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Epigenetics profilling

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https://www.readbyqxmd.com/read/29332359/novel-molecular-and-metabolic-aspects-in-osteosarcoma
#1
Evangelos Tsiambas, Panagiotis P Fotiades, Chrissa Sioka, Dimitrios Kotrotsios, Evangelia Gkika, Andreas Fotopoulos, Stylianos N Mastronikolis, Ilianna E Armata, Evangelos Giotakis, Vasileios Ragos
Osteosarcoma (OS) is the most frequent bone-forming malignancy in children and adolescents. Concerning its molecular landscape, there is no a direct relationship with a specific gene, but a combination of genetic events. A broad spectrum of activated oncogenes and downregulated suppressor genes has been already explored and considered crucial for its progressive pathogenesis. Mechanisms of gene deregulation include amplifications, point mutations, allelic losses and also epigenetic abnormalities such as aberrant promoter methylation...
November 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29331675/module-analysis-captures-pancancer-genetically-and-epigenetically-deregulated-cancer-driver-genes-for-smoking-and-antiviral-response
#2
Magali Champion, Kevin Brennan, Tom Croonenborghs, Andrew J Gentles, Nathalie Pochet, Olivier Gevaert
The availability of increasing volumes of multi-omics profiles across many cancers promises to improve our understanding of the regulatory mechanisms underlying cancer. The main challenge is to integrate these multiple levels of omics profiles and especially to analyze them across many cancers. Here we present AMARETTO, an algorithm that addresses both challenges in three steps. First, AMARETTO identifies potential cancer driver genes through integration of copy number, DNA methylation and gene expression data...
December 1, 2017: EBioMedicine
https://www.readbyqxmd.com/read/29329322/methylene-tetrahydrofolate-reductase-contributes-to-allergic-airway-disease
#3
Kenneth R Eyring, Brent S Pedersen, Kenneth N Maclean, Sally P Stabler, Ivana V Yang, David A Schwartz
RATIONALE: Environmental exposures strongly influence the development and progression of asthma. We have previously demonstrated that mice exposed to a diet enriched with methyl donors during vulnerable periods of fetal development can enhance the heritable risk of allergic airway disease through epigenetic changes. There is conflicting evidence on the role of folate (one of the primary methyl donors) in modifying allergic airway disease. OBJECTIVES: We hypothesized that blocking folate metabolism through the loss of methylene-tetrahydrofolate reductase (Mthfr) activity would reduce the allergic airway disease phenotype through epigenetic mechanisms...
2018: PloS One
https://www.readbyqxmd.com/read/29325629/bioinformatics-and-genomic-databases
#4
Jason Chen, Giovanni Coppola
High-throughput, low-cost sequencing technologies have begun to yield new insights into biology and medicine. New data enable the interrogation of the molecular biology of disease from DNA to RNA to protein, charting the central dogma. This chapter reviews some of the key advances and resources in the application of bioinformatics to understanding, and ultimately diagnosing and treating, diseases of the nervous system. Array genotyping, exome sequencing, and whole-genome sequencing, in both disease and healthy populations, have enabled the interpretation of new genetic data...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#5
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29324471/sellar-region-atypical-teratoid-rhabdoid-tumors-atrt-in-adults-display-dna-methylation-profiles-of-the-atrt-myc-subgroup
#6
Pascal D Johann, Susanne Bens, Florian Oyen, Rabea Wagener, Caterina Giannini, Arie Perry, Jack M Raisanen, Gerald F Reis, Sumihito Nobusawa, Kazunori Arita, Jörg Felsberg, Guido Reifenberger, Abbas Agaimy, Rolf Buslei, David Capper, Stefan M Pfister, Reinhard Schneppenheim, Reiner Siebert, Michael C Frühwald, Werner Paulus, Marcel Kool, Martin Hasselblatt
Atypical teratoid/rhabdoid tumor (ATRT) is a highly malignant brain tumor predominantly encountered in infants. Mutations of the SMARCB1 gene are the characteristic genetic lesion. A small group of ATRT stands out clinically, because these tumors are located in the sellar region of adults. To investigate if sellar region ATRT in adults represents a molecular distinct entity, we characterized molecular alterations in 7 sellar region ATRTs in adults as compared with 150 pediatric ATRTs and 47 pituitary adenomas using SMARCB1 sequencing, multiplex ligation-dependent probe amplification and fluorescence in situ hybridization as well as DNA methylation profiling...
January 10, 2018: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29320577/genome-wide-profiling-of-the-piwi-interacting-rna-mrna-regulatory-networks-in-epithelial-ovarian-cancers
#7
Garima Singh, Jyoti Roy, Pratiti Rout, Bibekanand Mallick
PIWI-interacting (piRNAs), ~23-36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29318561/analysis-of-somatic-dna-methylation-alterations-of-genes-encoding-cell-surface-metallopeptidases-in-colorectal-cancer
#8
Sergio Alonso, Beatriz González, Andreu Alibés, Manuel Perucho
The genome of cancer cells accumulates numerous genetic and epigenetic somatic alterations ultimately conferring capabilities for unrestrained growth, invasion of local tissues, migration, and colonization of distant organs. Many of these new capabilities require the disruption of the cell-to-cell interactions between the cancer cell and its microenvironment. These interactions are mediated, among other factors, by the activity of extracellular enzymes that reshape not only the extracellular compartment of the cancer cells but also that of the neighboring non-cancerous stroma cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29317756/non-coding-rnas-predict-recurrence-free-survival-of-patients-with-hypoxic-tumours
#9
Victor D Martinez, Natalie S Firmino, Erin A Marshall, Kevin W Ng, Brennan J Wadsworth, Christine Anderson, Wan L Lam, Kevin L Bennewith
Hypoxia promotes tumour aggressiveness and reduces patient survival. A spectrum of poor outcome among patients with hypoxic tumours suggests that additional factors modulate how tumours respond to hypoxia. PIWI-interacting RNAs (piRNAs) are small non-coding RNAs with a pivotal role in genomic stability and epigenetic regulation of gene expression. We reported that cancer type-specific piRNA signatures vary among patients. However, remarkably homogenous piRNA profiles are detected across patients with renal cell carcinoma, a cancer characterized by constitutive upregulation of hypoxia-related signaling induced by common mutation or loss of von Hippel-Lindau factor (VHL)...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317608/epigenetics-and-cerebral-organoids-promising-directions-in-autism-spectrum-disorders
#10
REVIEW
Sheena Louise Forsberg, Mirolyuba Ilieva, Tanja Maria Michel
Autism spectrum disorders (ASD) affect 1 in 68 children in the US according to the Centers for Disease Control and Prevention (CDC). It is characterized by impairments in social interactions and communication, restrictive and repetitive patterns of behaviors, and interests. Owing to disease complexity, only a limited number of treatment options are available mainly for children that alleviate but do not cure the debilitating symptoms. Studies confirm a genetic link, but environmental factors, such as medications, toxins, and maternal infection during pregnancy, as well as birth complications also play a role...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29317265/wound-regeneration-deficit-in-rats-correlates-with-low-morphogenetic-potential-and-distinct-transcriptome-profile-of-epidermis
#11
Christian F Guerrero-Juarez, Aliaksandr A Astrowski, Rabi Murad, Christina T Dang, Vera O Shatrova, Aksana Astrowskaja, Chae Ho Lim, Raul Ramos, Xiaojie Wang, Yuchen Liu, Hye-Lim Lee, Kim T Pham, Tsai-Ching Hsi, Ji Won Oh, Daniel Crocker, Ali Mortazavi, Mayumi Ito, Maksim V Plikus
Large excisional wounds in mice prominently regenerate new hair follicles (HFs) and fat, yet humans are deficient for this regenerative behavior. Currently, wound-induced regeneration remains a clinically desirable, but only partially understood phenomenon. We show that large excisional wounds in rats, across seven strains fail to regenerate new HFs. We compared wound transcriptomes between mice and rats at the time of scab detachment, which coincides with the onset of HF regeneration in mice. In both species, wound dermis and epidermis share core dermal and epidermal transcriptional programs respectively, yet prominent inter-species differences exist...
January 6, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29316435/molecular-predictors-of-gastric-neoplastic-progression
#12
Paul Lochhead, Emad M El-Omar
In this issue of Cancer Cell, Huang et al. describe comprehensive genetic and epigenetic profiling of gastric intestinal metaplasia lesions from a longitudinal cohort in which outcome data allowed for identification of potential markers of gastric neoplastic progression.
January 8, 2018: Cancer Cell
https://www.readbyqxmd.com/read/29315816/uncovering-the-potential-of-cd44v-syne1-mir34a-axis-in-salivary-fluids-of-oral-cancer-patients
#13
Kavan Shah, Shanaya Patel, Bansri Modi, Franky Shah, Rakesh Rawal
OBJECTIVES: Late stage diagnosis is one of the major confounders for poor prognosis of oral cancer patients owing to lack of a biomarker to diagnose this disease at an early stage. Moreover, till date invasive biopsies are the only option to assess disease occurrence and progression in this malignancy. Thus, this study aims to identify and assess potential salivary markers in OSCC patients in order to open newer avenues in the field of non-invasive biopsies. METHODOLOGY: Bioinformatic based analysis were performed to identify potential biomarkers that could be assessed in OSCC patients...
January 8, 2018: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/29315310/dysregulation-of-valvular-interstitial-cell-let-7c-mir-17-mir-20a-and-mir-30d-in-naturally-occurring-canine-myxomatous-mitral-valve-disease
#14
Vicky K Yang, Albert K Tai, Terry P Huh, Dawn M Meola, Christine M Juhr, Nicholas A Robinson, Andrew M Hoffman
Canine myxomatous mitral valve disease (MMVD) resembles the early stages of myxomatous pathology seen in human non-syndromic mitral valve prolapse, a common valvular heart disease in the adult human population. Canine MMVD is seen in older subjects, suggesting age-related epigenetic dysregulation leading to derangements in valvular cell populations and matrix synthesis or degradation. We hypothesized that valvular interstitial cells (VICs) undergo disease-relevant changes in miRNA expression. In primary VIC lines from diseased and control valves, miRNA expression was profiled using RT-qPCR and next generation sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29315108/review-of-molecular-classification-and-treatment-implications-of-pediatric-brain-tumors
#15
Ana S Guerreiro Stucklin, Vijay Ramaswamy, Craig Daniels, Michael D Taylor
PURPOSE OF REVIEW: Brain tumors are the most common solid tumors and leading cause of cancer-related death in children. The advent of large-scale genomics has resulted in a plethora of profiling studies that have mapped the genetic and epigenetic landscapes of pediatric brain tumors, ringing in a new era of precision diagnostics and targeted therapies. In this review, we highlight the most recent findings, focusing on studies published after 2015, and discuss how new evidence is changing the care of children with brain tumors...
February 2018: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/29313708/human-lung-dna-methylation-quantitative-trait-loci-colocalize-with-copd-genome-wide-association-loci
#16
Jarrett D Morrow, Kimberly Glass, Michael H Cho, Craig P Hersh, Victor Pinto-Plata, Bartolome Celli, Nathaniel Marchetti, Gerard Criner, Raphael Bueno, George Washko, Augustine M K Choi, John Quackenbush, Edwin K Silverman, Dawn L DeMeo
RATIONALE: As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD and sub-genome-wide significant loci may play a role in pathogenesis. OBJECTIVES: Regulatory annotation with epigenetic evidence may give priority for further investigation, particularly for GWAS associations in non-coding regions...
January 9, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29313067/combinatorial-effects-of-histone-deacetylase-inhibitors-hdaci-vorinostat-and-entinostat-and-adaphostin-are-characterized-by-distinct-redox-alterations
#17
Nilsa Rivera-Del Valle, Tiewei Cheng, Mary E Irwin, Hayley Donnella, Melissa M Singh, Joya Chandra
PURPOSE: Amongst the epigenetically targeted therapies, targeting of the histone deacetylases (HDACs) has yielded numerous drugs for clinical use in hematological malignancies, but none as yet for acute lymphocytic leukemia (ALL). Single agent activity of HDAC inhibitors (HDACi) has been elusive in ALL, and has prompted study of combinatorial strategies. Because several HDACi raise levels of intracellular oxidative stress, we evaluated combinations of two structurally distinct HDACi with the redox active compound adaphostin in ALL...
January 8, 2018: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/29310721/the-utility-of-dna-extracted-from-saliva-for-genome-wide-molecular-research-platforms
#18
Fiona J Bruinsma, Jihoon E Joo, Ee Ming Wong, Graham G Giles, Melissa C Southey
OBJECTIVE: The study aimed to investigate the suitability of DNA extracted from saliva for high throughput molecular genotyping and DNA methylation platforms by comparing its performance with that of DNA extracted from blood. The genome-wide methylation profile, using the Infinium HumanMethylation450 Beadchip array® (Illumina, San Diego, CA), was measured for 20 DNA samples. Common genetic variation was measured, using the Infinium HumanCore Beadchip® (Illumina, San Diego, CA) for 4 samples (matching samples from 2 people)...
January 8, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29310712/genome-wide-screening-of-dna-methylation-in-bovine-blastocysts-with-different-kinetics-of-development
#19
Jessica Ispada, Camila Bruna de Lima, Marc-André Sirard, Patrícia Kubo Fontes, Marcelo Fábio Gouveia Nogueira, Kelly Annes, Marcella Pecora Milazzotto
BACKGROUND: The timing of the first cell divisions may predict the developmental potential of an embryo, including its ability to establish pregnancy. Besides differences related to metabolism, stress, and survival, embryos with different speeds of development present distinct patterns of gene expression, mainly related to energy and lipid metabolism. As gene expression is regulated by epigenetic factors, and that includes DNA methylation patterns, in this study we compared the global DNA methylation profile of embryos with different kinetics of development in order to identify general pathways and regions that are most influenced by this phenotype...
January 8, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29308326/depletion-of-tumor-associated-macrophages-switches-the-epigenetic-profile-of-pancreatic-cancer-infiltrating-t-cells-and-restores-their-anti-tumor-phenotype
#20
Simone Borgoni, Andrea Iannello, Santina Cutrupi, Paola Allavena, Maurizio D'Incalci, Francesco Novelli, Paola Cappello
Pancreatic Ductal Adenocarcinoma (PDA) is characterized by a complex tumor microenvironment that supports its progression, aggressiveness and resistance to therapies. The delicate interplay between cancer and immune cells creates the conditions for PDA development, particularly due to the functional suppression of T cell anti-tumor effector activity. However, some of the mechanisms involved in this process are still poorly understood. In this study, we analyze whether the functional and epigenetic profile of T cells that infiltrate PDA is modulated by the microenvironment, and in particular by tumor-associated macrophages (TAMs)...
2018: Oncoimmunology
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