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Grabia S, Smyczynska U, Pagacz K, Fendler W. NormiRazor: tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies. BMC Bioinformatics 2020; 21:425. [PMID: 32993488 PMCID: PMC7523363 DOI: 10.1186/s12859-020-03743-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Multi-gene expression assays are an attractive tool in revealing complex regulatory mechanisms in living organisms. Normalization is an indispensable step of data analysis in all those studies, since it removes unwanted, non-biological variability from data. In targeted qPCR assays it is typically performed with respect to prespecified reference genes, but the lack of robust strategy of their selection is reported in literature, especially in studies concerning circulating microRNAs (miRNA). Unfortunately, this problem impedes translation of scientific discoveries on miRNA biomarkers into widely available laboratory assays. Previous studies concluded that averaged expressions of multi-miRNA combinations are more stable references than single genes. However, due to the number of such combinations the computational load is considerable and may be hindering for objective reference selection in large datasets. Existing implementations of normalization algorithms (geNorm, NormFinder and BestKeeper) have poor performance and may require days to compute stability values for all potential reference as the evaluation is performed sequentially. RESULTS We designed NormiRazor - an integrative tool which implements those methods in a parallel manner on a graphics processing unit (GPU) using CUDA platform. We tested our approach on publicly available miRNA expression datasets. As a result, the times of executions on 8 datasets containing from 50 to 400 miRNAs (subsets of GSE68314) decreased 18.7 ±0.6 (mean ±SD), 104.7 ±4.2 and 76.5 ±2.2 times for geNorm, BestKeeper and NormFinder with respect to previous Python implementation. To allow for easy access to normalization pipeline for biomedical researchers we implemented NormiRazor as an online platform where a user could normalize their datasets based on the automatically selected references. It is available at norm.btm.umed.pl, together with instruction manual and exemplary datasets. CONCLUSIONS NormiRazor allows for an easy, informed choice of reference genes for qPCR transcriptomic studies. As such it can improve comparability and repeatability of experiments and in longer perspective help translate newly discovered biomarkers into readily available assays.
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Affiliation(s)
- Szymon Grabia
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
- Institute of Applied Computer Science, Lodz University of Technology, 18/22 Stefanowskiego St., Lodz, 90-537 Poland
| | - Urszula Smyczynska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
| | - Konrad Pagacz
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki i Wigury St., Warsaw, 02-091 Poland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka St., Lodz, 92-215 Poland
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, 450 Brookline Av., Boston, MA 02215 USA
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Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
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Zhang T, Ma G, Zhang Y, Huo H, Zhao Y. miR-599 inhibits proliferation and invasion of glioma by targeting periostin. Biotechnol Lett 2017; 39:1325-1333. [PMID: 28597372 DOI: 10.1007/s10529-017-2365-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To explore the molecular mechanism of microRNA-599(miR-599) in the migration and invasion of glioma. RESULT Clinicopathological characteristics of 33 patients were analyzed. Based on reverse transcription-PCR, miR-599 was down-regulated in glioma tissues compared with adjacent normal brain tissues (P < 0.001). Moreover, negative correlations between miR-599 and periostin protein expression in glioma tissues (P < 0.01) and necrosis by magnetic resonance imaging (P < 0.05) were observed. Transwell and wound healing assays showed that overexpression of miR-599 inhibited glioma cell migration and invasion. miR-599 down-regulated periostin expression by targeting the 3'-untranslated region. Additionally, re-expression of periostin partial reversed the suppressive effect of miR-599 on migration and invasion in vitro and in vivo. CONCLUSION microRNA-599 inhibits proliferation and invasion by down-regulating periostin expression in vitro and in vivo.
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Affiliation(s)
- Tingting Zhang
- School of Basic Medical Science; School of Information Science and Engineering, Central South University, Changsha, Hunan Province, 410078, China
| | - Guangtao Ma
- Department of Neurosurgery, Daqing Oil Field General Hospital, Daqing, Heilongjiang Province, 163000, China
| | - Yan Zhang
- Department of The Heart of Non-invasive Examination, Daqing Oil Field General Hospital, Daqing, Heilongjiang Province, 163000, China
| | - Hongda Huo
- Daqing Convalescence Hospital, Daqing, Heilongjiang Province, 163000, China
| | - Yuqian Zhao
- School of Information Science and Engineering, Central South University, Tongzipo Road No.172, Changsha, Hunan Province, 410078, China.
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Zatelli MC, Grossrubatscher EM, Guadagno E, Sciammarella C, Faggiano A, Colao A. Circulating tumor cells and miRNAs as prognostic markers in neuroendocrine neoplasms. Endocr Relat Cancer 2017; 24:R223-R237. [PMID: 28389504 DOI: 10.1530/erc-17-0091] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/07/2017] [Indexed: 01/02/2023]
Abstract
The prognosis of neuroendocrine neoplasms (NENs) is widely variable and has been shown to associate with several tissue- and blood-based biomarkers in different settings. The identification of prognostic factors predicting NEN outcome is of paramount importance to select the best clinical management for these patients. Prognostic markers have been intensively investigated, also taking advantage of the most modern techniques, in the perspective of personalized medicine and appropriate resource utilization. This review summarizes the available data on the possible role of circulating tumor cells and microRNAs as prognostic markers in NENs.
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Affiliation(s)
- Maria Chiara Zatelli
- Department of Medical SciencesSection of Endocrinology and Internal Medicine, University of Ferrara, Ferrara, Italy
| | | | - Elia Guadagno
- Department of Advanced Biomedical SciencesPathology Section, University of Naples Federico II, Naples, Italy
| | | | - Antongiulio Faggiano
- Thyroid and Parathyroid Surgery UnitIstituto Nazionale per lo Studio e la Cura Dei Tumori 'Fondazione G. Pascale' - IRCCS, Naples, Italy
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Nassirpour R, Homer BL, Mathur S, Li Y, Li Z, Brown T, Carraher D, Warneke J, Bailey S, Percival K, O'Neil SP, Whiteley LO. Identification of Promising Urinary MicroRNA Biomarkers in Two Rat Models of Glomerular Injury. Toxicol Sci 2015; 148:35-47. [PMID: 26253709 DOI: 10.1093/toxsci/kfv167] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that regulate protein levels posttranscriptionally. 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. Here, changes in miRNA expression patterns are described in 2 different rodent models of glomerular injury (acute puromycin aminonucleoside nephropathy and passive Heymann nephritis). By employing 2 different modes of glomerular insult, oxidative stress and immune-mediated toxicity, miRNA changes in both isolated glomeruli as well as urine specimens allow for identification of urinary miRNA biomarkers that are suggestive of drug-induced injury specifically to the glomerulus. Subsets of glomerular urinary miRNAs associated with these different modes of glomerular toxicity seem to be dependent on the mechanism of the induced injury, while 9 miRNAs that changed early in both glomerular and urine specimens were common to both studies. We further show that the miRNAs identified as mechanism-specific early glomerular injury biomarkers target key pathways and transcripts relevant to the type of insult, while the insult-independent changes might serve as ideal glomerular injury biomarkers.
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Affiliation(s)
| | - Bruce L Homer
- *Drug Safety, Pfizer Worldwide Research and Development
| | - Sachin Mathur
- Business Technology, Pfizer Research and Development, Andover, Massachusetts 01810; and
| | - Yizheng Li
- Business Technology, Pfizer Research and Development, Andover, Massachusetts 01810; and
| | - Zhonghan Li
- *Drug Safety, Pfizer Worldwide Research and Development
| | - Tom Brown
- Drug Safety, Pfizer Research and Development, Groton, Connecticut 06340
| | | | - James Warneke
- *Drug Safety, Pfizer Worldwide Research and Development
| | - Steven Bailey
- *Drug Safety, Pfizer Worldwide Research and Development
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Usó M, Jantus-Lewintre E, Sirera R, Bremnes RM, Camps C. miRNA detection methods and clinical implications in lung cancer. Future Oncol 2015; 10:2279-92. [PMID: 25471039 DOI: 10.2217/fon.14.93] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Therefore, advances in the diagnosis and treatment of the disease are urgently needed. miRNAs are a family of small, noncoding RNAs that regulate gene expression at the transcriptional level. miRNAs have been reported to be deregulated and to play a critical role in different types of cancer, including lung cancer. Thus, miRNA profiling in lung cancer patients has become the core of several investigations. To this end, the development of a multitude of platforms for miRNA profiling analysis has been essential. This article focuses on the different technologies available for assessing miRNAs and the most important results obtained to date in lung cancer.
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Affiliation(s)
- Marta Usó
- Molecular Oncology Laboratory, Fundación para la Investigación del Hospital General Universitario de Valencia, Av. Tres Cruces s/n, 46014 Valencia, Spain
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Flowers E, Won GY, Fukuoka Y. MicroRNAs associated with exercise and diet: a systematic review. Physiol Genomics 2015; 47:1-11. [PMID: 25465031 PMCID: PMC7199230 DOI: 10.1152/physiolgenomics.00095.2014] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/26/2014] [Indexed: 11/22/2022] Open
Abstract
MicroRNAs are posttranscriptional regulators of gene expression. MicroRNAs reflect individual biologic adaptation to exposures in the environment. As such, measurement of circulating microRNAs presents an opportunity to evaluate biologic changes associated with behavioral interventions (i.e., exercise, diet) for weight loss. The aim of this study was to perform a systematic review of the literature to summarize what is known about circulating microRNAs associated with exercise, diet, and weight loss. We performed a systematic review of three scientific databases. We included studies reporting on circulating microRNAs associated with exercise, diet, and weight loss in humans. Of 1,219 studies identified in our comprehensive database search, 14 were selected for inclusion. Twelve reported on microRNAs associated with exercise, and two reported on microRNAs associated with diet and weight loss. The majority of studies used a quasiexperimental, cross-sectional design. There were numerous differences in the type and intensity of exercise and dietary interventions, the biologic source of microRNAs, and the methodological approaches used quantitate microRNAs. Data from several studies support an association between circulating microRNAs and exercise. The evidence for an association between circulating microRNAs and diet is weaker because of a small number of studies. Additional research is needed to validate previous observations using methodologically rigorous approaches to microRNA quantitation to determine the specific circulating microRNA signatures associated with behavioral approaches to weight loss. Future directions include longitudinal studies to determine if circulating microRNAs are predictive of response to behavioral interventions.
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Affiliation(s)
- Elena Flowers
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, California;
| | - Gloria Y Won
- Fishbon Library, University of California, San Francisco, California; and
| | - Yoshimi Fukuoka
- Institute for Health and Aging/Department of Social & Behavioral Sciences, University of California, San Francisco, California
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