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Licholai S, Blaż M, Kapelak B, Sanak M. Unbiased Profile of MicroRNA Expression in Ascending Aortic Aneurysm Tissue Appoints Molecular Pathways Contributing to the Pathology. Ann Thorac Surg 2016; 102:1245-52. [PMID: 27234576 DOI: 10.1016/j.athoracsur.2016.03.061] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 01/19/2016] [Accepted: 03/16/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Complex etiopathogenesis of ascending aortic aneurysm suggests contribution of epigenetic mechanisms in its development. Several studies appointed microRNAs (miRs) as essential epigenetic factors in various human diseases; however, little is known about their role in ascending aortic aneurysm. Therefore, the aim of this study was to perform unbiased molecular screening of miRs expression in aneurysmal tissue and establish their functions on a transcriptional level. METHODS Samples of ascending aortic tissue were obtained from 15 patients, and total RNA was isolated separately from aneurysmal and unaffected aortic tissue obtained from the same patient. Expression of the complete panel of human miRs was assessed by quantitative real-time polymerase chain reaction. Using bioinformatic tools, 13 genes were selected that were putatively regulated by overexpressed miRs. Expression level of transcripts were evaluated by quantitative real-time polymerase chain reaction and correlated with their targeting miRs. RESULTS Overexpression of 10 miRs distinguished aneurysmal tissue from the unchanged one. These miRs were involved in cell senescence (miR-191-5p), maintenance of vascular integrity (miR-126-3p and miR-374-5p), nitric oxide-dependent vascular relaxation (miR-21-5p), smooth muscle differentiation, and contractility (miR-145- 3p, miR-29c-3p, miR-133a-3p, miR-186-5p, miR-143-3p, and miR-24-3p), and correlated with abundance of its miR targets. CONCLUSIONS Altered expression of particular miRs selectively in the affected tissue indicate their role as factors that trigger pathways of aneurysmal transformation. Limited reparative properties due to overexpression of miR-191 may play a crucial role for aneurysm enlargement, whereas nitric oxide-dependent relaxation of vascular smooth muscle mediated by miR-21 offers an attractive explanation of the aneurysm's initiation, and is confirmed in experimental conditions.
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Affiliation(s)
- Sabina Licholai
- Division of Molecular Biology and Clinical Genetics, Department of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Michal Blaż
- Students' Research Group, Division of Molecular Biology and Clinical Genetics, Department of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Boguslaw Kapelak
- Department of Cardiovascular Surgery and Transplantology, Jagiellonian University, John Paul II Hospital in Krakow, Krakow, Poland
| | - Marek Sanak
- Division of Molecular Biology and Clinical Genetics, Department of Medicine, Jagiellonian University Medical College, Krakow, Poland.
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Nollet E, Hoymans VY, Van Craenenbroeck AH, Vrints CJ, Van Craenenbroeck EM. Improving stem cell therapy in cardiovascular diseases: the potential role of microRNA. Am J Physiol Heart Circ Physiol 2016; 311:H207-18. [PMID: 27208159 DOI: 10.1152/ajpheart.00239.2016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/11/2016] [Indexed: 11/22/2022]
Abstract
The initial promising prospect of autologous bone marrow-derived stem cell therapy in the setting of cardiovascular diseases has been overshadowed by functional shortcomings of the stem cell product. As powerful epigenetic regulators of (stem) cell function, microRNAs are valuable targets for novel therapeutic strategies. Indeed, modulation of specific miRNA expression could contribute to improved therapeutic efficacy of stem cell therapy. First, this review elaborates on the functional relevance of miRNA dysregulation in bone marrow-derived progenitor cells in different cardiovascular diseases. Next, we provide a comprehensive overview of the current evidence on the effect of specific miRNA modulation in several types of progenitor cells on cardiac and/or vascular regeneration. By elaborating on the cardioprotective regulation of progenitor cells on cardiac miRNAs, more insight in the underlying mechanisms of stem cell therapy is provided. Finally, some considerations are made regarding the potential of circulating miRNAs as regulators of the miRNA signature of progenitor cells in cardiovascular diseases.
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Affiliation(s)
- Evelien Nollet
- Laboratory of Cellular and Molecular Cardiology, Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium; Cardiovascular Diseases, Department of Translational Pathophysiological Research, University of Antwerp, Antwerp, Belgium
| | - Vicky Y Hoymans
- Laboratory of Cellular and Molecular Cardiology, Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium; Cardiovascular Diseases, Department of Translational Pathophysiological Research, University of Antwerp, Antwerp, Belgium
| | - Amaryllis H Van Craenenbroeck
- Cardiovascular Diseases, Department of Translational Pathophysiological Research, University of Antwerp, Antwerp, Belgium; Department of Nephrology, Antwerp University Hospital, Antwerp, Belgium; Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, Antwerp, Belgium; and
| | - Christiaan J Vrints
- Laboratory of Cellular and Molecular Cardiology, Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium; Cardiovascular Diseases, Department of Translational Pathophysiological Research, University of Antwerp, Antwerp, Belgium; Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium
| | - Emeline M Van Craenenbroeck
- Laboratory of Cellular and Molecular Cardiology, Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium; Cardiovascular Diseases, Department of Translational Pathophysiological Research, University of Antwerp, Antwerp, Belgium; Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium
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The Discovery of Novel Genomic, Transcriptomic, and Proteomic Biomarkers in Cardiovascular and Peripheral Vascular Disease: The State of the Art. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7829174. [PMID: 27298828 PMCID: PMC4889798 DOI: 10.1155/2016/7829174] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/26/2016] [Accepted: 05/05/2016] [Indexed: 12/14/2022]
Abstract
Cardiovascular disease (CD) and peripheral vascular disease (PVD) are leading causes of mortality and morbidity in western countries and also responsible of a huge burden in terms of disability, functional decline, and healthcare costs. Biomarkers are measurable biological elements that reflect particular physiological or pathological states or predisposition towards diseases and they are currently widely studied in medicine and especially in CD. In this context, biomarkers can also be used to assess the severity or the evolution of several diseases, as well as the effectiveness of particular therapies. Genomics, transcriptomics, and proteomics have opened new windows on disease phenomena and may permit in the next future an effective development of novel diagnostic and prognostic medicine in order to better prevent or treat CD. This review will consider the current evidence of novel biomarkers with clear implications in the improvement of risk assessment, prevention strategies, and medical decision making in the field of CD.
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MicroRNA-194 Modulates Glucose Metabolism and Its Skeletal Muscle Expression Is Reduced in Diabetes. PLoS One 2016; 11:e0155108. [PMID: 27163678 PMCID: PMC4862646 DOI: 10.1371/journal.pone.0155108] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/25/2016] [Indexed: 11/29/2022] Open
Abstract
Background The regulation of microRNAs (miRNAs) at different stages of the progression of type 2 diabetes mellitus (T2DM) and their role in glucose homeostasis was investigated. Methods Microarrays were used to assess miRNA expression in skeletal muscle biopsies taken from healthy individuals and patients with pre-diabetes or T2DM, and insulin resistant offspring of rat dams fed a high fat diet during pregnancy. Results Twenty-three miRNAs were differentially expressed in patients with T2DM, and 7 in the insulin resistant rat offspring compared to their controls. Among these, only one miRNA was similarly regulated: miR-194 expression was significantly reduced by 25 to 50% in both the rat model and in human with pre-diabetes and established diabetes. Knockdown of miR-194 in L6 skeletal muscle cells induced an increase in basal and insulin-stimulated glucose uptake and glycogen synthesis. This occurred in conjunction with an increased glycolysis, indicated by elevated lactate production. Moreover, oxidative capacity was also increased as we found an enhanced glucose oxidation in presence of the mitochondrial uncoupler FCCP. When miR-194 was down-regulated in vitro, western blot analysis showed an increased phosphorylation of AKT and GSK3β in response to insulin, and an increase in expression of proteins controlling mitochondrial oxidative phosphorylation. Conclusions Type 2 diabetes mellitus is associated with regulation of several miRNAs in skeletal muscle. Interestingly, miR-194 was a unique miRNA that appeared regulated across different stages of the disease progression, from the early stages of insulin resistance to the development of T2DM. We have shown miR-194 is involved in multiple aspects of skeletal muscle glucose metabolism from uptake, through to glycolysis, glycogenesis and glucose oxidation, potentially via mechanisms involving AKT, GSK3 and oxidative phosphorylation. MiR-194 could be down-regulated in patients with early features of diabetes as an adaptive response to facilitate tissue glucose uptake and metabolism in the face of insulin resistance.
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Abstract
With the impressive advancement in high-throughput 'omics' technologies over the past two decades, epigenetic mechanisms have emerged as the regulatory interface between the genome and environmental factors. These mechanisms include DNA methylation, histone modifications, ATP-dependent chromatin remodeling and RNA-based mechanisms. Their highly interdependent and coordinated action modulates the chromatin structure controlling access of the transcription machinery and thereby regulating expression of target genes. Given the rather limited proliferative capability of human cardiomyocytes, epigenetic regulation appears to play a particularly important role in the myocardium. The highly dynamic nature of the epigenome allows the heart to adapt to environmental challenges and to respond quickly and properly to cardiac stress. It is now becoming evident that histone-modifying and chromatin-remodeling enzymes as well as numerous non-coding RNAs play critical roles in cardiac development and function, while their dysregulation contributes to the onset and development of pathological cardiac remodeling culminating in HF. This review focuses on up-to-date knowledge about the epigenetic mechanisms and highlights their emerging role in the healthy and failing heart. Uncovering the determinants of epigenetic regulation holds great promise to accelerate the development of successful new diagnostic and therapeutic strategies in human cardiac disease.
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Affiliation(s)
- José Marín-García
- The Molecular Cardiology and Neuromuscular Institute, 75 Raritan Ave., Highland Park, NJ, 08904, USA,
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206
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miR-21-3p controls sepsis-associated cardiac dysfunction via regulating SORBS2. J Mol Cell Cardiol 2016; 94:43-53. [DOI: 10.1016/j.yjmcc.2016.03.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 12/23/2022]
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Steinkraus BR, Toegel M, Fulga TA. Tiny giants of gene regulation: experimental strategies for microRNA functional studies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2016; 5:311-62. [PMID: 26950183 PMCID: PMC4949569 DOI: 10.1002/wdev.223] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/19/2015] [Accepted: 11/28/2015] [Indexed: 12/11/2022]
Abstract
The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high-throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA-target binding events in vivo drove the emergence of a slew of high-throughput multiplex strategies, which now provide a viable prospect for elucidating genome-wide miRNA-target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post-transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high-precision interference with their direct, endogenous targets. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Toegel
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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Pulignani S, Vecoli C, Sabina S, Foffa I, Ait-Ali L, Andreassi MG. 3'UTR SNPs and Haplotypes in the GATA4 Gene Contribute to the Genetic Risk of Congenital Heart Disease. ACTA ACUST UNITED AC 2016; 69:760-5. [PMID: 27118528 DOI: 10.1016/j.rec.2016.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/22/2015] [Indexed: 01/19/2023]
Abstract
INTRODUCTION AND OBJECTIVES Single-nucleotide polymorphisms within a microRNA binding site can have different effects on gene expression, influencing the risk of disease. This study aimed to evaluate the association between single-nucleotide polymorphisms and haplotypes in the 3'UTR of the GATA4 gene and congenital heart disease risk. METHODS Bioinformatics algorithms were used to analyze single-nucleotide polymorphisms in putative microRNA-binding sites of GATA4 3'UTR and to calculate the difference in free energy of hybridization (ΔFE, kcal/mol) for each wild-type vs the variant allele. RESULTS The study population comprised 146 Caucasian patients (73 males; 6.68 ± 7.79 years) and a 265 healthy newborn participants (147 males). The sum of all |ΔFE| was considered to predict the biological importance of single-nucleotide polymorphisms binding more microRNAs. Next, the 4 polymorphisms (+1158C > T, +1256 A > T, +1355 G > A, +1521C > G) with the highest predicted |ΔFEtot| (9.91, 14.85, 11.03, 21.66kcal/mol, respectively) were genotyped in a case-control study (146 patients and 250 controls). Applying a correction for multiple testing only the +1158 T allele was found to be associated with a reduced risk showing significant difference between patients and controls. Haplotype analysis showed that the T-T-G-C haplotype (more uncommon in congenital heart diseases than in controls) was associated with a significantly decreased risk (P = .03), while the rare C-A-A-C haplotype, which was very uncommon in controls (0.3%) compared with the disease (2.4%), was associated with a 4-fold increased risk of disease (P = .04). CONCLUSIONS Common variants in 3'UTR of the GATA4 gene jointly interact, affecting the congenital heart disease susceptibility, probably by altering microRNA posttranscriptional regulation.
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Affiliation(s)
- Silvia Pulignani
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
| | - Cecilia Vecoli
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy.
| | - Saverio Sabina
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
| | - Ilenia Foffa
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
| | - Lamia Ait-Ali
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
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Lukasik A, Wójcikowski M, Zielenkiewicz P. Tools4miRs - one place to gather all the tools for miRNA analysis. Bioinformatics 2016; 32:2722-4. [PMID: 27153626 PMCID: PMC5013900 DOI: 10.1093/bioinformatics/btw189] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/04/2016] [Indexed: 01/08/2023] Open
Abstract
Summary: MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data. Availability and Implementation: Tools4miRs is implemented in Python using Django and is freely available at tools4mirs.org. Contact: piotr@ibb.waw.pl Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anna Lukasik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Maciej Wójcikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, 02-096 Warsaw, Poland
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Iacomino G, Russo P, Stillitano I, Lauria F, Marena P, Ahrens W, De Luca P, Siani A. Circulating microRNAs are deregulated in overweight/obese children: preliminary results of the I.Family study. GENES AND NUTRITION 2016; 11:7. [PMID: 27551310 PMCID: PMC4968450 DOI: 10.1186/s12263-016-0525-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/08/2016] [Indexed: 01/06/2023]
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs involved in the modulation of gene expression and in the control of numerous cell functions. Alterations of miRNA patterns frequently occur in cancer and metabolic disorders, including obesity. Recent studies showed remarkable stability of miRNAs in both plasma and serum making them suitable as potential circulating biomarkers for a variety of diseases and conditions. The aim of this study was to assess the profile of circulating miRNAs expressed in plasma samples of overweight or obese (OW/Ob) and normal weight (NW) prepubertal children from a European cohort (www.ifamilystudy.eu). The project, aimed to assess the determinants of eating behavior in children and adolescents of eight European countries, is built on the IDEFICS cohort (www.ideficsstudy.eu), established in 2006. Among the participants of the I.Family Italian Cohort, ten OW/Ob (age 10.7 ± 1.5 years, BMI 31.6 ± 4.3 kg/m2) and ten NW (age 10.5 ± 2.7 years, BMI 16.4 ± 1.7 kg/m2) children were selected for the study. Gene arrays were employed to differentially screen the expression of 372 miRNAs in pooled plasma samples. Deregulated miRNAs (p < 0.05) were further validated in the individual samples using a real-time PCR (RT-qPCR) approach. Results Using a significance threshold of p < 0.05 and a fold-change threshold of ± 4.0, we preliminarily identified in the pooled samples eight miRNAs that differed between the OW/Ob and NW groups. The validation by RT-qPCR in the individual plasma samples showed a twofold upregulation of miR-31-5p, a threefold upregulation of miR-2355-5p, and a 0.5-fold downregulation of miR-206 in OW/Ob as compared with NW. The molecular functions of these differentially expressed plasma miRNAs as well as their expected mRNA targets were predicted by bioinformatics tools. Conclusions This pilot study shows that three circulating miRNAs are differentially regulated in OW/Ob as compared with NW children. Although causal pathways cannot be firmly inferred by these results, that deserve confirmation in larger samples, it is conceivable that circulating miRNAs may be novel biomarkers of obesity and related metabolic disturbances. Electronic supplementary material The online version of this article (doi:10.1186/s12263-016-0525-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giuseppe Iacomino
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
| | - Paola Russo
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
| | - Ilaria Stillitano
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
| | - Fabio Lauria
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
| | - Pasquale Marena
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
| | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany ; Institute of Statistics, Faculty of Mathematics and Computer Science, University Bremen, Bremen, Germany
| | | | - Alfonso Siani
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
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Amacher DE. A 2015 survey of established or potential epigenetic biomarkers for the accurate detection of human cancers. Biomarkers 2016; 21:387-403. [PMID: 26983778 DOI: 10.3109/1354750x.2016.1153724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Context The silencing or activation of cancer-associated genes by epigenetic mechanisms can ultimately lead to the clonal expansion of cancer cells. Objective The aim of this review is to summarize all relevant epigenetic biomarkers that have been proposed to date for the diagnosis of some prevalent human cancers. Methods A Medline search for the terms epigenetic biomarkers, human cancers, DNA methylation, histone modifications and microRNAs was performed. Results One hundred fifty-seven relevant publications were found and reviewed. Conclusion To date, a significant number of potential epigenetic cancer biomarkers of human cancer have been investigated, and some have advanced to clinical implementation.
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Gjymishka A, Pi L, Oh SH, Jorgensen M, Liu C, Protopapadakis Y, Patel A, Petersen BE. miR-133b Regulation of Connective Tissue Growth Factor: A Novel Mechanism in Liver Pathology. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:1092-102. [PMID: 26945106 DOI: 10.1016/j.ajpath.2015.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/30/2015] [Accepted: 12/28/2015] [Indexed: 02/07/2023]
Abstract
miRNAs are involved in liver regeneration, and their expression is dysregulated in hepatocellular carcinoma (HCC). Connective tissue growth factor (CTGF), a direct target of miR-133b, is crucial in the ductular reaction (DR)/oval cell (OC) response for generating new hepatocyte lineages during liver injury in the context of hepatotoxin-inhibited hepatocyte proliferation. Herein, we investigate whether miR-133b regulation of CTGF influences HCC cell proliferation and migration, and DR/OC response. We analyzed miR-133b expression and found it to be down-regulated in HCC patient samples and induced in the rat DR/OC activation model of 2-acetylaminofluorene with partial hepatectomy. Furthermore, overexpression of miR-133b via adenoviral system in vitro led to decreased CTGF expression and reduced proliferation and Transwell migration of both HepG2 HCC cells and WBF-344 rat OCs. In vivo, overexpression of miR-133b in DR/OC activation models of 2-acetylaminofluorene with partial hepatectomy in rats, and 3,5-diethoxycarbonyl-1,4-dihydrocollidine in mice, led to down-regulation of CTGF expression and OC proliferation. Collectively, these results show that miR-133b regulation of CTGF is a novel mechanism critical for the proliferation and migration of HCC cells and OC response.
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Affiliation(s)
- Altin Gjymishka
- Department of Pediatrics, University of Florida, Gainesville, Florida
| | - Liya Pi
- Department of Pediatrics, University of Florida, Gainesville, Florida
| | - Seh-Hoon Oh
- Department of Pediatrics, University of Florida, Gainesville, Florida
| | - Marda Jorgensen
- Department of Pediatrics, University of Florida, Gainesville, Florida
| | - Chen Liu
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida
| | | | - Ashnee Patel
- Department of Pediatrics, University of Florida, Gainesville, Florida
| | - Bryon E Petersen
- Department of Pediatrics, University of Florida, Gainesville, Florida.
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Rudnicki M, Perco P, D Haene B, Leierer J, Heinzel A, Mühlberger I, Schweibert N, Sunzenauer J, Regele H, Kronbichler A, Mestdagh P, Vandesompele J, Mayer B, Mayer G. Renal microRNA- and RNA-profiles in progressive chronic kidney disease. Eur J Clin Invest 2016; 46:213-26. [PMID: 26707063 DOI: 10.1111/eci.12585] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 12/20/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) contribute to chronic kidney disease (CKD) progression via regulating mRNAs involved in renal homeostasis. However, their association with clinical outcome remains poorly understood. MATERIALS AND METHODS We performed miRNA and mRNA expression profiling on renal biopsy sections by qPCR (miRNA) and microarrays (mRNA) in a discovery (n = 43) and in a validation (n = 29) cohort. miRNAs differentiating stable and progressive cases were inversely correlated with putative target mRNAs, which were further characterized by pathway analysis using KEGG pathways. RESULTS miR-30d, miR-140-3p, miR-532-3p, miR-194, miR-190, miR-204 and miR-206 were downregulated in progressive cases. These seven miRNAs correlated with upregulated 29 target mRNAs involved in inflammatory response, cell-cell interaction, apoptosis and intra-cellular signalling. In particular, miR-206 and miR-532-3p were associated with distinct biological processes via the expression of their target mRNAs: Reduced expression of miR-206 in progressive disease correlated with the upregulation of target mRNAs participating in inflammatory pathways (CCL19, CXCL1, IFNAR2, NCK2, PTK2B, PTPRC, RASGRP1 and TNFRSF25). Progressive cases also showed a lower expression of miR-532-3p and an increased expression of target transcripts involved in apoptosis pathways (MAP3K14, TNFRSF10B/TRAIL-R2, TRADD and TRAF2). In the validation cohort, we confirmed the decreased expression of miR-206 and miR-532-3p, and the inverse correlation of these miRNAs with the expression of nine of the 12 target genes. The levels of the identified miRNAs and the target mRNAs correlated with clinical parameters and histological damage indices. CONCLUSIONS These results suggest the involvement of specific miRNAs and mRNAs in biological pathways associated with the progression of CKD.
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Affiliation(s)
- Michael Rudnicki
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Paul Perco
- Emergentec Biodevelopment GmbH, Vienna, Austria
| | | | - Johannes Leierer
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | | | | | - Ninella Schweibert
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Judith Sunzenauer
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria.,Department of Nephrology, KH Elisabethinen, Linz, Austria
| | - Heinz Regele
- Institute of Pathology, Medical University Vienna, Vienna, Austria
| | - Andreas Kronbichler
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | | | | | - Bernd Mayer
- Emergentec Biodevelopment GmbH, Vienna, Austria
| | - Gert Mayer
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
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Leistner DM, Boeckel JN, Reis SM, Thome CE, De Rosa R, Keller T, Palapies L, Fichtlscherer S, Dimmeler S, Zeiher AM. Transcoronary gradients of vascular miRNAs and coronary atherosclerotic plaque characteristics. Eur Heart J 2016; 37:1738-49. [DOI: 10.1093/eurheartj/ehw047] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 12/23/2015] [Indexed: 11/13/2022] Open
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Sewelam N, Kazan K, Schenk PM. Global Plant Stress Signaling: Reactive Oxygen Species at the Cross-Road. FRONTIERS IN PLANT SCIENCE 2016; 7:187. [PMID: 26941757 PMCID: PMC4763064 DOI: 10.3389/fpls.2016.00187] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/04/2016] [Indexed: 05/18/2023]
Abstract
Current technologies have changed biology into a data-intensive field and significantly increased our understanding of signal transduction pathways in plants. However, global defense signaling networks in plants have not been established yet. Considering the apparent intricate nature of signaling mechanisms in plants (due to their sessile nature), studying the points at which different signaling pathways converge, rather than the branches, represents a good start to unravel global plant signaling networks. In this regard, growing evidence shows that the generation of reactive oxygen species (ROS) is one of the most common plant responses to different stresses, representing a point at which various signaling pathways come together. In this review, the complex nature of plant stress signaling networks will be discussed. An emphasis on different signaling players with a specific attention to ROS as the primary source of the signaling battery in plants will be presented. The interactions between ROS and other signaling components, e.g., calcium, redox homeostasis, membranes, G-proteins, MAPKs, plant hormones, and transcription factors will be assessed. A better understanding of the vital roles ROS are playing in plant signaling would help innovate new strategies to improve plant productivity under the circumstances of the increasing severity of environmental conditions and the high demand of food and energy worldwide.
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Affiliation(s)
- Nasser Sewelam
- Botany Department, Faculty of Science, Tanta UniversityTanta, Egypt
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization Agriculture, Queensland Bioscience Precinct, St LuciaQLD, Australia
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, BrisbaneQLD, Australia
| | - Peer M. Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, BrisbaneQLD, Australia
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216
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Abstract
The worldwide increase in the prevalence of obesity and type 2 diabetes and the associated elevated risk of cardiovascular disease (CVD) has emphasized the need to seek new therapeutic targets to offset the negative impact on human health outcomes. In this regards, microRNAs (miRNAs), a class of small noncoding RNAs that mediate posttranscriptional gene silencing, have received considerable interest. miRNAs repress gene expression by their ability to pair with target sequences in the 3' untranslated region of the messenger RNA. miRNAs play a crucial role in the biogenesis and function of the cardiovascular system and are implicated as dynamic regulators of cardiac and vascular signaling and pathophysiology. Numerous miRNAs have been identified as novel biomarkers and potential therapeutic targets for CVD. In this review, we discuss the contribution of miRNAs to the regulation of CVD, their role in macrovascular/microvascular (dys)function, their potential as important biomarkers for the early detection of CVD, and, finally, as therapeutic targets.
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217
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microRNA-29b Mediates the Antifibrotic Effect of Tanshinone IIA in Postinfarct Cardiac Remodeling. J Cardiovasc Pharmacol 2016; 65:456-64. [PMID: 25636075 DOI: 10.1097/fjc.0000000000000214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Tanshinone IIA (TSN) is one of the main components isolated from Danshen, which is widely used for the treatment of cardiovascular diseases. The transforming growth factor beta (TGF-β) signaling pathway and microRNA (miR)-29b play important roles in the progression of cardiac fibrosis and the modulation of cardiac fibroblast (CF) function. Our study investigated the role of miR-29b in the cardioprotective effects of TSN in postinfarct cardiac remodeling. METHODS AND RESULTS Echocardiography demonstrated that medium-dose TSN (TSN-M) and high-dose TSN (TSN-H) significantly inhibited postinfarct cardiac fibrosis and improved the impaired left ventricular function in rats subjected to acute myocardial infarction. Moreover, quantitative real-time polymerase chain reaction and Western blot demonstrated that TSN-M and TSN-H downregulated the expression of TGF-β1, Col1a1, Col3a1, and α-SMA but upregulated the expression of miR-29b. CFs treated with TSN showed inhibited TGF-β signaling pathway, downregulated expression of Col1a1, Col3a1, and α-SMA, and upregulated miR-29b expression in vitro. Furthermore, treatment with a miR-29b inhibitor dramatically inhibited these TSN-induced antifibrotic effects, suggesting that miR-29b may be responsible for the antifibrotic effects of TSN. In addition, treatment with Smad3 siRNA significantly inhibited miR-29b expression in CFs, which implies that Smad3 signaling promotes miR-29b expression on CFs. CONCLUSIONS TSN exerts antifibrotic effects in postinfarct cardiac fibrosis by upregulating the expression of miR-29b, which is mediated by the TGF-β-Smad3 signaling pathway.
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218
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Nakou ES, Parthenakis FI, Kallergis EM, Marketou ME, Nakos KS, Vardas PE. Healthy aging and myocardium: A complicated process with various effects in cardiac structure and physiology. Int J Cardiol 2016; 209:167-75. [PMID: 26896615 DOI: 10.1016/j.ijcard.2016.02.039] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/25/2015] [Accepted: 02/02/2016] [Indexed: 02/08/2023]
Abstract
It is known that there is an ongoing increase in life expectancy worldwide, especially in the population older than 65years of age. Cardiac aging is characterized by a series of complex pathophysiological changes affecting myocardium at structural, cellular, molecular and functional levels. These changes make the aged myocardium more susceptible to stress, leading to a high prevalence of cardiovascular diseases (heart failure, atrial fibrillation, left ventricular hypertrophy, coronary artery disease) in the elderly population. The aging process is genetically programmed but modified by environmental influences, so that the rate of aging can vary widely among people. We summarized the entire data concerning all the multifactorial changes in aged myocardium and highlighting the recent evidence for the pathophysiological basis of cardiac aging. Keeping an eye on the clinical side, this review will explore the potential implications of the age-related changes in the clinical management and on novel therapeutic strategies potentially deriving from the scientific knowledge currently acquired on cardiac aging process.
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Affiliation(s)
- E S Nakou
- Department of Cardiology, Heraklion University Hospital, 7100, Voutes, Heraklion-Crete, Greece.
| | - F I Parthenakis
- Department of Cardiology, Heraklion University Hospital, 7100, Voutes, Heraklion-Crete, Greece
| | - E M Kallergis
- Department of Cardiology, Heraklion University Hospital, 7100, Voutes, Heraklion-Crete, Greece
| | - M E Marketou
- Department of Cardiology, Heraklion University Hospital, 7100, Voutes, Heraklion-Crete, Greece
| | - K S Nakos
- Department of Cardiology, Heraklion University Hospital, 7100, Voutes, Heraklion-Crete, Greece
| | - P E Vardas
- Department of Cardiology, Heraklion University Hospital, 7100, Voutes, Heraklion-Crete, Greece
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219
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Glover AR, Hassan N, Joo LJS, Kwok G, Zhao JT, Sidhu SB. Could miRNA replacement be a novel therapy for adrenocortical carcinoma? INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2016. [DOI: 10.2217/ije.15.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Adrenocortical carcinoma (ACC) has poor outcomes and there is a need for novel effective treatments for metastatic disease and adjuvant therapy. miRNAs are small endogenous noncoding RNAs that control gene expression. miRNAs are dysregulated in all cancers and manipulation of miRNA levels is under investigation as a novel therapy in other cancers with poor outcomes such as mesothelioma. In this review, the rationale for miRNA therapy will be presented along with the current understanding of the role of miRNA dysregulation and miRNA regulation of ACC. Potential therapeutic approaches of miRNA therapy using established delivery systems such as liposomes and targeted nanocells will be presented, along with the future challenges of establishing miRNA therapy in clinical trials for ACC.
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Affiliation(s)
- Anthony R Glover
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
- University of Sydney Endocrine Surgery Unit, Royal North Shore Hospital, Sydney, NSW, Australia
- Sydney Vital Translational Research Unit, Northern Sydney Local Health District, Cancer Institute NSW, Australia
| | - Nunki Hassan
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
| | - Lauren Jin Suk Joo
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
| | - Grace Kwok
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
| | - Jing Ting Zhao
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
- Sydney Vital Translational Research Unit, Northern Sydney Local Health District, Cancer Institute NSW, Australia
| | - Stan B Sidhu
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
- University of Sydney Endocrine Surgery Unit, Royal North Shore Hospital, Sydney, NSW, Australia
- Sydney Vital Translational Research Unit, Northern Sydney Local Health District, Cancer Institute NSW, Australia
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miR-26a suppresses EMT by disrupting the Lin28B/let-7d axis: potential cross-talks among miRNAs in IPF. J Mol Med (Berl) 2016; 94:655-65. [PMID: 26787543 DOI: 10.1007/s00109-016-1381-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 12/20/2015] [Accepted: 01/11/2016] [Indexed: 12/31/2022]
Abstract
UNLABELLED Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and highly lethal fibrotic lung disease with unknown cause or cure. Although some microRNAs (miRNAs), such as miR-26a and let-7d, have been confirmed, the contribution to the pathophysiological processes of IPF, the roles of miRNAs and intrinsic links between them in fibrotic lung diseases are not yet well understood. In this study, we found that Lin28B could induce the process of epithelial-mesenchymal transition (EMT) by inhibiting let-7d, whereas inhibition of Lin28B mitigated TGF-β1-induced fibrogenesis and attenuated EMT in both cultured A549 cells and MLE-12 cells. More importantly, over-expression of miR-26a could simultaneously enhance the expression of let-7d in A549 cells, and further study confirmed that Lin28B was one of the direct targets of miR-26a, which mediates, at least in part, the regulatory effects of miR-26a on the biogenesis of let-7d. Finally, we constructed a regulatory network among miRNAs involved in the progression of IPF. Taken together, our study deciphered the essential role of Lin28B in the pathogenesis of EMT, and unraveled a novel mechanism that miR-26a is a modulator of let-7d. This study also defines the miRNAs network involved in IPF, which may have implications for developing new strategies for pulmonary fibrosis. KEY MESSAGE Upregulation of Lin28B contributes to idiopathic pulmonary fibrosis. Lin28B causes epithelial-mesenchymal transition (EMT) by inhibition of let-7d. Lin28B is one of the targets of microRNA-26a. miR-26a enhances the expression of let-7d via targeting regulation of Lin28B. A regulatory network among miRNAs involved in the progression of IPF.
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221
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Rotllan N, Price N, Pati P, Goedeke L, Fernández-Hernando C. microRNAs in lipoprotein metabolism and cardiometabolic disorders. Atherosclerosis 2016; 246:352-60. [PMID: 26828754 DOI: 10.1016/j.atherosclerosis.2016.01.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 12/18/2022]
Abstract
Circulating levels of low-density lipoprotein cholesterol (LDL), and high-density lipoprotein cholesterol (HDL) are two of the most important risk factors for the development of cardiovascular disease (CVD), the leading cause of death worldwide. Recently, miRNAs have emerged as critical regulators of cholesterol metabolism and promising therapeutic targets for the treatment of CVD. A great deal of work has established numerous miRNAs as important regulators of HDL metabolism. This includes miRNAs that target ABCA1, a critical factor for HDL biogenesis and reverse cholesterol transport (RCT), the process through which cells, including arterial macrophages, efflux cellular cholesterol for transport to and removal by the liver. The most well studied of these miRNAs, miR-33, has been demonstrated to target ABCA1, as well as numerous other genes involved in metabolic function and RCT, and therapeutic inhibition of miR-33 was found to increase HDL levels in mice and non-human primates. Moreover, numerous studies have demonstrated the beneficial effects of miR-33 inhibition or knockout on reducing atherosclerotic plaque burden. Even more recent work has identified miRNAs that regulate LDL cholesterol levels, including direct modulation of LDL uptake in the liver through targeting of the LDL receptor. Among these, inhibition of miR-128-1, miR-148a, or miR-185 was found to reduce plasma LDL levels, and inhibition of miR-185 was further demonstrated to reduce atherosclerotic plaque size in ApoE(-/-) mice. Due to their ability to target many different genes, miRNAs have the ability to mediate complex physiologic changes through simultaneous regulation of multiple interrelated pathways. Of particular importance for CVD, inhibition of miR-148a may prove an important therapeutic approach for combating dyslipidemia, as this has been demonstrated to both raise plasma HDL levels and lower LDL levels in mice by targeting both ABCA1 and LDLR, respectively. In this review we highlight recent advances in our understanding of how miRNAs regulate cholesterol metabolism and the development of atherosclerotic plaques and discuss the potential of anti-miRNA therapies for the treatment and prevention of CVD.
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Affiliation(s)
- Noemi Rotllan
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA; Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan Price
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA; Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Paramita Pati
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA; Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Leigh Goedeke
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA; Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA; Integrative Cell Signaling and Neurobiology of Metabolism Program, Section of Comparative Medicine and Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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Abstract
Biomarkers are measurable characteristics reflective of the physiological or diseased state and a crucial feature in rendering personalized medicine more precise. Dysregulated expression of circulating microRNAs (miRNAs) in bodily fluids is being explored as noninvasive clinical biomarker for a variety of disorders including chronic pain. High-precision qPCR-based signal amplification of these miRNAs enables the detection of small changes making them ideal biomarker candidates. Presence of circulating miRNAs in exosomes, small vesicles that mediate intercellular communication, opens up novel avenues for target intervention and biomarker discovery. miRNA signatures specific to different pain conditions, and their reversal on treatment in patients and animal models can be beneficial in patient stratification, prognosis, and in bridging preclinical and clinical results. Identification of multiple miRNAs as opposed to reliance on one specific molecule as a biomarker could improve treatment efficacies in an extremely heterogeneous pain patient population. Additionally, owing to the stability of miRNAs, retrospective studies could be performed using banked samples from completed clinical trials. Irrespective of the phase and outcome, these studies can provide insights on molecular underpinnings influencing treatment outcome, or specific therapeutic intervention. Identification of miRNAs altered in chronic pain states will have a significant impact on the identification of right leads, targets, doses, and patients. Effective implementation of miRNA-based biomarkers would provide treatment guidance for clinicians, better clinical trial designs for pharmaceutical companies, all leading to individualized care and better treatment outcome for chronic pain patients.
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Affiliation(s)
- Sujay Ramanathan
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Seena K Ajit
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.
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223
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Busch A, Busch M, Scholz CJ, Kellersmann R, Otto C, Chernogubova E, Maegdefessel L, Zernecke A, Lorenz U. Aneurysm miRNA Signature Differs, Depending on Disease Localization and Morphology. Int J Mol Sci 2016; 17:ijms17010081. [PMID: 26771601 PMCID: PMC4730325 DOI: 10.3390/ijms17010081] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/18/2015] [Accepted: 01/04/2016] [Indexed: 12/27/2022] Open
Abstract
Limited comprehension of aneurysm pathology has led to inconclusive results from clinical trials. miRNAs are key regulators of post-translational gene modification and are useful tools in elucidating key features of aneurysm pathogenesis in distinct entities of abdominal and popliteal aneurysms. Here, surgically harvested specimens from 19 abdominal aortic aneurysm (AAA) and 8 popliteal artery aneurysm (PAA) patients were analyzed for miRNA expression and histologically classified regarding extracellular matrix (ECM) remodeling and inflammation. DIANA-based computational target prediction and pathway enrichment analysis verified our results, as well as previous ones. miRNA-362, -19b-1, -194, -769, -21 and -550 were significantly down-regulated in AAA samples depending on degree of inflammation. Similar or inverse regulation was found for miR-769, 19b-1 and miR-550, -21, whereas miR-194 and -362 were unaltered in PAA. In situ hybridization verified higher expression of miR-550 and -21 in PAA compared to AAA and computational analysis for target genes and pathway enrichment affirmed signal transduction, cell-cell-interaction and cell degradation pathways, in line with previous results. Despite the vague role of miRNAs for potential diagnostic and treatment purposes, the number of candidates from tissue signature studies is increasing. Tissue morphology influences subsequent research, yet comparison of distinct entities of aneurysm disease can unravel core pathways.
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Affiliation(s)
- Albert Busch
- Department for General, Visceral, Vascular & Paediatric Surgery, University Hospital of Würzburg, Würzburg 97080, Germany.
| | - Martin Busch
- Rudolf Virchow-Center, University of Würzburg, Würzburg 97080, Germany.
| | - Claus-Jürgen Scholz
- IZKF Laboratory for Microarray Applications, University Hospital Würzburg, Würzburg 97080, Germany.
| | - Richard Kellersmann
- Department for General, Visceral, Vascular & Paediatric Surgery, University Hospital of Würzburg, Würzburg 97080, Germany.
| | - Christoph Otto
- Department for General, Visceral, Vascular & Paediatric Surgery, University Hospital of Würzburg, Würzburg 97080, Germany.
| | - Ekaterina Chernogubova
- Department of Medicine, Center for Molecular Medicine (L8:03), Karolinska Institute, Stockholm 12065, Sweden.
| | - Lars Maegdefessel
- Department of Medicine, Center for Molecular Medicine (L8:03), Karolinska Institute, Stockholm 12065, Sweden.
| | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg 97080, Germany.
| | - Udo Lorenz
- Department for General, Visceral, Vascular & Paediatric Surgery, University Hospital of Würzburg, Würzburg 97080, Germany.
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Lee S, Hwang S, Yu HJ, Oh D, Choi YJ, Kim MC, Kim Y, Ryu DY. Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition. PLoS One 2016; 11:e0146374. [PMID: 26731407 PMCID: PMC4711666 DOI: 10.1371/journal.pone.0146374] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/16/2015] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) in blood plasma are stable under high levels of ribonuclease activity and could function in tissue-to-tissue communication, suggesting that they may have distinctive structural characteristics compared with non-circulating miRNAs. In this study, the expression of miRNAs in horse plasma and their characteristic nucleotide composition were examined and compared with non-plasma miRNAs. Highly expressed plasma miRNA species were not part of the abundant group of miRNAs in non-plasma tissues, except for the eca-let-7 family. eca-miR-486-5p, -92a, and -21 were among the most abundant plasma miRNAs, and their human orthologs also belong to the most abundant group of miRNAs in human plasma. Uracil and guanine were the most common nucleotides of both plasma and non-plasma miRNAs. Cytosine was the least common in plasma and non-plasma miRNAs, although levels were higher in plasma miRNAs. Plasma miRNAs also showed higher expression levels of miRNAs containing adenine and cytosine repeats, compared with non-plasma miRNAs. These observations indicate that miRNAs in the plasma have a unique nucleotide composition.
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Affiliation(s)
- Seungwoo Lee
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Seungwoo Hwang
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hee Jeong Yu
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Dayoung Oh
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Yu Jung Choi
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Myung-Chul Kim
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Yongbaek Kim
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Doug-Young Ryu
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
- * E-mail:
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Xu W, Luo F, Sun B, Ye H, Li J, Shi L, Liu Y, Lu X, Wang B, Wang Q, Liu Q, Zhang A. HIF-2α, acting via miR-191, is involved in angiogenesis and metastasis of arsenite-transformed HBE cells. Toxicol Res (Camb) 2016; 5:66-78. [PMID: 30090327 PMCID: PMC6060623 DOI: 10.1039/c5tx00225g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022] Open
Abstract
Arsenic is a well established human carcinogen that causes diseases of the lung. Some studies have suggested that hypoxia-inducible factors (HIFs) and microRNAs (miRNAs) are involved in human lung cancer; however, their molecular mechanisms that causally contribute to arsenite-caused malignant transformation of cells remain unclear. To elucidate the mechanisms of angiogenesis and metastasis of lung cancer caused by arsenite, we investigated the role of HIF-2α regulation of miRNA-191 (miR-191) in the angiogenic and metastatic properties of human bronchial epithelial (HBE) cells transformed by arsenite. In HBE cells, HIF-2α binds to the hypoxia response element (HRE) in the promoter region of miR-191 and initiates transcription of miR-191. Blocking of HIF-2α with siRNA inhibited the up-regulation of miR-191, Wilms' tumor 1 (WT1) protein, matrix metalloproteinase 9 (MMP-9), vascular endothelial growth factor (VEGF), and the down-regulation of brain acid-soluble protein 1 (BASP1). In arsenite-transformed HBE (T-HBE) cells, down-regulation of HIF-2α by siRNA blocked the process of angiogenesis and decreased their neoplastic properties and metastatic capacity, which were reversed by over-expression of miR-191 or by up-regulating WT1. Thus, HIF-2α up-regulates WT1 via miR-191, both of which are involved in the angiogenesis and metastasis of T-HBE cells. The results present a better understanding of the processes involved in lung cancer caused by arsenite exposure.
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Affiliation(s)
- Wenchao Xu
- Institute of Toxicology , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China
- The Key Laboratory of Modern Toxicology , Ministry of Education , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China . ; ; Tel: +86-25-8686-8424
| | - Fei Luo
- Institute of Toxicology , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China
- The Key Laboratory of Modern Toxicology , Ministry of Education , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China . ; ; Tel: +86-25-8686-8424
| | - Baofei Sun
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control , Ministry of Education , School of Public Health , Guiyang Medical University , Guiyang 550025 , Guizhou , People's Republic of China . ; ; Tel: +86-851-8841-6171
| | - Hua Ye
- School of Medicine , Yangzhou University , Yangzhou 225009 , Jiangsu , People's Republic of China
| | - Jun Li
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control , Ministry of Education , School of Public Health , Guiyang Medical University , Guiyang 550025 , Guizhou , People's Republic of China . ; ; Tel: +86-851-8841-6171
| | - Le Shi
- Institute of Toxicology , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China
- The Key Laboratory of Modern Toxicology , Ministry of Education , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China . ; ; Tel: +86-25-8686-8424
| | - Yi Liu
- Institute of Toxicology , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China
- The Key Laboratory of Modern Toxicology , Ministry of Education , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China . ; ; Tel: +86-25-8686-8424
| | - Xiaolin Lu
- Institute of Toxicology , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China
- The Key Laboratory of Modern Toxicology , Ministry of Education , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China . ; ; Tel: +86-25-8686-8424
| | - Bairu Wang
- Institute of Toxicology , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China
- The Key Laboratory of Modern Toxicology , Ministry of Education , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China . ; ; Tel: +86-25-8686-8424
| | - Qingling Wang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control , Ministry of Education , School of Public Health , Guiyang Medical University , Guiyang 550025 , Guizhou , People's Republic of China . ; ; Tel: +86-851-8841-6171
| | - Qizhan Liu
- Institute of Toxicology , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China
- The Key Laboratory of Modern Toxicology , Ministry of Education , School of Public Health , Nanjing Medical University , Nanjing 211166 , Jiangsu , People's Republic of China . ; ; Tel: +86-25-8686-8424
| | - Aihua Zhang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control , Ministry of Education , School of Public Health , Guiyang Medical University , Guiyang 550025 , Guizhou , People's Republic of China . ; ; Tel: +86-851-8841-6171
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Abstract
PURPOSE OF REVIEW The use of adeno-associated virus (AAV) as an efficient, cardiotropic, and safe vector, coupled with the identification of key molecular targets, has placed gene-based therapies within reach of cardiovascular diseases. The purpose of this review is to provide a focused update on the current advances related to AAV-mediated gene therapy in cardiovascular diseases, and particularly in heart failure (HF), wherein gene therapy has recently made important progress. RECENT FINDINGS Multiple successful preclinical studies suggest a potential utility of AAV gene therapy for arrhythmias and biological heart pacing, as well as RNA overexpression. Moreover, AAV-mediated overexpression of several molecular targets involved in HF has demonstrated promising results in clinically relevant large animal models. In humans, a safe and successful completion of a phase 2 clinical trial targeting the sarcoplasmic reticulum calcium ATPase pump with AAV has been reported. Serial studies are ongoing to further prove the efficacy of AAV-mediated sarcoplasmic reticulum calcium ATPase pump gene transfer in human HF. SUMMARY Significant progress in clinical translation of AAV-mediated cardiac gene therapy has been achieved in recent years. This will prompt further clinical trials, and positive results could open a new era for cardiac gene therapy.
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Schulte C, Westermann D, Blankenberg S, Zeller T. Diagnostic and prognostic value of circulating microRNAs in heart failure with preserved and reduced ejection fraction. World J Cardiol 2015; 7:843-860. [PMID: 26730290 PMCID: PMC4691811 DOI: 10.4330/wjc.v7.i12.843] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/28/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023] Open
Abstract
microRNAs (miRNAs) are powerful regulators of posttranscriptional gene expression and play an important role in pathophysiological processes. Circulating miRNAs can be quantified in body liquids and are promising biomarkers in numerous diseases. In cardiovascular disease miRNAs have been proven to be reliable diagnostic biomarkers for different disease entities. In cardiac fibrosis (CF) and heart failure (HF) dysregulated circulating miRNAs have been identified, indicating their promising applicability as diagnostic biomarkers. Some miRNAs were successfully tested in risk stratification of HF implementing their potential use as prognostic biomarkers. In this respect miRNAs might soon be implemented in diagnostic clinical routine. In the young field of miRNA based research advances have been made in identifying miRNAs as potential targets for the treatment of experimental CF and HF. Promising study results suggest their potential future application as therapeutic agents in treatment of cardiovascular disease. This article summarizes the current state of the various aspects of miRNA research in the field of CF and HF with reduced ejection fraction as well as preserved ejection fraction. The review provides an overview of the application of circulating miRNAs as biomarkers in CF and HF and current approaches to therapeutically utilize miRNAs in this field of cardiovascular disease.
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228
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Arias N, Aguirre L, Fernández-Quintela A, González M, Lasa A, Miranda J, Macarulla MT, Portillo MP. MicroRNAs involved in the browning process of adipocytes. J Physiol Biochem 2015; 72:509-21. [PMID: 26695012 DOI: 10.1007/s13105-015-0459-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/13/2015] [Indexed: 12/25/2022]
Abstract
The present review focuses on the role of miRNAs in the control of white adipose tissue browning, a process which describes the recruitment of adipocytes showing features of brown adipocytes in white adipose tissue. MicroRNAs (miRNAs) are a class of short non-coding RNAs (19-22 nucleotides) involved in gene regulation. Although the main effect of miRNAs is the inhibition of the translational machinery, thereby preventing the production of the protein product, the activation of protein translation has also been described in the literature. In addition to modifying translation, miRNAs binding to its target mRNAs also trigger the recruitment and association of mRNA decay factors, leading to mRNA destabilization, degradation, and thus to the decrease in expression levels. Although a great number of miRNAs have been reported to potentially regulate genes that play important roles in the browning process, only a reduced number of studies have demonstrated experimentally an effect on this process associated to changes in miRNA expressions, so far.
These studies have shown, by using either primary adipocyte cultures or experimental models of mice (KO mice, mice overexpressing a specific miRNA), that miR-196a, miR-26, and miR-30 are needed for browning process development. By contrast, miR-155, miR-133, miR-27b, and miR-34 act as negative regulators of this process [corrected]. Further studies are needed to fully describe the miRNA network-involved white adipose tissue browning regulation.
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Affiliation(s)
- N Arias
- Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria-Gasteiz, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - L Aguirre
- Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria-Gasteiz, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - A Fernández-Quintela
- Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria-Gasteiz, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - M González
- Nutrition and Food Science, Faculty of Biochemistry and Biological Sciences, National University of Litoral, Santa Fe, Argentina
| | - A Lasa
- Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria-Gasteiz, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - J Miranda
- Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria-Gasteiz, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - M T Macarulla
- Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria-Gasteiz, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - M P Portillo
- Nutrition and Obesity Group, Department of Nutrition and Food Sciences, University of Basque Country (UPV/EHU) and Lucio Lascaray Research Center, Vitoria-Gasteiz, Spain. .,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.
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Su XW, Chan AHY, Lu G, Lin M, Sze J, Zhou JY, Poon WS, Liu Q, Zheng VZY, Wong GKC. Circulating microRNA 132-3p and 324-3p Profiles in Patients after Acute Aneurysmal Subarachnoid Hemorrhage. PLoS One 2015; 10:e0144724. [PMID: 26675167 PMCID: PMC4682983 DOI: 10.1371/journal.pone.0144724] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023] Open
Abstract
Background Aneurysmal subarachnoid hemorrhage (SAH) is a highly morbid and fatal condition with high rate of cognitive impairment and negative impact in quality of life among survivors. Delayed cerebral infarction (DCI) is one the major factors for these negative outcomes. In this study we compared the circulating microRNA profiles of SAH patients and healthy individuals, and the circulating microRNA profiles of SAH patients with and without DCI. Methods Peripheral blood samples on Day 7 after the onset of SAH were subjected to microarray analysis with Affymetrix miRNA 3.0 array and quantitative PCR analysis. SAH patients with (N = 20) and without DCI (N = 20) and Healthy controls (N = 20) were included for analyses. Results We demonstrated that 99 miRNAs were found to be dysregulated in the SAH patient group with DCI. 81 miRNAs were upregulated and 18 were downregulated. Findings from KEGG pathway analysis showed that miRNAs and target genes for axon guidance and TGF-beta signaling were involved, implying that the resulted differential miRNA expression pattern reflect the results of SAH instead of etiology of the disease. miR-132-3p and miR-324-3p showed distinctive upregulations in qPCR [miR-132: 9.5 fold (95%CI: 2.3 to 16.7) in DCI group and 3.4 fold (95%CI: 1.0 to 5.8) in Non-DCI group; miR-324: 4924 fold (95%CI: 2620 to 7228) in DCI group and 4545 fold (95%CI: 2408 to 6683) in non-DCI group]. However, there were no significant differences in fold changes between SAH patients with and without DCI [fold change ratios (mean+/-SD): 2.7+/-4.2 and 1.1+/-1.1 for miRNA-132 and miRNA-324]. Conclusion Our study demonstrated that as compared to healthy control, miR-132 and miR-324 showed a upregulation in both SAH DCI and Non-DCI groups. However, the differences between the SAH DCI and non-DCI groups were not statistically significant.
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Affiliation(s)
- Xian Wei Su
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
| | - Anna Ho Yin Chan
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
| | - Gang Lu
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
- School of Biomedical Science, The Chinese University of Hong Kong, HKSAR, China
| | - Marie Lin
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
| | - Johnny Sze
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
| | - Jing Ye Zhou
- School of Biomedical Science, The Chinese University of Hong Kong, HKSAR, China
| | - Wai Sang Poon
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
| | - Qiang Liu
- School of Biomedical Science, The Chinese University of Hong Kong, HKSAR, China
| | - Vera Zhi Yuan Zheng
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
| | - George Kwok Chu Wong
- Division of Neurosurgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, HKSAR, China
- * E-mail:
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McKiernan PJ, Greene CM. High-throughput profiling for discovery of non-coding RNA biomarkers of lung disease. Expert Rev Mol Diagn 2015; 16:173-85. [PMID: 26581119 DOI: 10.1586/14737159.2016.1122526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In respiratory medicine there is a need for clinical biomarkers for diagnosis, prognosis and assessment of response to therapy. Noncoding RNA (ncRNA) is expressed in all human cells; two major classes--long ncRNA and microRNA--are detectable extracellularly in the circulation and other biofluids. Altered ncRNA expression is associated with lung disease; collectively this indicates that ncRNA represents a potential biomarker class. This article presents and compares existing platforms for detection and quantification of ncRNA, specifically hybridization, qRT-PCR and RNA sequencing, and outlines methods for data interpretation and normalization. Each approach has merits and shortcomings, which can affect the choice of method when embarking on a biomarker study. Biomarker properties and pre-analytical considerations for ncRNA profiling are also presented. Since a variety of profiling approaches are available, careful study and experimental design are important. Finally, challenges and goals for reliable, standardized high-throughput ncRNA profiling in biofluids as lung disease biomarkers are reviewed.
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Affiliation(s)
- Paul J McKiernan
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
| | - Catherine M Greene
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
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231
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Xiao J, Bei Y, Liu J, Dimitrova-Shumkovska J, Kuang D, Zhou Q, Li J, Yang Y, Xiang Y, Wang F, Yang C, Yang W. miR-212 downregulation contributes to the protective effect of exercise against non-alcoholic fatty liver via targeting FGF-21. J Cell Mol Med 2015; 20:204-16. [PMID: 26648452 PMCID: PMC4727558 DOI: 10.1111/jcmm.12733] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/03/2015] [Indexed: 12/17/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is associated with obesity and lifestyle, while exercise is beneficial for NAFLD. Dysregulated microRNAs (miRs) control the pathogenesis of NAFLD. However, whether exercise could prevent NAFLD via targeting microRNA is unknown. In this study, normal or high-fat diet (HF) mice were either subjected to a 16-week running program or kept sedentary. Exercise attenuated liver steatosis in HF mice. MicroRNA array and qRT-PCR demonstrated that miR-212 was overexpressed in HF liver, while reduced by exercise. Next, we investigated the role of miR-212 in lipogenesis using HepG2 cells with/without long-chain fatty acid treatment (± FFA). FFA increased miR-212 in HepG2 cells. Moreover, miR-212 promoted lipogenesis in HepG2 cells (± FFA). Fibroblast growth factor (FGF)-21, a key regulator for lipid metabolism, was negatively regulated by miR-212 at protein level in HepG2 cells. Meanwhile, FFA downregulated FGF-21 both at mRNA and protein levels in HepG2 cells. Also, FGF-21 protein level was reduced in HF liver, while reversed by exercise in vivo. Furthermore, siRNA-FGF-21 abolished the lipogenesis-reducing effect of miR-212 inhibitor in HepG2 cells (± FFA), validating FGF-21 as a target gene of miR-212. These data link the benefit of exercise and miR-212 downregulation in preventing NAFLD via targeting FGF-21.
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Affiliation(s)
- Junjie Xiao
- Regeneration and Ageing Lab, Experimental Center of Life Sciences, School of Life Science, Shanghai University, Shanghai, China.,Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Yihua Bei
- Regeneration and Ageing Lab, Experimental Center of Life Sciences, School of Life Science, Shanghai University, Shanghai, China.,Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jingqi Liu
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jasmina Dimitrova-Shumkovska
- Regeneration and Ageing Lab, Experimental Center of Life Sciences, School of Life Science, Shanghai University, Shanghai, China.,Department of Experimental Biochemistry and Physiology, Faculty of Natural Sciences and Mathematics, University Ss Cyril and Methodius, Skopje, Republic of Macedonia
| | - Dapeng Kuang
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiulian Zhou
- Regeneration and Ageing Lab, Experimental Center of Life Sciences, School of Life Science, Shanghai University, Shanghai, China.,Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jin Li
- Regeneration and Ageing Lab, Experimental Center of Life Sciences, School of Life Science, Shanghai University, Shanghai, China.,Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Yanning Yang
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology and Department of Biochemistry, Nanjing University, Nanjing, China
| | - Fei Wang
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Changqing Yang
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenzhuo Yang
- Division of Gastroenterology and Hepatology, Digestive Disease Institute, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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Mukhadi S, Hull R, Mbita Z, Dlamini Z. The Role of MicroRNAs in Kidney Disease. Noncoding RNA 2015; 1:192-221. [PMID: 29861424 PMCID: PMC5932548 DOI: 10.3390/ncrna1030192] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/28/2015] [Accepted: 11/08/2015] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that regulate pathophysiological processes that suppress gene expression by binding to messenger RNAs. These biomolecules can be used to study gene regulation and protein expression, which will allow better understanding of many biological processes such as cell cycle progression and apoptosis that control the fate of cells. Several pathways have also been implicated to be involved in kidney diseases such as Transforming Growth Factor-β, Mitogen-Activated Protein Kinase signaling, and Wnt signaling pathways. The discovery of miRNAs has provided new insights into kidney pathologies and may provide new innovative and effective therapeutic strategies. Research has demonstrated the role of miRNAs in a variety of kidney diseases including renal cell carcinoma, diabetic nephropathy, nephritic syndrome, renal fibrosis, lupus nephritis and acute pyelonephritis. MiRNAs are implicated as playing a role in these diseases due to their role in apoptosis, cell proliferation, differentiation and development. As miRNAs have been detected in a stable condition in different biological fluids, they have the potential to be tools to study the pathogenesis of human diseases with a great potential to be used in disease prognosis and diagnosis. The purpose of this review is to examine the role of miRNA in kidney disease.
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Affiliation(s)
- Sydwell Mukhadi
- Forensic Science Laboratory, 730 Pretorius street, Arcadia 0083, South Africa.
| | - Rodney Hull
- College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X6, Florida 1709, Johannesburg 1709, South Africa.
| | - Zukile Mbita
- Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Private Bag x1106, Sovenga 0727, South Africa.
| | - Zodwa Dlamini
- Research, Innovation & Engagements Portfolio, Mangosuthu University of Technology, Durban 4031, South Africa.
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233
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Kuschnerus K, Landmesser U, Kränkel N. Vascular repair strategies in type 2 diabetes: novel insights. Cardiovasc Diagn Ther 2015; 5:374-86. [PMID: 26543824 DOI: 10.3978/j.issn.2223-3652.2015.05.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Impaired functions of vascular cells are responsible for the majority of complications in patients with type 2 diabetes (T2D). Recently a better understanding of mechanisms contributing to development of vascular dysfunction and the role of systemic inflammatory activation and functional alterations of several secretory organs, of which adipose tissue has more recently been investigated, has been achieved. Notably, the progression of vascular disease within the context of T2D appears to be driven by a multitude of incremental signaling shifts. Hence, successful therapies need to target several mechanisms in parallel, and over a long time period. This review will summarize the latest molecular strategies and translational developments of cardiovascular therapy in patients with T2D.
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Affiliation(s)
- Kira Kuschnerus
- Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Medizinische Klinik für Kardiologie, Berlin, Germany
| | - Ulf Landmesser
- Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Medizinische Klinik für Kardiologie, Berlin, Germany
| | - Nicolle Kränkel
- Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Medizinische Klinik für Kardiologie, Berlin, Germany
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234
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Ding XQ, Ge PC, Liu Z, Jia H, Chen X, An FH, Li LH, Chen ZH, Mao HW, Li ZY, Gu Y, Zhu TB, Li CJ, Wang LS, Ma WZ, Yang ZJ, Jia EZ. Interaction between microRNA expression and classical risk factors in the risk of coronary heart disease. Sci Rep 2015; 5:14925. [PMID: 26446730 PMCID: PMC4597355 DOI: 10.1038/srep14925] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 09/09/2015] [Indexed: 01/07/2023] Open
Abstract
The aim of this study was to identify the synergistic effect of microRNA expression with classical risk factors of coronary heart disease (CHD) and to explore their diagnostic value for coronary stenotic lesions in subjects with CHD. Plasma samples were obtained from 66 subjects with CHD and from 58 control individuals. A quantitative reverse-transcription PCR (RT-qPCR) assay was conducted to confirm the relative expressions of the known CHD-related miRNAs. The severity of coronary atherosclerosis was based on the Gensini scoring system. The expression of miR-125b in plasma of the CHD group was lower than that of the non-CHD group (0.14 ± 0.09 vs. 0.18 ± 0.10, p = 0.055), and the miR-125b levels significantly decreased following an increasing Gensini score (P = 0.037). Spearman correlation analyses indicated the Gensini score was negatively associated with miR-125b (r = −0.215, p = 0.017). Of all the miRNAs, miR-125b showed the lowest AUC (0.405; 95% CI: 0.305 ~ 0.506, p = 0.070). We found several synergistic effects between miR-125b and classical risk factors, such as age, sex, CR, FBG and HDL-C; the proportion of CHD attributable to the interaction of miR-125b and age was as high as 80%. Therefore, miR-125b was shown to play an important role in individual’s susceptibility to developing CHD.
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Affiliation(s)
- Xiao-Qing Ding
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Peng-Cheng Ge
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Zhe Liu
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Heng Jia
- Kangda school, Nanjing Medical University, Lianyungang 222000, Jiangsu Province, China
| | - Xi Chen
- Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210029, Jiangsu Province, China
| | - Feng-Hui An
- Friendship Hospital of Ili Kazakh Autonomous Prefecture, Yining 835000, Xinjiang, China
| | - Li-Hua Li
- Friendship Hospital of Ili Kazakh Autonomous Prefecture, Yining 835000, Xinjiang, China
| | - Zhao-Hong Chen
- Friendship Hospital of Ili Kazakh Autonomous Prefecture, Yining 835000, Xinjiang, China
| | - Hong-Wei Mao
- Friendship Hospital of Ili Kazakh Autonomous Prefecture, Yining 835000, Xinjiang, China
| | - Zhao-Yang Li
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Yan Gu
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Tie-Bing Zhu
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Chun-Jian Li
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Lian-Sheng Wang
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Wen-Zhu Ma
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Zhi-Jian Yang
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - En-Zhi Jia
- First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
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235
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Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers. Forensic Sci Int Genet 2015; 18:21-32. [DOI: 10.1016/j.fsigen.2014.11.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
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236
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Page A, Mann DA. Epigenetic regulation of liver fibrosis. Clin Res Hepatol Gastroenterol 2015; 39 Suppl 1:S64-8. [PMID: 26189981 DOI: 10.1016/j.clinre.2015.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/10/2015] [Indexed: 02/04/2023]
Abstract
Fibrosis is a common and important pathology associated with progressive chronic liver diseases and underlies the development of cirrhosis and hepatocellular carcinoma. Research into the molecular regulation of fibrosis has discovered that it is under the control of a number of epigenetic mechanisms including DNA methylation, histone modifications and the activities of non-coding RNAs. A deeper understanding of how epigenetic regulators such as DNA methyltranserases, methyl-DNA binding proteins, histone modifying enzymes and regulatory RNA molecules impact on the fibrogenic process is expected to result in new biomarkers for disease progression as well as novel therapeutic targets. The aim of this mini-review is to briefly introduce the reader to the major epigenetic regulators so far identified as being implicated in fibrosis.
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Affiliation(s)
- Agata Page
- Fibrosis Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Derek A Mann
- Fibrosis Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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miRNA-based therapies: strategies and delivery platforms for oligonucleotide and non-oligonucleotide agents. Future Med Chem 2015; 6:1967-84. [PMID: 25495987 DOI: 10.4155/fmc.14.116] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The discovery of miRNAs as important regulatory agents for gene expression has expanded the therapeutic opportunities for oligonucleotides. In contrast to siRNA, miRNA-targeted therapy is able to influence not only a single gene, but entire cellular pathways or processes. It is possible to supplement downregulated or non-functional miRNAs by synthetic oligonucleotides, as well as alleviating effects caused by overexpression of malignant miRNAs through artificial antagonists, either oligonucleotides or small molecules. Chemical oligonucleotide modifications together with an efficient delivery system seem to be mandatory for successful therapeutic application. While miRNA-based therapy benefits from the decades of research spent on other therapeutic oligonucleotides, there are some specific challenges associated with miRNA therapy, mainly caused by the short target sequence. The current status and recent progress of miRNA-targeted therapeutics is described and future challenges and potential applications in treatment of cancer and viral infections are discussed.
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239
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Liu Q, Du GQ, Zhu ZT, Zhang C, Sun XW, Liu JJ, Li X, Wang YS, Du WJ. Identification of apoptosis-related microRNAs and their target genes in myocardial infarction post-transplantation with skeletal myoblasts. J Transl Med 2015; 13:270. [PMID: 26286600 PMCID: PMC4539916 DOI: 10.1186/s12967-015-0603-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 07/10/2015] [Indexed: 11/13/2022] Open
Abstract
Background Skeletal myoblasts (SkMs) has
provided a promising treatment for myocardial infarction (MI). Functioning as posttranscriptional regulators, microRNAs (miRNAs) play important roles in cardiac repairment and stem cell regulation. However, the correlation between miRNAs and their targeted genes in SkM cell therapy for MI was not fully understood. Methods We explored the cardioprotection by SkMs in infracted rats and determined cardiac functions at 4 weeks. In addition, we compared the expression profiles of miRNAs and mRNAs in post-MI rats with or without SkM cell therapy using microarray. The concordance between miRNA expression and mRNA levels of potential target genes was confirmed by quantitative real-time PCR. Results Quantitative echocardiography and histology showed improved cardiac function, attenuated heart infarcted area and inhibited cardiomyocyte apoptosis in the SkM group, compared with MI group. We identified that 160 miRNAs were differentially expressed in MI group as compared to the control group and 78 miRNAs were differentially expressed in the SkM treated group as compared to the untreated post-MI. We focused on a novel set of apoptosis-associated miRNAs and their target genes, among which 4 miRNAs (miR-30a-5p, miR-30c-5p, miR-145-5p, miR-140-3p), except one (miR-143-3p), were downregulated in the SkM treated group as compared to the untreated group. Furthermore, we found seven genes including Angptl4, Dpep1, Egr1, Eif5a, Tsc22d3, Irs2 and Cebpb that showed a linear correlation with which miRNAs. Conclusions The downregulation of apoptosis-regulatory miRNAs and in turn upregulation of target genes may partially account for rescue effect of SKM therapy for MI. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0603-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qi Liu
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Guo Qing Du
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Ultrasound, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Zhi Tao Zhu
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiac Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - ChunYang Zhang
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Xiao Wei Sun
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Jing Jin Liu
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Xia Li
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Yong Shun Wang
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Wen Juan Du
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China. .,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
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M'Baya-Moutoula E, Louvet L, Metzinger-Le Meuth V, Massy ZA, Metzinger L. High inorganic phosphate concentration inhibits osteoclastogenesis by modulating miR-223. Biochim Biophys Acta Mol Basis Dis 2015; 1852:2202-12. [PMID: 26255635 DOI: 10.1016/j.bbadis.2015.08.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/21/2015] [Accepted: 08/05/2015] [Indexed: 01/08/2023]
Abstract
Chronic kidney disease-mineral and bone disorder (CKD-MBD) is a common complication of CKD, and uremic toxins have been shown to be instrumental in this process. We have previously shown that miR-223 is increased in smooth muscle cells subjected to the uremic toxin inorganic phosphate (Pi). In the present study we investigated the influence of this miRNA in osteoclastogenesis in order to elucidate its role in the course of CKD-MBD. RT-qPCR demonstrated that high Pi concentration decreased miR-223 expression in differentiated RAW 264.7 cells. Up- and down-regulation of miR-223 was performed using specific pre-miR and anti-miR-223. Differentiation of monocyte/macrophage precursors was assessed by using RAW 264.7 cells and peripheral blood mononuclear cells (PBMC). TRAP activity and bone resorption were used to measure osteoclast activity. Pi induced a marked decrease in osteoclastogenesis in RAW cells and miR-223 levels were concomitantly decreased. Anti-miR-223 treatment inhibited osteoclastogenesis in the same way as Pi. In contrast, overexpression of miR-223 triggered differentiation, as reflected by TRAP activity. We showed that miR-223 affected the expression of its target genes NFIA and RhoB, but also osteoclast marker genes and the Akt signalling pathway, which induces osteoclastogenesis. These results were confirmed by measuring bone resorption activity of human PBMC differentiated into osteoclasts. We thus demonstrate a role of miR-223 in osteoclast differentiation, with rational grounds to use deregulation of this miRNA to selectively increase osteoclast-like activity in calcified vessels of CKD-MBD. This approach could alleviate vascular calcification without altering bone structure.
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Affiliation(s)
| | - Loïc Louvet
- INSERM U1088, CURS, CHU Amiens Sud, Avenue René Laënnec, Salouel, F-80054 Amiens, France
| | - Valérie Metzinger-Le Meuth
- INSERM U1088, CURS, CHU Amiens Sud, Avenue René Laënnec, Salouel, F-80054 Amiens, France; University Paris 13, UFR SMBH, 74 rue Marcel Cachin, F-93017 Bobigny, France
| | - Ziad A Massy
- INSERM U1088, CURS, CHU Amiens Sud, Avenue René Laënnec, Salouel, F-80054 Amiens, France; Division of Nephrology, Ambroise Paré Hospital, Paris Ile de France Ouest (UVSQ) University, 09 Avenue Charles de Gaulle 92100 Boulogne Billancourt Cedex, France
| | - Laurent Metzinger
- INSERM U1088, CURS, CHU Amiens Sud, Avenue René Laënnec, Salouel, F-80054 Amiens, France; Centre De Biologie Humaine (CBH), Amiens University Hospital, F-80054 Amiens, France.
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Zhao X, Wang K, Hu F, Qian C, Guan H, Feng K, Zhou Y, Chen Z. MicroRNA-101 protects cardiac fibroblasts from hypoxia-induced apoptosis via inhibition of the TGF-β signaling pathway. Int J Biochem Cell Biol 2015; 65:155-64. [DOI: 10.1016/j.biocel.2015.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/26/2015] [Accepted: 06/04/2015] [Indexed: 12/12/2022]
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Henrici A, Montalbano R, Neureiter D, Krause M, Stiewe T, Slater EP, Quint K, Ocker M, Di Fazio P. The pan-deacetylase inhibitor panobinostat suppresses the expression of oncogenic miRNAs in hepatocellular carcinoma cell lines. Mol Carcinog 2015; 54:585-97. [PMID: 24375802 DOI: 10.1002/mc.22122] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/18/2013] [Accepted: 11/26/2013] [Indexed: 02/05/2023]
Abstract
Deacetylase inhibitors (DACi) are a new class of drugs with a broad spectrum of mechanisms that favor their application in cancer therapy. Currently, the exact mechanisms and cellular effects of DACi have not been fully elucidated. In addition to their effects on histone acetylation, DACi can interfere with gene expression via miRNA pathways. Treatment with panobinostat (LBH589), a novel potent DACi, led to the highly aberrant modulation of several miRNAs in hepatocellular carcinoma (HCC) cell lines as shown by miRNA array analysis. Among them, hsa-miR-19a, hsa-miR-19b1 and the corresponding precursors were down-regulated by panobinostat in TP53(-/-) Hep3B and TP53(+/+) HepG2 cell lines; hsa-miR30a-5p mature form only was suppressed in both HCC cell lines, as confirmed by further RT-qPCR analysis. In HCC cell lines, panobinostat caused the upregulation of the predicted miRNA targets APAF1 and Beclin1 protein levels. Transfection with oligonucleotides mimicking these miRNAs led to an increase in the viability rate of both cell lines as analyzed by impedance-based real-time cell analysis. In addition, transfecting miRNA mimicking oligonucleotides resulted in the decrease of APAF1, Beclin1 and PAK6 at the protein level, proving the regulating influence of the investigated miRNAs on gene final products. The overexpression of the above mentioned oncomiRs in Hep3B and HepG2 cell lines leads to cell proliferation and downregulation of cell death associated proteins. In our model, panobinostat exerts its anti-cancer effect by suppressing these miRNAs and restoring the expression of their corresponding tumor suppressor targets.
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Affiliation(s)
- Alexander Henrici
- Institute for Surgical Research, Philipps University of Marburg, Marburg, Germany
| | - Roberta Montalbano
- Institute for Surgical Research, Philipps University of Marburg, Marburg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University of Marburg, Marburg, Germany
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Private Medical University, Salzburg, Austria
| | - Michael Krause
- Institute of Molecular Biology and Tumor Research, Philipps University of Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Biology and Tumor Research, Philipps University of Marburg, Marburg, Germany
| | - Emily Prentice Slater
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University of Marburg, Marburg, Germany
| | - Karl Quint
- Institute for Surgical Research, Philipps University of Marburg, Marburg, Germany
| | - Matthias Ocker
- Institute for Surgical Research, Philipps University of Marburg, Marburg, Germany
| | - Pietro Di Fazio
- Institute for Surgical Research, Philipps University of Marburg, Marburg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University of Marburg, Marburg, Germany
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Angelini TG, Emanueli C. MicroRNAs as clinical biomarkers? Front Genet 2015; 6:240. [PMID: 26236333 PMCID: PMC4500989 DOI: 10.3389/fgene.2015.00240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/29/2015] [Indexed: 12/28/2022] Open
Affiliation(s)
| | - Costanza Emanueli
- Bristol Heart Institute, School of Clinical Sciences, University of Bristol Bristol, UK ; National Heart and Lung Institute, Imperial College London London, UK
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Kurakula K, Goumans MJ, Ten Dijke P. Regulatory RNAs controlling vascular (dys)function by affecting TGF-ß family signalling. EXCLI JOURNAL 2015; 14:832-50. [PMID: 26862319 PMCID: PMC4743484 DOI: 10.17179/excli2015-423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 06/30/2015] [Indexed: 01/15/2023]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide. Over the last few years, microRNAs (miRNAs) have emerged as master regulators of gene expression in cardiovascular biology and disease. miRNAs are small endogenous non-coding RNAs that usually bind to 3′ untranslated region (UTR) of their target mRNAs and inhibit mRNA stability or translation of their target genes. miRNAs play a dynamic role in the pathophysiology of many CVDs through their effects on target mRNAs in vascular cells. Recently, numerous miRNAs have been implicated in the regulation of the transforming growth factor-β (TGF-β)/bone morphogenetic protein (BMP) signalling pathway which plays crucial roles in diverse biological processes, and is involved in pathogenesis of many diseases including CVD. This review gives an overview of current literature on the role of miRNAs targeting TGF-β/BMP signalling in vascular cells, including endothelial cells and smooth muscle cells. We also provide insight into how this miRNA-mediated regulation of TGF-β/BMP signalling might be used to harness CVD.
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Affiliation(s)
- Kondababu Kurakula
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie-Jose Goumans
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Ten Dijke
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
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Potus F, Ruffenach G, Dahou A, Thebault C, Breuils-Bonnet S, Tremblay È, Nadeau V, Paradis R, Graydon C, Wong R, Johnson I, Paulin R, Lajoie AC, Perron J, Charbonneau E, Joubert P, Pibarot P, Michelakis ED, Provencher S, Bonnet S. Downregulation of MicroRNA-126 Contributes to the Failing Right Ventricle in Pulmonary Arterial Hypertension. Circulation 2015; 132:932-43. [PMID: 26162916 DOI: 10.1161/circulationaha.115.016382] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 07/06/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Right ventricular (RV) failure is the most important factor of both morbidity and mortality in pulmonary arterial hypertension (PAH). However, the underlying mechanisms resulting in the failed RV in PAH remain unknown. There is growing evidence that angiogenesis and microRNAs are involved in PAH-associated RV failure. We hypothesized that microRNA-126 (miR-126) downregulation decreases microvessel density and promotes the transition from a compensated to a decompensated RV in PAH. METHODS AND RESULTS We studied RV free wall tissues from humans with normal RV (n=17), those with compensated RV hypertrophy (n=8), and patients with PAH with decompensated RV failure (n=14). Compared with RV tissues from patients with compensated RV hypertrophy, patients with decompensated RV failure had decreased miR-126 expression (quantitative reverse transcription-polymerase chain reaction; P<0.01) and capillary density (CD31(+) immunofluorescence; P<0.001), whereas left ventricular tissues were not affected. miR-126 downregulation was associated with increased Sprouty-related EVH1 domain-containing protein 1 (SPRED-1), leading to decreased activation of RAF (phosphorylated RAF/RAF) and mitogen-activated protein kinase (MAPK); (phosphorylated MAPK/MAPK), thus inhibiting the vascular endothelial growth factor pathway. In vitro, Matrigel assay showed that miR-126 upregulation increased angiogenesis of primary cultured endothelial cells from patients with decompensated RV failure. Furthermore, in vivo miR-126 upregulation (mimic intravenous injection) improved cardiac vascular density and function of monocrotaline-induced PAH animals. CONCLUSIONS RV failure in PAH is associated with a specific molecular signature within the RV, contributing to a decrease in RV vascular density and promoting the progression to RV failure. More importantly, miR-126 upregulation in the RV improves microvessel density and RV function in experimental PAH.
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Affiliation(s)
- François Potus
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Grégoire Ruffenach
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Abdellaziz Dahou
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Christophe Thebault
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Sandra Breuils-Bonnet
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Ève Tremblay
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Valérie Nadeau
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Renée Paradis
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Colin Graydon
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Ryan Wong
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Ian Johnson
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Roxane Paulin
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Annie C Lajoie
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Jean Perron
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Eric Charbonneau
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Philippe Joubert
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Philippe Pibarot
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Evangelos D Michelakis
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.)
| | - Steeve Provencher
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.).
| | - Sébastien Bonnet
- From Pulmonary Hypertension Research Group of the Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University, Quebec City, QC, Canada (F.P., G.R., A.D., C.T., S.B.-B., E.T., V.N., R. Paradis, C.G., R.W., I.J., A.C.L., J.P., E.C., P.J., P.P., S.P., S.B.); and Vascular Biology Research Group, Department of Medicine, University of Alberta, Edmonton, AB, Canada (R. Paulin, E.D.M.).
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Hubé F, Francastel C. "Pocket-sized RNA-Seq": A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest. Noncoding RNA 2015; 1:127-138. [PMID: 29861419 PMCID: PMC5932543 DOI: 10.3390/ncrna1020127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/03/2015] [Accepted: 06/23/2015] [Indexed: 12/28/2022] Open
Abstract
Currently, the discovery of new small ncRNAs requires high throughput methods even in the case of focused research on the regulation of specific genes or set of genes. We propose herein a simple, rapid, efficient, and cost effective method to clone and sequence single, yet unknown, small ncRNA. This technique that we called “Pocket-sized RNA-Seq” or psRNA-seq is based on in vitro transcription, RNA pull down and adapted RACE-PCR methods that allow its implementation using either available commercial kits or in-house reagents.
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Affiliation(s)
- Florent Hubé
- University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France.
- Epigénétique et Destin Cellulaire, CNRS UMR 7216, 75013 Paris, France.
| | - Claire Francastel
- University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France.
- Epigénétique et Destin Cellulaire, CNRS UMR 7216, 75013 Paris, France.
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Miller KJ, Brown DA, Ibrahim MM, Ramchal TD, Levinson H. MicroRNAs in skin tissue engineering. Adv Drug Deliv Rev 2015; 88:16-36. [PMID: 25953499 DOI: 10.1016/j.addr.2015.04.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 04/04/2015] [Accepted: 04/25/2015] [Indexed: 01/08/2023]
Abstract
35.2 million annual cases in the U.S. require clinical intervention for major skin loss. To meet this demand, the field of skin tissue engineering has grown rapidly over the past 40 years. Traditionally, skin tissue engineering relies on the "cell-scaffold-signal" approach, whereby isolated cells are formulated into a three-dimensional substrate matrix, or scaffold, and exposed to the proper molecular, physical, and/or electrical signals to encourage growth and differentiation. However, clinically available bioengineered skin equivalents (BSEs) suffer from a number of drawbacks, including time required to generate autologous BSEs, poor allogeneic BSE survival, and physical limitations such as mass transfer issues. Additionally, different types of skin wounds require different BSE designs. MicroRNA has recently emerged as a new and exciting field of RNA interference that can overcome the barriers of BSE design. MicroRNA can regulate cellular behavior, change the bioactive milieu of the skin, and be delivered to skin tissue in a number of ways. While it is still in its infancy, the use of microRNAs in skin tissue engineering offers the opportunity to both enhance and expand a field for which there is still a vast unmet clinical need. Here we give a review of skin tissue engineering, focusing on the important cellular processes, bioactive mediators, and scaffolds. We further discuss potential microRNA targets for each individual component, and we conclude with possible future applications.
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Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C. Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing. BMC Med Genomics 2015; 8:35. [PMID: 26130076 PMCID: PMC4487992 DOI: 10.1186/s12920-015-0109-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/16/2015] [Indexed: 02/08/2023] Open
Abstract
Background Small ncRNAs (sncRNAs) offer great hope as biomarkers of disease and response to treatment. This has been highlighted in the context of several medical conditions such as cancer, liver disease, cardiovascular disease, and central nervous system disorders, among many others. Here we assessed several steps involved in the development of an ncRNA biomarker discovery pipeline, ranging from sample preparation to bioinformatic processing of small RNA sequencing data. Methods A total of 45 biological samples were included in the present study. All libraries were prepared using the Illumina TruSeq Small RNA protocol and sequenced using the HiSeq2500 or MiSeq Illumina sequencers. Small RNA sequencing data was validated using qRT-PCR. At each stage, we evaluated the pros and cons of different techniques that may be suitable for different experimental designs. Evaluation methods included quality of data output in relation to hands-on laboratory time, cost, and efficiency of processing. Results Our results show that good quality sequencing libraries can be prepared from small amounts of total RNA and that varying degradation levels in the samples do not have a significant effect on the overall quantification of sncRNAs via NGS. In addition, we describe the strengths and limitations of three commercially available library preparation methods: (1) Novex TBE PAGE gel; (2) Pippin Prep automated gel system; and (3) AMPure XP beads. We describe our bioinformatics pipeline, provide recommendations for sequencing coverage, and describe in detail the expression and distribution of all sncRNAs in four human tissues: whole-blood, brain, heart and liver. Conclusions Ultimately this study provides tools and outcome metrics that will aid researchers and clinicians in choosing an appropriate and effective high-throughput sequencing quantification method for various study designs, and overall generating valuable information that can contribute to our understanding of small ncRNAs as potential biomarkers and mediators of biological functions and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0109-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Pablo Lopez
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Alpha Diallo
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada.
| | - Cristiana Cruceanu
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Laura M Fiori
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada.
| | - Sylvie Laboissiere
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Isabelle Guillet
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Joelle Fontaine
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany.
| | - Gustavo Turecki
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Carl Ernst
- McGill Group for Suicide Studies (MGSS), Douglas Mental Health University Institute, McGill University, Frank B Common Pavilion, Room F-2101.2, 6875 LaSalle Boulevard, Montreal, QC, H4H 1R3, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada.
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Hwang CK, Wagley Y, Law PY, Wei LN, Loh HH. Analysis of epigenetic mechanisms regulating opioid receptor gene transcription. Methods Mol Biol 2015; 1230:39-51. [PMID: 25293314 DOI: 10.1007/978-1-4939-1708-2_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Opioid drugs are generally used for moderate and severe pain reductions which act through opioid receptors. Studies on transcriptional regulation of opioid receptors are still invaluable because not only transcription is the first step to produce protein products in cells, but the receptor transcription levels also affect the pain reduction by opioids, as observed in studies of heterozygous opioid receptor knockout mice.There are growing evidences that epigenetic regulation has played significant roles in transcriptional regulation of genes, including opioid receptors. In general, epigenetic mechanisms include three main regulatory factors: DNA methylation, chromatin modification, and noncoding RNAs (such as microRNA). From previous studies of ours and others on opioid receptors, those epigenetic factors were clearly involved in regulating opioid receptor expression in vivo and in vitro. In this chapter, among those three techniques we describe more details of DNA methylation methods because of emerging concepts of DNA methylation with the recent discovery of 5-hydroxymethylcytosine converting enzyme, TET1. Another analytical method of the epigenetic factors, chromatin modification, will be described briefly and information of analyzing noncoding RNAs is briefly mentioned in Subheading 1.
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Affiliation(s)
- Cheol Kyu Hwang
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church St. SE, Minneapolis, MN, 55455, USA,
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