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CpG Islands

Trine B Rounge, Christian M Page, Maija Lepistö, Pekka Ellonen, Bettina K Andreassen, Elisabete Weiderpass
AIM: We performed an epigenome-wide association study within the Finnish Health in Teens cohort to identify differential DNA methylation and its association with BMI in adolescents. MATERIALS & METHODS: Differential DNA methylation analyses of 3.1 million CpG sites were performed in saliva samples from 50 lean and 50 heavy adolescent girls by genome-wide targeted bisulfite-sequencing. RESULTS: We identified 100 CpG sites with p-values < 0...
October 20, 2016: Epigenomics
Mathieu Fonteneau, Dominique Filliol, Patrick Anglard, Katia Befort, Pascal Romieu, Jean Zwiller
DNA methylation is a major epigenetic process which regulates the accessibility of genes to the transcriptional machinery. In the present study, we investigated whether modifying the global DNA methylation pattern in the brain would alter cocaine intake by rats, using the cocaine self-administration test. The data indicate that treatment of rats with the DNA methyltransferase inhibitors 5-aza-2'-deoxycytidine and zebularine actually enhanced the reinforcing properties of cocaine. To get some insights about the underlying neurobiological mechanisms, a genome-wide methylation analysis was undertaken in the prefrontal cortex of rats self-administering cocaine and treated or not with 5-aza-2'-deoxycytidine...
October 20, 2016: Genes, Brain, and Behavior
A Sangalli, G Malerba, G Tessari, M Rodolfo, M Gomez-Lira
No abstract text is available yet for this article.
October 20, 2016: Experimental Dermatology
Yongchang Zheng, Qianqian Huang, Zijian Ding, Tingting Liu, Chenghai Xue, Xinting Sang, Jin Gu
The alteration of DNA methylation landscape is a key epigenetic event in cancer. As the accumulation of large-scale genome-wide DNA methylation data from clinical samples, we are able to characterize the patterns of DNA methylation alterations for identifying candidate epigenetic markers and drivers. In this survey, we take hepatocellular carcinoma (HCC) as an example to show the basic steps of analyzing the DNA methylation patterns in cancer across multiple data sets. We collected three genome-wide DNA methylation data sets with ∼800 clinical samples and the corresponding gene expression data sets...
October 19, 2016: Briefings in Bioinformatics
Matthew Gordon Varga, Maria Blanca Piazuelo, Judith Romero-Gallo, Alberto G Delgado, Giovanni Suarez, Morgan E Whitaker, Uma S Krishna, Rachna V Patel, Eric P Skaar, Keith T Wilson, Holly M Scott Algood, Richard M Peek
Helicobacter pylori induces chronic gastritis in humans and infection can persist for decades. One H. pylori strain-specific constituent that augments disease risk is the cag pathogenicity island. The cag island encodes a type IV secretion system (T4SS) that translocates DNA into host cells. Toll-like receptor 9 (TLR9) is an innate immune receptor that detects hypo-methylated CpG DNA motifs. In this study, we sought to define the role of the H. pylori cag T4SS on TLR9-mediated responses in vivo H. pylori strain PMSS1 or its cagE(-) mutant, which fails to assemble a T4SS, were used to infect wild-type or Tlr9(-/-) C57BL/6 mice...
October 6, 2016: American Journal of Physiology. Gastrointestinal and Liver Physiology
Hirokazu Muraoka, Kazuhiro Hasegawa, Shu Wakino
OBJECTIVE: Nicotinamide phosphoribosyltransferase (Nampt) cooperates with a longevity gene, Sirt1, to exert the potentiation of stress resistance. We have reported that the high expression level of Nampt in PTs contributes to the sufficient supply of NMN to glomeruli. We also showed that downregulation of Nampt and NMN in PT in DN leads to glomerular damages (Nature Medicine 2013). However, the regulation mechanisms of Nampt expression remain unknown. DESIGN AND METHOD: We investigated how Nampt expression is consistently retained at high levels in PTs under normal conditions and how Nampt levels are decreased in DN...
September 2016: Journal of Hypertension
Satoshi Umemura
Primary aldosteronism (PA) is a heterogeneous group of disorders including both sporadic and familial forms (familial hyperaldosteronism type I, II and III). PA is the most frequent endocrine cause of secondary hypertension and associated with a higher rate of cardiovascular complications, compared with essential hypertension.Here I review the recent progress in understanding of the genetic and molecular mechanisms leading to autonomous aldosterone production in PA.Systematic screening detects primary aldosteronism in 5 to 10% of all patients with hypertension and in approximately 20% of patients with resistant hypertension...
September 2016: Journal of Hypertension
Yoshiki Nando, Jiro Watari, Chiyomi Ito, Ken Hara, Takahisa Yamasaki, Takuya Okugawa, Takashi Kondo, Tomoaki Kono, Katsuyuki Tozawa, Toshihiko Tomita, Yoshio Ohda, Tadayuki Oshima, Hirokazu Fukui, Nagahide Matsubara, Naohiro Tomita, Seiichi Hirota, Hiroto Miwa
It is recommended that small (6-10 mm) lesions be treated with endoscopic resection (ER), while diminutive (≤ 5 mm) lesions are not currently an indication for ER according to the Japanese guidelines. The aim of this study was to evaluate the molecular alterations, and therefore treatment indications, in diminutive vs. small tubular adenoma (TA). We prospectively analyzed genetic instability, including microsatellite instability (MSI) and loss of heterozygosity, methylation status, KRAS/BRAF mutations, and Ki-67 staining in 96 TAs without a villous component...
October 13, 2016: Human Pathology
Jezkova Eva, Kajo Karol, Zubor Pavol, Grendar Marian, Malicherova Bibiana, Mendelova Andrea, Dokus Karol, Lasabova Zora, Plank Lukas, Danko Jan
Breast cancer is a heterogeneous disease with very different responses to therapy and different length of survival. In many cases, however, the determination of the stage and histopathological characteristics of breast cancer is insufficient to predict prognosis and response to treatment for the vast heterogeneity of the disease. To understand the molecular signature of subtypes of breast cancer, we attempted to identify the methylation status of key tumour suppressor gene Ras association (RalGDS/AF-6) domain family member 1 isoform a (RASSF1A) and a member of the paired-like homeodomain transcription factor family which functions in left-right asymmetry development (PITX2) and to correlate results with known clinicopathological features of breast cancer...
October 15, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Susanne A Bengesser, Eva Z Reininghaus, Nina Lackner, Armin Birner, Frederike T Fellendorf, Martina Platzer, Nora Kainzbauer, Bernhard Tropper, Christa Hörmanseder, Robert Queissner, Hans-Peter Kapfhammer, Sandra J Wallner-Liebmann, Robert Fuchs, Erwin Petek, Christian Windpassinger, Mario Schnalzenberger, Bernd Reininghaus, Bernd Evert, Andreas Waha
OBJECTIVES: The clock gene ARNTL is associated with the transcription activation of monoamine oxidase A according to previous literature. Thus, we hypothesised that methylation of ARNTL may differ between bipolar disorder (BD) and controls. METHODS: The methylation status of one CpG island covering the first exon of ARNTL (PS2) and one site in the 5' region of ARNTL (cg05733463) were analysed in patients with BD (n = 151) versus controls (n = 66). Methylation analysis was performed by bisulphite-conversion of DNA from fasting blood with the EpiTect Bisulfite Kit, PCR and pyrosequencing...
October 14, 2016: World Journal of Biological Psychiatry
Xin Li, Yun Liu, Tal Salz, Kasper D Hansen, Andrew P Feinberg
DNA methylation at the 5-postion of cytosine (5mC) is an epigenetic modification that regulates gene expression and cellular plasticity in development and disease. The ten-eleven translocation (TET) gene family oxidizes 5mC to 5-hydroxymethylcytosine (5hmC), providing an active mechanism for DNA demethylation, and may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation and hydroxymethylation maps at single-base resolution in paired human liver and lung normal and cancer...
October 13, 2016: Genome Research
Ruoxu Dou, Reiko Nishihara, Yin Cao, Tsuyoshi Hamada, Kosuke Mima, Atsuhiro Masuda, Yohei Masugi, Yan Shi, Mancang Gu, Wanwan Li, Annacarolina da Silva, Katsuhiko Nosho, Xuehong Zhang, Jeffrey A Meyerhardt, Edward L Giovannucci, Andrew T Chan, Charles S Fuchs, Zhi Rong Qian, Shuji Ogino
Experimental evidence suggests that the let-7 family of noncoding RNAs suppresses adaptive immune responses, contributing to immune evasion by the tumor. We hypothesized that the amount of let-7a and let-7b expression in colorectal carcinoma might be associated with limited T-lymphocyte infiltrates in the tumor microenvironment and worse clinical outcome. Utilizing the molecular pathological epidemiology resources of 795 rectal and colon cancers in two U.S.-nationwide prospective cohort studies, we measured tumor-associated let-7a and let-7b expression levels by quantitative reverse-transcription PCR, and CD3(+), CD8(+), CD45RO (PTPRC)(+), and FOXP3(+) cell densities by tumor tissue microarray immunohistochemistry and computer-assisted image analysis...
October 13, 2016: Cancer Immunology Research
Inessa Skrypkina, Liudmyla Tsyba, Kateryna Onyshchenko, Dmytro Morderer, Olena Kashparova, Oleksii Nikolaienko, Grigory Panasenko, Sergii Vozianov, Alina Romanenko, Alla Rynditch
The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls...
2016: Disease Markers
Yuan Xue, Ming-Jie Wang, Su-Yuan Huang, Zhi-Tao Yang, De-Min Yu, Yue Han, Ming-Yu Zhu, Dao Huang, Dong-Hua Zhang, Qi-Ming Gong, Xin-Xin Zhang
BACKGROUND: CpG islands in hepatitis B virus (HBV) genome are potential targets for methylation mediated gene silencing, and may be involved in the pathogenesis of HBV infection. To date, their characteristics in HBV quasispecies (QS) remain largely unknown. The purpose of this study was to investigate the characteristics of CpG islands in HBV QS. METHODS: Forty patients diagnosed as acute hepatitis B (AHB, n = 10), immune-tolerant HBV carriers (IT, n = 9), chronic hepatitis B (CHB, n = 11), or acute on chronic liver failure (ACLF, n = 10), were enrolled in this case-control study...
2016: SpringerPlus
M Shao, X P Lyu, Q K Yang, W T Zhu, J Song, Y K Kong, J Wang, L Sun, F Wang
Objective: To investigate the impact of promoter CpG island methylation on ABO mRNA expression in leukemia. Methods: 25 cases of leukemia and 20 cases of normal control were studied, and the leukemia cell lines K562、HL-60 and Jurkat were treated with different concentrations of decitabine. PCR-SSP was used to identify ABO genotype, RQ-PCR for ABO mRNA expression and bisulfite sequencing PCR for DNA methylation status. Results: ① The methylation of ABO promoter in acute myeloid leukemia patients (10 cases) and acute lymphoblastic leukemia patients (10 cases) were 53...
September 14, 2016: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
Masaru Takabatake, Benjamin J Blyth, Kazuhiro Daino, Tatsuhiko Imaoka, Mayumi Nishimura, Masahiro Fukushi, Yoshiya Shimada
Several lines of evidence indicate one's age at exposure to radiation strongly modifies the risk of radiation-induced breast cancer. We previously reported that rat mammary carcinomas induced by pre- and post-pubertal irradiation have distinct gene expression patterns, but the changes underlying these differences have not yet been characterized. The aim of this investigation was to see if differences in CpG DNA methylation were responsible for the differences in gene expression between age at exposure groups observed in our previous study...
2016: PloS One
Vincent Huin, Vincent Deramecourt, Dominique Caparros-Lefebvre, Claude-Alain Maurage, Charles Duyckaerts, Eniko Kovari, Florence Pasquier, Valérie Buée-Scherrer, Julien Labreuche, Hélène Behal, Luc Buée, Claire-Marie Dhaenens, Bernard Sablonnière
BACKGROUND: Progressive supranuclear palsy (PSP) is a rare neurodegenerative disease causing parkinsonian symptoms. Altered DNA methylation of the microtubule-associated protein tau gene correlates with the expression changes in Alzheimer's disease and Parkinson's disease brains. However, few studies examine the sequences beyond the constitutive promoter. OBJECTIVES: Because activating different microtubule-associated protein tau gene control regions via methylation might regulate the differential tau expression constituting the specific signatures of individual tauopathies, we compared methylation of a candidate promoter, intron 0...
October 6, 2016: Movement Disorders: Official Journal of the Movement Disorder Society
Shahla Masood, Ehab El-Gabry, Chuhua Zhang, Zhiqiang Wang
BACKGROUND: It is documented that in tumor cell lines, the hTERT gene exhibits prominent methylation at a CpG island rich region about -600 bp upstream of the transcription start site, but mixed or allelically absent around ±150 bp region. Given the potential clinical implications of the findings in breast cancer diagnostics, we set out to investigate if such findings are reproducible on primary surgically resected invasive breast carcinomas. METHODS: The cohort consisted of 50 cases of freshly sampled and formalin-fixed paraffin embedded (FFPE) invasive breast cancers and normal tissue...
November 2016: Laboratory Medicine
H Zhang, P F Jin, L L Niu, L Li, L J Wang, Y Chen, G J Zhang, H P Zhang, T Zhong
DIO3 gene encoding type 3 iodothyronine deiodinase is an imprinted gene, located in the DLK1-DIO3 (delta-like 1 homolog-type 3 iodothyronine deiodinase) imprinted domain, and is potentially involved in degrading excessive amounts of thyroid hormone to protect embryogenesis. However, the underlying regulatory mechanism of the imprinted DIO3 gene expression during fetal and neonatal development in goats has not been elucidated. In this study, we explored the DNA methylation patterns of the caprine DIO3 intragenic CpG island and quantified gene expression level in six tissues from Chinese Nanjiang Yellow 3-day old kids...
September 2, 2016: Genetics and Molecular Research: GMR
Ling-Hao Zhao, Xiao Liu, He-Xin Yan, Wei-Yang Li, Xi Zeng, Yuan Yang, Jie Zhao, Shi-Ping Liu, Xue-Han Zhuang, Chuan Lin, Chen-Jie Qin, Yi Zhao, Ze-Ya Pan, Gang Huang, Hui Liu, Jin Zhang, Ruo-Yu Wang, Yun Yang, Wen Wen, Gui-Shuai Lv, Hui-Lu Zhang, Han Wu, Shuai Huang, Ming-Da Wang, Liang Tang, Hong-Zhi Cao, Ling Wang, T P Lee, Hui Jiang, Ye-Xiong Tan, Sheng-Xian Yuan, Guo-Jun Hou, Qi-Fei Tao, Qin-Guo Xu, Xiu-Qing Zhang, Meng-Chao Wu, Xun Xu, Jun Wang, Huan-Ming Yang, Wei-Ping Zhou, Hong-Yang Wang
Hepatitis B virus (HBV) can integrate into the human genome, contributing to genomic instability and hepatocarcinogenesis. Here by conducting high-throughput viral integration detection and RNA sequencing, we identify 4,225 HBV integration events in tumour and adjacent non-tumour samples from 426 patients with HCC. We show that HBV is prone to integrate into rare fragile sites and functional genomic regions including CpG islands. We observe a distinct pattern in the preferential sites of HBV integration between tumour and non-tumour tissues...
October 5, 2016: Nature Communications
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