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Epigenetic markers

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https://www.readbyqxmd.com/read/27922854/identification-of-hiv-infection-related-dna-methylation-sites-and-advanced-epigenetic-aging-in-hiv-treatment-na%C3%A3-ve-u-s-veterans
#1
Kristin N Nelson, Qin Hui, David Rimland, Ke Xu, Matthew S Freiberg, Amy C Justice, Vincent C Marconi, Yan V Sun
OBJECTIVE: HIV-positive individuals are at higher risk than healthy persons for aging-related diseases, including myocardial infarction and non-AIDS defining cancers. Recent evidence suggests that HIV infection may modulate changes in the host cell epigenome, and these changes represent a potential mechanism through which HIV infection accelerates aging. We assessed the difference in DNAm age, an aging marker involving multiple age-related CpG sites, among antiretroviral treatment (ART) naïve HIV-positive and HIV-negative individuals in a cohort of veterans from the Veterans Aging Cohort Study (VACS)...
December 5, 2016: AIDS
https://www.readbyqxmd.com/read/27921030/describing-the-stem-cell-potency-the-various-methods-of-functional-assessment-and-in-silico-diagnostics
#2
REVIEW
Vimal K Singh, Abhishek Saini, Manisha Kalsan, Neeraj Kumar, Ramesh Chandra
Stem cells are defined by their capabilities to self-renew and give rise to various types of differentiated cells depending on their potency. They are classified as pluripotent, multipotent, and unipotent as demonstrated through their potential to generate the variety of cell lineages. While pluripotent stem cells may give rise to all types of cells in an organism, Multipotent and Unipotent stem cells remain restricted to the particular tissue or lineages. The potency of these stem cells can be defined by using a number of functional assays along with the evaluation of various molecular markers...
2016: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/27918480/cord-blood-dna-methylation-biomarkers-for-predicting-neurodevelopmental-outcomes
#3
REVIEW
Nicolette A Hodyl, Claire T Roberts, Tina Bianco-Miotto
Adverse environmental exposures in pregnancy can significantly alter the development of the fetus resulting in impaired child neurodevelopment. Such exposures can lead to epigenetic alterations like DNA methylation, which may be a marker of poor cognitive, motor and behavioral outcomes in the infant. Here we review studies that have assessed DNA methylation in cord blood following maternal exposures that may impact neurodevelopment of the child. We also highlight some key studies to illustrate the potential for DNA methylation to successfully identify infants at risk for poor outcomes...
December 3, 2016: Genes
https://www.readbyqxmd.com/read/27915480/genetic-and-epigenetic-alterations-in-bladder-cancer
#4
REVIEW
Hong-Tao Li, Christopher E Duymich, Daniel J Weisenberger, Gangning Liang
Bladder cancer is one of the most common cancers worldwide, with a high rate of recurrence and poor outcomes as a result of relapse. Bladder cancer patients require lifelong invasive monitoring and treatment, making bladder cancer one of the most expensive malignancies. Lines of evidence increasingly point to distinct genetic and epigenetic alteration patterns in bladder cancer, even between the different stages and grades of disease. In addition, genetic and epigenetic alterations have been demonstrated to play important roles during bladder tumorigenesis...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27913608/the-clinical-utility-of-circulating-neuroendocrine-gene-transcript-analysis-in-well-differentiated-paragangliomas-and-pheochromocytomas
#5
M Pęczkowska, J Cwikla, M Kidd, A Lewczuk, A Kolasinska-Ćwikła, D Niec, I Michałowska, A Prejbisz, A Januszewicz, J Chiarelli, L Bodei, I Modlin
CONTEXT: Paragangliomas and pheochromocytomas (PPGLs) exhibit variable malignancy, which is difficult to determine by histopathology, amine measurements or tissue genetic analyses. OBJECTIVE: To evaluate whether a 51-neuroendocrine gene blood analysis has clinical utility as a diagnostic and prognostic marker. DESIGN: Prospective cohort study. Well-differentiated PPGLs (n = 32), metastatic (n = 4); SDHx mutation (n = 25); 12 biochemically active, Lanreotide treated (n = 4)...
February 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/27913493/novel-agents-in-follicular-lymphoma-choosing-the-best-target
#6
Laurie H Sehn
Outcomes in patients with follicular lymphoma (FL) have improved dramatically over the last decade. However, novel agents are greatly needed for those who exhibit treatment resistance, in order to minimize lifelong toxicity and to enable combinations that may allow us to achieve the elusive goal of cure. Biological advances have led to the discovery of a large number of potential therapeutic targets and the development of a plethora of novel agents designed to exploit these processes. Possible targets include tumor cell surface markers, key components of intracellular pathways and epigenetic mechanisms, and reactive cells of the microenvironment...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27912315/genetics-of-infectious-and-inflammatory-diseases-overlapping-discoveries-from-association-and-exome-sequencing-studies
#7
David Langlais, Nassima Fodil, Philippe Gros
Genome technologies have defined a complex genetic architecture in major infectious, inflammatory, and autoimmune disorders. High density marker arrays and Immunochips have powered genome-wide association studies (GWAS) that have mapped nearly 450 genetic risk loci in 22 major inflammatory diseases, including a core of common genes that play a central role in pathological inflammation. Whole-exome and whole-genome sequencing have identified more than 265 genes in which mutations cause primary immunodeficiencies and rare forms of severe inflammatory bowel disease...
December 1, 2016: Annual Review of Immunology
https://www.readbyqxmd.com/read/27909741/the-role-of-epigenetic-modifiers-in-extended-cultures-of-functional-hepatocyte-like-cells-derived-from-human-neonatal-mesenchymal-stem-cells
#8
M Cipriano, J C Correia, S P Camões, N G Oliveira, P Cruz, H Cruz, M Castro, J L Ruas, J M Santos, J P Miranda
The development of predictive in vitro stem cell-derived hepatic models for toxicological drug screening is an increasingly important topic. Herein, umbilical cord tissue-derived mesenchymal stem cells (hnMSCs) underwent hepatic differentiation using an optimized three-step core protocol of 24 days that mimicked liver embryogenesis with further exposure to epigenetic markers, namely the histone deacetylase inhibitor trichostatin A (TSA), the cytidine analogue 5-azacytidine (5-AZA) and dimethyl sulfoxide (DMSO)...
December 1, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27903268/long-term-outdoor-air-pollution-and-dna-methylation-in-circulating-monocytes-results-from-the-multi-ethnic-study-of-atherosclerosis-mesa
#9
Gloria C Chi, Yongmei Liu, James W MacDonald, R Graham Barr, Kathleen M Donohue, Mark D Hensley, Lifang Hou, Charles E McCall, Lindsay M Reynolds, David S Siscovick, Joel D Kaufman
BACKGROUND: DNA methylation may mediate effects of air pollution on cardiovascular disease. The association between long-term air pollution exposure and DNA methylation in monocytes, which are central to atherosclerosis, has not been studied. We investigated the association between long-term ambient air pollution exposure and DNA methylation (candidate sites and global) in monocytes of adults (aged ≥55). METHODS: One-year average ambient fine particulate matter (PM2...
December 1, 2016: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/27903230/glucocorticoid-receptor-interacting-co-regulators-putative-candidates-for-future-drug-targeting-therapy
#10
Alessia Di Silvestre, Marianna Lucafò, Sara De Iudicibus, Alessandro Ventura, Stefano Martelossi, Gabriele Stocco, Giuliana Decorti
Glucocorticoids (GCs) are largely used in different inflammatory, autoimmune and proliferative diseases. To date their mechanism of action is not completely clear and more studies are necessary, in particular to explain the great interindividual variability in clinical response. In this panorama the glucocorticoid receptor (GR) has an important role: in fact it regulates the pharmacological response thanks to the capability to interact with different molecules (DNA, RNA, ncRNA and proteins) that are known to influence its activity...
November 29, 2016: Mini Reviews in Medicinal Chemistry
https://www.readbyqxmd.com/read/27899259/overexpression-of-the-long-non-coding-rna-spry4-it1-promotes-tumor-cell-proliferation-and-invasion-by-activating-ezh2-in-hepatocellular-carcinoma
#11
Meng Zhou, Xiao-Yu Zhang, Xi Yu
BACKGROUND: Increasing evidences have demonstrated that the dysregulation of long non-coding RNAs (lncRNAs) may act as an important role in tumor progression. The long non-coding RNA SPRY4 intronic transcript 1 (SPRY4-IT1) has been reported in some cancer including regulating cell growth, differentiation, apoptosis, and cancer progression. However, the expression and function of SPRY4-IT1 in the progression of hepatocellular carcinoma (HCC) remain largely unknown. METHODS: The lncRNA SPRY4-IT1 was detected by quantitative real time PCR (qRT-PCR) in HCC cell lines, CCK8 cell proliferation and transwell invasion assays were performed to detect the GC cell proliferation and invasion abilities...
November 26, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27898666/algorithm-optimization-in-methylation-detection-with-multiple-rt-qpcr
#12
Lele Song, Yuemin Li, Jia Jia, Guangpeng Zhou, Jianming Wang, Qian Kang, Peng Jin, Jianqiu Sheng, Guoxiang Cai, Sanjun Cai, Xiaoliang Han
Epigenetic markers based on differential methylation of DNA sequences are used in cancer screening and diagnostics. Detection of abnormal methylation at specific loci by real-time quantitative polymerase chain reaction (RT-qPCR) has been developed to enable high-throughput cancer screening. For tests that combine the results of multiple PCR replicates into a single reportable result, both individual PCR cutoff and weighting of the individual PCR result are essential to test outcome. In this opportunistic screening study, we tested samples from 1133 patients using the triplicate Epi proColon assay with various algorithms and compared it with the newly developed single replicate SensiColon assay that measures methylation status of the same SEPT9 gene sequence...
2016: PloS One
https://www.readbyqxmd.com/read/27896998/methyldmv-simultaneous-detection-of-differential-dna-methylation-and-variability-with-confounder-adjustment
#13
Pei Fen Kuan, Junyan Song, Shuyao He
DNA methylation has emerged as promising epigenetic markers for disease diagnosis. Both the differential mean (DM) and differential variability (DV) in methylation have been shown to contribute to transcriptional aberration and disease pathogenesis. The presence of confounding factors in large scale EWAS may affect the methylation values and hamper accurate marker discovery. In this paper, we propose a exible framework called methylDMV which allows for confounding factors adjustment and enables simultaneous characterization and identification of CpGs exhibiting DM only, DV only and both DM and DV...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896277/prediction-of-bacillus-calmette-guerin-response-in-patients-with-bladder-cancer-after-transurethral-resection-of-bladder-tumor-by-using-genetic-variation-based-on-genomic-studies
#14
REVIEW
Ning Zhang, Guangliang Jiang, Xu Liu, Rong Na, Xiang Wang, Jianfeng Xu
Purpose. We aimed to comprehensively review contemporary literature on genetic and epigenetic biomarkers associated with the prediction of Bacillus Calmette-Guerin (BCG) response after the transurethral resection of a bladder tumor and to discuss the application of these biomarkers in precision cancer care for bladder cancer. Method. We performed a systematic review of published literatures in the databases PubMed and Embase by using the following key words: bladder cancer, BCG, gene, and methylation. Studies associated with cell lines, animal models, and muscle invasive bladder cancer were excluded...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27889662/pediatric-pineal-germinomas-epigenetic-and-genomic-approach
#15
Monserrat Pérez-Ramírez, Alejo Justino Hernández-Jiménez, Armando Guerrero-Guerrero, Alicia Georgina Siordia-Reyes, Marta Elena Hernández-Caballero, Antonio García-Méndez, Fernando Chico-Ponce de León, Fabio Abdel Salamanca-Gómez, Normand García-Hernández
OBJECTIVE: We identify and correlate chromosomal alterations, methylation patterns and gene expression in pediatric pineal germinomas. METHODS: CGH microarray, methylation and gene expression were performed through the Agilent platform. The results were analyzed with MatLab software, MapViewer, DAVID, GeneCards and Hippie. RESULTS: Amplifications were found in 1q24.2, 1q31.3, 2p11.2, 3p22.2, 7p13, 7p15.2, 8p22, 12p13.2, 14q24.3 y 22q12; and deletions were found in 1q21...
November 19, 2016: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/27887750/chronic-kidney-disease
#16
REVIEW
Angela C Webster, Evi V Nagler, Rachael L Morton, Philip Masson
The definition and classification of chronic kidney disease (CKD) have evolved over time, but current international guidelines define this condition as decreased kidney function shown by glomerular filtration rate (GFR) of less than 60 mL/min per 1·73 m(2), or markers of kidney damage, or both, of at least 3 months duration, regardless of the underlying cause. Diabetes and hypertension are the main causes of CKD in all high-income and middle-income countries, and also in many low-income countries. Incidence, prevalence, and progression of CKD also vary within countries by ethnicity and social determinants of health, possibly through epigenetic influence...
November 22, 2016: Lancet
https://www.readbyqxmd.com/read/27885689/pathogenesis-and-diagnosis-of-placental-disorders-is-related-to-abnormal-methylation-at-promoters-of-placental-vascularization-mediating-genes
#17
Beenish Rahat, Rauf Ahmad Najar, Abid Hamid, Rashmi Bagga, Jyotdeep Kaur
OBJECTIVES: To investigate the role of methylation levels at promoter regions of placental vascularization genes (VEGF, EGFR and c-jun) in pathogenesis and diagnosis of placental disorders. METHODS: We analyzed DNA and histone methylation at promoters of VEGF, EGFR and c-jun via methylation-sensitive high resolution melting and chromatin immunoprecipitation assay in pregnant women with normal pregnancy in first, second and third trimester (n = 30 in each group) and pregnant women with pregnancy complicated with preeclampsia (n = 30) and hydatidiform mole (n = 15)...
November 24, 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27884142/dna-methylation-patterns-associated-with-oxidative-stress-in-an-ageing-population
#18
Åsa K Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind, Erik Ingelsson
BACKGROUND: Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease...
November 25, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27883060/environmental-intervention-as-a-therapy-for-adverse-programming-by-ancestral-stress
#19
J Keiko McCreary, Zachary T Erickson, YongXin Hao, Yaroslav Ilnytskyy, Igor Kovalchuk, Gerlinde A S Metz
Ancestral stress can program stress sensitivity and health trajectories across multiple generations. While ancestral stress is uncontrollable to the filial generations, it is critical to identify therapies that overcome transgenerational programming. Here we report that prenatal stress in rats generates a transgenerationally heritable endocrine and epigenetic footprint and elevated stress sensitivity which can be alleviated by beneficial experiences in later life. Ancestral stress led to downregulated glucocorticoid receptor and prefrontal cortex neuronal densities along with precocious development of anxiety-like behaviours...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27882781/age-related-epigenetic-drift-and-phenotypic-plasticity-loss-implications-in-prevention-of-age-related-human-diseases
#20
Yuanyuan Li, Trygve O Tollefsbol
Aging is considered as one of the most important developmental processes in organisms and is closely associated with global deteriorations of epigenetic markers such as aberrant methylomic patterns. This altered epigenomic state, referred to 'epigenetic drift', reflects deficient maintenance of epigenetic marks and contributes to impaired cellular and molecular functions in aged cells. Epigenetic drift-induced abnormal changes during aging are scantily repaired by epigenetic modulators. This inflexibility in the aged epigenome may lead to an age-related decline in phenotypic plasticity at the cellular and molecular levels due to epigenetic drift...
November 24, 2016: Epigenomics
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