression leading to mitochondrial dysfunction. Methylation of CpG sites within these genes may interact with these factors to affect cancer risk. MATERIALS & METHODS: Among 385 men, we identified 84 incidents of cancers (predominantly prostate and nonmelanoma skin). We examined associations between leukocyte DNA methylation of 41 CpGs from PGC1A and PGC1B with telomere length, mitochondrial 8-OHdG lesions, mitochondrial abundance and cancer incidence...
June 2018: Epigenomics
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