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Al Gashaamy ZJ, Alomar T, Al-Sinjary L, Wazzan M, Saeed MH, Al-Rawi NH. MicroRNA expression in apical periodontitis and pulpal inflammation: a systematic review. PeerJ 2023; 11:e14949. [PMID: 36890871 PMCID: PMC9987318 DOI: 10.7717/peerj.14949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
Background The aim of this systematic review is to determine microRNAs (miRs) that are differently expressed between diseased pulpal and periapical tissues. Design This systematic review used PubMed, Scopus, EBSCO, ProQuest, Cochrane database as well as manual searching to extract studies from January 2012 up to February 2022. Results A total of 12 studies met the eligibility criteria were included. All selected studies were of case-control type. Twenty-four miRNAs associated with apical periodontitis, 11 were found to be upregulatedand 13 were downregulated. Four out of the 44 miRs associated with pulpal inflammation were upregulated, whereas forty were downregulated. Six miRs, namely hsa-miR-181b, hsa-miR-181c,hsa-miR-455-3p,hsa-miR-128-3p, hsa-miR199a-5p, and hsa-miR-95, exhibited considerable downregulation in both periapical and pulp tissues. Conclusion MiRs have been investigated for their role in pulpal and periapical biology and may be utilised in diagnostic and therapeutic purposes. Further investigations are required to determine why certain irreversible pulpitis situations progress to apical periodontitis and others do not, based on the various miR expressions. Moreover, clinical and laboratory trials are needed to support this theory.
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Affiliation(s)
- Zainab Jamal Al Gashaamy
- Oral & Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Tiba Alomar
- Oral & Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Linah Al-Sinjary
- Oral & Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad Wazzan
- Oral & Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Musab Hamed Saeed
- Department of Clinical Science, College of Dentistry, Ajman University, Ajman, United Arab Emirates.,Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Natheer H Al-Rawi
- Oral & Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, United Arab Emirates
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2
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Shen J, Lou H, Yu Q, Yao H, Yuan J. The Connection between High Myopia Patients and MiR-708a or MiR-148 Expression Levels in Aqueous Studies of Visual Acuity. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3363830. [PMID: 36277877 PMCID: PMC9584676 DOI: 10.1155/2022/3363830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/13/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022]
Abstract
Myopia goes far beyond the inconvenience it brings. It is a prevailing and vision-threatening eye disease, especially in Asia. Aberrantly expressed miR-708a and miR-148 are critical for accurate diagnosis, good prognosis, and precise response prediction of myopia. In this paper, we aim to examine the potential contributions of miR-708a, miR-148a, and PAX6 to high myopia (HM). First, aqueous samples were taken from 25 exclusively HM eyes and 25 exclusively cataract eyes. For next-generation sequencing and bioinformatics analysis, RNA from sample 30one was used. Twenty more samples were used for RT-qPCR. 341 miRNAs in total were found in HM eyes; 249 mature miRNAs and 17 new miRNAs showed differential expression. The expression of hsa-miR-127-3p, hsa-let-7i-5p, and hsa-miR-98-5p was identified using RT-qPCR. MiR-708a and miR-148, which may be linked to the development of myopia and serve as possible biomarkers, are notably highly expressed in atrial tissues of HM patients. Our findings may help deepen the understanding of the mechanisms behind the high expression of miR-708a and miR-148 in atrial tissues of patients with HM.
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Affiliation(s)
- Jiang Shen
- Department of Ophthalmology, Ningbo Eye Hospital, Ningbo, 315040 Zhejiang, China
| | - Hong Lou
- Department of Ophthalmology, Ningbo Eye Hospital, Ningbo, 315040 Zhejiang, China
| | - Qihua Yu
- Department of Ophthalmology, Ningbo Eye Hospital, Ningbo, 315040 Zhejiang, China
| | - Hongyan Yao
- Department of Ophthalmology, Ningbo Eye Hospital, Ningbo, 315040 Zhejiang, China
| | - Jianshu Yuan
- Department of Ophthalmology, Ningbo Eye Hospital, Ningbo, 315040 Zhejiang, China
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3
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Lu Q, Chen Z, Ji D, Mao Y, Jiang Q, Yang Z, Loor JJ. Progress on the Regulation of Ruminant Milk Fat by Noncoding RNAs and ceRNAs. Front Genet 2021; 12:733925. [PMID: 34790222 PMCID: PMC8591074 DOI: 10.3389/fgene.2021.733925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022] Open
Abstract
Milk fat is not only a key factor affecting the quality of fresh milk but also a major target trait forbreeding. The regulation of milk fat involves multiple genes, network regulation and signal transduction. To explore recent discoveries of pathway regulation, we reviewed the published literature with a focus on functional noncoding RNAs and epigenetic regulation in ruminants. Results indicate that miRNAs play key roles in the regulation of milk fat synthesis and catabolism in ruminants. Although few data are available, merging evidence indicates that lncRNAs and circRNAs act on milk fat related genes through indirect action with microRNAs or RNAs in the ceRNA network to elicit positive effects on transcription. Although precise regulatory mechanisms remain unclear, most studies have focused on the regulation of the function of target genes through functional noncoding RNAs. Data to help identify factors that can regulate their own expression and function or to determine whether self-regulation involves positive and/or negative feedback are needed. Despite the growing body of research on the role of functional noncoding RNA in the control of ruminant milk fat, most data are still not translatable for field applications. Overall, the understanding of mechanisms whereby miRNA, lncRNA, circRNA, and ceRNA regulate ruminant milk fat remains an exciting area of research.
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Affiliation(s)
- QinYue Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Dejun Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Qianming Jiang
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Juan J Loor
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
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4
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Hu C, Zhang L, Yang Z, Song Z, Zhang Q, He Y. Graphene oxide-based qRT-PCR assay enables the sensitive and specific detection of miRNAs for the screening of ovarian cancer. Anal Chim Acta 2021; 1174:338715. [PMID: 34247740 DOI: 10.1016/j.aca.2021.338715] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/01/2022]
Abstract
Circulating microRNAs (miRNAs) have the potential to become reliable and noninvasive biomarkers for ovarian cancer (OC) diagnosis; however, the conventional miRNAs detection techniques exhibit enduring limitations of low sensitivity and specificity. Graphene oxide (GO), a novel nanomaterial, is at the forefront of material design for extensive biomedical applications. Owing to the excellent water affinity and single-stranded DNA (ssDNA) adsorption characteristics of GO, we designed and developed a GO-based qRT-PCR assay for the detection of miRNAs associated with OC. In the GO-based qRT-PCR system, GO could significantly improve the sensitivity and specificity of the qRT-PCR assay by noncovalently interacting with primers and ssDNA and reducing the occurrence of non-specific amplification. Moreover, the detection of miRNAs associated with OC confirmed that GO-based qRT-PCR assay could differentiate benign ovarian tumors from OC (sensitivity, 0.91; specificity, 1.00). Collectively, these findings provide robust evidence that GO-based qRT-PCR assay can be effectively used as a promising method to detect miRNAs for the screening of OC patients.
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Affiliation(s)
- Chenyan Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Linlin Zhang
- Department of Gynecology, People's Hospital of Mianzhu City, Deyang, Sichuan, 618200, China
| | - Zhongzhu Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Zhen Song
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Qin Zhang
- Department of Gynecology, People's Hospital of Mianzhu City, Deyang, Sichuan, 618200, China
| | - Yang He
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China.
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Shen Z, Silva RM. MicroRNAs: emerging players in apical periodontitis. J Appl Oral Sci 2021; 29:e20201058. [PMID: 33886945 PMCID: PMC8054647 DOI: 10.1590/1678-7757-2020-1058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Apical periodontitis is an inflammatory disorder of periradicular tissues developed from endodontic infections. Understanding its pathophysiology and the underlying molecular mechanisms is key to the advancement of endodontics. MicroRNAs (miRNAs), a group of evolutionarily conserved small non-coding RNAs, may be phenotypically and functionally associated with the pathogenesis of apical periodontitis. Several studies have focused on the role of miRNAs in the pulp and periradicular biology, and they have demonstrated their essential functions, such as initiating odontogenic differentiation and promoting pro- or anti-inflammatory responses in pulpitis. Up to date, over 2,000 miRNAs have been discovered in humans; however, only few have been reported to associate with apical periodontitis. Therefore, identifying miRNAs involved in diseased apical tissues and conducting functional studies are important in expanding our current knowledge of pulp and periradicular biology and exploring novel therapeutic avenues. In this review, we revisit current models of apical periodontitis and miRNA biogenesis, analyze existing evidence of the involvement of miRNAs in diseased apical tissues, and discuss their diverse functions and potential values. Based on their sheer abundance, prolonged stability in biofluid, and relative ease of sampling, miRNAs may be a useful tool to be developed as diagnostic biomarkers for apical periodontitis. Furthermore, it can be used as therapeutic targets in conjunction with conventional endodontic therapies.
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Affiliation(s)
- Zhen Shen
- The University of Texas Health Science Center at Houston, Department of Endodontics, Houston, TX, United States
| | - Renato Menezes Silva
- The University of Texas Health Science Center at Houston, Department of Endodontics, Houston, TX, United States.,The University of Texas Health Science Center at Houston, Center for Craniofacial Research, Houston, TX, United States
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6
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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7
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Shen Z, Wichnieski C, Carneiro E, Garlet GP, Letra A, Silva RM. Expression Profiling and Functional Characterization of MicroRNAs in Apical Periodontitis. J Endod 2020; 47:263-271. [PMID: 33245973 DOI: 10.1016/j.joen.2020.11.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION MicroRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs that may orchestrate the pathogenesis of apical periodontitis (AP). This study aimed to identify differentially expressed miRNAs and investigate their target gene pathways in AP. METHODS Total RNA was extracted from 10 human AP and 2 healthy apical tissues (controls) and subjected to miRNA sequencing for the identification of differentially expressed miRNAs (>1.5-fold changes). The function of the most up-regulated miRNA was further studied in vitro. miR-10a-5p mimics and inhibitors were introduced to human stem cells from the apical papilla and K-562 cells challenged with lipopolysaccharide, and expressions of predicted target genes were examined via quantitative reverse-transcription polymerase chain reaction and RNA sequencing. RESULTS A total of 852 miRNAs were identified, of which 12 were significantly up-regulated (1.54- to 8.44-fold) and 94 were significantly down-regulated (0.14- to 0.67-fold) in AP. Predicted target genes of these miRNAs are involved in inflammation, pain, and related pathways. miR-10a-5p showed the highest expression levels in AP. Overexpression of miR-10a-5p in LPS-challenged stem cells from the apical papilla resulted in down-regulation of messenger RNA levels of TNFA and up-regulation of interleukin IL10. RNA sequencing of K-562 cells treated with miR-10a-5p mimics and inhibitors identified miR-10a-5p target genes associated with multiple pathways, including macrophage-mediated inflammation and coagulation pathways. CONCLUSIONS Over 100 miRNAs were differentially expressed in AP and appeared to be involved with modulation of genes in inflammatory and immune pathways. MiR-10a-5p was the most significantly up-regulated miRNA in AP and may play a critical role in suppressing inflammation and promoting healing.
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Affiliation(s)
- Zhen Shen
- Department of Endodontics, University of Texas Health Science Center at Houston, School of Dentistry at Houston, Houston, Texas
| | - Caroline Wichnieski
- Department of Endodontics, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Everdan Carneiro
- Department of Endodontics, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Gustavo P Garlet
- Department of Biological Sciences, School of Dentistry of Bauru, University of São Paulo, Bauru, São Paulo, Brazil
| | - Ariadne Letra
- Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, Texas; Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry at Houston, Houston, Texas
| | - Renato M Silva
- Department of Endodontics, University of Texas Health Science Center at Houston, School of Dentistry at Houston, Houston, Texas; Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, Texas.
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8
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Bauer M, Vaxevanis C, Heimer N, Al-Ali HK, Jaekel N, Bachmann M, Wickenhauser C, Seliger B. Expression, Regulation and Function of microRNA as Important Players in the Transition of MDS to Secondary AML and Their Cross Talk to RNA-Binding Proteins. Int J Mol Sci 2020; 21:ijms21197140. [PMID: 32992663 PMCID: PMC7582632 DOI: 10.3390/ijms21197140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Myelodysplastic syndromes (MDS), heterogeneous diseases of hematopoietic stem cells, exhibit a significant risk of progression to secondary acute myeloid leukemia (sAML) that are typically accompanied by MDS-related changes and therefore significantly differ to de novo acute myeloid leukemia (AML). Within these disorders, the spectrum of cytogenetic alterations and oncogenic mutations, the extent of a predisposing defective osteohematopoietic niche, and the irregularity of the tumor microenvironment is highly diverse. However, the exact underlying pathophysiological mechanisms resulting in hematopoietic failure in patients with MDS and sAML remain elusive. There is recent evidence that the post-transcriptional control of gene expression mediated by microRNAs (miRNAs), long noncoding RNAs, and/or RNA-binding proteins (RBPs) are key components in the pathogenic events of both diseases. In addition, an interplay between RBPs and miRNAs has been postulated in MDS and sAML. Although a plethora of miRNAs is aberrantly expressed in MDS and sAML, their expression pattern significantly depends on the cell type and on the molecular make-up of the sample, including chromosomal alterations and single nucleotide polymorphisms, which also reflects their role in disease progression and prediction. Decreased expression levels of miRNAs or RBPs preventing the maturation or inhibiting translation of genes involved in pathogenesis of both diseases were found. Therefore, this review will summarize the current knowledge regarding the heterogeneity of expression, function, and clinical relevance of miRNAs, its link to molecular abnormalities in MDS and sAML with specific focus on the interplay with RBPs, and the current treatment options. This information might improve the use of miRNAs and/or RBPs as prognostic markers and therapeutic targets for both malignancies.
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Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06112 Halle, Germany; (M.B.); (C.W.)
| | - Christoforos Vaxevanis
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
| | - Nadine Heimer
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
| | - Haifa Kathrin Al-Ali
- Department of Hematology/Oncology, University Hospital Halle, 06112 Halle, Germany; (H.K.A.-A.); (N.J.)
| | - Nadja Jaekel
- Department of Hematology/Oncology, University Hospital Halle, 06112 Halle, Germany; (H.K.A.-A.); (N.J.)
| | - Michael Bachmann
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, 01328 Dresden, Germany;
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06112 Halle, Germany; (M.B.); (C.W.)
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany
- Correspondence: ; Tel.: +49-345-557-4054
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9
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Liu Y, Wang Y, Chen Y, Fang X, Wen T, Xiao M, Chen S, Zhang X. Discovery and Validation of Circulating Hsa-miR-210-3p as a Potential Biomarker for Primary Open-Angle Glaucoma. Invest Ophthalmol Vis Sci 2019; 60:2925-2934. [PMID: 31284309 DOI: 10.1167/iovs.19-26663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Blood-based examination tools for glaucoma diagnosis in clinical practice, which can be useful for screening patients when traditional ophthalmic examinations cannot be utilized, are not available thus far. This study aimed to identify circulating microRNAs (miRNAs) associated with primary open-angle glaucoma (POAG) and explore their utility as diagnostic markers. Methods A total of 136 POAG patients and controls were enrolled. Next-generation RNA sequencing was used to explore the expression profile of circulating miRNAs in the sequencing set, and potential miRNAs from independent samples in both the screening and validation sets were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Receiver operating characteristic (ROC) analysis was used to evaluate the ability of certain miRNAs to distinguish POAG patients from control subjects. Results Using sequencing and qRT-PCR, hsa-miR-210-3p was found to be elevated in POAG patients in all sets. ROC analysis of the screening and validation sets revealed that hsa-miR-210-3p differentiated between POAG patients and matched controls with an area under the curve (AUC) of 0.846 (sensitivity: 84.6%; specificity: 80.8%) and 0.813 (sensitivity: 84.8%; specificity: 69.7%), respectively. In case of all nonsequencing participants, analysis revealed that hsa-miR-210-3p differentiated between severe POAG patients and controls with an AUC of 0.880 (sensitivity: 85.4%; specificity: 85.7%). In addition, the expression of hsa-miR-210-3p was associated with visual field defects of |mean deviation| (β = 0.237; P = 0.022) and average retinal nerve fiber layer thickness (β = -5.792; P = 0.014). Conclusions Circulating hsa-miR-210-3p may serve as a potential diagnostic marker for POAG (especially for severe POAG patients).
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Affiliation(s)
- Yaoming Liu
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yayi Wang
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yang Chen
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiuli Fang
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Tao Wen
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Mianli Xiao
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shida Chen
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiulan Zhang
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
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10
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Chen L, Heikkinen L, Wang C, Yang Y, Sun H, Wong G. Trends in the development of miRNA bioinformatics tools. Brief Bioinform 2019; 20:1836-1852. [PMID: 29982332 PMCID: PMC7414524 DOI: 10.1093/bib/bby054] [Citation(s) in RCA: 344] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.
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Affiliation(s)
- Liang Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Liisa Heikkinen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Changliang Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Yang Yang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Huiyan Sun
- Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
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11
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Chen S, Yuan M, Liu Y, Zhao X, Lian P, Chen Y, Liu B, Lu L. Landscape of microRNA in the aqueous humour of proliferative diabetic retinopathy as assessed by next-generation sequencing. Clin Exp Ophthalmol 2019; 47:925-936. [PMID: 31081578 DOI: 10.1111/ceo.13554] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND The microRNAs (miRNA) have been found to play an important role in the pathogenesis of diabetic retinopathy. We try to explore the miRNA and piwi-interacting RNA (piRNA) profile in the aqueous humour of proliferative diabetic retinopathy (PDR) using next-generation sequencing (NGS). METHODS Aqueous humour samples were collected from nine PDR eyes and nine cataract control eyes, and NGS was performed. Quantitative polymerase chain reaction (qPCR) was used to validate the sequencing results. An oxygen-induced retinopathy (OIR) model was used to validate the angiogenesis related miRNA. RESULTS In total, 484 miRNAs were differently expressed between the PDR eyes and cataract control eyes, including 210 mature miRNAs and 274 novel miRNAs. Furthermore, eight miRNAs and 30 piRNAs were identified as the most differently expressed between the two groups (P > .85). This differential expression of miRNA was predicted to regulate Rho protein signal transduction, neurotransmitter uptake and histone lysine methylation. Relative expression patterns of miR-184, -150-5p and -93-5p were confirmed by qPCR. A reduced expression of miR-93-5p was confirmed in the OIR model. CONCLUSIONS This study comprehensively demonstrated the miRNA and piRNA expression profile of the aqueous humour of PDR eyes, which may serve as a potential biomarker and involved in the pathogenesis of PDR.
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Affiliation(s)
- Shida Chen
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Miner Yuan
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Yaoming Liu
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Xiujuan Zhao
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Ping Lian
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Yang Chen
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Bingqian Liu
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Lin Lu
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
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12
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Liu Y, Chen Y, Wang Y, Zhang X, Gao K, Chen S, Zhang X. microRNA Profiling in Glaucoma Eyes With Varying Degrees of Optic Neuropathy by Using Next-Generation Sequencing. Invest Ophthalmol Vis Sci 2019; 59:2955-2966. [PMID: 30025119 DOI: 10.1167/iovs.17-23599] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To explore the microRNA (miRNA) profile and its putative role in glaucomatous optic neuropathy by using next-generation sequencing. Methods Aqueous humor (AH) samples were collected from 19 primary open-angle glaucoma (POAG) eyes and 17 cataract eyes before surgery. Next-generation sequencing was performed for RNA samples extracted from 18 AH samples, and the bioinformatics approach was applied for samples with adequate clean data output. The other 18 samples were used for quantitative PCR validation of sequencing results. Results In total, 12 (six POAG and six cataract controls) samples with sufficient clean data output after sequencing were used for further data analysis. Four hundred sixty-six and 480 mature miRNAs were detected in the POAG and cataract control groups, respectively. Among them, 164 miRNAs were detected in all POAG samples, and 96 miRNAs were detected in all cataract control samples. Furthermore, 88 miRNAs were identified as differently expressed between POAG and cataract control eyes. In addition, 16 miRNAs were differently expressed between POAG eyes with severe visual field damage and eyes with moderate visual field damage. This differential expression was predicted to regulate thiamine metabolism, purine metabolism, and transcriptional misregulation. Relative expression patterns of hsa-miR-184, hsa-miR-486-5p, and hsa-miR-93-5p were confirmed by quantitative PCR. Conclusions This study comprehensively demonstrated the miRNA expression profile in the AH of POAG eyes, especially the differential expression of miRNA in eyes with varying degrees of visual field damage, which, together with the underlying miRNA-related pathways, indicate new targets for the pathogenesis and progression of POAG.
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Affiliation(s)
- Yaoming Liu
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yang Chen
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yayi Wang
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xinyu Zhang
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Kai Gao
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shida Chen
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiulan Zhang
- Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, People's Republic of China
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13
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Lan L, Guo Q, Nie H, Zhou C, Cai Q, Huang J, Meng X. Linear-hairpin variable primer RT-qPCR for MicroRNA. Chem Sci 2018; 10:2034-2043. [PMID: 30842860 PMCID: PMC6375362 DOI: 10.1039/c8sc04621b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/02/2018] [Indexed: 12/31/2022] Open
Abstract
Here, we present a highly specific, sensitive and cost-effective system to quantify microRNA (miRNA) expression based on two-step RT-qPCR with EvaGreen detection chemistry, called linear-hairpin variable primer RT-qPCR.
Here, we present a highly specific, sensitive and cost-effective system to quantify microRNA (miRNA) expression based on two-step RT-qPCR with EvaGreen detection chemistry, called linear-hairpin variable primer RT-qPCR. It takes advantage of the novel designed variable primer, which is initially designed to be linear, extending to form a hairpin structure and replacing the target miRNA for cyclic RT. Then the RT product is quantified by conventional EvaGreen based qPCR. The results show that this method has a dynamic range of 8 logs and the sensitivity is sufficient to directly detect down to 4 target miRNA molecules with a total analysis time of less than 2 hours. It is capable of discriminating between similar miRNAs, leading to an accurate representation of the mature miRNA content in a sample. The RT step can be multiplexed and the 8 miRNA profiles measured in 7 mouse tissues by this method show an excellent correlation with the commercial standard TaqMan RT-qPCR assays (r2 = 0.9881).
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Affiliation(s)
- Lin Lan
- College of Biology , Hunan University , Changsha , P. R. China .
| | - Qiuping Guo
- College of Biology , Hunan University , Changsha , P. R. China . .,State Key Laboratory of Chemo/Biosensing and Chemometrics , P. R. China.,Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , P. R. China
| | - Hemin Nie
- College of Biology , Hunan University , Changsha , P. R. China .
| | - Chang Zhou
- School of Life Sciences , Hunan Normal University , Changsha , P. R. China
| | - Qingyun Cai
- College of Chemistry and Chemical Engineering , Hunan University , Changsha , P. R. China . .,State Key Laboratory of Chemo/Biosensing and Chemometrics , P. R. China
| | - Jin Huang
- College of Chemistry and Chemical Engineering , Hunan University , Changsha , P. R. China . .,State Key Laboratory of Chemo/Biosensing and Chemometrics , P. R. China.,Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , P. R. China
| | - Xiangxian Meng
- College of Biology , Hunan University , Changsha , P. R. China .
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14
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Li X, Kleeman S, Coburn SB, Fumagalli C, Perner J, Jammula S, Pfeiffer RM, Orzolek L, Hao H, Taylor PR, Miremadi A, Galeano-Dalmau N, Lao-Sirieix P, Tennyson M, MacRae S, Cook MB, Fitzgerald RC. Selection and Application of Tissue microRNAs for Nonendoscopic Diagnosis of Barrett's Esophagus. Gastroenterology 2018; 155:771-783.e3. [PMID: 29906417 PMCID: PMC6120784 DOI: 10.1053/j.gastro.2018.05.050] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS MicroRNA (miRNA) is highly stable in biospecimens and provides tissue-specific profiles, making it a useful biomarker of carcinogenesis. We aimed to discover a set of miRNAs that could accurately discriminate Barrett's esophagus (BE) from normal esophageal tissue and to test its diagnostic accuracy when applied to samples collected by a noninvasive esophageal cell sampling device. METHODS We analyzed miRNA expression profiles of 2 independent sets of esophageal biopsy tissues collected during endoscopy from 38 patients with BE and 26 patients with normal esophagus (controls) using Agilent microarray and Nanostring nCounter assays. Consistently up-regulated miRNAs were quantified by real-time polymerase chain reaction in esophageal tissues collected by Cytosponge from patients with BE vs without BE. miRNAs were expressed from plasmids and antisense oligonucleotides were expressed in normal esophageal squamous cells; effects on proliferation and gene expression patterns were analyzed. RESULTS We identified 15 miRNAs that were significantly up-regulated in BE vs control tissues. Of these, 11 (MIR215, MIR194, MIR 192, MIR196a, MIR199b, MIR10a, MIR145, MIR181a, MIR30a, MIR7, and MIR199a) were validated in Cytosponge samples. The miRNAs with the greatest increases in BE tissues (7.9-fold increase in expression or more, P < .0001: MIR196a, MIR192, MIR194, and MIR215) each identified BE vs control tissues with area under the curve (AUC) values of 0.82 or more. We developed an optimized multivariable logistic regression model, based on expression levels of 6 miRNAs (MIR7, MIR30a, MIR181a, MIR192, MIR196a, and MIR199a), that identified patients with BE with an AUC value of 0.89, 86.2% sensitivity, and 91.6% specificity. Expression level of MIR192, MIR196a, MIR199a, combined that of trefoil factor 3, identified patients with BE with an AUC of 0.93, 93.1% sensitivity, and 93.7% specificity. Hypomethylation was observed in the promoter region of the highly up-regulated cluster MIR192-MIR194. Overexpression of these miRNAs in normal esophageal squamous cells increased their proliferation, via GRHL3 and PTEN signaling. CONCLUSIONS In analyses of miRNA expression patterns of BE vs non-BE tissues, we identified a profile that can identify Cytosponge samples from patients with BE with an AUC of 0.93. Expression of MIR194 is increased in BE samples via epigenetic mechanisms that might be involved in BE pathogenesis.
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Affiliation(s)
- Xiaodun Li
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Sam Kleeman
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Sally B. Coburn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Carlo Fumagalli
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Juliane Perner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sriganesh Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Linda Orzolek
- Johns Hopkins Medical Institutions Deep Sequencing and Microarray Core, Baltimore, Maryland
| | - Haiping Hao
- Johns Hopkins Medical Institutions Deep Sequencing and Microarray Core, Baltimore, Maryland
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | | | - Núria Galeano-Dalmau
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Pierre Lao-Sirieix
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Maria Tennyson
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Shona MacRae
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland,Reprint requests Address requests for reprints to: Michael B. Cook, PhD, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK,Rebecca C. Fitzgerald, MD, MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, UK CB2 0XZ.
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15
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MiR-99b-5p and miR-203a-3p Function as Tumor Suppressors by Targeting IGF-1R in Gastric Cancer. Sci Rep 2018; 8:10119. [PMID: 29973668 PMCID: PMC6031697 DOI: 10.1038/s41598-018-27583-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/05/2018] [Indexed: 01/19/2023] Open
Abstract
MicroRNAs (miRNAs) have been explored in many critical cellular processes, including proliferation and apoptosis. The purpose of this study was to detect the biological function and regulation of miR-99b-5p and miR-203a-3p in gastric cancer (GC). Here, we demonstrated that miR-99b-5p/203a-3p were downregulated in both GC tissues and cell lines. MiR-99b-5p/203a-3p overexpression reduced GC cell proliferation and cell cycle progression in vitro. Notably, we combined bioinformatics tools with biological validation assays to demonstrate that insulin-like growth factor 1 receptor (IGF-1R) is a direct co-target and functional mediator of miR-99b-5p/203a-3p in GC cells. Mechanistically, the AKT pathway, which is downstream of IGF-1R, is essential for the functional roles of miR-99b-5p/203a-3p in GC cells. Taken together, our data revealed that IGF-1R is a direct co-target of miR-99b-5p/203a-3p, and miR-99b-5p/203a-3p may function as tumor suppressive miRNAs by negatively regulating IGF-1R expression in GC cells.
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16
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Kalariya N, Brassil K, Calin G. MicroRNAs: Clinical Trials and Potential Applications
. Clin J Oncol Nurs 2018; 21:554-559. [PMID: 28945717 DOI: 10.1188/17.cjon.554-559] [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] [Indexed: 11/17/2022]
Abstract
MicroRNAs are novel biomolecules with a crucial function in normal cellular physiology and in pathophysiologic conditions, including cancer. Since the first report on the link between microRNAs and cancer was published in 2002, research has revealed the potential clinical implications of microRNAs. Oncology nurses play an important role in educating patients and their families about possible applications of microRNAs in oncology.
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17
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Chen L, Yang J, Lü J, Cao S, Zhao Q, Yu Z. Identification of aberrant circulating miRNAs in Parkinson's disease plasma samples. Brain Behav 2018; 8:e00941. [PMID: 29670823 PMCID: PMC5893342 DOI: 10.1002/brb3.941] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 01/12/2018] [Accepted: 01/14/2018] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE To detect the aberrant expression of circulating miRNAs and explore the potential early diagnostic biomarkers in patients with Parkinson's disease (PD). METHODS Plasma samples were collected from 25 treatment-naïve PD-diagnosed patients and 25 healthy controls followed by a real-time PCR-based miRNA screening analysis of neuron disease-related miRNAs. RESULTS A subset of miRNAs with aberrant expression levels in the plasma of PD-diagnosed patients were identified including upregulation of miR-27a and downregulation of let-7a, let-7f, miR-142-3p, and miR-222 with the AUC values more than 0.8 derived from the receiver operating characteristic curves. CONCLUSIONS The high sensitivity and specificity of the circulating miRNAs may enable early diagnosis of PD. The study provides a group of novel miRNA candidates for detecting PD.
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Affiliation(s)
- Lei Chen
- Department of NeurologyTianjin Huan Hu Hospital Jinnan District, Tianjin China.,Tianjin Key Laboratory of Cerebrovascular and Neurodegenerative Diseases Tianjin China
| | - Junxiu Yang
- Department of Neurology Hospital of Integrated Traditional and Western Medicine Cangzhou China
| | - Jinhui Lü
- Research Center for Translational Medicine East Hospital Tongji University School of Medicine Shanghai China
| | - Shanshan Cao
- Department of NeurologyTianjin Huan Hu Hospital Jinnan District, Tianjin China.,Tianjin Key Laboratory of Cerebrovascular and Neurodegenerative Diseases Tianjin China
| | - Qian Zhao
- Research Center for Translational Medicine East Hospital Tongji University School of Medicine Shanghai China
| | - Zuoren Yu
- Research Center for Translational Medicine East Hospital Tongji University School of Medicine Shanghai China
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18
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Androvic P, Valihrach L, Elling J, Sjoback R, Kubista M. Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification. Nucleic Acids Res 2017; 45:e144. [PMID: 28911110 PMCID: PMC5587787 DOI: 10.1093/nar/gkx588] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/28/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on two-step RT-qPCR with SYBR-green detection chemistry called Two-tailed RT-qPCR. It takes advantage of novel, target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of seven logs and a sensitivity sufficient to detect down to ten target miRNA molecules. It is capable to capture the full isomiR repertoire, leading to accurate representation of the complete miRNA content in a sample. The reverse transcription step can be multiplexed and the miRNA profiles measured with Two-tailed RT-qPCR show excellent correlation with the industry standard TaqMan miRNA assays (r2 = 0.985). Moreover, Two-tailed RT-qPCR allows for rapid testing with a total analysis time of less than 2.5 hours.
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Affiliation(s)
- Peter Androvic
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc 783 71, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic
| | | | | | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,TATAA Biocenter AB, Gothenburg 411 03, Sweden
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19
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Differential expression of miR-184 in temporal lobe epilepsy patients with and without hippocampal sclerosis - Influence on microglial function. Sci Rep 2016; 6:33943. [PMID: 27666871 PMCID: PMC5036198 DOI: 10.1038/srep33943] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/06/2016] [Indexed: 12/21/2022] Open
Abstract
Epilepsy is one of the most common neurological disorders characterized by recurrent seizures due to neuronal hyperexcitability. Here we compared miRNA expression patterns in mesial temporal lobe epilepsy with and without hippocampal sclerosis (mTLE + HS and mTLE −HS) to investigate the regulatory mechanisms differentiating both patient groups. Whole genome miRNA sequencing in surgically resected hippocampi did not reveal obvious differences in expression profiles between the two groups of patients. However, one microRNA (miR-184) was significantly dysregulated, which was confirmed by qPCR. We observed that overexpression of miR-184 inhibited cytokine release after LPS stimulation in primary microglial cells, while it did not affect the viability of murine primary neurons and primary astrocytes. Pathway analysis revealed that miR-184 is potentially involved in the regulation of inflammatory signal transduction and apoptosis. Dysregulation of some the potential miR-184 target genes was confirmed by qPCR and 3′UTR luciferase reporter assay. The reduced expression of miR-184 observed in patients with mTLE + HS together with its anti-inflammatory effects indicate that miR-184 might be involved in the modulation of inflammatory processes associated with hippocampal sclerosis which warrants further studies elucidating the role of miR-184 in the pathophysiology of mTLE.
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20
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Svoboda P. A toolbox for miRNA analysis. FEBS Lett 2015; 589:1694-701. [DOI: 10.1016/j.febslet.2015.04.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/28/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022]
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21
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Pimentel F, Bonilla P, Ravishankar YG, Contag A, Gopal N, LaCour S, Lee T, Niemz A. Technology in MicroRNA Profiling: Circulating MicroRNAs as Noninvasive Cancer Biomarkers in Breast Cancer. ACTA ACUST UNITED AC 2014; 20:574-88. [PMID: 25524488 DOI: 10.1177/2211068214561788] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Indexed: 12/13/2022]
Abstract
This report describes technologies to identify and quantify microRNAs (miRNAs) as potential cancer biomarkers, using breast cancer as an example. Most breast cancer patients are not diagnosed until the disease has advanced to later stages, which decreases overall survival rates. Specific miRNAs are up- or downregulated in breast cancer patients at various stages, can be detected in plasma and serum, and have shown promising preliminary clinical sensitivity and specificity for early cancer diagnosis or staging. Nucleic acid testing methods to determine relative concentrations of selected miRNAs include reverse transcription, followed by quantitative PCR (RT-qPCR), microarrays, and next-generation sequencing (NGS). Of these methods, NGS is the most powerful approach for miRNA biomarker discovery, whereas RT-qPCR shows the most promise for eventual clinical diagnostic applications.
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Affiliation(s)
- Fernando Pimentel
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Patricia Bonilla
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | | | - Alec Contag
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Nimish Gopal
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Sarah LaCour
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Trenton Lee
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
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22
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Chandran PA, Keller A, Weinmann L, Seida AA, Braun M, Andreev K, Fischer B, Horn E, Schwinn S, Junker M, Houben R, Dombrowski Y, Dietl J, Finotto S, Wölfl M, Meister G, Wischhusen J. The TGF-β-inducible miR-23a cluster attenuates IFN-γ levels and antigen-specific cytotoxicity in human CD8⁺ T cells. J Leukoc Biol 2014; 96:633-45. [PMID: 25030422 DOI: 10.1189/jlb.3a0114-025r] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cytokine secretion and degranulation represent key components of CD8(+) T-cell cytotoxicity. While transcriptional blockade of IFN-γ and inhibition of degranulation by TGF-β are well established, we wondered whether TGF-β could also induce immune-regulatory miRNAs in human CD8(+) T cells. We used miRNA microarrays and high-throughput sequencing in combination with qRT-PCR and found that TGF-β promotes expression of the miR-23a cluster in human CD8(+) T cells. Likewise, TGF-β up-regulated expression of the cluster in CD8(+) T cells from wild-type mice, but not in cells from mice with tissue-specific expression of a dominant-negative TGF-β type II receptor. Reporter gene assays including site mutations confirmed that miR-23a specifically targets the 3'UTR of CD107a/LAMP1 mRNA, whereas the further miRNAs expressed in this cluster-namely, miR-27a and -24-target the 3'UTR of IFN-γ mRNA. Upon modulation of the miR-23a cluster by the respective miRNA antagomirs and mimics, we observed significant changes in IFN-γ expression, but only slight effects on CD107a/LAMP1 expression. Still, overexpression of the cluster attenuated the cytotoxic activity of antigen-specific CD8(+) T cells. These functional data thus reveal that the miR-23a cluster not only is induced by TGF-β, but also exerts a suppressive effect on CD8(+) T-cell effector functions, even in the absence of TGF-β signaling.
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Affiliation(s)
- P Anoop Chandran
- Graduate School of Life Sciences (GSLS), University of Würzburg, Germany; Department of Obstetrics and Gynecology
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Lasse Weinmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ahmed Adel Seida
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research
| | - Matthias Braun
- Pediatric Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital
| | - Katerina Andreev
- Laboratory of Cellular and Molecular Lung Immunology, Institute of Molecular Pneumology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; and
| | | | - Evi Horn
- Department of Obstetrics and Gynecology
| | - Stefanie Schwinn
- Pediatric Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital
| | - Markus Junker
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research
| | - Roland Houben
- Department of Dermatology, University of Würzburg Medical School, Würzburg, Germany
| | - Yvonne Dombrowski
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research
| | | | - Susetta Finotto
- Laboratory of Cellular and Molecular Lung Immunology, Institute of Molecular Pneumology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; and
| | - Matthias Wölfl
- Pediatric Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital
| | - Gunter Meister
- Max Planck Institute of Biochemistry, Martinsried, Germany; Department of Biochemistry, University of Regensburg, Germany
| | - Jörg Wischhusen
- Department of Obstetrics and Gynecology, Interdisciplinary Center for Clinical Research,
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Degliangeli F, Pompa PP, Fiammengo R. Nanotechnology-based strategies for the detection and quantification of microRNA. Chemistry 2014; 20:9476-92. [PMID: 24989446 DOI: 10.1002/chem.201402649] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression, and many pathological conditions, including cancer, are characterized by altered miRNA expression levels. Therefore, accurate and sensitive quantification of miRNAs may result in correct disease diagnosis establishing these small noncoding RNA transcripts as valuable biomarkers. Aiming at overcoming some limitations of conventional quantification strategies, nanotechnology is currently providing numerous significant alternatives to miRNA sensing. In this review an up-to-date account of nanotechnology-based strategies for miRNA detection and quantification is given. The topics covered are: nanoparticle-based approaches in solution, sensing based on nanostructured surfaces, combined nanoparticle/surface sensing approaches, and single-molecule approaches.
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Affiliation(s)
- Federica Degliangeli
- Center for Biomolecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia (IIT), Via Barsanti, 73010 Arnesano (Lecce) (Italy)
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Pagani M, Rossetti G, Panzeri I, de Candia P, Bonnal RJP, Rossi RL, Geginat J, Abrignani S. Role of microRNAs and long-non-coding RNAs in CD4(+) T-cell differentiation. Immunol Rev 2013; 253:82-96. [PMID: 23550640 DOI: 10.1111/imr.12055] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
CD4(+) T lymphocytes orchestrate adaptive immune responses by differentiating into various subsets of effector T cells such as T-helper 1 (Th1), Th2, Th17, and regulatory T cells. These subsets have been generally described by master transcription factors that dictate the expression of cytokines and receptors, which ultimately define lymphocyte effector functions. However, the view of T-lymphocyte subsets as stable and terminally differentiated lineages has been challenged by increasing evidence of functional plasticity within CD4(+) T-cell subsets, which implies flexible programming of effector functions depending on time and space of T-cell activation. An outstanding question with broad basic and traslational implications relates to the mechanisms, besides transcriptional regulation, which define the plasticity of effector functions. In this study, we discuss the emerging role of regulatory non-coding RNAs in T-cell differentiation and plasticity. Not only microRNAs have been proven to be important for CD4(+) T-cell differentiation, but it is also likely that the overall T-cell functioning is the result of a multilayered network composed by coding RNAs as well as by short and long non-coding RNAs. The integrated study of all the nodes of this network will provide a comprehensive view of the molecular mechanisms underlying T-cell functions in health and disease.
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25
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Hermansen SK, Kristensen BW. MicroRNA biomarkers in glioblastoma. J Neurooncol 2013; 114:13-23. [PMID: 23700324 DOI: 10.1007/s11060-013-1155-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/12/2013] [Indexed: 12/27/2022]
Abstract
Recent research suggests that deregulation of microRNAs (miRNAs) is involved in initiation and progression of many cancers, including gliomas and that miRNAs hold great potential as future diagnostic and therapeutic tools in cancer. MiRNAs are a class of short non-coding RNA sequences (18-24 nucleotides), which base-pair to target messenger RNA (mRNA) and thereby cause translational repression or mRNA degradation based on the level of complementarity between strands. Profiling miRNAs in clinical glioblastoma samples has shown aberrant expression of numerous miRNAs when compared to normal brain tissues. Understanding these alterations is key to developing new biomarkers and intelligent treatment strategies. This review presents an overview of current knowledge about miRNA alterations in glioblastoma while focusing on the clinical future of miRNAs as biomarkers and discussing the strengths and weaknesses of various methods used in evaluating their expression.
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Affiliation(s)
- Simon Kjær Hermansen
- Department of Pathology, Odense University Hospital, Winsløwparken 15, 3. Floor, 5000, Odense C, Denmark.
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Jimenez-Mateos E, Henshall D. Epilepsy and microRNA. Neuroscience 2013; 238:218-29. [DOI: 10.1016/j.neuroscience.2013.02.027] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/18/2013] [Accepted: 02/15/2013] [Indexed: 12/11/2022]
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Burgos KL, Javaherian A, Bomprezzi R, Ghaffari L, Rhodes S, Courtright A, Tembe W, Kim S, Metpally R, Van Keuren-Jensen K. Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing. RNA (NEW YORK, N.Y.) 2013; 19:712-22. [PMID: 23525801 PMCID: PMC3677285 DOI: 10.1261/rna.036863.112] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
There has been a growing interest in using next-generation sequencing (NGS) to profile extracellular small RNAs from the blood and cerebrospinal fluid (CSF) of patients with neurological diseases, CNS tumors, or traumatic brain injury for biomarker discovery. Small sample volumes and samples with low RNA abundance create challenges for downstream small RNA sequencing assays. Plasma, serum, and CSF contain low amounts of total RNA, of which small RNAs make up a fraction. The purpose of this study was to maximize RNA isolation from RNA-limited samples and apply these methods to profile the miRNA in human CSF by small RNA deep sequencing. We systematically tested RNA isolation efficiency using ten commercially available kits and compared their performance on human plasma samples. We used RiboGreen to quantify total RNA yield and custom TaqMan assays to determine the efficiency of small RNA isolation for each of the kits. We significantly increased the recovery of small RNA by repeating the aqueous extraction during the phenol-chloroform purification in the top performing kits. We subsequently used the methods with the highest small RNA yield to purify RNA from CSF and serum samples from the same individual. We then prepared small RNA sequencing libraries using Illumina's TruSeq sample preparation kit and sequenced the samples on the HiSeq 2000. Not surprisingly, we found that the miRNA expression profile of CSF is substantially different from that of serum. To our knowledge, this is the first time that the small RNA fraction from CSF has been profiled using next-generation sequencing.
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Affiliation(s)
| | - Ashkan Javaherian
- Translational Genomics Research Institute, Phoenix, Arizona 85003, USA
| | - Roberto Bomprezzi
- Barrow Neurological Institute at St. Joseph’s Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Layla Ghaffari
- Translational Genomics Research Institute, Phoenix, Arizona 85003, USA
| | - Susan Rhodes
- Barrow Neurological Institute at St. Joseph’s Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Amanda Courtright
- Translational Genomics Research Institute, Phoenix, Arizona 85003, USA
| | - Waibhav Tembe
- Translational Genomics Research Institute, Phoenix, Arizona 85003, USA
| | - Seungchan Kim
- Translational Genomics Research Institute, Phoenix, Arizona 85003, USA
| | - Raghu Metpally
- Translational Genomics Research Institute, Phoenix, Arizona 85003, USA
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MicroRNA profiling methods applied to recent studies of fetal mouse submandibular gland development. J Oral Biosci 2012. [DOI: 10.1016/j.job.2012.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues. PLoS One 2012; 7:e45105. [PMID: 23028787 PMCID: PMC3441572 DOI: 10.1371/journal.pone.0045105] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 08/14/2012] [Indexed: 01/06/2023] Open
Abstract
Background Microarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been systematically compared but only in few cases using clinical samples. Methodology/Principal Findings We investigated the inter-platform reproducibility of four miRNA microarray platforms (Agilent, Exiqon, Illumina, and Miltenyi), comparing nine paired tumor/normal colon tissues. The most concordant and selected discordant miRNAs were further studied by quantitative RT-PCR. Globally, a poor overlap among differentially expressed miRNAs identified by each platform was found. Nevertheless, for eight miRNAs high agreement in differential expression among the four platforms and comparability to qRT-PCR was observed. Furthermore, most of the miRNA sets identified by each platform are coherently enriched in data from the other platforms and the great majority of colon cancer associated miRNA sets derived from the literature were validated in our data, independently from the platform. Computational integration of miRNA and gene expression profiles suggested that anti-correlated predicted target genes of differentially expressed miRNAs are commonly enriched in cancer-related pathways and in genes involved in glycolysis and nutrient transport. Conclusions Technical and analytical challenges in measuring miRNAs still remain and further research is required in order to increase consistency between different microarray-based methodologies. However, a better inter-platform agreement was found by looking at miRNA sets instead of single miRNAs and through a miRNAs – gene expression integration approach.
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