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DNA methylation miRNA

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https://www.readbyqxmd.com/read/28106826/colorectal-carcinoma-a-general-overview-and-future-perspectives-in-colorectal-cancer
#1
REVIEW
Inés Mármol, Cristina Sánchez-de-Diego, Alberto Pradilla Dieste, Elena Cerrada, María Jesús Rodriguez Yoldi
Colorectal cancer (CRC) is the third most common cancer and the fourth most common cause of cancer-related death. Most cases of CRC are detected in Western countries, with its incidence increasing year by year. The probability of suffering from colorectal cancer is about 4%-5% and the risk for developing CRC is associated with personal features or habits such as age, chronic disease history and lifestyle. In this context, the gut microbiota has a relevant role, and dysbiosis situations can induce colonic carcinogenesis through a chronic inflammation mechanism...
January 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28059592/mutual-regulation-of-micrornas-and-dna-methylation-in-human-cancers
#2
Sumei Wang, Wanyin Wu, Francois X Claret
microRNAs (miRNAs) and DNA methylation are the two epigenetic modifications that have emerged in recent years as the most critical players in the regulation of gene expression. Compelling evidence has indicated the roles of miRNAs and DNA methylation in modulating cellular transformation and tumorigenesis. miRNAs act as negative regulators of gene expression and are involved in the regulation of both physiological conditions and during diseases, such as cancer, inflammatory diseases, and psychiatric disorders, among others...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28058582/genome-wide-dna-methylation-patterns-analysis-of-noncoding-rnas-in-temporal-lobe-epilepsy-patients
#3
Wenbiao Xiao, Yuze Cao, Hongyu Long, Zhaohui Luo, Shuyu Li, Na Deng, Jianjian Wang, Xiaoyan Lu, Tianfeng Wang, Shangwei Ning, Lihua Wang, Bo Xiao
Temporal lobe epilepsy (TLE) is the most common form of adult epilepsy and frequently evolving drug resistance. Although there is growing consensus that noncoding ribonucleic acids (ncRNAs) are modulators of TLE, the knowledge about the deoxyribonucleic acid (DNA) methylation patterns of ncRNAs in TLE remains limited. In the current study, we constructed DNA methylation profiles from 30 TLE patients and 30 healthy controls for ncRNAs, primarily focusing on long ncRNAs (lncRNAs) and microRNAs (miRNAs), by reannotating data of DNA methylation BeadChip...
January 5, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28052018/targeting-micrornas-a-new-action-mechanism-of-natural-compounds
#4
REVIEW
Qian Lin, Leina Ma, Zhantao Liu, Zhihong Yang, Jin Wang, Jia Liu, Guohui Jiang
Unlike genetics, epigenetics involves the modification of genome without changes in DNA sequences, including DNA methylation, histone modification, chromatin remodeling and noncoding RNA regulation. MicroRNA (miRNA), a member of noncoding RNAs superfamily, participates in RNA interference through a unique mechanism. Currently, microRNAs have been found to be regulated by some natural compounds. Through altering the expression of miRNAs and influencing the downstream signaling pathways or target genes, several natural compounds exhibit its bioactivity in the prevention, diagnosis, therapy, prognosis and drug resistance of human diseases, such as cancer...
December 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/28049580/epigenetic-regulation-on-the-gene-expression-signature-in-esophagus-adenocarcinoma
#5
Ting Xi, Guizhi Zhang
BACKGROUND: Understanding the molecular mechanisms represents an important step in the development of diagnostic and therapeutic measures of esophagus adenocarcinoma (NOS). The objective of this study is to identify the epigenetic regulation on gene expression in NOS, shedding light on the molecular mechanisms of NOS. METHODS: In this study, 78 patients with NOS were included and the data of mRNA, miRNA and DNA methylation of were downloaded from The Cancer Genome Atlas (TCGA)...
December 19, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28049410/tcga2bed-extracting-extending-integrating-and-querying-the-cancer-genome-atlas
#6
Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, Emanuel Weitschek
BACKGROUND: Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. RESULTS: We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28045918/response-of-mirna-22-3p-and-mirna-149-5p-to-folate-deficiency-and-the-differential-regulation-of-mthfr-expression-in-normal-and-cancerous-human-hepatocytes
#7
Chao Li, Juan Ni, Yao-Xian Liu, Han Wang, Zi-Qing Liang, Xu Wang
BACKGROUND/AIMS: Folic acid (FA) is a core micronutrient involved in DNA synthesis/methylation, and the metabolism of FA is responsible for genomic stability. MicroRNAs may affect gene expression during folate metabolism when cellular homeostasis is changed. This study aimed to reveal the relationship between FA deficiency and the expression of miR-22-p/miR-149-5p and the targeted regulation of miR-22-3p/miR-149-5p on the key folate metabolic gene Methylenetetrahydrofolate reductase (MTHFR)...
2017: PloS One
https://www.readbyqxmd.com/read/28045116/comparative-analysis-of-dna-methylome-and-transcriptome-of-skeletal-muscle-in-lean-obese-and-mini-type-pigs
#8
Yalan Yang, Guoming Liang, Guanglin Niu, Yuanyuan Zhang, Rong Zhou, Yanfang Wang, Yulian Mu, Zhonglin Tang, Kui Li
DNA methylation plays a pivotal role in biological processes by affecting gene expression. However, how DNA methylation mediates phenotype difference of skeletal muscle between lean-, obese-, and mini-type pigs remains unclear. We systematically carried out comparative analysis of skeletal muscle by integrating analysis of genome-wide DNA methylation, mRNA, lncRNA and miRNA profiles in three different pig breeds (obese-type Tongcheng, lean-type Landrace, and mini-type Wuzhishan pigs). We found that the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress and muscle development...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28035070/elucidation-of-the-genetic-and-epigenetic-landscape-alterations-in-rna-binding-proteins-in-glioblastoma
#9
Shruti Bhargava, Vikas Patil, Kulandaivelu Mahalingam, Kumaravel Somasundaram
RNA binding proteins (RBPs) have been implicated in cancer development. An integrated bioinformatics analysis of RBPs (n = 1756) in various datasets (n = 11) revealed several genetic and epigenetically altered events among RBPs in glioblastoma (GBM). We identified 13 mutated and 472 differentially regulated RBPs in GBM samples. Mutations in AHNAK predicted poor prognosis. Copy number variation (CNV), DNA methylation and miRNA targeting contributed to RBP differential regulation. Two sets of differentially regulated RBPs that may be implicated in initial astrocytic transformation and glioma progression were identified...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28031532/cell-free-methylation-markers-with-diagnostic-and-prognostic-potential-in-hepatocellular-carcinoma
#10
Chang-Yi Lu, Shih-Ya Chen, Hui-Ling Peng, Pu-Yeh Kan, Wan-Chi Chang, Chia-Jui Yen
Hepatocellular carcinoma (HCC) is a highly malignant tumor with poor prognosis and high mortality. There is a dearth of effective early diagnostic tools, so liver resection surgery and liver transplantation are the only effective medical treatments. The most commonly used marker for HCC detection is serum alpha fetoprotein (AFP), which has low sensitivity and specificity. Because aberrant DNA methylation of genes and miRNAs occurs early in most cancers, we explored whether circulating methylation markers could be promising clinical tools for HCC diagnosis...
December 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/28000890/combined-analysis-of-gene-expression-mirna-expression-and-dna-methylation-profiles-of-osteosarcoma
#11
Wenpeng Zhang, Shiliang Han, Kang Sun
Osteosarcoma (OS) is a common primary malignancy in children and adolescents with relative high survival rate after chemotherapy. While the toxicity of chemotherapy and personalized different response to chemotherapy makes it difficult for the selection of therapeutics and improvement of diagnosis. In this study, we conducted a combined analysis of three types of microarray datasets (gene expression, microRNA (miRNA) expression and DNA methylation) from the Gene Expression Omnibus (GEO). The differential expression genes (DEGs) and miRNAs (DEMI) were screened out via the limma package and differential methylation sites (DMS) were identified by the IMA package...
February 2017: Oncology Reports
https://www.readbyqxmd.com/read/27998789/dna-methylation-contributes-to-deregulation-of-12-cancer-associated-micrornas-and-breast-cancer-progression
#12
Irina V Pronina, Vitaly I Loginov, Alexey M Burdennyy, Marina V Fridman, Vera N Senchenko, Tatiana P Kazubskaya, Nikolay E Kushlinskii, Alexey A Dmitriev, Eleonora A Braga
The methylation of promoter CpG islands and the interaction between microRNAs (miRNAs) and messenger RNAs (mRNAs) of target genes are considered two crucial mechanisms for gene and pathway deregulation in malignant tumors. The aim of this study was to analyze the role of promoter methylation in altering the expression of 13 miRNAs that are associated with breast cancer (BC): miR-124, -125b, -127, -132, -137, -148a, -191, -193a, -203, -212, -34b, -375, -9. The role of methylation in the deregulation of these miRNAs has not been previously assessed in the representative set of BC samples...
March 10, 2017: Gene
https://www.readbyqxmd.com/read/27993167/prognostic-value-of-cross-omics-screening-for-kidney-clear-cell-renal-cancer-survival
#13
Slavica Dimitrieva, Ralph Schlapbach, Hubert Rehrauer
BACKGROUND: Kidney renal clear cell carcinoma (KIRC) is a type of cancer that is resistant to chemotherapy and radiotherapy and has limited treatment possibilities. Large-scale molecular profiling of KIRC tumors offers a great potential to uncover the genetic and epigenetic changes underlying this disease and to improve the clinical management of KIRC patients. However, in practice the clinicians and researchers typically focus on single-platform molecular data or on a small set of genes...
December 20, 2016: Biology Direct
https://www.readbyqxmd.com/read/27992519/site-dependent-differences-in-dna-methylation-and-their-impact-on-plant-establishment-and-phosphorus-nutrition-in-populus-trichocarpa
#14
Brigitte Schönberger, Xiaochao Chen, Svenja Mager, Uwe Ludewig
The propagation via clonal stem cuttings is a frequent practice in tree plantations. Despite their clonal origin, the trees establish differently according to weather, temperature and nutrient availability, as well as the presence of various stresses. Here, clonal Populus trichocarpa (cv. Muhle Larson) cuttings from different sites were transferred into a common, fully nutrient supplied environment. Despite identical underlying genetics, stem cuttings derived from sites with lower phosphorus availability established worse, independent of phosphorus (P) level after transplantation...
2016: PloS One
https://www.readbyqxmd.com/read/27989132/dietary-phytochemicals-and-cancer-chemoprevention-a-perspective-on-oxidative-stress-inflammation-and-epigenetics
#15
Wenji Li, Yue Guo, Chengyue Zhang, Renyi Wu, Anne Yuqing Yang, John Gaspar, Ah-Ng Tony Kong
Oxidative stress occurs when cellular reactive oxygen species levels exceed the self-antioxidant capacity of the body. Oxidative stress induces many pathological changes, including inflammation and cancer. Chronic inflammation is believed to be strongly associated with the major stages of carcinogenesis. The nuclear factor erythroid 2-related factor 2 (Nrf2) pathway plays a crucial role in regulating oxidative stress and inflammation by manipulating key antioxidant and detoxification enzyme genes via the antioxidant response element...
December 19, 2016: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/27983682/zebrafish-as-an-in-vivo-model-to-assess-epigenetic-effects-of-ionizing-radiation
#16
REVIEW
Eva Yi Kong, Shuk Han Cheng, Kwan Ngok Yu
Exposure to ionizing radiations (IRs) is ubiquitous in our environment and can be categorized into "targeted" effects and "non-targeted" effects. In addition to inducing deoxyribonucleic acid (DNA) damage, IR exposure leads to epigenetic alterations that do not alter DNA sequence. Using an appropriate model to study the biological effects of radiation is crucial to better understand IR responses as well as to develop new strategies to alleviate exposure to IR. Zebrafish, Danio rerio, is a scientific model organism that has yielded scientific advances in several fields and recent studies show the usefulness of this vertebrate model in radiation biology...
December 15, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27942223/silencing-of-mir-1247-by-dna-methylation-promoted-non-small-cell-lung-cancer-cell-invasion-and-migration-by-effects-of-stmn1
#17
Juan Zhang, Jun Fu, Yuliang Pan, Xi Zhang, Liangfang Shen
MicroRNAs (miRNAs) play an important role in cancer development and progression, altering several biological functions by affecting targets through either degradation of mRNAs or suppression of protein translation. One such miRNA, miR-1247, is downregulated in various cancers, but its biological role in non-small-cell lung cancer (NSCLC) is unknown. This study found that the expression of miR-1247 was significantly reduced in NSCLC cell lines and tumor tissues compared with matched normal lung tissues and cell lines as a result of DNA hypermethylation...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27910778/mirsnps-of-mir1274-and-mir3202-genes-that-target-mecp2-and-dnmt3b-are-associated-with-lung-cancer-risk-a-study-conducted-on-massarray-genotyping
#18
Cansu Ozbayer, Irfan Degirmenci, Derya Ustuner, Guntulu Ak, Faruk Saydam, Ertugrul Colak, Hasan Veysi Gunes, Muzaffer Metintas
Genetic variants of miRNAs that target DNMTs and MBDs involved in DNA methylation were scanned with current databases, and 35 miRSNPs in 22 miRNA genes were identified. The aim of the study was to determine the association between these variants of miRNA genes and lung cancer (LC). DNA samples were isolated from blood samples and genotyped using a Sequenom MassARRAY System. An association between the rs188912830 gene variant of miR3202 that targets the MeCP2 protein and LC was indicated in both subtypes. The presence of the C-allele in patients with LC and its subtypes was significantly lower, and the absence of the C-allele was determined to increase the risk of LC by 7,429-times compared to the presence (p=0,010)...
2016: Journal of Environmental Pathology, Toxicology and Oncology
https://www.readbyqxmd.com/read/27904681/mir-330-3p-inhibits-gastric-cancer-progression-through-targeting-msi1
#19
Aoran Guan, Hui Wang, Xun Li, Hui Xie, Ruotian Wang, Yankun Zhu, Ruhong Li
Increasing evidences demonstrated that microRNAs (miRNAs) play critical roles in the human tumor development and progression. In our study, we found that miR-330-3p expression was downregulated in gastric cancer cell lines and tissues. Ectopic expression of miR-330-3p suppressed the gastric cancer cell proliferation, colony formation and migration. Overexpression of miR-330-3p promoted E-cadherin expression and inhibited the expression of N-cadherin, vimentin and snail. We identified Musashi-1 (MSI1) as a direct target gene of miR-330-3p in gastric cancer cell...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27904521/epigenetic-modifications-in-adipose-tissue-relation-to-obesity-and-diabetes
#20
Marta A Kasinska, Jozef Drzewoski, Agnieszka Sliwinska
The growing number of people suffering from obesity and type 2 diabetes mellitus (T2DM) is a global health problem that results in increased mortality from their complications, mainly cardiovascular diseases. Although the relationship between obesity and T2DM is well established, the common molecular pathomechanisms are still under investigation. Recently, it has been suggested that epigenetic modifications may be involved in both obesity and T2DM development. Epigenetics plays a pivotal role in the regulation of gene expression by the reversible modifications of chromatin structure without any changes in DNA sequence...
December 1, 2016: Archives of Medical Science: AMS
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