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Epigenetic markers

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https://www.readbyqxmd.com/read/28219347/aquaculture-genomics-genetics-and-breeding-in-the-united-states-current-status-challenges-and-priorities-for-future-research
#1
EDITORIAL
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad, Marta Gomez-Chiarri, Kamal Gosh, Ximing Guo, Perry Hackett, Terry Hanson, Dennis Hedgecock, Tiffany Howard, Leigh Holland, Molly Jackson, Yulin Jin, Karim Kahlil, Thomas Kocher, Tim Leeds, Ning Li, Lauren Lindsey, Shikai Liu, Zhanjiang Liu, Kyle Martin, Romi Novriadi, Ramjie Odin, Yniv Palti, Eric Peatman, Dina Proestou, Guyu Qin, Benjamin Reading, Caird Rexroad, Steven Roberts, Mohamed Salem, Andrew Severin, Huitong Shi, Craig Shoemaker, Sheila Stiles, Suxu Tan, Kathy F J Tang, Wilawan Thongda, Terrence Tiersch, Joseph Tomasso, Wendy Tri Prabowo, Roger Vallejo, Hein van der Steen, Khoi Vo, Geoff Waldbieser, Hanping Wang, Xiaozhu Wang, Jianhai Xiang, Yujia Yang, Roger Yant, Zihao Yuan, Qifan Zeng, Tao Zhou
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28216432/epigenetic-modification-by-dietary-factors-implications-in-metabolic-syndrome
#2
REVIEW
Jae-Ho Park, Soon-Hee Kim, Myeong Soo Lee, Myung-Sunny Kim
Dietary factors play a role in normal biological processes and are involved in the regulation of pathological progression over a lifetime. Evidence has emerged indicating that dietary factor-dependent epigenetic modifications can significantly affect genome stability and the expression of mRNA and proteins, which are involved in metabolic dysfunction. Since metabolic syndrome is a progressive phenotype characterized by insulin resistance, obesity, hypertension, dyslipidemia, or type 2 diabetes, gene-diet interactions are important processes involved in the initiation of particular symptoms of metabolic syndrome and their progression...
February 16, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28214526/recent-advances-in-human-genetics-and-epigenetics-of-adiposity-pathway-to-precision-medicine
#3
Tove Fall, Michael Mendelson, Elizabeth K Speliotes
Obesity is a heritable trait that contributes to substantial global morbidity and mortality. Here, we summarize findings from the last decade of genetic and epigenetic research focused on unravelling the underpinnings of adiposity. More than 140 genetic regions are now known to influence adiposity traits. The genetics of general adiposity, as measured by body mass index, and that of abdominal obesity, as measured by waist to hip ratio, have distinct biological backgrounds. Expression of genes associated with general adiposity are enriched in the nervous system...
February 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28211484/regulation-of-mrna-splicing-by-mecp2-via-epigenetic-modifications-in-the-brain
#4
Tian-Lin Cheng, Jingqi Chen, Huida Wan, Bin Tang, Weidong Tian, Lujian Liao, Zilong Qiu
Mutations of X-linked gene Methyl CpG binding protein 2 (MECP2) are the major causes of Rett syndrome (RTT), a severe neurodevelopmental disorder. Duplications of MECP2-containing genomic segments lead to severe autistic symptoms in human. MECP2-coding protein methyl-CpG-binding protein 2 (MeCP2) is involved in transcription regulation, microRNA processing and mRNA splicing. However, molecular mechanisms underlying the involvement of MeCP2 in mRNA splicing in neurons remain largely elusive. In this work we found that the majority of MeCP2-associated proteins are involved in mRNA splicing using mass spectrometry analysis with multiple samples from Mecp2-null rat brain, mouse primary neuron and human cell lines...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209718/demethylation-of-h3k27-is-essential-for-the-induction-of-direct-cardiac-reprogramming-by-mir-combo
#5
Sophie Dal-Pra, Conrad P Hodgkinson, Maria Mirotsou, Imke Kirste, Victor J Dzau
Rationale: Direct reprogramming of cardiac fibroblasts to cardac omyocytes has recently emerged as a novel and promising approach to regenerate the injured myocardium. We have previously demonstrated the feasibility of this approach in vitro and in vivo using a combination of four microRNAs (miR-1, miR-133, miR-208 and miR-499) that we named miR combo. However, the mechanism of miR combo mediated direct cardiac reprogramming is currently unknown. Objective: Here we investigated the possibility that miR combo initiated direct cardiac reprogramming through an epigenetic mechanism...
February 16, 2017: Circulation Research
https://www.readbyqxmd.com/read/28199764/clinical-markers-of-asthma-and-ige-assessed-in-parents-before-conception-predicts-asthma-and-hay-fever-in-the-offspring
#6
Randi J Bertelsen, Marta Rava, Anne Elie Carsin, Simone Accordini, Bryndis Benediktsdóttir, Julia Dratva, Karl A Franklin, Joachim Heinrich, Mathias Holm, Christer Janson, Ane Johannessen, Deborah L Jarvis, Rain Jogi, Benedicte Leynaert, Dan Norback, Ernst Reidar Omenaas, Chantal Raherison, José Luis Sánchez-Ramos, Vivi Schlünssen, Torben Sigsgaard, Shyamali C Dharmage, Cecilie Svanes
BACKGROUND: Mice models suggest epigenetic inheritance induced by parental allergic disease activity. However, we know little of how parental disease activity before conception influences offspring's asthma and allergy in humans. OBJECTIVE: We aimed to assess the associations of parental asthma severity, bronchial hyperresponsiveness (BHR), and total and specific IgEs, measured before conception vs after birth, with offspring asthma and hay fever. METHODS: The study included 4293 participants (mean age 34, 47% men) from the European Community Respiratory Health Survey (ECRHS) with information on asthma symptom severity, BHR, total and specific IgEs from 1991-1993, and data on 9100 offspring born 1972-2012...
February 15, 2017: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28199193/epigenetic-and-risk-factors-of-testicular-germ-cell-tumors-a-brief-review
#7
Daniel Adrian Landero-Huerta, Rosa Maria Vigueras-Villasenor, Emiy Yokoyama-Rebollar, Elena Arechaga-Ocampo, Julio Cesar Rojas-Castaneda, Francisco Jimenez-Trejo, Margarita Chavez-Saldana
Testicular germ cell cancer (TGCT) is the most common malignancy among young adult males, which has become important due to its increased incidence and mortality in the population worldwide. The etiology is multifactorial. Recent studies have shown some associations between the development of isolated TGCT and certain risk factors, such as exposure to endocrine disruptors, cryptorchidism, and family history of cancer, in order to identify the key pieces in carcinogenesis. Some of the most important findings in recent years is the association of different genes, such as c-KIT/KITLG, expression of the miR-371-373 cluster and protein expression as c-KIT and POU5F1 in the development of this neoplasia, and the identification of new molecular markers as TGFBR3 gene, identifying aberrant methylation patterns in promoter regions of several genes, expression of miR-1297 which regulates PTEN and protein expression as DMTR1...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28198450/identification-of-methylation-driven-differentially-expressed-stxbp6-as-a-novel-biomarker-in-lung-adenocarcinoma
#8
Govinda Lenka, Mong-Hsun Tsai, Hsin-Chieh Lin, Jen-Hao Hsiao, Yi-Ching Lee, Tzu-Pin Lu, Jang-Ming Lee, Chung-Ping Hsu, Liang-Chuan Lai, Eric Y Chuang
DNA methylation is an essential epigenetic marker associated with the silencing of gene expression. Although various genome-wide studies revealed aberrantly methylated gene targets as molecular biomarkers for early detection, the survival rate of lung cancer patients is still poor. In order to identify methylation-driven biomarkers, genome-wide changes in DNA methylation and differential expression in 32 pairs of lung adenocarcinoma and adjacent normal lung tissue in non-smoking women were examined. This concurrent analysis identified 21 negatively correlated probes (r ≤ -0...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194967/multicellular-tumor-spheroids-combined-with-mass-spectrometric-histone-analysis-to-evaluate-epigenetic-drugs
#9
Peter E Feist, Simone Sidoli, Xin Liu, Monica M Schroll, Sharif Rahmy, Rina Fujiwara, Benjamin A Garcia, Amanda B Hummon
Multicellular tumor spheroids (MCTS) are valuable in vitro tumor models frequently used to evaluate the penetration and efficacy of therapeutics. In this study, we evaluated potential differences in epigenetic markers, i.e., histone post-translational modifications (PTMs), in the layers of the HCT116 colon carcinoma MCTS. Cells were grown in agarose-coated 96 well plates, forming reproducible 1-mm-diameter MCTS. The MCTS were fractionated into three radially concentric portions, generating samples containing cells from the core, the mid and the external layers...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193841/dual-roles-of-akirin2-during-xenopus-neural-development
#10
Xiaoliang Liu, Yingjie Xia, Jixin Tang, Li Ma, Chaocui Li, Pengcheng Ma, Bingyu Mao
To ensure correct spatial and temporal patterning, embryos must maintain pluripotent cell populations and control when cells undergo commitment. The newly identified nucleoprotein Akirin has been shown to modulate the innate immune response through epigenetic regulation and to play important roles in other physiological processes, but its role in neural development remains unknown. Here, we show that Akirin2 is required for neural development in Xenopus and knockdown of Akirin2 expands the expression of the neural progenitor marker Sox2 and inhibits expression of the differentiated neuronal marker N-tubulin...
February 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28193206/inducing-goat-pluripotent-stem-cells-with-four-transcription-factor-mrnas-that-activate-endogenous-promoters
#11
Hao Chen, Qisheng Zuo, Yingjie Wang, Jiuzhou Song, Huilin Yang, Yani Zhang, Bichun Li
BACKGROUND: Traditional approaches for generating goat pluripotent stem cells (iPSCs) suffer from complexity and low preparation efficiency. Therefore, we tried to derive goat iPSCs with a new method by transfecting exogenous Oct4, Sox2, Klf4 and c-Myc mRNAs into goat embryonic fibroblasts (GEFs), and explore the mechanisms regarding the transcription regulation of the reprogramming factors in goat iPSCs induction. RESULTS: mRNAs of the four reprogramming factors were transfected into GEFs, and were localized in nucleus with approximately 90% transfection efficiency...
February 13, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28192422/identification-of-quiescent-and-spatially-restricted-mammary-stem-cells-that-are-hormone-responsive
#12
Nai Yang Fu, Anne C Rios, Bhupinder Pal, Charity W Law, Paul Jamieson, Ruijie Liu, François Vaillant, Felicity Jackling, Kevin He Liu, Gordon K Smyth, Geoffrey J Lindeman, Matthew E Ritchie, Jane E Visvader
Despite accumulating evidence for a mammary differentiation hierarchy, the basal compartment comprising stem cells remains poorly characterized. Through gene expression profiling of Lgr5(+) basal epithelial cells, we identify a new marker, Tetraspanin8 (Tspan8). Fractionation based on Tspan8 and Lgr5 expression uncovered three distinct mammary stem cell (MaSC) subsets in the adult mammary gland. These exist in a largely quiescent state but differ in their reconstituting ability, spatial localization, and their molecular and epigenetic signatures...
February 13, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28186085/hepatitis-b-virus-x-protein-mediated-non-coding-rna-aberrations-in-the-development-of-human-hepatocellular-carcinoma
#13
REVIEW
Bei Zhang, Siqi Han, Bing Feng, Xiaoyuan Chu, Longbang Chen, Rui Wang
Hepatitis B virus (HBV) has an important role in the development of human hepatocellular carcinoma (HCC). Accumulated evidence has shown that HBV-encoded X protein (HBx) can induce both genetic alterations in tumor suppressor genes and oncogenes, as well as epigenetic aberrations in HCC pathogens. Non-coding RNAs (ncRNAs) mainly include microRNAs and long non-coding RNAs (lncRNAs). Although ncRNAs cannot code proteins, growing evidence has shown that they have various important biological functions in cell proliferation, cell cycle control, anti-apoptosis, epithelial-mesenchymal transition, tumor invasion and metastasis...
February 10, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28183455/cardiometabolic-risk-markers-adipocyte-fatty-acid-binding-protein-afabp-and-the-impact-of-high-intensity-interval-training-hiit-in-obese-adolescents
#14
Susann Blüher, Jakob Käpplinger, Sabine Herget, Sandra Reichardt, Yvonne Böttcher, Andrea Grimm, Jürgen Kratzsch, David Petroff
OBJECTIVE: The impact of high-intensity interval training (HIIT) as well as the association between the adipocyte fatty binding protein (aFABP) and cardiometabolic risk factors in overweight adolescents was investigated. METHODS: Twenty-eight adolescents (13-18years; BMI≥90th percentile according to German reference values) were offered HIIT twice weekly for 6months. At baseline and after program completion, anthropometric, clinical and metabolic characteristics were assessed and a fasting blood sample was obtained...
March 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28178884/improved-post-thaw-function-and-epigenetic-changes-in-mesenchymal-stromal-cells-cryopreserved-using-multicomponent-osmolyte-solutions
#15
Kathryn Pollock, Rebekah Samsonraj, Amel Dudakovic, Roman Thaler, Aron Stumbras, David McKenna, Peter Dosa, Andre van Wijnen, Allison Hubel
Current methods for freezing mesenchymal stromal cells (MSCs) result in poor post-thaw function, which limits the clinical utility of these cells. This investigation develops a novel approach to preserve MSCs using combinations of sugars, sugar alcohols and small molecule additives. MSCs frozen using these solutions exhibit improved post-thaw attachment and a more normal alignment of the actin cytoskeleton compared to cells exposed to dimethylsulfoxide (DMSO). Osteogenic and chondrogenic differentiation assays show that cells retain their mesenchymal lineage properties...
February 8, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28176655/epigenetics-in-clinical-management-of-children-and-adolescents-with-brain-tumors
#16
Andres Morales La Madrid, Mark W Kieran
Central nervous system (CNS) tumors represent the second most prevalent group of cancers in children and adolescents, yet account for the majority of childhood cancer-related deaths and considerable morbidity among survivors, due to high-intensity non-selective standard therapies delivered to immature nervous system structures undergoing development. These tumors arise at different ages -not infrequently very early in life-, in different locations and cellular contexts, have varied cell types of origin, and have heterogeneous responses to the "classic" current therapeutic approaches...
February 3, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28176651/lung-cancer-stem-cells-an-epigenetic-perspective
#17
Samriddhi Shukla, Sajid Khan, Sonam Sinha, Syed Musthapa Meeran
Lung cancer remains the major cause of human mortality among all the cancer types despite the colossal amount of efforts to prevent the cancer onset and to provide the appropriate cure. Recent reports have identified that important contributors of lung cancer-related mortality are the drug resistance and aggressive tumor relapse, the characteristics contributed by the presence of lung cancer stem cells (CSCs). The identification of lung CSCs is inherently complex due to the quiescent nature of lung epithelium, which makes the distinction between the normal lung epithelium and lung CSCs difficult...
February 5, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28176646/epigenetic-regulation-of-emt-in-non-small-cell-lung-cancer
#18
Karen O'Leary, Alice Shia, Peter Schmid
Lung cancer remains the most diagnosed cancer in the world, with a high mortality rate and fewer therapeutic options. The most common lung cancer is non-small cell, which can consist of adenocarcinoma, squamous cell carcinoma and large cell lung carcinoma. As per all solid tumours, the changes that occur for the initiation and metastasis of lung cancer can be described using the EMT (epithelial mesenchymal transition). Cells progressing through EMT lose their epithelial cell characteristics, expressing more mesenchymal markers and are phenotypically different...
February 3, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28174608/genome-wide-dna-methylation-profile-identified-a-unique-set-of-differentially-methylated-immune-genes-in-oral-squamous-cell-carcinoma-patients-in-india
#19
Baidehi Basu, Joyeeta Chakraborty, Aditi Chandra, Atul Katarkar, Jadav Ritesh Kumar Baldevbhai, Debjit Dhar Chowdhury, Jay Gopal Ray, Keya Chaudhuri, Raghunath Chatterjee
BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and validated in an additional 53 well-differentiated OSCC and adjacent normal samples...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28167342/cellular-transformation-of-human-mammary-epithelial-cells-by-satb2
#20
Wei Yu, Yiming Ma, Augusto C Ochoa, Sharmila Shankar, Rakesh K Srivastava
Breast tumors are heterogeneous and carry a small population of progenitor cells that can produce various subtypes of breast cancer. SATB2 (special AT-rich binding protein-2) is a newly identified transcription factor and epigenetic regulator. It is highly expressed in embryonic stem cells, but not in adult tissues, and regulates pluripotency-maintaining factors. However, the molecular mechanisms by which SATB2 induces transformation of human mammary epithelial cells (HMECs) leading to malignant phenotype are unknown...
February 1, 2017: Stem Cell Research
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