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Epigenetic marker

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https://www.readbyqxmd.com/read/29679205/changes-in-the-position-and-volume-of-inactive-x-chromosomes-during-the-g0-g1-transition
#1
Guoliang Lyu, Tan Tan, Yiting Guan, Lei Sun, Qianjin Liang, Wei Tao
In female mammals, each cell silences one X chromosome by converting it into transcriptionally inert heterochromatin. The inactivation is concomitant with epigenetic changes including methylation of specific histone residues and incorporation of macroH2A. Such epigenetic changes may exert influence on the positioning of the inactive X chromosome (Xi) within the nucleus beyond the level of chromatin structure. However, the dynamic positioning of the inactive X chromosome during cell cycle remains unclear. Here, we show that H3K27me3 is a cell-cycle-independent marker for the inactivated X chromosomes in WI38 cells...
April 21, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29672679/disease-prediction-by-cell-free-dna-methylation
#2
Hao Feng, Peng Jin, Hao Wu
Disease diagnosis using cell-free DNA (cfDNA) has been an active research field recently. Most existing approaches perform diagnosis based on the detection of sequence variants on cfDNA; thus, their applications are limited to diseases associated with high mutation rate such as cancer. Recent developments start to exploit the epigenetic information on cfDNA, which could have substantially wider applications. In this work, we provide thorough reviews and discussions on the statistical method developments and data analysis strategies for using cfDNA epigenetic profiles, in particular DNA methylation, to construct disease diagnostic models...
April 16, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29672536/development-of-a-quantitative-pachytene-chromosome-map-and-its-unification-with-somatic-chromosome-and-linkage-maps-of-rice-oryza-sativa-l
#3
Nobuko Ohmido, Aiko Iwata, Seiji Kato, Toshiyuki Wako, Kiichi Fukui
A quantitative pachytene chromosome map of rice (Oryza sativa L.) was developed using imaging methods. The map depicts not only distribution patterns of chromomeres specific to pachytene chromosomes, but also the higher order information of chromosomal structures, such as heterochromatin (condensed regions), euchromatin (decondensed regions), the primary constrictions (centromeres), and the secondary constriction (nucleolar organizing regions, NOR). These features were image analyzed and quantitatively mapped onto the map by Chromosome Image Analyzing System ver...
2018: PloS One
https://www.readbyqxmd.com/read/29670281/identification-of-the-tumour-transition-states-occurring-during-emt
#4
Ievgenia Pastushenko, Audrey Brisebarre, Alejandro Sifrim, Marco Fioramonti, Tatiana Revenco, Soufiane Boumahdi, Alexandra Van Keymeulen, Daniel Brown, Virginie Moers, Sophie Lemaire, Sarah De Clercq, Esmeralda Minguijón, Cédric Balsat, Youri Sokolow, Christine Dubois, Florian De Cock, Samuel Scozzaro, Federico Sopena, Angel Lanas, Nicky D'Haene, Isabelle Salmon, Jean-Christophe Marine, Thierry Voet, Panagiota A Sotiropoulou, Cédric Blanpain
In cancer, the epithelial-to-mesenchymal transition (EMT) is associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However, there is no direct in vivo evidence for this idea. Here we screen a large panel of cell surface markers in skin and mammary primary tumours, and identify the existence of multiple tumour subpopulations associated with different EMT stages: from epithelial to completely mesenchymal states, passing through intermediate hybrid states...
April 18, 2018: Nature
https://www.readbyqxmd.com/read/29670108/down-regulation-of-a-pro-apoptotic-pathway-regulated-by-pcaf-ada3-in-early-stage-gastric-cancer
#5
Daniella Brasacchio, Rita A Busuttil, Tahereh Noori, Ricky W Johnstone, Alex Boussioutas, Joseph A Trapani
The loss of p300/CBP-associated protein (PCAF) expression is associated with poor clinical outcome in gastric cancer, and a potential bio-marker for invasive and aggressive tumors. However, the mechanism linking loss of PCAF to the onset of gastric cancer has not been identified. Given that PCAF and its binding partner transcriptional adaptor protein 3 (ADA3) were recently shown to regulate the intrinsic (mitochondrial) pathway to apoptosis via epigenetic regulation of phosphofurin acidic cluster sorting proteins 1 and 2 (PACS1, PACS2), we analyzed PCAF, ADA3, and PACS1/2 expression in 99 patient-matched surgical samples ranging from normal gastric mucosa, through pre-malignant chronic gastritis and intestinal metaplasia to stage I-III invasive cancers...
April 18, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29669575/effects-of-senolytic-drugs-on-human-mesenchymal-stromal-cells
#6
Clara Grezella, Eduardo Fernandez-Rebollo, Julia Franzen, Mónica Sofia Ventura Ferreira, Fabian Beier, Wolfgang Wagner
BACKGROUND: Senolytic drugs are thought to target senescent cells and might thereby rejuvenate tissues. In fact, such compounds were suggested to increase health and lifespan in various murine aging models. So far, effects of senolytic drugs have not been analysed during replicative senescence of human mesenchymal stromal cells (MSCs). METHODS: In this study, we tested four potentially senolytic drugs: ABT-263 (navitoclax), quercetin, nicotinamide riboside, and danazol...
April 18, 2018: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29669262/dna-mismatch-repair-in-cancer
#7
REVIEW
Marina Baretti, Dung T Le
Microsatellite instability (MSI) refers to the hypermutator phenotype secondary to frequent polymorphism in short repetitive DNA sequences and single nucleotide substitution, as consequence of DNA mismatch repair (MMR) deficiency. MSI secondary to germline mutation in DNA MMR proteins is the molecular fingerprint of Lynch Syndrome (LS), while epigenetic inactivation of these genes is more commonly found in sporadic MSI tumors. MSI occurs at different frequencies across malignancies, although original methods to assess MSI or MMR deficiency have been developed mostly in LS related cancers...
April 15, 2018: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/29669110/chronic-occupational-exposure-endured-by-tobacco-farmers-from-brazil-and-association-with-dna-damage
#8
Vívian F Silva Kahl, Varinderpal Singh Dhillon, Daniel Simon, Fernanda Rabaioli da Silva, Mirian Salvador, Cátia Dos Santos Branco, Mónica Cappetta, Wilner Martínez-López, Flávia V Thiesen, Johnny F Dias, Claudia Telles de Souza, Michael Fenech, Juliana da Silva
Tobacco farming is an important economic income in Brazil, although it has been challenged as regard the occupational exposure to both pesticides and nicotine endured by farmers. Chronic occupational exposure to complex mixtures can lead to health hazardous. We examined genomic instability and epigenetic changes in tobacco farmers occupationally exposed to pesticide mixtures and nicotine at tobacco fields. DNA damage was assessed by alkaline comet assay in blood cells. Genomic DNA was isolated, and telomere length was measured using quantitative polymerase chain reaction assay...
April 13, 2018: Mutagenesis
https://www.readbyqxmd.com/read/29666172/genetic-editing-of-colonic-organoids-provides-a-molecularly-distinct-and-orthotopic-preclinical-model-of-serrated-carcinogenesis
#9
Tamsin R M Lannagan, Young K Lee, Tongtong Wang, Jatin Roper, Mark L Bettington, Lochlan Fennell, Laura Vrbanac, Lisa Jonavicius, Roshini Somashekar, Krystyna Gieniec, Miao Yang, Jia Q Ng, Nobumi Suzuki, Mari Ichinose, Josephine A Wright, Hiroki Kobayashi, Tracey L Putoczki, Yoku Hayakawa, Simon J Leedham, Helen E Abud, Ömer H Yilmaz, Julie Marker, Sonja Klebe, Pratyaksha Wirapati, Siddhartha Mukherjee, Sabine Tejpar, Barbara A Leggett, Vicki L J Whitehall, Daniel L Worthley, Susan L Woods
OBJECTIVE: Serrated colorectal cancer (CRC) accounts for approximately 25% of cases and includes tumours that are among the most treatment resistant and with worst outcomes. This CRC subtype is associated with activating mutations in the mitogen-activated kinase pathway gene, BRAF , and epigenetic modifications termed the CpG Island Methylator Phenotype, leading to epigenetic silencing of key tumour suppressor genes. It is still not clear which (epi-)genetic changes are most important in neoplastic progression and we begin to address this knowledge gap herein...
April 17, 2018: Gut
https://www.readbyqxmd.com/read/29665672/regulatory-network-of-arf-in-cancer-development
#10
Aram Ko, Su Yeon Han, Jaewhan Song
ARF is a tumor suppressor protein that has a pivotal role in the prevention of cancer development through regulating cell proliferation, senescence, and apoptosis. As a factor that induces senescence, the role of ARF as a tumor suppressor is closely linked to the p53-MDM2 axis, which is a key process that restrains tumor formation. Thus, many cancer cells either lack a functional ARF or p53, which enables them to evade cell oncogenic stress-mediated cycle arrest, senescence, or apoptosis. In particular, the ARF gene is a frequent target of genetic and epigenetic alterations including promoter hypermethylation or gene deletion...
April 18, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29665409/epigenomic-biomarkers-for-prognostication-and-diagnosis-of-gastrointestinal-cancers
#11
REVIEW
Chi Chun Wong, Weilin Li, Bertina Chan, Jun Yu
Altered epigenetic regulation is central to many human diseases, including cancer. Over the past two decade, major advances have been made in our understanding of the role of epigenetic alterations in carcinogenesis, particularly for DNA methylation, histone modifications and non-coding RNAs. Aberrant hypermethylation of DNA at CpG islands is a well-established phenomenon that mediates transcriptional silencing of tumor suppressor genes, and it is an early event integral to gastrointestinal cancer development...
April 14, 2018: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29665055/s6k1-controls-epigenetic-plasticity-for-the-expression-of-pancreatic-%C3%AE-%C3%AE-cell-marker-genes
#12
Sang Ah Yi, Jieun Lee, Jong Woo Park, Jihoon Han, Min Gyu Lee, Ki Hong Nam, Jee Hun Park, Hwamok Oh, Sung Jin Ahn, Saetbyul Kim, So Hee Kwon, Dong-Gyu Jo, Jeung-Whan Han
The failure of insulin production by pancreatic β cells is a common hallmark of type 1 diabetes mellitus (T1DM). Because administration of exogenous insulin is associated with diabetes-derived complications, endogenous α to β cell transition can be an attractive alternative. Although decreased β cell size and hypoinsulinaemia have been observed in S6K1-deficient mice, the molecular mechanism underlying the involvement of S6K1 in the transcriptional regulation of insulin remains elusive. Here, we show that the hypoinsulinaemic phenotype of S6K1-deficient mice stems from the dysregulated transcription of a set of genes required for insulin and glucagon production...
April 17, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29653143/phenotypic-characterization-of-the-sirc-statens-seruminstitut-rabbit-cornea-cell-line-reveals-a-mixed-epithelial-and-fibroblastic-nature
#13
Melania Olivieri, Martina Cristaldi, Salvatore Pezzino, Dario Rusciano, Barbara Tomasello, Carmelina Daniela Anfuso, Gabriella Lupo
The aim of the present study was to investigate, in the Statens Seruminstitut Rabbit Cornea (SIRC) cell line, the presence of epithelial and fibroblastic markers, comparing their levels with those of the human Retinal Pigmented Epithelial (ARPE-19) cell line, and the Human Keratocyte (HK) cell line, respectively. SIRC cells, often described as of epithelial origin, are used as a corneal epithelial barrier model to study the permeability of ophthalmic drugs. However, they show a morphology that is more consistent with a fibroblastic cell phenotype, similar to corneal keratocytes...
April 10, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29651348/dna-methylation-status-of-the-interspersed-repetitive-sequences-for-line-1-alu-herv-e-and-herv-k-in-trabeculectomy-specimens-from-glaucoma-eyes
#14
Sunee Chansangpetch, Sasiprapa Prombhul, Visanee Tantisevi, Pimpayao Sodsai, Anita Manassakorn, Nattiya Hirankarn, Shan C Lin
Background/Aims: Epigenetic mechanisms via DNA methylation may be related to glaucoma pathogenesis. This study aimed to determine the global DNA methylation level of the trabeculectomy specimens among patients with different types of glaucoma and normal subjects. Methods: Trabeculectomy sections from 16 primary open-angle glaucoma (POAG), 12 primary angle-closure glaucoma (PACG), 16 secondary glaucoma patients, and 10 normal controls were assessed for DNA methylation using combined-bisulfite restriction analysis...
2018: Journal of Ophthalmology
https://www.readbyqxmd.com/read/29643973/epigenetic-versus-genetic-deregulation-of-the-keap1-nrf2-axis-in-solid-tumors-focus-on-methylation-and-noncoding-rnas
#15
REVIEW
F P Fabrizio, A Sparaneo, D Trombetta, L A Muscarella
Oxidative and electrophilic changes in cells are mainly coordinated by the KEAP1/NRF2 (Kelch-like erythroid-derived cap-n-collar homology- (ECH-) associated protein-1/nuclear factor (erythroid-derived 2)-like 2) axis. The physical interaction between these two proteins promotes the expression of several antioxidant defense genes in response to exogenous and endogenous insults. Recent studies demonstrated that KEAP1/NRF2 axis dysfunction is also strongly related to tumor progression and chemo- and radiotherapy resistance of cancer cells...
2018: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/29628786/personalized-medicine-in-oncology-new-perspectives-in-management-of-gliomas
#16
REVIEW
Justyna Gil, Izabela Laczmanska, Karolina A Pesz, Maria M Sasiadek
Studies on genetic and epigenetic mechanisms of carcinogenesis have led to the discovery of crucial genetic events for many of particular malignancies. This was followed by invention of new therapeutic approaches based on molecular mechanisms underlying cancer development and progression that bears the name of personalised medicine. In the case of gliomas, ascertainment of genetic/epigenetic markers was the basis for re-classification of tumours that until now depended on histopathological analysis. This article reviews recent advances in personalised medicine and the new World Health Organisation classification of gliomas...
March 2018: Contemporary Oncology Współczesna Onkologia
https://www.readbyqxmd.com/read/29627753/cr-vi-induced-methylation-and-down-regulation-of-dna-repair-genes-and-its-association-with-markers-of-genetic-damage-in-workers-and-16hbe-cells
#17
Guiping Hu, Ping Li, Xiaoxing Cui, Yang Li, Ji Zhang, Xinxiao Zhai, Shanfa Yu, Shichuan Tang, Zuchang Zhao, Jing Wang, Guang Jia
To examine the mechanism of hexavalent chromium [Cr(VI)]-induced carcinogenesis, a cross-sectional study in workers with or without exposure to Cr(VI) as well as in vitro administration of Cr(VI) in 16HBE cells was conducted. We explored the associations between Cr(VI) exposure, methylation modification of DNA repair genes and their expression levels, and genetic damage. Results showed that hypermethylation of CpG sites were observed in both occupationally exposed workers and 16HBE cells administrated Cr(VI)...
April 5, 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29622848/the-hdac-inhibitor-saha-prevents-colonic-inflammation-by-suppressing-pro-inflammatory-cytokines-and-chemokines-in-dss-induced-colitis
#18
Mohmand Noor Ali, Narantsog Choijookhuu, Hideaki Takagi, Naparee Srisowanna, Mai Nguyen Nhat Huynh, Yuya Yamaguchi, Phyu Synn Oo, Myat Tin Htwe Kyaw, Katsuaki Sato, Ryoji Yamaguchi, Yoshitaka Hishikawa
Inflammatory bowel disease (IBD) is an inflammatory disorder of the gastrointestinal tract that is caused by multiple factors, including dysfunction of the immune system and genetic and epigenetic alterations. Aberrant epigenetic regulation, especially histone acetylation, was found in biopsies from IBD patients and mouse models of colitis, suggesting that an epigenetic treatment approach may be useful for IBD therapy. Therefore, we investigated the effects of the histone deacetylase (HDAC) inhibitor, suberoylanilide hydroxamic acid (SAHA), in a mouse model of dextran sulfate sodium (DSS)-induced colitis...
February 27, 2018: Acta Histochemica et Cytochemica
https://www.readbyqxmd.com/read/29615864/molecular-neuropathology-of-astrocytes-and-oligodendrocytes-in-alcohol-use-disorders
#19
REVIEW
José J Miguel-Hidalgo
Postmortem studies reveal structural and molecular alterations of astrocytes and oligodendrocytes in both the gray and white matter (GM and WM) of the prefrontal cortex (PFC) in human subjects with chronic alcohol abuse or dependence. These glial cellular changes appear to parallel and may largely explain structural and functional alterations detected using neuroimaging techniques in subjects with alcohol use disorders (AUDs). Moreover, due to the crucial roles of astrocytes and oligodendrocytes in neurotransmission and signal conduction, these cells are very likely major players in the molecular mechanisms underpinning alcoholism-related connectivity disturbances between the PFC and relevant interconnecting brain regions...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29615218/placental-promoter-methylation-of-dna-repair-genes-and-prenatal-exposure-to-particulate-air-pollution-an-environage-cohort-study
#20
Kristof Y Neven, Nelly D Saenen, Letitzia Tarantini, Bram G Janssen, Wouter Lefebvre, Charlotte Vanpoucke, Valentina Bollati, Tim S Nawrot
BACKGROUND: Exposure to particulate air pollution has been linked with risk of carcinogenesis. Damage to repair pathways might have long-term adverse health effects. We aimed to investigate the association of prenatal exposure to air pollution with placental mutation rate and the DNA methylation of key placental DNA repair genes. METHODS: This cohort study used data from the ongoing ENVironmental Influence ON early AGEing (ENVIRONAGE) birth cohort, which enrols pairs of mothers and neonates (singleton births only) at the East-Limburg Hospital (Genk, Belgium)...
April 2018: Lancet. Planetary Health
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