Wednesday, December 5, 2018

Environmental epigenomics and disease susceptibility session at Epigenetics 2019

Epidemiological evidence increasingly suggests that environmental exposures early in development have a role in susceptibility to disease in later life. In addition, some of these environmental effects seem to be passed on through subsequent generations. Epigenetic modifications provide a plausible link between the environment and alterations in gene expression that might lead to disease phenotypes. An increasing body of evidence from animal studies supports the role of environmental epigenetics in disease susceptibility. Furthermore, recent studies have demonstrated for the first time that heritableenvironmentally induced epigenetic modifications underlie reversible transgenerational alterations in phenotype. Methods are now becoming available to investigate the relevance of these phenomena to human disease.

Friday, November 30, 2018

Cytotoxicity & Transcriptomic Analysis of Silver Nanoparticles in Mouse Embryonic Fibroblast Cells

The rapid development of nanotechnology has led to the use of silver nanoparticles (AgNPs) in biomedical applications, including antibacterial, antiviral, anti-inflammatory & anticancer therapies. The molecular mechanism of AgNPs-induced cytotoxicity has not been studied thoroughly using a combination of cellular assays & RNA sequencing (RNA-Seq) analysis. In this study, we prepared AgNPs using myricetin, an anti-oxidant polyphenol & studied their effects on NIH3T3 mouse embryonic fibroblasts as an in vitro model system to explore the potential biomedical applications of AgNPs. AgNPs induced loss of cell viability and cell proliferation in a dose-dependent manner, as evident by increased leakage of lactate dehydrogenase (LDH) from cells. Reactive oxygen species (ROS) were a potential source of cytotoxicity. AgNPs also incrementally increased oxidative stress & the level of malondialdehyde, depleted glutathione and superoxide dismutase, reduced mitochondrial membrane potential and adenosine triphosphate (ATP), and caused DNA damage by increasing the level of 8-hydroxy-2'-deoxyguanosine and the expressions of the p53 and p21 genes in NIH3T3 cells. Thus, activation of oxidative stress may be crucial for NIH3T3 cytotoxicity. Interestingly, gene ontology (GO) term analysis revealed alterations in epigenetics-related biological processes including nucleosome assembly & DNA methylation due to AgNPs exposure. This study is the first demonstration that AgNPs can alter bulk histone gene expression. Therefore, our genome-scale study suggests that the apoptosis observed in NIH3T3 cells treated with AgNPs is mediated by the repression of genes required for cell survival and the aberrant enhancement of nucleosome assembly components to induce apoptosis.

 Epigenetics 2019

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Thursday, November 29, 2018

Epigenetic regulation of FOXA2 in endometrial cancer

FOXA2 is a pioneer transcription factor that plays an important role in normal development and in adult tissues. The Cancer Genome Atlas project identified FOXA2 as a “significantly mutated gene” in endometrial cancer, with the majority of mutations being loss-of-function defects. Epigenetic silencing of genes associated with methylation of CpG-rich promoter regions is seen in cancers. We sought to analyze the FOXA2promoter region for methylation and to determine the relationship between methylation and mRNA and protein expression.

 Epigenetics 2019

Wednesday, November 28, 2018

Chromatin imaging and new advancements for imaging the nucleome

Synergistic developments in advanced fluorescent imaging & labeling techniques enable direct visualization of the chromatin structure & dynamics at the nanoscale level & in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement & can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulatedemission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global & sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy & enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential & combinatorial labeling, direct characterization of the DNA domain volume & length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions.

 Epigenetics 2019

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Monday, November 26, 2018

The Emerging Role of Epitranscriptomics in Cancer

Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (mA) is the most frequent, especially among mRNAs. mA has been demonstrated to play important roles in many physiological procedure and several disease states, including various cancer models (from solid to liquid tumors). Tumor cells' epitranscriptome is indeed disrupted in a way to promote cancer-prone features, by means of up/downregulating mA-related players: the so-called writers, readers and erasers. These proteins modulate mA establishment, removal and determine mRNAs fate, acting in a context-dependent manner, so that a single player may act as an oncogenic signal in one tumor model (methyltransferase like 3 (METTL3) in lung cancer) and as a tumor suppressor in another context (METTL3 in glioblastoma). Despite recent advances, however, little attention has been directed towards urological cancer. By means of a thorough analysis of the publicly available TCGA (The Cancer Genome Atlas) database, we disclosed the most relevant players in four major urogenital neoplasms-kidney, bladder, prostate and testicular cancer-for prognostic, subtype discrimination and survival purposes. In all tumor models assessed, the most promising player was shown to be Vir like mA methyltransferase associated (VIRMA), which could constitute a potential target for personalized therapies.

 Epigenetics 2019

Saturday, November 24, 2018

Cyto-genotoxic & DNA methylation changes induced by different crystal phases of TiO2-np in bronchial epithelial cells

With the expansion in use of TiO2-np, a superior comprehension of their wellbeing is vital. In the present study the impact of different crystal phases of TiO2-np (anatase, rutile and anatase: rutile mixture; 20-26nm) were studied for cyto-genotoxicity and global DNA methylation and hydroxymethylation. Cytotoxic response was observed at a concentration of 25μg/ml for the particles tested. Results of comet and micronucleus (with and without CytB) assays revealed significant genotoxic effect of these particles. Flow cytometry revealed cell cycle arrest in the S-phase. Based on the results, toxicity of the particles could be correlated with their physico-chemical properties (i.e. smaller size and hydrodynamic diameter and larger surface area), anatase form being the most toxic. From the results of the cyto-genotoxicity assays, concentrations were determined for the epigenetic study. Effect on global DNA methylation and hydroxymethylation levels were studied at cyto-genotoxic (25μg/ml), genotoxic (12.5μg/ml) and sub cyto-genotoxic (3.25μg/ml) concentrations using LC-MS/MS analysis. Though no significant changes were observed for 3h treatment schedule; significant hypomethylation were observed at 24h for anatase (significant at 3.25 and 25μg/ml), rutile (significant at 3.25 and 25μg/ml) and anatase: rutile mixture (significant at 25μg/ml) forms. The results suggest that epigenetic changes could occur at sub cyto-genotoxic concentrations. And hence for complete characterization of nanoparticle toxicity, epigenetic studies should be performed along with conventional toxicity testing methods.

 Epigenetics 2019

Thursday, November 22, 2018

Brain disorders & Epigenetics

All creatures have body weights of polychlorinated biphenyls (PCBs) regardless of their boycott decades prior. These and current endocrine-upsetting synthetic compounds (EDCs, for example, the fungicide vinclozolin (VIN) bother hormone flagging and prompt dysfunctions following pre-birth exposures. Past direct exposures, transgenerational ailment phenotypes can hold on for various ages without consequent introduction. The instruments of activity of these EDCs vary: VIN is hostile to androgenic while the PCB blend Aroclor 1221 (A1221) is pitifully estrogenic. In view of restricted proof for the legacy of epimutations in germline, we gauged DNA methylation in cerebrum and sperm of rodents. Pregnant dams were uncovered from day 8-18 of growth to low measurements of VIN, A1221, or the vehicle. To deliver fatherly ancestries, uncovered F1 guys were reproduced with untreated females, making the F2 and in this way F3 ages. In grown-up F1 and F3 guys, develop sperm was gathered, and mind cores engaged with nervousness and social practices (CA3 of the hippocampus; focal amygdala) were chosen for examines of epimutations in CpG islands utilizing decreased portrayal bisulfite sequencing. In F1 sperm, VIN and PCBs incited differential methylation in 215 and 284 CpG islands, individually, contrasted with vehicle. The dominant part of impacts were related with hypermethylation. Less epimutations were recognized in the cerebrum. A subset of differentially methylated areas were held from the F1 to the F3 age, recommending a typical component of EDC and germline epigenome cooperation. In this manner, EDCs can cause heritable epimutations in the sperm that may encapsulate the future phenotype of cerebrum conduct issue caused by direct or transgenerational exposures.

 Epigenetics 2019

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