MicroRNA profiling: Approaches and considerations

Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Nature Reviews Genetics (Impact Factor: 36.98). 04/2012; 13(5):358-69. DOI: 10.1038/nrg3198
Source: PubMed


MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate the expression of thousands of genes in a broad range of organisms in both normal physiological contexts and in disease contexts. miRNA expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and also show promise as biomarkers for disease. Technological advances have spawned a multitude of platforms for miRNA profiling, and an understanding of the strengths and pitfalls of different approaches can aid in their effective use. Here, we review the major considerations for carrying out and interpreting results of miRNA-profiling studies.

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    • "Forensic RNA analysis is increasingly being used for more definitive body fluid identification (BFID) with a focus on messenger RNA (mRNA) [1] [2] [3] [4] [5] and more increasingly on microRNA (miRNA) [6– 11]. MicroRNA is, in theory, the preferred marker to target as it is more stable due to its small size ($22–26 bp) and relatively high copy numbers within the cells [11] [12] [13] [14] [15] [16] [17]. There are some concerns relating to its species specificity, but this may be resolved by using a single channel simultaneous extraction technique [18] and the associated DNA profile, which is human specific. "
    • "Levels of either free miRNAs bound only to a protein complex such as Argonaute (Ago) or miRNAs within EVs have been assayed for correlation to a wide variety of diseases. In the oncology literature , hundreds of studies have been performed generating a variety of outcomes of both positive and negative associations of miRNAs, much of which has been questioned on methodologic grounds [21] [22] [23]. miRNAs as blood-based biomarkers have also been investigated in a huge variety of nonneoplastic diseases ranging from Alzheimer's disease to zinc depletion. "
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    ABSTRACT: microRNAs (miRNAs) are a class of small regulatory RNAs that decrease protein translation to fine-tune cellular function. Recently, miRNAs were found to transfer from a donor cell into a recipient cell via exosomes and microparticles. These microvesicles are found in blood, urine, saliva, and other fluid compartments. miRNAs are delivered with intact functionality and have been repeatedly shown to regulate protein expression in recipient cells in a paracrine fashion. Thus, transported miRNAs are a new class of cell-to-cell regulatory species. Exosomal miRNA transfer is now being reported in cardiovascular systems and disease. In the blood vessels, this transfer modulates atherosclerosis and angiogenesis. In the heart, it modulates heart failure, myocardial infarction, and response to ischemic preconditioning. This review describes our current understanding of extracellular vesicle miRNA transfer, demonstrating the roles of miR-126, miR-146a, miR-143, and other miRNAs being shuttled from endothelial cells, stem cells, fibroblasts and others into myocytes, endothelial cells, and smooth muscle cells to activate cellular changes and modulate disease phenotypes. Copyright © 2015. Published by Elsevier Inc.
    Cardiovascular pathology: the official journal of the Society for Cardiovascular Pathology 04/2015; 24(4). DOI:10.1016/j.carpath.2015.04.007 · 2.00 Impact Factor
    • "The upregulation (overexpression) of specific miRNAs could lead to the repression of tumor suppressor gene-expression, and conversely the down-regulation of specific miRNAs could result in an increase of oncogene expression; both these situations induce subsequent malignant effects on cell proliferation, differentiation, and apoptosis that lead to tumor growth and progress [5] [6]. Since their discovery, miRNAs are recognized as crucial regulators of geneexpression that regulate a range of processes [7]. Nowadays, it is evident that miRNAs regulate diverse cellular pathways and are widely believed to regulate most biological processes [8] [9] [10]. "
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    ABSTRACT: Wilms tumor, or nephroblastoma, is a cancer of the kidneys that typically occurs in children and rarely in adults. Around 10% of Wilms tumor patients are diagnosed having a concurrent syndrome that enhances the risk of Wilms tumor. A screening method for early detection of Wilms tumor in these patients would be beneficial, since the size or stage of a tumor is related to outcome. We introduce a miRNA pathway analysis methodology that takes into account the topology and regulation mechanisms of the gene regulatory networks and identify disrupted sub-paths in known pathways, using miRNA expressions. The methodology was applied on a miRNA-expression study and a predictive model was developed, using machine-learning (decision-tree induction) approaches. The model is able to identify putative mechanisms that underlie and govern the Wilms tumor phenotype, and discriminate between diseased and healthy subjects. Initial experimental results are promising and in line with the relevant biomedical literature.
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