Potential pitfalls in microRNA profiling

Department of Microbiology, UNC-Chapel Hill, Chapel Hill, NC, USA.
WIREs RNA (Impact Factor: 6.02). 09/2012; 3(5):601-16. DOI: 10.1002/wrna.1120
Source: PubMed


MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally influence a wide range of cellular processes such as the host response to viral infection, innate immunity, cell cycle progression, migration, and apoptosis through the inhibition of target mRNA translation. Owing to the growing number of miRNAs and identification of their functional roles, miRNA profiling of many different sample types has become more expansive, especially with relevance to disease signatures. In this review, we address some of the advantages and potential pitfalls of the currently available methods for miRNA expression profiling. Some of the topics discussed include isomiRNAs, comparison of different profiling platforms, normalization strategies, and issues with regard to sample preparation and experimental analyses. WIREs RNA 2011 DOI: 10.1002/wrna.1120
For further resources related to this article, please visit the WIREs website.

Download full-text


Available from: Dirk P Dittmer, Apr 26, 2014
  • Source
    • "It is difficult to compare these studies directly due to differences in cells, experimental methods and profiling techniques (qPCR versus microarray). Differences in profiling techniques alone are known to contribute to the variation of datasets [70]. Smith et al. reported that a molecule termed hs_154 was significantly induced following WNV infection [37]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The innate immune response to West Nile virus (WNV) infection involves recognition through toll-like receptors (TLRs) and RIG-I-like receptors (RLRs), leading to establishment of an antiviral state. MiRNAs (miRNAs) have been shown to be reliable biomarkers of TLR activation. Here, we sought to evaluate the contribution of TLR3 and miRNAs to the host response to WNV infection. We first analyzed HEK293-NULL and HEK293-TLR3 cells for changes in the innate immune response to infection. The presence of TLR3 did not seem to affect WNV load, infectivity or phosphorylation of IRF3. Analysis of experimentally validated NFκB-responsive genes revealed a WNV-induced signature largely independent of TLR3. Since miRNAs are involved in viral pathogenesis and the innate response to infection, we sought to identify changes in miRNA expression upon infection in the presence or absence of TLR3. MiRNA profiling revealed 70 miRNAs induced following WNV infection in a TLR3-independent manner. Further analysis of predicted gene targets of WNV signature miRNAs revealed genes highly associated with pathways regulating cell death, viral pathogenesis and immune cell trafficking.
    PLoS ONE 08/2014; 9(8):e104770. DOI:10.1371/journal.pone.0104770 · 3.23 Impact Factor
  • Source
    • "Thus, many factors should be considered when choosing a platform. Recently, the current knowledge of the relevant methodologies and potential pitfalls in miRNA profiling were extensively reviewed (Chugh and Dittmer, 2012). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Trinucleotide repeat expansion disorders (TREDs) constitute a group of dominantly inherited neurological diseases that are incurable and ultimately fatal. The underlying cause of TREDs is an expansion of trinucleotide repeats that may occur in the coding and non-coding regions of human genes. MicroRNAs (miRNAs) have emerged as potent regulators of gene expression at the posttranscriptional level. They are involved in a variety of physiological and pathological processes in humans, and the alteration of miRNA expression is considered to be a hallmark of many diseases, including TREDs. This review summarizes the current knowledge regarding the involvement of miRNAs in the pathogenesis of TREDs and the experimentally proven associations between specific miRNAs and particular disorders that have been reported to date.
    Applied RNAi: From Fundamental Research to Therapeutic Applications, Edited by Patrick Arbuthnot, Marc S. Weinberg, 06/2014: chapter 12: pages 227–246; Caister Academic Press., ISBN: 978-1-908230-43-0 / Ebook 978-1-908230-67-6
  • Source
    • "This technique relies on the production of cDNA libraries, which are amplified by PCR. This opens the possibility of testing global miRNA levels in samples with little starting material, but it suffers from nonlinearity in the measurement process [9], with miRNAs expressed at very high or very low levels being the most affected by this issue. Likewise, technical issues, particularly concerning variability in adapter ligation and differences in enzymatic efficiency, can affect this technique. "
    [Show abstract] [Hide abstract]
    ABSTRACT: MicroRNAs (miRNAs) have emerged as key genetic regulators of a wide variety of biological processes, including growth, proliferation, and survival. Recent advances have led to the recognition that miRNAs can act as potent oncogenes and tumor suppressors, playing crucial roles in the initiation, maintenance, and progression of the oncogenic state in a variety of cancers. Determining how miRNA expression and function is altered in cancer is an important goal, and a necessary prerequisite to the development and adoption of miRNA-based therapeutics in the clinic. Highly promising clinical applications of miRNAs are the use of miRNA signatures as biomarkers for cancer (for example, for early detection or diagnosis), and therapeutic supplementation or inhibition of specific miRNAs to alter the cancer phenotype. In this review, we discuss the main methods used for miRNA profiling, and examine key miRNAs that are commonly altered in a variety of tumors. Current studies underscore the functional versatility and potency of miRNAs in various aspects of the cancer phenotype, pointing to their potential clinical applications. Consequently, we discuss the application of miRNAs as biomarkers, clinical agents, and therapeutic targets, highlighting both the enormous potential and major challenges in this field.
    Genome Medicine 12/2013; 5(12):111. DOI:10.1186/gm516 · 5.34 Impact Factor
Show more