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Epigenomics

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https://www.readbyqxmd.com/read/28885036/postnatal-diet-remodels-hepatic-dna-methylation-in-metabolic-pathways-established-by-a-maternal-high-fat-diet
#1
Laura Moody, Hong Chen, Yuan-Xiang Pan
AIM: We investigate how postweaning diet may modify the epigenetic landscape to meet metabolic demands later in life. METHODS: Sprague-Dawley rats were exposed to a high-fat (HF) diet during gestation and lactation. At weaning, male offspring were placed either on an HF diet (HF/HF) or a control diet (HF/C). Methylation-dependent immunoprecipitation sequencing and methylation-sensitive restriction enzyme sequencing were used to quantify hepatic DNA methylation. RESULTS: Out of the 3966 identified differentially methylated regions, 37% were mapped to gene bodies while 6% fell within promoter or downstream regions...
September 8, 2017: Epigenomics
https://www.readbyqxmd.com/read/28882057/interethnic-dna-methylation-difference-and-its-implications-in-pharmacoepigenetics
#2
Shih-Kai Chu, Hsin-Chou Yang
AIM: This is the first systematic study to examine the population differentiation effect of DNA methylation on the treatment response and drug absorption, distribution, metabolism and excretion in multiple tissue types and cancer types. MATERIALS & METHODS: We analyzed the whole methylome and transcriptome data of primary tumor tissues of four cancer types (breast, colon, head & neck and uterine corpus) and lymphoblastoid cell lines for African and European ancestry populations...
September 8, 2017: Epigenomics
https://www.readbyqxmd.com/read/28877608/genome-wide-integrative-analysis-identified-snp-mirna-mrna-interaction-networks-in-peripheral-blood-mononuclear-cells
#3
Xiang Lin, Wei Xia, Wei Ji, Fang-Fei Xie, Pei He, Xiao-Wei Zhu, Yong-Hong Zhang, Fei-Yan Deng, Shu-Feng Lei
AIM: To detect SNP-miRNA-mRNA interaction networks and to elucidate miRNA-mediated regulation effects on mRNA expression. MATERIALS & METHODS: In human peripheral blood mononuclear cells of 43 females, SNP-miRNA-mRNA interaction networks were established through an integrative analysis. Then causal inference test was followed to detect miRNA-mediated effects on mRNA expressions. RESULTS: About 167 trios corresponding to 56 SNPs, 20 miRNAs and 47 target-mRNAs have the SNP-miRNA-mRNA interactions, but only 22 trios have miRNA-mediated effects between SNP and mRNA...
September 7, 2017: Epigenomics
https://www.readbyqxmd.com/read/28877596/what-the-human-sperm-methylome-tells-us
#4
Cristina Camprubí, Riccardo Aiese Cigliano, Albert Salas-Huetos, Nicolas Garrido, Joan Blanco
AIM: To characterize the sperm methylome in semen samples from 19 donors with proven fertility. MATERIALS & METHODS: Bisulfite-converted sperm DNA was hybridized on the HumanMethylation450 Infinium BeadChip platform. CpG fluorescence intensities were extracted and converted to β-values. RESULTS: The sperm methylome is highly homogeneous and hypomethylated. Genes with hypomethylated promoters are ontologically associated to biological functions related to spermatogenesis and embryogenesis...
September 7, 2017: Epigenomics
https://www.readbyqxmd.com/read/28875726/elevated-expression-of-a-pharmacologic-polycomb-signature-predicts-poor-prognosis-in-gastric-and-breast-cancer
#5
Pier-Luc Clermont, Lorenzo Fornaro, Francesco Crea
AIM: Polycomb Group complexes are epigenetic repressors that silence tumor suppressive genes. Studies demonstrated that pharmacologic inhibition of Polycomb Group complexes with 3-deazaneplanocin A (DZNeP) induces cancer cell death by re-expressing silenced genes. Here we evaluate the prognostic significance of DZNeP target genes in gastric and breast cancer. Patients & methods/materials: The prognostic impact of a DZNeP-regulated gene signature was investigated using the KM Plotter and cBio Portal resources containing microarray data from tumor tissue...
September 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/28875715/the-emerging-molecular-biology-toolbox-for-the-study-of-long-noncoding-rna-biology
#6
Ezio T Fok, Janine Scholefield, Stephanie Fanucchi, Musa M Mhlanga
Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely...
September 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/28875708/fkbp5-methylation-as-a-possible-marker-for-cortisol-state-and-transient-cortisol-exposure-in-healthy-human-subjects
#7
Britta K Winkler, Hendrik Lehnert, Henrik Oster, Henriette Kirchner, Birgit Harbeck
Current glucocorticoid replacement regimens, in adrenal insufficiency, fail to mimic the physiological cortisol secretion, thereby fostering serious side effects. AIM: To experimentally evaluate the impact of CpG methylation within the FKBP5 gene as a possible short- and long-term marker for cortisol exposure in humans. MATERIALS & METHODS: An ACTH-stimulation test was carried out and methylation status of the FKBP5 gene in leukocytes was determined. RESULTS: A negative correlation between basal levels of methylation and serum cortisol was observed...
September 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/28874065/associations-between-adiposity-and-repetitive-element-dna-methylation-in-healthy-postmenopausal-women
#8
Devon J Boyne, Christine M Friedenreich, John B McIntyre, Kerry S Courneya, Will D King
AIM: To describe the association between adiposity and repetitive element DNA methylation in healthy postmenopausal women. PATIENTS & METHODS: A cross-sectional study was conducted using baseline information from 289 women who participated in the Alberta Physical Activity and Breast Cancer Prevention trial. RESULTS: After adjusting for important confounders,  long interspersed nuclear element-1 methylation was positively associated with intra-abdominal fat area (p = 0...
September 6, 2017: Epigenomics
https://www.readbyqxmd.com/read/28809130/long-noncoding-rna-a-new-contributor-and-potential-therapeutic-target-in-fibrosis
#9
Xiaoying Jiang, Fujun Zhang
Fibrosis is the excess deposition of extracellular matrix components which occur in multiple organs and ultimately leads to organ failure. Long noncoding RNAs (lncRNAs) are a kind of noncoding RNAs longer than approximately 200 nucleotides with no protein-encoding capacity. A growing body of evidence suggests that lncRNAs are also involved in tissues fibrosis in several organs, such as lungs fibrosis, liver fibrosis, renal fibrosis and cardiac fibrosis. In this review, we summarized the current studies of lncRNAs in the process of fibrosis and hopefully aid in better understanding the molecular mechanism of fibrosis and provide a basis to explore new therapeutic targets of fibrosis...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28809129/effect-of-methotrexate-vitamin-b12-on-dna-methylation-as-a-potential-factor-in-leukemia-treatment-related-neurotoxicity
#10
Victoria J Forster, Alex McDonnell, Rachel Theobald, Jill A McKay
Methotrexate (MTX) is administered to treat childhood acute lymphoblastic leukemia (ALL). It acts by inhibiting dihydrofolate reductase which reduces methyltetrahydrofolate, a key component in one carbon metabolism, thus reducing cell proliferation. Further perturbations to one carbon metabolism, such as reduced vitamin B12 levels via the use of nitrous oxide for sedation during childhood ALL treatment, may increase neurotoxicity risk. With B12 as an enzymatic cofactor, methyltetrahydrofolate is essential to produce methionine, which is critical for DNA methylation...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28809127/the-correlation-of-methylation-levels-measured-using-illumina-450k-and-epic-beadchips-in-blood-samples
#11
Mark W Logue, Alicia K Smith, Erika J Wolf, Hannah Maniates, Annjanette Stone, Steven A Schichman, Regina E McGlinchey, William Milberg, Mark W Miller
AIM: We examined concordance of methylation levels across the Illumina Infinium HumanMethylation450 BeadChip and the Infinium MethylationEPIC BeadChip. METHODS: We computed the correlation for 145 whole blood DNA samples at each of the 422,524 CpG sites measured by both chips. RESULTS: The correlation at some sites was high (up to r = 0.95), but many sites had low correlation (55% had r < 0.20). The low correspondence between 450K and EPIC measured methylation values at many loci was largely due to the low variability in methylation values for the majority of the CpG sites in blood...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28809126/comprehensive-epigenetic-analysis-of-the-signature-genes-in-lung-adenocarcinoma
#12
Yunfeng Zhang, Weidong Zhao, Jia Zhang
AIM: This study aimed to explore the epigenetic modifications of signature genes in lung adenocarcinoma. MATERIALS & METHODS: The data of miRNA expression, mRNA expression and DNA methylation were downloaded from The Cancer Genome Atlas. Differential analysis was performed, followed by correlation analysis of miRNA-mRNA and DNA methylation-mRNA. RESULTS: A total of 14 significant inverse correlations between gene expression and DNA methylation were identified, the expressions of which were selected for further validation via GSE27262, displaying similar pattern with that of the integrated analysis...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28803498/screening-circular-rna-related-to-chemotherapeutic-resistance-in-breast-cancer
#13
Danfeng Gao, Xiufen Zhang, Beibei Liu, Dong Meng, Kai Fang, Zijian Guo, Lihua Li
AIM: We aimed to identify circular RNAs (circRNAs) associated with breast cancer chemoresistance. MATERIALS & METHODS: CircRNA microarray expression profiles were obtained from Adriamycin (ADM) resistant MCF-7 breast cancer cells (MCF-7/ADM) and parental MCF-7 cells and were validated using quantitative real-time reverse transcription PCR. The expression data were analyzed bioinformatically. RESULTS: We detected 3093 circRNAs and identified 18 circRNAs that are differentially expressed between MCF-7/ADM and MCF-7 cells; after validating by quantitative real-time reverse transcription PCR, we predicted the possible miRNAs and potential target genes of the seven upregulated circRNAs using TargetScan and miRanda...
August 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/28803494/prognostic-dna-methylation-markers-for-renal-cell-carcinoma-a-systematic-review
#14
Sophie C Joosten, Ivette Ag Deckers, Maureen J Aarts, Ann Hoeben, Joep G van Roermund, Kim M Smits, Veerle Melotte, Manon van Engeland, Vivianne C Tjan-Heijnen
AIM: Despite numerous published prognostic methylation markers for renal cell carcinoma (RCC), none of these have yet changed patient management. Our aim is to systematically review and evaluate the literature on prognostic DNA methylation markers for RCC. MATERIALS & METHODS: We conducted an exhaustive search of PubMed, EMBASE and MEDLINE up to April 2017 and identified 49 publications. Studies were reviewed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, assessed for their reporting quality using the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) criteria, and were graded to determine the level of evidence (LOE) for each biomarker...
August 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/28799791/unique-aspects-of-the-epigenetic-code-in-the-brain
#15
Nasser H Zawia
No abstract text is available yet for this article.
August 11, 2017: Epigenomics
https://www.readbyqxmd.com/read/28768424/surgical-salvage-of-recurrence-after-resection-of-colorectal-liver-metastases-incidence-and-outcomes
#16
Nuh N Rahbari, Michael I D'Angelica
Surgical resection remains the primary curative treatment option for patients with colorectal liver metastases. While the majority of patients will develop tumor relapse within or outside of the liver after hepatic metastasectomy, a subset of these patients may be amenable to salvage surgical resection. However, outcomes for this approach are not well defined. In this article, we summarize the current evidence for the incidence, feasibility and outcomes of salvage resection for recurrence after initial resection of colorectal liver metastases...
August 3, 2017: Epigenomics
https://www.readbyqxmd.com/read/28762778/epigenomic-analysis-in-a-cell-based-model-reveals-the-roles-of-h3k9me3-in-breast-cancer-transformation
#17
Qing-Lan Li, Pin-Ji Lei, Quan-Yi Zhao, Lianyun Li, Gang Wei, Min Wu
AIM: Epigenetic marks are critical regulators of chromatin and gene activity. Their roles in normal physiology and disease states, including cancer development, still remain elusive. Herein, the epigenomic change of H3K9me3, as well as its potential impacts on gene activity and genome stability, was investigated in an in vitro breast cancer transformation model. METHODS: The global H3K9me3 level was studied with western blotting. The distribution of H3K9me3 on chromatin and gene expression was studied with ChIP-Seq and RNA-Seq, respectively...
August 1, 2017: Epigenomics
https://www.readbyqxmd.com/read/28758427/genome-wide-dna-methylation-profiling-of-the-regenerative-mrl-mpj-mouse-and-two-normal-strains
#18
Bartosz Górnikiewicz, Anna Ronowicz, Piotr Madanecki, Paweł Sachadyn
AIM: We aimed to identify the pivotal differences in the DNA methylation profiles between the regeneration capable MRL/MpJ mouse and reference mouse strains. MATERIALS & METHODS: Global DNA methylation profiling was performed in ear pinnae, bone marrow, spleen, liver and heart from uninjured adult females of the MRL/MpJ and C57BL/6J and BALB/c. RESULTS & CONCLUSION: A number of differentially methylated regions (DMRs) distinguishing between the MRL/MpJ mouse and both references were identified...
July 31, 2017: Epigenomics
https://www.readbyqxmd.com/read/28758420/mir-377-reverses-cancerous-phenotypes-of-pancreatic-cells-via-suppressing-dnmt1-and-demethylating-tumor-suppressor-genes
#19
Masoumeh Azizi, Pezhman Fard-Esfahani, Habibollah Mahmoodzadeh, Mohammad Sadegh Fazeli, Kayhan Azadmanesh, Sirous Zeinali, Ladan Teimoori-Toolabi
AIM: The aim was to investigate the effect of miR-377 on DNMT1 expression and cancer phenotype in pancreatic cancer cells. MATERIALS & METHODS: Real-time PCR, luciferase assay, MTT and Annexin-PI staining were used. RESULTS: Decreased miR-377 and increased DNMT1 (verified as a target for mir-377) levels in pancreatic cancer tissues and cell lines in comparison with normal tissues was confirmed to be influenced by promoter methylation. Also hypermethylation of BNIP3, SPARC, TFPI2 and PENK promoters was observed in tumor samples but not in normal tissues which negatively correlated with their expression...
July 31, 2017: Epigenomics
https://www.readbyqxmd.com/read/28749190/are-there-any-hottips-for-defining-coding-potential-of-lncrnas-or-just-a-lot-of-hotair
#20
Rebecca L Mather, Mark Hirst, Francesco Crea
No abstract text is available yet for this article.
July 27, 2017: Epigenomics
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