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MicroRNA

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https://www.readbyqxmd.com/read/28340487/microrna-4739-regulates-osteogenic-and-adipocytic-differentiation-of-immortalized-human-bone-marrow-stromal-cells-via-targeting-lrp3
#1
Mona Elsafadi, Muthurangan Manikandan, Nehad M Alajez, Rimi Hamam, Raed Abu Dawud, Abdullah Aldahmash, Zafar Iqbal, Musaad Alfayez, Moustapha Kassem, Amer Mahmood
Understanding the regulatory networks underlying lineage differentiation and fate determination of human bone marrow stromal cells (hBMSC) is a prerequisite for their therapeutic use. The goal of the current study was to unravel the novel role of the low-density lipoprotein receptor-related protein 3 (LRP3) in regulating the osteogenic and adipogenic differentiation of immortalized hBMSCs. Gene expression profiling revealed significantly higher LRP3 levels in the highly osteogenic hBMSC clone imCL1 than in the less osteogenic clone imCL2, as well as a significant upregulation of LRP3 during the osteogenic induction of the imCL1 clone...
March 8, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28340087/nutrigenomic-point-of-view-on-effects-and-mechanisms-of-action-of-ruminant-trans-fatty-acids-on-insulin-resistance-and-type-2-diabetes
#2
Bénédicte L Tremblay, Iwona Rudkowska
Evidence from observational studies suggests beneficial effects of ruminant trans fatty acids (rTFA) on insulin resistance (IR) and type 2 diabetes (T2D). However, beneficial effects of rTFA are not always observed in cell, animal, and human studies. This narrative review presents potential mechanisms of action of rTFA using nutrigenomics and microRNA results in an integrative model. In addition, the review presents factors, including measures of IR and T2D, dose and duration of studies, as well as health status, ethnicity, and genotypes of subjects, that may help explain the heterogeneity in response to rTFA supplementation...
March 7, 2017: Nutrition Reviews
https://www.readbyqxmd.com/read/28339741/shear-stress-regulated-mir-27b-controls-pericyte-recruitment-by-repressing-sema6a-and-sema6d
#3
Shemsi Demolli, Anuradha Doddaballapur, Kavi Devraj, Konstantin Stark, Yosif Manavski, Annekathrin Eckart, Christoph Zehendner, Tina Lucas, Thomas Korff, Markus Hecker, Steffen Massberg, Stefan Liebner, David Kaluza, Reinier A Boon, Stefanie Dimmeler
Aims: Vessel maturation involves the recruitment of mural cells such as pericytes and smooth muscle cells. Laminar shear stress is a major trigger for vessel maturation, but the molecular mechanisms by which shear stress affects recruitment of pericytes are unclear. MicroRNAs (miRs) are small non-coding RNAs, which post-transcriptionally control gene expression. The aim of the present study was to unveil the mechanism by which shear stress-regulated microRNAs contribute to vessel maturation...
February 23, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28339495/microrna-expression-profiles-identify-disease-specific-alterations-in-systemic-lupus-erythematosus-and-primary-sj%C3%A3-gren-s-syndrome
#4
Ji-Qing Chen, Gábor Papp, Szilárd Póliska, Krisztina Szabó, Tünde Tarr, Bálint László Bálint, Péter Szodoray, Margit Zeher
The discovery of microRNAs (miRNAs) and their critical role in genetic control opened new avenues in understanding of various biological processes including immune cell lineage commitment, differentiation, proliferation and apoptosis. However, a given miRNA may have hundreds of different mRNA targets and a target might be regulated by multiple miRNAs, thus the characterisation of dysregulated miRNA expression profiles could give a better insight into the development of immunological disturbances in autoimmune diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28339468/pbmda-a-novel-and-effective-path-based-computational-model-for-mirna-disease-association-prediction
#5
Zhu-Hong You, Zhi-An Huang, Zexuan Zhu, Gui-Ying Yan, Zheng-Wei Li, Zhenkun Wen, Xing Chen
In the recent few years, an increasing number of studies have shown that microRNAs (miRNAs) play critical roles in many fundamental and important biological processes. As one of pathogenetic factors, the molecular mechanisms underlying human complex diseases still have not been completely understood from the perspective of miRNA. Predicting potential miRNA-disease associations makes important contributions to understanding the pathogenesis of diseases, developing new drugs, and formulating individualized diagnosis and treatment for diverse human complex diseases...
March 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28339187/accurate-mirna-analysis-in-crude-cell-lysate-by-capillary-electrophoresis-based-hybridization-assay-in-comparison-with-quantitative-reverse-transcription-polymerase-chain-reaction
#6
Liang Hu, Alexander S Stasheuski, David W Wegman, Nan Wu, Burton B Yang, Heyam Hayder, Chun Peng, Stanley K Liu, George M Yousef, Sergey N Krylov
Accurate quantitation of microRNA (miRNA) in tissue samples is required for validation and clinical use of miRNA-based disease biomarkers. Since sample processing, such as RNA extraction, introduces undesirable biases, it is advantageous to measure miRNA in a crude cell lysate. Here we report on accurate miRNA quantitation in crude cell lysate by a CE-based hybridization assay termed direct quantitative analysis of multiple miRNAs (DQAMmiR). Accuracy and precision of miRNA quantitation were determined for miRNA samples in a crude cell lysate, RNA extract from the lysate, and a pure buffer...
March 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28335522/extracellular-vesicles-deliver-host-and-virus-rna-and-regulate-innate-immune-response
#7
REVIEW
Takahisa Kouwaki, Masaaki Okamoto, Hirotake Tsukamoto, Yoshimi Fukushima, Hiroyuki Oshiumi
The innate immune system plays a crucial role in controlling viral infection. Pattern recognition receptors (PRRs), such as Toll-like receptors and RIG-I-like receptors, sense viral components called pathogen-associated molecular patterns (PAMPs) and trigger signals to induce innate immune responses. Extracellular vesicles (EVs), including exosomes and microvesicles, deliver functional RNA and mediate intercellular communications. Recent studies have revealed that EVs released from virus-infected cells deliver viral RNA to dendritic cells and macrophages, thereby activating PRRs in recipient cells, which results in the expression of type I interferon and pro-inflammatory cytokines...
March 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335496/quantitative-analysis-of-the-kshv-transcriptome-following-primary-infection-of-blood-and-lymphatic-endothelial-cells
#8
A Gregory Bruce, Serge Barcy, Terri DiMaio, Emilia Gan, H Jacques Garrigues, Michael Lagunoff, Timothy M Rose
The transcriptome of the Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters...
March 19, 2017: Pathogens
https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#9
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335259/lipid-nanovectors-to-deliver-rna-oligonucleotides-in-cancer
#10
REVIEW
Virginia Campani, Giuseppina Salzano, Sara Lusa, Giuseppe De Rosa
The growing knowledge on the mechanisms of gene silencing and gene regulation by non-coding RNAs (ncRNA), mainly small interfering RNA (siRNA) and microRNA (miRNA), is providing a significant boost to the development of new therapeutic strategies for the treatment of cancer. However, the design of RNA-based therapeutics is hampered by biopharmaceutical issues, thus requiring the use of suitable delivery strategies. In this regards, lipid nanovectors have been successfully investigated to deliver RNA in different forms of cancer...
July 9, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335016/trna-derived-small-rnas-target-transposable-element-transcripts
#11
German Martinez, Sarah G Choudury, R Keith Slotkin
tRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are processed by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334969/a-single-mir390-targeting-event-is-sufficient-for-triggering-tas3-tasirna-biogenesis-in-arabidopsis
#12
Felipe Fenselau de Felippes, Antonin Marchais, Alexis Sarazin, Stefan Oberlin, Olivier Voinnet
In plants, tasiRNAs form a class of endogenous secondary siRNAs produced through the action of RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) upon microRNA-mediated cleavage of non-coding TAS RNAs. In Arabidopsis thaliana, TAS1, TAS2 and TAS4 tasiRNA production proceeds via a single cleavage event mediated by 22nt-long or/and asymmetric miRNAs in an ARGONAUTE-1 (AGO1)-dependent manner. By contrast, tasiRNA production from TAS3 seems to follow the so-called 'two-hit' process, where dual targeting of TAS3, specifically mediated by the 21nt-long, symmetric miR390, initiates AGO7-dependent tasiRNA production...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334781/auf1-facilitates-microrna-mediated-gene-silencing
#13
Kyung-Won Min, Myung Hyun Jo, Soochul Shin, Sylvia Davila, Richard W Zealy, Soo Im Kang, Lawson T Lloyd, Sungchul Hohng, Je-Hyun Yoon
Eukaryotic mRNA decay is tightly modulated by RNA-binding proteins (RBPs) and microRNAs (miRNAs). RBP AU-binding factor 1 (AUF1) has four isoforms resulting from alternative splicing and is critical for miRNA-mediated gene silencing with a distinct preference of target miRNAs. Previously, we have shown that AUF1 facilitates miRNA loading to Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex. Here, we further demonstrate that depletion of AUF1 abolishes the global interaction of miRNAs and AGO2...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334721/microrna-9-inhibits-nlrp3-inflammasome-activation-in-human-atherosclerosis-inflammation-cell-models-through-the-jak1-stat-signaling-pathway
#14
Yue Wang, Zhihua Han, Yuqi Fan, Junfeng Zhang, Kan Chen, Lin Gao, Huasu Zeng, Jiatian Cao, Changqian Wang
BACKGROUND/AIMS: MicroRNA-9 (miR-9) is involved in inflammatory reaction in atherosclerosis; however, its function and regulatory mechanisms remain unclear. We aimed to uncover the exact roles of miR-9 and downstream signaling pathways using in vitro human atherosclerosis models. METHODS: We used oxidized low-density lipoprotein (oxLDL)-stimulated human THP-1 derived macrophages, oxLDL-stimulated human primary peripheral blood monocytes and lipopolysaccharides (LPS) or Alum-stimulated human THP-1 derived macrophages as in vitro atherosclerosis inflammation models...
March 27, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28334640/mirnas-in-synapse-development-and-synaptic-plasticity
#15
REVIEW
Zhonghua Hu, Zheng Li
Synapses are functional units of the nervous system, through which information is transferred between neurons. The development and activity-dependent modification of synapses require temporally and spatially controlled modulation of gene expression. microRNAs (miRNAs) have emerged as essential regulators of gene expression. They are small non-coding RNAs that regulate mRNA stability and translation by interacting with the 3' untranslated region (3' UTR) of mRNAs. miRNAs are located to neuronal processes to regulate protein synthesis locally and their expression is regulated by synaptic activity...
March 20, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28334134/a-compilation-of-web-based-research-tools-for-mirna-analysis
#16
Vaibhav Shukla, Vinay Koshy Varghese, Shama Prasada Kabekkodu, Sandeep Mallya, Kapaettu Satyamoorthy
Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features...
February 25, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28334118/individualized-analysis-of-differentially-expressed-mirnas-with-application-to-the-identification-of-mirnas-deregulated-commonly-in-lung-cancer-tissues
#17
Haidan Yan, Hao Cai, Qingzhou Guan, Jun He, Juan Zhang, You Guo, Haiyan Huang, Xiangyu Li, Yawei Li, Yunyan Gu, Lishuang Qi, Zheng Guo
Identifying differentially expressed microRNAs (DE miRNAs) between cancer samples and normal controls is a common way to investigate carcinogenesis mechanisms. However, for a DE miRNA detected at the population-level, we do not know whether it is DE in a particular cancer sample. Here, based on the finding that the within-sample relative expression orderings of miRNA pairs are highly stable in a particular type of normal tissues but widely disrupted in the corresponding cancer tissues, we proposed a method, called RankMiRNA, to identify DE miRNAs in each cancer tissue compared with its own normal state...
February 23, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334047/clinical-validation-of-chemotherapy-predictors-developed-on-global-microrna-expression-in-the-nci60-cell-line-panel-tested-in-ovarian-cancer
#18
Kira Philipsen Prahm, Claus Høgdall, Mona Aarenstrup Karlsen, Ib Jarle Christensen, Guy Wayne Novotny, Steen Knudsen, Anker Hansen, Peter Buhl Jensen, Thomas Jensen, Mansoor Raza Mirza, Anne Weng Ekmann-Gade, Lotte Nedergaard, Estrid Høgdall
OBJECTIVE: Ovarian cancer is the leading cause of death among gynecologic malignancies. This is partly due to a non-durable response to chemotherapy. Prediction of resistance to chemotherapy could be a key role in more personalized treatment. In the current study we aimed to examine if microRNA based predictors could predict resistance to chemotherapy in ovarian cancer, and to investigate if the predictors could be prognostic factors for progression free and overall survival. METHODS: Predictors of chemotherapy-resistance were developed based on correlation between miRNA expression and differences in measured growth inhibition in a variety of human cancer cell lines in the presence of Carboplatin, Paclitaxel and Docetaxel...
2017: PloS One
https://www.readbyqxmd.com/read/28333977/transition-into-inflammatory-cancer-associated-adipocytes-in-breast-cancer-microenvironment-requires-microrna-regulatory-mechanism
#19
Jiwoo Lee, Bok Sil Hong, Han Suk Ryu, Han-Byoel Lee, Minju Lee, In Ae Park, Jisun Kim, Wonshik Han, Dong-Young Noh, Hyeong-Gon Moon
The role of adipocytes in cancer microenvironment has gained focus during the recent years. However, the characteristics of the cancer-associated adipocytes (CAA) in human breast cancer tissues and the underlying regulatory mechanism are not clearly understood. We reviewed pathology specimens of breast cancer patients to understand the morphologic characteristics of CAA, and profiled the mRNA and miRNA expression of CAA by using indirect co-culture system in vitro. The CAAs in human breast cancers showed heterogeneous topographic relationship with breast cancer cells within the breast microenvironment...
2017: PloS One
https://www.readbyqxmd.com/read/28333713/micrornas-and-lipid-metabolism
#20
Binod Aryal, Abhishek K Singh, Noemi Rotllan, Nathan Price, Carlos Fernández-Hernando
PURPOSE OF REVIEW: Work over the past decade has identified the important role of microRNAs (miRNAS) in regulating lipoprotein metabolism and associated disorders including metabolic syndrome, obesity, and atherosclerosis. This review summarizes the most recent findings in the field, highlighting the contribution of miRNAs in controlling LDL-cholesterol (LDL-C) and HDL-cholesterol (HDL-C) metabolism. RECENT FINDINGS: A number of miRNAs have emerged as important regulators of lipid metabolism, including miR-122 and miR-33...
March 22, 2017: Current Opinion in Lipidology
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