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Methylation DNA

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https://www.readbyqxmd.com/read/29350455/a-novel-prognostic-six-cpg-signature-in-glioblastomas
#1
An-An Yin, Nan Lu, Amandine Etcheverry, Marc Aubry, Jill Barnholtz-Sloan, Lu-Hua Zhang, Jean Mosser, Wei Zhang, Xiang Zhang, Yu-He Liu, Ya-Long He
AIMS: We aimed to identify a clinically useful biomarker using DNA methylation-based information to optimize individual treatment of patients with glioblastoma (GBM). METHODS: A six-CpG panel was identified by incorporating genome-wide DNA methylation data and clinical information of three distinct discovery sets and was combined using a risk-score model. Different validation sets of GBMs and lower-grade gliomas and different statistical methods were implemented for prognostic evaluation...
January 19, 2018: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/29350283/epigenetic-regulation-of-neuroblastoma-development
#2
REVIEW
Durinck Kaat, Speleman Frank
In recent years, technological advances have enabled a detailed landscaping of the epigenome and the mechanisms of epigenetic regulation that drive normal cell function, development and cancer. Rather than merely a structural entity to support genome compaction, we now look at chromatin as a very dynamic and essential constellation that is actively participating in the tight orchestration of transcriptional regulation as well as DNA replication and repair. The unique feature of chromatin flexibility enabling fast switches towards more or less restricted epigenetic cellular states is, not surprisingly, intimately connected to cancer development and treatment resistance, and the central role of epigenetic alterations in cancer is illustrated by the finding that up to 50% of all mutations across cancer entities affect proteins controlling the chromatin status...
January 19, 2018: Cell and Tissue Research
https://www.readbyqxmd.com/read/29348893/diagnostic-accuracy-of-dna-methylation-in-detection-of-gastric-cancer-a-meta-analysis
#3
Weiling Hu, Wenfang Zheng, Qifang Liu, Hua Chu, Shujie Chen, John J Kim, Jiaguo Wu, Jianmin Si
Emerging studies demonstrate the diagnostic utility of DNA methylation-based blood test for gastric cancer. The aim of the meta-analysis is to evaluate the accuracy of blood DNA methylation markers for detecting patients with gastric cancer. A systematic literature search to November 2016 that evaluated DNA methylation markers utilizing blood specimen to detect gastric cancer were selected to derive pooled sensitivities and specificities. 32 studies including 4,172 patients (gastric cancer (N = 2,098), control (N = 2,074)) met the study criteria...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348853/3d-cultivation-of-nsclc-cell-lines-induce-gene-expression-alterations-of-key-cancer-associated-pathways-and-mimic-in-vivo-conditions
#4
Gabriele Gamerith, Johannes Rainer, Julia M Huber, Hubert Hackl, Zlatko Trajanoski, Stefan Koeck, Edith Lorenz, Johann Kern, Reinhard Kofler, Jens M Kelm, Heinz Zwierzina, Arno Amann
This work evaluated gene expression differences between a hanging-drop 3D NSCLC model and 2D cell cultures and their in-vivo relevance by comparison to patient-derived data from The Cancer Genome Atlas. Gene expression of 2D and 3D cultures for Colo699 and A549 were assessed using Affymetrix HuGene 1.0 ST gene chips. Biostatistical analyses tested for reproducibility, comparability and significant differences in gene expression profiles between cell lines, experiments and culture methods. The analyses revealed a high interassay correlation within specific culture systems proving a high validity...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348462/piperlongumine-and-p53-reactivator-apr-246-selectively-induce-cell-death-in-hnscc-by-targeting-gstp1
#5
Wei Hang, Zhi-Xian Yin, Gang Liu, Qinghua Zeng, Xiang-Feng Shen, Qian-Hui Sun, Dong-Dong Li, Yong-Ping Jian, Yang-He Zhang, Yi-Shu Wang, Cheng-Shi Quan, Rui-Xun Zhao, Yu-Lin Li, Zhi-Xiang Xu
TP53 mutations frequently occur in head and neck squamous cell carcinoma (HNSCC) patients without human papillomavirus infection. The recurrence rate for these patients is distinctly high. It has been actively explored to identify agents that target TP53 mutations and restore wild-type (WT) TP53 activities in HNSCC. PRIMA-1 (p53-reactivation and induction of massive apoptosis-1) and its methylated analogue PRIMA-1Met (also called APR-246) were found to be able to reestablish the DNA-binding activity of p53 mutants and reinstate the functions of WT p53...
January 18, 2018: Oncogene
https://www.readbyqxmd.com/read/29348151/ahrr-hypomethylation-lung-function-lung-function-decline-and-respiratory-symptoms
#6
Jakob B Kodal, Camilla J Kobylecki, Signe Vedel-Krogh, Børge G Nordestgaard, Stig E Bojesen
Introduction: Epigenome wide association studies have shown a consistent association between smoking exposure and hypomethylation in the aryl hydrocarbon receptor repressor(AHRR) gene(cg05575921). We tested the hypothesis that AHRR hypomethylation is associated with low lung function, steeper lung function decline, and respiratory symptoms in the general population.Methods:AHRR methylation extent was measured in 9113 individuals from the 1991-1994 examination of the Copenhagen City Heart Study, using bisulfite treated leucocyte DNA...
January 18, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/29347875/universal-informative-cpg-sites-for-inferring-tumor-purity-from-dna-methylation-microarray-data
#7
Haixia Dou, Yun Fang, Xiaoqi Zheng
Tumor purity is an intrinsic property of tumor samples and potentially has severe impact on many types of data analysis. We have previously developed a statistical method, InfiniumPurify, which could infer purity of a tumor sample given its tumor type (available in TCGA) or a set of informative CpG (iDMC) sites. However, in many clinical practices, researchers may focus on a specific type of tumor samples that is not included in TCGA, and samples which are too few to identify reliable iDMCs. This greatly restricts the application of InfiniumPurify in cancer research...
December 28, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#8
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29345269/tributyltin-induces-epigenetic-changes-and-decreases-the-expression-of-nuclear-respiratory-factor-1
#9
Saki Hanaoka, Keishi Ishida, Saki Tanaka, Shuichiro Sakamoto, Katsuhiro Okuda, Seigo Sanoh, Shigeru Ohta, Yaichiro Kotake
Tributyltin (TBT), a common organotin environmental pollutant, has been widely used as a component of marine antifouling paints. We previously reported that exposure to TBT inhibits the expression and DNA binding of nuclear respiratory factor-1 (NRF-1) and causes neurotoxicity. In the present study, we focused on the epigenetic effects of TBT and investigated whether TBT decreases NRF-1 expression via epigenetic modifications in SH-SY5Y human neuroblastoma cells. First, we found that exposure to 300 nM TBT decreases NRF-1 expression...
January 18, 2018: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29344930/maternal-prenatal-stress-and-infant-dna-methylation-a-systematic-review
#10
REVIEW
David W Sosnowski, Carolyn Booth, Timothy P York, Ananda B Amstadter, Wendy Kliewer
Maternal prenatal stress has been linked to a variety of infant postnatal outcomes, partially through alterations in fetal HPA axis functioning; yet the underlying pathobiology remains elusive. Current literature posits DNA methylation as a candidate mechanism through which maternal prenatal stress can influence fetal HPA axis functioning. The goal of this systematic review was to summarize the literature examining the associations among maternal prenatal stress, DNA methylation of commonly studied HPA axis candidate genes, and infant HPA axis functioning...
January 18, 2018: Developmental Psychobiology
https://www.readbyqxmd.com/read/29344904/mgmt-assessment-in-pituitary-adenomas-comparison-of-different-immunohistochemistry-fixation-chemicals
#11
Alexander S G Micko, Romana Höftberger, Adelheid Wöhrer, Matthias Millesi, Engelbert Knosp, Stefan Wolfsberger
PURPOSE: Despite the established role of O6-methyl-guanine-DNA methyltransferase (MGMT) as a marker for temozolomide response, consensus of the most reliable method to assess MGMT expression in pituitary adenomas is still missing. Currently, immunohistochemistry (IHC) assessment of formaldehyde fixed tissue samples is most widely used in a semiquantitative description. As formaldehyde fails to completely preserve nucleic acids, RCL2, an alcohol-based formaldehyde-free fixative, has been proposed as a more reliable alternative in terms of cell stability...
January 17, 2018: Pituitary
https://www.readbyqxmd.com/read/29344884/analyzing-dna-methylation-patterns-during-tumor-evolution
#12
Heng Pan, Olivier Elemento
Epigenetic modifications play a key role in cellular development and tumorigenesis. Recent large-scale genomic studies have shown that mutations in players of the epigenetic machinery and concomitant perturbation of epigenomic patterning are frequent events in tumors. Among epigenetic marks, DNA methylation is one of the best studied. Hyper- and hypo-methylation events of specific regulatory elements (such as promoters and enhancers) are sometimes thought to be correlated with expression of nearby genes. High-throughput bisulfite converted sequencing is currently the technology of choice for studying DNA methylation in base-pair resolution and on whole-genome scale...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344860/laser-microdissection-for-human-papillomavirus-hpv-genotyping-attribution-and-methylation-pattern-analyses-of-squamous-intraepithelial-lesions
#13
Monica Molano, Suzanne M Garland, Alyssa M Cornall
Human papillomavirus (HPV) is a nearly ubiquitous infectious organism. It is estimated that 80% of sexually active adults will be exposed to anogenital HPVs in their lifetime, and detection of multiple genotypes in an anogenital sample is common. Detection and genotyping of HPV is usually performed by DNA testing, and less frequently by mRNA testing. HPV genotype testing and characterization of DNA methylation patterns of HPV-related lesions can provide important biological, epidemiological, and potentially relevant clinical information in individuals and populations...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344347/epigenetic-alterations-in-tramp-mice-epigenome-dna-methylation-profiling-using-medip-seq
#14
Wenji Li, Ying Huang, Davit Sargsyan, Tin Oo Khor, Yue Guo, Limin Shu, Anne Yuqing Yang, Chengyue Zhang, Ximena Paredes-Gonzalez, Michael Verzi, Ronald P Hart, Ah-Ng Kong
Purpose: We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods: Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq)...
2018: Cell & Bioscience
https://www.readbyqxmd.com/read/29344314/aberrant-expression-and-dna-methylation-of-lipid-metabolism-genes-in-pcos-a-new-insight-into-its-pathogenesis
#15
Jie-Xue Pan, Ya-Jing Tan, Fang-Fang Wang, Ning-Ning Hou, Yu-Qian Xiang, Jun-Yu Zhang, Ye Liu, Fan Qu, Qing Meng, Jian Xu, Jian-Zhong Sheng, He-Feng Huang
Background: Polycystic ovary syndrome (PCOS), whose etiology remains uncertain, is a highly heterogenous and genetically complex endocrine disorder. The aim of this study was to identify differentially expressed genes (DEGs) in granulosa cells (GCs) from PCOS patients and make epigenetic insights into the pathogenesis of PCOS. Results: Included in this study were 110 women with PCOS and 119 women with normal ovulatory cycles undergoing in vitro fertilization acting as the control group...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29344313/dna-methylation-as-a-predictor-of-fetal-alcohol-spectrum-disorder
#16
Alexandre A Lussier, Alexander M Morin, Julia L MacIsaac, Jenny Salmon, Joanne Weinberg, James N Reynolds, Paul Pavlidis, Albert E Chudley, Michael S Kobor
Background: Fetal alcohol spectrum disorder (FASD) is a developmental disorder that manifests through a range of cognitive, adaptive, physiological, and neurobiological deficits resulting from prenatal alcohol exposure. Although the North American prevalence is currently estimated at 2-5%, FASD has proven difficult to identify in the absence of the overt physical features characteristic of fetal alcohol syndrome. As interventions may have the greatest impact at an early age, accurate biomarkers are needed to identify children at risk for FASD...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29344260/dr2-blocker-thioridazine-a-promising-drug-for-ovarian-cancer-therapy
#17
Min Yong, Tinghe Yu, Si Tian, Shuaibin Liu, Jiao Xu, Jianguo Hu, Lina Hu
Dopamine receptor 2 (DR2) may be a biomarker for various types of cancer. Ovarian cancer cells overexpress DR2; therefore, blocking DR2 may be a novel treatment strategy for ovarian cancer. Thioridazine, a DR2 blocker, has antineoplastic activity in a variety of cancer cells. In view of the requirement for novel therapeutic agents in ovarian cancer, the present study aimed to determine the potential effects of thioridazine in vitro and in vivo. It was revealed that the DR2 blocker thioridazine induced cell death in a dose-dependent manner in ovarian cancer cells...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344216/hypermethylation-downregulates-p2x7-receptor-expression-in-astrocytoma
#18
Jing Liu, Ningning Li, Ruofan Sheng, Rui Wang, Zude Xu, Ying Mao, Yin Wang, Ying Liu
The present study investigated the altered expression of p2X purinoceptor (P2X7R) in astrocytoma. Reverse transcription-quantitative polymerase chain reaction and western blot analysis were used to determine the P2X7R expression in glioblastoma (GBM) and surrounding normal brain tissue. DNA methylation levels of P2X7R gene promoter in GBM were analyzed using a Sequenom MassARRAY® System. Immunohistochemistry (IHC) was used to detect the expression of P2X7R in astrocytoma at different malignancy grades, including diffuse astrocytoma, anaplastic astrocytoma and GBM...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343995/humanmethylation450k-array-identified-biomarkers-predict-tumour-recurrence-progression-at-initial-diagnosis-of-high-risk-non-muscle-invasive-bladder-cancer
#19
Mark O Kitchen, Richard T Bryan, Richard D Emes, Christopher J Luscombe, K K Cheng, Maurice P Zeegers, Nicholas D James, Lyndon M Gommersall, Anthony A Fryer
Background: High-risk non-muscle invasive bladder cancer (HR-NMIBC) is a clinically unpredictable disease. Despite clinical risk estimation tools, many patients are undertreated with intra-vesical therapies alone, whereas others may be over-treated with early radical surgery. Molecular biomarkers, particularly DNA methylation, have been reported as predictive of tumour/patient outcomes in numerous solid organ and haematologic malignancies; however, there are few reports in HR-NMIBC and none using genome-wide array assessment...
2018: Biomarkers in Cancer
https://www.readbyqxmd.com/read/29343972/targeting-histone-methyltransferase-and-demethylase-in-acute-myeloid-leukemia-therapy
#20
REVIEW
Germana Castelli, Elvira Pelosi, Ugo Testa
Acute myeloid leukemia (AML) is a clonal disorder of myeloid progenitors characterized by the acquisition of chromosomal abnormalities, somatic mutations, and epigenetic changes that determine a consistent degree of biological and clinical heterogeneity. Advances in genomic technologies have increasingly shown the complexity and heterogeneity of genetic and epigenetic alterations in AML. Among the genetic alterations occurring in AML, frequent are the genetic alterations at the level of various genes involved in the epigenetic control of the DNA methylome and histone methylome...
2018: OncoTargets and Therapy
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