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Epigenetic markers

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https://www.readbyqxmd.com/read/29035547/pharmacokinetics-and-pharmacodynamics-of-the-triterpenoid-ursolic-acid-in-regulating-the-anti-oxidant-anti-inflammatory-and-epigenetic-gene-responses-in-rat-leukocytes
#1
Chengyue Zhang, Chao Wang, Wenji Li, Renyi Wu, Yue Guo, David Cheng, Yuqing Yang, Ioannis P Androulakis, Ah-Ng Kong
The triterpenoid ursolic acid (UA) has been proposed as a potential cancer chemopreventive agent in many preclinical and clinical studies. In the present work, we aimed to characterize the pharmacokinetics (PK) of UA and to quantitatively assess the anti-oxidative and anti-inflammatory effects of UA, which are potentially linked to its chemopreventive efficacy. UA was administered intravenously (i.v., 20 mg/kg) or by oral gavage (100 mg/kg) to male Sprague-Dawley rats, and blood samples were collected at a series of designated time points...
October 16, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29035444/circulating-micrornas-expressions-as-genetic-biomarkers-in-pancreatic-cancer-patients-continuous-non-invasive-monitoring
#2
REVIEW
Mihai Sandesc, Anca Dinu, Alexandru F Rogobete, Ovidiu H Bedreag, Dorel Sandesc, Marius Papurica, Lavinia M Bratu, Silvius Negoita, Corina Vernic, Sonia E Popovici, Dan Corneci
BACKGROUND: Pancreatic cancer is one of the most important causes of death worldwide. The main cause is late detection. Also, an important factor playing a role in altering the clinical status of these patients is the lack of methods for the evaluation of therapeutic response. A marker that can be useful, both in early diagnosis and in evaluating and monitoring non-invasive treatment response, is analyzing the expression of miRNAs. In this paper, we summarize genetic and epigenetic aspects of miRNAs in pancreatic cancer...
October 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/29035356/circulating-tumour-dna-methylation-markers-for-diagnosis-and-prognosis-of-hepatocellular-carcinoma
#3
Rui-Hua Xu, Wei Wei, Michal Krawczyk, Wenqiu Wang, Huiyan Luo, Ken Flagg, Shaohua Yi, William Shi, Qingli Quan, Kang Li, Lianghong Zheng, Heng Zhang, Bennett A Caughey, Qi Zhao, Jiayi Hou, Runze Zhang, Yanxin Xu, Huimin Cai, Gen Li, Rui Hou, Zheng Zhong, Danni Lin, Xin Fu, Jie Zhu, Yaou Duan, Meixing Yu, Binwu Ying, Wengeng Zhang, Juan Wang, Edward Zhang, Charlotte Zhang, Oulan Li, Rongping Guo, Hannah Carter, Jian-Kang Zhu, Xiaoke Hao, Kang Zhang
An effective blood-based method for the diagnosis and prognosis of hepatocellular carcinoma (HCC) has not yet been developed. Circulating tumour DNA (ctDNA) carrying cancer-specific genetic and epigenetic aberrations may enable a noninvasive 'liquid biopsy' for diagnosis and monitoring of cancer. Here, we identified an HCC-specific methylation marker panel by comparing HCC tissue and normal blood leukocytes and showed that methylation profiles of HCC tumour DNA and matched plasma ctDNA are highly correlated...
October 9, 2017: Nature Materials
https://www.readbyqxmd.com/read/29034211/the-role-of-atrx-in-glioma-biology
#4
REVIEW
Pravanya Nandakumar, Alireza Mansouri, Sunit Das
The current World Health Organization classification of CNS tumors has made a tremendous leap from past editions by incorporating molecular criteria in addition to the pre-existing histological parameters. The revised version has had a particular impact on the classification of diffuse low-grade gliomas and their high-grade variants. The ATRX status is one of the critical markers that define the molecular classification of gliomas. In this review, we will first provide an overview of the role of ATRX in regular cell biology...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29030490/early-sex-dependent-differences-in-response-to-environmental-stress
#5
Serafin Pérez-Cerezales, Priscila Ramos-Ibeas, Dimitrios Rizos, Pat Lonergan, Pablo Bermejo-Alvarez, Alfonso Gutierrez-Adan
Developmental plasticity enables the appearance of long-term effects in offspring caused by exposure to environmental stressors during embryonic and foetal life. These long-term effects can be traced to pre- and post-implantation development, and in both cases the effects are usually sex-specific. During preimplantation development, male and female embryos exhibit an extensive transcriptional dimorphism mainly driven by incomplete X-chromosome inactivation. These early developmental stages are crucial for the establishment of epigenetic marks that will be conserved throughout development, making it a particularly susceptible period for the appearance of long-term epigenetic-based phenotypes...
October 13, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/29027325/ecological-plant-epigenetics-evidence-from-model-and-non-model-species-and-the-way-forward
#6
Christina L Richards, Conchita Alonso, Claude Becker, Oliver Bossdorf, Etienne Bucher, Maria Colomé-Tatché, Walter Durka, Jan Engelhardt, Bence Gaspar, Andreas Gogol-Döring, Ivo Grosse, Thomas P van Gurp, Katrin Heer, Ilkka Kronholm, Christian Lampei, Vít Latzel, Marie Mirouze, Lars Opgenoorth, Ovidiu Paun, Sonja J Prohaska, Stefan A Rensing, Peter F Stadler, Emiliano Trucchi, Kristian Ullrich, Koen J F Verhoeven
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation...
October 12, 2017: Ecology Letters
https://www.readbyqxmd.com/read/29027120/elucidating-the-preadipocyte-and-its-role-in-adipocyte-formation-a-comprehensive-review
#7
REVIEW
Christos N Sarantopoulos, Derek A Banyard, Mary E Ziegler, Beatrice Sun, Ashkaun Shaterian, Alan D Widgerow
Adipogenesis is a complex process whereby the multipotent adipose-derived stem cell is converted to a preadipocyte before terminal differentiation into the mature adipocyte. Preadipocytes are present throughout adult life, exhibit adipose fat depot specificity, and differentiate and proliferate from distinct progenitor cells. The mechanisms that promote preadipocyte commitment and maturation involve numerous protein factor regulators, epigenetic factors, and miRNAs. Detailed characterization of this process is currently an area of intense research and understanding the roles of preadipocytes in tissue plasticity may provide insight into novel approaches for tissue engineering, regenerative medicine and treating a host of obesity-related conditions...
October 13, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/29026078/deciphering-tal-effectors-for-5-methylcytosine-and-5-hydroxymethylcytosine-recognition
#8
Yuan Zhang, Lulu Liu, Shengjie Guo, Jinghui Song, Chenxu Zhu, Zongwei Yue, Wensheng Wei, Chengqi Yi
DNA recognition by transcription activator-like effector (TALE) proteins is mediated by tandem repeats that specify nucleotides through repeat-variable diresidues. These repeat-variable diresidues form direct and sequence-specific contacts to DNA bases; hence, TALE-DNA interaction is sensitive to DNA chemical modifications. Here we conduct a thorough investigation, covering all theoretical repeat-variable diresidue combinations, for their recognition capabilities for 5-methylcytosine and 5-hydroxymethylcytosine, two important epigenetic markers in higher eukaryotes...
October 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29024663/role-of-the-astroglial-glutamate-exchanger-xct-in-ventral-hippocampus-in-resilience-to-stress
#9
Carla Nasca, Benedetta Bigio, Danielle Zelli, Paolo de Angelis, Timothy Lau, Masahiro Okamoto, Hideyo Soya, Jason Ni, Lars Brichta, Paul Greengard, Rachael L Neve, Francis S Lee, Bruce S McEwen
We demonstrate that stress differentially regulates glutamate homeostasis in the dorsal and ventral hippocampus and identify a role for the astroglial xCT in ventral dentate gyrus (vDG) in stress and antidepressant responses. We provide an RNA-seq roadmap for the stress-sensitive vDG. The transcription factor REST binds to xCT promoter in co-occupancy with the epigenetic marker H3K27ac to regulate expression of xCT, which is also reduced in a genetic mouse model of inherent susceptibility to depressive-like behavior...
October 11, 2017: Neuron
https://www.readbyqxmd.com/read/29018782/comparison-of-blueberry-vaccinium-spp-and-vitamin-c-via-antioxidative-and-epigenetic-effects-in-human
#10
Minju Kim, Hyunkyung Na, Hiroshi Kasai, Kazuaki Kawai, Yun-Shan Li, Mihi Yang
BACKGROUND: Chemopreventive effects and the underlying mechanisms of blueberry (Vaccinium spp.) are not clearly understood in human. We hypothesized blueberry would work via antioxidative and epigenetic modulation, which is similar to vitamin C. METHODS: We performed a pilot and non-inferiority study in healthy young women (n = 12), who consumed vitamin C (1 g/d) or 240 mL of blueberry juice (total polyphenols 300 mg and proanthocyanidin 76 mg/d) for 2 weeks. We analyzed 8-hydroxydeoxyguanosine (8-OHdG) and malondialdehyde (MDA) levels in their urine, and global and specific DNA methylation at the NAD(P)H quinone oxidoreductase 1 (NQO1), methylenetetrahydrofolate reductase (MTHFR), or DNA methyltransferase 1 (DNMT1) genes in their blood...
September 2017: Journal of Cancer Prevention
https://www.readbyqxmd.com/read/29017567/impairment-of-igf2-gene-expression-in-prostate-cancer-is-triggered-by-epigenetic-dysregulation-of-igf2-dmr0-and-its-interaction-with-klf4
#11
Undraga Schagdarsurengin, Angela Lammert, Natalie Schunk, Diana Sheridan, Stefan Gattenloehner, Klaus Steger, Florian Wagenlehner, Temuujin Dansranjavin
BACKGROUND: Human cancer cells often exhibit impaired IGF2 expression and the underlying mechanisms are multifaceted and complex. Besides the well-known imprinting control region IGF2/H19-ICR, the involvement of a differentially methylated region in the promoter P0 of IGF2 gene (IGF2-DMR0) has been suggested. Here, we evaluate several mechanisms potentially leading to up- and/or down-regulation of IGF2 expression in prostate cancer and present a novel role of Kruppel-like factor 4 (KLF4) as a transcriptional regulator of IGF2 binding in IGF2-DMR0...
October 10, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/28994788/evaluating-primary-blast-effects-in-vitro
#12
Niall J Logan, Hari Arora, Claire A Higgins
Exposure to blast events can cause severe trauma to vital organs such as the lungs, ears, and brain. Understanding the mechanisms behind such blast-induced injuries is of great importance considering the recent trend towards the use of explosives in modern warfare and terrorist-related incidents. To fully understand blast-induced injury, we must first be able to replicate such blast events in a controlled environment using a reproducible method. In this technique using shock tube equipment, shock waves at a range of pressures can be propagated over live cells grown in 2D, and markers of cell viability can be immediately analyzed using a redox indicator assay and the fluorescent imaging of live and dead cells...
September 18, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28992396/alcohol-feeding-in-mice-promotes-colonic-hyperpermeability-and-changes-in-colonic-organoid-stem-cell-fate
#13
Christopher B Forsyth, Maliha Shaikh, Faraz Bishehsari, Garth Swanson, Robin M Voigt, Hemraj Dodiya, Peter Wilkinson, Beata Samelco, Shiwen Song, Ali Keshavarzian
BACKGROUND: Alcohol increases intestinal permeability to pro-inflammatory microbial products that promote liver disease, even after a period of sobriety. We sought to test the hypothesis that alcohol affects intestinal stem cells using an in vivo model and ex vivo organoids generated from jejunum and colon from mice fed chronic alcohol. METHODS: Mice were fed a control or an alcohol diet. Intestinal permeability, liver steatosis/inflammation, and stool short chain fatty acids (SCFA) were measured...
October 9, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28990796/homocysteine-levels-associate-with-subtle-changes-in-leukocyte-dna-methylation-an-epigenome-wide-analysis
#14
Pooja R Mandaviya, Dylan Aïssi, Koen F Dekkers, Roby Joehanes, Silva Kasela, Vinh Truong, Lisette Stolk, Diana van Heemst, M Arfan Ikram, Jan Lindemans, P Eline Slagboom, David-Alexandre Trégouët, André G Uitterlinden, Chen Wei, Phil Wells, France Gagnon, Marleen Mj van Greevenbroek, Bastiaan T Heijmans, Lili Milani, Pierre-Emmanuel Morange, Joyce Bj van Meurs, Sandra G Heil
AIM: Homocysteine (Hcy) is a sensitive marker of one-carbon metabolism. Higher Hcy levels have been associated with global DNA hypomethylation. We investigated the association between plasma Hcy and epigenome-wide DNA methylation in leukocytes. METHODS: Methylation was measured using Illumina 450 k arrays in 2035 individuals from six cohorts. Hcy-associated differentially methylated positions and regions were identified using meta-analysis. RESULTS: Three differentially methylated positions cg21607669 (SLC27A1), cg26382848 (AJUBA) and cg10701000 (KCNMA1) at chromosome 19, 14 and 10, respectively, were significantly associated with Hcy...
October 9, 2017: Epigenomics
https://www.readbyqxmd.com/read/28986789/establishment-of-the-crispr-cas9-system-for-targeted-gene-disruption-and-gene-tagging
#15
Eric Ehrke-Schulz, Maren Schiwon, Claudia Hagedorn, Anja Ehrhardt
CRISPR/Cas9 RNA-guided nucleases refashioned in vivo gene editing approaches for specific gene disruption, gene correction, or gene addition. Moreover, chimeric Cas9 proteins can be applied to direct fused cis-acting effector protein domains, enzymes, or fluorescent markers to DNA to target sequences to regulate gene expression, to introduce epigenetic changes, or to fluorescently label DNA sequences of interest. Here we show how to design guide RNAs for specific DNA targeting. We provide a protocol to customize the CRISPR/Cas9 machinery encoded on commercially available plasmids and present how to test the targeting efficiency of Cas9 with a target-specific gRNA by testing mutation induction efficiency...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984297/expression-patterns-of-class-i-histone-deacetylases-in-osteosarcoma-a-novel-prognostic-marker-with-potential-therapeutic-implications
#16
Parunya Chaiyawat, Dumnoensun Pruksakorn, Areerak Phanphaisarn, Pimpisa Teeyakasem, Jeerawan Klangjorhor, Jongkolnee Settakorn
Epigenetic aberrations are recognized as having pivotal roles in cancer etiology and progression. Histone deacetylases are among the most studied epigenetic modulators in various cancer types. The expression levels of class I histone deacetylase isoforms 1, 2, and 3 in patient-derived primary osteosarcoma cells (6 cases) was investigated, comparing them to normal bone graft-derived osteoblasts (6 cases) using the immunoblotting technique. Expression profiles of histone deacetylases in high-grade osteosarcoma tissue of 89 patients were examined and their association with clinicopathologic parameters and the patient survival was evaluated...
October 6, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28979686/methylation-mediated-silencing-of-mir-124-facilitates-chondrogenesis-by-targeting-nfatc1-under-hypoxic-conditions
#17
Ming Gong, Tangzhao Liang, Song Jin, Xuejun Dai, Zhiyu Zhou, Manman Gao, Sheng Huang, Jiaquan Luo, Lijin Zou, Xuenong Zou
Chondrogenic differentiation of mesenchymal stem cells is regulated by many different pathways. Recent studies have established that hypoxia and epigenetic alterations potently affect expression of chondrogenesis marker genes. Sox9 is generally regarded as a master regulator of chondrogenesis and microRNA-124 (miRNA-124) regulates gene expression in murine bone marrow-derived mesenchymal stem cells. Therefore, in this study we investigated whether epigenetic regulation of miRNA-124 could affect the expression of Sox9 and thereby regulate chondrogenesis...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28978863/myeloid-neoplasms-in-the-world-health-organization-2016-classification
#18
Norio Asou
In the 2016 revision of the World Health Organization (WHO) classification, the categories of myeloid neoplasms have not been revised significantly from the 2008 fourth edition. However, recent discovery of molecular abnormalities provides a new perspective regarding the diagnostic and prognostic markers. In myeloproliferative neoplasms, the identification of CALR gene mutation, in addition to the JAK2 and MPL mutations, has impacted the diagnostic criteria. In myelodysplastic syndromes and acute myeloid leukemia, in addition to alterations in the transcription factors and signal transduction pathways, discovery of gene mutations in the epigenetic regulators that are involved in DNA methylation, histone modification, cohesin complex, and RNA splicing, by comprehensive genetic analyses, has improved our understanding of the pathobiology of these diseases...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28978636/ezh2-modifies-sunitinib-resistance-in-renal-cell-carcinoma-by-kinome-reprogramming
#19
Remi Adelaiye-Ogala, Justin Budka, Nur P Damayanti, Justine Arrington, Mary W Ferris, Chuan-Chih Hsu, Sreenivasulu Chintala, Ashley R Orillion, Kiersten Marie Miles, Li Shen, May Elbanna, Eric Ciamporcero, Sreevani Arisa, Piergiorgio Pettazzoni, Giulio F Draetta, Mukund Seshadri, Bradley A Hancock, Milan Radovich, Janaiah Kota, Michael Buck, Heike Keilhack, Brian P McCarthy, Scott A Persohn, Paul R Territo, Yong Zang, Joseph Irudayaraj, Andy W Tao, Peter Hollenhorst, Roberto Pili
Acquired and intrinsic resistance to receptor tyrosine kinase inhibitors (RTKi) represent a major hurdle in improving the management of clear cell renal cell carcinoma (ccRCC). Recent reports suggest that drug resistance is driven by tumor adaptation via epigenetic mechanisms that activate alternative survival pathways. The histone methyl transferase EZH2 is frequently altered in many cancers including ccRCC. To evaluate its role in ccRCC resistance to RTKi, we established and characterized a spontaneously metastatic, patient-derived xenograft (PDX) model that is intrinsically resistant to the RTKI sunitinib but not to the VEGF therapeutic antibody bevacizumab...
October 4, 2017: Cancer Research
https://www.readbyqxmd.com/read/28978033/mysm1-2a-dub-is-an-epigenetic-regulator-in-human-melanoma-and-contributes-to-tumor-cell-growth
#20
Christina Wilms, Carsten M Kroeger, Adelheid V Hainzl, Ishani Banik, Clara Bruno, Ioanna Krikki, Vida Farsam, Meinhard Wlaschek, Martina V Gatzka
Histone modifying enzymes, such as histone deacetylases (HDACs) and polycomb repressive complex (PRC) components, have been implicated in regulating tumor growth, epithelial-mesenchymal transition, tumor stem cell maintenance, or repression of tumor suppressor genes - and may be promising targets for combination therapies of melanoma and other cancers. According to recent findings, the histone H2A deubiquitinase 2A-DUB/Mysm1 interacts with the p53-axis in hematopoiesis and tissue differentiation in mice, in part by modulating DNA-damage responses in stem cell and progenitor compartments...
September 15, 2017: Oncotarget
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