151
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Yu T, Tang C, Zhang Y, Zhang R, Yan W. Microfluidics-based digital quantitative PCR for single-cell small RNA quantification. Biol Reprod 2018; 97:490-496. [PMID: 29024970 DOI: 10.1093/biolre/iox102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/29/2017] [Indexed: 01/02/2023] Open
Abstract
Quantitative analyses of small RNAs at the single-cell level have been challenging because of limited sensitivity and specificity of conventional real-time quantitative PCR methods. A digital quantitative PCR (dqPCR) method for miRNA quantification has been developed, but it requires the use of proprietary stem-loop primers and only applies to miRNA quantification. Here, we report a microfluidics-based dqPCR (mdqPCR) method, which takes advantage of the Fluidigm BioMark HD system for both template partition and the subsequent high-throughput dqPCR. Our mdqPCR method demonstrated excellent sensitivity and reproducibility suitable for quantitative analyses of not only miRNAs but also all other small RNA species at the single-cell level. Using this method, we discovered that each sperm has a unique miRNA profile.
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Affiliation(s)
- Tian Yu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Chong Tang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Ying Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Ruirui Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.,Department of Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
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152
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Role of MicroRNAs in Renal Parenchymal Diseases-A New Dimension. Int J Mol Sci 2018; 19:ijms19061797. [PMID: 29914215 PMCID: PMC6032378 DOI: 10.3390/ijms19061797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 11/18/2022] Open
Abstract
Since their discovery in 1993, numerous microRNAs (miRNAs) have been identified in humans and other eukaryotic organisms, and their role as key regulators of gene expression is still being elucidated. It is now known that miRNAs not only play a central role in the processes that ensure normal development and physiology, but they are often dysregulated in various diseases. In this review, we present an overview of the role of miRNAs in normal renal development and physiology, in maladaptive renal repair after injury, and in the pathogenesis of renal parenchymal diseases. In addition, we describe methods used for their detection and their potential as therapeutic targets. Continued research on renal miRNAs will undoubtedly improve our understanding of diseases affecting the kidneys and may also lead to new therapeutic agents.
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153
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de Ronde MWJ, Ruijter JM, Moerland PD, Creemers EE, Pinto-Sietsma SJ. Study Design and qPCR Data Analysis Guidelines for Reliable Circulating miRNA Biomarker Experiments: A Review. Clin Chem 2018; 64:1308-1318. [PMID: 29903876 DOI: 10.1373/clinchem.2017.285288] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/08/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND In the past decade, the search for circulating microRNA (miRNA) biomarkers has yielded numerous associations between miRNAs and different types of disease. However, many of these relations could not be replicated in subsequent studies under similar experimental conditions. Although this lack of replicability may be explained by the variation in experimental design and analysis methods, guidelines on the most appropriate design and analysis methods to study circulating miRNAs are scarce. CONTENT miRNA biomarker experiments generally consist of a discovery phase and a validation phase. In the discovery phase, typically hundreds of miRNAs are measured in parallel to identify candidate biomarkers. Because of the costs of such high-throughput experiments, the number of individuals included in those studies is often too small, which can easily lead to false positives and false negatives. In the validation phase, a small number of identified biomarker candidates are measured in a large cohort of cases and controls, generally by quantitative PCR (qPCR). Although qPCR is a sensitive method to measure miRNAs in the circulation, experimental design and qPCR data analysis remain challenging. Omitting some crucial steps in the design and analysis of the qPCR experiment or performing them incorrectly can cause serious biases, ultimately leading to false conclusions. SUMMARY In this review, we aim to expose and discuss the most common sources of interstudy variation in miRNA research from a methodological point of view and to provide guidelines on how to perform these steps correctly to increase replicability of studies on circulating miRNAs.
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Affiliation(s)
- Maurice W J de Ronde
- Departments of Vascular Medicine.,Clinical Epidemiology, Biostatistics and Bioinformatics
| | | | | | - Esther E Creemers
- Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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154
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Pedersen NJ, Jensen DH, Lelkaitis G, Kiss K, Charabi BW, Ullum H, Specht L, Schmidt AY, Nielsen FC, von Buchwald C. MicroRNA-based classifiers for diagnosis of oral cavity squamous cell carcinoma in tissue and plasma. Oral Oncol 2018; 83:46-52. [PMID: 30098778 DOI: 10.1016/j.oraloncology.2018.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 04/27/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) hold promise as diagnostic cancer biomarkers. Here we aimed to define the miRNome in oral squamous cell carcinoma (OSCC) and normal oral mucosa (NOM), and to identify and validate new diagnostic miRNAs and miRNA combinations in formalin-fixed paraffin-embedded (FFPE) tissue samples and plasma samples. METHODS We performed next-generation miRNA sequencing in FFPE tissue samples of OSCC (n = 80) and NOM (n = 8). Our findings were validated by quantitative polymerase chain reaction (qPCR) analysis of OSCC (n = 195) and NOM (n = 103) FFPE tissue samples, and plasma samples from OSCC patients (n = 55) and healthy persons (n = 18). RESULTS The OSCC miRNome included 567 miRNAs, 66 of which were differentially expressed between OSCC and NOM. Using qPCR data, we constructed receiver operating curves to classify patients as NOM or OSCC based on miRNA combinations. The area under the curve was of 0.92 from FFPE tissue (miR-204-5p, miR-370, miR-1307, miR-193b-3p, and miR-144-5p), and 1.0 from plasma samples (miR-30a-5p and miR-769-5p). Model calibration and discrimination were evaluated using 10-fold cross-validation. CONCLUSIONS Analysis of the miRNome from many OSCC cases improves our knowledge of the importance of individual miRNAs and their predictive potential in OSCC. We successfully identified miRNA classifiers in FFPE OSCC tissue and plasma with a high discriminatory ability between OSCC and NOM. The proposed combination of miR-30a-5p and miR-769-5p in plasma from OSCC patients could serve as a minimal invasive biomarker for diagnosis and control of T-site recurrences.
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Affiliation(s)
- Nicklas Juel Pedersen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - David Hebbelstrup Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Giedrius Lelkaitis
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Katalin Kiss
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Wittenborg Charabi
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Ullum
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lena Specht
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Ane Yde Schmidt
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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155
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Vestal B, Russell P, Radcliffe R, Bemis L, Saba L, Kechris K. miRNA-regulated transcription associated with mouse strains predisposed to hypnotic effects of ethanol. Brain Behav 2018; 8:e00989. [PMID: 30106247 PMCID: PMC5991579 DOI: 10.1002/brb3.989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 01/18/2018] [Accepted: 03/24/2018] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Studying innate sensitivity to ethanol can be an important first step toward understanding alcohol use disorders. In brain, we investigated transcripts, with evidence of miRNA modulation related to a predisposition to the hypnotic effect of ethanol, as measured by loss of righting reflex (LORR). METHODS Expression of miRNAs (12 samples) and expression of mRNAs (353 samples) in brain were independently analyzed for an association with LORR in mice from the LXS recombinant inbred panel gathered across several small studies. These results were then integrated via a meta-analysis of miRNA-mRNA target pairs identified in miRNA-target interaction databases. RESULTS We found 112 significant miRNA-mRNA pairs where a large majority of miRNAs and mRNAs were highly interconnected. Most pairs indicated a pattern of increased levels of miRNAs and reduced levels of mRNAs being associated with more alcohol-sensitive strains. For example, CaMKIIn1 was targeted by multiple miRNAs associated with LORR. CAMK2N1 is an inhibitor of CAMK2, which among other functions, phosphorylates, or binds to GABAA and NMDA receptors. CONCLUSIONS Our results suggest a novel role of miRNA-mediated regulation of an inhibitor of CAMK2 and its downstream targets including the GABAA and NMDA receptors, which have been previously implicated to have a role in ethanol-induced sedation and sensitivity.
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MESH Headings
- Alcoholism/genetics
- Animals
- Calcium-Calmodulin-Dependent Protein Kinase Type 2/antagonists & inhibitors
- Ethanol/pharmacology
- Female
- GABA-A Receptor Antagonists/pharmacology
- Gene Expression Regulation
- Genetic Predisposition to Disease/genetics
- Hypnotics and Sedatives/pharmacology
- Mice
- Mice, Inbred Strains
- MicroRNAs/genetics
- MicroRNAs/metabolism
- MicroRNAs/physiology
- RNA, Messenger/metabolism
- Receptors, GABA-A/drug effects
- Receptors, GABA-A/genetics
- Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors
- Receptors, N-Methyl-D-Aspartate/drug effects
- Receptors, N-Methyl-D-Aspartate/genetics
- Reflex, Righting/drug effects
- Reflex, Righting/genetics
- Transcription, Genetic/genetics
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Affiliation(s)
- B. Vestal
- Center for Genes, Environment and HealthNational Jewish HealthDenverColorado
- Department of Biostatistics and InformaticsUniversity of Colorado Denver Anschutz Medical CampusAuroraColorado
| | - P. Russell
- Department of Biostatistics and InformaticsUniversity of Colorado Denver Anschutz Medical CampusAuroraColorado
| | - R.A. Radcliffe
- Department of Pharmaceutical SciencesUniversity of Colorado Denver Anschutz Medical CampusAuroraColorado
| | - L. Bemis
- Department of Biomedical SciencesUniversity of Minnesota Medical School Duluth CampusDuluthMinnesota
| | - L.M. Saba
- Department of Pharmaceutical SciencesUniversity of Colorado Denver Anschutz Medical CampusAuroraColorado
| | - K. Kechris
- Department of Biostatistics and InformaticsUniversity of Colorado Denver Anschutz Medical CampusAuroraColorado
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156
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Non-coding RNAs and exercise: pathophysiological role and clinical application in the cardiovascular system. Clin Sci (Lond) 2018; 132:925-942. [DOI: 10.1042/cs20171463] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/18/2022]
Abstract
There is overwhelming evidence that regular exercise training is protective against cardiovascular disease (CVD), the main cause of death worldwide. Despite the benefits of exercise, the intricacies of their underlying molecular mechanisms remain largely unknown. Non-coding RNAs (ncRNAs) have been recognized as a major regulatory network governing gene expression in several physiological processes and appeared as pivotal modulators in a myriad of cardiovascular processes under physiological and pathological conditions. However, little is known about ncRNA expression and role in response to exercise. Revealing the molecular components and mechanisms of the link between exercise and health outcomes will catalyse discoveries of new biomarkers and therapeutic targets. Here we review the current understanding of the ncRNA role in exercise-induced adaptations focused on the cardiovascular system and address their potential role in clinical applications for CVD. Finally, considerations and perspectives for future studies will be proposed.
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157
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Opoku-Damoah Y, Assanhou AG, Sooro MA, Baduweh CA, Sun C, Ding Y. Functional Diagnostic and Therapeutic Nanoconstructs for Efficient Probing of Circulating Tumor Cells. ACS APPLIED MATERIALS & INTERFACES 2018; 10:14231-14247. [PMID: 29557165 DOI: 10.1021/acsami.7b17896] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The circulation of tumor cells in peripheral blood is mostly recognized as a prerequisite for cancer progression or systemic invasion, and it correlates with the pivotal hallmark of malignancies known as metastasis. Multiple detection schemes for circulating tumor cells (CTCs) have emerged as the most discerning criteria for monitoring the outcome of anticancer therapy. Therefore, there has been a tremendous increase in the use of robust nanostructured platforms for observation of these mobile tumor cells through various simultaneous diagnosis and treatment regimens developed from conventional techniques. This review seeks to give detailed information about the nature of CTCs as well as techniques for exploiting specific biomarkers to help monitor cancer via detection, capturing, and analysis of unstable tumor cells. We will further discuss nanobased diagnostic interventions and novel platforms which have recently been developed from versatile nanomaterials such as polymer nanocomposites, metal organic frameworks, bioderived nanomaterials and other physically responsive particles with desirable intrinsic and external properties. Herein, we will also include in vivo nanotheranostic platforms which have received a lot of attention because of their enormous clinical potential. In all, this review sums up the general potential of key promising nanoinspired systems as well as other advanced strategies under research and those in clinical use.
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Affiliation(s)
- Yaw Opoku-Damoah
- Australian Institute for Bioengineering & Nanotechnology , The University of Queensland , St. Lucia , Brisbane, QLD 4072
| | - Assogba G Assanhou
- UFR Pharmacie, Falculté des Sciences de la Santé , Université d'Abomey-Calavi , 01BP188 Cotonou , Benin
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158
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Benway CJ, Iacomini J. Defining a microRNA-mRNA interaction map for calcineurin inhibitor induced nephrotoxicity. Am J Transplant 2018; 18:796-809. [PMID: 28925592 DOI: 10.1111/ajt.14503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/21/2017] [Accepted: 09/04/2017] [Indexed: 02/06/2023]
Abstract
Calcineurin inhibitors induce nephrotoxicity through poorly understood mechanisms thereby limiting their use in transplantation and other diseases. Here we define a microRNA (miRNA)-messenger RNA (mRNA) interaction map that facilitates exploration into the role of miRNAs in cyclosporine-induced nephrotoxicity (CIN) and the gene pathways they regulate. Using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP), we isolated RNAs associated with Argonaute 2 in the RNA-induced silencing complex (RISC) of cyclosporine A (CsA) treated and control human proximal tubule cells and identified mRNAs undergoing active targeting by miRNAs. CsA causes specific changes in miRNAs and mRNAs associated with RISC, thereby altering post-transcriptional regulation of gene expression. Pathway enrichment analysis identified canonical pathways regulated by miRNAs specifically following CsA treatment. RNA-seq performed on total RNA indicated that only a fraction of total miRNAs and mRNAs are actively targeted in the RISC, indicating that PAR-CLIP more accurately defines meaningful targeting interactions. Our data also revealed a role for miRNAs in calcineurin-independent regulation of JNK and p38 MAPKs caused by targeting of MAP3K1. Together, our data provide a novel resource and unique insights into molecular pathways regulated by miRNAs in CIN. The gene pathways and miRNAs defined may represent novel targets to reduce calcineurin induced nephrotoxicity.
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Affiliation(s)
- Christopher J Benway
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, MA, USA.,Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - John Iacomini
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, MA, USA.,Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA.,Graduate Program in Immunology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA.,Tufts University School of Medicine, Boston, MA, USA
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159
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Mitchell CJ, D'Souza RF, Schierding W, Zeng N, Ramzan F, O'Sullivan JM, Poppitt SD, Cameron-Smith D. Identification of human skeletal muscle miRNA related to strength by high-throughput sequencing. Physiol Genomics 2018; 50:416-424. [PMID: 29602299 DOI: 10.1152/physiolgenomics.00112.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The loss of muscle size, strength, and quality with aging is a major determinant of morbidity and mortality in the elderly. The regulatory pathways that impact the muscle phenotype include the translational regulation maintained by microRNAs (miRNA). Yet the miRNAs that are expressed in human skeletal muscle and relationship to muscle size, strength, and quality are unknown. Using next-generation sequencing, we selected the 50 most abundantly expressed miRNAs and then analyzed them in vastus lateralis muscle, obtained by biopsy from middle-aged males ( n = 48; 50.0 ± 4.3 yr). Isokinetic strength testing and midthigh computed tomography was undertaken for muscle phenotype analysis. Muscle attenuation was measured by computerized tomography and is inversely proportional to myofiber lipid content. miR-486-5p accounted for 21% of total miR sequence reads, with miR-10b-5p, miR-133a-3p, and miR-22-3p accounting for a further 15, 12, and 10%, respectively. Isokinetic knee extension strength and muscle cross-sectional area were positively correlated with miR-100-5p, miR-99b-5p, and miR-191-5p expression. Muscle attenuation was negatively correlated to let-7f-5p, miR-30d-5p, and miR-125b-5p expression. In silico analysis implicates miRNAs related to strength and muscle size in the regulation of mammalian target of rapamycin, while miRNAs related to muscle attenuation may have potential roles regulating the transforming growth factor-β/SMAD3 pathway.
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Affiliation(s)
| | | | | | - Nina Zeng
- Liggins Institute, University of Auckland , Auckland , New Zealand
| | - Farha Ramzan
- Liggins Institute, University of Auckland , Auckland , New Zealand
| | | | - Sally D Poppitt
- School of Biological Sciences, University of Auckland , Auckland , New Zealand.,Riddet Institute , Palmerston North , New Zealand
| | - David Cameron-Smith
- Liggins Institute, University of Auckland , Auckland , New Zealand.,Food & Bio-based Products Group, AgResearch, Palmerston North , New Zealand.,Riddet Institute , Palmerston North , New Zealand
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160
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Bai S, Xu B, Guo Y, Qiu J, Yu W, Xie G. High-Discrimination Factor Nanosensor Based on Tetrahedral DNA Nanostructures and Gold Nanoparticles for Detection of MiRNA-21 in Live Cells. Theranostics 2018; 8:2424-2434. [PMID: 29721089 PMCID: PMC5928899 DOI: 10.7150/thno.23852] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/25/2018] [Indexed: 12/28/2022] Open
Abstract
While detection of microRNA with or without signal amplification is highly informative, nanosensors with high specificity for cell-specific RNA detection are rare. Methods: In this study, a tetrahedral DNA nanostructure (TDN) with a specific function was combined with gold nanoparticles (Au-NP) possessing fluorescence quenching effects and a large surface area to fabricate a fluorescence resonance energy transfer based nanosensor (Au-TDNN). The presence of miR-21 (target) can separate the fluorescent dye-labeled detection probe on Au-TDNNs from Au-NPs, which separates the donor and acceptor, thus inducing an intensive fluorescence signal. High specificity for discerning point mutation targets was achieved by rationally designing the nucleic acid strand displacement reaction to occur spontaneously with ΔG0 ≈ 0 based on thermodynamic parameters; under this condition, slight thermodynamic changes caused by base mismatch exert significant effects on hybridization yield. Results: Chemically synthesized DNA of three single-base-changed analogues of target, let-7d, and miR-200b were tested. A discrimination factor (DF) of 15.4 was produced by the expected detection probe on Au-NPs for proximal single-base mismatch. As the control group, the DF produced by an ordinary detection probe on Au-NPs only reached 2.4. The feasibility of the proposed strategy was also confirmed using hepatocyte cancer cells (HepG2). Conclusion: This improved nanosensor opens a new avenue for the specific and easy detection of microRNA in live cells.
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161
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Yu S, Wang Y, Jiang LP, Bi S, Zhu JJ. Cascade Amplification-Mediated In Situ Hot-Spot Assembly for MicroRNA Detection and Molecular Logic Gate Operations. Anal Chem 2018; 90:4544-4551. [DOI: 10.1021/acs.analchem.7b04930] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sha Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yingying Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Sai Bi
- Collaborative Innovation Center for Marine Biomass Fiber, Materials and Textiles of Shandong Province, College of Chemistry and Chemical Engineering, Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Qingdao University, Qingdao 266071, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, China
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162
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MicroRNA Expression Profiling of the Armed Forces Health Surveillance Branch Cohort for Identification of "Enviro-miRs" Associated With Deployment-Based Environmental Exposure. J Occup Environ Med 2018; 58:S97-S103. [PMID: 27501110 DOI: 10.1097/jom.0000000000000764] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The aim of this study was to identify serum microRNA (miRNA) biomarkers that indicate deployment-associated exposures in service members at military installations with open burn pits. Another objective was to determine detection rates of miRNAs in Department of Defense Serum Repository (DoDSR) samples with a high-throughput methodology. METHODS Low-volume serum samples (n = 800) were profiled by miRNA-capture isolation, pre-amplification, and measurement by a quantitative PCR-based OpenArray platform. Normalized quantitative cycle values were used for differential expression analysis between groups. RESULTS Assay specificity, dynamic range, reproducibility, and detection rates by OpenArray passed target desired specifications. Serum abundant miRNAs were consistently measured in study specimens. Four miRNAs were differentially expressed in the case deployment group subjects. CONCLUSIONS miRNAs are suitable RNA species for biomarker discovery in the DoDSR serum specimens. Serum miRNAs are candidate biomarkers for deployment and environmental exposure in military service members.
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163
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Single-Step Incubation Determination of miRNAs in Cancer Cells Using an Amperometric Biosensor Based on Competitive Hybridization onto Magnetic Beads. SENSORS 2018; 18:s18030863. [PMID: 29543716 PMCID: PMC5877363 DOI: 10.3390/s18030863] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 12/20/2022]
Abstract
This work reports an amperometric biosensor for the determination of miRNA-21, a relevant oncogene. The methodology involves a competitive DNA-target miRNA hybridization assay performed on the surface of magnetic microbeads (MBs) and amperometric transduction at screen-printed carbon electrodes (SPCEs). The target miRNA competes with a synthetic fluorescein isothiocyanate (FITC)-modified miRNA with an identical sequence for hybridization with a biotinylated and complementary DNA probe (b-Cp) immobilized on the surface of streptavidin-modified MBs (b-Cp-MBs). Upon labeling, the FITC-modified miRNA attached to the MBs with horseradish peroxidase (HRP)-conjugated anti-FITC Fab fragments and magnetic capturing of the MBs onto the working electrode surface of SPCEs. The cathodic current measured at −0.20 V (versus the Ag pseudo-reference electrode) was demonstrated to be inversely proportional to the concentration of the target miRNA. This convenient biosensing method provided a linear range between 0.7 and 10.0 nM and a limit of detection (LOD) of 0.2 nM (5 fmol in 25 μL of sample) for the synthetic target miRNA without any amplification step. An acceptable selectivity towards single-base mismatched oligonucleotides, a high storage stability of the b-Cp-MBs, and usefulness for the accurate determination of miRNA-21 in raw total RNA (RNAt) extracted from breast cancer cells (MCF-7) were demonstrated.
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164
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Pine PS, Lund SP, Parsons JR, Vang LK, Mahabal AA, Cinquini L, Kelly SC, Kincaid H, Crichton DJ, Spira A, Liu G, Gower AC, Pass HI, Goparaju C, Dubinett SM, Krysan K, Stass SA, Kukuruga D, Van Keuren-Jensen K, Courtright-Lim A, Thompson KL, Rosenzweig BA, Sorbara L, Srivastava S, Salit ML. Summarizing performance for genome scale measurement of miRNA: reference samples and metrics. BMC Genomics 2018; 19:180. [PMID: 29510677 PMCID: PMC5838960 DOI: 10.1186/s12864-018-4496-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measurement assurance are critical components of genome-scale measurements. Here, we evaluated the utility of a set of total RNA samples, designed with between-sample differences in the relative abundance of miRNAs, as process controls. RESULTS Three pure total human RNA samples (brain, liver, and placenta) and two different mixtures of these components were evaluated as measurement assurance control samples on multiple measurement systems at multiple sites and over multiple rounds. In silico modeling of mixtures provided benchmark values for comparison with physical mixtures. Biomarker development laboratories using next-generation sequencing (NGS) or genome-scale hybridization assays participated in the study and returned data from the samples using their routine workflows. Multiplexed and single assay reverse-transcription PCR (RT-PCR) was used to confirm in silico predicted sample differences. Data visualizations and summary metrics for genome-scale miRNA profiling assessment were developed using this dataset, and a range of performance was observed. These metrics have been incorporated into an online data analysis pipeline and provide a convenient dashboard view of results from experiments following the described design. The website also serves as a repository for the accumulation of performance values providing new participants in the project an opportunity to learn what may be achievable with similar measurement processes. CONCLUSIONS The set of reference samples used in this study provides benchmark values suitable for assessing genome-scale miRNA profiling processes. Incorporation of these metrics into an online resource allows laboratories to periodically evaluate their performance and assess any changes introduced into their measurement process.
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Affiliation(s)
- P Scott Pine
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA.
| | - Steven P Lund
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jerod R Parsons
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA
| | - Lindsay K Vang
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA
| | - Ashish A Mahabal
- Center for Data Driven Discovery, California Institute of Technology, Pasadena, CA, USA
| | - Luca Cinquini
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Sean C Kelly
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Heather Kincaid
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Daniel J Crichton
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Avrum Spira
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Gang Liu
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Adam C Gower
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, NYU Langone Medical Center, New York, NY, USA
| | - Chandra Goparaju
- Department of Cardiothoracic Surgery, NYU Langone Medical Center, New York, NY, USA
| | - Steven M Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Sanford A Stass
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Debra Kukuruga
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Karol L Thompson
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Barry A Rosenzweig
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Lynn Sorbara
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Marc L Salit
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, 443 Via Ortega, Stanford, CA, 94305, USA
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165
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Analysis of meat quality traits and gene expression profiling of pigs divergent in residual feed intake. Meat Sci 2018; 137:265-274. [DOI: 10.1016/j.meatsci.2017.11.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/08/2017] [Accepted: 11/16/2017] [Indexed: 11/19/2022]
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166
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Choi W, Yeom SY, Kim J, Jung S, Jung S, Shim TS, Kim SK, Kang JY, Lee SH, Cho IJ, Choi J, Choi N. Hydrogel micropost-based qPCR for multiplex detection of miRNAs associated with Alzheimer's disease. Biosens Bioelectron 2018; 101:235-244. [DOI: 10.1016/j.bios.2017.10.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/14/2017] [Accepted: 10/16/2017] [Indexed: 12/19/2022]
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167
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Park Y, Lee CY, Kang S, Kim H, Park KS, Park HG. Universal, colorimetric microRNA detection strategy based on target-catalyzed toehold-mediated strand displacement reaction. NANOTECHNOLOGY 2018; 29:085501. [PMID: 29269591 DOI: 10.1088/1361-6528/aaa3a3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, we developed a novel, label-free, and enzyme-free strategy for the colorimetric detection of microRNA (miRNA), which relies on a target-catalyzed toehold-mediated strand displacement (TMSD) reaction. The system employs a detection probe that specifically binds to the target miRNA and sequentially releases a catalyst strand (CS) intended to trigger the subsequent TMSD reaction. Thus, the presence of target miRNA releases the CS that mediates the formation of an active G-quadruplex DNAzyme which is initially caged and inactivated by a blocker strand. In addition, a fuel strand that is supplemented for the recycling of the CS promotes another TMSD reaction, consequently generating a large number of active G-quadruplex DNAzymes. As a result, a distinct colorimetric signal is produced by the ABTS oxidation promoted by the peroxidase mimicking activity of the released G-quadruplex DNAzymes. Based on this novel strategy, we successfully detected miR-141, a promising biomarker for human prostate cancer, with high selectivity. The diagnostic capability of this system was also demonstrated by reliably determining target miR-141 in human serum, showing its great potential towards real clinical applications. Importantly, the proposed approach is composed of separate target recognition and signal transduction modules. Thus, it could be extended to analyze different target miRNAs by simply redesigning the detection probe while keeping the same signal transduction module as a universal signal amplification unit, which was successfully demonstrated by analyzing another target miRNA, let-7d.
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Affiliation(s)
- Yeonkyung Park
- Department of Chemical and Biomolecular Engineering (BK21+Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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168
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Lusardi TA, Phillips JI, Wiedrick JT, Harrington CA, Lind B, Lapidus JA, Quinn JF, Saugstad JA. MicroRNAs in Human Cerebrospinal Fluid as Biomarkers for Alzheimer's Disease. J Alzheimers Dis 2018; 55:1223-1233. [PMID: 27814298 DOI: 10.3233/jad-160835] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Currently available biomarkers of Alzheimer's disease (AD) include cerebrospinal fluid (CSF) protein analysis and amyloid PET imaging, each of which has limitations. The discovery of extracellular microRNAs (miRNAs) in CSF raises the possibility that miRNA may serve as novel biomarkers of AD. OBJECTIVE Investigate miRNAs in CSF obtained from living donors as biomarkers for AD. METHODS We profiled miRNAs in CSF from 50 AD patients and 49 controls using TaqMan® arrays. Replicate studies performed on a subset of 32 of the original CSF samples verified 20 high confidence miRNAs. Stringent data analysis using a four-step statistical selection process including log-rank and receiver operating characteristic (ROC) tests, followed by random forest tests, identified 16 additional miRNAs that discriminate AD from controls. Multimarker modeling evaluated linear combinations of these miRNAs via best-subsets logistic regression, and computed area under the ROC (AUC) curve ascertained classification performance. The influence of ApoE genotype on miRNA biomarker performance was also evaluated. RESULTS We discovered 36 miRNAs that discriminate AD from control CSF. 20 of these retested in replicate studies verified differential expression between AD and controls. Stringent statistical analysis also identified these 20 miRNAs, and 16 additional miRNA candidates. Top-performing linear combinations of 3 and 4 miRNAs have AUC of 0.80-0.82. Addition of ApoE genotype to the model improved performance, i.e., AUC of 3 miRNA plus ApoE4 improves to 0.84. CONCLUSIONS CSF miRNAs can discriminate AD from controls. Combining miRNAs improves sensitivity and specificity of biomarker performance, and adding ApoE genotype improves classification.
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Affiliation(s)
- Theresa A Lusardi
- Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Jay I Phillips
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jack T Wiedrick
- Biostatistics, School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | | | - Babett Lind
- Department of Neurology, Layton Aging and Alzheimer's Center, Oregon Health & Science University, Portland, OR, USA
| | - Jodi A Lapidus
- Biostatistics, School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Joseph F Quinn
- Department of Neurology, Layton Aging and Alzheimer's Center, Oregon Health & Science University, Portland, OR, USA.,Department of Neurology, Portland VA Medical Center, Portland, OR, USA
| | - Julie A Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, USA
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169
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Zouari M, Campuzano S, Pingarrón J, Raouafi N. Ultrasensitive determination of microribonucleic acids in cancer cells with nanostructured-disposable electrodes using the viral protein p19 for recognition of ribonucleic acid/microribonucleic acid homoduplexes. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2017.12.190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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170
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Ankasha SJ, Shafiee MN, Wahab NA, Ali RAR, Mokhtar NM. Post-transcriptional regulation of microRNAs in cancer: From prediction to validation. Oncol Rev 2018; 12:344. [PMID: 29989022 PMCID: PMC6037043 DOI: 10.4081/oncol.2018.344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/01/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNA (miRNA) is a small non-coding RNA with an established function to regulate genes at the post-transcriptional level leading to suppression or degradation of its messenger RNA expression (mRNA). Its dysregulation plays a vital role in a variety of biological and pathological processes including cancer. A lot of algorithms have been established to predict the target sites of miRNA, but experimentally identifying and validating its target region is still lacking. Guidance in experimental procedures is really needed to find genuine miRNA targets. Therefore, in this review, we provide an outline on the workflow in predicting and validating the targeted sites of miRNA using several methods as a guideline for the scientists. The final outcome of this type of experiment is essential to explore the major impact of miRNAmRNA interaction involved in the biological processes and to assist miRNA-based drug development in the future.
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Affiliation(s)
| | - Mohamad Nasir Shafiee
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University Kebangsaan
| | | | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, University Kebangsaan, Malaysia
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171
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Salinas-Santander M, Trevino V, De la Rosa-Moreno E, Verduzco-Garza B, Sánchez-Domínguez CN, Cantú-Salinas C, Ocampo-Garza J, Lagos-Rodríguez A, Ocampo-Candiani J, Ortiz-López R. CAPN3, DCT, MLANA and TYRP1 are overexpressed in skin of vitiligo vulgaris Mexican patients. Exp Ther Med 2018; 15:2804-2811. [PMID: 29456684 PMCID: PMC5795480 DOI: 10.3892/etm.2018.5764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/05/2018] [Indexed: 12/18/2022] Open
Abstract
Vitiligo is a disorder causing skin depigmentation, in which several factors have been proposed for its pathogenesis: Environmental, genetic and biological aspects of melanocytes, even those of the surrounding keratinocytes. However, the lack of understanding of the mechanisms has complicated the task of predicting the development and progression. The present study used microarray analysis to characterize the transcriptional profile of skin from Vitiligo Vulgaris (VV) patients and the identified transcripts were validated using targeted high-throughput RNA sequencing in a broader set of patients. For microarrays, mRNA was taken from 20 skin biopsies of 10 patients with VV (pigmented and depigmented skin biopsy of each), and 5 biopsies of healthy subjects matched for age and sex were used as a control. A signature was identified that contains the expression pattern of 722 genes between depigmented vitiligo skin vs. healthy control, 1,108 between the pigmented skin of vitiligo vs. healthy controls and 1,927 between pigmented skin, depigmented vitiligo and healthy controls (P<0.05; false discovery rate, <0.1). When comparing the pigmented and depigmented skin of patients with vitiligo, which reflects the real difference between both skin types, 5 differentially expressed genes were identified and further validated in 45 additional VV patients by RNA sequencing. This analysis showed significantly higher RNA levels of calpain-3, dopachrome tautomerase, melan-A and tyrosinase-related protein-1 genes. The data revealed that the pigmented skin of vitiligo is already affected at the level of gene expression and that the main differences between pigmented and non-pigmented skin are explained by the expression of genes associated with pigment metabolism.
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Affiliation(s)
- Mauricio Salinas-Santander
- Departamento de Bioquímica y Medicina Molecular, Universidad Autónoma de Nuevo León, Facultad de Medicina, Monterrey, Nuevo León 64460, México.,Departamento de Investigación, Facultad de Medicina Unidad Saltillo, Universidad Autónoma de Coahuila, Saltillo, Coahuila 25000, México
| | - Víctor Trevino
- Grupo de Investigación en Bioinformática, Escuela de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México
| | - Eduardo De la Rosa-Moreno
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Bárbara Verduzco-Garza
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Celia N Sánchez-Domínguez
- Departamento de Bioquímica y Medicina Molecular, Universidad Autónoma de Nuevo León, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Cristina Cantú-Salinas
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Jorge Ocampo-Garza
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Armando Lagos-Rodríguez
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Jorge Ocampo-Candiani
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Rocio Ortiz-López
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México.,Escuela de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México
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172
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Ivanov MK, Titov SE, Glushkov SA, Dzyubenko VV, Malek AV, Arkhangelskaya PA, Samsonov RB, Mikhetko AA, Bakhidze EV, Berlev IV, Kolesnikov NN. Detection of high-grade neoplasia in air-dried cervical PAP smears by a microRNA-based classifier. Oncol Rep 2018; 39:1099-1111. [PMID: 29328473 PMCID: PMC5802032 DOI: 10.3892/or.2018.6214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/29/2017] [Indexed: 01/17/2023] Open
Abstract
Recent studies have shown that changes in the expression levels of certain microRNAs correlate with the degree of severity of cervical lesions. The aim of the present study was to develop a microRNA-based classifier for the detection of high-grade cervical intraepithelial neoplasia (CIN ≥2) in cytological samples from patients with different high-risk human papillomavirus (HR-HPV) viral loads. For this purpose, raw RT-qPCR data for 25 candidate microRNAs, U6 snRNA and human DNA in air-dried PAP smears from 174 women with different cervical cytological diagnoses, 144 of which were HR-HPV-positive [40 negative for intraepithelial lesion or malignancy (NILM), 34 low-grade squamous intraepithelial lesions (L-SIL), 57 high-grade squamous intraepithelial lesions (H-SIL), 43 invasive cancers], were statistically processed. The expression level changes of various individual microRNAs were found to be significantly correlated with the cytological diagnosis but the statistical significance of this correlation was critically dependent on the normalization strategy. We developed a linear classifier based on the paired ratios of 8 microRNA concentrations and cellular DNA content. The classifier determines the dimensionless coefficient (DF value), which increases with the severity of cervical lesion. The high- and low-grade CINs were better distinguished by the microRNA classifier than by the measurement of individual microRNA levels with the use of traditional normalization methods. The diagnostic sensitivity of detecting high-grade lesions (CIN ≥2) with the developed microRNA classifier was 83.4%, diagnostic specificity 81.2%, ROC AUC=0.913. The analysis can be performed with the same nucleic acid preparation as used for HPV testing. No statistically significant correlation of the DF value and HR-HPV DNA load was found. The DF value and the HR HPV presence and viral DNA load may be regarded as independent criteria that can complement each other in molecular screening for high-grade cervical intraepithelial neoplasia. Although it has several limitations, the present study showed that the small-scale analysis of microRNA signatures performed by simple PCR-based methods may be useful for improving the diagnostic/prognostic value of cervical screening.
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Affiliation(s)
| | | | | | | | - Anastasia V Malek
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | | | - Roman B Samsonov
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Andrey A Mikhetko
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Elena V Bakhidze
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Igor V Berlev
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Nikolay N Kolesnikov
- Institute of Molecular and Cellular Biology, Siberian Branch of The Russian Academy of Sciences, 630090 Novosibirsk, Russia
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173
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Lewis JB, Jimenez FR, Merrell BJ, Kimbler B, Arroyo JA, Reynolds PR. The expression profile of Claudin family members in the developing mouse lung and expression alterations resulting from exposure to secondhand smoke (SHS). Exp Lung Res 2018; 44:13-24. [DOI: 10.1080/01902148.2017.1409846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Joshua B. Lewis
- Department of Physiology and Developmental Biology, Lung and Placenta Research Laboratory, Brigham Young University, Provo, Utah, USA
| | - Felix R. Jimenez
- Department of Physiology and Developmental Biology, Lung and Placenta Research Laboratory, Brigham Young University, Provo, Utah, USA
| | - Brigham J. Merrell
- Department of Physiology and Developmental Biology, Lung and Placenta Research Laboratory, Brigham Young University, Provo, Utah, USA
| | - Brent Kimbler
- Department of Physiology and Developmental Biology, Lung and Placenta Research Laboratory, Brigham Young University, Provo, Utah, USA
| | - Juan A. Arroyo
- Department of Physiology and Developmental Biology, Lung and Placenta Research Laboratory, Brigham Young University, Provo, Utah, USA
| | - Paul R. Reynolds
- Department of Physiology and Developmental Biology, Lung and Placenta Research Laboratory, Brigham Young University, Provo, Utah, USA
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174
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Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells. Genes (Basel) 2018; 9:genes9010025. [PMID: 29315258 PMCID: PMC5793178 DOI: 10.3390/genes9010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 12/27/2022] Open
Abstract
The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO) cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK), while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.
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175
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Yang VK, Tai AK, Huh TP, Meola DM, Juhr CM, Robinson NA, Hoffman AM. Dysregulation of valvular interstitial cell let-7c, miR-17, miR-20a, and miR-30d in naturally occurring canine myxomatous mitral valve disease. PLoS One 2018; 13:e0188617. [PMID: 29315310 PMCID: PMC5760013 DOI: 10.1371/journal.pone.0188617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
Canine myxomatous mitral valve disease (MMVD) resembles the early stages of myxomatous pathology seen in human non-syndromic mitral valve prolapse, a common valvular heart disease in the adult human population. Canine MMVD is seen in older subjects, suggesting age-related epigenetic dysregulation leading to derangements in valvular cell populations and matrix synthesis or degradation. We hypothesized that valvular interstitial cells (VICs) undergo disease-relevant changes in miRNA expression. In primary VIC lines from diseased and control valves, miRNA expression was profiled using RT-qPCR and next generation sequencing. VICs from diseased valves showed phenotypic changes consistent with myofibroblastic differentiation (vimentinlow+, α-SMAhigh+), increases in senescence markers (p21, SA-β-gαl), and decreased cell viability and proliferation potential. RT-qPCR and miRNA sequencing analyses both showed significant (p<0.05) downregulation of let-7c, miR-17, miR-20a, and miR-30d in VICs from diseased valves compared to controls. Decreased let-7c, miR-17, and miR-20a may contribute to myofibroblastic differentiation in addition to cell senescence, and decreased miR-30d may disinhibit cell apoptosis. These data support the hypothesis that epigenetic dysregulation plays an important role in age-related canine MMVD.
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Affiliation(s)
- Vicky K. Yang
- Department of Clinical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
- * E-mail:
| | - Albert K. Tai
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Terry P. Huh
- Department of Clinical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Dawn M. Meola
- Department of Clinical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Christine M. Juhr
- Department of Clinical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Nicholas A. Robinson
- Department of Biomedical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Andrew M. Hoffman
- Department of Clinical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
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176
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Abstract
MicroRNAs are a class of small noncoding RNAs that function as regulators involving in many biological processes. The evaluation of miRNAs and their targets has been aided by miRNA expression profiling studies including multiplex PCR, microarrays, and recent next-generation sequencing tools. Next-generation sequencing has enabled us to profile thousands of genes in a single experiment and overcome the background signal and cross-hybridization issues of microarrays. Next-generation sequencing also allows for the simultaneous confirmation of known miRNAs and discovery of new miRNAs, and significantly reduces costs while providing billions of nucleotide information within a single experiment. Here we describe a detailed procedure of generation of miRNA library for next-generation sequencing to increase the efficiency of adapter ligation and finally construct a more specific cDNA library for sequencing and analyses for miRNA expression profiling.
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Affiliation(s)
- Poching Liu
- DNA Sequencing and Genomics Core-NHLBI, National Institute of Health, Bethesda, MD, USA.
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177
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Zheng A, Zhang X, Huang Y, Cai Z, Liu X, Liu J. Polydopamine-assisted versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy. RSC Adv 2018; 8:6781-6788. [PMID: 35540353 PMCID: PMC9078363 DOI: 10.1039/c8ra00261d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/30/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs play an important role in various biological processes, and their aberrant expression is closely associated with various human diseases, especially cancer. Real-time monitoring of microRNAs in living cells may help us to understand their role in cellular processes, which can further provide a basis for diagnosis and treatment. In this study, polydopamine was used to assist the versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy. Polydopamine can be covalently linked with a thiol-terminated nucleic acid probe through the Michael addition reaction under slightly alkaline conditions. This modification is mild and can be performed directly in an aqueous solution, which can better resist hydrolysis than the traditional modification processes, resulting in a nanoprobe with better stability and higher loading of nucleic acids. This prepared nanoprobe can easily enter cells without transfection agents and then realize the imaging of intracellular miRNA through fluorescence restoration. Moreover, the coating of PDA can enhance the photothermal conversion efficiency of the nanoprobe, making it suitable for photothermal therapy of cancer. It is expected that the PDA-based versatile modification can help to construct a promising platform for tumor imaging and treatment. Polydopamine can assist the versatile modification of a nucleic acid probe for intracellular miRNA responsed fluorescence imaging and enhanced photothermal therapy.![]()
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Affiliation(s)
- Aixian Zheng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Xiaolong Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Yanbing Huang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
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178
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Snijders C, Bassil KC, de Nijs L. Methodologies of Neuroepigenetic Research: Background, Challenges and Future Perspectives. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:15-27. [DOI: 10.1016/bs.pmbts.2018.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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179
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Cui L, Markou A, Stratton CW, Lianidou E. Diagnosis and Assessment of Microbial Infections with Host and Microbial MicroRNA Profiles. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7119978 DOI: 10.1007/978-3-319-95111-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) encoded by viral genome or host have been found participating in host-microbe interactions. Differential expression profiles of miRNAs were shown linking to specific disease pathologies which indicated its potency as diagnostic/prognostic biomarkers of infectious disease. This was emphasized by the discovery of circulating miRNAs which were found to be remarkably stable in mammalian biofluids. Standardized methods of miRNA quantification including RNA isolation should be established before they will be ready for use in clinical practice.
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180
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Abstract
Identifying microRNA (miRNA) signatures in animal tissues is an essential first step in studies assessing post-transcriptional regulation of gene expression in health or disease. Small RNA sequencing (sRNA-Seq) is a next-generation sequencing-based technology that is currently considered the most powerful and versatile tool for miRNA profiling. Here, we describe a sRNA-Seq protocol including RNA purification from mammalian tissues, library preparation, and raw data analysis.
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Affiliation(s)
- Lucas Carminatti Pantaleão
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Susan E Ozanne
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
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181
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Atkin SL, Ramachandran V, Yousri NA, Benurwar M, Simper SC, McKinlay R, Adams TD, Najafi-Shoushtari SH, Hunt SC. Changes in Blood microRNA Expression and Early Metabolic Responsiveness 21 Days Following Bariatric Surgery. Front Endocrinol (Lausanne) 2018; 9:773. [PMID: 30687230 PMCID: PMC6338028 DOI: 10.3389/fendo.2018.00773] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 12/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Early metabolic responses following bariatric surgery appear greater than expected given the initial weight loss and coincide with improvement in diabetes. We hypothesized that small non-coding microRNA changes might contribute to regulating mechanisms for metabolic changes and weight loss in patients with severe obesity and diabetes. Methods: Twenty-nine type 2 patients with severe obesity (mean BMI 46.2 kg/m2) and diabetes underwent Roux-en-Y gastric bypass (RYGB) surgery. Clinical measurements and fasting blood samples were taken preoperatively and at day 21 postoperatively. Normalization of fasting glucose and HbA1c following bariatric surgery (short-term diabetes remission) was defined as withdrawal of anti-diabetic medication and fasting glucose < 100 mg/dL (5.6 mmol/L) or HbA1c < 6.0%. MicroRNA expression was determined by quantitative polymerase chain reaction and tested for significant changes after surgery. Results: BMI decreased by 3.8 kg/m2 21 days postoperatively. Eighteen of 29 RYGB (62%) had short-term diabetes remission. Changes from pre- to post-surgery in 32 of 175 microRNAs were nominally significant (p < 0.05). Following multiple comparison adjustment, changes in seven microRNAs remained significant: miR-7-5p, let-7f-5p, miR-15b-5p, let-7i-5p, miR-320c, miR-205-5p, and miR-335-5p. Four pathways were over-represented by these seven microRNAs, including diabetes and insulin resistance pathways. Conclusion: Seven microRNAs showed significant changes 21 days after bariatric surgery. Functional pathways of the altered microRNAs were associated with diabetes-, pituitary-, and liver-related disease, with expression in natural killer cells, and pivotal intestinal pathology suggesting possible mechanistic roles in early diabetes responses following bariatric surgery.
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Affiliation(s)
- Stephen L. Atkin
- Department of Medicine, Weill Cornell Medicine, Doha, Qatar
- *Correspondence: Stephen L. Atkin
| | - Vimal Ramachandran
- Department of Cell and Developmental Biology, Weill Cornell Medicine, Doha, Qatar
- MicroRNA Core Laboratory, Weill Cornell Medicine, Doha, Qatar
| | - Noha A. Yousri
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
| | - Manasi Benurwar
- Department of Cell and Developmental Biology, Weill Cornell Medicine, Doha, Qatar
- MicroRNA Core Laboratory, Weill Cornell Medicine, Doha, Qatar
| | - Steven C. Simper
- Rocky Mountain Associated Physicians, Inc., Salt Lake City, UT, United States
| | - Rodrick McKinlay
- Rocky Mountain Associated Physicians, Inc., Salt Lake City, UT, United States
| | - Ted D. Adams
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States
- Intermountain LiveWell Center, Intermountain Healthcare, Salt Lake City, UT, United States
| | - S. Hani Najafi-Shoushtari
- Department of Cell and Developmental Biology, Weill Cornell Medicine, Doha, Qatar
- MicroRNA Core Laboratory, Weill Cornell Medicine, Doha, Qatar
| | - Steven C. Hunt
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States
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182
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Wang LJ, Li SC, Lee MJ, Chou MC, Chou WJ, Lee SY, Hsu CW, Huang LH, Kuo HC. Blood-Bourne MicroRNA Biomarker Evaluation in Attention-Deficit/Hyperactivity Disorder of Han Chinese Individuals: An Exploratory Study. Front Psychiatry 2018; 9:227. [PMID: 29896131 PMCID: PMC5987559 DOI: 10.3389/fpsyt.2018.00227] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 05/08/2018] [Indexed: 12/14/2022] Open
Abstract
Background: Attention-deficit/hyperactivity disorder (ADHD) is a highly genetic neurodevelopmental disorder, and its dysregulation of gene expression involves microRNAs (miRNAs). The purpose of this study was to identify potential miRNAs biomarkers and then use these biomarkers to establish a diagnostic panel for ADHD. Design and methods: RNA samples from white blood cells (WBCs) of five ADHD patients and five healthy controls were combined to create one pooled patient library and one control library. We identified 20 candidate miRNAs with the next-generation sequencing (NGS) technique (Illumina). Blood samples were then collected from a Training Set (68 patients and 54 controls) and a Testing Set (20 patients and 20 controls) to identify the expression profiles of these miRNAs with real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). We used receiver operating characteristic (ROC) curves and the area under the curve (AUC) to evaluate both the specificity and sensitivity of the probability score yielded by the support vector machine (SVM) model. Results: We identified 13 miRNAs as potential ADHD biomarkers. The ΔCt values of these miRNAs in the Training Set were integrated to create a biomarker model using the SVM algorithm, which demonstrated good validity in differentiating ADHD patients from control subjects (sensitivity: 86.8%, specificity: 88.9%, AUC: 0.94, p < 0.001). The results of the blind testing showed that 85% of the subjects in the Testing Set were correctly classified using the SVM model alignment (AUC: 0.91, p < 0.001). The discriminative validity is not influenced by patients' age or gender, indicating both the robustness and the reliability of the SVM classification model. Conclusion: As measured in peripheral blood, miRNA-based biomarkers can aid in the differentiation of ADHD in clinical settings. Additional studies are needed in the future to clarify the ADHD-associated gene functions and biological mechanisms modulated by miRNAs.
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Affiliation(s)
- Liang-Jen Wang
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Chinese Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Min-Jing Lee
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Miao-Chun Chou
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Wen-Jiun Chou
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Sheng-Yu Lee
- Department of Psychiatry, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Psychiatry, College of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Wei Hsu
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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183
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Cieślik M, Chinnaiyan AM. Cancer transcriptome profiling at the juncture of clinical translation. Nat Rev Genet 2017; 19:93-109. [PMID: 29279605 DOI: 10.1038/nrg.2017.96] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methodological breakthroughs over the past four decades have repeatedly revolutionized transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples. These transcriptomes provide a link between cellular phenotypes and their molecular underpinnings, such as mutations. In the context of cancer, this link represents an opportunity to dissect the complexity and heterogeneity of tumours and to discover new biomarkers or therapeutic strategies. Here, we review the rationale, methodology and translational impact of transcriptome profiling in cancer.
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Affiliation(s)
- Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan.,Comprehensive Cancer Center, University of Michigan.,Department of Urology, University of Michigan.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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184
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Mobuchon L, Le Guillou S, Marthey S, Laubier J, Laloë D, Bes S, Le Provost F, Leroux C. Sunflower oil supplementation affects the expression of miR-20a-5p and miR-142-5p in the lactating bovine mammary gland. PLoS One 2017; 12:e0185511. [PMID: 29281677 PMCID: PMC5744907 DOI: 10.1371/journal.pone.0185511] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022] Open
Abstract
Oil supplementation in dairy cattle diets is used to modulate milk fat composition, as well as the expression of mammary lipogenic genes, whose regulation remains unclear. MiRNAs are small non-coding RNA considered as crucial regulators of gene expression, offering clues to explain the mechanism underlying gene nutriregulation. The present study was designed to identify miRNAs whose expression in the cow mammary gland is modulated by sunflower oil supplementation. MiRNomes were obtained using RNAseq technology from the mammary gland of lactating cows receiving a low forage diet, supplemented or not with 4% sunflower oil. Among the 272 miRNAs characterized, eight were selected for RT-qPCR validations, showing the significant down-regulation of miR-142-5p and miR-20a-5p by sunflower supplementation. These two miRNAs are predicted to target genes whose expression was reported as differentially expressed by sunflower supplementation. Among their putative targets, ELOVL6 gene involved in lipid metabolism has been studied. However, a first analysis did not show its significant down-regulation, in response to the over-expression of miR-142-5p, of miR-20a-5p, or both, in a bovine mammary epithelial cell line. However, a clearer understanding of the miRNA expression by lipid supplementation would help to decipher the regulation of lactating cow mammary gland in response to nutrition.
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Affiliation(s)
- Lenha Mobuchon
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- INRA, UMR1213 Herbivores, Saint Genès Champanelle, France
- Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | | | - Sylvain Marthey
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Johann Laubier
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Denis Laloë
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sébastien Bes
- INRA, UMR1213 Herbivores, Saint Genès Champanelle, France
- Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | | | - Christine Leroux
- INRA, UMR1213 Herbivores, Saint Genès Champanelle, France
- Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
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185
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Kok MGM, de Ronde MWJ, Moerland PD, Ruijter JM, Creemers EE, Pinto-Sietsma SJ. Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 15:1-5. [PMID: 29276692 PMCID: PMC5737945 DOI: 10.1016/j.bdq.2017.11.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/02/2017] [Accepted: 11/27/2017] [Indexed: 02/08/2023]
Abstract
Since the discovery of microRNAs (miRNAs), circulating miRNAs have been proposed as biomarkers for disease. Consequently, many groups have tried to identify circulating miRNA biomarkers for various types of diseases including cardiovascular disease and cancer. However, the replicability of these experiments has been disappointingly low. In order to identify circulating miRNA candidate biomarkers, in general, first an unbiased high-throughput screen is performed in which a large number of miRNAs is detected and quantified in the circulation. Because these are costly experiments, many of such studies have been performed using a low number of study subjects (small sample size). Due to lack of power in small sample size experiments, true effects are often missed and many of the detected effects are wrong. Therefore, it is important to have a good estimate of the appropriate sample size for a miRNA high-throughput screen. In this review, we discuss the effects of small sample sizes in high-throughput screens for circulating miRNAs. Using data from a miRNA high-throughput experiment on isolated monocytes, we illustrate that the implementation of power calculations in a high-throughput miRNA discovery experiment will avoid unnecessarily large and expensive experiments, while still having enough power to be able to detect clinically important differences.
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Affiliation(s)
- M G M Kok
- Departments of Vascular Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - M W J de Ronde
- Departments of Vascular Medicine, University of Amsterdam, Amsterdam, The Netherlands.,Departments of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| | - P D Moerland
- Departments of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| | - J M Ruijter
- Departments of Anatomy, Embryology and Physiology, University of Amsterdam, Amsterdam, The Netherlands
| | - E E Creemers
- Departments of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - S J Pinto-Sietsma
- Departments of Vascular Medicine, University of Amsterdam, Amsterdam, The Netherlands.,Departments of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
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186
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Crouser ED, Hamzeh NY, Maier LA, Julian MW, Gillespie M, Rahman M, Baxter D, Wu X, Nana-Sinkam SP, Wang K. Exosomal MicroRNA for Detection of Cardiac Sarcoidosis. Am J Respir Crit Care Med 2017; 196:931-934. [PMID: 28245138 DOI: 10.1164/rccm.201611-2183le] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | | | | | - Mark W Julian
- 1 Ohio State University Wexner Medical Center Columbus, Ohio
| | | | - Mohammad Rahman
- 1 Ohio State University Wexner Medical Center Columbus, Ohio
| | - David Baxter
- 3 Institute for Systems Biology Seattle, Washington and
| | - Xiaogang Wu
- 3 Institute for Systems Biology Seattle, Washington and
| | | | - Kai Wang
- 3 Institute for Systems Biology Seattle, Washington and
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187
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miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget 2017; 7:25930-48. [PMID: 27036018 PMCID: PMC5041955 DOI: 10.18632/oncotarget.8412] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/13/2016] [Indexed: 12/13/2022] Open
Abstract
Ovarian cancer presents as an aggressive, advanced stage cancer with widespread metastases that depend primarily on multicellular spheroids in the peritoneal fluid. To identify new druggable pathways related to metastatic progression and spheroid formation, we integrated microRNA and mRNA sequencing data from 293 tumors from The Cancer Genome Atlas (TCGA) ovarian cancer cohort. We identified miR-509-3p as a clinically significant microRNA that is more abundant in patients with favorable survival in both the TCGA cohort (P = 2.3E–3), and, by in situ hybridization (ISH), in an independent cohort of 157 tumors (P < 1.0E–3). We found that miR-509-3p attenuated migration and disrupted multi-cellular spheroids in HEYA8, OVCAR8, SKOV3, OVCAR3, OVCAR4 and OVCAR5 cell lines. Consistent with disrupted spheroid formation, in TCGA data miR-509-3p's most strongly anti-correlated predicted targets were enriched in components of the extracellular matrix (ECM). We validated the Hippo pathway effector YAP1 as a direct miR-509-3p target. We showed that siRNA to YAP1 replicated 90% of miR-509-3p-mediated migration attenuation in OVCAR8, which contained high levels of YAP1 protein, but not in the other cell lines, in which levels of this protein were moderate to low. Our data suggest that the miR-509-3p/YAP1 axis may be a new druggable target in cancers with high YAP1, and we propose that therapeutically targeting the miR-509-3p/YAP1/ECM axis may disrupt early steps in multi-cellular spheroid formation, and so inhibit metastasis in epithelial ovarian cancer and potentially in other cancers.
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188
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miRNome Profiling in Bicuspid Aortic Valve-Associated Aortopathy by Next-Generation Sequencing. Int J Mol Sci 2017; 18:ijms18112498. [PMID: 29165337 PMCID: PMC5713463 DOI: 10.3390/ijms18112498] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 01/05/2023] Open
Abstract
The molecular mechanisms underlying thoracic aortic aneurysm (TAA) in patients with bicuspid aortic valve (BAV) are incompletely characterized. MicroRNAs (miRNAs) may play a major role in the different pathogenesis of aortopathy. We sought to employ next-generation sequencing to analyze the entire miRNome in TAA tissue from patients with BAV and tricuspid aortic valve (TAV). In the discovery stage, small RNA sequencing was performed using the Illumina MiSeq platform in 13 TAA tissue samples (seven patients with BAV and six with TAV). Gene ontology (GO) and KEGG pathway analysis were used to identify key pathways and biological functions. Validation analysis was performed by qRT-PCR in an independent cohort of 30 patients with BAV (26 males; 59.5 ± 12 years) and 30 patients with TAV (16 males; 68.5 ± 9.5 years). Bioinformatic analysis identified a total of 489 known mature miRNAs and five novel miRNAs. Compared to TAV samples, 12 known miRNAs were found to be differentially expressed in BAV, including two up-regulated and 10 down-regulated (FDR-adjusted p-value ≤ 0.05 and fold change ≥ 1.5). GO and KEGG pathway enrichment analysis (FDR-adjusted p-value < 0.05) identified different target genes and pathways linked to BAV and aneurysm formation, including Hippo signaling pathway, ErbB signaling, TGF-beta signaling and focal adhesion. Validation analysis of selected miRNAs confirmed the significant down-regulation of miR-424-3p (p = 0.01) and miR-3688-3p (p = 0.03) in BAV patients as compared to TAV patients. Our study provided the first in-depth screening of the whole miRNome in TAA specimens and identified specific dysregulated miRNAs in BAV patients.
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189
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MiR-301b-3p/3584-5p enhances low-dose mono-n-butyl phthalate (MBP)-induced proliferation by targeting Rasd1 in Sertoli cells. Toxicol In Vitro 2017; 47:79-88. [PMID: 29162477 DOI: 10.1016/j.tiv.2017.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/09/2017] [Accepted: 11/15/2017] [Indexed: 02/02/2023]
Abstract
To investigate the possible molecular mechanism of low concentration plasticizer mono-n-butyl phthalate (MBP) -induced juvenile Sertoli cells (SCs) proliferation, we evaluated global alterations of miRNA and mRNA expression in rat SCs treated with 0.1mM MBP. Microarray analysis revealed that miR-3584-5p and miR-301b-3p were up-regulated and their common target gene Dexamethasone-induced Ras-related protein 1 (Rasd1) was down-regulated. Further work suggested that SCs proliferation induced by low concentration MBP in vitro might be mediated by Rasd1 regulating ERK1/2 signaling pathway. The present study is first to investigate the effect of low-dose MBP on SCs proliferation and may enhance our understanding on the modes of action of low concentration MBP on male reproductive system. We hope the results will contribute to explain the causes of precocious puberty and testicular tumors induced by exogenous chemicals.
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190
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Vargas E, Torrente-Rodríguez RM, Ruiz-Valdepeñas Montiel V, Povedano E, Pedrero M, Montoya JJ, Campuzano S, Pingarrón JM. Magnetic Beads-Based Sensor with Tailored Sensitivity for Rapid and Single-Step Amperometric Determination of miRNAs. Int J Mol Sci 2017; 18:ijms18112151. [PMID: 29120349 PMCID: PMC5713197 DOI: 10.3390/ijms18112151] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/08/2017] [Accepted: 10/09/2017] [Indexed: 02/06/2023] Open
Abstract
This work describes a sensitive amperometric magneto-biosensor for single-step and rapid determination of microRNAs (miRNAs). The developed strategy involves the use of direct hybridization of the target miRNA (miRNA-21) with a specific biotinylated DNA probe immobilized on streptavidin-modified magnetic beads (MBs), and labeling of the resulting heteroduplexes with a specific DNA–RNA antibody and the bacterial protein A (ProtA) conjugated with an horseradish peroxidase (HRP) homopolymer (Poly-HRP40) as an enzymatic label for signal amplification. Amperometric detection is performed upon magnetic capture of the modified MBs onto the working electrode surface of disposable screen-printed carbon electrodes (SPCEs) using the H2O2/hydroquinone (HQ) system. The magnitude of the cathodic signal obtained at −0.20 V (vs. the Ag pseudo-reference electrode) demonstrated linear dependence with the concentration of the synthetic target miRNA over the 1.0 to 100 pM range. The method provided a detection limit (LOD) of 10 attomoles (in a 25 μL sample) without any target miRNA amplification in just 30 min (once the DNA capture probe-MBs were prepared). This approach shows improved sensitivity compared with that of biosensors constructed with the same anti-DNA–RNA Ab as capture instead of a detector antibody and further labeling with a Strep-HRP conjugate instead of the Poly-HRP40 homopolymer. The developed strategy involves a single step working protocol, as well as the possibility to tailor the sensitivity by enlarging the length of the DNA/miRNA heteroduplexes using additional probes and/or performing the labelling with ProtA conjugated with homopolymers prepared with different numbers of HRP molecules. The practical usefulness was demonstrated by determination of the endogenous levels of the mature target miRNA in 250 ng raw total RNA (RNAt) extracted from human mammary epithelial normal (MCF-10A) and cancer (MCF-7) cells and tumor tissues.
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Affiliation(s)
- Eva Vargas
- Department of Analytical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain.
| | - Rebeca M Torrente-Rodríguez
- Department of Analytical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain.
| | | | - Eloy Povedano
- Department of Analytical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain.
| | - María Pedrero
- Department of Analytical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain.
| | - Juan J Montoya
- Cannan Research and Investment & Faculty of Medicine, University Complutense of Madrid, 28040 Madrid, Spain.
| | - Susana Campuzano
- Department of Analytical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain.
| | - José M Pingarrón
- Department of Analytical Chemistry, Faculty of Chemistry, University Complutense of Madrid, 28040 Madrid, Spain.
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191
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Marzinotto I, Pellegrini S, Brigatti C, Nano R, Melzi R, Mercalli A, Liberati D, Sordi V, Ferrari M, Falconi M, Doglioni C, Ravassard P, Piemonti L, Lampasona V. miR-204 is associated with an endocrine phenotype in human pancreatic islets but does not regulate the insulin mRNA through MAFA. Sci Rep 2017; 7:14051. [PMID: 29070792 PMCID: PMC5656581 DOI: 10.1038/s41598-017-13622-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/07/2017] [Indexed: 11/09/2022] Open
Abstract
miR-204 has been proposed to modulate insulin expression in human pancreatic islets by regulating the expression of the MAFA transcript, and in turn insulin transcription. We investigated miR-204 expression in pancreatic endocrine tumors (PET), a panel of human tissues, tissues derived from pancreatic islet purification, and in induced pluripotent stem cells (iPSCs) differentiated towards a pancreatic endocrine phenotype by quantitative real time RT-PCR or droplet digital PCR (ddPCR). In addition, we evaluated the effect of miR-204 up- or down-regulation in purified human islets and in the EndoC-βH1 cell line, as an experimental model of human pancreatic β cells. Our results confirm that miR-204 was enriched in insulin producing PET, in β cells within healthy pancreatic islets, and highly expressed in EndoC-βH1 cells. Moreover, in iPSCs miR-204 increased stepwise upon stimulated differentiation to insulin producing cells. However, up- or down-regulation of miR-204 in human islets and in EndoC-βH1 cells resulted in modest and not significant changes of the MAFA and INS mRNAs measured by ddPCR or c-peptide release. Our data confirm the association of miR-204 with a β cell endocrine phenotype in human pancreatic islets, but do not support its direct role in regulating the levels of insulin mRNA through MAFA.
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Affiliation(s)
- Ilaria Marzinotto
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Human Pathologies Genomic Diagnostics unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Pellegrini
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Brigatti
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Rita Nano
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Melzi
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessia Mercalli
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Liberati
- Human Pathologies Genomic Diagnostics unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Sordi
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maurizio Ferrari
- Human Pathologies Genomic Diagnostics unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Falconi
- Vita-Salute San Raffaele University, Milan, Italy.,Department of Surgery, Division of Pancreatic Surgery, San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Doglioni
- Vita-Salute San Raffaele University, Milan, Italy.,Unit of Pathology, San Raffaele Scientific Institute, Milan, Italy
| | - Philippe Ravassard
- Institut du Cerveau et de la Moelle épinière (ICM), Biotechnology & Biotherapy Team, Université Pierre et Marie Curie, Paris, France
| | - Lorenzo Piemonti
- Diabetes Research Institute, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy. .,Vita-Salute San Raffaele University, Milan, Italy.
| | - Vito Lampasona
- Human Pathologies Genomic Diagnostics unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy.
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192
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Darvasi O, Szabo PM, Nemeth K, Szabo K, Spisak S, Liko I, Czirjak S, Racz K, Igaz P, Patocs A, Butz H. Limitations of high throughput methods for miRNA expression profiles in non-functioning pituitary adenomas. Pathol Oncol Res 2017; 25:169-182. [PMID: 29043608 DOI: 10.1007/s12253-017-0330-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 10/02/2017] [Indexed: 12/24/2022]
Abstract
Microarray, RT-qPCR based arrays and next-generation-sequencing (NGS) are available high-throughput methods for miRNA profiling (miRNome). Analytical and biological performance of these methods were tested in identification of biologically relevant miRNAs in non-functioning pituitary adenomas (NFPA). miRNome of 4 normal pituitary (NP) and 8 NFPA samples was determined by these platforms and expression of 21 individual miRNAs was measured on 30 (20 NFPA and 10 NP) independent samples. Complex bioinformatics was used. 132 and 137 miRNAs were detected by all three platforms in NP and NFPA, respectively, of which 25 were differentially expressed (fold change > 2). The strongest correlation was observed between microarray and TaqMan-array, while the data obtained by NGS were the most discordant despite of various bioinformatics settings. As a technical validation we measured the expression of 21 selected miRNAs by individual RT-qPCR and we were able to validate 35.1%, 76.2% and 71.4% of the miRNAs revealed by SOLiD, TLDA and microarray result, respectively. We performed biological validation using an extended number of samples (20 NFPAs and 8 NPs). Technical and biological validation showed high correlation (p < 0.001; R = 0.96). Pathway and network analysis revealed several common pathways but no pathway showed the same activation score. Using the 25 platform-independent miRNAs developmental pathways were the top functional categories relevant for NFPA genesis. The difference among high-throughput platforms is of great importance and selection of screening method can influence experimental results. Validation by another platform is essential in order to avoid or to minimalize the platform specific errors.
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Affiliation(s)
- O Darvasi
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - P M Szabo
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - K Nemeth
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - K Szabo
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - S Spisak
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - I Liko
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - S Czirjak
- National Institute of Neurosurgery, Budapest, Hungary
| | - K Racz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - P Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - A Patocs
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Semmelweis University, Department of Laboratory Medicine, 46 Szentkirályi Str, Budapest, H-1088, Hungary
| | - Henriett Butz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.
- Semmelweis University, Department of Laboratory Medicine, 46 Szentkirályi Str, Budapest, H-1088, Hungary.
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193
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Ragusa M, Barbagallo C, Cirnigliaro M, Battaglia R, Brex D, Caponnetto A, Barbagallo D, Di Pietro C, Purrello M. Asymmetric RNA Distribution among Cells and Their Secreted Exosomes: Biomedical Meaning and Considerations on Diagnostic Applications. Front Mol Biosci 2017; 4:66. [PMID: 29046875 PMCID: PMC5632685 DOI: 10.3389/fmolb.2017.00066] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/20/2017] [Indexed: 12/17/2022] Open
Abstract
Over the past few years, exosomes and their RNA cargo have been extensively studied because of the fascinating biological roles they play in cell-to-cell communication, including the signal exchange among cancer, stromal, and immune cells, leading to modifications of tumor microenvironment. RNAs, especially miRNAs, stored within exosomes, seem to be among the main determinants of such signaling: their sorting into exosomes appears to be cell-specific and related to cellular physiopathology. Accordingly, the identification of exosomal miRNAs in body fluids from pathological patients has become one of the most promising activity in the field of biomarker discovery. Several analyses on the qualitative and quantitative distribution of RNAs between cells and their secreted exosomes have given rise to questions on whether and how accurately exosomal RNAs would represent the transcriptomic snapshot of the physiological and pathological status of secreting cells. Although the exact molecular mechanisms of sorting remain quite elusive, many papers have reported an evident asymmetric quantitative distribution of RNAs between source cells and their exosomes. This phenomenon could depend both on passive and active sorting mechanisms related to: (a) RNA turnover; (b) maintaining the cytoplasmic miRNA:target equilibrium; (c) removal of RNAs not critical or even detrimental for normal or diseased cells. These observations represent very critical issues in the exploitation of exosomal miRNAs as cancer biomarkers. In this review, we will discuss how much the exosomal and corresponding donor cell transcriptomes match each other, to better understand the actual reliability of exosomal RNA molecules as pathological biomarkers reflecting a diseased status of the cells.
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Affiliation(s)
- Marco Ragusa
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy.,IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Italy
| | - Cristina Barbagallo
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Matilde Cirnigliaro
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Rosalia Battaglia
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Duilia Brex
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Angela Caponnetto
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Davide Barbagallo
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Cinzia Di Pietro
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Michele Purrello
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
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194
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Shah P, Bristow MR, Port JD. MicroRNAs in Heart Failure, Cardiac Transplantation, and Myocardial Recovery: Biomarkers with Therapeutic Potential. Curr Heart Fail Rep 2017; 14:454-464. [DOI: 10.1007/s11897-017-0362-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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195
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Single-step, homogeneous and sensitive detection for microRNAs with dual-recognition steps based on luminescence resonance energy transfer (LRET) using upconversion nanoparticles. Biosens Bioelectron 2017; 100:475-481. [PMID: 28963965 DOI: 10.1016/j.bios.2017.09.039] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/08/2017] [Accepted: 09/20/2017] [Indexed: 01/23/2023]
Abstract
A single-step, homogeneous and sensitive LRET assay is presented for the detection of miRNAs. The amplification-free assay provides a unique combination of high specificity with dual-recognition approach of different hybridization and ligation steps and preventing background auto-fluorescence in biological samples using upconversion nanoparticles (UCNPs) as signal-producing nanoprobes. The assay probe is composed of signal-producing unit (a pair of homogeneous upconversion luminescence resonance energy transfer (UC-LRET)-based oligonucleotides) and recognition unit (two adaptor oligonucleotides). In the presence of target miRNAs, the probe and target miRNAs leads to the formation of stable double-strands and semi-stable adaptor-miRNAs complexes with an adaptor nick. Ligation of the nick using ligase cause the formation of stable double-strands, resulting in UCNPs-to-dye UC-LRET for detection of the miRNAs with near-infrared radiation (980nm). Sensitive detection of miRNA-21 at concentrations of 200pM to 1.4nM and detection limits of 0.095nM with good precision of 3.9% (RSD) for seven repeated measurements of 500pM miRNAs demonstrate the feasibility of both high throughput and point-of-care clinical diagnostics. The homogeneous UC-LRET assay without any washing can be extended to the application in other important types of nucleic acid analysis.
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196
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Fujise K, Kikuchi Y, Kokubu E, Okamoto-Shibayama K, Ishihara K. Effect of extracytoplasmic function sigma factors on autoaggregation, hemagglutination, and cell surface properties of Porphyromonas gingivalis. PLoS One 2017; 12:e0185027. [PMID: 28931045 PMCID: PMC5607195 DOI: 10.1371/journal.pone.0185027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 09/05/2017] [Indexed: 01/05/2023] Open
Abstract
Porphyromonas gingivalis is a bacterium frequently isolated from chronic periodontal lesions and is involved in the development of chronic periodontitis. To colonize the gingival crevice, P. gingivalis has to adapt to environmental stresses. Microbial gene expression is regulated by transcription factors such as those in two-component systems and extracytoplasmic function (ECF) sigma factors. ECF sigma factors are involved in the regulation of environmental stress response genes; however, the roles of individual ECF sigma factors are largely unknown. The purpose of this study was to investigate the functions, including autoaggregation, hemagglutination, gingipain activity, susceptibility to antimicrobial agents, and surface structure formation, of P. gingivalis ECF sigma factors encoded by SigP (PGN_0274), SigCH (PGN_0319), PGN_0450, PGN_0970, and SigH (PGN_1740). Various physiological aspects of the sigP mutant were affected; autoaggregation was significantly decreased at 60 min (p < 0.001), hemagglutination activity was markedly reduced, and enzymatic activities of Kgp and Rgps were significantly decreased (p < 0.001). The other mutants also showed approximately 50% reduction in Rgps activity. Kgp activity was significantly reduced in the sigH mutant (p < 0.001). No significant differences in susceptibilities to tetracycline and ofloxacin were observed in the mutants compared to those of the wild-type strain. However, the sigP mutant displayed an increased susceptibility to ampicillin, whereas the PGN_0450 and sigH mutants showed reduced susceptibility. Transmission electron microscopy images revealed increased levels of outer membrane vesicles formed at the cell surfaces of the sigP mutant. These results indicate that SigP is important for bacterial surface-associated activities, including gingipain activity, autoaggregation, hemagglutination, vesicle formation, and antimicrobial susceptibility.
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Affiliation(s)
- Kazutaka Fujise
- Department of Microbiology, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan
| | - Yuichiro Kikuchi
- Department of Microbiology, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan.,Oral Health Science Center, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan
| | - Eitoyo Kokubu
- Department of Microbiology, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan.,Oral Health Science Center, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan
| | | | - Kazuyuki Ishihara
- Department of Microbiology, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan.,Oral Health Science Center, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan
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197
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Kumar G, Chaudhary KK, Misra K, Tripathi A. Next-Generation Sequencing for Drug Designing and Development: An Omics Approach for Cancer Treatment. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.709.723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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198
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Multiplex quantitative analysis of microRNA expression via exponential isothermal amplification and conformation-sensitive DNA separation. Sci Rep 2017; 7:11396. [PMID: 28900270 PMCID: PMC5595994 DOI: 10.1038/s41598-017-11895-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/01/2017] [Indexed: 12/02/2022] Open
Abstract
Expression profiling of multiple microRNAs (miRNAs) generally provides valuable information for understanding various biological processes. Thus, it is necessary to develop a sensitive and accurate miRNA assay suitable for multiplexing. Isothermal exponential amplification reaction (EXPAR) has received significant interest as an miRNA analysis method because of high amplification efficiency. However, EXPAR cannot be used for a broader range of applications owing to limitations such as complexity of probe design and lack of proper detection method for multiplex analysis. Here, we developed a sensitive and accurate multiplex miRNA profiling method using modified isothermal EXPAR combined with high-resolution capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP). To increase target miRNA specificity, a stem-loop probe was introduced instead of a linear probe in isothermal EXPAR to allow specific amplification of multiple miRNAs with minimal background signals. CE-SSCP, a conformation-dependent separation method, was used for detection. Since CE-SSCP eliminates the need for probes to have different lengths, easier designing of probes with uniform amplification efficiency was possible. Eight small RNAs comprising six miRNAs involved in Caenorhabditis elegans development and two controls were analyzed. The expression patterns obtained using our method were concordant with those reported in previous studies, thereby supporting the proposed method’s robustness and utility.
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199
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Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks. PLoS One 2017; 12:e0183103. [PMID: 28817636 PMCID: PMC5560700 DOI: 10.1371/journal.pone.0183103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/19/2017] [Indexed: 01/17/2023] Open
Abstract
Co-expression networks have long been used as a tool for investigating the molecular circuitry governing biological systems. However, most algorithms for constructing co-expression networks were developed in the microarray era, before high-throughput sequencing-with its unique statistical properties-became the norm for expression measurement. Here we develop Bayesian Relevance Networks, an algorithm that uses Bayesian reasoning about expression levels to account for the differing levels of uncertainty in expression measurements between highly- and lowly-expressed entities, and between samples with different sequencing depths. It combines data from groups of samples (e.g., replicates) to estimate group expression levels and confidence ranges. It then computes uncertainty-moderated estimates of cross-group correlations between entities, and uses permutation testing to assess their statistical significance. Using large scale miRNA data from The Cancer Genome Atlas, we show that our Bayesian update of the classical Relevance Networks algorithm provides improved reproducibility in co-expression estimates and lower false discovery rates in the resulting co-expression networks. Software is available at www.perkinslab.ca.
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200
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Balacescu O, Petrut B, Tudoran O, Feflea D, Balacescu L, Anghel A, Sirbu IO, Seclaman E, Marian C. Urinary microRNAs for prostate cancer diagnosis, prognosis, and treatment response: are we there yet? WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [DOI: 10.1002/wrna.1438] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/27/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Ovidiu Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Bogdan Petrut
- Department of Urology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Oana Tudoran
- Department of Functional Genomics, Proteomics and Experimental Pathology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Dragos Feflea
- Department of Urology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Loredana Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Andrei Anghel
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
| | - Ioan O. Sirbu
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
| | - Edward Seclaman
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
| | - Catalin Marian
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
- Division of Cancer Prevention and Control; The Ohio State University Comprehensive Cancer Center; Columbus OH USA
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