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Epigenomics

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https://www.readbyqxmd.com/read/28809130/long-noncoding-rna-a-new-contributor-and-potential-therapeutic-target-in-fibrosis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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/28799802/the-influence-of-an-epigenetics-diet-on-the-cancer-epigenome
#7
Kayla A Lewis, Trygve O Tollefsbol
No abstract text is available yet for this article.
August 11, 2017: Epigenomics
https://www.readbyqxmd.com/read/28799801/cross-generational-effects-of-alcohol-dependence-in-humans-on-hras-and-tp53-methylation-in-offspring
#8
Shirley Y Hill, Gregory Rompala, Gregg E Homanics, Nicholas Zezza
AIM: We hypothesized that cross-generational effects of alcohol exposure could alter DNA methylation and expression of the HRAS oncogene and TP53 tumor suppressor gene that drive cancer development. METHODS: DNA methylation of the HRAS and TP53 genes was tested in samples from young participants (Mean age of 13.4 years). RESULTS: Controlling for both personal use and maternal use of substances during pregnancy, familial alcohol dependence was associated with hypomethylation of CpG sites in the HRAS promoter region and hypermethylation of the TP53 gene...
August 11, 2017: Epigenomics
https://www.readbyqxmd.com/read/28799793/towards-quantitative-analysis-of-gene-regulation-by-enhancers
#9
Ekaterina V Nizovtseva, Stefjord Todolli, Wilma K Olson, Vasily M Studitsky
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
August 11, 2017: Epigenomics
https://www.readbyqxmd.com/read/28799791/unique-aspects-of-the-epigenetic-code-in-the-brain
#10
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
#11
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
#12
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
#13
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
#14
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
#15
Rebecca L Mather, Mark Hirst, Francesco Crea
No abstract text is available yet for this article.
July 27, 2017: Epigenomics
https://www.readbyqxmd.com/read/28749187/differential-methylation-of-lncrna-kcnq1ot1-promoter-polymorphism-was-associated-with-symptomatic-cardiac-long-qt
#16
Eliecer Coto, David Calvo, Julián R Reguero, César Morís, Jose M Rubín, Carmen Díaz-Corte, Helena Gil-Peña, Belén Alosno, Sara Iglesias, Juan Gómez
AIM: To investigate whether the differential methylation of KCNQ1OT1 was associated with the risk of symptomatic long QTc. PATIENTS & METHODS: We investigated the methylation status of KCNQ1OT1 in a cohort of patients (n = 131) with a symptomatic prolonged QTc. All the patients were genotyped for a common promoter polymorphism (rs11023840). They were also genotyped for DNA digested with the methylation-sensitive HpaII restriction enzyme. RESULTS: We found a significant higher frequency of AA genotype (p = 0...
July 27, 2017: Epigenomics
https://www.readbyqxmd.com/read/28749184/is-cellular-heterogeneity-merely-a-confounder-to-be-removed-from-epigenome-wide-association-studies
#17
Joanna D Holbrook, Rae-Chi Huang, Sheila J Barton, Richard Saffery, Karen A Lillycrop
Excitement about DNA methylation biomarkers has been tempered by a growing appreciation of the complex causal relations with cell fate. Intersample differences in DNA methylation can be partitioned into those that are independent of cellular heterogeneity and those that are caused by differential mixtures of cell types. Generally, the field has assumed that the former are more likely to be causative of disease. The latter has been considered a likely consequence of disease and a confounder to be removed. We argue that the conceptual separation of these signals is artificial and not necessarily informative about causation...
July 27, 2017: Epigenomics
https://www.readbyqxmd.com/read/28749179/analysis-of-microrna-expression-and-micronuclei-frequency-in-workers-exposed-to-vinyl-chloride-monomer-in-china
#18
Nan-Nan Feng, Yan Fang, Ya-Nan Zhang, Xiao-Wen Xu, Yong Li, Jin-Wei Wang, Yong-Liang Li, Paul Brandt-Rauf, Zhao-Lin Xia
AIM: To identify differently expressed miRNAs associated with vinyl chloride monomer (VCM) and micronuclei (MN) frequency. METHOD: In discovery stage, we used microarray to detect miRNAs expression in peripheral blood lymphocytes between six low and six high VCM-exposed workers grouped by medium cumulative exposure dose. Then we validated four miRNAs using real-time quantitative reverse transcription PCR (qRT-PCR) and detected the micronuclei frequencies using cytokinesis-block micronucleus assay in 94 VCM-exposed workers and 53 healthy control subjects...
July 27, 2017: Epigenomics
https://www.readbyqxmd.com/read/28699367/a-comprehensive-review-of-lysine-specific-demethylase-1-and-its-roles-in-cancer
#19
Amir Hosseini, Saverio Minucci
Histone methylation plays a key role in the regulation of chromatin structure, and its dynamics regulates important cellular processes. The investigation of the role of alterations in histone methylation in cancer has led to the identification of histone methyltransferases and demethylases as promising novel targets for therapy. Lysine-specific demethylase 1(LSD1, also known as KDM1A) is the first discovered histone lysine demethylase, with the ability to demethylase H3K4me1/2 and H3K9me1/2 at target loci in a context-dependent manner...
July 12, 2017: Epigenomics
https://www.readbyqxmd.com/read/28651445/cellular-reprogramming-technology-for-dissecting-cancer-epigenome-in-vivo
#20
Kenji Ito, Yasuhiro Yamada
Decades of studies have shown that epigenetic alterations play a significant role on cancer development both in vitro and in vivo. However, considering that many cancers harbor mutations at epigenetic modifier genes and that transcription factor-mediated gene regulations are tightly coupled with epigenetic modifications, the majority of epigenetic alterations in cancers could be the consequence of the dysfunction or dysregulation of epigenetic modifiers caused by genetic abnormalities. Therefore, it remains unclear whether bona fide epigenetic abnormalities have causal roles on cancer development...
June 27, 2017: Epigenomics
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