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Epigenetic markers

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https://www.readbyqxmd.com/read/28339768/the-transcription-factor-olig2-is-important-for-the-biology-of-diffuse-intrinsic-pontine-gliomas
#1
Jane L Anderson, Ranjithmenon Muraleedharan, Nicole Oatman, Amanda Klotter, Satarupa Sengupta, Ronald R Waclaw, Jianqiang Wu, Rachid Drissi, Lili Miles, Eric H Raabe, Matthew L Weirauch, Maryam Fouladi, Lionel M Chow, Lindsey Hoffman, Mariko DeWire, Biplab Dasgupta
Background.: Diffuse intrinsic pontine glioma (DIPG) is a high-grade brainstem glioma of children with dismal prognosis. There is no single unifying model about the cell of origin of DIPGs. Proliferating cells in the developing human and mouse pons, the site of DIPGs, express neural stem/progenitor cell (NPC) markers, including Sox2, nestin, vimentin, Olig2, and glial fibrillary acidic protein, in an overlapping and non-overlapping manner, suggesting progenitor cell heterogeneity in the pons...
February 23, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28337379/long-intergenic-non-coding-rna-00152-promotes-renal-cell-carcinoma-progression-by-epigenetically-suppressing-p16-and-negatively-regulates-mir-205
#2
Yongjun Wang, Jianzhen Liu, Hongzhong Bai, Yi Dang, Pei Lv, Shucai Wu
Long non-coding RNAs (lncRNAs) have been reported to play important roles in the tumorigenesis and development of several human cancers. Long intergenic non-coding RNA 152 (LINC00152) is significantly up-regulated in some solid tumors. However, the role of LINC00152 in the pathogenesis and development of renal cell carcinoma (RCC) remains largely unclear. In the study, we showed that LINC00152 expression was up-regulated in RCC tissues compared with adjacent normal tissues and revealed that LINC00152 expression was positively correlated with lymph node metastasis, higher TNM stage, and poor over survival (OS) time in RCC patients...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28335509/novel-diagnostic-and-predictive-biomarkers-in-pancreatic-adenocarcinoma
#3
REVIEW
John C Chang, Madappa Kundranda
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease for a multitude of reasons including very late diagnosis. This in part is due to the lack of understanding of the biological behavior of PDAC and the ineffective screening for this disease. Significant efforts have been dedicated to finding the appropriate serum and imaging biomarkers to help early detection and predict response to treatment of PDAC. Carbohydrate antigen 19-9 (CA 19-9) has been the most validated serum marker and has the highest positive predictive value as a stand-alone marker...
March 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28334849/icf-specific-dnmt3b-dysfunction-interferes-with-intragenic-regulation-of-mrna-transcription-and-alternative-splicing
#4
Sole Gatto, Miriam Gagliardi, Monica Franzese, Sylwia Leppert, Mariarosaria Papa, Marco Cammisa, Giacomo Grillo, Guillame Velasco, Claire Francastel, Shir Toubiana, Maurizio D'Esposito, Claudia Angelini, Maria R Matarazzo
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown...
March 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334074/genome-wide-analysis-reveals-that-exon-methylation-facilitates-its-selective-usage-in-the-human-transcriptome
#5
Shengli Li, Jiwei Zhang, Shenglin Huang, Xianghuo He
DNA methylation, especially in promoter regions, is a well-characterized epigenetic marker related to gene expression regulation in eukaryotes. However, the role of intragenic DNA methylation in the usage of corresponding exons still remains elusive. In this study, we described the DNA methylome across 10 human tissues. The human genome showed both conserved and varied methylation levels among these tissues. We found that the methylation densities in promoters and first exons were negatively correlated with the corresponding gene expression level...
February 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28332209/quantitation-and-mapping-of-the-epigenetic-marker-5-hydroxymethylcytosine
#6
Ying Qing, Zhiqi Tian, Ying Bi, Yongyao Wang, Jiangang Long, Chun-Xiao Song, Jiajie Diao
We here review primary methods used in quantifying and mapping 5-hydroxymethylcytosine (5hmC), including global quantification, restriction enzyme-based detection, and methods involving DNA-enrichment strategies and the genome-wide sequencing of 5hmC. As discovered in the mammalian genome in 2009, 5hmC, oxidized from 5-methylcytosine (5mC) by ten-eleven translocation (TET) dioxygenases, is increasingly being recognized as a biomarker in biological processes from development to pathogenesis, as its various detection methods have shown...
March 23, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28331559/tumor-suppressor-genes-in-familial-adenomatous-polyposis
#7
REVIEW
Nahal Eshghifar, Naser Farrokhi, Tahereh Naji, Mohammadreza Zali
Colorectal cancer (CRC) is mostly due to a series of genetic alterations that are being greatly under the influence of the environmental factors. These changes, mutational or epigenetic modifications at transcriptional forefront and/or post-transcriptional effects via miRNAs, include inactivation and the conversion of proto-oncogene to oncogenes, and/or inactivation of tumor suppressor genes (TSG). Here, a thorough review was carried out on the role of TSGs with the focus on the APC as the master regulator, mutated genes and mal-/dysfunctional pathways that lead to one type of hereditary form of the CRC; namely familial adenomatous polyposis (FAP)...
2017: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28330124/somaclonal-variations-and-their-applications-in-horticultural-crops-improvement
#8
REVIEW
Hare Krishna, Mahdi Alizadeh, Dhurendra Singh, Udayvir Singh, Nitesh Chauhan, Maliheh Eftekhari, Radha Kishan Sadh
The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28326594/hypoacetylation-of-acetyl-histone-h3-h3k9ac-as-marker-of-poor-prognosis-in-oral-cancer
#9
Liana Preto Webber, Vivian Petersen Wagner, Marina Curra, Pablo Agustin Vargas, Luise Meurer, Vinícius Coelho Carrard, Cristiane Helena Squarize, Rogério Moraes Castilho, Manoela Domingues Martins
AIMS: Epigenetics refers to changes in cell characteristics that occur independently of modifications to the DNA sequence. Oral carcinogenesis is influenced by modifications in epigenetic mechanisms, including changes in histones, which are proteins that support chromatin remodeling for the dynamic regulation of gene expression and silencing. The dysregulation of histone acetylation can lead to the uncontrolled activity of different genes, thereby triggering events associated with malignant transformation...
March 22, 2017: Histopathology
https://www.readbyqxmd.com/read/28320828/malaria-epigenetics
#10
Alfred Cortés, Kirk W Deitsch
Organisms with identical genome sequences can show substantial differences in their phenotypes owing to epigenetic changes that result in different use of their genes. Epigenetic regulation of gene expression plays a key role in the control of several fundamental processes in the biology of malaria parasites, including antigenic variation and sexual differentiation. Some of the histone modifications and chromatin-modifying enzymes that control the epigenetic states of malaria genes have been characterized, and their functions are beginning to be unraveled...
March 20, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28319413/aberrant-promoter-hypermethylation-of-p16-survivin-and-retinoblastoma-in-gastric-cancer
#11
L Guo, C Huang, Q J Ji
BACKGROUND: Gastric cancer is common and can be found throughout the world. Notoriously like other cancers, gastric cancer is a consequence of cellular regulation disorder. Epigenetics, including many oncogenes or tumour suppressor genes, can provide some clues for this kind of disorder. DNA methylation, especially promoter methylation, which causes the silence/decrease of tumour related genes, has become a focus in various tumour types. The aim of this study was to investigate promoter methylation of certain genes: p16, survivin, retinoblastoma (Rb), all of which have been regarded as genes related to gastric cancer...
2017: Bratislavské Lekárske Listy
https://www.readbyqxmd.com/read/28316600/methylation-of-foxp3-tsdr-underlies-the-impaired-suppressive-function-of-tregs-from-long-term-belatacept-treated-kidney-transplant-patients
#12
Evelyn Katy Alvarez Salazar, Arimelek Cortés-Hernández, Germán Rodrigo Alemán-Muench, Josefina Alberú, Jesús R Rodríguez-Aguilera, Félix Recillas-Targa, Victoria Chagoya de Sánchez, Eric Cuevas, Eduardo Mancilla-Urrea, María Pérez García, Guillermo Mondragón-Ramírez, Mario Vilatobá, Ian Bostock, Erick Hernández-Méndez, David De Rungs, Eduardo A García-Zepeda, Gloria Soldevila
Regulatory T cells (Tregs) are considered key players in the prevention of allograft rejection in transplanted patients. Belatacept (BLT) is an effective alternative to calcineurin inhibitors that appears to preserve graft survival and function; however, the impact of this drug in the homeostasis of Tregs in transplanted patients remains controversial. Here, we analyzed the phenotype, function, and the epigenetic status of the Treg-specific demethylated region (TSDR) in FOXP3 of circulating Tregs from long-term kidney transplant patients under BLT or Cyclosporine A treatment...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28315825/effects-of-florida-red-tides-on-histone-variant-expression-and-dna-methylation-in-the-eastern-oyster-crassostrea-virginica
#13
Rodrigo Gonzalez-Romero, Victoria Suarez-Ulloa, Javier Rodriguez-Casariego, Daniel Garcia-Souto, Gabriel Diaz, Abraham Smith, Juan Jose Pasantes, Gary Rand, Jose M Eirin-Lopez
Massive algal proliferations known as Harmful Algal Blooms (HABs) represent one of the most important threats to coastal areas. Among them, the so-called Florida Red Tides (FRTs, caused by blooms of the dinoflagellate Karenia brevis and associated brevetoxins) are particularly detrimental in the southeastern U.S., causing high mortality rates and annual losses in excess of $40 million. The ability of marine organisms to cope with environmental stressors (including those produced during HABs) is influenced by genetic and epigenetic mechanisms, the latter resulting in phenotypic changes caused by heritable modifications in gene expression, without involving changes in the genetic (DNA) sequence...
March 7, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28314271/identification-of-methylation-profiles-of-cancer-related-genes-in-circulating-tumor-cells-population
#14
Anna Lyberopoulou, Michail Galanopoulos, Gerasimos Aravantinos, George E Theodoropoulos, Evangelos Marinos, Efstathios P Efstathopoulos, Maria Gazouli
BACKGROUND: We performed an epigenetic analysis of the first exon of the hVIM gene and the SFRP2 in circulating tumor cells (CTCs) and correlation with the corresponding primary colorectal cancer (CRC) tissue. PATIENTS AND METHODS: CTCs detection in 52 colorectal cancer patients was managed by a multi-marker immunomagnetic method with the use of quantum dots (QDs). To determine methylation levels we used high-resolution melting (HRM) technology. RESULTS: In the case of VIM we found 76...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28302141/dna-hypomethylation-and-aberrant-expression-of-the-human-endogenous-retrovirus-ervwe1-syncytin-1-in-seminomas
#15
Martina Benešová, Kateřina Trejbalová, Denisa Kovářová, Zdenka Vernerová, Tomáš Hron, Dana Kučerová, Jiří Hejnar
BACKGROUND: Syncytin-1 and 2, human fusogenic glycoproteins encoded by the env genes of the endogenous retroviral loci ERVWE1 and ERVFRDE1, respectively, contribute to the differentiation of multinucleated syncytiotrophoblast in chorionic villi. In non-trophoblastic cells, however, the expression of syncytins has to be suppressed to avoid potential pathogenic effects. Previously, we have shown that the transcriptional suppression of ERVWE1 promoter is controlled epigenetically by DNA methylation and chromatin modifications...
March 17, 2017: Retrovirology
https://www.readbyqxmd.com/read/28295500/sperm-dna-methylation-of-h19-imprinted-gene-and-male-infertility
#16
F Nasri, B Gharesi-Fard, B Namavar Jahromi, M A Farazi-Fard, M Banaei, M Davari, S Ebrahimi, Z Anvar
Infertility affects up to 15% of reproductive-aged couples worldwide, with male factor being detected in 40%-50% of the cases. Proper sperm production is associated with the establishment of appropriate epigenetic marks in developing germ cells. Several studies have demonstrated the association between abnormal spermatogenesis and epigenetic disturbances with the major focus on DNA methylation. Imprinted genes are expressed in a parent-of-origin-specific manner, and the role of their DNA methylation in proper spermatogenesis has been documented recently...
March 15, 2017: Andrologia
https://www.readbyqxmd.com/read/28292683/lower-inflammatory-markers-in-women-with-antenatal-depression-brings-the-m1-m2-balance-into-focus-from-a-new-direction
#17
Åsa Edvinsson, Emma Bränn, Charlotte Hellgren, Eva Freyhult, Richard White, Masood Kamali-Moghaddam, Jocelien Olivier, Jonas Bergquist, Adrian E Boström, Helgi B Schiöth, Alkistis Skalkidou, Janet L Cunningham, Inger Sundström-Poromaa
BACKGROUND: Antenatal depression and use of serotonin reuptake inhibitors (SSRI) in pregnancy have both been associated with an increased risk of poor pregnancy outcomes, such as preterm birth and impaired fetal growth. While the underlying biological pathways for these complications are poorly understood, it has been hypothesized that inflammation may be a common physiological pathway. The aim of the present study was to assess peripheral inflammatory markers in healthy women, women with antenatal depression, and in women using SSRI during pregnancy...
February 28, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28292214/adamtsl5-and-cdh11-putative-epigenetic-markers-for-therapeutic-resistance-in-acute-lymphoblastic-leukemia
#18
Maha Abdullah, Chee Wei Choo, Hamidah Alias, Eni Juraidah Abdul Rahman, Hishamshah Mohd Ibrahim, Rahman Jamal, Noor Hamidah Hussin
BACKGROUND AND OBJECTIVES: DNA hypermethylation has been linked to poor treatment outcome in childhood acute lymphoblastic leukemia (ALL). Genes differentially methylated in the chemoresponsive pre-B-ALL compared to chemoresistant pre-B-ALL cases provide potential prognostic markers. METHODS: DNA methylation profiles of five B-ALL childhood patients who achieved morphological complete remission (chemoresponsive) and five B-ALL patients who did not (chemoresistant) after induction treatments as well as four normal controls were compared on 27 000 CpG sites microarray chips...
March 15, 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28291773/comprehensive-molecular-exploration-identified-promoter-dna-methylation-of-the-crbp1-gene-as-a-determinant-of-radiation-sensitivity-in-rectal-cancer
#19
K Yokoi, K Yamashita, S Ishii, T Tanaka, N Nishizawa, A Tsutsui, H Miura, H Katoh, T Yamanashi, M Naito, T Sato, T Nakamura, M Watanabe
BACKGROUND: Neoadjuvant chemoradiotherapy (NCRT) for advanced rectal cancer (RC) is a well-evidenced therapy; however, some RC patients have no therapeutic response. Patient selection for NCRT so that non-responsive patients are excluded has been subjective. To date, no molecular markers indicating radiation sensitivity have been reported. METHODS: We irradiated six colorectal cancer (CRC) cell lines and identified HCT116 cells as radiation-sensitive and HCT15 and DLD-1 cells as radiation resistant...
March 14, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28288848/bcl11b-mediated-epigenetic-repression-is-a-crucial-target-for-histone-deacetylase-inhibitors-in-cutaneous-t-cell-lymphoma
#20
Wenjing Fu, Shengguo Yi, Lei Qiu, Jingru Sun, Ping Tu, Yang Wang
The treatment options for advanced cutaneous T-cell lymphoma (CTCL) are limited due to its unclear pathogenesis. HDAC inhibitors (HDACi) are recently developed therapeutics approved for refractory CTCL. However, the response rate is relatively low and unpredictable. Previously, we discovered that BCL11B, a key T-cell development regulator, was aberrantly overexpressed in mycosis fungoides (MF), the most common CTCL, as compared with benign inflammatory skin. In the current study, we identified positive correlation between BCL11B expression and the sensitivity to HDACi in CTCL lines...
March 10, 2017: Journal of Investigative Dermatology
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