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Dna methylation

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https://read.qxmd.com/read/32227582/pirna-63076-contributes-to-pulmonary-arterial-smooth-muscle-cell-proliferation-through-acyl-coa-dehydrogenase
#1
Cui Ma, Lixin Zhang, Xiaoying Wang, Siyu He, June Bai, Qian Li, Min Zhang, Chen Zhang, Xiufeng Yu, Junting Zhang, Wei Xin, Yiying Li, Daling Zhu
Piwi-interacting RNAs (piRNAs) are thought to be germline-specific and to be involved in maintaining genome stability during development. Recently, piRNA expression has been identified in somatic cells in diverse organisms. However, the roles of piRNAs in pulmonary arterial smooth muscle cell (PASMC) proliferation and the molecular mechanism underlying the hypoxia-regulated pathological process of pulmonary hypertension are not well understood. Using hypoxic animal models, cell and molecular biology, we obtained the first evidence that the expression of piRNA-63076 was up-regulated in hypoxia and was positively correlated with cell proliferation...
March 30, 2020: Journal of Cellular and Molecular Medicine
https://read.qxmd.com/read/32227215/experimental-parasite-infection-causes-genome-wide-changes-in-dna-methylation
#2
Kostas Sagonas, Britta S Meyer, Joshka Kaufmann, Tobias L Lenz, Robert Häsler, Christophe Eizaguirre
Parasites are arguably among the strongest drivers of natural selection, constraining hosts to evolve resistance and tolerance mechanisms. Although, the genetic basis of adaptation to parasite infection has been widely studied, little is known about how epigenetic changes contribute to parasite resistance and eventually, adaptation. Here, we investigated the role of host DNA methylation modifications to respond to parasite infections. In a controlled infection experiment, we used the three-spined stickleback fish, a model species for host-parasite studies, and their nematode parasite Camallanus lacustris...
March 30, 2020: Molecular Biology and Evolution
https://read.qxmd.com/read/32226940/ex-vivo-ultrasonic-samples-of-human-brain-tumors-in-the-molecular-era
#3
Alastair J Kirby, José P Lavrador, Istvan Bodi, Francesco Vergani, Ranjeev Bhangoo, Keyoumars Ashkan, Gerald T Finnerty
Background: Gliomas are composed of multiple clones of tumor cells. This intratumor heterogeneity contributes to the ability of gliomas to resist treatment. It is vital that gliomas are fully characterized at a molecular level when a diagnosis is made to maximize treatment effectiveness. Methods: We collected ultrasonic tissue fragments during glioma surgery. Large tissue fragments were separated in the operating theater and bathed continuously in oxygenated artificial cerebrospinal fluid to keep them alive...
February 8, 2020: Neuro-oncology advances
https://read.qxmd.com/read/32226505/promoter-hypermethylation-of-chodl-contributes-to-carcinogenesis-and-indicates-poor-survival-in-patients-with-early-stage-colorectal-cancer
#4
Xinyue Zhang, Kaiming Wu, Yuhua Huang, Lixia Xu, Xiaoxing Li, Ning Zhang
Aims: Aberrant hypermethylation of CpG islands is an important hallmark of colorectal cancer (CRC). We previously utilized methyl-DNA immunoprecipitation assays to identify a novel methylated gene, chondrolectin (CHODL), preferentially methylated in human CRC. In this study, we examined the epigenetic inactivation, biological effects and prognostic significance of CHODL in CRC. Main methods: The methylation status of CHODL in CRC was evaluated by bisulfite genomic sequencing (BGS). The functions of CHODL in CRC were determined by proliferation, apoptosis, cell migration and invasion assays...
2020: Journal of Cancer
https://read.qxmd.com/read/32226501/effect-of-celsr3-on-the-cell-cycle-and-apoptosis-of-hepatocellular-carcinoma-cells
#5
Zucheng Xie, Yiwu Dang, Huayu Wu, Rongquan He, Jie Ma, Zhigang Peng, Minhua Rong, Zhekun Li, Jiapeng Yang, Yizhao Jiang, Gang Chen, Lihua Yang
Cadherin EGF LAG seven-pass G-type receptor 3 (CELSR3) has been reported in cancers but its role and potential molecular mechanism in hepatocellular carcinoma (HCC) is unclear. Therefore, we aimed to investigate the clinical value and molecular mechanism of CELSR3 in HCC using an in vitro experiment, a meta-analysis and bioinformatics. The in vitro experiment determined the promoting effect of CELSR3 in the proliferation, invasion, and migration of HCC cells. CELSR3 knockout causes S-phage arrest in HCC cells...
2020: Journal of Cancer
https://read.qxmd.com/read/32226395/air-exposure-affects-physiological-responses-innate-immunity-apoptosis-and-dna-methylation-of-kuruma-shrimp-marsupenaeus-japonicus
#6
Panpan Wang, Jun Wang, Yongquan Su, Zhixin Liu, Yong Mao
Air exposure stress is a common phenomenon for commercial crustacean species in aquaculture and during waterless transportation. However, the antioxidant responses to air exposure discussed in previous studies may be insufficient to present the complexities involved in this process. The comprehensive immune responses, especially considering the immune genes, cell apoptosis, and epigenetic changes, are still unknown. Accordingly, we investigated the multifaceted responses of Marsupenaeus japonicus to air exposure...
2020: Frontiers in Physiology
https://read.qxmd.com/read/32226301/circulating-tumor-dna-as-an-emerging-liquid-biopsy-biomarker-for-early-diagnosis-and-therapeutic-monitoring-in-hepatocellular-carcinoma
#7
REVIEW
Xiaolin Wu, Jiahui Li, Asmae Gassa, Denise Buchner, Hakan Alakus, Qiongzhu Dong, Ning Ren, Ming Liu, Margarete Odenthal, Dirk Stippel, Christiane Bruns, Yue Zhao, Roger Wahba
As one of the most common malignant tumors worldwide, hepatocellular carcinoma (HCC) is known for its poor prognosis due to diagnosis only in advanced stages. Nearly 50% of the patients with the first diagnosis of HCC die within a year. Currently, the advancements in the integration of omics information have begun to transform the clinical management of cancer patients. Molecular profiling for HCC patients is in general obtained from resected tumor materials or biopsies. However, the resected tumor tissue is limited and can only be obtained through surgery, so that dynamic monitoring of patients cannot be performed...
2020: International Journal of Biological Sciences
https://read.qxmd.com/read/32226259/a-novel-mutation-in-acat1-causing-beta-ketothiolase-deficiency-in-a-4-year-old-sri-lankan-boy-with-metabolic-ketoacidosis
#8
Thivanka Vishwani Manawadu, Eresha Jasinge, Meranthi Fernando, Pradeep Gamage, Anusha Varuni Gunarathne
Beta-ketothiolase (mitochondrial acetoacetyl-CoA thiolase, T2) deficiency is a rare genetic disorder of ketone utilization and isoleucine catabolism caused by mutations in the ACAT1 gene. Here we report the first Sri Lankan case of T2 deficiency confirmed by genetic analysis. A 4-year-old boy presented with the first episode of severe metabolic ketoacidosis after a febrile illness. On admission, the child was drowsy and had circulatory collapse needing intubation. Initial investigations were not detective of a cause and symptomatic management did not improve the condition...
April 2020: Indian Journal of Clinical Biochemistry: IJCB
https://read.qxmd.com/read/32226005/dna-methylation-and-cis-regulation-of-gene-expression-by-prostate-cancer-risk-snps
#9
James Y Dai, Xiaoyu Wang, Bo Wang, Wei Sun, Kristina M Jordahl, Suzanne Kolb, Yaw A Nyame, Jonathan L Wright, Elaine A Ostrander, Ziding Feng, Janet L Stanford
Genome-wide association studies have identified more than 100 SNPs that increase the risk of prostate cancer (PrCa). We identify and compare expression quantitative trait loci (eQTLs) and CpG methylation quantitative trait loci (meQTLs) among 147 established PrCa risk SNPs in primary prostate tumors (n = 355 from a Seattle-based study and n = 495 from The Cancer Genome Atlas, TCGA) and tumor-adjacent, histologically benign samples (n = 471 from a Mayo Clinic study). The role of DNA methylation in eQTL regulation of gene expression was investigated by data triangulation using several causal inference approaches, including a proposed adaptation of the Causal Inference Test (CIT) for causal direction...
March 30, 2020: PLoS Genetics
https://read.qxmd.com/read/32225116/epigenetic-regulation-of-auxin-induced-somatic-embryogenesis-in-plants
#10
REVIEW
Barbara Wójcikowska, Anna M Wójcik, Małgorzata D Gaj
Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling...
March 26, 2020: International Journal of Molecular Sciences
https://read.qxmd.com/read/32225105/regulative-loop-between-%C3%AE-catenin-and-protein-tyrosine-receptor-type-%C3%AE-in-chronic-myeloid-leukemia
#11
Luisa Tomasello, Marzia Vezzalini, Christian Boni, Massimiliano Bonifacio, Luigi Scaffidi, Mohamed Yassin, Nader Al-Dewik, Paul Takam Kamga, Mauro Krampera, Claudio Sorio
Protein tyrosine phosphatase receptor type γ (PTPRG) is a tumor suppressor gene, down-regulated in Chronic Myeloid Leukemia (CML) cells by the hypermethylation of its promoter region. β-catenin (CTNNB1) is a critical regulator of Leukemic Stem Cells (LSC) maintenance and CML proliferation. This study aims to demonstrate the antagonistic regulation between β-catenin and PTPRG in CML cells. The specific inhibition of PTPRG increases the activation state of BCR-ABL1 and modulates the expression of the BCR-ABL1- downstream gene β-Catenin...
March 26, 2020: International Journal of Molecular Sciences
https://read.qxmd.com/read/32224912/dna-methylation-in-the-diagnosis-of-monogenic-diseases
#12
REVIEW
Flavia Cerrato, Angela Sparago, Francesca Ariani, Fulvia Brugnoletti, Luciano Calzari, Fabio Coppedè, Alessandro De Luca, Cristina Gervasini, Emiliano Giardina, Fiorella Gurrieri, Cristiana Lo Nigro, Giuseppe Merla, Monica Miozzo, Silvia Russo, Eugenio Sangiorgi, Silvia M Sirchia, Gabriella Maria Squeo, Silvia Tabano, Elisabetta Tabolacci, Isabella Torrente, Maurizio Genuardi, Giovanni Neri, Andrea Riccio
DNA methylation in the human genome is largely programmed and shaped by transcription factor binding and interaction between DNA methyltransferases and histone marks during gamete and embryo development. Normal methylation profiles can be modified at single or multiple loci, more frequently as consequences of genetic variants acting in cis or in trans, or in some cases stochastically or through interaction with environmental factors. For many developmental disorders, specific methylation patterns or signatures can be detected in blood DNA...
March 26, 2020: Genes
https://read.qxmd.com/read/32224873/blood-free-circulating-dna-testing-of-methylated-runx3-is-useful-for-diagnosing-early-gastric-cancer
#13
Eizaburou Hideura, Yutaka Suehiro, Jun Nishikawa, Takuya Shuto, Hiroyuki Fujimura, Shunsuke Ito, Atsushi Goto, Kouichi Hamabe, Issei Saeki, Takeshi Okamoto, Shingo Higaki, Ikuei Fujii, Chieko Suzuki, Tomomi Hoshida, Toshihiko Matsumoto, Taro Takami, Isao Sakaida, Takahiro Yamasaki
The main modalities for gastric cancer screening are limited to upper gastrointestinal endoscopy and contrast radiography. The former is invasive, and the latter has high false-negative rates. Thus, alternative diagnostic strategies are required. One solution may be a liquid biopsy. Methylated RUNX3 is a well-known biomarker of gastric cancer but it is very difficult to detect with conventional bisulfite-based methylation assays when only a small amount of serum is available. We developed the combined restriction digital PCR (CORD) assay, a new methylation assay allowing for the counting of as little as one copy of a methylated gene in a small sample of DNA without necessitating DNA bisulfite treatment...
March 26, 2020: Cancers
https://read.qxmd.com/read/32223500/dietary-inclusion-of-plant-ingredients-induces-epigenetic-changes-in-the-intestine-of-zebrafish
#14
Anusha K S Dhanasiri, Xianquan Chen, Dalia Dahle, Prabhugouda Siriyappagouder, Christiane K Fæste, Jorge M O Fernandes
Epigenetic modifications, such as DNA methylation, can be regulated by nutrition and dietary factors. There has been a large increase in the use of sustainable plant-based protein sources in fish feed due to limitations of fishmeal resources that are needed to sustain a rapidly growing aquaculture industry. With this huge transition from marine ingredients to plant-based diets, fish are abruptly introduced to changes in dietary composition and exposed to a variety of phytochemicals, some of which reported to cause epigenetic changes in mammals...
March 28, 2020: Epigenetics: Official Journal of the DNA Methylation Society
https://read.qxmd.com/read/32223478/circulating-tumour-dna-alterations-as-biomarkers-for-head-and-neck-cancer-a-systematic-review
#15
Amalie Hartvig Pall, Kathrine Kronberg Jakobsen, Christian Grønhøj, Christian von Buchwald
Background: Head and neck squamous cell carcinoma (HNSCC) is a significant global burden. The development of a diagnostic or recurrence monitoring test could evolve from the exploitation of molecular markers such as tumour-specific DNA alterations in plasma. The aim of this study was to report specific genetic alterations of DNA in plasma from HNSCC patients, report the diagnostic accuracy, and discuss potentials for a diagnostic or recurrence monitoring test based on circulating tumour DNA (ctDNA). Methods: A systematic search was performed in PubMed, Embase, and Cochrane Library for articles published in English between 1 January 1980 and 24 October 2018...
March 30, 2020: Acta Oncologica
https://read.qxmd.com/read/32222987/shedding-light-on-the-chromatin-changes-that-modulate-shade-responses
#16
Jaime F Martínez-García, Jordi Moreno-Romero
Perception of vegetation proximity or plant shade informs of potential competition for resources by the neighboring vegetation. As vegetation proximity impacts on both light quantity and quality, perception of this cue by plant photoreceptors reprograms development to result in responses that allow plants to compete with the neighboring vegetation. Developmental reprogramming involves massive and rapid changes in gene expression, with the concerted action of photoreceptors and downstream transcription factors...
March 28, 2020: Physiologia Plantarum
https://read.qxmd.com/read/32222976/a-prospective-evaluation-of-serum-methionine-related-metabolites-in-relation-to-pancreatic-cancer-risk-in-two-prospective-cohort-studies
#17
Joyce Y Huang, Hung N Luu, Lesley M Butler, Øivind Midttun, Arve Ulvik, Renwei Wang, Aizhen Jin, Yu-Tang Gao, Yuting Tan, Per M Ueland, Woon-Puay Koh, Jian-Min Yuan
Deficiencies in methyl donor status may render DNA methylation changes and DNA damage, leading to carcinogenesis. Epidemiological studies reported that higher dietary intake of choline is associated with lower risk of pancreatic cancer, but no study has examined the association of serum choline and its metabolites with risk of pancreatic cancer. Two parallel case-control studies, one nested within the Shanghai Cohort Study (129 cases and 258 controls) and the other within the Singapore Chinese Health Study (58 cases and 104 controls), were conducted to evaluate the associations of baseline serum concentrations of choline, betaine, methionine, total methyl donors (i...
March 29, 2020: International Journal of Cancer. Journal International du Cancer
https://read.qxmd.com/read/32222762/comparison-of-dna-methylation-patterns-of-parentally-imprinted-genes-in-placenta-derived-from-ivf-conceptions-in-two-different-culture-media
#18
Callista L Mulder, Tess M Wattimury, Aldo Jongejan, Cindy M de Winter-Korver, Saskia K M van Daalen, Robert B Struijk, Susanne C M Borgman, Yvonne Wurth, Dimitri Consten, Jannie van Echten-Arends, Sebastiaan Mastenbroek, John C M Dumoulin, Sjoerd Repping, Ans M M van Pelt, Aafke P A van Montfoort
STUDY QUESTION: Is there a difference in DNA methylation status of imprinted genes in placentas derived from IVF conceptions where embryo culture was performed in human tubal fluid (HTF) versus G5 culture medium? SUMMARY ANSWER: We found no statistically significant differences in the mean DNA methylation status of differentially methylated regions (DMRs) associated with parentally imprinted genes in placentas derived from IVF conceptions cultured in HTF versus G5 culture medium...
March 29, 2020: Human Reproduction
https://read.qxmd.com/read/32222282/virus-mediated-dnmt1-and-dnmt3a-deletion-disrupts-excitatory-synaptogenesis-and-synaptic-function-in-primary-cultured-hippocampal-neurons
#19
Wei Sun, Qingnuan Kong, Meng Zhang, Xue Mi, Xiaomin Sun, Ming Yu, Tengbo Yu, Yu Zhou
Dnmt1, Dnmt3a and Dnmt3b are main genes encoding DNA methyltransferases (Dnmts) which catalyze DNA methylation and regulate gene expression without changing DNA sequence. Our previous study disclosed that double knockout of Dnmt1 and Dnmt3a in forebrain excitatory neurons impaired synaptic plasticity and led to hippocampus-dependent learning and memory deficits, however the underlying synaptic mechanisms remain uncertain. In this study, we selectively knocked down the expression of Dnmt1 and Dnmt3a in primary cultured hippocampal neurons derived from embryonic Dnmt1,3a2flox/2flox mice by transfection with Cre-expressing virus, to study the effect of Dnmts and mediated DNA methylation on synaptogenesis and synaptic function...
March 25, 2020: Biochemical and Biophysical Research Communications
https://read.qxmd.com/read/32221967/resources-for-functional-genomic-studies-of-health-and-development-in-nonhuman-primates
#20
Anna J Jasinska
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs)...
March 27, 2020: American Journal of Physical Anthropology
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