1
|
Mansueto G, Fusco G, Colonna G. A Tiny Viral Protein, SARS-CoV-2-ORF7b: Functional Molecular Mechanisms. Biomolecules 2024; 14:541. [PMID: 38785948 PMCID: PMC11118181 DOI: 10.3390/biom14050541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study presents the interaction with the human host metabolism of SARS-CoV-2 ORF7b protein (43 aa), using a protein-protein interaction network analysis. After pruning, we selected from BioGRID the 51 most significant proteins among 2753 proven interactions and 1708 interactors specific to ORF7b. We used these proteins as functional seeds, and we obtained a significant network of 551 nodes via STRING. We performed topological analysis and calculated topological distributions by Cytoscape. By following a hub-and-spoke network architectural model, we were able to identify seven proteins that ranked high as hubs and an additional seven as bottlenecks. Through this interaction model, we identified significant GO-processes (5057 terms in 15 categories) induced in human metabolism by ORF7b. We discovered high statistical significance processes of dysregulated molecular cell mechanisms caused by acting ORF7b. We detected disease-related human proteins and their involvement in metabolic roles, how they relate in a distorted way to signaling and/or functional systems, in particular intra- and inter-cellular signaling systems, and the molecular mechanisms that supervise programmed cell death, with mechanisms similar to that of cancer metastasis diffusion. A cluster analysis showed 10 compact and significant functional clusters, where two of them overlap in a Giant Connected Component core of 206 total nodes. These two clusters contain most of the high-rank nodes. ORF7b acts through these two clusters, inducing most of the metabolic dysregulation. We conducted a co-regulation and transcriptional analysis by hub and bottleneck proteins. This analysis allowed us to define the transcription factors and miRNAs that control the high-ranking proteins and the dysregulated processes within the limits of the poor knowledge that these sectors still impose.
Collapse
Affiliation(s)
- Gelsomina Mansueto
- Dipartimento di Scienze Mediche e Chirurgiche Avanzate, Università della Campania, L. Vanvitelli, 80138 Naples, Italy;
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Giovanni Colonna
- Medical Informatics AOU, Università della Campania, L. Vanvitelli, 80138 Naples, Italy
| |
Collapse
|
2
|
Ye Q, Raese RA, Luo D, Feng J, Xin W, Dong C, Qian Y, Guo NL. MicroRNA-Based Discovery of Biomarkers, Therapeutic Targets, and Repositioning Drugs for Breast Cancer. Cells 2023; 12:1917. [PMID: 37508580 PMCID: PMC10378316 DOI: 10.3390/cells12141917] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer treatment can be improved with biomarkers for early detection and individualized therapy. A set of 86 microRNAs (miRNAs) were identified to separate breast cancer tumors from normal breast tissues (n = 52) with an overall accuracy of 90.4%. Six miRNAs had concordant expression in both tumors and breast cancer patient blood samples compared with the normal control samples. Twelve miRNAs showed concordant expression in tumors vs. normal breast tissues and patient survival (n = 1093), with seven as potential tumor suppressors and five as potential oncomiRs. From experimentally validated target genes of these 86 miRNAs, pan-sensitive and pan-resistant genes with concordant mRNA and protein expression associated with in-vitro drug response to 19 NCCN-recommended breast cancer drugs were selected. Combined with in-vitro proliferation assays using CRISPR-Cas9/RNAi and patient survival analysis, MEK inhibitors PD19830 and BRD-K12244279, pilocarpine, and tremorine were discovered as potential new drug options for treating breast cancer. Multi-omics biomarkers of response to the discovered drugs were identified using human breast cancer cell lines. This study presented an artificial intelligence pipeline of miRNA-based discovery of biomarkers, therapeutic targets, and repositioning drugs that can be applied to many cancer types.
Collapse
Affiliation(s)
- Qing Ye
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Rebecca A Raese
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Dajie Luo
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Juan Feng
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Wenjun Xin
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Chunlin Dong
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Yong Qian
- Health Effects Laboratory Division, National Institute for Occupational and Safety & Health, Morgantown, WV 26505, USA
| | - Nancy Lan Guo
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
- Department of Occupational and Environmental Health Sciences, School of Public Health, West Virginia University, Morgantown, WV 26506, USA
| |
Collapse
|
3
|
Attomolar sensitivity microRNA detection using real-time digital microarrays. Sci Rep 2022; 12:16220. [PMID: 36171215 PMCID: PMC9519543 DOI: 10.1038/s41598-022-19912-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/06/2022] [Indexed: 11/08/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of noncoding, functional RNAs. With recent developments in molecular biology, miRNA detection has attracted significant interest, as hundreds of miRNAs and their expression levels have shown to be linked to various diseases such as infections, cardiovascular disorders and cancers. A powerful and high throughput tool for nucleic acid detection is the DNA microarray technology. However, conventional methods do not meet the demands in sensitivity and specificity, presenting significant challenges for the adaptation of miRNA detection for diagnostic applications. In this study, we developed a highly sensitive and multiplexed digital microarray using plasmonic gold nanorods as labels. For proof of concept studies, we conducted experiments with two miRNAs, miRNA-451a (miR-451) and miRNA-223-3p (miR-223). We demonstrated improvements in sensitivity in comparison to traditional end-point assays that employ capture on solid phase support, by implementing real-time tracking of the target molecules on the sensor surface. Particle tracking overcomes the sensitivity limitations for detection of low-abundance biomarkers in the presence of low-affinity but high-abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$\sim$$\end{document}∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.
Collapse
|
4
|
Habib S, Singh M. Carbon-based Nanomaterials for delivery of small RNA molecules: a focus on potential cancer treatment applications. Pharm Nanotechnol 2022; 10:PNT-EPUB-124198. [PMID: 35670355 DOI: 10.2174/2211738510666220606102906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/17/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleic acid-mediated therapy holds immense potential in the treatment of recalcitrant human diseases such as cancer. This is underscored by advances in understanding the mechanisms of gene regulation. In particular, the endogenous protective mechanism of gene silencing known as RNA interference (RNAi) has been extensively exploited. METHODS We review here the developments from 2011 to 2021, in the use of nanographene oxide, carbon nanotubes, fullerenes, carbon nanohorns, carbon nanodots and nanodiamonds for the delivery of therapeutic small RNA molecules. RESULTS Appropriately designed effector molecules such as small interfering RNA (siRNA), can, in theory, silence the expression of any disease-causing gene. Alternatively, siRNA can be generated in vivo through the introduction of plasmid-based short hairpin RNA (shRNA) expression vectors. Other small RNAs such as micro RNA (miRNA) also function in post-transcriptional gene regulation and are aberrantly expressed under disease conditions. The miRNA-based therapy involves either restoration of miRNA function through the introduction of miRNA mimics; or the inhibition of miRNA function by delivering anti-miRNA oligomers. However, the large size, hydrophilicity, negative charge and nuclease-sensitivity of nucleic acids necessitate an appropriate carrier for their introduction as medicine into cells. CONCLUSION While numerous organic and inorganic materials have been investigated for this purpose, the perfect carrier agent remains elusive. In recent years, carbon-based nanomaterials have received widespread attention in biotechnology due to their tunable surface characteristics, mechanical, electrical, optical and chemical properties.
Collapse
Affiliation(s)
- Saffiya Habib
- Nano-Gene and Drug Delivery Laboratory, Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Moganavelli Singh
- Nano-Gene and Drug Delivery Laboratory, Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| |
Collapse
|
5
|
Wei JJ. Linking altered microRNA expression to racial disparities in uterine serous carcinoma. Gynecol Oncol 2021; 163:446-447. [PMID: 34836615 DOI: 10.1016/j.ygyno.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022]
Affiliation(s)
- Jian-Jun Wei
- Department of Pathology, Department Obstetrics and Gynecology, Northwestern University, Feinberg School of Medicine, 251 East Huron Street, Feinberg 7-334, Chicago, IL 60611, USA.
| |
Collapse
|
6
|
Tran HV, Piro B. Recent trends in application of nanomaterials for the development of electrochemical microRNA biosensors. Mikrochim Acta 2021; 188:128. [PMID: 33740140 DOI: 10.1007/s00604-021-04784-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/10/2021] [Indexed: 01/10/2023]
Abstract
The biology of the late twentieth century was marked by the discovery in 1993 of a new class of small non-coding ribonucleic acids (RNAs) which play major roles in regulating the translation and degradation of messenger RNAs. These small RNAs (18-25 nucleotides), called microRNAs (miRNAs), are implied in several biological processes such as differentiation, metabolic homeostasis, or cellular apoptosis and proliferation. The discovery in 2008 that the presence of miRNAs in body fluids could be correlated with cancer (prostate, breast, colon, lung, etc.) or other diseases (diabetes, heart diseases, etc.) has made them new key players as biomarkers. Therefore, miRNA detection is of considerable significance in both disease diagnosis and in the study of miRNA function. Until these days, more than 1200 miRNAs have been identified. However, traditional methods developed for conventional DNA does not apply satisfactorily for miRNA, in particular due to the low expression level of these miRNA in biofluids, and because they are very short strands. Electrochemical biosensors can provide this sensitivity and also offer the advantages of mass fabrication, low-cost, and potential decentralized analysis, which has wide application for microRNAs sensing, with many promising results already reported. The present review summarizes some newly developed electrochemical miRNA detection methods.
Collapse
Affiliation(s)
- Hoang Vinh Tran
- School of Chemical Engineering, Hanoi University of Science and Technology (HUST), 1st Dai Co Viet Road, Hanoi, Vietnam.
| | - Benoit Piro
- ITODYS, CNRS, Université de Paris, F-75006, Paris, France
| |
Collapse
|
7
|
Coccia E, Masanas M, López-Soriano J, Segura MF, Comella JX, Pérez-García MJ. FAIM Is Regulated by MiR-206, MiR-1-3p and MiR-133b. Front Cell Dev Biol 2021; 8:584606. [PMID: 33425889 PMCID: PMC7785887 DOI: 10.3389/fcell.2020.584606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/27/2020] [Indexed: 12/17/2022] Open
Abstract
Apoptosis plays an important role during development, control of tissue homeostasis and in pathological contexts. Apoptosis is executed mainly through the intrinsic pathway or the death receptor pathway, i.e., extrinsic pathway. These processes are tightly controlled by positive and negative regulators that dictate pro- or anti-apoptotic death receptor signaling. One of these regulators is the Fas Apoptotic Inhibitory Molecule (FAIM). This death receptor antagonist has two main isoforms, FAIM-S (short) which is the ubiquitously expressed, and a longer isoform, FAIM-L (long), which is mainly expressed in the nervous system. Despite its role as a death receptor antagonist, FAIM also participates in cell death-independent processes such as nerve growth factor-induced neuritogenesis or synaptic transmission. Moreover, FAIM isoforms have been implicated in blocking the formation of protein aggregates under stress conditions or de-regulated in certain pathologies such as Alzheimer’s and Parkinson’s diseases. Despite the role of FAIM in physiological and pathological processes, little is known about the molecular mechanisms involved in the regulation of its expression. Here, we seek to investigate the post-transcriptional regulation of FAIM isoforms by microRNAs (miRNAs). We found that miR-206, miR-1-3p, and miR-133b are direct regulators of FAIM expression. These findings provide new insights into the regulation of FAIM and may provide new opportunities for therapeutic intervention in diseases in which the expression of FAIM is altered.
Collapse
Affiliation(s)
- Elena Coccia
- Cell Signaling and Apoptosis Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marc Masanas
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-UAB, Barcelona, Spain
| | - Joaquín López-Soriano
- Cell Signaling and Apoptosis Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Miguel F Segura
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-UAB, Barcelona, Spain
| | - Joan X Comella
- Cell Signaling and Apoptosis Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M José Pérez-García
- Cell Signaling and Apoptosis Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| |
Collapse
|
8
|
Jebelli A, Oroojalian F, Fathi F, Mokhtarzadeh A, Guardia MDL. Recent advances in surface plasmon resonance biosensors for microRNAs detection. Biosens Bioelectron 2020; 169:112599. [DOI: 10.1016/j.bios.2020.112599] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022]
|
9
|
Park HJ, Lee SS. Detection of miR‐155 Using Two Types of Electrochemical Approaches. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hyeoun Ji Park
- Department of Pharmaceutical Engineering Soonchunhhyang University Chungnam 31538 South Korea
| | - Soo Suk Lee
- Department of Pharmaceutical Engineering Soonchunhhyang University Chungnam 31538 South Korea
| |
Collapse
|
10
|
A label-free mass spectrometry detection of microRNA by signal switching from high-molecular-weight polynucleotides to highly sensitive small molecules. Talanta 2020; 224:121899. [PMID: 33379105 DOI: 10.1016/j.talanta.2020.121899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are associated with various cellular processes and have been recognized as potential biomarkers for many human diseases. The sensitive and accurate determination of miRNA expression levels in biological specimens is highly significant for understanding their biological functions and clinical diagnosis. Mass spectrometry (MS) has shown its potential to study bioactive molecules, however, direct MS analysis of miRNAs is often hampered by limited sensitivity. For sensitive detection of miRNAs, indirect methods are generally employed through the use of DNA probes labeled with peptides or metal elements. In this work, we proposed a novel MS-based label-free strategy for miRNA quantification. A dual-amplification system was developed by using a padlock probe containing the poly(thymine) sequence in combination with rolling circle amplification (RCA). The specific recognition of target miRNA by the padlock probes produced long single-stranded DNAs containing poly (adenine) segments, which guaranteed the specificity of detection and realized primary amplification. Then the RCA products were extracted and treated with acid to release a large number of free adenines as reporter molecules for secondary signal amplification. Overall, the quantification of target miRNA was carried out by signal switching from high-molecular-weight RCA products to highly sensitive small molecule of adenine. The developed method achieved a linear detection range from 200 amol to 100 fmol for miRNA-21 with a limit of detection of 50 amol, and successfully applied to detect endogenous miRNA-21 levels from lung cancer cells. Overall, the present study provides a sensitive, specific MS-based method for miRNA detection and holds great potential for further application of MS technology to detect other biomarkers in biomedical research and early clinical diagnosis.
Collapse
|
11
|
Obrador E, Salvador R, Villaescusa JI, Soriano JM, Estrela JM, Montoro A. Radioprotection and Radiomitigation: From the Bench to Clinical Practice. Biomedicines 2020; 8:E461. [PMID: 33142986 PMCID: PMC7692399 DOI: 10.3390/biomedicines8110461] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
The development of protective agents against harmful radiations has been a subject of investigation for decades. However, effective (ideal) radioprotectors and radiomitigators remain an unsolved problem. Because ionizing radiation-induced cellular damage is primarily attributed to free radicals, radical scavengers are promising as potential radioprotectors. Early development of such agents focused on thiol synthetic compounds, e.g., amifostine (2-(3-aminopropylamino) ethylsulfanylphosphonic acid), approved as a radioprotector by the Food and Drug Administration (FDA, USA) but for limited clinical indications and not for nonclinical uses. To date, no new chemical entity has been approved by the FDA as a radiation countermeasure for acute radiation syndrome (ARS). All FDA-approved radiation countermeasures (filgrastim, a recombinant DNA form of the naturally occurring granulocyte colony-stimulating factor, G-CSF; pegfilgrastim, a PEGylated form of the recombinant human G-CSF; sargramostim, a recombinant granulocyte macrophage colony-stimulating factor, GM-CSF) are classified as radiomitigators. No radioprotector that can be administered prior to exposure has been approved for ARS. This differentiates radioprotectors (reduce direct damage caused by radiation) and radiomitigators (minimize toxicity even after radiation has been delivered). Molecules under development with the aim of reaching clinical practice and other nonclinical applications are discussed. Assays to evaluate the biological effects of ionizing radiations are also analyzed.
Collapse
Affiliation(s)
- Elena Obrador
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain; (E.O.); (R.S.); (J.M.E.)
| | - Rosario Salvador
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain; (E.O.); (R.S.); (J.M.E.)
| | - Juan I. Villaescusa
- Service of Radiological Protection, Clinical Area of Medical Image, La Fe University Hospital, 46026 Valencia, Spain;
- Biomedical Imaging Research Group GIBI230, Health Research Institute (IISLaFe), La Fe University Hospital, 46026 Valencia, Spain
| | - José M. Soriano
- Food & Health Lab, Institute of Materials Science, University of Valencia, 46980 Valencia, Spain;
- Joint Research Unit in Endocrinology, Nutrition and Clinical Dietetics, University of Valencia-Health Research Institute IISLaFe, 46026 Valencia, Spain
| | - José M. Estrela
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain; (E.O.); (R.S.); (J.M.E.)
| | - Alegría Montoro
- Service of Radiological Protection, Clinical Area of Medical Image, La Fe University Hospital, 46026 Valencia, Spain;
- Biomedical Imaging Research Group GIBI230, Health Research Institute (IISLaFe), La Fe University Hospital, 46026 Valencia, Spain
| |
Collapse
|
12
|
Torma F, Gombos Z, Jokai M, Berkes I, Takeda M, Mimura T, Radak Z, Gyori F. The roles of microRNA in redox metabolism and exercise-mediated adaptation. JOURNAL OF SPORT AND HEALTH SCIENCE 2020; 9:405-414. [PMID: 32780693 PMCID: PMC7498669 DOI: 10.1016/j.jshs.2020.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/03/2020] [Accepted: 02/10/2020] [Indexed: 05/10/2023]
Abstract
MicroRNAs (miRs) are small regulatory RNA transcripts capable of post-transcriptional silencing of mRNA messages by entering a cellular bimolecular apparatus called RNA-induced silencing complex. miRs are involved in the regulation of cellular processes producing, eliminating or repairing the damage caused by reactive oxygen species, and they are active players in redox homeostasis. Increased mitochondrial biogenesis, function and hypertrophy of skeletal muscle are important adaptive responses to regular exercise. In the present review, we highlight some of the redox-sensitive regulatory roles of miRs.
Collapse
Affiliation(s)
- Ferenc Torma
- Research Center of Molecular Exercise Science, University of Physical Education, Budapest 1123, Hungary
| | - Zoltan Gombos
- Research Center of Molecular Exercise Science, University of Physical Education, Budapest 1123, Hungary
| | - Matyas Jokai
- Research Center of Molecular Exercise Science, University of Physical Education, Budapest 1123, Hungary
| | - Istvan Berkes
- Research Center of Molecular Exercise Science, University of Physical Education, Budapest 1123, Hungary
| | - Masaki Takeda
- Faculty of Health and Sports Science, Doshisha University, Kyotanabe 610-0394, Japan
| | - Tatsuya Mimura
- Faculty of Sport and Health Sciences, Osaka Sangyo University, Osaka 573-1004, Japan
| | - Zsolt Radak
- Research Center of Molecular Exercise Science, University of Physical Education, Budapest 1123, Hungary; Faculty of Sport Sciences, Waseda University, Tokorozawa, Saitama 359-1192, Japan; Institute of Physical Education and Sport Science, JGYPK, University of Szeged, Szeged 6726, Hungary.
| | - Ferenc Gyori
- Institute of Physical Education and Sport Science, JGYPK, University of Szeged, Szeged 6726, Hungary
| |
Collapse
|
13
|
Park HJ, Lee SS. QCM sensing of miR-21 by formation of microRNA-DNA hybrid duplexes and intercalation on surface-functionalized pyrene. Analyst 2020; 144:6936-6943. [PMID: 31617512 DOI: 10.1039/c9an01645g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that serve as important biomarkers for a variety of diseases such as cancer and vascular disease. However, sensitive and accurate detection of miR-21 is very challenging in that up-regulation of miR-21 is highly associated with several types of malignant tumors. Here, quartz crystal microbalance (QCM) biosensors were developed for sensitive and specific detection of miR-21 through formation of miR-21-DNA hybrid duplexes and non-specific intercalation of surface-modified pyrene molecules. High selectivity for miR-21 over other miRNAs came from the specific hybridization between miR-21 and gold nanoparticle (AuNP)-conjugated complementary oligonucleotides of miR-21. High sensitivity was obtained through formation of intercalated complexes on the surface with subsequent gold staining signal amplification. Under optimum condition using this strategic approach, our novel QCM biosensors could detect miR-21 concentration as low as 3.6 pM in the entire linear range from 2.5 pM to 2.5 μM with a correlation coefficient of 0.989. In addition, these sensors did not work at all for other miRNAs based on their high selectivity. miR-21 in human brain total RNA and total RNA extracted from A549 cell line could also be successfully detected. Therefore, miRNA detection technology using QCM biosensors and their detection mechanisms have potential as alternatives in biological studies and clinical diagnosis.
Collapse
Affiliation(s)
- Hyeoun Ji Park
- Department of Pharmaceutical Engineering, Soonchunhyang University, 22 Soonchunhyang-ro, Shinchang-myeon, Asan-si, Chungcheongnam-do 31538, Republic of Korea.
| | | |
Collapse
|
14
|
Sánchez-Visedo A, Gallego B, Royo LJ, Soldado A, Valledor M, Ferrero FJ, Campo JC, Costa-Fernández JM, Fernández-Argüelles MT. Visual detection of microRNA146a by using RNA-functionalized gold nanoparticles. Mikrochim Acta 2020; 187:192. [PMID: 32124045 DOI: 10.1007/s00604-020-4148-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/26/2020] [Indexed: 01/07/2023]
Abstract
Gold nanoparticles of different sizes have been synthesized and surface-functionalized with selected RNA probes in order to develop a rapid, low-cost and sensitive method for detection of microRNA146a (miR146a). The strategy is based on the change of colour that can be observed visually after aggregation of the RNA modified-gold nanoparticles (AuNPs) in presence of miR146a. Experimental conditions have been carefully selected in order to obtain a good sensitivity that allows to perform visual detection of microRNA at the nM level, achieving a detection limit of 5 nM. Good repeatability and selectivity versus other sequences that only differ from miR146a in 3 bases was achieved. miR146a has been described as one of the main microRNA involved in the immune response of bovine mastitis, being expressed in tissue, blood and milk samples. The method was successfully applied to the detection of miR146a in raw cow milk samples. The present scheme constitutes a rapid and low-cost alternative to perform highly sensitive detection of microRNA without the need of instrumentation and amplification steps for the early detection of bovine mastitis in the agrofood industry. Graphical abstract Schematic representation of the assay based on aggregation of RNA-modified gold nanoparticles (blue) in presence of microRNA146a generating a dark blue spot onto a solid support, versus a pink spot observed in absence of miR146a due to dispersed gold nanoparticles (red).
Collapse
Affiliation(s)
- Adrián Sánchez-Visedo
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - Borja Gallego
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - Luis José Royo
- Department of Animal Nutrition, Grassland and Forages, Regional Institute for Research and Agro-Food Development (SERIDA), Carretera Oviedo S/N, 33300, Villaviciosa (Asturias), Spain.
| | - Ana Soldado
- Department of Animal Nutrition, Grassland and Forages, Regional Institute for Research and Agro-Food Development (SERIDA), Carretera Oviedo S/N, 33300, Villaviciosa (Asturias), Spain
| | - Marta Valledor
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus Gijón, 33204, Gijón, Spain
| | - Francisco Javier Ferrero
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus Gijón, 33204, Gijón, Spain
| | - Juan Carlos Campo
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus Gijón, 33204, Gijón, Spain
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - María Teresa Fernández-Argüelles
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain.
| |
Collapse
|
15
|
Grunt M, Failla AV, Stevic I, Hillebrand T, Schwarzenbach H. A novel assay for exosomal and cell-free miRNA isolation and quantification. RNA Biol 2020; 17:425-440. [PMID: 31986967 DOI: 10.1080/15476286.2020.1721204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The use of disease-specific signatures of microRNAs (miRNAs) in exosomes has become promising for clinical applications, either as biomarkers or direct therapeutic targets. However, a new approach for exosome enrichment and quantification of miRNAs is urgently needed for its clinical application, since the commercial techniques have shortcomings in quantity and quality. To overcome these deficiencies, we developed a new method for purification of exosomes with subsequent miRNA extraction, followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR), and compared our assays with commercial techniques. For the establishment of these methods, numerous reagents, parameters, and combinations thereof were examined. Our new technique for exosome extraction is based on a mannuronate-guluronate polymer (MGP) which avoids co-precipitating plasma proteins. Quality, concentration and biological activity of the isolated exosomes were examined by Western blot, Nanoparticle Tracking Analysis (NTA), and confocal microscopy. A combination of chaotropic and non-chaotropic salts was used to extract miRNAs from plasma, serum, and exosomes, allowing the exclusion of hazardous components, such as phenol/chloroform. The performance of the miRNAs extraction was verified by RT-qPCR. The chemistry and TaqMan probe were also optimized for RT-qPCR. Sensitivity, efficiency, and linearity of RT-qPCR were tested on serial dilutions of synthetic miR-16 and miR-142. Our established procedure covers all steps of miRNA analyses, and measures the levels of either cell-free and exosomal miRNAs in plasma, serum and other body fluids with high performance.
Collapse
Affiliation(s)
- Magdalena Grunt
- Research and Development, AJ Innuscreen GmbH, Berlin, Germany
| | | | - Ines Stevic
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timo Hillebrand
- Research and Development, AJ Innuscreen GmbH, Berlin, Germany
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
16
|
MiR-205 Dysregulations in Breast Cancer: The Complexity and Opportunities. Noncoding RNA 2019; 5:ncrna5040053. [PMID: 31752366 PMCID: PMC6958506 DOI: 10.3390/ncrna5040053] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNAs that downregulate target gene expression by imperfect base-pairing with the 3' untranslated regions (3'UTRs) of target gene mRNAs. MiRNAs play important roles in regulating cancer cell proliferation, stemness maintenance, tumorigenesis, cancer metastasis, and cancer therapeutic resistance. While studies have shown that dysregulation of miRNA-205-5p (miR-205) expression is controversial in different types of human cancers, it is generally observed that miR-205-5p expression level is downregulated in breast cancer and that miR-205-5p exhibits a tumor suppressive function in breast cancer. This review focuses on the role of miR-205-5p dysregulation in different subtypes of breast cancer, with discussions on the effects of miR-205-5p on breast cancer cell proliferation, epithelial-mesenchymal transition (EMT), metastasis, stemness and therapy-resistance, as well as genetic and epigenetic mechanisms that regulate miR-205-5p expression in breast cancer. In addition, the potential diagnostic and therapeutic value of miR-205-5p in breast cancer is also discussed. A comprehensive list of validated miR-205-5p direct targets is presented. It is concluded that miR-205-5p is an important tumor suppressive miRNA capable of inhibiting the growth and metastasis of human breast cancer, especially triple negative breast cancer. MiR-205-5p might be both a potential diagnostic biomarker and a therapeutic target for metastatic breast cancer.
Collapse
|
17
|
Madadi S, Schwarzenbach H, Lorenzen J, Soleimani M. MicroRNA expression studies: challenge of selecting reliable reference controls for data normalization. Cell Mol Life Sci 2019; 76:3497-3514. [PMID: 31089747 PMCID: PMC11105490 DOI: 10.1007/s00018-019-03136-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/13/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023]
Abstract
Accurate determination of microRNA expression levels is a prerequisite in using these small non-coding RNA molecules as novel biomarkers in disease diagnosis and prognosis. Quantitative PCR is the method of choice for measuring the expression levels of microRNAs. However, a major obstacle that affects the reliability of results is the lack of validated reference controls for data normalization. Various non-coding RNAs have previously been used as reference controls, but their use may lead to variations and lack of comparability of microRNA data among the studies. Despite the growing number of studies investigating microRNA profiles to discriminate between healthy and disease stages, robust reference controls for data normalization have so far not been established. In the present article, we provide an overview of different reference controls used in various diseases, and highlight the urgent need for the identification of suitable reference controls to produce reliable data. Our analysis shows, among others, that RNU6 is not an ideal normalizer in studies using patient material from different diseases. Finally, our article tries to disclose the challenges to find a reference control which is uniformly and stably expressed across all body tissues, fluids, and diseases.
Collapse
Affiliation(s)
- Soheil Madadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Johan Lorenzen
- Department of Nephrology, University Hospital Zürich, Zurich, Switzerland
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran.
| |
Collapse
|
18
|
Recent progress in microRNA-based delivery systems for the treatment of human disease. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-019-0024-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
19
|
Cai S, Ye J, Al-Maskri AAA, Sun L, Zeng S. A conformational switch-based aptasensor for the chemiluminescence detection of microRNA. LUMINESCENCE 2019; 34:823-829. [PMID: 31290225 DOI: 10.1002/bio.3677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/15/2019] [Accepted: 06/06/2019] [Indexed: 01/21/2023]
Abstract
A simple microRNA (miRNA) aptasensor has been developed combining the conformational switch of a streptavidin aptamer and isothermal strand displacement amplification. In the presence of its target miRNA, the allosteric molecular beacon (aMB) probe immobilized on the plate can be 'switched on' and release the streptavidin aptamer. At the same time, Klenow fragment (3'→5' exo-) is utilized to initiate DNA-strand displacement, which starts the target recycling process. Based on the aptamer' high binding affinity and subsequent catalytic chemiluminescence (CL) detection, this CL strategy is highly specific in distinguishing mature miRNAs in same family. It exhibits a dynamic range of four orders of magnitude with a detection limit of 50 fM, and shows great potential for miRNA-related clinical practices and biochemical research.
Collapse
Affiliation(s)
- Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
20
|
Jimenez V, Jambrina C, Casana E, Sacristan V, Muñoz S, Darriba S, Rodó J, Mallol C, Garcia M, León X, Marcó S, Ribera A, Elias I, Casellas A, Grass I, Elias G, Ferré T, Motas S, Franckhauser S, Mulero F, Navarro M, Haurigot V, Ruberte J, Bosch F. FGF21 gene therapy as treatment for obesity and insulin resistance. EMBO Mol Med 2019; 10:emmm.201708791. [PMID: 29987000 PMCID: PMC6079533 DOI: 10.15252/emmm.201708791] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Prevalence of type 2 diabetes (T2D) and obesity is increasing worldwide. Currently available therapies are not suited for all patients in the heterogeneous obese/T2D population, hence the need for novel treatments. Fibroblast growth factor 21 (FGF21) is considered a promising therapeutic agent for T2D/obesity. Native FGF21 has, however, poor pharmacokinetic properties, making gene therapy an attractive strategy to achieve sustained circulating levels of this protein. Here, adeno-associated viral vectors (AAV) were used to genetically engineer liver, adipose tissue, or skeletal muscle to secrete FGF21. Treatment of animals under long-term high-fat diet feeding or of ob/ob mice resulted in marked reductions in body weight, adipose tissue hypertrophy and inflammation, hepatic steatosis, inflammation and fibrosis, and insulin resistance for > 1 year. This therapeutic effect was achieved in the absence of side effects despite continuously elevated serum FGF21. Furthermore, FGF21 overproduction in healthy animals fed a standard diet prevented the increase in weight and insulin resistance associated with aging. Our study underscores the potential of FGF21 gene therapy to treat obesity, insulin resistance, and T2D.
Collapse
Affiliation(s)
- Veronica Jimenez
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Claudia Jambrina
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Estefania Casana
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Victor Sacristan
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Sergio Muñoz
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Sara Darriba
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Jordi Rodó
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Cristina Mallol
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Miquel Garcia
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Xavier León
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Sara Marcó
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Albert Ribera
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Ivet Elias
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Alba Casellas
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Ignasi Grass
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Gemma Elias
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Tura Ferré
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Sandra Motas
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Sylvie Franckhauser
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Francisca Mulero
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.,Molecular Imaging Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marc Navarro
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.,Department of Animal Health and Anatomy, School of Veterinary Medicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Virginia Haurigot
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Jesus Ruberte
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.,Department of Animal Health and Anatomy, School of Veterinary Medicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Fatima Bosch
- Center of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Bellaterra, Spain .,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| |
Collapse
|
21
|
Wu Y, Li Y, Han H, Zhao C, Zhang X. Dual cycle amplification and dual signal enhancement assisted sensitive SERS assay of MicroRNA. Anal Biochem 2018; 564-565:16-20. [PMID: 30312618 DOI: 10.1016/j.ab.2018.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/09/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022]
Abstract
A sensitive surface-enhanced Raman scattering (SERS) approach has been developed for detection of microRNA (miRNA) based on target-triggered dual signal amplification including strand displancement amplification (SDA) and hybridization chain reaction (HCR). With the assistant of polymerase and nicking endonuclease (NEase), target miRNA combines with the single stranded template DNA to generate a great amount of trigger DNA which can induce HCR. Coupled the dual cycle amplification of SDA and HCR with the dual enhancement of gold nanoparticles (AuNPs), a low detection limit of 0.5 fM for miRNA is obtained using the proposed strategy. With high sensitivity, universality, rapid analysis, and high selectivity, this method has a great potential for detecting biomolecules with trace amounts in bioanalysis and clinical biomedicine.
Collapse
Affiliation(s)
- Yingdi Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Ying Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Huixia Han
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Caisheng Zhao
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Xiaoru Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| |
Collapse
|
22
|
An innovative paradigm of methods in microRNAs detection: highlighting DNAzymes, the illuminators. Biosens Bioelectron 2018; 107:123-144. [DOI: 10.1016/j.bios.2018.02.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 12/15/2022]
|
23
|
Ahn JH, Kwak J, Lee JH, Lee SS. Efficient and accurate analysis of microRNA using a specific extension sequence. Mol Biol Rep 2018; 45:611-619. [PMID: 29846878 DOI: 10.1007/s11033-018-4200-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/23/2018] [Indexed: 01/01/2023]
Abstract
We present here on an innovative assay for detecting miRNAs using a uniquely designed specific extension sequence that provides high efficiency and accuracy. This assay consists of poly(A) tailing and reverse transcription followed by real-time PCR. In the first step of this reaction, target miRNAs are poly(A) tailed by poly(A) polymerase followed by cDNA synthesis using poly(T) adaptors. In the second step, cDNA is hybridized to the 3'-end of a specific extension sequence that contains part of a miRNA sequence; this cDNA-specific extension sequence hybrid forms the novel PCR template. The PCR template is amplified in a SYBR Green-based quantitative real-time PCR with universal forward and reverse primers. The miR-106b in human brain total RNA could be detected quantitatively in the range of seven orders of magnitude with high linearity and reproducibility. This innovative extension-based assay has several performance advantages over the poly(A) tailing method that include lower CT values, clear gel electrophoresis images, and distinct nucleotide peaks in sequencing chromatograms.
Collapse
Affiliation(s)
- Jae Hyun Ahn
- HeimBiotek, Inc., A-201 Pangyo Silicon Park, Bundang-gu, Senognam-si, Kyeonggi-do, 13486, Republic of Korea
| | - Jiwon Kwak
- Department of Pharmaceutical Engineering, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan-si, Chungcheongnam-do, 31538, Republic of Korea
| | - Jae-Hoon Lee
- HeimBiotek, Inc., A-201 Pangyo Silicon Park, Bundang-gu, Senognam-si, Kyeonggi-do, 13486, Republic of Korea
| | - Soo Suk Lee
- Department of Pharmaceutical Engineering, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan-si, Chungcheongnam-do, 31538, Republic of Korea.
| |
Collapse
|
24
|
MicroRNA-216a Inhibits NF-κB-Mediated Inflammatory Cytokine Production in Teleost Fish by Modulating p65. Infect Immun 2018; 86:IAI.00256-18. [PMID: 29632247 DOI: 10.1128/iai.00256-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/08/2023] Open
Abstract
Inflammation is the host self-protection mechanism to eliminate pathogen invasion. The excessive inflammatory response can result in uncontrolled inflammation, autoimmune diseases, or pathogen dissemination. Recent studies have widely shown that microRNAs (miRNAs) contribute to the regulation of inflammation in mammals by repressing gene expression at the posttranscriptional level. However, the miRNA-mediated mechanism in the inflammatory response in fish remains hazy. In the present study, the regulatory mechanism of the miR-216a-mediated inflammatory response in teleost fish was addressed. We found that the expression of miR-216a could be significantly upregulated in the miiuy croaker after challenge with Vibrio anguillarum and lipopolysaccharide. Bioinformatics predictions demonstrated a potential binding site of miR-216a in the 3' untranslated region of the p65 gene, and the result was further confirmed by luciferase assay. Moreover, both the mRNA and protein levels of p65 in macrophages were downregulated by miR-216a. Deletion mutant analysis of the miR-216a promoter showed that the Ap1 and Sp1 transcription factor binding sites are indispensable for the transcription of miR-216a. Further study revealed that overexpression of miR-216a suppresses inflammatory cytokine expression and negatively regulates NF-κB signaling, which inhibit an excessive inflammatory response. The collective results indicate that miR-216a plays a role as a negative regulator involved in modulating the bacterium-induced inflammatory response.
Collapse
|
25
|
Herkenhoff ME, Oliveira AC, Nachtigall PG, Costa JM, Campos VF, Hilsdorf AWS, Pinhal D. Fishing Into the MicroRNA Transcriptome. Front Genet 2018; 9:88. [PMID: 29616080 PMCID: PMC5868305 DOI: 10.3389/fgene.2018.00088] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/02/2018] [Indexed: 01/18/2023] Open
Abstract
In the last decade, several studies have been focused on revealing the microRNA (miRNA) repertoire and determining their functions in farm animals such as poultry, pigs, cattle, and fish. These small non-protein coding RNA molecules (18-25 nucleotides) are capable of controlling gene expression by binding to messenger RNA (mRNA) targets, thus interfering in the final protein output. MiRNAs have been recognized as the main regulators of biological features of economic interest, including body growth, muscle development, fat deposition, and immunology, among other highly valuable traits, in aquatic livestock. Currently, the miRNA repertoire of some farmed fish species has been identified and characterized, bringing insights about miRNA functions, and novel perspectives for improving health and productivity. In this review, we summarize the current advances in miRNA research by examining available data on Neotropical and other key species exploited by fisheries and in aquaculture worldwide and discuss how future studies on Neotropical fish could benefit from this knowledge. We also make a horizontal comparison of major results and discuss forefront strategies for miRNA manipulation in aquaculture focusing on forward-looking ideas for forthcoming research.
Collapse
Affiliation(s)
- Marcos E. Herkenhoff
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Arthur C. Oliveira
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Pedro G. Nachtigall
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Juliana M. Costa
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Vinicius F. Campos
- Laboratory of Structural Genomics (GenEstrut), Graduate Program of Biotechnology, Technology Developmental Center, Federal University of Pelotas, Pelotas, Brazil
| | | | - Danillo Pinhal
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| |
Collapse
|
26
|
Le BH, Seo YJ. Highly sensitive MicroRNA 146a detection using a gold nanoparticle-based CTG repeat probing system and isothermal amplification. Anal Chim Acta 2017; 999:155-160. [PMID: 29254567 DOI: 10.1016/j.aca.2017.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/10/2017] [Accepted: 11/09/2017] [Indexed: 12/13/2022]
Abstract
We have developed a gold nanoparticle (AuNP)-based CTG repeat probing system displaying high quenching capability and combined it with isothermal amplification for the detection of miRNA 146a. This method of using a AuNP-based CTG repeat probing system with isothermal amplification allowed the highly sensitive (14 aM) and selective detection of miRNA 146a. A AuNP-based CTG repeat probing system having a hairpin structure and a dTF fluorophore exhibited highly efficient quenching because the CTG repeat-based stable hairpin structure imposed a close distance between the AuNP and the dTF residue. A small amount of miRNA 146a induced multiple copies of the CAG repeat sequence during rolling circle amplification; the AuNP-based CTG repeat probing system then bound to the complementary multiple-copy CAG repeat sequence, thereby inducing a structural change from a hairpin to a linear structure with amplified fluorescence. This AuNP-based CTG probing system combined with isothermal amplification could also discriminate target miRNA 146a from one- and two-base-mismatched miRNAs (ORN 1 and ORN 2, respectively). This simple AuNP-based CTG probing system, combined with isothermal amplification to induce a highly sensitive change in fluorescence, allows the detection of miRNA 146a with high sensitivity (14 aM) and selectivity.
Collapse
Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea; Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea.
| |
Collapse
|
27
|
Kim KJ, Kwak J, Lee JH, Lee SS. Real-time qRT-PCR assay for the detection of miRNAs using bi-directional extension sequences. Anal Biochem 2017; 536:32-35. [DOI: 10.1016/j.ab.2017.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/08/2017] [Accepted: 08/11/2017] [Indexed: 02/06/2023]
|
28
|
Yan H, Xu Y, Lu Y, Xing W. Reduced Graphene Oxide-Based Solid-Phase Extraction for the Enrichment and Detection of microRNA. Anal Chem 2017; 89:10137-10140. [PMID: 28933157 DOI: 10.1021/acs.analchem.7b03138] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are endogenous molecules with regulatory functions. The purification and enrichment of miRNA are essential for its precise and sensitive detection. miRNA isolated using commercial kits contains abundant interfering RNAs, and the concentration of miRNA may not be adequate for detection. Herein, we prepared a reduced graphene oxide (rGO)-based magnetic solid-phase extraction material for the enrichment and ultrasensitive detection of miRNA from intricate nucleic acid solutions. In situ reverse transcription (RT) was developed as the most efficient approach to desorb miRNA from rGO among the methods that are compatible for the subsequent amplification reported thus far. Additionally, rolling circle amplification and qPCR were used to detect let-7a with a decrease of the limit of detection by 24.7- and 31.3-fold, respectively. This material was also successfully used to extract and detect miRNA from total RNA isolated from human plasma. Our results show that the material prepared in this study has the potential for cancer biopsy in clinics and the discovery of new miRNAs in scientific research.
Collapse
Affiliation(s)
- He Yan
- School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University , Beijing 100084, China
| | - Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University , Beijing 100084, China
| | - Wanli Xing
- Department of Biomedical Engineering, School of Medicine, Tsinghua University , Beijing 100084, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou 310003, China.,National Engineering Research Center for Beijing Biochip Technology , Beijing 102206, China
| |
Collapse
|
29
|
Wang Y, Lau C, Lu J. Target-initiated labeling for the dual-amplified detection of multiple microRNAs. Anal Chim Acta 2017; 992:76-84. [PMID: 29054152 DOI: 10.1016/j.aca.2017.08.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/21/2017] [Accepted: 08/16/2017] [Indexed: 12/21/2022]
Abstract
Herein we exploited a novel target-initiated labeling strategy for the multiplex detection of microRNAs (miRNAs) by coupling duplex-specific nuclease (DSN) with terminal deoxynucleotidyl transferase (TdT). In the presence of target miRNA, the immobilized and 3'-blocked capture probes hybridized with target and thus the formed DNA-RNA hybrid was recognized by DSN. DSN mediated the digestion of 3'-phosphated capture probes (CPs) in the hybrids and synchronously target was released and recycled for another round of hybridization and cleavage. The cleaved CP fragments with a free 3'-OH were then elongated and labeled with multiple biotin-dUTP nucleotides by TdT. Fluorescence reporter streptavidin-phycoerythin was finally added to react with the immobilized biotins and render fluorescence signals. This dual-amplification labeling strategy was successfully demonstrated to sensitively detect multiple miRNAs, taking advantage of DSN-mediated target recycling and TdT-catalyzed multiple signal modification with analysis by a commercial Luminex xMAP array platform. Our experimental results showed the simultaneous quantitative measurement of three sequence-specific miRNAs at concentrations from 1 pM to 2.5 nM. Attempts were also made to directly detect miRNAs in total RNA extracted from cancer cells. The dual-amplification labeling strategy reported here shows a great potential for the development of a method for the multiplexed, sensitive, selective, and simple analysis of multiple miRNAs in tissues or cells for biomedical research and clinical early diagnosis.
Collapse
Affiliation(s)
- Yinan Wang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Choiwan Lau
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
| | - Jianzhong Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
| |
Collapse
|
30
|
Liu X, Tian R, Gao J, Liu D, Wang Z. Multiplexed detection of microRNAs by a competitive DNA microarray-based resonance light scattering assay. Analyst 2017; 142:4529-4535. [DOI: 10.1039/c7an01152k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A competitive DNA microarray-based resonance light scattering assay is developed for the selective and sensitive detection of multiple microRNAs.
Collapse
Affiliation(s)
- Xia Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Rongrong Tian
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Jiaxue Gao
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| |
Collapse
|
31
|
Zhang XX, Deng LH, Chen WW, Shi N, Jin T, Lin ZQ, Ma Y, Jiang K, Yang XN, Xia Q. Circulating microRNA 216 as a Marker for the Early Identification of Severe Acute Pancreatitis. Am J Med Sci 2016; 353:178-186. [PMID: 28183420 DOI: 10.1016/j.amjms.2016.12.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 12/04/2016] [Accepted: 12/08/2016] [Indexed: 02/05/2023]
Abstract
BACKGROUND To study the value of circulating microRNA 216 (miR-216) as a marker for the severity of acute pancreatitis (AP) in both murine models and patients. MATERIALS AND METHODS Mice with AP were induced by intraperitoneal injection of 50μg/kg/hour cerulean either 7 times, sacrificed at 8, 9, 10, 11 or 12 hours after the first injection, or 12 times, sacrificed at 24 hours after the first injection. Plasma samples and data from patients with AP were obtained from a prospective cohort. Quantitative reverse transcription polymerase chain reaction was used to determine the miR-216a and miR-216b level. RESULTS The upregulation of miR-216a and miR-216b in the serum of mice was induced by cerulean injection in both the 7- and 12-injection groups (P < 0.05). The downregulation of miR-216a in pancreatic tissues of mice with AP was detected (P < 0.05), but no difference was observed in pancreatic miR-216b levels among any of the groups (all P > 0.05). The serum miR-216a level was positively correlated with pancreatic histopathology severity scores, and was negatively correlated with pancreatic miR-216a (r = -0.483, P = 0.009). The plasma miR-216a level was significantly upregulated in patients with severe AP (SAP) compared with patients with mild AP (MAP) or moderate severe AP (MSAP) (SAP versus MAP, P = 0.04; SAP versus MSAP, P = 0.00), but no difference was seen between patients with MAP and those with MSAP (P = 0.73). CONCLUSIONS Circulating miR-216a might be a potential biomarker for the early identification of SAP.
Collapse
Affiliation(s)
- Xiao-Xin Zhang
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Li-Hui Deng
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China.
| | - Wei-Wei Chen
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Na Shi
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Tao Jin
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Zi-Qi Lin
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Yun Ma
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Kun Jiang
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Xiao-Nan Yang
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Qing Xia
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu, China.
| |
Collapse
|
32
|
Gareri C, De Rosa S, Indolfi C. MicroRNAs for Restenosis and Thrombosis After Vascular Injury. Circ Res 2016; 118:1170-84. [PMID: 27034278 DOI: 10.1161/circresaha.115.308237] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/01/2016] [Indexed: 12/21/2022]
Abstract
Percutaneous revascularization revolutionized the therapy of patients with coronary artery disease. Despite continuous technical advances that substantially improved patients' outcome after percutaneous revascularization, some issues are still open. In particular, restenosis still represents a challenge, even though it was dramatically reduced with the advent of drug-eluting stents. At the same time, drug-eluting stent thrombosis emerged as a major concern because of incomplete or delayed re-endothelialization after vascular injury. The discovery of microRNAs revealed a previously unknown layer of regulation for several biological processes, increasing our knowledge on the biological mechanisms underlying restenosis and stent thrombosis, revealing novel promising targets for more efficient and selective therapies. The present review summarizes recent experimental and clinical evidence on the role of microRNAs after arterial injury, focusing on practical aspects of their potential therapeutic application for selective inhibition of smooth muscle cell proliferation, enhancement of endothelial regeneration, and inhibition of platelet activation after coronary interventions. Application of circulating microRNAs as potential biomarkers is also discussed.
Collapse
Affiliation(s)
- Clarice Gareri
- From the Department of Medicine, Duke University, Durham, NC (C.G.); Division of Cardiology, Department of Medical and Surgical Science, "Magna Graecia" University, Catanzaro, Italy (S.D.R., C.I.); and URT-CNR, Department of Medicine, URT of Consiglio Nazionale delle Ricerche, Catanzaro, Italy (C.I.)
| | - Salvatore De Rosa
- From the Department of Medicine, Duke University, Durham, NC (C.G.); Division of Cardiology, Department of Medical and Surgical Science, "Magna Graecia" University, Catanzaro, Italy (S.D.R., C.I.); and URT-CNR, Department of Medicine, URT of Consiglio Nazionale delle Ricerche, Catanzaro, Italy (C.I.)
| | - Ciro Indolfi
- From the Department of Medicine, Duke University, Durham, NC (C.G.); Division of Cardiology, Department of Medical and Surgical Science, "Magna Graecia" University, Catanzaro, Italy (S.D.R., C.I.); and URT-CNR, Department of Medicine, URT of Consiglio Nazionale delle Ricerche, Catanzaro, Italy (C.I.).
| |
Collapse
|
33
|
Asghari F, Haghnavaz N, Baradaran B, Hemmatzadeh M, Kazemi T. Tumor suppressor microRNAs: Targeted molecules and signaling pathways in breast cancer. Biomed Pharmacother 2016; 81:305-317. [DOI: 10.1016/j.biopha.2016.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 12/19/2022] Open
|
34
|
Yu Y, Yao Y, Yan H, Wang R, Zhang Z, Sun X, Zhao L, Ao X, Xie Z, Wu Q. A Tumor-specific MicroRNA Recognition System Facilitates the Accurate Targeting to Tumor Cells by Magnetic Nanoparticles. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e318. [PMID: 27138178 PMCID: PMC5014513 DOI: 10.1038/mtna.2016.28] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 03/22/2016] [Indexed: 12/25/2022]
Abstract
Targeted therapy for cancer is a research area of great interest, and magnetic nanoparticles (MNPs) show great potential as targeted carriers for therapeutics. One important class of cancer biomarkers is microRNAs (miRNAs), which play a significant role in tumor initiation and progression. In this study, a cascade recognition system containing multiple plasmids, including a Tet activator, a lacI repressor gene driven by the TetOn promoter, and a reporter gene repressed by the lacI repressor and influenced by multiple endogenous miRNAs, was used to recognize cells that display miRNA signals that are characteristic of cancer. For this purpose, three types of signal miRNAs with high proliferation and metastasis abilities were chosen (miR-21, miR-145, and miR-9). The response of this system to the human breast cancer MCF-7 cell line was 3.2-fold higher than that to the human breast epithelial HBL100 cell line and almost 7.5-fold higher than that to human embryonic kidney HEK293T cells. In combination with polyethyleneimine-modified MNPs, this recognition system targeted the tumor location in situ in an animal model, and an ~42% repression of tumor growth was achieved. Our study provides a new combination of magnetic nanocarrier and gene therapy based on miRNAs that are active in vivo, which has potential for use in future cancer therapies.
Collapse
Affiliation(s)
- Yingting Yu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yi Yao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hao Yan
- Key Laboratory of Advanced Materials of Ministry of Education of China, School of Materials Science & Engineering, Tsinghua University, Beijing, China
| | - Rui Wang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhenming Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaodan Sun
- Key Laboratory of Advanced Materials of Ministry of Education of China, School of Materials Science & Engineering, Tsinghua University, Beijing, China
| | - Lingyun Zhao
- Key Laboratory of Advanced Materials of Ministry of Education of China, School of Materials Science & Engineering, Tsinghua University, Beijing, China
| | - Xiang Ao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhen Xie
- Bioinformatics Division/Center for Synthetic & Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, China
| | - Qiong Wu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
35
|
Egatz-Gomez A, Wang C, Klacsmann F, Pan Z, Marczak S, Wang Y, Sun G, Senapati S, Chang HC. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine. BIOMICROFLUIDICS 2016; 10:032902. [PMID: 27190565 PMCID: PMC4859827 DOI: 10.1063/1.4948525] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/20/2016] [Indexed: 05/05/2023]
Abstract
Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.
Collapse
Affiliation(s)
- Ana Egatz-Gomez
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Ceming Wang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Flora Klacsmann
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Zehao Pan
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Steve Marczak
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Yunshan Wang
- Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, USA
| | - Gongchen Sun
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Satyajyoti Senapati
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Hsueh-Chia Chang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| |
Collapse
|
36
|
Petty RD, McCarthy NE, Le Dieu R, Kerr JR. MicroRNAs hsa-miR-99b, hsa-miR-330, hsa-miR-126 and hsa-miR-30c: Potential Diagnostic Biomarkers in Natural Killer (NK) Cells of Patients with Chronic Fatigue Syndrome (CFS)/ Myalgic Encephalomyelitis (ME). PLoS One 2016; 11:e0150904. [PMID: 26967895 PMCID: PMC4788442 DOI: 10.1371/journal.pone.0150904] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/22/2016] [Indexed: 01/10/2023] Open
Abstract
Background Chronic Fatigue Syndrome (CFS/ME) is a complex multisystem disease of unknown aetiology which causes debilitating symptoms in up to 1% of the global population. Although a large cohort of genes have been shown to exhibit altered expression in CFS/ME patients, it is currently unknown whether microRNA (miRNA) molecules which regulate gene translation contribute to disease pathogenesis. We hypothesized that changes in microRNA expression in patient leukocytes contribute to CFS/ME pathology, and may therefore represent useful diagnostic biomarkers that can be detected in the peripheral blood of CFS/ME patients. Methods miRNA expression in peripheral blood mononuclear cells (PBMC) from CFS/ME patients and healthy controls was analysed using the Ambion Bioarray V1. miRNA demonstrating differential expression were validated by qRT-PCR and then replicated in fractionated blood leukocyte subsets from an independent patient cohort. The CFS/ME associated miRNA identified by these experiments were then transfected into primary NK cells and gene expression analyses conducted to identify their gene targets. Results Microarray analysis identified differential expression of 34 miRNA, all of which were up-regulated. Four of the 34 miRNA had confirmed expression changes by qRT-PCR. Fractionating PBMC samples by cell type from an independent patient cohort identified changes in miRNA expression in NK-cells, B-cells and monocytes with the most significant abnormalities occurring in NK cells. Transfecting primary NK cells with hsa-miR-99b or hsa-miR-330-3p, resulted in gene expression changes consistent with NK cell activation but diminished cytotoxicity, suggesting that defective NK cell function contributes to CFS/ME pathology. Conclusion This study demonstrates altered microRNA expression in the peripheral blood mononuclear cells of CFS/ME patients, which are potential diagnostic biomarkers. The greatest degree of miRNA deregulation was identified in NK cells with targets consistent with cellular activation and altered effector function.
Collapse
Affiliation(s)
- Robert D. Petty
- CFS Group, St George´s University of London, Cranmer Terrace, London, United Kingdom
- Centre for Haemato-Oncology, Bart’s cancer institute, Queen Mary University of London, London, United Kingdom
- * E-mail:
| | - Neil E. McCarthy
- Centre for Immunobiology, The Blizzard institute, Queen Mary University of London, London, United Kingdom
| | - Rifca Le Dieu
- Centre for Haemato-Oncology, Bart’s cancer institute, Queen Mary University of London, London, United Kingdom
| | - Jonathan R. Kerr
- CFS Group, St George´s University of London, Cranmer Terrace, London, United Kingdom
- Grupo de Salud Publica, Escuela de Medicine y Ciencias de la Salud, Universidad del Rosario, Quinta de Mutis, Bogotá 111221, Colombia
| |
Collapse
|
37
|
Hong C, Baek A, Hah SS, Jung W, Kim DE. Fluorometric Detection of MicroRNA Using Isothermal Gene Amplification and Graphene Oxide. Anal Chem 2016; 88:2999-3003. [DOI: 10.1021/acs.analchem.6b00046] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chaesun Hong
- Department
of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea
| | - Ahruem Baek
- Department
of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea
| | | | | | - Dong-Eun Kim
- Department
of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea
| |
Collapse
|
38
|
Glover AR, Hassan N, Joo LJS, Kwok G, Zhao JT, Sidhu SB. Could miRNA replacement be a novel therapy for adrenocortical carcinoma? INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2016. [DOI: 10.2217/ije.15.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Adrenocortical carcinoma (ACC) has poor outcomes and there is a need for novel effective treatments for metastatic disease and adjuvant therapy. miRNAs are small endogenous noncoding RNAs that control gene expression. miRNAs are dysregulated in all cancers and manipulation of miRNA levels is under investigation as a novel therapy in other cancers with poor outcomes such as mesothelioma. In this review, the rationale for miRNA therapy will be presented along with the current understanding of the role of miRNA dysregulation and miRNA regulation of ACC. Potential therapeutic approaches of miRNA therapy using established delivery systems such as liposomes and targeted nanocells will be presented, along with the future challenges of establishing miRNA therapy in clinical trials for ACC.
Collapse
Affiliation(s)
- Anthony R Glover
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
- University of Sydney Endocrine Surgery Unit, Royal North Shore Hospital, Sydney, NSW, Australia
- Sydney Vital Translational Research Unit, Northern Sydney Local Health District, Cancer Institute NSW, Australia
| | - Nunki Hassan
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
| | - Lauren Jin Suk Joo
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
| | - Grace Kwok
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
| | - Jing Ting Zhao
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
- Sydney Vital Translational Research Unit, Northern Sydney Local Health District, Cancer Institute NSW, Australia
| | - Stan B Sidhu
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St Leonards, NSW 2065, Australia
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, NSW, Australia
- University of Sydney Endocrine Surgery Unit, Royal North Shore Hospital, Sydney, NSW, Australia
- Sydney Vital Translational Research Unit, Northern Sydney Local Health District, Cancer Institute NSW, Australia
| |
Collapse
|
39
|
Seyhan AA. microRNAs with different functions and roles in disease development and as potential biomarkers of diabetes: progress and challenges. MOLECULAR BIOSYSTEMS 2016; 11:1217-34. [PMID: 25765998 DOI: 10.1039/c5mb00064e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Biomarkers provide information on early detection of diseases, in determining individuals at risk of developing complications or subtyping individuals for disease phenotypes. In addition, biomarkers may lead to better treatment strategies, personalized therapy, and improved outcome. A major gap in the field of biomarker development is that we have not identified appropriate (minimally invasive, life-style independent and informative) biomarkers for the underlying disease process(es) that can be measured in readily accessible samples (e.g. serum, plasma, blood, urine). miRNAs function as regulators in wide ranging cellular and physiological functions and also participate in many physiopathological processes and thus have been linked to many diseases including diabetes, metabolic and cardiovascular diseases, cancer, neurodegenerative diseases, and autoimmunity. Many miRNAs have been shown to have predictive value as potential biomarkers in a variety of diseases including diabetes, which are detectable in some instances many years before the manifestation of disease. Although some technical challenges still remain, due to their availability in the circulation, relative stability, and ease of detection; miRNAs have emerged as a promising new class of biomarkers to provide information on early detection of disease, monitoring disease progression, in determining individual's risk of developing complications or subtyping individuals for disease phenotypes, and to monitor response to therapeutic interventions. As a final note, most of the miRNAs reported in the literature have not yet been validated in sufficiently powered and longitudinal studies for specificity for that particular disease.
Collapse
Affiliation(s)
- Attila A Seyhan
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Sanford Burnham Institute, 301 E. Princeton Street, Orlando, FL 32804, USA.
| |
Collapse
|
40
|
Song Y, Liu KJ, Wang TH. Efficient synthesis of stably adenylated DNA and RNA adapters for microRNA capture using T4 RNA ligase 1. Sci Rep 2015; 5:15620. [PMID: 26500066 PMCID: PMC4620478 DOI: 10.1038/srep15620] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/29/2015] [Indexed: 11/09/2022] Open
Abstract
MicroRNA profiling methods have become increasingly important due to the rapid rise of microRNA in both basic and translational sciences. A critical step in many microRNA profiling assays is adapter ligation using pre-adenylated adapters. While pre-adenylated adapters can be chemically or enzymatically prepared, enzymatic adenylation is preferred due to its ease and high yield. However, previously reported enzymatic methods either require tedious purification steps or use thermostable ligases that can generate side products during the subsequent ligation step. We have developed a highly efficient, template- and purification-free, adapter adenylation method using T4 RNA ligase 1. This method is capable of adenylating large amounts of adapter at ~100% efficiency and can efficiently adenylate both DNA and RNA bases. We find that the adenylation reaction speed can differ between DNA and RNA and between terminal nucleotides, leading to bias if reactions are not allowed to run to completion. We further find that the addition of high PEG levels can effectively suppress these differences.
Collapse
Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kelvin J Liu
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA.,Circulomics Inc, Baltimore, MD, 21211, USA
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA.,Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA
| |
Collapse
|
41
|
Usó M, Jantus-Lewintre E, Sirera R, Bremnes RM, Camps C. miRNA detection methods and clinical implications in lung cancer. Future Oncol 2015; 10:2279-92. [PMID: 25471039 DOI: 10.2217/fon.14.93] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Therefore, advances in the diagnosis and treatment of the disease are urgently needed. miRNAs are a family of small, noncoding RNAs that regulate gene expression at the transcriptional level. miRNAs have been reported to be deregulated and to play a critical role in different types of cancer, including lung cancer. Thus, miRNA profiling in lung cancer patients has become the core of several investigations. To this end, the development of a multitude of platforms for miRNA profiling analysis has been essential. This article focuses on the different technologies available for assessing miRNAs and the most important results obtained to date in lung cancer.
Collapse
Affiliation(s)
- Marta Usó
- Molecular Oncology Laboratory, Fundación para la Investigación del Hospital General Universitario de Valencia, Av. Tres Cruces s/n, 46014 Valencia, Spain
| | | | | | | | | |
Collapse
|
42
|
MicroRNA-27a Contributes to Rhabdomyosarcoma Cell Proliferation by Suppressing RARA and RXRA. PLoS One 2015; 10:e0125171. [PMID: 25915942 PMCID: PMC4410939 DOI: 10.1371/journal.pone.0125171] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 03/21/2015] [Indexed: 12/21/2022] Open
Abstract
Background Rhabdomyosarcomas (RMS) are rare but very aggressive childhood tumors that arise as a consequence of a regulatory disruption in the growth and differentiation pathways of myogenic precursor cells. According to morphological criteria, there are two major RMS subtypes: embryonal RMS (ERMS) and alveolar RMS (ARMS) with the latter showing greater aggressiveness and metastatic potential with respect to the former. Efforts to unravel the complex molecular mechanisms underlying RMS pathogenesis and progression have revealed that microRNAs (miRNAs) play a key role in tumorigenesis. Methodology/Principal Findings The expression profiles of 8 different RMS cell lines were analyzed to investigate the involvement of miRNAs in RMS. The miRNA population from each cell line was compared to a reference sample consisting of a balanced pool of total RNA extracted from those 8 cell lines. Sixteen miRNAs whose expression discriminates between translocation-positive ARMS and negative RMS were identified. Attention was focused on the role of miR-27a that is up-regulated in the more aggressive RMS cell lines (translocation-positive ARMS) in which it probably acts as an oncogene. MiR-27a overexpressing cells showed a significant increase in their proliferation rate that was paralleled by a decrease in the number of cells in the G1 phase of the cell cycle. It was possible to demonstrate that miR-27a is implicated in cell cycle control by targeting the retinoic acid alpha receptor (RARA) and retinoic X receptor alpha (RXRA). Conclusions Study results have demonstrated that miRNA expression signature profiling can be used to classify different RMS subtypes and suggest that miR-27a may have a therapeutic potential in RMS by modulating the expression of retinoic acid receptors.
Collapse
|
43
|
Dusl M, Senderek J, Muller JS, Vogel JG, Pertl A, Stucka R, Lochmuller H, David R, Abicht A. A 3'-UTR mutation creates a microRNA target site in the GFPT1 gene of patients with congenital myasthenic syndrome. Hum Mol Genet 2015; 24:3418-26. [DOI: 10.1093/hmg/ddv090] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 03/08/2015] [Indexed: 01/07/2023] Open
|
44
|
Abstract
p19 is an RNA binding protein originally isolated from the Carnation Italian ring-spot virus (CIRV). It has been shown that p19 is a plant RNA-silencing suppressor that binds small interfering RNA (siRNA) with high affinity. A bifunctional p19 fusion protein, with an N-terminal maltose binding protein (MBP) and a C-terminal chitin binding domain (CBD) allows protein purification and binding of p19 to chitin magnetic beads via the chitin binding domain. The fusion p19 protein recognizes and binds double-stranded RNAs (dsRNA) in the size range of 20-23 nucleotides, but does not bind single strand RNA (ssRNA) or dsDNA. Furthermore, p19 can also bind mRNA, if there is a 19 bp blunt RNA duplex at the exact end of the RNA. Binding specificity of the p19 fusion protein for small dsRNA allows for detection of siRNAs derived either from exogenous or endogenous long dsRNA or microRNAs when hybridized to a complementary RNA. Here we describe a robust method using p19 and radioactive RNA probes to detect siRNAs in the sub-femtomole range and in the presence of a million-fold excess of total RNA. Unlike most nucleic acid detection methods, p19 selects for RNA hybrids of correct length and structure. This chapter describes the potential of p19 fusion protein to detect miRNAs, isolate exogenous or endogenous siRNAs, and purify longer RNAs that contain a 19-bp terminal RNA duplex.
Collapse
Affiliation(s)
- Jingmin Jin
- Division of RNA Biology, New England Biolabs, Ipswich, MA, USA
| | | | | |
Collapse
|
45
|
Zhang J, Ning X, Cui W, Bi M, Zhang D, Zhang J. Transforming growth factor (TGF)-β-induced microRNA-216a promotes acute pancreatitis via Akt and TGF-β pathway in mice. Dig Dis Sci 2015; 60:127-35. [PMID: 25501921 DOI: 10.1007/s10620-014-3261-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/18/2014] [Indexed: 12/26/2022]
Abstract
BACKGROUND Both transforming growth factor β (TGF-β) and MicroRNA-216a (miR-216a) were reported to be upregulated during acute pancreatitis (AP). Moreover, miR-216a can be induced by TGF-β. AIM This study aimed to investigate how TGF-β and miR-216a involved in the pathogenesis of AP both in a mouse model and in rat pancreatic acinar AR42J cells. METHODS Cerulein-induced AP mouse model was established and pretreated with a TGF-β inhibitor, SB431542. Serum amylase, lipase, tumor necrosis factor (TNF)-α, interleukin 6 (IL-6), TGF-β and histopathological changes of pancreas were determined. Expression of miR-216a was detected by quantitative real-time RT-PCR. Bioinformatics was utilized to predict the targets of miR-216a. Expression levels of phosphatase and tensin homolog (PTEN), mothers against decapentaplegic homolog 7 (Smad7), TGF-β receptor I, total Akt and pAkt were detected by Western blot. RESULTS SB431542 significantly decreased serum amylase, lipase, TNF-α, IL-6, TGF-β, histopathological changes of pancreas and expression of miR-216a in cerulein-induced mouse (P < 0.05). TGF-β induced miR-216a in AR42J cells. PTEN and Smad7 were identified to be the possible targets of miR-216a. Transfection of miR-216a mimics (or inhibitors) in AR42J cells downregulated (or upregulated) the expression of PTEN and Smad7, thus affected the expression of downstream pAkt and TGF-β receptor I. The expression changes of these protein caused by miR-216a can be regulated by SB431542 both in mouse model and AR42J cells. CONCLUSIONS TGF-β promotes AP by inducing miR-216a targeting PTEN and Smad7, thus through PI3K/Akt and TGF-β feedback pathway.
Collapse
Affiliation(s)
- Jian Zhang
- Department of General Surgery, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, 266003, Shandong Province, People's Republic of China,
| | | | | | | | | | | |
Collapse
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Xu J, Chen X, Li D, Chen Q, Zhou Z, Hou D, Wang J, Zhang Q, Zen K, Zhang CY. Small RNA existed in commercial reverse transcriptase: primary evidence of functional small RNAs. Protein Cell 2014; 6:1-5. [PMID: 25412770 PMCID: PMC4286138 DOI: 10.1007/s13238-014-0116-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Jie Xu
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Xi Chen
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Donghai Li
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Qun Chen
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Zhen Zhou
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Dongxia Hou
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Jin Wang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Qipeng Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Ke Zen
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| | - Chen-Yu Zhang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093 China
| |
Collapse
|
48
|
Orang AV, Safaralizadeh R, Hosseinpour Feizi MA. Insights into the diverse roles of miR-205 in human cancers. Asian Pac J Cancer Prev 2014; 15:577-83. [PMID: 24568460 DOI: 10.7314/apjcp.2014.15.2.577] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The recent discovery of tiny microRNAs (miRNAs) has brought about awareness of a new class of regulators of diverse pathways in many physiological and pathological processes, such as tumorigenesis. They modulate gene expression by targeting plethora of mRNAs, mostly reducing the protein yield of a targeted mRNA. With accumulation of information on characteristics of miR-205, complex and in some cases converse roles of miR-205 in tumor initiation, progression and metastasis are emerging. miR-205 acts either as an oncogene via facilitating tumor initiation and proliferation, or in some cases as a tumor suppressor through inhibiting proliferation and invasion. The aim of this review is to discuss miR-205 roles in different types of cancers. Given the critical effects of deregulated miR-205 on processes involved in tumorigenesis, they hold potential as novel therapeutic targets and biomarkers.
Collapse
Affiliation(s)
- Ayla Valinezhad Orang
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Islamic Republic of Iran E-mail :
| | | | | |
Collapse
|
49
|
Capillary electrophoresis methods for microRNAs assays: a review. Anal Chim Acta 2014; 852:1-7. [PMID: 25441872 DOI: 10.1016/j.aca.2014.08.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 08/07/2014] [Accepted: 08/13/2014] [Indexed: 12/23/2022]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that conduct important roles in many cellular processes such as development, proliferation, differentiation, and apoptosis. In particular, circulating miRNAs have been proposed as biomarkers for cancer, diabetes, cardiovascular disease, and other illnesses. Therefore, determination of miRNA expression levels in various biofluids is important for the investigation of biological processes in health and disease and for discovering their potential as new biomarkers and drug targets. Capillary electrophoresis (CE) is emerging as a useful analytical tool for analyzing miRNA because of its simple sample preparation steps and efficient resolution of a diverse size range of compounds. In particular, CE with laser-induced fluorescence detection is a promising and relatively rapidly developing tool with the potential to provide high sensitivity and specificity in the analysis of miRNAs. This paper covers a short overview of the recent developments and applications of CE systems in miRNA studies in biological and biomedical areas.
Collapse
|
50
|
Soares RJ, Cagnin S, Chemello F, Silvestrin M, Musaro A, De Pitta C, Lanfranchi G, Sandri M. Involvement of microRNAs in the regulation of muscle wasting during catabolic conditions. J Biol Chem 2014; 289:21909-25. [PMID: 24891504 PMCID: PMC4139209 DOI: 10.1074/jbc.m114.561845] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Loss of muscle proteins and the consequent weakness has important clinical consequences in diseases such as cancer, diabetes, chronic heart failure, and in aging. In fact, excessive proteolysis causes cachexia, accelerates disease progression, and worsens life expectancy. Muscle atrophy involves a common pattern of transcriptional changes in a small subset of genes named atrophy-related genes or atrogenes. Whether microRNAs play a role in the atrophy program and muscle loss is debated. To understand the involvement of miRNAs in atrophy we performed miRNA expression profiling of mouse muscles under wasting conditions such as fasting, denervation, diabetes, and cancer cachexia. We found that the miRNA signature is peculiar of each catabolic condition. We then focused on denervation and we revealed that changes in transcripts and microRNAs expression did not occur simultaneously but were shifted. Indeed, whereas transcriptional control of the atrophy-related genes peaks at 3 days, changes of miRNA expression maximized at 7 days after denervation. Among the different miRNAs, microRNA-206 and -21 were the most induced in denervated muscles. We characterized their pattern of expression and defined their role in muscle homeostasis. Indeed, in vivo gain and loss of function experiments revealed that miRNA-206 and miRNA-21 were sufficient and required for atrophy program. In silico and in vivo approaches identified transcription factor YY1 and the translational initiator factor eIF4E3 as downstream targets of these miRNAs. Thus miRNAs are important for fine-tuning the atrophy program and their modulation can be a novel potential therapeutic approach to counteract muscle loss and weakness in catabolic conditions.
Collapse
Affiliation(s)
- Ricardo José Soares
- From the Dulbecco Telethon Institute, Venetian Institute of Molecular Medicine, 35129 Padova, Italy, the Ph.D. Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Stefano Cagnin
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy
| | - Francesco Chemello
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy
| | - Matteo Silvestrin
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy
| | - Antonio Musaro
- the DAHFMO-Unit of Histology and Medical Embryology, Sapienza University, 00161 Roma, Italy, and
| | - Cristiano De Pitta
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy,
| | - Gerolamo Lanfranchi
- the Department of Biology and CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy,
| | - Marco Sandri
- From the Dulbecco Telethon Institute, Venetian Institute of Molecular Medicine, 35129 Padova, Italy, the Department of Biomedical Sciences and the Institute of Neuroscience, Consiglio Nazionale delle Ricerche, 35121 Padova, Italy, the Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| |
Collapse
|