301
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Wu K, Xing F, Wu SY, Watabe K. Extracellular vesicles as emerging targets in cancer: Recent development from bench to bedside. Biochim Biophys Acta Rev Cancer 2017; 1868:538-563. [PMID: 29054476 DOI: 10.1016/j.bbcan.2017.10.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 12/16/2022]
Abstract
Extracellular vesicles (EVs) have emerged as important players of cancer initiation and progression through cell-cell communication. They have been recognized as critical mediators of extracellular communications, which promote transformation, growth invasion, and drug-resistance of cancer cells. Interestingly, the secretion and uptake of EVs are regulated in a more controlled manner than previously anticipated. EVs are classified into three groups, (i) exosomes, (ii) microvesicles (MVs), and (iii) apoptotic bodies (ABs), based on their sizes and origins, and novel technologies to isolate and distinguish these EVs are evolving. The biologically functional molecules harbored in these EVs, including nucleic acids, lipids, and proteins, have been shown to induce key signaling pathways in both tumor and tumor microenvironment (TME) cells for exacerbating tumor development. While tumor cell-derived EVs are capable of reprogramming stromal cells to generate a proper tumor cell niche, stromal-derived EVs profoundly affect the growth, resistance, and stem cell properties of tumor cells. This review summarizes and discusses these reciprocal communications through EVs in different types of cancers. Further understanding of the pathophysiological roles of different EVs in tumor progression is expected to lead to the discovery of novel biomarkers in liquid biopsy and development of tumor specific therapeutics. This review will also discuss the translational aspects of EVs and therapeutic opportunities of utilizing EVs in different cancer types.
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Affiliation(s)
- Kerui Wu
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC, USA
| | - Fei Xing
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC, USA
| | - Shih-Ying Wu
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC, USA
| | - Kounosuke Watabe
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC, USA.
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302
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Lange T, Stracke S, Rettig R, Lendeckel U, Kuhn J, Schlüter R, Rippe V, Endlich K, Endlich N. Identification of miR-16 as an endogenous reference gene for the normalization of urinary exosomal miRNA expression data from CKD patients. PLoS One 2017; 12:e0183435. [PMID: 28859135 PMCID: PMC5578666 DOI: 10.1371/journal.pone.0183435] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/03/2017] [Indexed: 12/14/2022] Open
Abstract
Chronic kidney disease (CKD) is a severe disorder with an increasing incidence worldwide. An early detection may help to prevent its progression and to minimize the risk of cardiovascular diseases as one of the major comorbidities. Recently, extracellular miRNAs like urinary exosomal miRNAs became of great interest as non-invasive biomarkers which can be determined by RT-qPCR. But until now, there is no consensus regarding the normalization of miRNAs isolated from body fluids. The present study analyzed the miRNAs miR-16, miR-92a, miR-21, miR-124a and the small nuclear RNA RNU6B for their applicability as an endogenous reference gene in expression studies of exosomal miRNAs isolated from CKD patients. For this purpose, miRNA expression levels were determined by RT-qPCR after the isolation of urinary exosomes from 33 CKD patients and from 5 healthy controls. Expression data was analyzed with the normalization determination software NormFinder, BestKeeper, GeNorm and DeltaCt. Our results revealed an abundant expression of the four candidate miRNAs in urinary exosomes and no detectable expression of RNU6B. We identified miR-16 as the most stable endogenous reference gene in our data set, making it a suitable endogenous reference gene for miRNA studies of urinary exosomes derived from CKD patients.
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Affiliation(s)
- Tim Lange
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Sylvia Stracke
- Department of Internal Medicine A, Nephrology, University Medicine Greifswald, Greifswald, Germany
| | - Rainer Rettig
- Institute of Physiology, University Medicine Greifswald, Karlsburg, Germany
| | - Uwe Lendeckel
- Department of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Jana Kuhn
- Clinic for Diabetes and Metabolic Diseases, Karlsburg Hospital Dr. Guth GmbH & Co KG, Karlsburg, Germany
| | - Rabea Schlüter
- Imaging Centre of the Department of Biology, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Volkhard Rippe
- Centre for Human Genetics, University of Bremen, Bremen, Germany
| | - Karlhans Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Nicole Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
- * E-mail:
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303
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Pergoli L, Cantone L, Favero C, Angelici L, Iodice S, Pinatel E, Hoxha M, Dioni L, Letizia M, Albetti B, Tarantini L, Rota F, Bertazzi PA, Tirelli AS, Dolo V, Cattaneo A, Vigna L, Battaglia C, Carugno M, Bonzini M, Pesatori AC, Bollati V. Extracellular vesicle-packaged miRNA release after short-term exposure to particulate matter is associated with increased coagulation. Part Fibre Toxicol 2017; 14:32. [PMID: 28899404 PMCID: PMC5594543 DOI: 10.1186/s12989-017-0214-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Exposure to particulate matter (PM) is associated with increased incidence of cardiovascular disease and increased coagulation, but the molecular mechanisms underlying these associations remain unknown. Obesity may increase susceptibility to the adverse effects of PM exposure, exacerbating the effects on cardiovascular diseases. Extracellular vesicles (EVs), which travel in body fluids and transfer microRNAs (miRNAs) between tissues, might play an important role in PM-induced cardiovascular risk. We sought to determine whether the levels of PM with an aerodynamic diameter ≤ 10 μm (PM10) are associated with changes in fibrinogen levels, EV release, and the miRNA content of EVs (EV-miRNAs), investigating 1630 overweight/obese subjects from the SPHERE Study. RESULTS Short-term exposure to PM10 (Day before blood drawing) was associated with an increased release of EVs quantified by nanoparticle tracking analysis, especially EVs derived from monocyte/macrophage components (CD14+) and platelets (CD61+) which were characterized by flow cytometry. We first profiled miRNAs of 883 subjects by the QuantStudio™ 12 K Flex Real Time PCR System and the top 40 EV-miRNAs were validated through custom miRNA plates. Nine EV-miRNAs (let-7c-5p; miR-106a-5p; miR-143-3p; miR-185-5p; miR-218-5p; miR-331-3p; miR-642-5p; miR-652-3p; miR-99b-5p) were downregulated in response to PM10 exposure and exhibited putative roles in cardiovascular disease, as highlighted by integrated network analysis. PM10 exposure was significantly associated with elevated fibrinogen levels, and five of the nine downregulated EV-miRNAs were mediators between PM10 exposure and fibrinogen levels. CONCLUSIONS Research on EVs opens a new path to the investigation of the adverse health effects of air pollution exposure. EVs have the potential to act both as markers of PM susceptibility and as potential molecular mechanism in the chain of events connecting PM exposure to increased coagulation, which is frequently linked to exposure and CVD development.
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Affiliation(s)
- Laura Pergoli
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Laura Cantone
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Chiara Favero
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Laura Angelici
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Simona Iodice
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy
| | - Eva Pinatel
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate, Milan, Italy
| | - Mirjam Hoxha
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Laura Dioni
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Marilena Letizia
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Benedetta Albetti
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Letizia Tarantini
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Federica Rota
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy
| | - Pier Alberto Bertazzi
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy
| | - Amedea Silvia Tirelli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy
| | - Vincenza Dolo
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Andrea Cattaneo
- Department of Science and High Technology, University of Insubria, Como, Italy
| | - Luisella Vigna
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy
| | - Cristina Battaglia
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129, Milan, Italy
| | - Michele Carugno
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy
| | - Matteo Bonzini
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy
| | - Angela Cecilia Pesatori
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy
| | - Valentina Bollati
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122, Milan, Italy. .,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Occupational Medicine, Milan, Italy.
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304
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Laganà A, Dirksen WP, Supsavhad W, Yilmaz AS, Ozer HG, Feller JD, Vala KA, Croce CM, Rosol TJ. Discovery and characterization of the feline miRNAome. Sci Rep 2017; 7:9263. [PMID: 28835705 PMCID: PMC5569061 DOI: 10.1038/s41598-017-10164-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 08/07/2017] [Indexed: 12/28/2022] Open
Abstract
The domestic cat is an important human companion animal that can also serve as a relevant model for ~250 genetic diseases, many metabolic and degenerative conditions, and forms of cancer that are analogous to human disorders. MicroRNAs (miRNAs) play a crucial role in many biological processes and their dysregulation has a significant impact on important cellular pathways and is linked to a variety of diseases. While many species already have a well-defined and characterized miRNAome, miRNAs have not been carefully studied in cats. As a result, there are no feline miRNAs present in the reference miRNA databases, diminishing the usefulness of medical research on spontaneous disease in cats for applicability to both feline and human disease. This study was undertaken to define and characterize the cat miRNAome in normal feline tissues. High-throughput sequencing was performed on 12 different normal cat tissues. 271 candidate feline miRNA precursors, encoding a total of 475 mature sequences, were identified, including several novel cat-specific miRNAs. Several analyses were performed to characterize the discovered miRNAs, including tissue distribution of the precursors and mature sequences, genomic distribution of miRNA genes and identification of clusters, and isomiR characterization. Many of the miRNAs were regulated in a tissue/organ-specific manner.
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Affiliation(s)
- Alessandro Laganà
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Wessel P Dirksen
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Wachiraphan Supsavhad
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Ayse Selen Yilmaz
- Department of Biomedical Informatics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Hatice G Ozer
- Department of Biomedical Informatics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - James D Feller
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Kiersten A Vala
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Thomas J Rosol
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
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305
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Reference miRNAs for colorectal cancer: analysis and verification of current data. Sci Rep 2017; 7:8413. [PMID: 28827728 PMCID: PMC5567181 DOI: 10.1038/s41598-017-08784-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) hold great promise in cancer research. The use of appropriate reference miRNAs for normalization of qPCR data is crucial for accurate expression analysis. We present here analysis and verification of current data, proposing a workflow strategy for identification of reference miRNAs in colorectal cancer (CRC). We performed a systematic review of studies aimed to identify stable reference miRNAs in CRC through high-throughput screening. Among the candidate miRNAs selected from the literature we excluded those predicted to target oncogenes or tumor suppressor gene. We then assessed the expression levels of the remaining candidates in exosomes, plasma and tissue samples from CRC patients and healthy controls. The expression stability was evaluated by box-plot, ∆Cq analysis, NormFinder and BestKeeper statistical algorithms. The effects of normalisers on the relative quantification of the oncogenic miR-1290 was also assessed. Our results consistently showed that different combinations of miR-520d, miR-1228 and miR-345 provided the most stably expressed reference miRNAs in the three biological matrices. We identified suitable reference miRNAs for future miRNA expression studies in exosomes plasma and tissues CRC samples. We also provided a novel conceptual framework that overcome the need of performing ex novo identification of suitable reference genes in single experimental systems.
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306
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An integrated expression atlas of miRNAs and their promoters in human and mouse. Nat Biotechnol 2017; 35:872-878. [PMID: 28829439 DOI: 10.1038/nbt.3947] [Citation(s) in RCA: 353] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/25/2017] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
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307
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Ivica J, Williamson PTF, de Planque MRR. Salt Gradient Modulation of MicroRNA Translocation through a Biological Nanopore. Anal Chem 2017; 89:8822-8829. [DOI: 10.1021/acs.analchem.7b01246] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Josip Ivica
- Electronics
and Computer Science, ‡Centre for Biological Sciences, and §Institute for
Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Philip T. F. Williamson
- Electronics
and Computer Science, ‡Centre for Biological Sciences, and §Institute for
Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Maurits R. R. de Planque
- Electronics
and Computer Science, ‡Centre for Biological Sciences, and §Institute for
Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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308
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Cirnigliaro M, Barbagallo C, Gulisano M, Domini CN, Barone R, Barbagallo D, Ragusa M, Di Pietro C, Rizzo R, Purrello M. Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder. Front Mol Neurosci 2017; 10:250. [PMID: 28848387 PMCID: PMC5554380 DOI: 10.3389/fnmol.2017.00250] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022] Open
Abstract
Given its prevalence and social impact, Autism Spectrum Disorder (ASD) is drawing much interest. Molecular basis of ASD is heterogeneous and only partially known. Many factors, including disorders comorbid with ASD, like TS (Tourette Syndrome), complicate ASD behavior-based diagnosis and make it vulnerable to bias. To further investigate ASD etiology and to identify potential biomarkers to support its precise diagnosis, we used TaqMan Low Density Array technology to profile serum miRNAs from ASD, TS, and TS+ASD patients, and unaffected controls (NCs). Through validation assays in 30 ASD, 24 TS, and 25 TS+ASD patients and 25 NCs, we demonstrated that miR-140-3p is upregulated in ASD vs.: NC, TS, and TS+ASD (Tukey's test, p-values = 0.03, = 0.01, < 0.0001, respectively). ΔCt values for miR-140-3p and YGTSS (Yale Global Tic Severity Scale) scores are positively correlated (Spearman r = 0.33; Benjamini-Hochberg p = 0.008) and show a linear relationship (p = 0.002). Network functional analysis showed that nodes controlled by miR-140-3p, especially CD38 and NRIP1 which are its validated targets, are involved in processes convergingly dysregulated in ASD, such as synaptic plasticity, immune response, and chromatin binding. Biomarker analysis proved that serum miR-140-3p can discriminate among: (1) ASD and NC (Area under the ROC curve, AUC: 0.70; sensitivity: 63.33%; specificity: 68%); (2) ASD and TS (AUC: 0.72; sensitivity: 66.66%; specificity: 70.83%); (3) ASD and TS+ASD (AUC: 0.78; sensitivity: 73.33%; specificity: 76%). Characterization of miR-140-3p network would contribute to further clarify ASD etiology. Serum miR-140-3p could represent a potential non-invasive biomarker for ASD, easy to test through liquid biopsy.
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Affiliation(s)
- Matilde Cirnigliaro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Cristina Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Mariangela Gulisano
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Carla N Domini
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Rita Barone
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy.,Associazione Oasi Maria SS. Onlus (IRCCS), Institute for Research on Mental Retardation and Brain AgingTroina, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Renata Rizzo
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Michele Purrello
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
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309
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Cowled C, Foo CH, Deffrasnes C, Rootes CL, Williams DT, Middleton D, Wang LF, Bean AGD, Stewart CR. Circulating microRNA profiles of Hendra virus infection in horses. Sci Rep 2017; 7:7431. [PMID: 28785041 PMCID: PMC5547158 DOI: 10.1038/s41598-017-06939-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Hendra virus (HeV) is an emerging zoonotic pathogen harbored by Australian mainland flying foxes. HeV infection can cause lethal disease in humans and horses, and to date all cases of human HeV disease have resulted from contact with infected horses. Currently, diagnosis of acute HeV infections in horses relies on the productive phase of infection when virus shedding may occur. An assay that identifies infected horses during the preclinical phase of infection would reduce the risk of zoonotic viral transmission during management of HeV outbreaks. Having previously shown that the host microRNA (miR)-146a is upregulated in the blood of HeV-infected horses days prior to the detection of viremia, we have profiled miRNAs at the transcriptome-wide level to comprehensively assess differences between infected and uninfected horses. Next-generation sequencing and the miRDeep2 algorithm identified 742 mature miRNA transcripts corresponding to 593 miRNAs in whole blood of six horses (three HeV-infected, three uninfected). Thirty seven miRNAs were differentially expressed in infected horses, two of which were validated by qRT-PCR. This study describes a methodology for the transcriptome-wide profiling of miRNAs in whole blood and supports the notion that measuring host miRNA expression levels may aid infectious disease diagnosis in the future.
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Affiliation(s)
- Christopher Cowled
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia.
| | - Chwan-Hong Foo
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Celine Deffrasnes
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | | | - David T Williams
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Deborah Middleton
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Andrew G D Bean
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Cameron R Stewart
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
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310
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Identification of aminosulfonylarylisoxazole as microRNA-31 regulators. PLoS One 2017; 12:e0182331. [PMID: 28783765 PMCID: PMC5544221 DOI: 10.1371/journal.pone.0182331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/17/2017] [Indexed: 12/28/2022] Open
Abstract
The discovery of small-molecule regulators of microRNAs remains challenging, but a few have been reported. Herein, we describe small-molecule inhibitors of miR-31, a tumor-associated microRNA (miRNA), identified by high-throughput screening using a cell-based reporter assay. Aminosulfonylarylisoxazole compounds exhibited higher specificity for miR-31 than for six other miRNAs, i.e., miR-15a, miR-16, miR-21, miR-92a-1, miR-146a, and miR-155, and increased the expression of miR-31 target genes. The down-regulation of mature miR-31 was observed, while its precursor form increased following treatment with the compounds. Thus, the compounds may target the processing of pre-miR-31 into mature miR-31 and thereby inhibit the production of mature miR-31.
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311
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Wu CW, Cao X, Berger CK, Foote PH, Mahoney DW, Simonson JA, Anderson BW, Yab TC, Taylor WR, Boardman LA, Kisiel JB, Ahlquist DA. Novel Approach to Fecal Occult Blood Testing by Assay of Erythrocyte-Specific microRNA Markers. Dig Dis Sci 2017; 62:1985-1994. [PMID: 28660489 PMCID: PMC6021130 DOI: 10.1007/s10620-017-4627-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/23/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Fecal occult blood testing (FOBT) has historically relied on methods to detect hemoglobin with no fundamental innovations in decades. AIM To examine microRNA (miRNA) as a new marker class for FOBT. METHODS Candidate miRNA markers were identified by small RNA sequencing of human whole blood compared to colorectal epithelia. Markers were tested in human blood cell subsets and blood from non-human species. We assessed assay linearity in blood spiking and marker stability in stool over incubation experiments. Levels of candidate erythrocyte markers were explored in stools from colorectal cancer (CRC) cases and controls. RESULTS Based on small RNA sequencing and validation RT-qPCR, expression level of each of the top blood-enriched markers (hsa-miR-144-3p, 144-5p, 451a, 486-5p, 363-3p, 20b-5p) could perfectly discriminate blood from colorectal epithelia. All six markers arose from and showed specificity to human erythrocytes. Marker levels increased linearly with erythrocyte concentration in saline or stool and demonstrated a broader dynamic range than did immunochemical test for hemoglobin. Degradation of markers occurred in stool but was reduced with preservative buffers. Erythrocyte marker candidates for stool testing were selected in an exploratory set of stools (20 CRC, 40 normal). Candidates were then further tested in a feasibility set (29 CRC, 31 advanced adenoma, and 115 normal); a miRNA panel (hsa-miR-451a, 144-5p, and 200b-3p as normalizer) yielded an AUC of 0.89 (95% CI 0.82-0.95, P < .0001) for CRC. CONCLUSIONS A novel miRNA-based approach accurately quantifies fecal blood levels over a broad, clinically relevant range.
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Affiliation(s)
- Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Xiaoming Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Calise K. Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Patrick H. Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Douglas W. Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Julie A. Simonson
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Bradley W. Anderson
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Tracy C. Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - William R. Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Lisa A. Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - David A. Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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312
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Non-coding RNAs as Biomarkers for Colorectal Cancer Screening and Early Detection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 937:153-70. [PMID: 27573899 DOI: 10.1007/978-3-319-42059-2_8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Early detection of colorectal cancer (CRC) is the key for prevention and the ability to impact long-term survival of CRC patients. Current CRC screening modalities are inadequate for global application because of low sensitivity and specificity in case of conventional stool-based screening tests, and high costs and a low participation compliance in colonoscopy. An accurate stool- or blood-based screening test with use of innovative biomarkers is an appealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher compliance rates. Non-coding RNAs (ncRNAs) have recently gained attention because of their involvement in different biological processes, such as proliferation, differentiation, migration, angiogenesis and apoptosis. An increasing number of studies have demonstrated that mutations or abnormal expression of ncRNAs are closely associated with various cancers, including CRC. The discovery that ncRNAs (mainly microRNAs) are stable in stool and in blood plasma and serum presents the opportunity to develop novel strategies taking advantage of circulating ncRNAs as early diagnostic biomarkers of CRC. This chapter is a comprehensive examination of aberrant ncRNAs expression levels in tumor tissue, stool and blood of CRC patients and a summary of the current findings on ncRNAs, including microRNAs, small nucleolar RNAs, small nuclear RNAs, Piwi-interacting RNAs, circular RNAs and long ncRNAs in regards to their potential usage for screening or early detection of CRC.
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313
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Chan SY, Snow JW. Formidable challenges to the notion of biologically important roles for dietary small RNAs in ingesting mammals. GENES AND NUTRITION 2017; 12:13. [PMID: 29308096 PMCID: PMC5753850 DOI: 10.1186/s12263-017-0561-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/19/2017] [Indexed: 02/07/2023]
Abstract
The notion of uptake of active diet-derived small RNAs (sRNAs) in recipient organisms could have significant implications for our understanding of oral therapeutics and nutrition, for the safe use of RNA interference (RNAi) in agricultural biotechnology, and for ecological relationships. Yet, the transfer and subsequent regulation of gene activity by diet-derived sRNAs in ingesting mammals are still heavily debated. Here, we synthesize current information based on multiple independent studies of mammals, invertebrates, and plants. Rigorous assessment of these data emphasize that uptake of active dietary sRNAs is neither a robust nor a prevalent mechanism to maintain steady-state levels in higher organisms. While disagreement still continues regarding whether such transfer may occur in specialized contexts, concerns about technical difficulties and a lack of consensus on appropriate methods have led to questions regarding the reproducibility and biologic significance of some seemingly positive results. For any continuing investigations, concerted efforts should be made to establish a strong mechanistic basis for potential effects of dietary sRNAs and to agree on methodological guidelines for realizing such proof. Such processes would ensure proper interpretation of studies aiming to prove dietary sRNA activity in mammals and inform potential for application in therapeutics and agriculture.
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Affiliation(s)
- Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, BST 1704.2, 200 Lothrop Street, Pittsburgh, PA 15261 USA
| | - Jonathan W Snow
- Department of Biology, Barnard College, New York, NY 10027 USA
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314
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Al-Qatati A, Akrong C, Stevic I, Pantel K, Awe J, Saranchuk J, Drachenberg D, Mai S, Schwarzenbach H. Plasma microRNA signature is associated with risk stratification in prostate cancer patients. Int J Cancer 2017; 141:1231-1239. [PMID: 28571116 DOI: 10.1002/ijc.30815] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 12/19/2022]
Abstract
The aim of this study was to establish a unique expression profile of circulating cell-free microRNAs (miRNAs) capable of differentiating between prostate cancer (PCa) patients with high-risk and intermediate-risk Gleason scores. MiRNA expression profiles were determined in plasma samples from 79 treatment-naïve PCa patients, 1-2 follow-up samples after radical prostatectomy (RP) from 51 out of the 79 PCa patients, and 33 healthy men, using a quantitative real-time PCR-based array containing 48 selected miRNAs. We identified 27 up- and 2 downregulated plasma miRNAs in PCa patients compared with healthy men. Most of the upregulated miRNA levels were also associated with increasing PSA levels and Gleason scores. Particularly, the levels of miR-16 (p = 0.002), miR-148a (p = 0.006) and miR-195 (p = 0.006) significantly correlated with high-risk Gleason scores, whereby miR-148a (p = 0.003) was also significantly associated with increasing PSA values. The high miRNA levels before RP remained increased in the postsurgical plasma samples. Our findings show a network of deregulated plasma miRNAs. In particular, miR-16, miR-148a and miR-195 are involved in the regulation of the PI3K/Akt signaling pathway. These miRNAs may be promising therapeutic targets for high-risk PCa stratification.
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Affiliation(s)
- Abeer Al-Qatati
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Christine Akrong
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Ines Stevic
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Julius Awe
- Manitoba Institute of Cell Biology, Cancer Care Manitoba, University of Manitoba, Winnipeg, Canada
| | - Jeff Saranchuk
- Manitoba Prostate Center, Cancer Care Manitoba, Winnipeg, Canada
| | | | - Sabine Mai
- Manitoba Institute of Cell Biology, Cancer Care Manitoba, University of Manitoba, Winnipeg, Canada
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
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315
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Mandilaras V, Vernon M, Meryet-Figuière M, Karakasis K, Lambert B, Poulain L, Oza A, Denoyelle C, Lheureux S. Updates and current challenges in microRNA research for personalized medicine in ovarian cancer. Expert Opin Biol Ther 2017. [DOI: 10.1080/14712598.2017.1340935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Victoria Mandilaras
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Mégane Vernon
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Matthieu Meryet-Figuière
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Katherine Karakasis
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Bernard Lambert
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
- Délégation régionale de Normandie, CNRS, Caen, France
| | - Laurent Poulain
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Amit Oza
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Christophe Denoyelle
- INSERM U1086 “ANTICIPE” (Interdisciplinary Research Unit for Cancers Prevention and Treatment, Axis BioTICLA “Biology and Innovative Therapeutics for Ovarian Cancers”), Normandie Univ, UNICAEN, Caen, France
- Comprehensive Cancer Centre François Baclesse, UNICANCER, Caen, France
| | - Stephanie Lheureux
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
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316
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Olaya LF, Hyett JA, McLennan SV. Effects of sample processing and storage on the integrity of cell-free miRNAs in maternal plasma. Prenat Diagn 2017; 37:744-749. [PMID: 28556966 DOI: 10.1002/pd.5075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/13/2017] [Accepted: 05/17/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cell-free fetal miRNAs have been identified as potential biomarkers for fetal abnormalities and/or placental function. Factors affecting the stability of cell-free fetal miRNA samples (type of collection tube and time interval between sampling and analysis) have not previously been reported. METHODS Blood from pregnant women (n = 12, 18 ± 4 weeks' gestation) was collected into two types of tube (EDTA and RNA BCT) and was stored at different temperatures for up to 72 h. Expression of seven apparently placental specific miRNAs was then measured to compare the effects of sampling and storage. These miRNAs were also assessed in non-pregnant women (n = 9). RESULTS The quantity of miRNA extracted was not affected by time or tube. Three miRNAs (miR-518b, miR-525 and miR-526a*) were measureable only in pregnant women, but miR-518b was not always present. Detailed study of the two pregnancy specific miRNAs showed no effect of tube type at 4 h. However, variability in miRNA level was observed with increased time and was significant for one miRNA in the BCT tube at >48 h (p < 0.005). CONCLUSION Some cffmiRNAs are placental specific, and these samples are stable when analyzed within 48 h of collection in either tube type. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Luisa F Olaya
- Discipline of Obstetrics, Gynaecology and Neonatology and Central Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia.,Department of Endocrinology, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan A Hyett
- Discipline of Obstetrics, Gynaecology and Neonatology and Central Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Susan V McLennan
- Department of Endocrinology, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia.,NSW Health Pathology, Chemical Pathology, RPA Hospital Camperdown, New South Wales, Australia
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317
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Armand-Labit V, Pradines A. Circulating cell-free microRNAs as clinical cancer biomarkers. Biomol Concepts 2017; 8:61-81. [DOI: 10.1515/bmc-2017-0002] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/21/2017] [Indexed: 12/23/2022] Open
Abstract
AbstractMicroRNAs (miRNAs) are non-coding small RNAs that are master regulators of genic expression and consequently of many cellular processes. But their expression is often deregulated in human tumors leading to cancer development. Recently miRNAs were discovered in body fluids (serum, plasma and others) and their levels have often been reported to be altered in patients. Circulating miRNAs became one of the most promising biomarkers in oncology for early diagnosis, prognosis and therapeutic response prediction. Here we describe the origins and roles of miRNAs, and summarize the most recent studies focusing on their usefulness as cancer biomarkers in lung, breast, colon, prostate, ovary cancers and melanoma. Lastly, we describe the main methodologies related to miRNA detection, which should be standardized for their use in clinical practice.
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Affiliation(s)
- Virginie Armand-Labit
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France
- Institut Claudius Regaud, IUCT-Oncopole, Laboratoire de Biologie Médicale Oncologique, Toulouse, France
| | - Anne Pradines
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France
- Institut Claudius Regaud, IUCT-Oncopole, Laboratoire de Biologie Médicale Oncologique, Toulouse, France
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318
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de Ronde MWJ, Ruijter JM, Lanfear D, Bayes-Genis A, Kok MGM, Creemers EE, Pinto YM, Pinto-Sietsma SJ. Practical data handling pipeline improves performance of qPCR-based circulating miRNA measurements. RNA (NEW YORK, N.Y.) 2017; 23:811-821. [PMID: 28202710 PMCID: PMC5393188 DOI: 10.1261/rna.059063.116] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/27/2017] [Indexed: 05/21/2023]
Abstract
Since numerous miRNAs have been shown to be present in circulation, these so-called circulating miRNAs have emerged as potential biomarkers for disease. However, results of qPCR studies on circulating miRNA biomarkers vary greatly and many experiments cannot be reproduced. Missing data in qPCR experiments often occur due to off-target amplification, nonanalyzable qPCR curves and discordance between replicates. The low concentration of most miRNAs leads to most, but not all missing data. Therefore, failure to distinguish between missing data due to a low concentration and missing data due to randomly occurring technical errors partly explains the variation within and between otherwise similar studies. Based on qPCR kinetics, an analysis pipeline was developed to distinguish missing data due to technical errors from missing data due to a low concentration of the miRNA-equivalent cDNA in the PCR reaction. Furthermore, this pipeline incorporates a method to statistically decide whether concentrations from replicates are sufficiently concordant, which improves stability of results and avoids unnecessary data loss. By going through the pipeline's steps, the result of each measurement is categorized as "valid, invalid, or undetectable." Together with a set of imputation rules, the pipeline leads to more robust and reproducible data as was confirmed experimentally. Using two validation approaches, in two cohorts totaling 2214 heart failure patients, we showed that this pipeline increases both the accuracy and precision of qPCR measurements. In conclusion, this statistical data handling pipeline improves the performance of qPCR studies on low-expressed targets such as circulating miRNAs.
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Affiliation(s)
- Maurice W J de Ronde
- Department of Vascular Medicine
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics
| | - Jan M Ruijter
- Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - David Lanfear
- Henry Ford Hospital, Heart and Vascular Institute, Detroit, Michigan 48202, USA
| | - Antoni Bayes-Genis
- Heart Failure Unit, Germans Trias i Pujol Hospital, 08916 Badalona, Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | | | - Esther E Creemers
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Yigal M Pinto
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Sara-Joan Pinto-Sietsma
- Department of Vascular Medicine
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics
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319
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Plasma Viral miRNAs Indicate a High Prevalence of Occult Viral Infections. EBioMedicine 2017; 20:182-192. [PMID: 28465156 PMCID: PMC5478184 DOI: 10.1016/j.ebiom.2017.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/30/2017] [Accepted: 04/10/2017] [Indexed: 11/22/2022] Open
Abstract
Prevalence of Kaposi sarcoma-associated herpesvirus (KSHV/HHV-8) varies greatly in different populations. We hypothesized that the actual prevalence of KSHV/HHV8 infection in humans is underestimated by the currently available serological tests. We analyzed four independent patient cohorts with post-surgical or post-chemotherapy sepsis, chronic lymphocytic leukemia and post-surgical patients with abdominal surgical interventions. Levels of specific KSHV-encoded miRNAs were measured by reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and KSHV/HHV-8 IgG were measured by immunoassay. We also measured specific miRNAs from Epstein Barr Virus (EBV), a virus closely related to KSHV/HHV-8, and determined the EBV serological status by ELISA for Epstein-Barr nuclear antigen 1 (EBNA-1) IgG. Finally, we identified the viral miRNAs by in situ hybridization (ISH) in bone marrow cells. In training/validation settings using independent multi-institutional cohorts of 300 plasma samples, we identified in 78.50% of the samples detectable expression of at least one of the three tested KSHV-miRNAs by RT-qPCR, while only 27.57% of samples were found to be seropositive for KSHV/HHV-8 IgG (P < 0.001). The prevalence of KSHV infection based on miRNAs qPCR is significantly higher than the prevalence determined by seropositivity, and this is more obvious for immuno-depressed patients. Plasma viral miRNAs quantification proved that EBV infection is ubiquitous. Measurement of viral miRNAs by qPCR has the potential to become the “gold” standard method to detect certain viral infections in clinical practice. There is no agreement on a standard assay to detect the true prevalence of Kaposi sarcoma-associated herpesvirus (KSHV) infection. Measurement of the viral miRNAs in plasma by RT-qPCR allows a direct and accurate assessment of viral infection. Measurement of the viral miRNAs in plasma by RT-qPCR shows prevalence of KSHV infection in immuno-depressed patients. Measurement of plasma viral miRNAs for viral infection assessment has the potential to become a “gold” standard method in the clinical practice.
Chronic viral infections represent risk factors for diseases and development of infection-related complications. There is no agreement on a standard assay to detect the true prevalence of Kaposi sarcoma-associated herpesvirus (KSHV) infection. The current method used in the clinical practice (ELISA-test) identifies a great geographic variation in KSHV seroprevalence and may underestimate the true-prevalence of KSHV infection. Here we showed that detection of plasma viral miRNAs levels for the identification of viral infection (e.g., KSHV, Epstein-Bar virus or EBV) is more accurate than the current method for detection of virus-derived antigen, especially in patients with low number of immune cells.
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320
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Kappel A, Keller A. miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects. Clin Chem Lab Med 2017; 55:636-647. [PMID: 27987355 DOI: 10.1515/cclm-2016-0467] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 12/27/2022]
Abstract
microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.
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Affiliation(s)
- Andreas Kappel
- Siemens Healthcare GmbH, Guenther-Scharowsky-Str.1, Erlangen
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbruecken
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321
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Batth IS, Mitra A, Manier S, Ghobrial IM, Menter D, Kopetz S, Li S. Circulating tumor markers: harmonizing the yin and yang of CTCs and ctDNA for precision medicine. Ann Oncol 2017; 28:468-477. [PMID: 27998963 DOI: 10.1093/annonc/mdw619] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Current trajectory of clinical care is heading in the direction of personalized medicine. In an ideal scenario, clinicians can obtain extensive diagnostic and prognostic information via minimally-invasive assays. Information available in the peripheral blood has the potential to bring us closer to this goal. In this review we highlight the contributions of circulating tumor cells and circulating tumor DNA and RNA (ctDNA/ctRNA) towards cancer therapeutic field. We discuss clinical relevance, summarize available and upcoming technologies, and hypothesize how future care could be impacted by a combined study.
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Affiliation(s)
- I S Batth
- Department of Pediatrics - Research, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Mitra
- Department of Pediatrics - Research, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Manier
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - I M Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - D Menter
- Department of Gastrointestinal (GI) Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Kopetz
- Department of Gastrointestinal (GI) Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Li
- Department of Pediatrics - Research, The University of Texas MD Anderson Cancer Center, Houston, USA
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322
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miRNAs as Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer: Current Perspectives. Target Oncol 2017; 12:179-200. [DOI: 10.1007/s11523-017-0478-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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323
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Scrutinio D, Conserva F, Passantino A, Iacoviello M, Lagioia R, Gesualdo L. Circulating microRNA-150-5p as a novel biomarker for advanced heart failure: A genome-wide prospective study. J Heart Lung Transplant 2017; 36:616-624. [PMID: 28259597 DOI: 10.1016/j.healun.2017.02.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Circulating microRNAs (miRs) are promising biomarkers for heart failure (HF). Previous studies have provided inconsistent miR "signatures." The phenotypic and pathophysiologic heterogeneity of HF may have contributed to this inconsistency. In this study we assessed whether advanced HF (AHF) patients present a distinct miR signature compared with healthy subjects (HS) and mild to moderate HF (MHF) patients. METHODS The study consisted of 2 phases: a screening phase and a validation phase. In the screening phase, 752 miRs were profiled in HS and MHF and AHF patients (N = 15), using the real-time quantitative polymerase chain reaction (RT-qPCR) technique and global mean normalization. In the validation phase, the miRs found to be significantly dysregulated in AHF patients compared with both HS and MHF patients were validated in 15 HS, 25 patients with MHF and 29 with AHF, using RT-qPCR, and normalizing to exogenous (cel-miR-39) and endogenous controls. RESULTS In the screening phase, 5 miRs were found to be significantly dysregulated: -26a-5p; -145-3p; -150-5p; -485-3p; and -487b-3p. In the validation phase, miR-150-5p was confirmed to be significantly downregulated in AHF patients when compared with both HS and MHF patients, irrespective of the normalization method used. miR-26a-5p was confirmed to be significantly dysregulated only when normalized to cell-miR-39. Dysregulation of the other miRs could not be confirmed. miR-150-5p was significantly associated with maladaptive remodeling, disease severity and outcome. CONCLUSIONS Our data suggest miR-150-5p as a novel circulating biomarker for AHF. The association of miR-150-5p with maladaptive remodeling, disease severity and outcome supports the pathophysiologic relevance of downregulated miR-150-5p expression to AHF.
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Affiliation(s)
- Domenico Scrutinio
- Department of Cardiology and Cardiac Rehabilitation. Scientific Clinical Institutes Maugeri, IRCCS Institute of Cassano Murge, Bari, Italy.
| | - Francesca Conserva
- Department of Cardiology and Cardiac Rehabilitation. Scientific Clinical Institutes Maugeri, IRCCS Institute of Cassano Murge, Bari, Italy; Division of Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Andrea Passantino
- Department of Cardiology and Cardiac Rehabilitation. Scientific Clinical Institutes Maugeri, IRCCS Institute of Cassano Murge, Bari, Italy
| | - Massimo Iacoviello
- Cardiology Unit, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Rocco Lagioia
- Department of Cardiology and Cardiac Rehabilitation. Scientific Clinical Institutes Maugeri, IRCCS Institute of Cassano Murge, Bari, Italy
| | - Loreto Gesualdo
- Division of Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
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324
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Masè M, Grasso M, Avogaro L, D’Amato E, Tessarolo F, Graffigna A, Denti MA, Ravelli F. Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation. Sci Rep 2017; 7:41127. [PMID: 28117343 PMCID: PMC5259703 DOI: 10.1038/srep41127] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/15/2016] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-Cq, GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions.
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Affiliation(s)
- Michela Masè
- Department of Physics, University of Trento, Trento, Italy
| | | | - Laura Avogaro
- Department of Physics, University of Trento, Trento, Italy
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Elvira D’Amato
- Department of Physics, University of Trento, Trento, Italy
| | - Francesco Tessarolo
- Healthcare Research and Innovation Program (IRCS-PAT), Bruno Kessler Foundation, Trento, Italy
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Angelo Graffigna
- Division of Cardiac Surgery, Santa Chiara Hospital, Trento, Italy
| | | | - Flavia Ravelli
- Department of Physics, University of Trento, Trento, Italy
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325
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Zendjabil M, Favard S, Tse C, Abbou O, Hainque B. [The microRNAs as biomarkers: What prospects?]. C R Biol 2017; 340:114-131. [PMID: 28081967 DOI: 10.1016/j.crvi.2016.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
MicroRNAs are nucleic acids of about twenty nucleotides that regulate about a third of the genome at the post-transcriptional level. Thanks to their different forms of transport, microRNAs are stable and can be detected in biological fluids such as blood, urine, cerebrospinal fluid, or saliva. In addition, the profile of circulating microRNAs is a specific part of the cells in which it is secreted and is modified according to the physiological or pathological conditions of these cells. MicroRNAs therefore appear as biomarkers of interest for many diseases. However, these applications face several challenges because there are currently considerable differences between the sample processing procedures, assay methods, and especially the result standardization strategies. This literature review aims to take stock of the current use of microRNAs as biomarkers mainly in biological fluids and address the perspectives that emerge from the fact that their vesicular circulating forms could be used to assess the state of the cells and the tissues that produce them.
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Affiliation(s)
- Mustapha Zendjabil
- Service de biochimie, établissement hospitalier universitaire (EHU) d'Oran, 1(er)-Novembre-1954, BP 4166 Ibn Rochd, Oran, Algérie.
| | - Séverine Favard
- Service de biochimie métabolique, hôpitaux universitaires Pitié-Salpêtrière-Charles-Foix, 47, boulevard de l'Hôpital, 75013 Paris, France
| | - Chantal Tse
- Service de biochimie métabolique, hôpitaux universitaires Pitié-Salpêtrière-Charles-Foix, 47, boulevard de l'Hôpital, 75013 Paris, France
| | - Omar Abbou
- Service de biochimie, établissement hospitalier universitaire (EHU) d'Oran, 1(er)-Novembre-1954, BP 4166 Ibn Rochd, Oran, Algérie
| | - Bernard Hainque
- Service de biochimie métabolique, hôpitaux universitaires Pitié-Salpêtrière-Charles-Foix, 47, boulevard de l'Hôpital, 75013 Paris, France
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326
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Sodi R, Eastwood J, Caslake M, Packard CJ, Denby L. Relationship between circulating microRNA-30c with total- and LDL-cholesterol, their circulatory transportation and effect of statins. Clin Chim Acta 2017; 466:13-19. [PMID: 28062296 DOI: 10.1016/j.cca.2016.12.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 12/30/2016] [Accepted: 12/30/2016] [Indexed: 01/20/2023]
Abstract
BACKGROUND Small non-coding microRNAs (miR) have important regulatory roles and are used as biomarkers of disease. We investigated the relationship between lipoproteins and circulating miR-30c, evaluated how they are transported in circulation and determined whether statins altered the circulating concentration of miR-30c. METHODS To determine the relationship between lipoproteins and circulating miR-30c, serum samples from 79 subjects recruited from a lipid clinic were evaluated. Ultracentrifugation and nanoparticle tracking analysis was used to evaluate the transportation of miR-30c in the circulation by lipoproteins and extracellular vesicles in three healthy volunteers. Using archived samples from previous studies, the effects of 40mg rosuvastatin (n=22) and 40mg pravastatin (n=24) on miR-30c expression was also examined. RNA extraction, reverse transcription-quantitative real-time polymerase chain reaction was carried out using standard procedures. RESULTS When stratified according to total cholesterol concentration, there was increased miR-30c expression in the highest compared to the lowest tertile (p=0.035). There was significant positive correlation between miR-30c and total- (r=0.367; p=0.002) and LDL-cholesterol (r=0.391; p=0.001). We found that miR-30c was transported in both exosomes and on HDL3. There was a 3.8-fold increased expression of circulating miR-30c after pravastatin treatment for 1year (p=0.005) but no significant change with atorvastatin after 8weeks (p=0.145). CONCLUSIONS This study shows for the first-time in humans that circulating miR-30c is significantly, positively correlated with total- and LDL-cholesterol implicating regulatory functions in lipid homeostasis. We show miR-30c is transported in both exosomes and on HDL3 and pravastatin therapy significantly increased circulating miR-30c expression adding to the pleiotropic dimensions of statins.
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Affiliation(s)
- Ravinder Sodi
- Department of Biochemistry, Royal Lancaster Infirmary & Furness General Hospital, University Hospitals of Morecambe Bay NHS Foundation Trust, Lancaster, United Kingdom; Lancaster Medical School, University of Lancaster, Lancaster, United Kingdom.
| | - Jarlath Eastwood
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Muriel Caslake
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Chris J Packard
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Laura Denby
- British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
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327
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Bell E, Watson HL, Bailey S, Murray MJ, Coleman N. A Robust Protocol to Quantify Circulating Cancer Biomarker MicroRNAs. Methods Mol Biol 2017; 1580:265-279. [PMID: 28439839 DOI: 10.1007/978-1-4939-6866-4_18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Reverse-transcriptase quantitative PCR (RT-qPCR) is a widely used method for quantifying microRNAs (miRNAs) in cells and tissues. However, the quantification of miRNAs in the circulation presents specific challenges. Here, we describe an optimized protocol using a small amount of input material to assess serum sample quality and quantify levels of a panel of up to 20 miRNAs. This is achieved by multiplexing Taqman miRNA stem-loop primers in the reverse transcription step. An additional multiplexed pre-amplification step is used to increase the sensitivity of the final quantification step, which is carried out using standard Taqman qPCR methodology.
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Affiliation(s)
- Emma Bell
- Department of Pathology, University of Cambridge, Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- AstraZeneca, Cambridge Science Park, Cambridge, CB4 0FZ, UK
| | - Hannah L Watson
- Department of Pathology, University of Cambridge, Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Shivani Bailey
- Department of Pathology, University of Cambridge, Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Matthew J Murray
- Department of Pathology, University of Cambridge, Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
- Department of Paediatrics, Haematology and Oncology, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
- Department of Histopathology, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.
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328
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Fiammengo R. Can nanotechnology improve cancer diagnosis through miRNA detection? Biomark Med 2017; 11:69-86. [DOI: 10.2217/bmm-2016-0195] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
miRNAs are key regulators of gene expression, and alterations in their expression levels correlate with the onset and progression of cancer. Although miRNAs have been proposed as biomarkers for cancer diagnosis, their application in routine clinical praxis is yet to come. Current quantification strategies have limitation, and there is a great interest in developing innovative ones. Since a few years, nanotechnology-based approaches for miRNA quantification are emerging at fast pace but there is urgent need to go beyond the proof-of-concept stage. Nanotechnology will have a strong impact on cancer diagnosis through miRNA detection only if it is demonstrated that the newly developed approaches are indeed working on ‘real-world’ samples under standardized conditions.
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Affiliation(s)
- Roberto Fiammengo
- Center for Biomolecular Nanotechnologies@UniLe – Istituto Italiano di Tecnologia (IIT), Via Barsanti, 73010 Arnesano, Lecce, Italy
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329
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Chen L, Jin Y, Wang L, Sun F, Yang X, Shi M, Zhan C, Shi Y, Wang Q. Identification of reference genes and miRNAs for qRT-PCR in human esophageal squamous cell carcinoma. Med Oncol 2016; 34:2. [PMID: 27889881 DOI: 10.1007/s12032-016-0860-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
It is important to select an appropriate reference gene and miRNA when using quantitative real-time polymerase chain reaction (qRT-PCR) to analyze gene and miRNA expression. However, many commonly used reference genes and miRNAs are not stably expressed and therefore not suitable for normalization or quantification of qRT-PCR data. This study aims to identify appropriate reference genes and miRNAs for use in human esophageal squamous carcinoma qRT-PCR analysis. Using data provided by The Cancer Genome Atlas, we identified DDX5, LAPTM4A, P4HB, RHOA, miR-28-5p, miR-34a-5p, and miR-186-5p as candidate reference genes and miRNAs. We used qRT-PCR to verify the expression levels of these candidates and another seven commonly used reference genes and miRNAs. A set of 50 paired human normal esophageal tissues and squamous cell carcinoma samples were used in the analysis. We then used geNorm and NormFinder to analyze the results. DDX5, LAPTM4A, RHOA, ACTB, RNU48, miR-28-5p, miR-34a-5p, and miR-186-5p were stably expressed, indicating they are suitable for used as references in qRT-PCR analysis of esophageal squamous cell carcinoma. However, expression levels of 18s rRNA, GAPDH, P4HB, 5s rRNA, U6, and RNU6B varied greatly between esophageal normal and squamous cell carcinoma samples, indicating that they are not suitable for use as references in the qRT-PCR analysis of esophageal squamous cell carcinoma.
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Affiliation(s)
- Li Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Yulin Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Lin Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Fenghao Sun
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Xiaodong Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
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330
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MicroRNAs in Coronary Heart Disease: Ready to Enter the Clinical Arena? BIOMED RESEARCH INTERNATIONAL 2016; 2016:2150763. [PMID: 27882321 PMCID: PMC5110879 DOI: 10.1155/2016/2150763] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/25/2016] [Indexed: 01/10/2023]
Abstract
Coronary artery disease (CAD) and its complication remain the leading cause of mortality in industrialized countries despite great advances in terms of diagnosis, prognosis, and treatment options. MicroRNAs (miRNAs), small noncoding RNAs, act as posttranscriptional gene expression modulators and have been implicated as key regulators in several physiological and pathological processes linked to CAD. Circulating miRNAs have been evaluated as promising novel biomarkers of CAD, acute coronary syndromes, and acute myocardial infarction, with prognostic implications. Several challenges related to technical aspects, miRNAs normalization, drugs interaction, and quality reporting of statistical multivariable analysis of the miRNAs observational studies remain unresolved. MicroRNA-based therapies in cardiovascular diseases are not ready yet for human trials but definitely appealing. Through this review we will provide clinicians with a concise overview of the pros and cons of microRNAs.
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331
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Leierer J, Mayer G, Kronbichler A. Primary focal segmental glomerulosclerosis: miRNAs and targeted therapies. Eur J Clin Invest 2016; 46:954-964. [PMID: 27651302 DOI: 10.1111/eci.12676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/07/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Primary focal segmental glomerulosclerosis (FSGS) is a common cause of nephrotic syndrome. AIMS The pathogenic steps leading to primary FSGS are still obscure, although evidence suggests that circulatory factor(s) are involved in the onset of disease. RESULTS Recent technical advances allow the analysis of miRNA expression in tissues and body fluids, leading to reports of miRNAs involved in the molecular mechanisms of FSGS-aetiopathogenesis. Moreover, investigations have also highlighted miRNAs that might serve as biomarkers for primary FSGS. DISCUSSION/CONCLUSIONS The aim of this review was to summarize reports showing a direct relation between miRNAs and primary FSGS. In addition, the impact of identified miRNAs on treatment response, prediction of the disease onset as well as the regulation in different disease activities is summarized.
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Affiliation(s)
- Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria.
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
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332
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Witwer KW, Halushka MK. Toward the promise of microRNAs - Enhancing reproducibility and rigor in microRNA research. RNA Biol 2016; 13:1103-1116. [PMID: 27645402 DOI: 10.1080/15476286.2016.1236172] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The fields of applied and translational microRNA research have exploded in recent years as microRNAs have been implicated across a spectrum of diseases. MicroRNA biomarkers, microRNA therapeutics, microRNA regulation of cellular physiology and even xenomiRs have stimulated great interest, which have brought many researchers into the field. Despite many successes in determining general mechanisms of microRNA generation and function, the application of microRNAs in translational areas has not had as much success. It has been a challenge to localize microRNAs to a given cell type within tissues and assay them reliably. At supraphysiologic levels, microRNAs may regulate hosts of genes that are not the physiologic biochemical targets. Thus the applied and translational microRNA literature is filled with pitfalls and claims that are neither scientifically rigorous nor reproducible. This review is focused on increasing awareness of the challenges of working with microRNAs in translational research and recommends better practices in this area of discovery.
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Affiliation(s)
- Kenneth W Witwer
- a Department of Molecular and Comparative Pathobiology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA.,b Department of Neurology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Marc K Halushka
- c Department of Pathology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
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333
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Occhipinti G, Giulietti M, Principato G, Piva F. The choice of endogenous controls in exosomal microRNA assessments from biofluids. Tumour Biol 2016; 37:11657-11665. [PMID: 27438704 DOI: 10.1007/s13277-016-5164-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/12/2016] [Indexed: 01/02/2023] Open
Abstract
The assessment of differentially expressed microRNAs in patients and healthy controls is important to identify potential tumor biomarkers. Recently, it has been shown that the microRNA levels in exosomes are more correlated with the clinical-pathological variables than vesicle-free microRNAs (miRNAs) in biofluids; therefore, there is an increasing interest in these specific evaluations. However, these measurements can be affected by experimental problems that not always are evaluated and/or by inadequate procedural choices. In particular, exosome isolation and miRNA extraction procedures are crucial to avoid contaminations, and even the choice of the most suitable purity controls is important. Moreover, a stable endogenous RNA should be used for normalization of miRNA expression obtained by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) in order to make these measures comparable among different samples. A rushed choice of the endogenous control can bias study conclusions without revealing inconsistencies. Unfortunately, a few studies systematically identified the best normalizer for their specific experimental context. Instead, sometimes, the normalization procedures were performed in a disputable way or the normalizer choices simply based on the previous literature. Here, we reviewed the studies where the exosomal miRNA profiling was assessed in human biofluids to point out the adopted procedures and the specific endogenous controls chosen for normalization.
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Affiliation(s)
- G Occhipinti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - M Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - G Principato
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - F Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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334
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Bignotti E, Calza S, Tassi RA, Zanotti L, Bandiera E, Sartori E, Odicino FE, Ravaggi A, Todeschini P, Romani C. Identification of stably expressed reference small non-coding RNAs for microRNA quantification in high-grade serous ovarian carcinoma tissues. J Cell Mol Med 2016; 20:2341-2348. [PMID: 27419385 PMCID: PMC5134371 DOI: 10.1111/jcmm.12927] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/13/2016] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) belong to a family of small non-coding RNAs (sncRNAs) playing important roles in human carcinogenesis. Multiple investigations reported miRNAs aberrantly expressed in several cancers, including high-grade serous ovarian carcinoma (HGS-OvCa). Quantitative PCR is widely used in studies investigating miRNA expression and the identification of reliable endogenous controls is crucial for proper data normalization. In this study, we aimed to experimentally identify the most stable reference sncRNAs for normalization of miRNA qPCR expression data in HGS-OvCa. Eleven putative reference sncRNAs for normalization (U6, SNORD48, miR-92a-3p, let-7a-5p, SNORD61, SNORD72, SNORD68, miR-103a-3p, miR-423-3p, miR-191-5p, miR-16-5p) were analysed on a total of 75 HGS-OvCa and 30 normal tissues, using a highly specific qPCR. Both the normal tissues considered to initiate HGS-OvCa malignant transformation, namely ovary and fallopian tube epithelia, were included in our study. Stability of candidate endogenous controls was evaluated using an equivalence test and validated by geNorm and NormFinder algorithms. Combining results from the three different statistical approaches, SNORD48 emerged as stably and equivalently expressed between malignant and normal tissues. Among malignant samples, considering groups based on residual tumour, miR-191-5p was identified as the most equivalent sncRNA. On the basis of our results, we support the use of SNORD48 as best reference sncRNA for relative quantification in miRNA expression studies between HGS-OvCa and normal controls, including the first time both the normal tissues supposed to be HGS-OvCa progenitors. In addition, we recommend miR-191-5p as best reference sncRNA in miRNA expression studies with prognostic intent on HGS-OvCa tissues.
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Affiliation(s)
- Eliana Bignotti
- Division of Obstetrics and Gynecology, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Stefano Calza
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Renata A Tassi
- "Angelo Nocivelli" Institute of Molecular Medicine, Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy
| | - Laura Zanotti
- "Angelo Nocivelli" Institute of Molecular Medicine, Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy
| | - Elisabetta Bandiera
- "Angelo Nocivelli" Institute of Molecular Medicine, Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy
| | - Enrico Sartori
- Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy
| | - Franco E Odicino
- Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy
| | - Antonella Ravaggi
- "Angelo Nocivelli" Institute of Molecular Medicine, Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy
| | - Paola Todeschini
- "Angelo Nocivelli" Institute of Molecular Medicine, Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy.,Doctorate School of Molecular and Translational Medicine, University of Milan, Milan, Italy
| | - Chiara Romani
- "Angelo Nocivelli" Institute of Molecular Medicine, Division of Obstetrics and Gynecology, University of Brescia, Brescia, Italy
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335
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Markou A, Zavridou M, Sourvinou I, Yousef G, Kounelis S, Malamos N, Georgoulias V, Lianidou E. Direct Comparison of Metastasis-Related miRNAs Expression Levels in Circulating Tumor Cells, Corresponding Plasma, and Primary Tumors of Breast Cancer Patients. Clin Chem 2016; 62:1002-11. [DOI: 10.1373/clinchem.2015.253716] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/04/2016] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Circulating tumor cells (CTCs) and microRNAs (miRNAs) are important in liquid biopsies in which peripheral blood is used to characterize the evolution of solid tumors. We evaluated the expression levels of miR-21, miR-146a, miR-200c, and miR-210 in CTCs of breast cancer patients with verified metastasis and compared their expression levels in corresponding plasma and primary tumors.
METHODS
Expression levels of the miRNAs were quantified by quantitative reverse transcription PCR (RT-qPCR) in (a) 89 primary breast tumors and 30 noncancerous breast tissues and (b) CTCs and corresponding plasma of 55 patients with metastatic breast cancer and 20 healthy donors. For 30 of these patients, CTCs, corresponding plasma, and primary tumor tissues were available.
RESULTS
In formalin-fixed, paraffin-embedded tissues, these miRNAs were differentially expressed between primary breast tumors and noncancerous breast tissues. miR-21 (P < 0.001) and miR-146a (P = 0.001) were overexpressed, whereas miR-200c (P = 0.004) and miR-210 (P = 0.002) were underexpressed. In multivariate analysis, miR-146a overexpression was significantly [hazard ratio 2.969 (1.231–7.157), P = 0.015] associated with progression-free survival. In peripheral blood, all miRNAs studied were overexpressed in both CTC and corresponding plasma. There was a significant association between miR-21 expression levels in CTCs and plasma for 36 of 55 samples (P = 0.008). In plasma, ROC curve analysis revealed that miR-21, miR-146a, and miR-210 could discriminate patients from healthy individuals.
CONCLUSIONS
Metastasis-related miRNAs are overexpressed in CTCs and corresponding plasma; miR-21 expression levels highly correlate in CTCs and plasma; and miR-21, miR-146a, and miR-210 are valuable plasma biomarkers for discriminating patients from healthy individuals.
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Affiliation(s)
- Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Martha Zavridou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Ioanna Sourvinou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - George Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Sofia Kounelis
- Oncology Unit and Pathology Department, Helena Venizelou Hospital, Athens, Greece
| | - Nikos Malamos
- Oncology Unit and Pathology Department, Helena Venizelou Hospital, Athens, Greece
| | - Vasilis Georgoulias
- Department of Medical Oncology, University General Hospital of Heraklion, Heraklion, Greece
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
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336
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Gorges TM, Stein A, Quidde J, Hauch S, Röck K, Riethdorf S, Joosse SA, Pantel K. Improved Detection of Circulating Tumor Cells in Metastatic Colorectal Cancer by the Combination of the CellSearch® System and the AdnaTest®. PLoS One 2016; 11:e0155126. [PMID: 27182774 PMCID: PMC4868337 DOI: 10.1371/journal.pone.0155126] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/25/2016] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the major causes of cancer-related death and reliable blood-based prognostic biomarkers are urgently needed. The enumeration and molecular characterization of circulating tumor cells (CTCs) has gained increasing interest in clinical practice. CTC detection by CellSearch® has already been correlated to an unfavorable outcome in metastatic CRC. However, the CTC detection rate in mCRC disease is low compared to other tumor entities. Thus, the use of alternative (or supplementary) assays might help to itemize the prognostic use of CTCs as blood-based biomarkers. In this study, blood samples from 47 mCRC patients were screened for CTCs using the FDA-cleared CellSearch® technology and / or the AdnaTest®. 38 samples could be processed in parallel. We demonstrate that a combined analysis of CellSearch® and the AdnaTest® leads to an improved detection of CTCs in our mCRC patient cohort (positivity rate CellSearch® 33%, AdnaTest® 30%, combined 50%). While CTCs detected with the CellSearch® system were significantly associated with progression-free survival (p = 0.046), a significant correlation regarding overall survival could be only seen when both assays were combined (p = 0.013). These findings could help to establish improved tools to detect CTCs as on-treatment biomarkers for clinical routine in future studies.
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Affiliation(s)
- Tobias M. Gorges
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Stein
- Department of Internal Medicine II and Clinic (Oncology Center), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Quidde
- Department of Internal Medicine II and Clinic (Oncology Center), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Katharina Röck
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A. Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail:
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337
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Towards a new standardized method for circulating miRNAs profiling in clinical studies: Interest of the exogenous normalization to improve miRNA signature accuracy. Mol Oncol 2016; 10:981-92. [PMID: 27083764 PMCID: PMC5423189 DOI: 10.1016/j.molonc.2016.03.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 01/15/2023] Open
Abstract
Circulating miRNAs are promising biomarkers in oncology but have not yet been implemented in the clinic given the lack of concordance across studies. In order to increase the cross‐studies reliability, we attempted to reduce and to control the circulating miRNA expression variability between patients. First, to maximize profiling signals and to reduce miRNA expression variability, three isolation kits were compared and the NucleoSpin® kit provided higher miRNA concentrations than the other widely used kits. Second, to control inter‐sample variability during the profiling step, the exogenous miRNAs normalization method commonly used for RT‐qPCR validation step was adapted to microarray experiments. Importantly, exogenous miRNAs presented two‐fold lower inter‐sample variability than the widely used endogenous miR‐16‐5p reflecting that the latter is subject to both biological and technical variability. Although Caenorhabditis elegans miRNAs isolation yields were heterogeneous, they correlated to each other and to their geometrical mean across samples. The normalization based on the geometrical mean of three exogenous miRNAs increased the correlation up‐to 0.97 between the microarrays and individual RT‐qPCR steps of circulating miRNAs expression. Overall, this new strategy open new avenue to identify reliable circulating miRNA signatures for translation into clinical practice. NucleoSpin kit offers the highest endogenous miRNA concentrations from serum/plasma. A common normalization based on exogenous miRNAs for discovery and validation steps. New strategy to increase both the signature accuracy and the overlap across studies.
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Meng X, Müller V, Milde-Langosch K, Trillsch F, Pantel K, Schwarzenbach H. Diagnostic and prognostic relevance of circulating exosomal miR-373, miR-200a, miR-200b and miR-200c in patients with epithelial ovarian cancer. Oncotarget 2016. [PMID: 26943577 DOI: 10.18632/oncotarget.7850]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Exosomes are membrane vesicles that mediate intercellular communication by transporting their molecular cargo from cell to cell. We investigated whether serum levels of exosomal miR-373, miR-200a, miR-200b and miR-200c and circulating exosomes have diagnostic and prognostic relevance in a cohort of 163 epithelial ovarian cancer (EOC) patients using TaqMan MicroRNA assays and ELISA. The serum concentrations of exosomal miR-373 (p = 0.0001), miR-200a (p = 0.0001), miR-200b (p = 0.0001) and miR-200c (p = 0.028) were significantly higher in EOC patients than healthy women. The levels of miR-200a (p = 0.0001), miR-200b (p = 0.0001) and miR-200c (p = 0.019) could distinguish between malignant and benign ovarian tumors. While the levels of miR-373 and miR-200a were increased in all FIGO/lymph node stages (p = 0.0001), the levels of miR-200b and miR-200c were higher in patients with FIGO stage III-IV (p = 0.0001, p = 0.008, respectively) including lymph node metastasis (p = 0.0001, p = 0.004, respectively) than FIGO stages I-II. The increased levels of miR-200b and miR-200c were also associated with CA125 values (p = 0.0001, p = 0.0001, respectively) and a shorter overall survival (p = 0.007, p = 0.017, respectively). The levels of exosomes were excessively elevated in EOC patients (p = 0.0001). In all three cohorts, they were positively associated with the serum levels of exosomal miR-373 (p = 0.004), miR-200a (p = 0.0001), miR-200b (p = 0.0001) and miR-200c (p = 0.008). In conclusion, the increased levels of exosomal miR-200b and miR-200c mainly observed in advanced EOC suggest that these microRNAs may be involved in tumor progression. The high concentrations of exosomes in EOC patients imply an excessive, active exosomal secretion in EOC.
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Affiliation(s)
- Xiaodan Meng
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Volkmar Müller
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Karin Milde-Langosch
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Fabian Trillsch
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
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339
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Diagnostic and prognostic relevance of circulating exosomal miR-373, miR-200a, miR-200b and miR-200c in patients with epithelial ovarian cancer. Oncotarget 2016. [PMID: 26943577 DOI: 10.18632/oncotarget.7850] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Exosomes are membrane vesicles that mediate intercellular communication by transporting their molecular cargo from cell to cell. We investigated whether serum levels of exosomal miR-373, miR-200a, miR-200b and miR-200c and circulating exosomes have diagnostic and prognostic relevance in a cohort of 163 epithelial ovarian cancer (EOC) patients using TaqMan MicroRNA assays and ELISA. The serum concentrations of exosomal miR-373 (p = 0.0001), miR-200a (p = 0.0001), miR-200b (p = 0.0001) and miR-200c (p = 0.028) were significantly higher in EOC patients than healthy women. The levels of miR-200a (p = 0.0001), miR-200b (p = 0.0001) and miR-200c (p = 0.019) could distinguish between malignant and benign ovarian tumors. While the levels of miR-373 and miR-200a were increased in all FIGO/lymph node stages (p = 0.0001), the levels of miR-200b and miR-200c were higher in patients with FIGO stage III-IV (p = 0.0001, p = 0.008, respectively) including lymph node metastasis (p = 0.0001, p = 0.004, respectively) than FIGO stages I-II. The increased levels of miR-200b and miR-200c were also associated with CA125 values (p = 0.0001, p = 0.0001, respectively) and a shorter overall survival (p = 0.007, p = 0.017, respectively). The levels of exosomes were excessively elevated in EOC patients (p = 0.0001). In all three cohorts, they were positively associated with the serum levels of exosomal miR-373 (p = 0.004), miR-200a (p = 0.0001), miR-200b (p = 0.0001) and miR-200c (p = 0.008). In conclusion, the increased levels of exosomal miR-200b and miR-200c mainly observed in advanced EOC suggest that these microRNAs may be involved in tumor progression. The high concentrations of exosomes in EOC patients imply an excessive, active exosomal secretion in EOC.
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340
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Raffort J, Lareyre F, Clement M, Mallat Z. Micro-RNAs in abdominal aortic aneurysms: insights from animal models and relevance to human disease. Cardiovasc Res 2016; 110:165-77. [PMID: 26965051 DOI: 10.1093/cvr/cvw046] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/28/2016] [Indexed: 01/09/2023] Open
Abstract
Abdominal aortic aneurysm (AAA) is a major health concern and may be associated with high rates of mortality linked to acute complications. Diagnosis and treatment are, respectively, based on imaging and surgical techniques. Drug-based therapies are still mostly ineffective, which highlight a real unmet need. Major pathophysiological mechanisms leading to aneurysm formation involve inflammatory processes, degradation of the extracellular matrix, and loss of smooth muscle cells. However, the precise cellular and molecular pathways are still poorly understood. Recently, microRNAs have emerged as major intracellular players in a wide range of biological processes, and their stability in extracellular medium within microvesicles has led to propose them as mediators of intercellular crosstalk and as potential biomarkers and therapeutic targets in a variety of disease settings. To date, several studies have been performed to address the involvement of micro-RNAs (miRs) in aneurysm formation and complications. Here, we discuss the roles and implications of miRs in animal models and their relevance to human AAA.
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Affiliation(s)
- Juliette Raffort
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK University of Nice-Sophia Antipolis, Medical School, Nice 06107, France INSERM U1081, CNRS UMR7284, IRCAN, Nice, France Clinical Chemistry Laboratory, University Hospital of Nice, Nice, France
| | - Fabien Lareyre
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK University of Nice-Sophia Antipolis, Medical School, Nice 06107, France INSERM U1081, CNRS UMR7284, IRCAN, Nice, France Department of Vascular Surgery, University Hospital of Nice, Nice, France
| | - Marc Clement
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge CB20 SZ, UK Institut National de la Santé et de la Recherche Médicale (Inserm), Unit 970, Paris Cardiovascular Research Center, Paris 75015, France
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Titov SE, Ivanov MK, Karpinskaya EV, Tsivlikova EV, Shevchenko SP, Veryaskina YA, Akhmerova LG, Poloz TL, Klimova OA, Gulyaeva LF, Zhimulev IF, Kolesnikov NN. miRNA profiling, detection of BRAF V600E mutation and RET-PTC1 translocation in patients from Novosibirsk oblast (Russia) with different types of thyroid tumors. BMC Cancer 2016; 16:201. [PMID: 26960768 PMCID: PMC4784369 DOI: 10.1186/s12885-016-2240-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 03/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The postoperative typing of thyroid lesions, which is instrumental in adequate patient treatment, is currently based on histologic examination. However, it depends on pathologist's qualification and can be difficult in some cases. Numerous studies have shown that molecular markers such as microRNAs and somatic mutations may be useful to assist in these cases, but no consensus exists on the set of markers that is optimal for that purpose. The aim of the study was to discriminate between different thyroid neoplasms by RT-PCR, using a limited set of microRNAs selected from literature. METHODS By RT-PCR we evaluated the relative levels of 15 microRNAs (miR-221, -222, -146b, -181b, -21, -187, -199b, -144, -192, -200a, -200b, -205, -141, -31, -375) and the presence of BRAF(V600E) mutation and RET-PTC1 translocation in surgically resected lesions from 208 patients from Novosibirsk oblast (Russia) with different types of thyroid neoplasms. Expression of each microRNA was normalized to adjacent non-tumor tissue. Three pieces of lesion tissue from each patient (39 goiters, 41 follicular adenomas, 16 follicular thyroid cancers, 108 papillary thyroid cancers, 4 medullary thyroid cancers) were analyzed independently to take into account method variation. RESULTS The diagnostic classifier based on profiling of 13 microRNAs was proposed, with total estimated accuracy varying from 82.7 to 99% for different nodule types. Relative expression of six microRNAs (miR-146b, -21, -221, -222, 375, -199b) appeared significantly different in BRAF(V600E)-positive samples (all classified as papillary thyroid carcinomas) compared to BRAF(V600E)-negative papillary carcinoma samples. CONCLUSIONS The results confirm practical feasibility of using molecular markers for typing of thyroid neoplasms and clarification of controversial cases.
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Affiliation(s)
- Sergei E Titov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia. .,JSC "Vector-Best", Koltsovo, Russia.
| | | | - Elena V Karpinskaya
- Novosibirsk Municipal Budgetary Healthcare Institution "Municipal Clinical Hospital #1", Novosibirsk, Russia
| | | | - Sergei P Shevchenko
- Novosibirsk Municipal Budgetary Healthcare Institution "Municipal Clinical Hospital #1", Novosibirsk, Russia
| | - Yulia A Veryaskina
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
| | - Larisa G Akhmerova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
| | - Tatiana L Poloz
- Non-governmental Healthcare Institution «Railroad Clinical Hospital on the Station Novosibirsk-Glavny", JSC Russian Railways, Novosibirsk, Russia
| | - Olesya A Klimova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.,JSC "Vector-Best", Koltsovo, Russia
| | | | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
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Huang SK, Hoon DSB. Liquid biopsy utility for the surveillance of cutaneous malignant melanoma patients. Mol Oncol 2016; 10:450-63. [PMID: 26778792 PMCID: PMC5307330 DOI: 10.1016/j.molonc.2015.12.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 01/01/2023] Open
Abstract
Cutaneous melanoma is one of the highest incident-rate cancers with increasing prevalence in Western societies. Despite the advent of new approved therapeutics, the 5-year overall survival rate of stage IV melanoma patients remains below 15%. Current treatments for late stage disease have shown higher efficacy when treated at a lower disease burden. Thus, blood-based biomarkers capable of detecting melanoma prior to clinically evident distant metastasis, will improve the treatment and outcomes for melanoma patients. To that end, effective treatment of melanoma necessitates identification of patients at risk for developing distant metastases. Furthermore, employing blood biomarkers that monitor cancer progression over the course of treatment is a promising solution to post-treatment drug resistance often developed in melanoma patients. Non-invasive blood biomarker assays allow for regular dynamic monitoring of disease. "Liquid Biopsy" of blood, which exploits circulating tumor cells (CTCs), cell-free circulating tumor DNA (ctDNA) and cell-free circulating microRNA (cmiRNA), has been shown to detect prognostic factors for relapse in AJCC stage III and stage IV melanoma patients. Moreover, molecular characterization of CTC and analysis of various forms of ctDNA present promising potential in development of individualized therapy for melanoma patients. New approaches such as massive parallel sequencing (MPS) provide a comprehensive view of the disease progression, allowing for the selection of therapeutic options for individual patients. With advancements of improving molecular assays, liquid biopsy analysis as a powerful, routine clinical assay for melanoma patients, is highly promising prospective.
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Affiliation(s)
- Sharon K Huang
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, United States
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, United States.
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343
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miR-16-5p Is a Stably-Expressed Housekeeping MicroRNA in Breast Cancer Tissues from Primary Tumors and from Metastatic Sites. Int J Mol Sci 2016; 17:ijms17020156. [PMID: 26821018 PMCID: PMC4783890 DOI: 10.3390/ijms17020156] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 01/24/2023] Open
Abstract
For quantitative microRNA analyses in formalin-fixed paraffin-embedded (FFPE) tissue, expression levels have to be normalized to endogenous controls. To investigate the most stably-expressed microRNAs in breast cancer and its surrounding tissue, we used tumor samples from primary tumors and from metastatic sites. MiRNA profiling using TaqMan(®) Array Human MicroRNA Cards, enabling quantification of 754 unique human miRNAs, was performed in FFPE specimens from 58 patients with metastatic breast cancer. Forty-two (72%) samples were collected from primary tumors and 16 (28%) from metastases. In a cross-platform analysis of a validation cohort of 32 FFPE samples from patients with early breast cancer genome-wide microRNA expression analysis using SurePrintG3 miRNA (8 × 60 K)(®) microarrays from Agilent(®) was performed. Eleven microRNAs could be detected in all samples analyzed. Based on NormFinder and geNorm stability values and the high correlation (rho ≥ 0.8) with the median of all measured microRNAs, miR-16-5p, miR-29a-3p, miR-126-3p, and miR-222-3p are suitable single gene housekeeper candidates. In the cross-platform validation, 29 human microRNAs were strongly expressed (mean log2-intensity > 10) and 21 of these microRNAs including miR-16-5p and miR-29a-3p were also stably expressed (CV < 5%). Thus, miR-16-5p and miR-29a-3p are both strong housekeeper candidates. Their Normfinder stability values calculated across the primary tumor and metastases subgroup indicate that miR-29a-3p can be considered as the strongest housekeeper in a cohort with mainly samples from primary tumors, whereas miR-16-5p might perform better in a metastatic sample enriched cohort.
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344
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Fabris L, Ceder Y, Chinnaiyan AM, Jenster GW, Sorensen KD, Tomlins S, Visakorpi T, Calin GA. The Potential of MicroRNAs as Prostate Cancer Biomarkers. Eur Urol 2016; 70:312-22. [PMID: 26806656 DOI: 10.1016/j.eururo.2015.12.054] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/29/2015] [Indexed: 12/20/2022]
Abstract
CONTEXT Short noncoding RNAs known as microRNAs (miRNAs) control protein expression through the degradation of RNA or the inhibition of protein translation. The miRNAs influence a wide range of biologic processes and are often deregulated in cancer. This family of small RNAs constitutes potentially valuable markers for the diagnosis, prognosis, and therapeutic choices in prostate cancer (PCa) patients, as well as potential drugs (miRNA mimics) or drug targets (anti-miRNAs) in PCa management. OBJECTIVE To review the currently available data on miRNAs as biomarkers in PCa and as possible tools for early detection and prognosis. EVIDENCE ACQUISITION A systematic review was performed searching the PubMed database for articles in English using a combination of the following terms: microRNA, miRNA, cancer, prostate cancer, miRNA profiling, diagnosis, prognosis, therapy response, and predictive marker. EVIDENCE SYNTHESIS We summarize the existing literature regarding the profiling of miRNA in PCa detection, prognosis, and response to therapy. The articles were reviewed with the main goal of finding a common recommendation that could be translated from bench to bedside in future clinical practice. CONCLUSIONS The miRNAs are important regulators of biologic processes in PCa progression. A common expression profile characterizing each tumor subtype and stage has still not been identified for PCa, probably due to molecular heterogeneity as well as differences in study design and patient selection. Large-scale studies that should provide additional important information are still missing. Further studies, based on common clinical parameters and guidelines, are necessary to validate the translational potential of miRNAs in PCa clinical management. Such common signatures are promising in the field and emerge as potential biomarkers. PATIENT SUMMARY The literature shows that microRNAs hold potential as novel biomarkers that could aid prostate cancer management, but additional studies with larger patient cohorts and common guidelines are necessary before clinical implementation.
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Affiliation(s)
- Linda Fabris
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yvonne Ceder
- Department of Laboratory Medicine, Lund, Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Comprehensive Cancer Center, and Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Guido W Jenster
- Department of Urology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Karina D Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Scott Tomlins
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Comprehensive Cancer Center, and Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tapio Visakorpi
- Prostate Cancer Research Center (PCRC), Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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