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Epigenetic markers

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https://www.readbyqxmd.com/read/29690914/klk10-exon-3-unmethylated-pcr-product-concentration-a-new-potential-early-diagnostic-marker-in-ovarian-cancer-a-pilot-study
#1
Mustafa A El Sherbini, Amal A Mansour, Maha M Sallam, Emtiaz A Shaban, Zeinab A Shehab ElDin, Amr H El-Shalakany
BACKGROUND: KLK10 exon 3 hypermethylation correlated to tumor-specific lack of KLK10 expression in cancer cell lines and primary tumors. In the present study we investigate the possible role of KLK10 exon 3 methylation in ovarian tumor diagnosis and prognosis. RESULTS: Qualitative methylation-specific PCR (MSP) results did not show statistically significant differences in patient group samples (normal and tumor) where all samples were positive only for the unmethylated-specific PCR except for two malignant samples that were either doubly positive (serous carcinoma) or doubly negative (Sertoli-Leydig cell tumor) for the two MSP tests...
April 24, 2018: Journal of Ovarian Research
https://www.readbyqxmd.com/read/29688621/an-epigenetic-signature-in-adipose-tissue-is-linked-to-nicotinamide-n-methyltransferase-gene-expression
#2
Ana B Crujeiras, Pavlos Pissios, Jose M Moreno-Navarrete, Angel Diaz-Lagares, Juan Sandoval, Antonio Gomez, Wilfredo Ricart, Manel Esteller, Felipe F Casanueva, Jose M Fernandez-Real
SCOPE: The enzyme nicotinamide N-methyltransferase (NNMT) is a major methyltransferase in adipose tissue. We hypothesized an epigenetic signature in association with NNMT gene expression in adipose tissue. METHODS AND RESULTS: The global human methylome was analyzed in visceral adipose tissue (VAT) from morbidly obese patients using the Infinium HumanMethylation450 BeadChip array (discovery cohort: n  =  11). The findings were confirmed in two additional independent cohorts (Cohort 1: n  =  60; BMI 20-60 kg/m2 and cohort 2: n  =  40; BMI >40 kg/m2 ) and validated after weight loss (using microarray data)...
April 24, 2018: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/29687310/genotype-and-phenotype-in-multiple-sclerosis-potential-for-disease-course-prediction
#3
REVIEW
Vilija G Jokubaitis, Yuan Zhou, Helmut Butzkueven, Bruce V Taylor
PURPOSE OF REVIEW: This review will examine the current evidence that genetic and/or epigenetic variation may influence the multiple sclerosis (MS) clinical course, phenotype, and measures of MS severity including disability progression and relapse rate. RECENT FINDINGS: There is little evidence that MS clinical phenotype is under significant genetic control. There is increasing evidence that there may be genetic determinants of the rate of disability progression...
April 24, 2018: Current Treatment Options in Neurology
https://www.readbyqxmd.com/read/29685967/germ-cell-tumour-subtypes-display-differential-expression-of-microrna371a-3p
#4
Bárbara Vilela-Salgueiro, Daniela Barros-Silva, João Lobo, Ana Laura Costa, Rita Guimarães, Mariana Cantante, Paula Lopes, Isaac Braga, Jorge Oliveira, Rui Henrique, Carmen Jerónimo
Testicular germ cell tumours (TGCTs) are a heterogeneous group of neoplasms, mostly affecting young men. Curability rates are high and adequate treatment relies on careful and accurate pathological and clinical assessment. Indeed, TGCTs' histopathological subtyping is critical for adequate therapeutic decision. Considering the limitation of currently available serum biomarkers, novel candidates have been proposed, most notably miR-371a-3p, which outperformed classical serum markers, but no detailed information concerning TGCT subtype was available...
June 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29685391/interactions-of-hp1-bound-to-h3k9me3-dinucleosome-by-molecular-simulations-and-biochemical-assays
#5
Shuhei Watanabe, Yuichi Mishima, Masahiro Shimizu, Isao Suetake, Shoji Takada
Heterochromatin protein 1 (HP1), associated with heterochromatin formation, recognizes an epigenetically repressive marker, trimethylated lysine 9 in histone H3 (H3K9me3), and generally contributes to long-term silencing. How HP1 induces heterochromatin is not fully understood. Recent experiments suggested that not one, but two nucleosomes provide a platform for this recognition. Integrating previous and new biochemical assays with computational modeling, we provide near-atomic structural models for HP1 binding to the dinucleosomes...
April 20, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29682093/dna-methylation-in-osteoarthritis-current-status-and-therapeutic-implications
#6
REVIEW
Antonio Miranda-Duarte
Background: Primary Osteoarthritis (OA) is a multifactorial disease in which genetic factors are strongly associated with its development; however, recently it has been observed that epigenetic modifications are also involved in the pathogenesis of OA. DNA methylation is related to gene silencing, and several studies have investigated its role in the loci of different pathways or molecules associated to OA. Objective: This review is focused on the current status of DNA methylation studies related to OA pathogenesis...
2018: Open Rheumatology Journal
https://www.readbyqxmd.com/read/29682090/the-neuropeptide-genes-sst-tac1-hcrt-npy-and-gal-are-powerful-epigenetic-biomarkers-in-head-and-neck-cancer-a-site-specific-analysis
#7
Kiyoshi Misawa, Masato Mima, Atsushi Imai, Daiki Mochizuki, Yuki Misawa, Shiori Endo, Ryuji Ishikawa, Takeharu Kanazawa, Hiroyuki Mineta
Background: Staging and pathological grading systems are convenient but imperfect predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). Identifying biomarkers for HNSCC that will progress and cause death is a critical research area, particularly if the biomarker can be linked to selection of patients. Therefore, to identify potential alternative prognostic markers, we investigated the methylation status of five neuropeptide gene promoters. The promoter methylation status was determined by quantitative methylation-specific PCR in 230 cases of HNSCC; 58 hypopharynx, 45 larynx, 56 oropharynx, and 71 oral cavity tumor samples were studied...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29682088/-gli2-promoter-hypermethylation-in-saliva-of-children-with-a-respiratory-allergy
#8
Sabine A S Langie, Matthieu Moisse, Katarzyna Szarc Vel Szic, Ellen Van Der Plas, Gudrun Koppen, Sofie De Prins, Tijs Louwies, Vera Nelen, Guy Van Camp, Diether Lambrechts, Greet Schoeters, Wim Vanden Berghe, Patrick De Boever
Background: The prevalence of respiratory allergy in children is increasing. Epigenetic DNA methylation changes are plausible underlying molecular mechanisms. Results: Saliva samples collected in substudies of two longitudinal birth cohorts in Belgium (FLEHS1 & FLEHS2) were used to discover and confirm DNA methylation signatures that can differentiate individuals with respiratory allergy from healthy subjects. Genome-wide analysis with Illumina Methylation 450K BeadChips revealed 23 differentially methylated gene regions (DMRs) in saliva from 11y old allergic children (N=26) vs...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29681542/dna-methylation-and-regulatory-elements-during-chicken-germline-stem-cell-differentiation
#9
Yanghua He, Qisheng Zuo, John Edwards, Keji Zhao, Jinzhi Lei, Wentao Cai, Qing Nie, Bichun Li, Jiuzhou Song
The production of germ cells in vitro would open important new avenues for stem biology and human medicine, but the mechanisms of germ cell differentiation are not well understood. The chicken, as a great model for embryology and development, was used in this study to help us explore its regulatory mechanisms. In this study, we reported a comprehensive genome-wide DNA methylation landscape in chicken germ cells, and transcriptomic dynamics was also presented. By uncovering DNA methylation patterns on individual genes, some genes accurately modulated by DNA methylation were found to be associated with cancers and virus infection, e...
April 17, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/29679205/changes-in-the-position-and-volume-of-inactive-x-chromosomes-during-the-g0-g1-transition
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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