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Epigenetics and diagnostic

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https://www.readbyqxmd.com/read/29772561/thyroid-cancer-phenotypes-in-relation-to-inflammation-and-autoimmunity
#1
Loredana Pagano, Chiara Mele, Maria Teresa Sama, Marco Zavattaro, Marina Caputo, Lucrezia De Marchi, Samuele Paggi, Flavia Prodam, Gianluca Aimaretti, Paolo Marzullo
Thyroid cancer represents the most frequent endocrine neoplasm and is epidemiologically linked to a growing incidence worldwide, which is only in part explained by the increased detection of small cancers in a preclinical stage. Understanding the molecular pathogenesis of well-differentiated thyroid cancers and poorly-differentiated thyroid cancers has prompted interest into the identification of crucial signaling pathways and molecular derangements related to genetic and epigenetic alterations. Increasing attention has been recently focused on inflammation and immunity as major culprit mechanisms involved in thyroid tumourigenesis, through the detection of activated immune cells, pro-inflammatory cytokines, as well as signal integrations between inflammatory and proliferative pathways within the thyroid tumour micro-environment...
June 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/29759571/prediction-models-for-endometrial-cancer-for-the-general-population-or-symptomatic-women-a-systematic-review
#2
REVIEW
Maaike Alblas, Kimberley B Velt, Nora Pashayan, Martin Widschwendter, Ewout W Steyerberg, Yvonne Vergouwe
OBJECTIVE: To provide an overview of prediction models for the risk of developing endometrial cancer in women of the general population or for the presence of endometrial cancer in symptomatic women. METHODS: We systematically searched the Embase and Pubmed database until September 2017 for relevant publications. We included studies describing the development, the external validation, or the updating of a multivariable model for predicting endometrial cancer in the general population or symptomatic women...
June 2018: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/29755768/detecting-promoter-methylation-pattern-of-apoptotic-genes-apaf1-and-caspase8-in-gastric-carcinoma-patients-undergoing-chemotherapy
#3
Fatemeh Azarkhazin, Golnaz Asaadi Tehrani
Background: DNA methylation patterns in cells dysregulation CpG island methylation of genes involved in cancer leads to increased levels of the cancer. Restoration of the apoptotic route in tumor cells of stomach in order for placing Casp8 and Apaf1 genes is a proper approach for new treatments of gastric cancer. The objective of the present study was to investigate the relationship between the pattern of methylation promoter in apoptotic genes of Casp8 and Apaf1 and gastric carcinoma in patients receiving chemotherapy...
April 2018: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/29742286/study-of-promoter-hypomethylation-profiles-of-ras-oncogenes-in-hepatocellular-carcinoma-derived-from-hepatitis-c-virus-genotype-3a-in-pakistani-population
#4
Maria Maryam, Muhammad Idrees
Epigenetic modifications such as DNA methylation contribute to progression of Hepatitis C virus (HCV) infection to life-threatening hepatocellular carcinoma (HCC), by promoting the silencing of tumor suppressor genes due to DNA hypermethylation and by causing genomic instability due to global hypomethylation. However few studies addressed promoter region hypomethylation status of the oncogenes involved in HCV derived HCC. In this study, we analyzed the promoter region methylation pattern of RAS oncogenes (HRAS, KRAS, NRAS) using methylation-specific PCR (MSP) for 50 Chronic HCV patients infected with genotype 3a (27 HCC patients and 23 Control non-HCC patients)...
May 9, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29741619/small-noncoding-rnas-in-fshd2-muscle-cells-reveal-both-dux4-and-smchd1-specific-signatures
#5
Jong-Won Lim, Chao-Jen Wong, Zizhen Yao, Rabi Tawil, Silvère M van der Maarel, Daniel G Miller, Stephen J Tapscott, Galina N Filippova
Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet...
May 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29740453/deoxyribonucleic-acid-methylation-in-systemic-lupus-erythematosus-implications-for-future-clinical-practice
#6
REVIEW
Emma Weeding, Amr H Sawalha
Differential deoxyribonucleic acid (DNA) methylation has emerged as a critical feature of systemic lupus erythematosus (SLE). Genome-wide DNA methylation studies have revealed methylation patterns characteristic of SLE-in particular, robust hypomethylation of interferon-regulated genes is a prominent finding in all cells of the immune system studied to date. These patterns reliably distinguish individuals with SLE from healthy controls and from individuals with other autoimmune diseases. For example, hypomethylation within IFI44L is both highly sensitive and highly specific for SLE, superior to currently available biomarkers...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29734178/long-non-coding-rna-sh3pxd2a-as1-promotes-cell-progression-partly-through-epigenetic-silencing-p57-and-klf2-in-colorectal-cancer
#7
Zhonghua Ma, Peng Peng, Jing Zhou, Bingqing Hui, Hao Ji, Juan Wang, Keming Wang
BACKGROUND/AIMS: Colorectal cancer (CRC) is one of the most commonly diagnosed malignancies worldwide. Current evidence has revealed the key roles of long non-coding RNAs (IncRNAs) in multiple cancers, including CRC. In this study we identified the lncRNA SH3PXD2A-AS1 as a novel molecule associated with CRC progression by analyzing the publicly available data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. METHODS: Quantitative real-time polymerase chain reaction (qRT-PCR) assays were performed to examine the expression levels of SH3PXD2A-AS1 in CRC tissue samples and CRC cell lines...
May 3, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29732534/epigenetic-loss-of-heparan-sulfate-3-o-sulfation-sensitizes-ovarian-carcinoma-to-oncogenic-signals-and-predicts-prognosis
#8
Rui-Lan Huang, Hsiang-Ju Chen, Lin-Yu Chen, Tai-Kuang Chao, Wei-Yu Lin, Phui-Ly Liew, Po-Hsuan Su, Yu-Chun Weng, Yu-Chi Wang, Chi-Chun Liao, Yaw-Wen Hsu, Hui- Chen Wang, Hung-Cheng Lai
Precision medicine requires markers for therapeutic guidance. The purpose of this study was to determine whether epithelial ovarian cancer (EOC) epigenetics can lead to the identification of biomarkers for precision medicine. Through integrative methylomics, we discovered and validated the epigenetic signature of NEFH and HS3ST2 as an independent prognostic factor for type II EOC in our dataset (n = 84), two independent methylomics datasets (total n = 467). Integrated transcriptomics dataset (n = 1147) and tissue microarrays (n = 54) of HS3ST2 also related to high-methylation statuses and the EOC prognosis...
May 7, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29732524/integrated-analysis-of-dynamic-fet-pet-ct-parameters-histology-and-methylation-profiling-of-44-gliomas
#9
Manuel Röhrich, Kristin Huang, Daniel Schrimpf, Nathalie L Albert, Thomas Hielscher, Andreas von Deimling, Ulrich Schüller, Antonia Dimitrakopoulou-Strauss, Uwe Haberkorn
PURPOSE: Dynamic 18 F-FET PET/CT is a powerful tool for the diagnosis of gliomas.18 F-FET PET time-activity curves (TAC) allow differentiation between histological low-grade gliomas (LGG) and high-grade gliomas (HGG). Molecular methods such as epigenetic profiling are of rising importance for glioma grading and subclassification. Here, we analysed dynamic 18 F-FET PET data, and the histological and epigenetic features of 44 gliomas. METHODS: Dynamic 18 F-FET PET was performed in 44 patients with newly diagnosed, untreated glioma: 10 WHO grade II glioma, 13 WHO grade III glioma and 21 glioblastoma (GBM)...
May 7, 2018: European Journal of Nuclear Medicine and Molecular Imaging
https://www.readbyqxmd.com/read/29725463/quantitative-assessment-of-gene-promoter-methylation-in-non-small-cell-lung-cancer-using-methylation-sensitive-high-resolution-melting
#10
Fangming Liu, Honglian Zhang, Shaohua Lu, Zhenhua Wu, Lin Zhou, Zule Cheng, Yanan Bai, Jianlong Zhao, Qiqing Zhang, Hongju Mao
DNA methylation is closely associated with aberrant epigenetic changes. Previous studies have identified various genes associated with non-small cell lung cancer (NSCLC), but the precise combination responsible for its etiology is still debated. The aim of the present study was to select a new set of NSCLC-related genes using methylation-sensitive high-resolution melting. The promoter methylation status of six selected genes, consisting of protocadherin γ subfamily B, 6 (PCDHGB6), homeobox A9 (HOXA9), O6 -methylguanine-DNA methyltransferase (MGMT), microRNA (miR)-126, suppressor of cytokine signaling 3 (SOCS3) and Ras association domain family member 5, also termed NORE1A, was evaluated in 54 NSCLC patients...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29721644/morphology-oriented-epigenetic-research
#11
REVIEW
Sohei Kitazawa, Ryuma Haraguchi, Riko Kitazawa
Cytosine methylation plays a major role in the regulation of sequential and tissue-specific expression of genes. De novo aberrant DNA methylation and demethylation are also crucial processes in tumorigenesis and tumor progression. The mechanisms of how and when such aberrant methylation and demethylation occur in tumor cells are still obscure, however. To evaluate subtle epigenetic alteration among minor subclonal populations, morphology-oriented epigenetic analysis is requisite, especially where heterogeneity and flexibility are as notable as in the process of cancer progression and cellular differentiation at critical stages...
May 2, 2018: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/29721069/release-of-micrornas-into-body-fluids-from-ten-organs-of-mice-exposed-to-cigarette-smoke
#12
Alberto Izzotti, Mariagrazia Longobardi, Sebastiano La Maestra, Rosanna T Micale, Alessandra Pulliero, Anna Camoirano, Marta Geretto, Francesco D'Agostini, Roumen Balansky, Mark Steven Miller, Vernon E Steele, Silvio De Flora
Purpose : MicroRNAs are small non-coding RNAs that regulate gene expression, thereby playing a role in a variety of physiological and pathophysiological states. Exposure to cigarette smoke extensively downregulates microRNA expression in pulmonary cells of mice, rats, and humans. Cellular microRNAs are released into body fluids, but a poor parallelism was previously observed between lung microRNAs and circulating microRNAs. The purpose of the present study was to validate the application of this epigenetic biomarker by using less invasive collection procedures...
2018: Theranostics
https://www.readbyqxmd.com/read/29709496/molecular-markers-associated-with-development-and-progression-of-potentially-premalignant-oral-epithelial-lesions-current-knowledge-and-future-implications
#13
REVIEW
Nikolaos G Nikitakis, Monica Pentenero, Maria Georgaki, Catherine F Poh, Douglas E Peterson, Paul Edwards, Mark Lingen, John J Sauk
Identification and management of potentially premalignant oral epithelial lesions (PPOELs) at highest risk of malignant transformation holds great promise for successful secondary prevention of oral squamous cell carcinoma, potentially reducing oral cancer morbidity and mortality. However, to date, neither clinical nor histopathologic validated risk predictors that can reliably predict which PPOELs will definitively progress to malignancy have been identified. In addition, the management of PPOELs remains a major challenge...
April 4, 2018: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/29707039/emerging-concepts-in-non-invasive-monitoring-of-crohn-s-disease
#14
REVIEW
Wojciech Marlicz, Karolina Skonieczna-Żydecka, Konstantinos John Dabos, Igor Łoniewski, Anastasios Koulaouzidis
Inflammatory bowel disease (IBD) is an umbrella term for Crohn's disease (CD) and ulcerative colitis (UC). In light of evolving epidemiology of CD, its clinical management is still complex and remains a challenge for contemporary physicians. With the advent of new diagnostic and treatment paradigms, there is a growing need for new biomarkers to guide decision-making, differential diagnosis, disease activity monitoring, as well as prognosis. However, both clinical and endoscopic scoring systems, widely utilized for disease monitoring and prognosis, have drawbacks and limitations...
2018: Therapeutic Advances in Gastroenterology
https://www.readbyqxmd.com/read/29706556/liquid-biopsies-dna-methylation-analyses-in-circulating-cell-free-dna
#15
REVIEW
Hu Zeng, Bo He, Chengqi Yi, Jinying Peng
Analysis of patient's materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potential for numerous diagnostic applications. Circulating cell-free DNA (cfDNA) is explored as a prognostic or predictive marker of liquid biopsies with the improvements in genomic and molecular methods. DNA methylation is an important epigenetic marker known to affect gene expression. cfDNA methylation detection is a very promising approach as abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis...
March 8, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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
#16
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/29686828/integrated-genome-wide-alu-methylation-and-transcriptome-profiling-analyses-reveal-novel-epigenetic-regulatory-networks-associated-with-autism-spectrum-disorder
#17
Thanit Saeliw, Chayanin Tangsuwansri, Surangrat Thongkorn, Weerasak Chonchaiya, Kanya Suphapeetiporn, Apiwat Mutirangura, Tewin Tencomnao, Valerie W Hu, Tewarit Sarachana
Background: Alu elements are a group of repetitive elements that can influence gene expression through CpG residues and transcription factor binding. Altered gene expression and methylation profiles have been reported in various tissues and cell lines from individuals with autism spectrum disorder (ASD). However, the role of Alu elements in ASD remains unclear. We thus investigated whether Alu elements are associated with altered gene expression profiles in ASD. Methods: We obtained five blood-based gene expression profiles from the Gene Expression Omnibus database and human Alu-inserted gene lists from the TranspoGene database...
2018: Molecular Autism
https://www.readbyqxmd.com/read/29686675/pathogenetic-and-clinical-aspects-of-anti-neutrophil-cytoplasmic-autoantibody-associated-vasculitides
#18
REVIEW
Peter Lamprecht, Anja Kerstein, Sebastian Klapa, Susanne Schinke, Christian M Karsten, Xinhua Yu, Marc Ehlers, Jörg T Epplen, Konstanze Holl-Ulrich, Thorsten Wiech, Kathrin Kalies, Tanja Lange, Martin Laudien, Tamas Laskay, Timo Gemoll, Udo Schumacher, Sebastian Ullrich, Hauke Busch, Saleh Ibrahim, Nicole Fischer, Katrin Hasselbacher, Ralph Pries, Frank Petersen, Gesche Weppner, Rudolf Manz, Jens Y Humrich, Relana Nieberding, Gabriela Riemekasten, Antje Müller
Anti-neutrophil cytoplasmic autoantibodies (ANCA) targeting proteinase 3 (PR3) and myeloperoxidase expressed by innate immune cells (neutrophils and monocytes) are salient diagnostic and pathogenic features of small vessel vasculitis, comprising granulomatosis with polyangiitis (GPA), microscopic polyangiitis, and eosinophilic GPA. Genetic studies suggest that ANCA-associated vasculitides (AAV) constitute separate diseases, which share common immunological and pathological features, but are otherwise heterogeneous...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29679470/molecular-progression-to-cervical-precancer-epigenetic-switch-or-sequential-model
#19
Belinda Nedjai, Caroline Reuter, Amar Ahmad, Rawinder Banwait, Rhian Warman, James Carton, Sabrina Boer, Jack Cuzick, Attila Lorincz
The evolution of precancerous cervical lesions is poorly understood. A widely held model of cervical intraepithelial neoplasia grade 3 (CIN3) development is sequential progression from normal through CIN1 and CIN2 to CIN3. Another hypothesis, the "molecular switch" model, postulates that CIN3 can evolve directly from human papillomavirus (HPV)-infected normal epithelium without progressing through CIN1 and CIN2. To shed light on this process, we compared DNA methylation of selected human biomarkers and HPV types in two groups of CIN1: CIN1 that were near or adjacent to CIN3 (adjacent-CIN1) and CIN1 that were the principal lesions with no CIN3 detected (principal-CIN1)...
April 21, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29672679/disease-prediction-by-cell-free-dna-methylation
#20
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
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