301
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Xu P, Billmeier M, Mohorianu I, Green D, Fraser WD, Dalmay T. An improved protocol for small RNA library construction using High Definition adapters. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/mngs-2015-0001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractNext generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules. One approach to reduce this ligation bias is to use a pool of adapters instead of a single adapter sequence, which allows many sRNAs to be ligated efficiently. We previously developed High Definition (HD) adapters for the Illumina sequencing platform, which contain degenerate nucleotides at the ligating ends of the adapters. However, the current commercial kits produced a large amount of 5’ adapter – 3’ adapter ligation product without the cDNA insert when HD adapters were used to replace the kit adapters. Here, we report a protocol to generate sRNA libraries using HD adapters with greatly reduced proportion of adapter-adapter products due to the degradation of nonligated 3’ adapters. The libraries can be completed within two days and can be used for various biological and clinical samples. As examples for using this protocol, we constructed sRNA libraries using total RNA extracted from cultured mammalian cells and plant leaf tissue.
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302
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Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation. PLoS One 2015; 10:e0122122. [PMID: 25836973 PMCID: PMC4383378 DOI: 10.1371/journal.pone.0122122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/19/2015] [Indexed: 11/19/2022] Open
Abstract
Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.
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303
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Challenges in using circulating miRNAs as cancer biomarkers. BIOMED RESEARCH INTERNATIONAL 2015; 2015:731479. [PMID: 25874226 PMCID: PMC4385632 DOI: 10.1155/2015/731479] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/06/2014] [Indexed: 02/06/2023]
Abstract
In the last years, circulating miRNAs have emerged as a new class of promising cancer biomarkers. Independent studies have shown the feasibility of using these small RNAs as tools for the diagnosis and prognosis of different types of malignancies as well as for predicting and possibly monitoring treatment response. However, despite an initial enthusiasm for their possible clinical application, widespread inconsistencies have been observed among the studies, and miRNA-based tools still represent the object of research within clinical diagnostic or treatment protocols. The poor overlap of results could be explained, at least in part, by preanalytical and analytical variables and donor-related factors that could generate artefacts, impairing an accurate quantification of circulating miRNAs. In fact, critical issues are represented by nonuniform sample choice, handling, and processing, as well as by blood cell contamination in sample preparation and lack of consensus for data normalization. In this review, we address the potential technical biases and individual-related parameters that can influence circulating miRNA studies' outcome. The exciting potential of circulating miRNAs as cancer biomarkers could confer an important advance in the disease management, but their clinical significance might not be proven without a global consensus of procedures and standardized protocols for their accurate detection.
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304
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MicroRNA-derived fragment length polymorphism assay. Sci Rep 2015; 5:9356. [PMID: 25790971 PMCID: PMC4366852 DOI: 10.1038/srep09356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/27/2015] [Indexed: 12/18/2022] Open
Abstract
MicroRNA (miRNA) studies are experiencing a transition from basic research applications to clinical applications. However, the lack of reliable and sensitive miRNA detection methods has become a bottleneck in the process. Here, we report an absolute quantification method based on the competitive PCR amplification of specific miRNAs and synthetic RNA spike-ins in a single reaction. RNA spike-ins are quantified as dynamic RNA copy number standards and are used to measure selected miRNAs free from the effects of intra-assay variables, including those from individual sample sources. Combined with the size differentiation power of capillary electrophoresis, the content of miRNAs was reproducibly measured, with verifiable detection limits of 10–46 copies over 5-log detection ranges. The direct measurements of miRNAs from 168 human serum samples and their considerable value as a diagnostic for bronchopneumonia and bronchiolitis demonstrate the potential of the assay in clinical applications.
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305
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High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute. Int J Genomics 2015; 2015:125048. [PMID: 25861616 PMCID: PMC4378336 DOI: 10.1155/2015/125048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/13/2015] [Accepted: 02/23/2015] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.
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306
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Schulte C, Zeller T. microRNA-based diagnostics and therapy in cardiovascular disease-Summing up the facts. Cardiovasc Diagn Ther 2015; 5:17-36. [PMID: 25774345 DOI: 10.3978/j.issn.2223-3652.2014.12.03] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/10/2014] [Indexed: 12/21/2022]
Abstract
Circulating microRNAs (miRNAs) are discussed as potential disease-specific biomarkers in cardiovascular disease. Their diagnostic value has been examined in numerous studies and animal models with respect to coronary artery disease (CAD) and myocardial infarction (MI) and the prognostic abilities of circulating miRNAs in risk stratification of future disease have been evaluated. Various miRNAs are described to complement protein-based biomarkers or classical risk factors in the diagnosis of CAD or MI and even represent potential new biomarkers in the discrimination of unstable angina pectoris (UAP). Signatures consisting of sets of multiple miRNAs seem to improve the predictive power compared to single miRNAs. Furthermore, the emerging field of miRNA-based therapeutics has reached cardiovascular research. The first promising in vitro results are raising hope for future clinical application. However, methods and material used for RNA isolation, miRNA detection and normalization steps still lack ways of standardization and need to be considered carefully. This article reviews the current knowledge of miRNAs in cardiovascular disease focusing on CAD and MI and will provide an overview regarding the use of circulating miRNAs as biomarkers and potential therapeutic targets in the field of CAD.
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Affiliation(s)
- Christian Schulte
- 1 Department of General and Interventional Cardiology, University Heart Center Hamburg Eppendorf, 20246 Hamburg, Germany ; 2 German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Hamburg, Germany
| | - Tanja Zeller
- 1 Department of General and Interventional Cardiology, University Heart Center Hamburg Eppendorf, 20246 Hamburg, Germany ; 2 German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Hamburg, Germany
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307
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Geraci NS, Tan JC, McDowell MA. Characterization of microRNA expression profiles in Leishmania-infected human phagocytes. Parasite Immunol 2015; 37:43-51. [PMID: 25376316 DOI: 10.1111/pim.12156] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/29/2014] [Indexed: 12/14/2022]
Abstract
Leishmania are intracellular protozoa that influence host immune responses eliciting parasite species-specific pathologies. MicroRNAs (miRNAs) are short single-stranded ribonucleic acids that complement gene transcripts to block protein translation and have been shown to regulate immune system molecular mechanisms. Human monocyte-derived dendritic cells (DC) and macrophages (MP) were infected in vitro with Leishmania major or Leishmania donovani parasites. Small RNAs were isolated from total RNA and sequenced to identify mature miRNAs associated with leishmanial infections. Normalized sequence read count profiles revealed a global downregulation in miRNA expression among host cells following infection. Most identified miRNAs were expressed at higher levels in L. donovani-infected cells relative to L. major-infected cells. Pathway enrichments using in silico-predicted gene targets of differentially expressed miRNAs showed evidence of potentially universal MAP kinase signalling pathway effects. Whereas JAK-STAT and TGF-β signalling pathways were more highly enriched using targets of miRNAs upregulated in L. donovani-infected cells, these data provide evidence in support of a selective influence on host cell miRNA expression and regulation in response to differential Leishmania infections.
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Affiliation(s)
- N S Geraci
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
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308
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Baril P, Ezzine S, Pichon C. Monitoring the spatiotemporal activities of miRNAs in small animal models using molecular imaging modalities. Int J Mol Sci 2015; 16:4947-72. [PMID: 25749473 PMCID: PMC4394458 DOI: 10.3390/ijms16034947] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/17/2015] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by binding mRNA targets via sequence complementary inducing translational repression and/or mRNA degradation. A current challenge in the field of miRNA biology is to understand the functionality of miRNAs under physiopathological conditions. Recent evidence indicates that miRNA expression is more complex than simple regulation at the transcriptional level. MiRNAs undergo complex post-transcriptional regulations such miRNA processing, editing, accumulation and re-cycling within P-bodies. They are dynamically regulated and have a well-orchestrated spatiotemporal localization pattern. Real-time and spatio-temporal analyses of miRNA expression are difficult to evaluate and often underestimated. Therefore, important information connecting miRNA expression and function can be lost. Conventional miRNA profiling methods such as Northern blot, real-time PCR, microarray, in situ hybridization and deep sequencing continue to contribute to our knowledge of miRNA biology. However, these methods can seldom shed light on the spatiotemporal organization and function of miRNAs in real-time. Non-invasive molecular imaging methods have the potential to address these issues and are thus attracting increasing attention. This paper reviews the state-of-the-art of methods used to detect miRNAs and discusses their contribution in the emerging field of miRNA biology and therapy.
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Affiliation(s)
- Patrick Baril
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, 45071 Orléans, France.
| | - Safia Ezzine
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, 45071 Orléans, France.
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, 45071 Orléans, France.
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309
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Duplex-specific nuclease-mediated bioanalysis. Trends Biotechnol 2015; 33:180-8. [DOI: 10.1016/j.tibtech.2014.12.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022]
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310
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Abstract
Methylation of N6-adenosine (m6A) has been observed in many different classes of RNA, but its prevalence in microRNAs (miRNAs) has not yet been studied. Here we show that a knockdown of the m6A demethylase FTO affects the steady-state levels of several miRNAs. Moreover, RNA immunoprecipitation with an anti-m6A-antibody followed by RNA-seq revealed that a significant fraction of miRNAs contains m6A. By motif searches we have discovered consensus sequences discriminating between methylated and unmethylated miRNAs. The epigenetic modification of an epigenetic modifier as described here adds a new layer to the complexity of the posttranscriptional regulation of gene expression.
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311
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miR-30 family microRNAs regulate myogenic differentiation and provide negative feedback on the microRNA pathway. PLoS One 2015; 10:e0118229. [PMID: 25689854 PMCID: PMC4331529 DOI: 10.1371/journal.pone.0118229] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/09/2015] [Indexed: 11/19/2022] Open
Abstract
microRNAs (miRNAs) are short non-coding RNAs that can mediate changes in gene expression and are required for the formation of skeletal muscle (myogenesis). With the goal of identifying novel miRNA biomarkers of muscle disease, we profiled miRNA expression using miRNA-seq in the gastrocnemius muscles of dystrophic mdx4cv mice. After identifying a down-regulation of the miR-30 family (miR-30a-5p, -30b, -30c, -30d and -30e) when compared to C57Bl/6 (WT) mice, we found that overexpression of miR-30 family miRNAs promotes differentiation, while inhibition restricts differentiation of myoblasts in vitro. Additionally, miR-30 family miRNAs are coordinately down-regulated during in vivo models of muscle injury (barium chloride injection) and muscle disuse atrophy (hindlimb suspension). Using bioinformatics tools and in vitro studies, we identified and validated Smarcd2, Snai2 and Tnrc6a as miR-30 family targets. Interestingly, we show that by targeting Tnrc6a, miR-30 family miRNAs negatively regulate the miRNA pathway and modulate both the activity of muscle-specific miR-206 and the levels of protein synthesis. These findings indicate that the miR-30 family may be an interesting biomarker of perturbed muscle homeostasis and muscle disease.
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312
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Melnikova NV, Dmitriev AA, Belenikin MS, Speranskaya AS, Krinitsina AA, Rachinskaia OA, Lakunina VA, Krasnov GS, Snezhkina AV, Sadritdinova AF, Uroshlev LA, Koroban NV, Samatadze TE, Amosova AV, Zelenin AV, Muravenko OV, Bolsheva NL, Kudryavtseva AV. Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L. Biochimie 2015; 109:36-41. [DOI: 10.1016/j.biochi.2014.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/26/2014] [Indexed: 10/24/2022]
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313
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In silico identification of conserved microRNAs and their targets in bovine fat tissue. Gene 2015; 559:119-28. [PMID: 25626178 DOI: 10.1016/j.gene.2015.01.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) represent a newly identified class of non-protein-coding ~22 nt small RNA which plays important roles in multiple biological processes by degrading targeted mRNA or repressing mRNA translation. Here we present EST (expressed sequence tags)-based and GSS (Genomic Survey Sequences)-based combined approach for the detection of conserved miRNAs of cattle. A total of 20 conserved miRNAs that belong to 18 miRNA families were detected following a range of filtering criteria; their functions were further predicted and analyzed. To confirm our prediction, a miRNA-detecting microarray was designed with probes complementary to previously known mature miRNA sequences from 131 organisms. After hybridizing with small RNAs extracted from beef cattle subcutaneous fat tissue, 219 (32.30%) miRNAs were detected in the 679 known Bos taurus miRNAs and all the miRNAs predicted above were also detected. Conformation of 22 most abundant miRNA expression by qRT-PCR indicated that they were highly accumulated not only in subcutaneous fat tissue but also in intramuscular fat tissue. Bioinformatics of KEGG pathway analysis suggested that 4 differential expression miRNAs (miR-143, miR-145, miR-2325c and miR-2361) involved in different pathways and target genes may regulate the fat deposition differently. Taken together, our results expand the number of known bovine miRNAs and provide a thorough account of the miRNA transcriptome in bovine adipose tissue.
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314
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Abstract
Molecular biomarkers are used routinely in the clinical management of several tumours such as prostate, colon, ovarian and pancreatic cancer but management decisions in bladder cancer remain dependent on clinical and pathological criteria, which are limited in their ability to predict outcomes. Molecular markers are urgently needed in detection, surveillance and prognostication of bladder cancer as well as to predict treatment response to intravesical and systemic therapies. Advances in cancer genomics and platforms for biomarker profiling have led to a plethora of biomarkers, which must now be rigorously validated in the clinical setting. Pre-clinical and clinical studies exploring the role of emerging targeted therapies to risk stratify and reduce cancer progression are also needed.
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315
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Essential Role of microRNA in Skin Physiology and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 888:307-30. [DOI: 10.1007/978-3-319-22671-2_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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316
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Hunt EA, Broyles D, Head T, Deo SK. MicroRNA Detection: Current Technology and Research Strategies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:217-37. [PMID: 25973944 DOI: 10.1146/annurev-anchem-071114-040343] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.
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Affiliation(s)
- Eric A Hunt
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, Florida 33136;
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317
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Aungier SR, Ohmori H, Clinton M, Mabbott NA. MicroRNA-100-5p indirectly modulates the expression of Il6, Ptgs1/2 and Tlr4 mRNA in the mouse follicular dendritic cell-like cell line, FL-Y. Immunology 2015; 144:34-44. [PMID: 24944008 PMCID: PMC4264908 DOI: 10.1111/imm.12342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/13/2014] [Accepted: 06/13/2014] [Indexed: 01/09/2023] Open
Abstract
Follicular dendritic cells (FDC) are important stromal cells within the B-cell follicles and germinal centres (GC) of secondary lymphoid tissues. FDC trap and retain native antigens on their surfaces in the form of immune complexes that they display to B cells, in order to select those cells with the highest antigen affinity. MicroRNAs are short, non-coding RNAs that are approximately 18-25 nucleotides in length that regulate gene expression at the post-transcriptional level by repressing the translation of target genes. In the current study, in vivo and in vitro systems were used to identify microRNAs that were potentially expressed by FDC. Constitutive lymphotoxin-β receptor (LTβR) stimulation is required to maintain FDC in their differentiated state. We show that the rapid de-differentiation of spleen FDC that accompanied LTβR-blockade, coincided with a significant decrease in the expression of mmu-miR-100-5p, mmu-miR-138-5p and mmu-miR-2137. These microRNAs were shown to be expressed in the FDC-like cell line, FL-YB, and specific inhibition of mmu-miR-100-5p significantly enhanced expression of Il6, Ptgs1/2 and Tlr4 mRNA in this cell line. The expression of Il6, Ptgs1/2 and Tlr4 by FDC play important roles in regulating GC size and promoting high-affinity antibody responses, so it is plausible that mmu-miR-100-5p may help to regulate the expression of these genes during GC reactions.
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Affiliation(s)
- Susan R Aungier
- The Roslin Institute and R(D)SVS, University of EdinburghMidlothian, UK
| | - Hitoshi Ohmori
- Department of Bioscience and Biotechnology, Okayama University Graduate School of Natural Science and TechnologyOkayama, Japan
| | - Michael Clinton
- The Roslin Institute and R(D)SVS, University of EdinburghMidlothian, UK
| | - Neil A Mabbott
- The Roslin Institute and R(D)SVS, University of EdinburghMidlothian, UK
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318
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Zhang H, Liu Y, Gao J, Zhen J. A sensitive SERS detection of miRNA using a label-free multifunctional probe. Chem Commun (Camb) 2015; 51:16836-9. [DOI: 10.1039/c5cc06225j] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A novel surface enhanced Raman scattering (SERS) detection method is fabricated for miRNA based on a smart multifunctional probe for dual cyclical nucleic acid strand-displacement polymerization (CNDP).
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Affiliation(s)
- Hao Zhang
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Yu Liu
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Jian Gao
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Junhui Zhen
- School of Medicine
- Shandong University
- Jinan 250012
- China
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319
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Fleischhacker M, Schmidt B. Extracellular Nucleic Acids and Cancer. ADVANCES IN PREDICTIVE, PREVENTIVE AND PERSONALISED MEDICINE 2015. [DOI: 10.1007/978-94-017-9168-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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320
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Butz H, Patócs A. Technical Aspects Related to the Analysis of Circulating microRNAs. EXPERIENTIA SUPPLEMENTUM (2012) 2015; 106:55-71. [PMID: 26608199 DOI: 10.1007/978-3-0348-0955-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Specific and sensitive noninvasive biofluid-based biomarkers are always needed in the laboratory diagnosis of diseases. Biomarkers are applied not only for diagnostic purposes but for stratifying a disease and for assessing the therapy response or disease progression. MicroRNAs (miRNAs) are short noncoding RNA molecules regulating gene expression posttranscriptionally. They are frequently dysregulated in many physiological and pathophysiological conditions. miRNAs are present in the circulation and in other biofluids that are common matrices for clinical laboratory testing that has raised the possibility that miRNAs may serve as novel biomarkers. Their excellent stability also supports the possibility that miRNAs once will be routinely used biomarkers in clinical practice. From an analytical point of view, there are many factors (starting material, sample storage and processing, different RNA extraction and detection methods, intra- and interassay variability, and assay interferences) to consider if a miRNA as biomarker is aimed to be introduced as a clinical laboratory test. Despite several pre-analytical and analytical factors that still need standardization, a significant number of studies have been published about the potential role of circulating miRNAs as biomarkers. Due to the lack of standardization of methods, there are a lot of discrepancies among results. In this chapter, we aimed to summarize the current findings about circulating miRNAs focusing on the analytical points related to miRNAs measurements from biofluids.
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Affiliation(s)
- Henriett Butz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Hungarian Academy of Sciences and Semmelweis University "Lendület" Hereditary Endocrine Tumors Research Group, Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 46 Szentkirályi Str., 1088, Budapest, Hungary
| | - Attila Patócs
- Hungarian Academy of Sciences and Semmelweis University "Lendület" Hereditary Endocrine Tumors Research Group, Budapest, Hungary.
- Department of Laboratory Medicine, Semmelweis University, 46 Szentkirályi Str., 1088, Budapest, Hungary.
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321
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Johansen I, Andreassen R. Validation of miRNA genes suitable as reference genes in qPCR analyses of miRNA gene expression in Atlantic salmon (Salmo salar). BMC Res Notes 2014; 8:945. [PMID: 25533334 PMCID: PMC4308020 DOI: 10.1186/1756-0500-7-945] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are an abundant class of endogenous small RNA molecules that downregulate gene expression at the post-transcriptional level. They play important roles by regulating genes that control multiple biological processes, and recent years there has been an increased interest in studying miRNA genes and miRNA gene expression. The most common method applied to study gene expression of single genes is quantitative PCR (qPCR). However, before expression of mature miRNAs can be studied robust qPCR methods (miRNA-qPCR) must be developed. This includes identification and validation of suitable reference genes. We are particularly interested in Atlantic salmon (Salmo salar). This is an economically important aquaculture species, but no reference genes dedicated for use in miRNA-qPCR methods has been validated for this species. Our aim was, therefore, to identify suitable reference genes for miRNA-qPCR methods in Salmo salar. Results We used a systematic approach where we utilized similar studies in other species, some biological criteria, results from deep sequencing of small RNAs and, finally, experimental validation of candidate reference genes by qPCR to identify the most suitable reference genes. Ssa-miR-25-3p was identified as most suitable single reference gene. The best combinations of two reference genes were ssa-miR-25-3p and ssa-miR-455-5p. These two genes were constitutively and stably expressed across many different tissues. Furthermore, infectious salmon anaemia did not seem to affect their expression levels. These genes were amplified with high specificity, good efficiency and the qPCR assays showed a good linearity when applying a simple cybergreen miRNA-PCR method using miRNA gene specific forward primers. Conclusions We have identified suitable reference genes for miRNA-qPCR in Atlantic salmon. These results will greatly facilitate further studies on miRNA genes in this species. The reference genes identified are conserved genes that are identical in their mature sequence in many aquaculture species. Therefore, they may also be suitable as reference genes in other teleosts. Finally, the systematic approach used in our study successfully identified suitable reference genes, suggesting that this may be a useful strategy to apply in similar validation studies in other aquaculture species. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-945) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Rune Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway.
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322
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Tavallaie R, De Almeida SRM, Gooding JJ. Toward biosensors for the detection of circulating microRNA as a cancer biomarker: an overview of the challenges and successes. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:580-92. [DOI: 10.1002/wnan.1324] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/09/2014] [Accepted: 10/29/2014] [Indexed: 01/07/2023]
Affiliation(s)
- Roya Tavallaie
- School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence for Bio-Nano Science and Technology; The University of New South Wales; Sydney NSW Australia
| | - Swahnnya R. M. De Almeida
- School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence for Bio-Nano Science and Technology; The University of New South Wales; Sydney NSW Australia
| | - J. Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence for Bio-Nano Science and Technology; The University of New South Wales; Sydney NSW Australia
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323
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Pimentel F, Bonilla P, Ravishankar YG, Contag A, Gopal N, LaCour S, Lee T, Niemz A. Technology in MicroRNA Profiling: Circulating MicroRNAs as Noninvasive Cancer Biomarkers in Breast Cancer. ACTA ACUST UNITED AC 2014; 20:574-88. [PMID: 25524488 DOI: 10.1177/2211068214561788] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Indexed: 12/13/2022]
Abstract
This report describes technologies to identify and quantify microRNAs (miRNAs) as potential cancer biomarkers, using breast cancer as an example. Most breast cancer patients are not diagnosed until the disease has advanced to later stages, which decreases overall survival rates. Specific miRNAs are up- or downregulated in breast cancer patients at various stages, can be detected in plasma and serum, and have shown promising preliminary clinical sensitivity and specificity for early cancer diagnosis or staging. Nucleic acid testing methods to determine relative concentrations of selected miRNAs include reverse transcription, followed by quantitative PCR (RT-qPCR), microarrays, and next-generation sequencing (NGS). Of these methods, NGS is the most powerful approach for miRNA biomarker discovery, whereas RT-qPCR shows the most promise for eventual clinical diagnostic applications.
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Affiliation(s)
- Fernando Pimentel
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Patricia Bonilla
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | | | - Alec Contag
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Nimish Gopal
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Sarah LaCour
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Trenton Lee
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
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324
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Assessing Agreement between miRNA Microarray Platforms. MICROARRAYS 2014; 3:302-21. [PMID: 27600350 PMCID: PMC4979053 DOI: 10.3390/microarrays3040302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/24/2014] [Accepted: 11/25/2014] [Indexed: 01/02/2023]
Abstract
Over the last few years, miRNA microarray platforms have provided great insights into the biological mechanisms underlying the onset and development of several diseases. However, only a few studies have evaluated the concordance between different microarray platforms using methods that took into account measurement error in the data. In this work, we propose the use of a modified version of the Bland–Altman plot to assess agreement between microarray platforms. To this aim, two samples, one renal tumor cell line and a pool of 20 different human normal tissues, were profiled using three different miRNA platforms (Affymetrix, Agilent, Illumina) on triplicate arrays. Intra-platform reliability was assessed by calculating pair-wise concordance correlation coefficients (CCC) between technical replicates and overall concordance correlation coefficient (OCCC) with bootstrap percentile confidence intervals, which revealed moderate-to-good repeatability of all platforms for both samples. Modified Bland–Altman analysis revealed good patterns of concordance for Agilent and Illumina, whereas Affymetrix showed poor-to-moderate agreement for both samples considered. The proposed method is useful to assess agreement between array platforms by modifying the original Bland–Altman plot to let it account for measurement error and bias correction and can be used to assess patterns of concordance between other kinds of arrays other than miRNA microarrays.
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325
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Role of microRNAs in cancers of the female reproductive tract: insights from recent clinical and experimental discovery studies. Clin Sci (Lond) 2014; 128:153-80. [PMID: 25294164 DOI: 10.1042/cs20140087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
microRNAs (miRNAs) are small RNA molecules that represent the top of the pyramid of many tumorigenesis cascade pathways as they have the ability to affect multiple, intricate, and still undiscovered downstream targets. Understanding how miRNA molecules serve as master regulators in these important networks involved in cancer initiation and progression open up significant innovative areas for therapy and diagnosis that have been sadly lacking for deadly female reproductive tract cancers. This review will highlight the recent advances in the field of miRNAs in epithelial ovarian cancer, endometrioid endometrial cancer and squamous-cell cervical carcinoma focusing on studies associated with actual clinical information in humans. Importantly, recent miRNA profiling studies have included well-characterized clinical specimens of female reproductive tract cancers, allowing for studies correlating miRNA expression with clinical outcomes. This review will summarize the current thoughts on the role of miRNA processing in unique miRNA species present in these cancers. In addition, this review will focus on current data regarding miRNA molecules as unique biomarkers associated with clinically significant outcomes such as overall survival and chemotherapy resistance. We will also discuss why specific miRNA molecules are not recapitulated across multiple studies of the same cancer type. Although the mechanistic contributions of miRNA molecules to these clinical phenomena have been confirmed using in vitro and pre-clinical mouse model systems, these studies are truly only the beginning of our understanding of the roles miRNAs play in cancers of the female reproductive tract. This review will also highlight useful areas for future research regarding miRNAs as therapeutic targets in cancers of the female reproductive tract.
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326
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Guerrini L, Krpetić Ž, van Lierop D, Alvarez-Puebla RA, Graham D. Direct Surface-Enhanced Raman Scattering Analysis of DNA Duplexes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408558] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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327
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Guerrini L, Krpetić Ž, van Lierop D, Alvarez-Puebla RA, Graham D. Direct Surface-Enhanced Raman Scattering Analysis of DNA Duplexes. Angew Chem Int Ed Engl 2014; 54:1144-8. [DOI: 10.1002/anie.201408558] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/30/2014] [Indexed: 01/04/2023]
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328
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Masood Y, Kqueen CY, Rajadurai P. Role of miRNA in head and neck squamous cell carcinoma. Expert Rev Anticancer Ther 2014; 15:183-97. [DOI: 10.1586/14737140.2015.978294] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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329
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Vescovo VD, Grasso M, Barbareschi M, Denti MA. MicroRNAs as lung cancer biomarkers. World J Clin Oncol 2014; 5:604-620. [PMID: 25302165 PMCID: PMC4129526 DOI: 10.5306/wjco.v5.i4.604] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/28/2014] [Accepted: 05/08/2014] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is the leading cause of cancer mortality worldwide. Its high mortality is due to the poor prognosis of the disease caused by a late disease presentation, tumor heterogeneities within histological subtypes, and the relatively limited understanding of tumor biology. Importantly, lung cancer histological subgroups respond differently to some chemotherapeutic substances and side effects of some therapies appear to vary between subgroups. Biomarkers able to stratify for the subtype of lung cancer, prognosticate the course of disease, or predict the response to treatment are in high demand. In the last decade, microRNAs (miRNAs), measured in resected tumor samples or in fine needle aspirate samples have emerged as biomarkers for tumor diagnosis, prognosis and prediction of response to treatment, due to the ease of their detection and in their extreme specificity. Moreover, miRNAs present in sputum, in plasma, in serum or in whole blood have increasingly been explored in the last five years as less invasive biomarkers for the early detection of cancers. In this review we cover the increasing amounts of data that have accumulated in the last ten years on the use of miRNAs as lung cancer biomarkers.
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330
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MiRNA profiles in cerebrospinal fluid from patients with central hypersomnias. J Neurol Sci 2014; 347:199-204. [PMID: 25451005 DOI: 10.1016/j.jns.2014.09.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 09/10/2014] [Accepted: 09/24/2014] [Indexed: 02/04/2023]
Abstract
MicroRNAs (miRNAs) are involved in the pathogenesis of many human diseases, including some neurological disorders. Recently, we have reported dysregulated miRNAs in plasma from patients with central hypersomnias including type 1 and type 2 narcolepsy, and idiopathic hypersomnia. This study addressed whether miRNA levels are altered in the cerebrospinal fluid (CSF) of patients with central hypersomnias. We conducted high-throughput analyses of miRNAs in CSF from patients using quantitative real-time polymerase chain reaction panels. We identified 13, 9, and 11 miRNAs with a more than two-fold change in concentration in CSF from patients with type 1 and type 2 narcolepsy and idiopathic hypersomnia, respectively, compared with matched healthy controls. Most miRNAs differed in more than one of the sleep disorders. However, all miRNAs were detected at low levels in CSF and varied between individuals. None of them showed significant differences in concentrations between groups after correcting for multiple testing, and none could be validated in an independent cohort. Nevertheless, approximately 60% of the most abundant miRNAs in the profile reported here have previously been identified in the CSF of healthy individuals, showing consistency with previous miRNA profiles found in CSF. In conclusion, we were not able to demonstrate distinct levels or patterns of miRNAs in CSF from central hypersomnia patients.
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331
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Zhao JJ, Carrasco RD. Crosstalk between microRNA30a/b/c/d/e-5p and the canonical Wnt pathway: implications for multiple myeloma therapy. Cancer Res 2014; 74:5351-8. [PMID: 25228654 DOI: 10.1158/0008-5472.can-14-0994] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dysregulation of transcription via the Wnt/β-catenin signaling pathway underlies the pathogenesis of a wide variety of frequent human cancers. These include epithelial carcinomas such as colorectal cancer and hematologic malignancies such as multiple myeloma. Thus, the Wnt/β-catenin in pathway potentially offers an attractive target for cancer therapy. This approach, however, has thus far proved challenging because the pathway plays a number of critical roles in physiologic homeostasis, [corrected] and because drugs that broadly target the pathway have unacceptable side effects. miRNAs function as regulators of gene expression and have also been implicated in the pathogenesis of multiple myeloma and other human cancers, offering the promise of novel therapeutic approaches if they can be applied effectively in vivo. Because BCL9 is a critical transcriptional coactivator of β-catenin that is aberrantly expressed in many human cancers but is of low abundance in normal tissues, [corrected] the Wnt/β-catenin/BCL9 complex has emerged as a promising and most likely relatively safe therapeutic target in cancers with dysregulated Wnt/β-catenin activity. This review discusses recent advances in the biology of Wnt inhibitors and the appealing possibility of a functional link between BCL9 and miRNA30a/b/c/d/e-5p that could be exploited for multiple myeloma therapy.
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Affiliation(s)
- Jian-Jun Zhao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ruben D Carrasco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
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332
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Boopathi T, Faria DG, Lee MD, Lee J, Chang M, Ki JS. A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79°N) in summer by using next-generation sequencing. Polar Biol 2014. [DOI: 10.1007/s00300-014-1576-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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333
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Biggar KK, Storey KB. New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview. Comput Struct Biotechnol J 2014; 11:138-46. [PMID: 25408848 PMCID: PMC4232569 DOI: 10.1016/j.csbj.2014.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/07/2014] [Accepted: 09/11/2014] [Indexed: 02/06/2023] Open
Abstract
Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.
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Affiliation(s)
| | - Kenneth B. Storey
- Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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334
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Sempere LF. Tissue slide-based microRNA characterization of tumors: how detailed could diagnosis become for cancer medicine? Expert Rev Mol Diagn 2014; 14:853-69. [PMID: 25090088 PMCID: PMC4364265 DOI: 10.1586/14737159.2014.944507] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
miRNAs are short, non-coding, regulatory RNAs that exert cell type-dependent, context-dependent, transcriptome-wide gene expression control under physiological and pathological conditions. Tissue slide-based assays provide qualitative (tumor compartment) and semi-quantitative (expression levels) information about altered miRNA expression at single-cell resolution in clinical tumor specimens. Reviewed here are key technological advances in the last 5 years that have led to implementation of fully automated, robust and reproducible tissue slide-based assays for in situ miRNA detection on US FDA-approved instruments; recent tissue slide-based discovery studies that suggest potential clinical applications of specific miRNAs in cancer medicine are highlighted; and the challenges in bringing tissue slide-based miRNA assays into the clinic are discussed, including clinical validation, biomarker performance, biomarker space and integration with other biomarkers.
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Affiliation(s)
- Lorenzo F Sempere
- Laboratory of microRNA Diagnostics and Therapeutics, Van Andel Research Institute, 333 Bostwick Ave, N.E, Grand Rapids, MI 49503, USA
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335
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Han HS, Jo YN, Lee JY, Choi SY, Jeong Y, Yun J, Lee OJ. Identification of suitable reference genes for the relative quantification of microRNAs in pleural effusion. Oncol Lett 2014; 8:1889-1895. [PMID: 25202432 PMCID: PMC4156210 DOI: 10.3892/ol.2014.2404] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 07/11/2014] [Indexed: 01/09/2023] Open
Abstract
Circulating cell-free microRNAs (miRNAs) are potential biomarkers of cancer. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is widely used in miRNA expression studies. The aim of this study was to identify suitable reference genes for RT-qPCR analyses of miRNA expression levels in pleural effusion. The expression levels of candidate reference miRNAs were investigated in 10 benign pleural effusion (BPE) and 10 lung adenocarcinoma-associated malignant pleural effusion (LA-MPE) samples using miRNA microarrays. The expression levels of candidate reference miRNAs, together with those of U6 small nuclear RNA (snRNA), RNU6B, RNU44 and RNU48 small RNAs, in 46 BPE and 45 LA-MPE samples were validated by RT-qPCR, and were analyzed using the NormFinder and BestKeeper algorithms. The impact of different normalization approaches on the detection of differential expression levels of miR-198 in BPE and LA-MPE samples was also assessed. As determined by the miRNA microarray data, five candidate reference miRNAs were identified. Following RT-qPCR validation, U6 snRNA, miR-192, miR-20a, miR-221, miR-222 and miR-16 were evaluated using the NormFinder and BestKeeper software programs. U6 snRNA and miR-192 were identified as single reference genes and the combination of these genes was preferred for the relative quantification of miRNA expression levels in pleural effusion. Normalization of miR-98 expression levels to those of U6 snRNA, miR-192 or a combination of these genes enabled the detection of a significant difference between BPE and LA-MPE samples. Therefore, U6 snRNA and miR-192 are recommended as reference genes for the relative quantification of miRNA expression levels in pleural effusion.
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Affiliation(s)
- Hye-Suk Han
- Department of Internal Medicine, College of Medicine, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Yeong Nang Jo
- Bioevaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 363-883, Republic of Korea
| | - Jin Yong Lee
- Public Health Medical Service, SMG-SNU Boramae Medical Center, Seoul 156-707, Republic of Korea
| | - Song-Yi Choi
- Department of Pathology, College of Medicine, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Yusook Jeong
- Department of Internal Medicine, College of Medicine, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Jieun Yun
- Bioevaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 363-883, Republic of Korea
| | - Ok-Jun Lee
- Department of Pathology, College of Medicine, Chungbuk National University, Cheongju 361-763, Republic of Korea
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336
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Plieskatt JL, Feng Y, Rinaldi G, Mulvenna JP, Bethony JM, Brindley PJ. Circumventing qPCR inhibition to amplify miRNAs in plasma. Biomark Res 2014; 2:13. [PMID: 25075309 PMCID: PMC4114091 DOI: 10.1186/2050-7771-2-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/11/2014] [Indexed: 01/05/2023] Open
Abstract
Background Circulating microRNAs (c-miRNAs) have be identified in saliva, urine and blood, which has led to increasing interest in their development as biomarkers for diverse diseases including cancers. One of the key advantages of c-miRNAs over other biomarkers is the ability to be amplified and quantified by quantitative PCR (qPCR). However, at phlebotomy when whole blood is dispensed into heparinized tubes, residual levels of the anti-coagulant lithium heparin may remain in the plasma and hence with RNA isolated from the plasma. This can confound the detection of c-miRNAs by qPCR because it inhibits reverse transcriptase (RT). Here we present a procedure, modified from earlier techniques, to detect c-miRNAs in plasma that improves sensitivity and streamlines performance. Findings Treatment of total RNA isolated from human blood plasma with Bacteroides heparinase I during reverse transcription at 37°C for one hour improved sensitivity and performance of the qPCR. This is in comparison to no treatment or treatment of the RNA prior to RT, which is the current suggested method and exposes plasma to Flavobacterium heparinum heparinase I for up to 2 hours before RT. This modest alteration improved qPCR performance and resulted in lowered threshold cycles (Ct) for detection of the target sequence, candidate c-miRNA biomarkers, and controls. It also reduced the expense and number of processing steps, shortening the duration of the assay and minimizing exposure of RNA to elevated temperatures. Conclusion Incorporating Bacteroides heparinase I treatment into conventional RT protocols targeting c-miRNA in plasma can be expected to expedite the discovery of biomarkers.
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Affiliation(s)
- Jordan L Plieskatt
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for the Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA
| | - Yanjun Feng
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for the Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA
| | - Gabriel Rinaldi
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for the Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA
| | - Jason P Mulvenna
- Infectious Disease and Cancer, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia ; The University of Queensland, School of Biomedical Sciences, Brisbane, Queensland, Australia
| | - Jeffrey M Bethony
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for the Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA
| | - Paul J Brindley
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for the Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA
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337
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Chandran PA, Keller A, Weinmann L, Seida AA, Braun M, Andreev K, Fischer B, Horn E, Schwinn S, Junker M, Houben R, Dombrowski Y, Dietl J, Finotto S, Wölfl M, Meister G, Wischhusen J. The TGF-β-inducible miR-23a cluster attenuates IFN-γ levels and antigen-specific cytotoxicity in human CD8⁺ T cells. J Leukoc Biol 2014; 96:633-45. [PMID: 25030422 DOI: 10.1189/jlb.3a0114-025r] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cytokine secretion and degranulation represent key components of CD8(+) T-cell cytotoxicity. While transcriptional blockade of IFN-γ and inhibition of degranulation by TGF-β are well established, we wondered whether TGF-β could also induce immune-regulatory miRNAs in human CD8(+) T cells. We used miRNA microarrays and high-throughput sequencing in combination with qRT-PCR and found that TGF-β promotes expression of the miR-23a cluster in human CD8(+) T cells. Likewise, TGF-β up-regulated expression of the cluster in CD8(+) T cells from wild-type mice, but not in cells from mice with tissue-specific expression of a dominant-negative TGF-β type II receptor. Reporter gene assays including site mutations confirmed that miR-23a specifically targets the 3'UTR of CD107a/LAMP1 mRNA, whereas the further miRNAs expressed in this cluster-namely, miR-27a and -24-target the 3'UTR of IFN-γ mRNA. Upon modulation of the miR-23a cluster by the respective miRNA antagomirs and mimics, we observed significant changes in IFN-γ expression, but only slight effects on CD107a/LAMP1 expression. Still, overexpression of the cluster attenuated the cytotoxic activity of antigen-specific CD8(+) T cells. These functional data thus reveal that the miR-23a cluster not only is induced by TGF-β, but also exerts a suppressive effect on CD8(+) T-cell effector functions, even in the absence of TGF-β signaling.
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Affiliation(s)
- P Anoop Chandran
- Graduate School of Life Sciences (GSLS), University of Würzburg, Germany; Department of Obstetrics and Gynecology
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Lasse Weinmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ahmed Adel Seida
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research
| | - Matthias Braun
- Pediatric Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital
| | - Katerina Andreev
- Laboratory of Cellular and Molecular Lung Immunology, Institute of Molecular Pneumology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; and
| | | | - Evi Horn
- Department of Obstetrics and Gynecology
| | - Stefanie Schwinn
- Pediatric Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital
| | - Markus Junker
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research
| | - Roland Houben
- Department of Dermatology, University of Würzburg Medical School, Würzburg, Germany
| | - Yvonne Dombrowski
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research
| | | | - Susetta Finotto
- Laboratory of Cellular and Molecular Lung Immunology, Institute of Molecular Pneumology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; and
| | - Matthias Wölfl
- Pediatric Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital
| | - Gunter Meister
- Max Planck Institute of Biochemistry, Martinsried, Germany; Department of Biochemistry, University of Regensburg, Germany
| | - Jörg Wischhusen
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research,
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338
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Riemondy K, Hoefert JE, Yi R. Not miR-ly micromanagers: the functions and regulatory networks of microRNAs in mammalian skin. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:849-65. [PMID: 25044412 DOI: 10.1002/wrna.1250] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 01/20/2023]
Abstract
The microRNA (miRNA) pathway is a widespread mechanism of post-transcriptional gene regulation in eukaryotic cells. In animals, each miRNA species can regulate hundreds of protein-coding genes, resulting in pervasive functions for miRNAs in numerous cellular processes. Since the identification of the first mammalian miRNA, the function of miRNAs in mammals has been a topic of great interest, both because of the versatile roles of miRNAs in biological systems, as well as the clinical potential of these regulatory RNAs. With well-defined cell lineages and the availability of versatile tools for both in vivo and in vitro studies, mammalian skin has emerged as an important system in which to examine miRNAs' functions in adult tissues. In this review, we discuss recent insights into the functions and regulatory networks of miRNAs in mammals, with a specific focus on murine skin development as a model system. We first introduce functional analyses of the miRNA biogenesis pathway in the skin, then highlight the functions of individual miRNAs in skin development, followed by an examination of miRNA roles in skin stress responses. We finish with a discussion of miRNA regulatory networks and emphasize future challenges and emerging technologies that permit the genome-wide study of miRNA functions and regulatory mechanisms in mammalian skin.
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Affiliation(s)
- Kent Riemondy
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
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339
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Degliangeli F, Pompa PP, Fiammengo R. Nanotechnology-based strategies for the detection and quantification of microRNA. Chemistry 2014; 20:9476-92. [PMID: 24989446 DOI: 10.1002/chem.201402649] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression, and many pathological conditions, including cancer, are characterized by altered miRNA expression levels. Therefore, accurate and sensitive quantification of miRNAs may result in correct disease diagnosis establishing these small noncoding RNA transcripts as valuable biomarkers. Aiming at overcoming some limitations of conventional quantification strategies, nanotechnology is currently providing numerous significant alternatives to miRNA sensing. In this review an up-to-date account of nanotechnology-based strategies for miRNA detection and quantification is given. The topics covered are: nanoparticle-based approaches in solution, sensing based on nanostructured surfaces, combined nanoparticle/surface sensing approaches, and single-molecule approaches.
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Affiliation(s)
- Federica Degliangeli
- Center for Biomolecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia (IIT), Via Barsanti, 73010 Arnesano (Lecce) (Italy)
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340
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Meder B, Backes C, Haas J, Leidinger P, Stähler C, Großmann T, Vogel B, Frese K, Giannitsis E, Katus HA, Meese E, Keller A. Influence of the confounding factors age and sex on microRNA profiles from peripheral blood. Clin Chem 2014; 60:1200-8. [PMID: 24987111 DOI: 10.1373/clinchem.2014.224238] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) measured from blood samples are promising minimally invasive biomarker candidates that have been extensively studied in several case-control studies. However, the influence of age and sex as confounding variables remains largely unknown. METHODS We systematically explored the impact of age and sex on miRNAs in a cohort of 109 physiologically unaffected individuals whose blood was characterized by microarray technology (stage 1). We also investigated an independent cohort from a different institution consisting of 58 physiologically unaffected individuals having a similar mean age but with a smaller age distribution. These samples were measured by use of high-throughput sequencing (stage 2). RESULTS We detected 318 miRNAs that were significantly correlated with age in stage 1 and, after adjustment for multiple testing of 35 miRNAs, remained statistically significant. Regarding sex, 144 miRNAs showed significant dysregulation. Here, no miRNA remained significant after adjustment for multiple testing. In the high-throughput datasets of stage 2, we generally observed a smaller number of significant associations, mainly as an effect of the smaller cohort size and age distribution. Nevertheless, we found 7 miRNAs that were correlated with age, of which 5 were concordant with stage 1. CONCLUSIONS The age distribution of individuals recruited for case-control studies needs to be carefully considered, whereas sex may be less confounding. To support the translation of miRNAs into clinical application, we offer a web-based application (http://www.ccb.uni-saarland.de/mirnacon) to test individual miRNAs or miRNA signatures for their likelihood of being influenced.
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Affiliation(s)
- Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany; Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Christina Backes
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Petra Leidinger
- Department of Human Genetics, Saarland University, Homburg, Germany
| | | | - Thomas Großmann
- Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
| | - Britta Vogel
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Karen Frese
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Evangelos Giannitsis
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany; Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrucken, Germany.
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341
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Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. Nat Methods 2014; 11:809-15. [PMID: 24973947 DOI: 10.1038/nmeth.3014] [Citation(s) in RCA: 468] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/22/2014] [Indexed: 11/08/2022]
Abstract
MicroRNAs are important negative regulators of protein-coding gene expression and have been studied intensively over the past years. Several measurement platforms have been developed to determine relative miRNA abundance in biological samples using different technologies such as small RNA sequencing, reverse transcription-quantitative PCR (RT-qPCR) and (microarray) hybridization. In this study, we systematically compared 12 commercially available platforms for analysis of microRNA expression. We measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples and synthetic spikes from microRNA family members with varying homology. We developed robust quality metrics to objectively assess platform performance in terms of reproducibility, sensitivity, accuracy, specificity and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals.
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342
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Nassirpour R, Mathur S, Gosink MM, Li Y, Shoieb AM, Wood J, O'Neil SP, Homer BL, Whiteley LO. Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms. BMC Genomics 2014; 15:485. [PMID: 24942259 PMCID: PMC4079956 DOI: 10.1186/1471-2164-15-485] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 06/09/2014] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small, non-coding RNAs that regulate protein levels post-transcriptionally. miRNAs play important regulatory roles in many cellular processes and have been implicated in several diseases. Recent studies have reported significant levels of miRNAs in a variety of body fluids, raising the possibility that miRNAs could serve as useful biomarkers. Next-generation sequencing (NGS) is increasingly employed in biomedical investigations. Although concordance between this platform and qRT-PCR based assays has been reported in high quality specimens, information is lacking on comparisons in biofluids especially urine. Here we describe the changes in miRNA expression patterns in a rodent model of renal tubular injury (gentamicin). Our aim is to compare RNA sequencing and qPCR based miRNA profiling in urine specimen from control and rats with confirmed tubular injury. Results Our preliminary examination of the concordance between miRNA-seq and qRT-PCR in urine specimen suggests minimal agreement between platforms probably due to the differences in sensitivity. Our results suggest that although miRNA-seq has superior specificity, it may not detect low abundant miRNAs in urine samples. Specifically, miRNA-seq did not detect some sequences which were identified by qRT-PCR. On the other hand, the qRT-PCR analysis was not able to detect the miRNA isoforms, which made up the majority of miRNA changes detected by NGS. Conclusions To our knowledge, this is the first time that miRNA profiling platforms including NGS have been compared in urine specimen. miRNAs identified by both platforms, let-7d, miR-203, and miR-320, may potentially serve as promising novel urinary biomarkers for drug induced renal tubular epithelial injury.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Laurence O Whiteley
- Drug Safety, Pfizer Worldwide Research and Development, 1 Burtt Rd, Andover, MA 01810, USA.
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343
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Waldron PR, Holodniy M. MicroRNA and hepatitis C virus--challenges in investigation and translation: a review of the literature. Diagn Microbiol Infect Dis 2014; 80:1-12. [PMID: 24996839 DOI: 10.1016/j.diagmicrobio.2014.05.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/22/2014] [Accepted: 05/27/2014] [Indexed: 12/25/2022]
Abstract
Investigations into the role of microRNA (miRNA) in hepatitis C virus (HCV) infection, disease pathogenesis and host immune and treatment response have potential to produce innovations in diagnosis, prognosis and therapy. However, investigational challenges remain in generating clinically useful and reproducible results. We review the literature with a primary emphasis on methods and technologies used to construct our current understanding of miRNA and HCV disease. A second emphasis is to understand potential clinical research applications and provide clarification of previous study results. Many miRNA have key roles in viral and immunopathogenesis of HCV infection across multiple tissue compartments. Controversy exists among published studies regarding relative measurements, temporal changes and biological significance of specific miRNA and HCV infection. To reconcile diverging data, additional research into optimal sample processing, in vitro models, techniques for microarray differential expression of miRNAs, practices for sample result normalization, and effect of HCV genotype variation on expression are all necessary. Microarray and miRNA isolation techniques should be selected based on ability to generate reproducible results in the sample type of interest. More direct comparisons of efficacy and reliability of various multiplex microarrays and an improved consensus around miRNA normalization and quantitation are necessary so that data can be compared across studies.
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Affiliation(s)
- Paul Ravi Waldron
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA.
| | - Mark Holodniy
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA; Office of Public Health, Department of Veterans Affairs, Washington, DC
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344
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Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics 2014; 15:423. [PMID: 24894665 PMCID: PMC4070549 DOI: 10.1186/1471-2164-15-423] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 05/27/2014] [Indexed: 01/21/2023] Open
Abstract
Background miRNAs play a key role in normal physiology and various diseases. miRNA profiling through next generation sequencing (miRNA-seq) has become the main platform for biological research and biomarker discovery. However, analyzing miRNA sequencing data is challenging as it needs significant amount of computational resources and bioinformatics expertise. Several web based analytical tools have been developed but they are limited to processing one or a pair of samples at time and are not suitable for a large scale study. Lack of flexibility and reliability of these web applications are also common issues. Results We developed a Comprehensive Analysis Pipeline for microRNA Sequencing data (CAP-miRSeq) that integrates read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, data visualization, variant detection in miRNA coding region, and more flexible differential expression analysis between experimental conditions. According to computational infrastructure, users can install the package locally or deploy it in Amazon Cloud to run samples sequentially or in parallel for a large number of samples for speedy analyses. In either case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses. Using well characterized data, we demonstrated the pipeline’s superior performances, flexibility, and practical use in research and biomarker discovery. Conclusions CAP-miRSeq is a powerful and flexible tool for users to process and analyze miRNA-seq data scalable from a few to hundreds of samples. The results are presented in the convenient way for investigators or analysts to conduct further investigation and discovery. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-423) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhifu Sun
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
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345
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Tsiliki G, Vlachakis D, Kossida S. On integrating multi-experiment microarray data. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20130136. [PMID: 24751870 PMCID: PMC3996576 DOI: 10.1098/rsta.2013.0136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
With the extensive use of microarray technology as a potential prognostic and diagnostic tool, the comparison and reproducibility of results obtained from the use of different platforms is of interest. The integration of those datasets can yield more informative results corresponding to numerous datasets and microarray platforms. We developed a novel integration technique for microarray gene-expression data derived by different studies for the purpose of a two-way Bayesian partition modelling which estimates co-expression profiles under subsets of genes and between biological samples or experimental conditions. The suggested methodology transforms disparate gene-expression data on a common probability scale to obtain inter-study-validated gene signatures. We evaluated the performance of our model using artificial data. Finally, we applied our model to six publicly available cancer gene-expression datasets and compared our results with well-known integrative microarray data methods. Our study shows that the suggested framework can relieve the limited sample size problem while reporting high accuracies by integrating multi-experiment data.
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Affiliation(s)
| | | | - Sophia Kossida
- Bioinformatics and Medical Informatics Group, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou 115 27, Greece
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346
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Sewer A, Gubian S, Kogel U, Veljkovic E, Han W, Hengstermann A, Peitsch MC, Hoeng J. Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression. BMC Res Notes 2014; 7:302. [PMID: 24886675 PMCID: PMC4077261 DOI: 10.1186/1756-0500-7-302] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/06/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. RESULTS Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the "common reference design" and processed as "pseudo-single-channel". They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription-polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. CONCLUSIONS Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository.
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Affiliation(s)
- Alain Sewer
- Philip Morris International Research & Development, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Sylvain Gubian
- Philip Morris International Research & Development, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Ulrike Kogel
- Philip Morris International Research & Development, Philip Morris Research Laboratories GmbH, Fuggerstrasse 3, 51149 Cologne, Germany
| | - Emilija Veljkovic
- Philip Morris International Research & Development, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Wanjiang Han
- Philip Morris International Research & Development, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Arnd Hengstermann
- Philip Morris International Research & Development, Philip Morris Research Laboratories GmbH, Fuggerstrasse 3, 51149 Cologne, Germany
| | - Manuel C Peitsch
- Philip Morris International Research & Development, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris International Research & Development, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
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347
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Duyu M, Durmaz B, Gunduz C, Vergin C, Yilmaz Karapinar D, Aksoylar S, Kavakli K, Cetingul N, Irken G, Yaman Y, Ozkinay F, Cogulu O. Prospective evaluation of whole genome microRNA expression profiling in childhood acute lymphoblastic leukemia. BIOMED RESEARCH INTERNATIONAL 2014; 2014:967585. [PMID: 24955371 PMCID: PMC4053274 DOI: 10.1155/2014/967585] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/07/2014] [Accepted: 04/22/2014] [Indexed: 12/31/2022]
Abstract
Dysregulation of microRNA (miRNA) expression contributes to the pathogenesis of several clinical conditions. The aim of this study is to evaluate the associations between miRNAs and childhood acute lymphoblastic leukemia (ALL) to discover their role in the course of the disease. Forty-three children with ALL and 14 age-matched healthy controls were included in the study. MicroRNA microarray expression profiling was used for peripheral blood and bone marrow samples. Aberrant miRNA expressions associated with the diagnosis and outcome were prospectively evaluated. Confirmation analysis was performed by real time RT-PCR. miR-128, miR-146a, miR-155, miR-181a, and miR-195 were significantly dysregulated in ALL patients at day 0. Following a six-month treatment period, the change in miRNA levels was determined by real time RT-PCR and expression of miR-146a, miR-155, miR-181a, and miR-195 significantly decreased. To conclude, these miRNAs not only may be used as biomarkers in diagnosis of ALL and monitoring the disease but also provide new insights into the potential roles of them in leukemogenesis.
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Affiliation(s)
- Muhterem Duyu
- Department of Pediatrics, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| | - Burak Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, 35100 Izmir, Turkey
| | - Cumhur Gunduz
- Department of Medical Biology, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| | - Canan Vergin
- Department of Pediatric Hematology, Behcet Uz Children's Hospital, 35210 Izmir, Turkey
| | | | - Serap Aksoylar
- Department of Pediatrics, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| | - Kaan Kavakli
- Department of Pediatrics, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| | - Nazan Cetingul
- Department of Pediatrics, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| | - Gulersu Irken
- Department of Pediatrics, Faculty of Medicine, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Yontem Yaman
- Department of Pediatric Hematology, Behcet Uz Children's Hospital, 35210 Izmir, Turkey
| | - Ferda Ozkinay
- Department of Pediatrics, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| | - Ozgur Cogulu
- Department of Pediatrics, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
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348
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Salas-Huetos A, Blanco J, Vidal F, Mercader JM, Garrido N, Anton E. New insights into the expression profile and function of micro-ribonucleic acid in human spermatozoa. Fertil Steril 2014; 102:213-222.e4. [PMID: 24794309 DOI: 10.1016/j.fertnstert.2014.03.040] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/28/2014] [Accepted: 03/18/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To characterize the microRNA (miRNA) expression profile in spermatozoa from human fertile individuals and their implications in human fertility. DESIGN The expression levels of 736 miRNAs were evaluated using TaqMan arrays. Ontologic analyses were performed to determine the presence of enriched biological processes among their targets. SETTING University research and clinical institutes. PATIENT(S) Ten individuals with normal seminogram, standard karyotype, and proven fertility. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Expression levels of 736 miRNAs, presence of enriched metabolic routes among their targets, homogeneity of the population, influence of demographic features in the results, presence of miRNA stable pairs, and best miRNA normalizing candidates. RESULT(S) A total of 221 miRNAs were consistently present in all individuals, 452 were only detected in some individuals, and 63 did not appear in any sample. The ontologic analysis of the 2,356 potential targets of the ubiquitous miRNAs showed an enrichment of processes related to cell differentiation, development, morphogenesis, and embryogenesis. None of the miRNAs were significantly correlated with age, semen volume, sperm concentration, motility, or morphology. Correlations between samples were statistically significant, indicating a high homogeneity of the population. A set of 48 miRNA pairs displayed a stable expression, a particular behavior that is discussed in relationship to their usefulness as fertility biomarkers. Hsa-miR-532-5p, hsa-miR-374b-5p, and hsa-miR-564 seemed to be the best normalizing miRNA candidates. CONCLUSION(S) Human sperm contain a stable population of miRNAs potentially related to embryogenesis and spermatogenesis.
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Affiliation(s)
- Albert Salas-Huetos
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Joan Blanco
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Francesca Vidal
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Josep M Mercader
- Joint Institution for Research in Biomedicine-Barcelona Supercomputing Center Program on Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Nicolás Garrido
- Laboratorio de Andrología y Banco de Semen, Instituto Valenciano de Infertilidad Valencia, Valencia, Spain
| | - Ester Anton
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain.
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349
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Xiao CL, Mai ZB, Lian XL, Zhong JY, Jin JJ, He QY, Zhang G. FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications. PLoS One 2014; 9:e94250. [PMID: 24743329 PMCID: PMC3990525 DOI: 10.1371/journal.pone.0094250] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/12/2014] [Indexed: 11/26/2022] Open
Abstract
Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT) based algorithms are fast but less robust. To have both advantages, we developed an algorithm FANSe2 with iterative mapping strategy based on the statistics of real-world sequencing error distribution to substantially accelerate the mapping without compromising the accuracy. Its sensitivity and accuracy are higher than the BWT-based algorithms in the tests using both prokaryotic and eukaryotic sequencing datasets. The gene identification results of FANSe2 is experimentally validated, while the previous algorithms have false positives and false negatives. FANSe2 showed remarkably better consistency to the microarray than most other algorithms in terms of gene expression quantifications. We implemented a scalable and almost maintenance-free parallelization method that can utilize the computational power of multiple office computers, a novel feature not present in any other mainstream algorithm. With three normal office computers, we demonstrated that FANSe2 mapped an RNA-seq dataset generated from an entire Illunima HiSeq 2000 flowcell (8 lanes, 608 M reads) to masked human genome within 4.1 hours with higher sensitivity than Bowtie/Bowtie2. FANSe2 thus provides robust accuracy, full indel sensitivity, fast speed, versatile compatibility and economical computational utilization, making it a useful and practical tool for deep sequencing applications. FANSe2 is freely available at http://bioinformatics.jnu.edu.cn/software/fanse2/.
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Affiliation(s)
- Chuan-Le Xiao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhi-Biao Mai
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xin-Lei Lian
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jia-Yong Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jing-jie Jin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (GZ); (Q-YH)
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (GZ); (Q-YH)
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350
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Song Y, Liu KJ, Wang TH. Elimination of ligation dependent artifacts in T4 RNA ligase to achieve high efficiency and low bias microRNA capture. PLoS One 2014; 9:e94619. [PMID: 24722341 PMCID: PMC3983213 DOI: 10.1371/journal.pone.0094619] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/18/2014] [Indexed: 01/22/2023] Open
Abstract
Adapter ligation is a critical first step in many microRNA analysis methods including microarray, qPCR, and sequencing. Previous studies have shown that ligation bias can have dramatic effects on both the fidelity of expression profiles and reproducibility across samples. We have developed a method for high efficiency and low bias microRNA capture by 3′ adapter ligation using T4 RNA ligase that does not require pooled adapters. Using a panel of 20 microRNA, we investigated the effects of ligase type, PEG concentration, ligase amount, adapter concentration, incubation time, incubation temperature, and adapter design on capture efficiency and bias. Of these factors, high PEG% was found to be critical in suppressing ligation bias. We obtained high average capture efficiency and low CV across the 20 microRNA panel, both in idealized buffer conditions (86%±10%) and total RNA spiking conditions (64%±17%). We demonstrate that this method is reliable across microRNA species that previous studies have had difficulty capturing and that our adapter design performs significantly better than the common adapter designs. Further, we demonstrate that the optimization methodology must be specifically designed for minimizing bias in order to obtain the ideal reaction parameters.
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Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kelvin J. Liu
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Circulomics Inc, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
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