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Clinical Epigenetics

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https://www.readbyqxmd.com/read/27999621/promoter-hypermethylation-of-shox2-and-sept9-is-a-potential-biomarker-for-minimally-invasive-diagnosis-in-adenocarcinomas-of-the-biliary-tract
#1
V Branchi, P Schaefer, A Semaan, A Kania, P Lingohr, J C Kalff, N Schäfer, G Kristiansen, D Dietrich, H Matthaei
BACKGROUND: Biliary tract carcinoma (BTC) is a fatal malignancy which aggressiveness contrasts sharply with its relatively mild and late clinical presentation. Novel molecular markers for early diagnosis and precise treatment are urgently needed. The purpose of this study was to evaluate the diagnostic and prognostic value of promoter hypermethylation of the SHOX2 and SEPT9 gene loci in BTC. METHODS: Relative DNA methylation of SHOX2 and SEPT9 was quantified in tumor specimens and matched normal adjacent tissue (NAT) from 71 BTC patients, as well as in plasma samples from an independent prospective cohort of 20 cholangiocarcinoma patients and 100 control patients...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27980696/characterization-of-tet-and-idh-gene-expression-in-chronic-lymphocytic-leukemia-comparison-with-normal-b-cells-and-prognostic-significance
#2
Michaël Van Damme, Emerence Crompot, Nathalie Meuleman, Marie Maerevoet, Philippe Mineur, Dominique Bron, Laurence Lagneaux, Basile Stamatopoulos
BACKGROUND: Chronic lymphocytic leukemia (CLL) is the most common hematological malignancy in western countries, characterized by a heterogeneous clinical course. Although genetic studies have identified chromosomal aberrations or specific mutations, epigenetic changes have been poorly characterized in CLL. METHODS: We assessed ten-eleven translocations (TET) 1, 2, and 3, isocitrate dehydrogenase (IDH) 1, and 2 messenger RNA (mRNA) expression using real-time PCR on purified leukemic B cells from 214 CLL patients (median follow-up = 75 months, range 1-380), normal peripheral blood B cells (n = 20), and umbilical cord blood B cells (n = 21)...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27980695/epigenome-wide-association-data-implicates-dna-methylation-mediated-genetic-risk-in-psoriasis
#3
Fusheng Zhou, Changbing Shen, Jingkai Xu, Jing Gao, Xiaodong Zheng, Randy Ko, Jinfa Dou, Yuyan Cheng, Caihong Zhu, Shuangjun Xu, Xianfa Tang, Xianbo Zuo, Xianyong Yin, Yong Cui, Liangdan Sun, Lam C Tsoi, Yi-Hsiang Hsu, Sen Yang, Xuejun Zhang
BACKGROUND: Psoriasis is a chronic inflammatory skin disease characterized by epidermal hyperproliferation and altered keratinocyte differentiation and inflammation and is caused by the interplay of genetic and environmental factors. Previous studies have revealed that DNA methylation (DNAm) and genetic makers are closely associated with psoriasis, and strong evidences have shown that DNAm can be controlled by genetic factors, which attracted us to evaluate the relationship among DNAm, genetic makers, and disease status...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27980694/a-methylation-pcr-method-determines-fmr1-activation-ratios-and-differentiates-premutation-allele-mosaicism-in-carrier-siblings
#4
Andrew G Hadd, Stela Filipovic-Sadic, Lili Zhou, Arianna Williams, Gary J Latham, Elizabeth Berry-Kravis, Deborah A Hall
BACKGROUND: Epigenetic modifications of the fragile X mental retardation 1 (FMR1) gene locus may impact the risk for reproductive and neurological disorders associated with expanded trinucleotide repeats and methylation status in the 5' untranslated region. FMR1 methylation is commonly assessed by Southern blot (SB) analysis, yet this method suffers a cumbersome workflow and relatively poor sizing resolution especially for premutation allele characteristic for fragile X-associated disorders...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27933111/aberrant-dna-hypermethylation-silenced-sox21-as1-gene-expression-and-its-clinical-importance-in-oral-cancer
#5
Cheng-Mei Yang, Tsung-Han Wang, Hung-Chih Chen, Sung-Chou Li, Ming-Chien Lee, Huei-Han Liou, Pei-Feng Liu, Yu-Kai Tseng, Yow-Ling Shiue, Luo-Ping Ger, Kuo-Wang Tsai
BACKGROUND: Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of this study was to identify the dysfunction of lncRNA in OSCC. RESULTS: We analyzed the transcriptome profiles of human OSCC tissues and paired adjacent normal tissues from two patients through a next-generation sequencing approach. A total of 14 lncRNAs were upregulated (fold change ≥3) and 13 were downregulated (fold change ≤-3) in OSCC tissues compared with the adjacent normal tissues...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27924165/assessment-of-global-dna-methylation-in-the-first-trimester-fetal-tissues-exposed-to-maternal-cigarette-smoking
#6
Svetlana Fa, Trine Vilsbøll Larsen, Katrine Bilde, Tina F Daugaard, Emil H Ernst, Rasmus H Olesen, Linn S Mamsen, Erik Ernst, Agnete Larsen, Anders L Nielsen
AIMS: Maternal cigarette smoking during pregnancy increases the risk of negative health consequences for the exposed child. Epigenetic mechanisms constitute a likely link between the prenatal exposure to maternal cigarette smoking and the increased risk in later life for diverse pathologies. Maternal smoking induces gene-specific DNA methylation alterations as well as global DNA hypermethylation in the term placentas and hypomethylation in the cord blood. Early pregnancy represents a developmental time where the fetal epigenome is remodeled and accordingly can be expected to be highly prone to exposures with an epigenetic impact...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27924164/smoking-associated-dna-methylation-markers-predict-lung-cancer-incidence
#7
Yan Zhang, Magdeldin Elgizouli, Ben Schöttker, Bernd Holleczek, Alexandra Nieters, Hermann Brenner
BACKGROUND: Newly established blood DNA methylation markers that are strongly associated with smoking might open new avenues for lung cancer (LC) screening. We aimed to assess the performance of the top hits from previous epigenome-wide association studies in prediction of LC incidence. In a prospective nested case-control study, DNA methylation at AHRR (cg05575921), 6p21.33 (cg06126421), and F2RL3 (cg03636183) were measured by pyrosequencing in baseline whole blood samples of 143 incident LC cases identified during 11 years of follow-up and 457 age- and sex-matched controls without diagnosis of LC until the end of follow-up...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27904655/increased-set1-binding-at-the-promoter-induces-aberrant-epigenetic-alterations-and-up-regulates-cyclic-adenosine-5-monophosphate-response-element-modulator-alpha-in-systemic-lupus-erythematosus
#8
Qing Zhang, Shu Ding, Huilin Zhang, Hai Long, Haijing Wu, Ming Zhao, Vera Chan, Chak-Sing Lau, Qianjin Lu
BACKGROUND: Up-regulated cyclic adenosine 5'-monophosphate response element modulator α (CREMα) which can inhibit IL-2 and induce IL-17A in T cells plays a critical role in the pathogenesis of systemic lupus erythematosus (SLE). This research aimed to investigate the mechanisms regulating CREMα expression in SLE. RESULTS: From the chromatin immunoprecipitation (ChIP) microarray data, we found a sharply increased H3 lysine 4 trimethylation (H3K4me3) amount at the CREMα promoter in SLE CD4+ T cells compared to controls...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27904654/augmentation-of-histone-deacetylase-3-hdac3-epigenetic-signature-at-the-interface-of-proinflammation-and-insulin-resistance-in-patients-with-type-2-diabetes
#9
Chandrakumar Sathishkumar, Paramasivam Prabu, Mahalingam Balakumar, Raji Lenin, Durai Prabhu, Ranjith Mohan Anjana, Viswanathan Mohan, Muthuswamy Balasubramanyam
BACKGROUND: A role of proinflammation has been implicated in the pathogenesis of diabetes, but the up-stream regulatory signals and molecular signatures are poorly understood. While histone modifications such as changes in histone deacetylase (HDAC) are emerging as novel epigenetic biomarkers, there is lack of studies to demonstrate their clinical relevance in diabetes. Therefore, we investigated the extent of HDAC machinery and inflammatory signals in peripheral blood mononuclear cells (PBMCs) from patients with type 2 diabetes mellitus (T2DM) compared to control subjects...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895808/mendelian-inheritance-of-trimodal-cpg-methylation-sites-suggests-distal-cis-acting-genetic-effects
#10
Shaza B Zaghlool, Mashael Al-Shafai, Wadha A Al Muftah, Pankaj Kumar, Christian Gieger, Melanie Waldenberger, Mario Falchi, Karsten Suhre
BACKGROUND: Environmentally influenced phenotypes, such as obesity and insulin resistance, can be transmitted over multiple generations. Epigenetic modifications, such as methylation of DNA cytosine-guanine (CpG) pairs, may be carriers of inherited information. At the population level, the methylation state of such "heritable" CpG sites is expected to follow a trimodal distribution, and their mode of inheritance should be Mendelian. METHODS: Using the Illumina Infinium 450 K DNA methylation array, we determined DNA CpG-methylation in blood cells from a family cohort 123 individuals of Arab ethnicity, including 18 elementary father-mother-child trios, we asked whether Mendelian inheritance of CpG methylation is observed, and most importantly, whether it is independent of any genetic signals...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895807/cpas-based-sequencing-on-the-bgiseq-500-to-explore-small-non-coding-rnas
#11
Tobias Fehlmann, Stefanie Reinheimer, Chunyu Geng, Xiaoshan Su, Snezana Drmanac, Andrei Alexeev, Chunyan Zhang, Christina Backes, Nicole Ludwig, Martin Hart, Dan An, Zhenzhen Zhu, Chongjun Xu, Ao Chen, Ming Ni, Jian Liu, Yuxiang Li, Matthew Poulter, Yongping Li, Cord Stähler, Radoje Drmanac, Xun Xu, Eckart Meese, Andreas Keller
BACKGROUND: We present the first sequencing data using the combinatorial probe-anchor synthesis (cPAS)-based BGISEQ-500 sequencer. Applying cPAS, we investigated the repertoire of human small non-coding RNAs and compared it to other techniques. RESULTS: Starting with repeated measurements of different specimens including solid tissues (brain and heart) and blood, we generated a median of 30.1 million reads per sample. 24.1 million mapped to the human genome and 23...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895806/genome-wide-epigenomic-profiling-for-biomarker-discovery
#12
REVIEW
René A M Dirks, Hendrik G Stunnenberg, Hendrik Marks
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895805/blood-based-dna-methylation-as-biomarker-for-breast-cancer-a-systematic-review
#13
REVIEW
Qiuqiong Tang, Jie Cheng, Xue Cao, Harald Surowy, Barbara Burwinkel
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27891194/erratum-to-donor-age-and-c1orf132-mir29b2c-determine-age-related-methylation-signature-of-blood-after-allogeneic-hematopoietic-stem-cell-transplantation
#14
Magdalena Spólnicka, Renata Zbieć Piekarska, Emilia Jaskuła, Grzegorz W Basak, Renata Jacewicz, Agnieszka Pięta, Żanetta Makowska, Maciej Jedrzejczyk, Agnieszka Wierzbowska, Agnieszka Pluta, Tadeusz Robak, Jarosław Berent, Wojciech Branicki, Wiesław Jędrzejczak, Andrzej Lange, Rafał Płoski
[This corrects the article DOI: 10.1186/s13148-016-0257-7.].
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27891193/in-epithelial-cancers-aberrant-col17a1-promoter-methylation-predicts-its-misexpression-and-increased-invasion
#15
Pulari U Thangavelu, Tibor Krenács, Eloise Dray, Pascal H G Duijf
BACKGROUND: Metastasis is a leading cause of death among cancer patients. In the tumor microenvironment, altered levels of extracellular matrix proteins, such as collagens, can facilitate the first steps of cancer cell metastasis, including invasion into surrounding tissue and intravasation into the blood stream. However, the degree of misexpression of collagen genes in tumors remains understudied, even though this knowledge could greatly facilitate the development of cancer treatment options aimed at preventing metastasis...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27891192/the-quest-for-an-effective-and-safe-personalized-cell-therapy-using-epigenetic-tools
#16
REVIEW
T A L Brevini, G Pennarossa, E F M Manzoni, C E Gandolfi, A Zenobi, F Gandolfi
In the presence of different environmental cues that are able to trigger specific responses, a given genotype has the ability to originate a variety of different phenotypes. This property is defined as plasticity and allows cell fate definition and tissue specialization. Fundamental epigenetic mechanisms drive these modifications in gene expression and include DNA methylation, histone modifications, chromatin remodeling, and microRNAs. Understanding these mechanisms can provide powerful tools to switch cell phenotype and implement cell therapy...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27891191/birth-weight-for-gestational-age-is-associated-with-dna-methylation-at-birth-and-in-childhood
#17
Golareh Agha, Hanine Hajj, Sheryl L Rifas-Shiman, Allan C Just, Marie-France Hivert, Heather H Burris, Xihong Lin, Augusto A Litonjua, Emily Oken, Dawn L DeMeo, Matthew W Gillman, Andrea A Baccarelli
BACKGROUND: Both higher and lower fetal growth are associated with cardio-metabolic health later in life, suggesting that prenatal developmental programming determines long-term cardiovascular disease risk. Epigenetic mechanisms, which orchestrate fetal growth and development, may offer insight on the early programming of health and disease. We investigated whether birth weight-for-gestational is associated with DNA methylation at birth and mid-childhood, measured via the Infinium 450K array...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27891190/cell-free-dna-promoter-hypermethylation-in-plasma-as-a-diagnostic-marker-for-pancreatic-adenocarcinoma
#18
Stine Dam Henriksen, Poul Henning Madsen, Anders Christian Larsen, Martin Berg Johansen, Asbjørn Mohr Drewes, Inge Søkilde Pedersen, Henrik Krarup, Ole Thorlacius-Ussing
BACKGROUND: Pancreatic cancer has a 5-year survival rate of only 5-7%. Difficulties in detecting pancreatic cancer at early stages results in the high mortality and substantiates the need for additional diagnostic tools. Surgery is the only curative treatment and unfortunately only possible in localized tumours. A diagnostic biomarker for pancreatic cancer will have a major impact on patient survival by facilitating early detection and the possibility for curative treatment. DNA promoter hypermethylation is a mechanism of early carcinogenesis, which can cause inactivation of tumour suppressor genes...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27891189/variations-in-dna-methylation-of-interferon-gamma-and-programmed-death-1-in-allograft-rejection-after-kidney-transplantation
#19
Karin Boer, L Elly A de Wit, Fleur S Peters, Dennis A Hesselink, Leo J Hofland, Michiel G H Betjes, Caspar W N Looman, Carla C Baan
BACKGROUND: The role of DNA methylation in the regulation of the anti-donor-directed immune response after organ transplantation is unknown. Here, we studied the methylation of two mediators of the immune response: the pro-inflammatory cytokine interferon γ (IFNγ) and the inhibitory receptor programmed death 1 (PD1) in naïve and memory CD8+ T cell subsets in kidney transplant recipients receiving immunosuppressive medication. Both recipients experiencing an episode of acute allograft rejection (rejectors) as well as recipients without rejection (non-rejectors) were included...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27822319/effect-of-prenatal-dha-supplementation-on-the-infant-epigenome-results-from-a-randomized-controlled-trial
#20
Susan J van Dijk, Jing Zhou, Timothy J Peters, Michael Buckley, Brodie Sutcliffe, Yalchin Oytam, Robert A Gibson, Andrew McPhee, Lisa N Yelland, Maria Makrides, Peter L Molloy, Beverly S Muhlhausler
BACKGROUND: Evidence is accumulating that nutritional exposures in utero can influence health outcomes in later life. Animal studies and human epidemiological studies have implicated epigenetic modifications as playing a key role in this process, but there are limited data from large well-controlled human intervention trials. This study utilized a large double-blind randomized placebo-controlled trial to test whether a defined nutritional exposure in utero, in this case docosahexaenoic acid (DHA), could alter the infant epigenome...
2016: Clinical Epigenetics
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