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miRNA analysis

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https://www.readbyqxmd.com/read/28329037/comprehensive-mirna-profiling-of-skeletal-muscle-and-serum-in-induced-and-normal-mouse-muscle-atrophy-during-aging
#1
Hwa Jin Jung, Kwang-Pyo Lee, Brandon Milholland, Yeo Jin Shin, Jae Sook Kang, Ki-Sun Kwon, Yousin Suh
Age-associated loss of muscle mass and function is a major cause of morbidity and mortality in the elderly adults. Muscular atrophy can also be induced by disuse associated with long-term bed rest or disease. Although miRNAs regulate muscle growth, regeneration, and aging, their potential role in acute muscle atrophy is poorly understood. Furthermore, alterations in circulating miRNA levels have been shown to occur during aging but their potential as noninvasive biomarkers for muscle atrophy remains largely unexplored...
March 10, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28329018/a-unique-microrna-profile-in-end-stage-heart-failure-indicates-alterations-in-specific-cardiovascular-signaling-networks
#2
Sathyamangla V Naga Prasad, Manveen K Gupta, Zhong-Hui Duan, Venkata Suresh K Surampudi, Chang-Gong Liu, Ashwin Kotwal, Christine S Moravec, Randall C Starling, Dianne M Perez, Subha Sen, Qingyu Wu, Edward F Plow, Sadashiva Karnik
It is well established that the gene expression patterns are substantially altered in cardiac hypertrophy and heart failure, however, less is known about the reasons behind such global differences. MicroRNAs (miRNAs) are short non-coding RNAs that can target multiple molecules to regulate wide array of proteins in diverse pathways. The goal of the study was to profile alterations in miRNA expression using end-stage human heart failure samples with an aim to build signaling network pathways using predicted targets for the altered miRNA and to determine nodal molecules regulating individual networks...
2017: PloS One
https://www.readbyqxmd.com/read/28327132/simultaneous-analysis-of-mirna-mrna-in-human-meningiomas-by-integrating-transcriptome-a-relationship-between-ptx3-and-mir-29c
#3
Altay Burak Dalan, Sukru Gulluoglu, Emre Can Tuysuz, Aysegul Kuskucu, Cumhur Kaan Yaltirik, Oguz Ozturk, Ugur Ture, Omer Faruk Bayrak
BACKGROUND: Although meningioma is a common disease, there is a lack of understanding of the underlying molecular mechanisms behind its initiation and progression. We used combined miRNA-mRNA transcriptome analysis to discover dysregulated genes and networks in meningiomas. METHODS: Fourteen fresh-frozen meningioma samples and one human meningeal cell line were analyzed by using miRNA and whole transcriptome microarray chips. Data was filtered and analyzed. Candidate miRNAs and mRNAs were selected for validation in fifty-eight patient samples...
March 21, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28325285/targeted-expression-of-mir-7-operated-by-ttf-1-promoter-inhibited-the-growth-of-human-lung-cancer-through-the-ndufa4-pathway
#4
Liangyu Lei, Chao Chen, Juanjuan Zhao, HaiRong Wang, Mengmeng Guo, Ya Zhou, Junming Luo, Jidong Zhang, Lin Xu
Targeted expression of gene technique is an important therapeutic strategy for lung cancer. MicroRNA-7 has been well documented as a promising tumor suppressor but never been test in specific gene-promoter-targeted expression in cancer gene therapy. Here, we first evaluated the efficacy of miR-7 expression operated by the promoter of TTF-1, a lineage-specific oncogene in lung cancer, in vitro using an eukaryotic vector of TTF-1-promoter-operated expression of miR-7 (termed as p-T-miR-7). Interestingly, using a nude mice model, the growth and metastasis of human lung cancer cells in vivo were significantly reduced in remote hypodermic injection of the p-T-miR-7 group, accompanied by increased expression of miR-7 and reduced transduction of the Akt and Erk pathway in situ...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28325277/reverse-expression-of-aging-associated-molecules-through-transfection-of-mirnas-to-aged-mice
#5
Jung-Hee Kim, Bo-Ram Lee, Eun-Sook Choi, Kyeong-Min Lee, Seong-Kyoon Choi, Jung Hoon Cho, Won Bae Jeon, Eunjoo Kim
Molecular changes during aging have been studied to understand the mechanism of aging progress. Herein, changes in microRNA (miRNA) expression in the whole blood of mice were studied to systemically reverse aging and propose them as non-invasive biomarkers. Through next-generation sequencing analysis, we selected 27 differentially expressed miRNAs during aging. The most recognized function involved was liver steatosis, a type of non-alcoholic fatty liver disease (NAFLD). Among 27 miRNAs, six were predicted to be involved in NAFLD, miR-16-5p, miR-17-5p, miR-21a-5p, miR-30c-5p, miR-103-3p, and miR-130a-3p; alterations in their blood and liver levels were confirmed by real-time qPCR...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28323882/mir-181-interacts-with-signaling-adaptor-molecule-denn-madd-and-enhances-tnf-induced-cell-death
#6
Samira Ghorbani, Farideh Talebi, Sedigheh Ghasemi, Ali Jahanbazi Jahan Abad, Mohammed Vojgani, Farshid Noorbakhsh
MicroRNAs are small noncoding RNAs, which regulate the expression of protein coding transcripts through mRNA degradation or translational inhibition. Numerous reports have highlighted the role of miRNAs in regulating cell death pathways including the expression of genes involved in the induction of apoptosis. Tumor necrosis factor alpha (TNF-α) is a proinflammatory cytokine which can send pro-death signals through its receptor TNFR1. Diverse adaptor molecules including DENN/MADD adaptor protein have been shown to modulate TNF-α pro-death signaling via recruitment of MAP kinases to TNFR1 and activation of pro-survival NFκB signaling...
2017: PloS One
https://www.readbyqxmd.com/read/28323040/-machine-learning-based-identification-of-endogenous-cellular-microrna-sponges-against-viral-micrornas
#7
Soowon Kang, Seunghyun Park, Sungroh Yoon, Hyeyoung Min
A "miRNA sponge" is an artificial oligonucleotide-based miRNA inhibitor containing multiple binding sites for a specific miRNA. Each miRNA sponge can bind and sequester several miRNA copies, thereby decreasing the cellular levels of the target miRNA. In addition to developing artificial miRNA sponges, scientists have sought endogenous RNA transcripts and found that long non-coding RNAs, competing endogenous RNAs, pseudogenes, circular RNAs, and coding RNAs could act as miRNA sponges under precise conditions...
March 17, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28321518/identification-and-characterization-of-durum-wheat-micrornas-in-leaf-and-root-tissues
#8
Veronica Fileccia, Edoardo Bertolini, Paolo Ruisi, Dario Giambalvo, Alfonso Salvatore Frenda, Gina Cannarozzi, Zerihun Tadele, Cristina Crosatti, Federico Martinelli
MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs...
March 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28321402/prognostic-role-of-the-microrna-200-family-in-various-carcinomas-a-systematic-review-and-meta-analysis
#9
REVIEW
Jung Soo Lee, Young-Ho Ahn, Hye Sung Won, Der Sheng Sun, Yeo Hyung Kim, Yoon Ho Ko
Background/Aims. The miRNA-200 (miR-200) family may act as key inhibitors of epithelial-to-mesenchymal transition. However, the potential prognostic value of miR-200s in various human malignancies remains controversial. This meta-analysis analyzed the associations between miR-200 levels and survival outcomes in a variety of tumors. Methods. Eligible published studies were identified by searching the Embase, PubMed, CINAHL, and Google scholar databases. Patient clinical data were pooled, and pooled hazard ratios (HRs) with 95% confidence intervals (95% CI) were used to calculate the strength of this association...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28321157/hsa-mir-183-is-frequently-methylated-and-related-to-poor-survival-in-human-hepatocellular-carcinoma
#10
Sumadi Lukman Anwar, Till Krech, Britta Hasemeier, Elisa Schipper, Nora Schweitzer, Arndt Vogel, Hans Kreipe, Reena Buurman, Britta Skawran, Ulrich Lehmann
AIM: To screen clinically relevant microRNAs (miRNAs) silenced by DNA methylation in human hepatocellular carcinoma (HCC). METHODS: Knockdown of DNA methyltransferases (DNMTs) using siRNAs and miRNA profiling in HCC cell lines were performed to identify DNA hypermethylation-mediated miRNA downregulation. Confirmation using individual quantitative real-time PCR (qRT-PCR) assays was then performed followed by DNA methylation quantification at the promoter of the miRNA genes...
March 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28320521/differential-mirna-expression-analysis-during-late-stage-terminal-hindgut-development-in-fetal-rats
#11
Shuguang Jin, Junxiang Wang, Hong Chen, Bo Xiang
BACKGROUND: Terminal hindgut deformity is the leading digestive tract malformation, however, the etiology and pathogenesis remained unknown. To date, gene expression abnormalities were considered the primary cause of these diseases. miRNAs have been found to play an important role in regulating the expression of genes. METHODS: A total of 24 pregnant rats were randomly divided into two groups. The experimental group (n=12) received 1% ethylenethiourea (125mg/kg) by gavage on gestational day 11, while the control group (n=12) received the same volume of distilled water...
March 12, 2017: Journal of Pediatric Surgery
https://www.readbyqxmd.com/read/28320388/exploring-the-fgfr3-related-oncogenic-mechanism-in-bladder-cancer-using-bioinformatics-strategy
#12
Wei Cao, Enguang Ma, Li Zhou, Tan Yuan, Chunying Zhang
BACKGROUND: Aberrant activation of fibroblast growth factor receptor 3 (FGFR3) is frequently observed in bladder cancer, but how it involved in carcinogenesis is not well understood. The current study was aimed to investigate the underlying mechanism on the progression of bladder cancer. METHODS: The GSE41035 dataset downloaded from Gene Expression Omnibus was used to identify the differentially expressed genes (DEGs) between bladder cancer cell line RT112 with or without depletion of FGFR3, and gene ontology enrichment analysis was performed...
March 20, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28320324/quickmirseq-a-pipeline-for-quick-and-accurate-quantification-of-both-known-mirnas-and-isomirs-by-jointly-processing-multiple-samples-from-microrna-sequencing
#13
Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent, Baohong Zhang
BACKGROUND: Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset. We implemented a pipeline called QuickMIRSeq for accurate quantification of known miRNAs and miRNA isoforms (isomiRs) from multiple samples simultaneously. RESULTS: QuickMIRSeq considers the unique nature of miRNAs and combines many important features into its implementation...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28319645/the-atypical-genesis-and-bioavailability-of-the-plant-based-small-rna-mir2911-bulking-up-while-breaking-down
#14
Jian Yang, Natee Kongchan, Cecilia Primo Planta, Joel R Neilson, Kendal D Hirschi
SCOPE: The uptake of dietary plant small RNAs (sRNAs) in consumers remains controversial, which is mainly due to low dietary content in combination with poor fractional absorption. MIR2911, among all the plant sRNAs including microRNAs, has been shown to be one of the most robustly absorbed sRNAs. Here we analyze the unusual abundance and unique genesis of MIR2911 during vegetable processing. METHODS AND RESULTS: Using qRT-PCR, the abundance of MIR2911 increased dramatically in macerated tissues while other microRNAs degraded...
March 20, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28319523/plasma-levels-of-microrna-155-are-upregulated-with-long-term-left-ventricular-assist-device-support
#15
Teresa Wang, Emily C OʼBrien, Joseph G Rogers, Daniel L Jacoby, Michael E Chen, Jeffrey M Testani, Dawn E Bowles, Carmelo A Milano, G Michael Felker, Chetan B Patel, Pramod N Bonde, Tariq Ahmad
Left ventricular assist device (LVAD) therapy unloads the failing heart but exposes the human body to unique pathophysiological demands such as continuous blood-flow and complete univentricular support, which are associated with increased risk of adverse clinical outcomes. MiRNAs are 22-23 nucleotide RNAs involved in regulation of multiple biological processes including the pathogenesis of heart failure (HF). Thus, measurement of miRNAs may have potential in both diagnostics as circulating biomarkers, and in therapeutics for targeted interventions...
March 17, 2017: ASAIO Journal: a Peer-reviewed Journal of the American Society for Artificial Internal Organs
https://www.readbyqxmd.com/read/28319142/microrna-32-promotes-calcification-in-vascular-smooth-muscle-cells-implications-as-a-novel-marker-for-coronary-artery-calcification
#16
Jianghua Liu, Xinhua Xiao, Yingying Shen, Ling Chen, Canxin Xu, Heng Zhao, Ying Wu, Qinghai Zhang, Jing Zhong, Zhenwang Tang, Changhui Liu, Qiang Zhao, Yi Zheng, Renxian Cao, Xuyu Zu
Cardiovascular calcification is one of the most severe outcomes associated with cardiovascular disease and often results in significant morbidity and mortality. Previous reports indicated that epigenomic regulation of microRNAs (miRNAs) might play important roles in vascular smooth muscle cell (VSMC) calcification. Here, we identified potential key miRNAs involved in vascular calcification in vivo and investigated the role of miR-32-5p (miR-32). According to microarray analysis, we observed increased expression of miR-125b, miR-30a, and miR-32 and decreased expression of miR-29a, miR-210, and miR-320 during the progression of vascularcalcification...
2017: PloS One
https://www.readbyqxmd.com/read/28315020/novel-biomarkers-for-non-functioning-invasive-pituitary-adenomas-were-identified-by-using-analysis-of-micrornas-expression-profile
#17
Silin Wu, Ye Gu, Yuying Huang, Tyh-Chai Wong, Hailin Ding, Tengfei Liu, Yu Zhang, Xiaobiao Zhang
The microRNAs (miRNAs) are involved in multiple pathological processes among various types of tumors. However, the functions of miRNAs in benign brain tumors are largely unexplored. In order to explore the pathogenesis of the invasiveness in non-functional pituitary adenoma (NFPA), the miRNAs expression profile was analyzed between invasive and non-invasive non-functional pituitary adenoma by miRNAs microarray. Six most significant differentially expressed miRNAs were identified including four upregulated miRNAs hsa-miR-181b-5p, hsa-miR-181d, hsa-miR-191-3p, and hsa-miR-598 and two downregulated miRNAs hsa-miR-3676-5p and hsa-miR-383...
March 17, 2017: Biochemical Genetics
https://www.readbyqxmd.com/read/28314792/comparative-profiling-of-small-rnas-of-pig-seminal-plasma-and-ejaculated-and-epididymal-sperm
#18
Cai Chen, Han Wu, Dan Shen, Saisai Wang, Li Zhang, Xiaoyan Wang, Bo Gao, Tianwen Wu, Bichun Li, Kui Li, Chengyi Song
The similarities and differences of small RNAs in seminal plasma, epididymal sperm and ejaculated sperm remain largely undefined. We conducted a systematic comparative analysis of small RNA profiles in pig ejaculated sperm, epididymal sperm and seminal plasma and found that the diversity distribution of small RNA species was generally similar, whereas the abundance of small RNAs is dramatically different across the three libraries; miRNAs and small RNAs derived from rRNA, tRNA, small nuclear RNA, 7SK RNA, NRON RNA and cis-regulatory RNA were enriched in the three libraries, but piRNA was absent...
March 17, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28306519/variability-in-variability-out-best-practice-recommendations-to-standardize-pre-analytical-variables-in-the-detection-of-circulating-and-tissue-micrornas
#19
Jenna Khan, Joshua A Lieberman, Christina M Lockwood
MicroRNAs (miRNAs) hold promise as biomarkers for a variety of disease processes and for determining cell differentiation. These short RNA species are robust, survive harsh treatment and storage conditions and may be extracted from blood and tissue. Pre-analytical variables are critical confounders in the analysis of miRNAs: we elucidate these and identify best practices for minimizing sample variation in blood and tissue specimens. Pre-analytical variables addressed include patient-intrinsic variation, time and temperature from sample collection to storage or processing, processing methods, contamination by cells and blood components, RNA extraction method, normalization, and storage time/conditions...
March 17, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28304398/characterization-of-the-polyphenol-oxidase-gene-family-reveals-a-novel-microrna-involved-in-posttranscriptional-regulation-of-ppos-in-salvia-miltiorrhiza
#20
Caili Li, Dongqiao Li, Jiang Li, Fenjuan Shao, Shanfa Lu
Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes...
March 17, 2017: Scientific Reports
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