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Epigenetics profilling

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https://www.readbyqxmd.com/read/29132323/integrative-microrna-and-mrna-deep-sequencing-expression-profiling-in-endemic-burkitt-lymphoma
#1
Cliff I Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A Otieno, John Michael Ong'echa, Ann M Moormann, Jeffrey A Bailey
BACKGROUND: Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells...
November 13, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29131015/therapeutic-response-to-paroxetine-in-major-depressive-disorder-predicted-by-dna-methylation
#2
Naohiro Takeuchi, Shinpei Nonen, Masaki Kato, Masataka Wakeno, Yoshiteru Takekita, Toshihiko Kinoshita, Fumihiko Kugawa
BACKGROUND: Antidepressants have variable therapeutic effects, depending on genetic and environmental factors. Approximately 30% of major depressive disorder (MDD) patients do not respond significantly to antidepressants such as paroxetine, a selective serotonin reuptake inhibitor (SSRI). However, the biological mechanisms behind this phenomenon are mostly unknown. Here, we examined the role of patients' epigenetic background in SSRI efficacy. METHODS: Genome-wide DNA methylation analysis of the peripheral blood of Japanese MDD patients was performed by using the Infinium HumanMethylation450 BeadChip...
November 4, 2017: Neuropsychobiology
https://www.readbyqxmd.com/read/29130343/defining-baseline-epigenetic-landscapes-in-the-rat-liver
#3
John P Thomson, Raffaele Ottaviano, Roland Buesen, Jonathan G Moggs, Michael Schwarz, Richard R Meehan
Characterization of the hepatic epigenome following exposure to chemicals and therapeutic drugs provides novel insights into toxicological and pharmacological mechanisms, however appreciation of genome-wide inter- and intra-strain baseline epigenetic variation, particularly in under-characterized species such as the rat is limited. Material & methods: To enhance the utility of epigenomic endpoints safety assessment, we map both DNA modifications (5-methyl-cytosine and 5-hydroxymethyl-cytosine) and enhancer related chromatin marks (H3K4me1 and H3K27ac) across multiple male and female rat livers for two important outbred laboratory rat strains (Sprague-Dawley and Wistar)...
November 13, 2017: Epigenomics
https://www.readbyqxmd.com/read/29126434/whole-blood-microrna-expression-pattern-differentiates-patients-with-rheumatoid-arthritis-their-seropositive-first-degree-relatives-and-healthy-unrelated-control-subjects
#4
Vidyanand Anaparti, Irene Smolik, Xiaobo Meng, Victor Spicer, Neeloffer Mookherjee, Hani El-Gabalawy
BACKGROUND: Epigenetic mechanisms can integrate gene-environment interactions that mediate disease transition from preclinical to clinically overt rheumatoid arthritis (RA). To better understand their role, we evaluated microRNA (miRNA, miR) expression profile in indigenous North American patients with RA who were positive for anticitrullinated protein antibodies; their autoantibody-positive, asymptomatic first-degree relatives (FDRs); and disease-free healthy control subjects (HCs). METHODS: Total RNA was isolated from whole blood samples obtained from HC (n = 12), patients with RA (n = 18), and FDRs (n = 12)...
November 10, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/29125853/whole-genome-dna-methylation-characteristics-in-pediatric-precursor-b-cell-acute-lymphoblastic-leukemia-bcp-all
#5
Radosław Chaber, Artur Gurgul, Grażyna Wróbel, Olga Haus, Anna Tomoń, Jerzy Kowalczyk, Tomasz Szmatoła, Igor Jasielczuk, Blanka Rybka, Renata Ryczan-Krawczyk, Ewa Duszeńko, Sylwia Stąpor, Krzysztof Ciebiera, Sylwia Paszek, Natalia Potocka, Christopher J Arthur, Izabela Zawlik
In addition to genetic alterations, epigenetic abnormalities have been shown to underlie the pathogenesis of acute lymphoblastic leukemia (ALL)-the most common pediatric cancer. The purpose of this study was to characterize the whole genome DNA methylation profile in children with precursor B-cell ALL (BCP ALL) and to compare this profile with methylation observed in normal bone marrow samples. Additional efforts were made to correlate the observed methylation patterns with selected clinical features. We assessed DNA methylation from bone marrow samples obtained from 38 children with BCP ALL at the time of diagnosis along with 4 samples of normal bone marrow cells as controls using Infinium MethylationEPIC BeadChip Array...
2017: PloS One
https://www.readbyqxmd.com/read/29123948/no-patient-left-behind-the-promise-of-immune-priming-with-epigenetic-agents
#6
REVIEW
Corey A Carter, Bryan T Oronsky, Joseph Roswarski, Arnold L Oronsky, Neil Oronsky, Jan Scicinski, Harry Lybeck, Michelle M Kim, Michelle Lybeck, Tony R Reid
Checkpoint inhibitors, monoclonal antibodies that inhibit PD-1 or CTLA-4, have revolutionized the treatment of multiple cancers. Despite the enthusiasm for the clinical successes of checkpoint inhibitors, and immunotherapy, in general, only a minority of patients with specific tumor types actually benefit from treatment. Emerging evidence implicates epigenetic alterations as a mechanism of clinical resistance to immunotherapy. This review presents evidence for that association, summarizes the epi-based mechanisms by which tumors evade immunogenic cell death, discusses epigenetic modulation as a component of an integrated strategy to boost anticancer T cell effector function in relation to a tumor immunosuppression cycle and, finally, makes the case that the success of this no-patient-left-behind strategy critically depends on the toxicity profile of the epigenetic agent(s)...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29123667/paternal-obesity-how-bad-is-it-for-sperm-quality-and-progeny-health
#7
Georges Raad, Mira Hazzouri, Silvia Bottini, Michele Trabucchi, Joseph Azoury, Valérie Grandjean
There is substantial evidence that paternal obesity is associated not only with an increased incidence of infertility, but also with an increased risk of metabolic disturbance in adult offspring. Apparently, several mechanisms may contribute to the sperm quality alterations associated with paternal obesity, such as physiological/hormonal alterations, oxidative stress, and epigenetic alterations. Along these lines, modifications of hormonal profiles namely reduced androgen levels and elevated estrogen levels, were found associated with lower sperm concentration and seminal volume...
2017: Basic and Clinical Andrology
https://www.readbyqxmd.com/read/29123172/transcriptomic-and-epigenetic-responses-to-short-term-nutrient-exercise-stress-in-humans
#8
R C Laker, C Garde, D M Camera, W J Smiles, J R Zierath, J A Hawley, R Barrès
High fat feeding impairs skeletal muscle metabolic flexibility and induces insulin resistance, whereas exercise training exerts positive effects on substrate handling and improves insulin sensitivity. To identify the genomic mechanisms by which exercise ameliorates some of the deleterious effects of high fat feeding, we investigated the transcriptional and epigenetic response of human skeletal muscle to 9 days of a high-fat diet (HFD) alone (Sed-HFD) or in combination with resistance exercise (Ex-HFD), using genome-wide profiling of gene expression and DNA methylation...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29121743/profiling-of-cardiovascular-and-cerebrovascular-disease-associated-microrna-expression-in-umbilical-cord-blood-in-gestational-hypertension-preeclampsia-and-fetal-growth-restriction
#9
Ilona Hromadnikova, Katerina Kotlabova, Katarina Ivankova, Yulia Vedmetskaya, Ladislav Krofta
BACKGROUND AND METHODS: Gene expression of 29 cardiovascular and cerebrovascular disease associated microRNAs was assessed in whole umbilical cord blood, compared between groups [47 gestational hypertension (GH), 56 preeclampsia (PE), 37 fetal growth restriction (FGR) and 44 normal pregnancies] and correlated with the severity of the disease with respect to clinical signs (mild PE vs. severe PE), delivery date (before and after 34weeks of gestation), and Doppler ultrasound parameters [pulsatility index (PI) in the umbilical artery, PI in the middle cerebral artery and the cerebroplacental ratio]...
December 15, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/29119291/determination-of-histone-epigenetic-marks-in-arabidopsis-and-tomato-genes-in-the-early-response-to-botrytis-cinerea
#10
Óscar Crespo-Salvador, Mónica Escamilla-Aguilar, Jaime López-Cruz, Gerardo López-Rodas, Carmen González-Bosch
Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea may contribute to find biomarkers of the early detection of this devastating pathogen. Recent studies have linked epigenetic modifications with plant responses to biotic stresses. Information about specific histone marks upon necrotrophic pathogens is scarce. Here we wondered whether the altered responsiveness of specific genes in plants infected with Botrytis cinerea was associated with changes in chromatin structure...
November 8, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29118760/septic-shock-and-the-aging-process-a-molecular-comparison
#11
Fabiano Pinheiro da Silva, Marcel Cerqueira César Machado
Aging is a continuous process promoted by both intrinsic and extrinsic factors that each trigger a multitude of molecular events. Increasing evidence supports a central role for inflammation in this progression. Here, we discuss how the low-grade chronic inflammation that characterizes aging is tightly interconnected with other important aspects of this process, such as DNA damage, mitochondrial dysfunction, and epigenetic changes. Similarly, inflammation also plays a critical role in many morbid conditions that affect patients who are admitted to Intensive Care...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29117997/metformin-an-anti-proliferative-agent-and-methylation-regulator-in-treating-prostatic-disease
#12
Zongwei Wang, Aria F Olumi
Existing drugs that have been used in clinical practice for other purposes can prove useful for reutilization, since much of the safety profile, pharmacokinetics have been completed. Therefore, the drugs can enter clinical practice for variety of causes with less regulatory burden. Metformin may prove to be such a drug where it may have a role in other diseases, beside management of diabetes. In this perspective, we provide our finding and understanding of metformin as an alternate way to treat urological abnormal proliferation...
November 8, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/29116514/combine-phage-antibody-display-library-selection-on-patient-tissue-specimens-with-laser-capture-microdissection-to-identify-novel-human-antibodies-targeting-clinically-relevant-tumor-antigens
#13
Yang Su, Scott Bidlingmaier, Nam-Kyung Lee, Bin Liu
A functional approach to generate tumor-targeting human monoclonal antibodies is through selection of phage antibody display libraries directly on tumor cells. Although technically convenient, the use of cancer cell lines for the selection has limitations as those cell lines often undergo genetic and epigenetic changes during prolonged in vitro culture and alter their cell surface antigen expression profile. The key is to develop a technology that allows selection of phage antibody display libraries on tumor cells in situ residing in their natural tissue microenvironment...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29114103/association-of-serotonin-transporter-gene-alujb-methylation-with-major-depression-amygdala-responsiveness-5-httlpr-rs25531-polymorphism-and-stress
#14
Ilona Schneider, Harald Kugel, Ronny Redlich, Dominik Grotegerd, Christian Bürger, Paul-Christian Bürkner, Nils Opel, Katharina Dohm, Dario Zaremba, Susanne Meinert, Nina Schröder, Anna Milena Straßburg, Kathrin Schwarte, Christiane Schettler, Oliver Ambrée, Stephan Rust, Katharina Domschke, Volker Arolt, Walter Heindel, Bernhard T Baune, Weiqi Zhang, Udo Dannlowski, Christa Hohoff
DNA methylation profiles of the serotonin transporter gene (SLC6A4) have been shown to alter SLC6A4 expression, drive antidepressant treatment response and modify brain functions. This study investigated whether methylation of an AluJb element in the SLC6A4 promotor was associated with major depressive disorder (MDD), amygdala reactivity to emotional faces, 5-HTTLPR/rs25531 polymorphism, and recent stress. MDD patients (n=122) and healthy controls (HC, n=176) underwent fMRI during an emotional face-matching task...
November 7, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29111977/nanos-promotes-epigenetic-reprograming-of-the-germline-by-down-regulation-of-the-thap-transcription-factor-lin-15b
#15
Chih-Yung Sean Lee, Tu Lu, Geraldine Seydoux
Nanos RNA-binding proteins are required for germline development in metazoans, but the underlying mechanisms remain poorly understood. We have profiled the transcriptome of primordial germ cells (PGCs) lacking the nanos homologs nos-1 and nos-2 in C. elegans. nos-1nos-2 PGCs fail to silence hundreds of transcripts normally expressed in oocytes. We find that this misregulation is due to both delayed turnover of maternal transcripts and inappropriate transcriptional activation. The latter appears to be an indirect consequence of delayed turnover of the maternally-inherited transcription factor LIN-15B, a synMuvB class transcription factor known to antagonize PRC2 activity...
November 7, 2017: ELife
https://www.readbyqxmd.com/read/29109980/the-abundance-of-metabolites-related-to-protein-methylation-correlates-with-the-metastatic-capacity-of-human-melanoma-xenografts
#16
Xiaolei Shi, Alpaslan Tasdogan, Fang Huang, Zeping Hu, Sean J Morrison, Ralph J DeBerardinis
Metabolic reprogramming is a major factor in transformation, and particular metabolic phenotypes correlate with oncogenotype, tumor progression, and metastasis. By profiling metabolites in 17 patient-derived xenograft melanoma models, we identified durable metabolomic signatures that correlate with biological features of the tumors. BRAF mutant tumors had metabolomic and metabolic flux features of enhanced glycolysis compared to BRAF wild-type tumors. Tumors that metastasized efficiently from their primary sites had elevated levels of metabolites related to protein methylation, including trimethyllysine (TML)...
November 2017: Science Advances
https://www.readbyqxmd.com/read/29108743/differentially-dna-methylation-changes-induced-in-vitro-by-traffic-derived-nanoparticulate-matter
#17
Xiaoning Lei, Joshua E Muscat, Bo Zhang, Xuyang Sha, Guangli Xiu
The cytotoxicity, apoptosis, reactive oxygen species (ROS) and DNA damage induced by the commercial diesel exhaust particulate matter (PM) (SRM2975) with concentrations ranging from 0.1μg·mL(-1) to 20μg·mL(-1) were assessed in human umbilical vein endothelial cells (HUVECs) in vitro. An epigenetics-wide investigation of DNA methylation profiles was also performed using a new methylation beadchip (Illumina 850K) to identify the health effects of traffic-derived nanoparticulate matter (nPM) with a concentration of 20μg·mL(-1)...
November 3, 2017: Toxicology
https://www.readbyqxmd.com/read/29108067/rapid-communication-the-correlation-between-histone-modifications-and-expression-of-key-genes-involved-in-accumulation-of-adipose-tissue-in-the-pig
#18
B Kociucka, J Stachecka, M Szydlowski, I Szczerbal
Histone modification is a well-known epigenetic mechanism involved in regulation of gene expression; however, it has been poorly studied in adipose tissues of the pig. Understanding the molecular background of adipose tissue development and function is essential for improving production efficiency and meat quality. The objective of this study was to identify the association between histone modification and the transcript level of genes important for lipid droplet formation and metabolism. Histone modifications at the promoter regions of 6 genes (, , , , , and ) were analyzed using a chromatin immunoprecipitation assay...
October 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/29106955/molecular-characterization-of-pod1-during-sex-development-in-chinese-tongue-sole-cynoglossus-semilaevis
#19
Linna Wang, Ying Zhu, Wenteng Xu, Changwei Shao, Zhongdian Dong, Hailong Li, Zhongkai Cui, Liang Meng, Hua Guo, Yongsheng Tian, Songlin Chen
Pod1 encodes a Class II bHLH transcription factor involved in the development of a number of tissues such as gonad, spleen, lungs and heart. However, to date, little is known about its function in teleosts. In this study, we cloned and characterized Pod1 gene from Cynoglossus semilaevis. This gene contains three exons and two introns, with the full-length cDNA of 918 nucleotides that encodes a 183 amino acid protein with a conserved bHLH domain. Realtime quantitative PCR revealed that Pod1 was predominantly expressed in the testes of C...
October 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29106556/location-matters-distinct-dna-methylation-patterns-in-gabaergic-interneuronal-populations-from-separate-microcircuits-within-the-human-hippocampus
#20
W Brad Ruzicka, Sivan Subburaju, Joseph T Coyle, Francine M Benes
Recent studies describe distinct DNA methylomes among phenotypic subclasses of neurons in the human brain, but variation in DNA methylation between common neuronal phenotypes distinguished by their function within distinct neural circuits remains an unexplored concept. Studies able to resolve epigenetic profiles at the level of microcircuits are needed to illuminate chromatin dynamics in the regulation of specific neuronal populations and circuits mediating normal and abnormal behaviors.The Illumina HumanMethylation450 BeadChip was used to assess genome-wide DNA methylation in stratum oriens GABAergic interneurons sampled by laser-microdissection from two discrete microcircuits along the trisynaptic pathway in postmortem human hippocampus from eight control, eight schizophrenia, and eight bipolar disorder subjects...
November 2, 2017: Human Molecular Genetics
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