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Häntzsch M, Tolios A, Beutner F, Nagel D, Thiery J, Teupser D, Holdt LM. Comparison of whole blood RNA preservation tubes and novel generation RNA extraction kits for analysis of mRNA and MiRNA profiles. PLoS One 2014; 9:e113298. [PMID: 25469788 PMCID: PMC4254602 DOI: 10.1371/journal.pone.0113298] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022] Open
Abstract
Background Whole blood expression profiling is frequently performed using PAXgene (Qiagen) or Tempus (Life Technologies) tubes. Here, we compare 6 novel generation RNA isolation protocols with respect to RNA quantity, quality and recovery of mRNA and miRNA. Methods 3 PAXgene and 3 Tempus Tubes were collected from participants of the LIFE study with (n = 12) and without (n = 35) acute myocardial infarction (AMI). RNA was extracted with 4 manual protocols from Qiagen (PAXgene Blood miRNA Kit), Life Technologies (MagMAX for Stabilized Blood Tubes RNA Isolation Kit), and Norgen Biotek (Norgen Preserved Blood RNA Purification Kit I and Kit II), and 2 (semi-)automated protocols on the QIAsymphony (Qiagen) and MagMAX Express-96 Magnetic Particle Processor (Life Technologies). RNA quantity and quality was determined. For biological validation, RNA from 12 representative probands, extracted with all 6 kits (n = 72), was reverse transcribed and mRNAs (matrix metalloproteinase 9, arginase 1) and miRNAs (miR133a, miR1), shown to be altered by AMI, were analyzed. Results RNA yields were highest using the Norgen Kit I with Tempus Tubes and lowest using the Norgen Kit II with PAXgene. The disease status was the second major determinant of RNA yields (LIFE-AMI 11.2 vs. LIFE 6.7 µg, p<0.001) followed by the choice of blood collection tube. (Semi-)automation reduced overall RNA extraction time but did not generally reduce hands-on-time. RNA yields and quality were comparable between manual and automated extraction protocols. mRNA expression was not affected by collection tubes and RNA extraction kits but by RT/qPCR reagents with exception of the Norgen Kit II, which led to mRNA depletion. For miRNAs, expression differences related to collection tubes (miR30b), RNA isolation (Norgen Kit II), and RT/qRT reagents (miR133a) were observed. Conclusion We demonstrate that novel generation RNA isolation kits significantly differed with respect to RNA recovery and affected miRNA but not mRNA expression profiles.
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Affiliation(s)
- Madlen Häntzsch
- LIFE – Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Alexander Tolios
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Frank Beutner
- LIFE – Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Department of Cardiology, Heart Center, University Leipzig, Leipzig, Germany
| | - Dorothea Nagel
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Joachim Thiery
- LIFE – Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Daniel Teupser
- LIFE – Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lesca M. Holdt
- LIFE – Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
- * E-mail:
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Up-regulation of brain-enriched miR-107 promotes excitatory neurotoxicity through down-regulation of glutamate transporter-1 expression following ischaemic stroke. Clin Sci (Lond) 2014; 127:679-89. [PMID: 24943094 DOI: 10.1042/cs20140084] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent studies have uncovered that accumulation of glutamate after ischaemic stroke is closely associated with the down-regulation of glutamate transporter-1 (GLT-1) expression, suggesting that GLT-1 expression critically controls glutamate accumulation and the abnormal glutamate transport-elicited neuronal cell excitotoxicity in patients with ischaemic stroke. However, it remains unknown how GLT-1 expression is regulated under ischaemic stroke conditions. In the present study, we screened the expression of nine brain-specific or brain-enriched miRNAs in a focal cerebral ischaemia/reperfusion (I/R) injury rat model, which showed glutamate accumulation and down-regulated GLT-1 expression as expected, and revealed that the miR-107 level was elevated in both brain tissue and plasma in the model. Next, we examined the functional relationship of miR-107 with GLT-1 expression in a nerve cell hypoxia/reoxygenation (H/R) injury model. H/R treatment increased apoptosis of the nerve cells concomitant with glutamate accumulation, miR-107 elevation and suppressed GLT-1 expression, mimicking our in vivo findings in the cerebral I/R injury rat model in vitro. Co-treating the cells with an miR-107 inhibitor blocked all of the effects, demonstrating that miR-107 functions to inhibit GLT-1 expression and elevate glutamate accumulation. To extend these animal and cell-based studies to clinical patients, we measured the plasma levels of miR-107 and glutamate, and observed that both miR-107 and glutamate were elevated in patients with ischaemic stroke. On the basis of these observations, we conclude that elevated miR-107 expression after ischaemic stroke accounts, at least partially, for glutamate accumulation through suppression of GLT-1 expression. Our findings also highlight that the plasma level of miR-107 may serve as a novel biomarker for monitoring excitotoxicity in patients with ischaemic stroke.
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Li J, Dong X, Wang Z, Wu J. MicroRNA-1 in Cardiac Diseases and Cancers. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2014; 18:359-63. [PMID: 25352753 PMCID: PMC4211117 DOI: 10.4196/kjpp.2014.18.5.359] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/17/2014] [Accepted: 08/09/2014] [Indexed: 11/15/2022]
Abstract
MicroRNAs (miRs) are endogenous ≈22-nt non-coding RNAs that participate in the regulation of gene expression at post-transcriptional level. MiR-1 is one of the muscle-specific miRs, aberrant expression of miR-1 plays important roles in many physiological and pathological processes. In this review, we focus on the recent studies about miR-1 in cardiac diseases and cancers. The findings indicate that miR-1 may be a novel, important biomarker, and a potential therapeutic target in cardiac diseases and cancers.
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Affiliation(s)
- Jianzhe Li
- Department of Pharmacy, Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi 530011, China
| | - Xiaomin Dong
- Department of Osteology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Zhongping Wang
- Department of Physiology and pathophysiology, school of Basic Medical Sciences, Jiujiang University, Jiujiang, Jiangxi 332000, China
| | - Jianhua Wu
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
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Balakathiresan NS, Chandran R, Bhomia M, Jia M, Li H, Maheshwari RK. Serum and amygdala microRNA signatures of posttraumatic stress: fear correlation and biomarker potential. J Psychiatr Res 2014; 57:65-73. [PMID: 24998397 DOI: 10.1016/j.jpsychires.2014.05.020] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/21/2014] [Accepted: 05/29/2014] [Indexed: 12/11/2022]
Abstract
Exposure to acute traumatic stress can cause permanent changes in neurological circuitry and may lead to the development of an anxiety disorder known as posttraumatic stress disorder (PTSD). Current diagnosis of PTSD is based on clinical or behavioral symptom assessment, however, these are not definitive due to overlapping symptoms with other psychiatric disorders or mild traumatic brain injury (mTBI). No FDA approved diagnostic tests or biomarkers are currently available for diagnosis of PTSD. Recently, circulating miRNAs have emerged as novel biomarkers of many diseases. In this study, we have examined the altered expression of serum and amygdala miRNAs in an animal model of PTSD. Differentially expressed and statistically significant miRNAs in serum were validated for their presence in amygdala of corresponding animals. A panel of nine stress-responsive miRNAs viz., miR-142-5p, miR-19b, miR-1928, miR-223-3p, miR-322∗, miR-324, miR-421-3p and miR-463∗ and miR-674∗ were identified, and may have potential as biomarker(s) for PTSD. Further validations by bioinformatics and system biology approaches indicate that five miRNAs such as miR-142-5p, miR-19b, miR-1928, miR-223 and miR-421-3p may play a potential role in the regulation of genes associated with delayed and exaggerated fear. To the best of our knowledge, this is the first report demonstrating the plausibility of using circulating miRNAs as biomarkers of PTSD.
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Affiliation(s)
- Nagaraja S Balakathiresan
- Department of Pathology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Raghavendar Chandran
- Department of Pathology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA; Biological Sciences Group, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Manish Bhomia
- Department of Pathology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Min Jia
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - He Li
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Radha K Maheshwari
- Department of Pathology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA.
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High association between human circulating microRNA-497 and acute myocardial infarction. ScientificWorldJournal 2014; 2014:931845. [PMID: 25110754 PMCID: PMC4119682 DOI: 10.1155/2014/931845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/19/2014] [Indexed: 12/27/2022] Open
Abstract
Recent papers have reported the fundamental roles of miR-497 in infarction which acute myocardial infarction (AMI) belongs to. However, the expression levels of miR-497 in AMI patients were unclear, especially the circulating miR-497 that was detectable in the human plasma. In this study, we focused on the expression levels of circulating miR-497 in AMI and the roles of plasma miR-497 as a promising biomarker for AMI. The plasma miR-497 levels were detected from 27 AMI patients and 31 healthy volunteers by qRT-PCR. The cTnI concentrations of these samples were also analyzed by ELISA. Results showed circulating miR-497 levels were upregulated in AMI patients at 4 h, 8 h, 12 h, and 24 h, by contrast to those in control. Interestingly, time courses of circulating miR-497 levels displayed similar trends to that of cTnI concentrations in AMI patients; further study revealed the high correlation between circulating miR-497 and cTnI concentrations (r = 0.573, P < 0.001). At last, the receiver operating characteristic (ROC) curve was performed and declared that there was a faithworthy sensitivity and specificity to identify the AMI patients by using circulating miR-497. In conclusion, circulating miR-497 might be a promising biomarker for AMI identification and there was high association between human miR-497 and acute myocardial infarction.
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Meder B, Backes C, Haas J, Leidinger P, Stähler C, Großmann T, Vogel B, Frese K, Giannitsis E, Katus HA, Meese E, Keller A. Influence of the confounding factors age and sex on microRNA profiles from peripheral blood. Clin Chem 2014; 60:1200-8. [PMID: 24987111 DOI: 10.1373/clinchem.2014.224238] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) measured from blood samples are promising minimally invasive biomarker candidates that have been extensively studied in several case-control studies. However, the influence of age and sex as confounding variables remains largely unknown. METHODS We systematically explored the impact of age and sex on miRNAs in a cohort of 109 physiologically unaffected individuals whose blood was characterized by microarray technology (stage 1). We also investigated an independent cohort from a different institution consisting of 58 physiologically unaffected individuals having a similar mean age but with a smaller age distribution. These samples were measured by use of high-throughput sequencing (stage 2). RESULTS We detected 318 miRNAs that were significantly correlated with age in stage 1 and, after adjustment for multiple testing of 35 miRNAs, remained statistically significant. Regarding sex, 144 miRNAs showed significant dysregulation. Here, no miRNA remained significant after adjustment for multiple testing. In the high-throughput datasets of stage 2, we generally observed a smaller number of significant associations, mainly as an effect of the smaller cohort size and age distribution. Nevertheless, we found 7 miRNAs that were correlated with age, of which 5 were concordant with stage 1. CONCLUSIONS The age distribution of individuals recruited for case-control studies needs to be carefully considered, whereas sex may be less confounding. To support the translation of miRNAs into clinical application, we offer a web-based application (http://www.ccb.uni-saarland.de/mirnacon) to test individual miRNAs or miRNA signatures for their likelihood of being influenced.
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Affiliation(s)
- Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany; Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Christina Backes
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Petra Leidinger
- Department of Human Genetics, Saarland University, Homburg, Germany
| | | | - Thomas Großmann
- Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
| | - Britta Vogel
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Karen Frese
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Evangelos Giannitsis
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany; Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrucken, Germany.
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Hu YW, Hu YR, Zhao JY, Li SF, Ma X, Wu SG, Lu JB, Qiu YR, Sha YH, Wang YC, Gao JJ, Zheng L, Wang Q. An agomir of miR-144-3p accelerates plaque formation through impairing reverse cholesterol transport and promoting pro-inflammatory cytokine production. PLoS One 2014; 9:e94997. [PMID: 24733347 PMCID: PMC3986368 DOI: 10.1371/journal.pone.0094997] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/20/2014] [Indexed: 12/13/2022] Open
Abstract
Aims ATP-binding cassette transporter A1 (ABCA1) mediates the efflux of cholesterol and phospholipids to lipid-poor apolipoproteins, which then form nascent HDL, a key step in the mechanism of reverse cholesterol transport (RCT). While a series of microRNAs (miRNAs) have been identified as potent post-transcriptional regulators of lipid metabolism, their effects on ABCA1 function and associated mechanisms remain unclear. Methods and Results ABCA1 was identified as a potential target of miR-144-3p, based on the results of bioinformatic analysis and the luciferase reporter assay, and downregulated after transfection of cells with miR-144-3p mimics, as observed with real-time PCR and western blot. Moreover, miR-144-3p mimics (agomir) enhanced the expression of inflammatory factors, including IL-1β, IL-6 and TNF-α, in vivo and in vitro, inhibited cholesterol efflux in THP-1 macrophage-derived foam cells, decreased HDL-C circulation and impaired RCT in vivo, resulting in accelerated pathological progression of atherosclerosis in apoE−/− mice. Clinical studies additionally revealed a positive correlation of circulating miR-144-3p with serum CK, CK-MB, LDH and AST in subjects with AMI. Conclusions Our findings clearly indicate that miR-144-3p is essential for the regulation of cholesterol homeostasis and inflammatory reactions, supporting its utility as a potential therapeutic target of atherosclerosis and a promising diagnostic biomarker of AMI.
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Affiliation(s)
- Yan-Wei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ya-Rong Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Yi Zhao
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shu-Fen Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xin Ma
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shao-Guo Wu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jing-Bo Lu
- Department of Vascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Rong Qiu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-Hua Sha
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-Chao Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ji-Juan Gao
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lei Zheng
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- * E-mail: (QW); (LZ)
| | - Qian Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- * E-mail: (QW); (LZ)
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Comprehensive characterization of serum microRNA profile in response to the emerging avian influenza A (H7N9) virus infection in humans. Viruses 2014; 6:1525-39. [PMID: 24699363 PMCID: PMC4014708 DOI: 10.3390/v6041525] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/13/2014] [Accepted: 03/18/2014] [Indexed: 12/20/2022] Open
Abstract
A novel avian-origin influenza A (H7N9) virus recently occurred in China and caused 137 human infection cases with a 32.8% mortality rate. Although various detection procedures have been developed, the pathogenesis of this emerging virus in humans remains largely unknown. In this study, we characterized serum microRNA (miRNA) profile in response to H7N9 virus infection using TaqMan Low Density Arrays. Upon infection, a total of 395 miRNAs were expressed in the serum pool of patients, far beyond the 221 in healthy controls. Among the 187 commonly expressed miRNAs, 146 were up-regulated and only 7 down-regulated in patients. Further analysis by quantitative RT-PCR revealed that the serum levels of miR-17, miR-20a, miR-106a and miR-376c were significantly elevated in patients compared with healthy individuals (p< 0.05). Receiver operating characteristic (ROC) curves were constructed to show that each miRNA could discriminate H7N9 patients from controls with area under the curve (AUC) values ranging from 0.622 to 0.898, whereas a combination of miR-17, miR-20a, miR-106a and miR-376c obtained a higher discriminating ability with an AUC value of 0.96. Our findings unravel the significant alterations in serum miRNA expression following virus infection and manifest great potential of circulating miRNAs for the diagnosis of viral diseases.
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