1
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Cerda A, Rivera M, Armijo G, Ibarra-Henriquez C, Reyes J, Blázquez-Sánchez P, Avilés J, Arce A, Seguel A, Brown AJ, Vásquez Y, Cortez-San Martín M, Cubillos FA, García P, Ferres M, Ramírez-Sarmiento CA, Federici F, Gutiérrez RA. An Open One-Step RT-qPCR for SARS-CoV-2 detection. PLoS One 2024; 19:e0297081. [PMID: 38271448 PMCID: PMC10810446 DOI: 10.1371/journal.pone.0297081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, demonstrating sensitivity comparable to a commercial kit routinely employed in clinical settings for patient diagnosis. Further evaluation on 40 clinical samples (20 positive and 20 negative) confirmed its comparable diagnostic accuracy. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.
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Affiliation(s)
- Ariel Cerda
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Grace Armijo
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina Ibarra-Henriquez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Avilés
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Aníbal Arce
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Aldo Seguel
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alexander J. Brown
- Department of Biomedical Research, National Jewish Health, Denver, CO, United States of America
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Yesseny Vásquez
- Escuela de Ciencias Médicas, Facultad de Medicina, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Marcelo Cortez-San Martín
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Francisco A. Cubillos
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Patricia García
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferres
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Ramírez-Sarmiento
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A. Gutiérrez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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2
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Cerda A, Rivera M, Armijo G, Ibarra-Henriquez C, Reyes J, Blázquez-Sánchez P, Avilés J, Arce A, Seguel A, Brown AJ, Vásquez Y, Cortez-San Martín M, Cubillos FA, García P, Ferres M, Ramírez-Sarmiento CA, Federici F, Gutiérrez RA. An Open One-Step RT-qPCR for SARS-CoV-2 detection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2021.11.29.21267000. [PMID: 34909786 PMCID: PMC8669853 DOI: 10.1101/2021.11.29.21267000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, and the kit showed comparable sensitivity to approved commercial kits. The One-Step RT-qPCR was then tested on clinical samples and demonstrated similar performance to commercial kits in terms of positive and negative calls. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.
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Affiliation(s)
- Ariel Cerda
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Maira Rivera
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Grace Armijo
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Catalina Ibarra-Henriquez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Javiera Reyes
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Avilés
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
| | - Aníbal Arce
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
| | - Aldo Seguel
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
| | - Alexander J. Brown
- Department of Biomedical Research, National Jewish Health, Denver, CO, USA
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yesseny Vásquez
- Escuela de Ciencias Médicas. Facultad de Medicina. Universidad de Santiago de Chile. USACH, Santiago, Chile
| | - Marcelo Cortez-San Martín
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Francisco A. Cubillos
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Patricia García
- Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferres
- Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Ramírez-Sarmiento
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A. Gutiérrez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio)
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
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3
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Da'as SI, Ahmed I, Hasan WH, Abdelrahman DA, Aliyev E, Nisar S, Bhat AA, Joglekar MV, Hardikar AA, Fakhro KA, Akil ASAS. The link between glycemic control measures and eye microvascular complications in a clinical cohort of type 2 diabetes with microRNA-223-3p signature. J Transl Med 2023; 21:171. [PMID: 36869348 PMCID: PMC9985290 DOI: 10.1186/s12967-023-03893-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/16/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is a critical healthcare challenge and priority in Qatar which is listed amongst the top 10 countries in the world, with its prevalence presently at 17% double the global average. MicroRNAs (miRNAs) are implicated in the pathogenesis of (T2D) and long-term microvascular complications including diabetic retinopathy (DR). METHODS In this study, a T2D cohort that accurately matches the characteristics of the general population was employed to find microRNA (miRNA) signatures that are correlated with glycemic and β cell function measurements. Targeted miRNA profiling was performed in (471) T2D individuals with or without DR and (491) (non-diabetic) healthy controls from the Qatar Biobank. Discovery analysis identified 20 differentially expressed miRNAs in T2D compared to controls, of which miR-223-3p was significantly upregulated (fold change:5.16, p = 3.6e-02) and positively correlated with glucose and hemoglobin A1c (HbA1c) levels (p-value = 9.88e-04 and 1.64e-05, respectively), but did not show any significant associations with insulin or C-peptide. Accordingly, we performed functional validation using a miR-223-3p mimic (overexpression) under control and hyperglycemia-induced conditions in a zebrafish model. RESULTS Over-expression of miR-223-3p alone was associated with significantly higher glucose (42.7 mg/dL, n = 75 vs 38.7 mg/dL, n = 75, p = 0.02) and degenerated retinal vasculature, and altered retinal morphology involving changes in the ganglion cell layer and inner and outer nuclear layers. Assessment of retinal angiogenesis revealed significant upregulation in the expression of vascular endothelial growth factor and its receptors, including kinase insert domain receptor. Further, the pancreatic markers, pancreatic and duodenal homeobox 1, and the insulin gene expressions were upregulated in the miR-223-3p group. CONCLUSION Our zebrafish model validates a novel correlation between miR-223-3p and DR development. Targeting miR-223-3p in T2D patients may serve as a promising therapeutic strategy to control DR in at-risk individuals.
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Affiliation(s)
- Sahar I Da'as
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.,Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, Sidra Medicine, P.O. Box 26999, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Ikhlak Ahmed
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Waseem H Hasan
- Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Doua A Abdelrahman
- Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Elbay Aliyev
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sabah Nisar
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ajaz Ahmad Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW, 2560, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW, 2560, Australia.,Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
| | - Khalid A Fakhro
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar.,Department of Genetic Medicine, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar. .,Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.
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4
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Farr RJ, Dahal S, Tribolet L, Bean AGD, Cowled C, Stewart CR. Profiling Host MicroRNA Responses to Henipavirus Infection. Methods Mol Biol 2023; 2682:261-279. [PMID: 37610588 DOI: 10.1007/978-1-0716-3283-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Diseases caused by henipaviruses feature incubation periods of up to 16 days, during which infected animals may show no apparent signs of disease yet be capable of transmitting the virus to humans. This risk has prompted research into host-derived biomarkers for early disease detection. Here, we describe a methodology for the assaying of host microRNAs (miRs), small non-coding RNAs that show promise as biomarkers for several human diseases and are responsive during early-stage henipavirus infection. In addition to their potential as disease biomarkers, miRNA profiling of henipavirus infections provides insight into cellular and immune pathways associated with disease pathogenesis.
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Affiliation(s)
- Ryan J Farr
- CSIRO Australian Animal Health Laboratory, Health & Biosecurity, Geelong, VIC, Australia
| | - Sudeep Dahal
- CSIRO Australian Animal Health Laboratory, Health & Biosecurity, Geelong, VIC, Australia
| | - Leon Tribolet
- CSIRO Australian Animal Health Laboratory, Health & Biosecurity, Geelong, VIC, Australia
| | - Andrew G D Bean
- CSIRO Australian Animal Health Laboratory, Health & Biosecurity, Geelong, VIC, Australia
| | - Christopher Cowled
- CSIRO Australian Animal Health Laboratory, Health & Biosecurity, Geelong, VIC, Australia
| | - Cameron R Stewart
- CSIRO Australian Animal Health Laboratory, Health & Biosecurity, Geelong, VIC, Australia.
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5
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The Intestinal Microbiota May Be a Potential Theranostic Tool for Personalized Medicine. J Pers Med 2022; 12:jpm12040523. [PMID: 35455639 PMCID: PMC9024566 DOI: 10.3390/jpm12040523] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/09/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
The human intestine is colonized by a huge number of microorganisms from the moment of birth. This set of microorganisms found throughout the human body, is called the microbiota; the microbiome indicates the totality of genes that the microbiota can express, i.e., its genetic heritage. Thus, microbiota participates in and influences the proper functioning of the organism. The microbiota is unique for each person; it differs in the types of microorganisms it contains, the number of each microorganism, and the ratio between them, but mainly it changes over time and under the influence of many factors. Therefore, the correct functioning of the human body depends not only on the expression of its genes but also on the expression of the genes of the microorganisms it coexists with. This fact makes clear the enormous interest of community science in studying the relationship of the human microbiota with human health and the incidence of disease. The microbiota is like a unique personalized “mold” for each person; it differs quantitatively and qualitatively for the microorganisms it contains together with the relationship between them, and it changes over time and under the influence of many factors. We are attempting to modulate the microbial components in the human intestinal microbiota over time to provide positive feedback on the health of the host, from intestinal diseases to cancer. These interventions to modulate the intestinal microbiota as well as to identify the relative microbiome (genetic analysis) can range from dietary (with adjuvant prebiotics or probiotics) to fecal transplantation. This article researches the recent advances in these strategies by exploring their advantages and limitations. Furthermore, we aim to understand the relationship between intestinal dysbiosis and pathologies, through the research of resident microbiota, that would allow the personalization of the therapeutic antibiotic strategy.
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6
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Mahani M, Khakbaz F, Ju H. Hairpin oligosensor using SiQDs: Förster resonance energy transfer study and application for miRNA-21 detection. Anal Bioanal Chem 2022; 414:2505-2512. [PMID: 35099583 DOI: 10.1007/s00216-022-03891-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/27/2021] [Accepted: 01/10/2022] [Indexed: 11/28/2022]
Abstract
MicroRNAs are known to be tumor suppressors and promoters and can be used as cancer markers. In this work, a novel oligosensor was designed using Si quantum dots (SiQDs) for the detection of miRNAs. Five-nanometer SiQDs were synthesized, with a band gap of 2.8 eV, fluorescence lifetime of 4.56 μs (τ1/2 = 3.26 μs), quantum yield of 25%, fluorescence rate constant of 6.25 × 104, and non-radiative rate constant of 1.60 × 105 s-1. They showed excellent water dispersibility, good stability (with 95% confidence for 6-month storage) without photobleaching, and high biocompatibility, with an IC50 value of 292.2 μg/L. The SiQDs and Black Hole Quencher-1 (BHQ1) were conjugated to the 5' and 3' terminals of an oligomer, respectively. The resulting hairpin molecular beacon showed resonance energy transfer efficiency of 63%. A distance of 0.91 R (Förster distance) between SiQD and BHQ1 was obtained. In the presence of a stoichiometric amount of the complementary oligonucleotide (ΔGhybridization = -35.09 kcal mol-1), 98% of the fluorescence was recovered due to loop opening of the hairpin structure. The probe showed good selectivity toward miRNA-21, with a limit of detection of 14.9 fM. The oligosensor recoveries of miRNA-21 spiked in human serum and urine were 94-98% and 93-108%, respectively.
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Affiliation(s)
- Mohamad Mahani
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Graduate University of Advanced Technology, Kerman, Iran.
| | - Faeze Khakbaz
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, 210023, China
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7
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Manipulating cellular microRNAs and analyzing high-dimensional gene expression data using machine learning workflows. STAR Protoc 2021; 2:100910. [PMID: 34746868 PMCID: PMC8554629 DOI: 10.1016/j.xpro.2021.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) are elements of the gene regulatory network and manipulating their abundance is essential toward elucidating their role in patho-physiological conditions. We present a detailed workflow that identifies important miRNAs using a machine learning algorithm. We then provide optimized techniques to validate the identified miRNAs through over-expression/loss-of-function studies. Overall, these protocols apply to any field in biology where high-dimensional data are produced. For complete details on the use and execution of this protocol, please refer to Wong et al. (2021a). LASSO and bootstrapping identify important miRNAs associated with gene of interest Generating puromycin resistant, doxycycline inducible, miRNA overexpressing cells Transient miRNA knockdown using LNA inhibitors in human primary cells Optimized reagent concentrations and cell densities for miRNA manipulation
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8
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Scott ES, Januszewski AS, Carroll LM, Fulcher GR, Joglekar MV, Hardikar AA, Jones TW, Davis EA, Jenkins AJ. Continuous subcutaneous insulin infusion alters microRNA expression and glycaemic variability in children with type 1 diabetes. Sci Rep 2021; 11:16656. [PMID: 34404828 PMCID: PMC8370996 DOI: 10.1038/s41598-021-95824-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/13/2021] [Indexed: 11/12/2022] Open
Abstract
To determine whether continuous subcutaneous insulin infusion (CSII) vs. multiple daily injections (MDI) therapy from near-diagnosis of type 1 diabetes is associated with reduced glycaemic variability (GV) and altered microRNA (miRNAs) expression. Adolescents (74% male) within 3-months of diabetes diagnosis (n = 27) were randomized to CSII (n = 12) or MDI. HbA1c, 1-5-Anhydroglucitol (1,5-AG), high sensitivity C-peptide and a custom TaqMan qPCR panel of 52 miRNAs were measured at baseline and follow-up (median (LQ-UQ); 535 (519–563) days). There were no significant differences between groups in baseline or follow-up HbA1c or C-peptide, nor baseline miRNAs. Mean ± SD 1,5-AG improved with CSII vs. MDI (3.1 ± 4.1 vs. − 2.2 ± − 7.0 mg/ml respectively, P = 0.029). On follow-up 11 miRNAs associated with diabetes vascular complications had altered expression in CSII-users. Early CSII vs. MDI use is associated with lower GV and less adverse vascular-related miRNAs. Relationships with future complications are of interest.
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Affiliation(s)
- Emma S Scott
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.,Department of Endocrinology and Diabetes, Royal North Shore Hospital, Sydney, Australia
| | - Andrzej S Januszewski
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.,Department of Medicine, St Vincent's Hospital, University of Melbourne, Melbourne, Australia
| | - Luke M Carroll
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Gregory R Fulcher
- Department of Endocrinology and Diabetes, Royal North Shore Hospital, Sydney, Australia.,Northern Clinical School, University of Sydney, Sydney, Australia
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Anandwardhan A Hardikar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Timothy W Jones
- University of Western Australia, Perth, Australia.,Diabetes and Endocrinology Services, Perth Children's Hospital, Perth, Australia.,Telethon Kids Institute, Perth, Australia
| | - Elizabeth A Davis
- University of Western Australia, Perth, Australia.,Diabetes and Endocrinology Services, Perth Children's Hospital, Perth, Australia.,Telethon Kids Institute, Perth, Australia
| | - Alicia J Jenkins
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Sydney, Australia. .,Department of Medicine, St Vincent's Hospital, University of Melbourne, Melbourne, Australia. .,NHMRC Clinical Trials Centre, The University of Sydney, Locked bag, 77, Camperdown, NSW, 1450, Australia.
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9
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Joglekar MV, Wong WKM, Ema FK, Georgiou HM, Shub A, Hardikar AA, Lappas M. Postpartum circulating microRNA enhances prediction of future type 2 diabetes in women with previous gestational diabetes. Diabetologia 2021; 64:1516-1526. [PMID: 33755745 DOI: 10.1007/s00125-021-05429-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022]
Abstract
AIMS/HYPOTHESIS Type 2 diabetes mellitus is a major cause of morbidity and death worldwide. Women with gestational diabetes mellitus (GDM) have greater than a sevenfold higher risk of developing type 2 diabetes in later life. Accurate methods for postpartum type 2 diabetes risk stratification are lacking. Circulating microRNAs (miRNAs) are well recognised as biomarkers/mediators of metabolic disease. We aimed to determine whether postpartum circulating miRNAs can predict the development of type 2 diabetes in women with previous GDM. METHODS In an observational study, plasma samples were collected at 12 weeks postpartum from 103 women following GDM pregnancy. Utilising a discovery approach, we measured 754 miRNAs in plasma from type 2 diabetes non-progressors (n = 11) and type 2 diabetes progressors (n = 10) using TaqMan-based real-time PCR on an OpenArray platform. Machine learning algorithms involving penalised logistic regression followed by bootstrapping were implemented. RESULTS Fifteen miRNAs were selected based on their importance in discriminating type 2 diabetes progressors from non-progressors in our discovery cohort. The levels of miRNA miR-369-3p remained significantly different (p < 0.05) between progressors and non-progressors in the validation sample set (n = 82; 71 non-progressors, 11 progressors) after adjusting for age and correcting for multiple comparisons. In a clinical model of prediction of type 2 diabetes that included six traditional risk factors (age, BMI, pregnancy fasting glucose, postpartum fasting glucose, cholesterol and triacylglycerols), the addition of the circulating miR-369-3p measured at 12 weeks postpartum improved the prediction of future type 2 diabetes from traditional AUC 0.83 (95% CI 0.68, 0.97) to an AUC 0.92 (95% CI 0.84, 1.00). CONCLUSIONS This is the first demonstration of miRNA-based type 2 diabetes prediction in women with previous GDM. Improved prediction will facilitate early lifestyle/drug intervention for type 2 diabetes prevention.
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Affiliation(s)
- Mugdha V Joglekar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
- Diabetes and Islet Biology Group, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Wilson K M Wong
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
- Diabetes and Islet Biology Group, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Fahmida K Ema
- Diabetes and Islet Biology Group, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Harry M Georgiou
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Alexis Shub
- Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia.
- Diabetes and Islet Biology Group, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia.
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.
| | - Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Heidelberg, VIC, Australia.
- Mercy Perinatal Research Centre, Mercy Hospital for Women, Heidelberg, VIC, Australia.
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10
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Januszewski AS, Cho YH, Joglekar MV, Farr RJ, Scott ES, Wong WKM, Carroll LM, Loh YW, Benitez-Aguirre PZ, Keech AC, O'Neal DN, Craig ME, Hardikar AA, Donaghue KC, Jenkins AJ. Insulin micro-secretion in Type 1 diabetes and related microRNA profiles. Sci Rep 2021; 11:11727. [PMID: 34083567 PMCID: PMC8175359 DOI: 10.1038/s41598-021-90856-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
The aim of this cross-sectional study was to compare plasma C-peptide presence and levels in people without diabetes (CON) and with Type 1 diabetes and relate C-peptide status to clinical factors. In a subset we evaluated 50 microRNAs (miRs) previously implicated in beta-cell death and associations with clinical status and C-peptide levels. Diabetes age of onset was stratified as adult (≥ 18 y.o) or childhood (< 18 y.o.), and diabetes duration was stratified as ≤ 10 years, 10–20 years and > 20 years. Plasma C-peptide was measured by ultrasensitive ELISA. Plasma miRs were quantified using TaqMan probe-primer mix on an OpenArray platform. C-peptide was detectable in 55.3% of (n = 349) people with diabetes, including 64.1% of adults and 34.0% of youth with diabetes, p < 0.0001 and in all (n = 253) participants without diabetes (CON). C-peptide levels, when detectable, were lower in the individuals with diabetes than in the CON group [median lower quartile (LQ)–upper quartile (UQ)] 5.0 (2.6–28.7) versus 650.9 (401.2–732.4) pmol/L respectively, p < 0.0001 and lower in childhood versus adult-onset diabetes [median (LQ–UQ) 4.2 (2.6–12.2) pmol/L vs. 8.0 (2.3–80.5) pmol/L, p = 0.02, respectively]. In the childhood-onset group more people with longer diabetes duration (> 20 years) had detectable C-peptide (60%) than in those with shorter diabetes duration (39%, p for trend < 0.05).
Nine miRs significantly correlated with detectable C-peptide levels in people with diabetes and 16 miRs correlated with C-peptide levels in CON. Our cross-sectional study results are supportive of (a) greater beta-cell function loss in younger onset Type 1 diabetes; (b) persistent insulin secretion in adult-onset diabetes and possibly regenerative secretion in childhood-onset long diabetes duration; and (c) relationships of C-peptide levels with circulating miRs. Confirmatory clinical studies and related basic science studies are merited.
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Affiliation(s)
- Andrzej S Januszewski
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia. .,Department of Medicine, University of Melbourne, Melbourne, VIC, Australia.
| | - Yoon Hi Cho
- Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia.,School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Ryan J Farr
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Emma S Scott
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Wilson K M Wong
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia.,School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Luke M Carroll
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Yik W Loh
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Paul Z Benitez-Aguirre
- Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Anthony C Keech
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - David N O'Neal
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Maria E Craig
- Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Anandwardhan A Hardikar
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia.,School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Department of Science and Environment, Roskilde University, Copenhagen, Denmark
| | - Kim C Donaghue
- Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia.,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Alicia J Jenkins
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia. .,Department of Medicine, University of Melbourne, Melbourne, VIC, Australia.
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11
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Shihana F, Wong WKM, Joglekar MV, Mohamed F, Gawarammana IB, Isbister GK, Hardikar AA, Seth D, Buckley NA. Urinary microRNAs as non-invasive biomarkers for toxic acute kidney injury in humans. Sci Rep 2021; 11:9165. [PMID: 33911095 PMCID: PMC8080685 DOI: 10.1038/s41598-021-87918-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/05/2021] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs in biofluids are potential biomarkers for detecting kidney and other organ injuries. We profiled microRNAs in urine samples from patients with Russell's viper envenoming or acute self-poisoning following paraquat, glyphosate, or oxalic acid [with and without acute kidney injury (AKI)] and on healthy controls. Discovery analysis profiled for 754 microRNAs using TaqMan OpenArray qPCR with three patients per group (12 samples in each toxic agent). From these, 53 microRNAs were selected and validated in a larger cohort of patients (Russell's viper envenoming = 53, paraquat = 51, glyphosate = 51, oxalic acid = 40) and 27 healthy controls. Urinary microRNAs had significantly higher expression in patients poisoned/envenomed by different nephrotoxic agents in both discovery and validation cohorts. Seven microRNAs discriminated severe AKI patients from no AKI for all four nephrotoxic agents. Four microRNAs (miR-30a-3p, miR-30a-5p, miR-92a, and miR-204) had > 17 fold change (p < 0.0001) and receiver operator characteristics area-under-curve (ROC-AUC) > 0.72. Pathway analysis of target mRNAs of these differentially expressed microRNAs showed association with the regulation of different nephrotoxic signaling pathways. In conclusion, human urinary microRNAs could identify toxic AKI early after acute injury. These urinary microRNAs have potential clinical application as early non-invasive diagnostic AKI biomarkers.
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Affiliation(s)
- Fathima Shihana
- Clinical Pharmacology and Toxicology Research Group, Biomedical Informatics and Digital Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia.
| | - Wilson K M Wong
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Fahim Mohamed
- Clinical Pharmacology and Toxicology Research Group, Biomedical Informatics and Digital Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
- Allied Health Sciences, Department of Pharmacy, University of Peradeniya, Peradeniya, Sri Lanka
- Australian Kidney Biomarker Reference Laboratory, Department of Nephrology, Prince of Wales Hospital and Clinical School, University of New South Wales, Sydney, Australia
| | - Indika B Gawarammana
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Geoffrey K Isbister
- Clinical Toxicology Research Group, University of Newcastle, Newcastle, NSW, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Devanshi Seth
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia
- Discipline of Clinical Medicine and Addiction Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Drug Health Services, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Nicholas A Buckley
- Clinical Pharmacology and Toxicology Research Group, Biomedical Informatics and Digital Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
- Drug Health Services, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
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12
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Wong WK, Joglekar MV, Saini V, Jiang G, Dong CX, Chaitarvornkit A, Maciag GJ, Gerace D, Farr RJ, Satoor SN, Sahu S, Sharangdhar T, Ahmed AS, Chew YV, Liuwantara D, Heng B, Lim CK, Hunter J, Januszewski AS, Sørensen AE, Akil AS, Gamble JR, Loudovaris T, Kay TW, Thomas HE, O'Connell PJ, Guillemin GJ, Martin D, Simpson AM, Hawthorne WJ, Dalgaard LT, Ma RC, Hardikar AA. Machine learning workflows identify a microRNA signature of insulin transcription in human tissues. iScience 2021; 24:102379. [PMID: 33981968 PMCID: PMC8082091 DOI: 10.1016/j.isci.2021.102379] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/19/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Dicer knockout mouse models demonstrated a key role for microRNAs in pancreatic β-cell function. Studies to identify specific microRNA(s) associated with human (pro-)endocrine gene expression are needed. We profiled microRNAs and key pancreatic genes in 353 human tissue samples. Machine learning workflows identified microRNAs associated with (pro-)insulin transcripts in a discovery set of islets (n = 30) and insulin-negative tissues (n = 62). This microRNA signature was validated in remaining 261 tissues that include nine islet samples from individuals with type 2 diabetes. Top eight microRNAs (miR-183-5p, -375-3p, 216b-5p, 183-3p, -7-5p, -217-5p, -7-2-3p, and -429-3p) were confirmed to be associated with and predictive of (pro-)insulin transcript levels. Use of doxycycline-inducible microRNA-overexpressing human pancreatic duct cell lines confirmed the regulatory roles of these microRNAs in (pro-)endocrine gene expression. Knockdown of these microRNAs in human islet cells reduced (pro-)insulin transcript abundance. Our data provide specific microRNAs to further study microRNA-mRNA interactions in regulating insulin transcription.
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Affiliation(s)
- Wilson K.M. Wong
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Mugdha V. Joglekar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Vijit Saini
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- School of Life Sciences and the Centre for Health Technologies, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, and Hong Kong Institute of Diabetes and Obesity, and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, Special Administrative Region, China
| | - Charlotte X. Dong
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Alissa Chaitarvornkit
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Grzegorz J. Maciag
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Dario Gerace
- School of Life Sciences and the Centre for Health Technologies, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Ryan J. Farr
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Sarang N. Satoor
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Subhshri Sahu
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Tejaswini Sharangdhar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Asma S. Ahmed
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Yi Vee Chew
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - David Liuwantara
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Benjamin Heng
- Faculty of Medicine Health and Human Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Chai K. Lim
- Faculty of Medicine Health and Human Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Julie Hunter
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, University of Sydney Medical School, Locked Bag #6, Newtown, NSW 2042, Australia
| | - Andrzej S. Januszewski
- NHMRC Clinical Trials Centre, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Anja E. Sørensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Ammira S.A. Akil
- Department of Human Genetics-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Jennifer R. Gamble
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, University of Sydney Medical School, Locked Bag #6, Newtown, NSW 2042, Australia
| | - Thomas Loudovaris
- St Vincent's Institute and The University of Melbourne Department of Medicine, 9 Princes Street, Fitzroy, VIC, Australia
| | - Thomas W. Kay
- St Vincent's Institute and The University of Melbourne Department of Medicine, 9 Princes Street, Fitzroy, VIC, Australia
| | - Helen E. Thomas
- St Vincent's Institute and The University of Melbourne Department of Medicine, 9 Princes Street, Fitzroy, VIC, Australia
| | - Philip J. O'Connell
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Gilles J. Guillemin
- Faculty of Medicine Health and Human Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - David Martin
- Upper GI Surgery, Strathfield Hospital, 2/3 Everton Road, Strathfield, NSW 2135, Australia
| | - Ann M. Simpson
- School of Life Sciences and the Centre for Health Technologies, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Wayne J. Hawthorne
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Louise T. Dalgaard
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Ronald C.W. Ma
- Department of Medicine and Therapeutics, and Hong Kong Institute of Diabetes and Obesity, and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, Special Administrative Region, China
| | - Anandwardhan A. Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW 2560, Australia
- Diabetes and Islet Biology group, Faculty of Medicine and Health, University of Sydney, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
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13
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Westaway JAF, Huerlimann R, Miller CM, Kandasamy Y, Norton R, Rudd D. Methods for exploring the faecal microbiome of premature infants: a review. Matern Health Neonatol Perinatol 2021; 7:11. [PMID: 33685524 PMCID: PMC7941982 DOI: 10.1186/s40748-021-00131-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.
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Affiliation(s)
- Jacob A F Westaway
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Roger Huerlimann
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
| | - Catherine M Miller
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia
| | - Yoga Kandasamy
- Townsville University Hospital, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Robert Norton
- Pathology Queensland, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Donna Rudd
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
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14
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Tribolet L, Kerr E, Cowled C, Bean AGD, Stewart CR, Dearnley M, Farr RJ. MicroRNA Biomarkers for Infectious Diseases: From Basic Research to Biosensing. Front Microbiol 2020; 11:1197. [PMID: 32582115 PMCID: PMC7286131 DOI: 10.3389/fmicb.2020.01197] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
In the pursuit of improved diagnostic tests for infectious diseases, several classes of molecules have been scrutinized as prospective biomarkers. Small (18–22 nucleotide), non-coding RNA transcripts called microRNAs (miRNAs) have emerged as promising candidates with extensive diagnostic potential, due to their role in numerous diseases, previously established methods for quantitation and their stability within biofluids. Despite efforts to identify, characterize and apply miRNA signatures as diagnostic markers in a range of non-infectious diseases, their application in infectious disease has advanced relatively slowly. Here, we outline the benefits that miRNA biomarkers offer to the diagnosis, management, and treatment of infectious diseases. Investigation of these novel biomarkers could advance the use of personalized medicine in infectious disease treatment, which raises important considerations for validating their use as diagnostic or prognostic markers. Finally, we discuss new and emerging miRNA detection platforms, with a focus on rapid, point-of-care testing, to evaluate the benefits and obstacles of miRNA biomarkers for infectious disease.
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Affiliation(s)
- Leon Tribolet
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Emily Kerr
- Institute for Frontier Materials, Deakin University, Geelong, VIC, Australia
| | - Christopher Cowled
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Andrew G D Bean
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Cameron R Stewart
- Health and Biosecurity, Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Megan Dearnley
- Diagnostics, Surveillance and Response (DSR), Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
| | - Ryan J Farr
- Diagnostics, Surveillance and Response (DSR), Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, VIC, Australia
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15
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Shihana F, Joglekar MV, Raubenheimer J, Hardikar AA, Buckley NA, Seth D. Circulating human microRNA biomarkers of oxalic acid-induced acute kidney injury. Arch Toxicol 2020; 94:1725-1737. [PMID: 32086547 DOI: 10.1007/s00204-020-02679-5] [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: 12/25/2019] [Accepted: 02/11/2020] [Indexed: 12/11/2022]
Abstract
Oxalic acid-induced nephrotoxicity and acute kidney injury result from formation of calcium oxalate crystals. Oxalic acid-induced acute kidney injury is a significant problem in many parts of the world. Circulating biomarkers that can accurately and reproducibly detect acute kidney injury are highly desirable. We used a high sensitivity discovery platform to identify signature microRNAs to distinguish healthy individuals never exposed to oxalic acid (n = 4) from those who were exposed to oxalic acid but had no injury (NOAKI; n = 4), moderate injury (AKIN2; n = 4) or severe injury (AKIN3; n = 4). Longitudinal analyses identified 4-8 h post-ingestion as the best time to detect AKIN2/3. We validated a signature of 53 microRNAs identified in the discovery, in a second cohort of individuals exposed to oxalic acid (NOAKI = 11, AKIN2 = 8 and AKIN3 = 18) and healthy controls (n = 19). Thirteen microRNAs were significantly downregulated in acute kidney injury patients compared to NOAKI within 8-h post-ingestion. Five microRNAs (miR-20a, miR-92a, miR-93, miR-195, miR-451) had a highly significant correlation with normalized urinary albumin, serum creatinine at 24 h and creatinine clearance. Logistic regression of these microRNAs had AUC-ROC of 0.85 predicting AKIN2/3 and discriminated patients from healthy controls (AUC-ROC = 0.93). mRNA targets of these microRNAs identified oxidative stress pathways of nephrotoxicity in proximal tubule and glomeruli nephrotoxicity. In conclusion, the downregulation of multiple circulating microRNAs in patients correlated with the severity of oxalic acid-induced acute kidney injury. A set of microRNAs (miR-20a, miR-92a, miR-93, miR-195, miR-451) could be promising biomarkers for early detection of oxalic acid-induced acute kidney injury.
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Affiliation(s)
- Fathima Shihana
- Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, The University of Sydney, Level 3, 1-3 Ross St (K06), Sydney, NSW, 2006, Australia. .,South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jacques Raubenheimer
- Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, The University of Sydney, Level 3, 1-3 Ross St (K06), Sydney, NSW, 2006, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Nicholas A Buckley
- Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, The University of Sydney, Level 3, 1-3 Ross St (K06), Sydney, NSW, 2006, Australia.,South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Devanshi Seth
- Discipline of Clinical Medicine and Addiction Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Drug Health Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,The Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia
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16
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Lin Q, Di YP. Determination and Quantification of Bacterial Virulent Gene Expression Using Quantitative Real-Time PCR. Methods Mol Biol 2020; 2102:177-193. [PMID: 31989555 DOI: 10.1007/978-1-0716-0223-2_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Polymerase chain reaction (PCR) plays significant roles in modern molecular biology. However, it is relatively cumbersome and less accurate to use the traditional PCR method in quantifying gene expression because it requires first generating a standard curve with multiple input controls showing linearity with amplified control PCR products on a electrophoresis gel to compare with the abundance of the to-be-determined gene transcript PCR amplicons. Quantitative real-time PCR (qRT-PCR) is a time-efficient and reliable tool for accurate quantification and comparison of gene (RNA transcript) expression from various biological samples. Current technology has simplified and expedited the qPCR process significantly. However, proper techniques and standard protocols are required in eliminating potentially erroneous experimental outcome. Here, we provide an example from a drug-treated bacterial gene expression study with detailed protocols to demonstrate real-time qPCR with SYBR™ Green and TaqMan®, two of the most adapted and well-established qPCR technologies. Relative quantification of gene (RNA transcript) expression using qRT-PCR is demonstrated in detail from sample preparations to data analysis.
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Affiliation(s)
- Qiao Lin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA.
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17
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Barraclough JY, Joan M, Joglekar MV, Hardikar AA, Patel S. MicroRNAs as Prognostic Markers in Acute Coronary Syndrome Patients-A Systematic Review. Cells 2019; 8:cells8121572. [PMID: 31817254 PMCID: PMC6952952 DOI: 10.3390/cells8121572] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 01/09/2023] Open
Abstract
Background: The potential utility of microRNAs (miRNAs) in the diagnosis, prognosis, and treatment of multiple disease states has been an area of great interest since their discovery. In patients with cardiovascular disease, there is a large pool of literature amassed from the last decade assessing their diagnostic and prognostic potential. This systematic review sought to determine whether existing literature supports the use of miRNAs as prognostic markers after an Acute Coronary Syndrome (ACS) presentation. Methods: A systematic review of published articles from 2005–2019 using MEDLINE and EMBASE databases was undertaken independently by two reviewers. Studies addressing prognosis in an ACS population yielded 32 studies and 2 systematic reviews. Results/conclusion: 23 prospective studies reported significant differences in miRNA levels and 16 compared the predictive power of miRNAs. The most common miRNAs assessed included miR-133a, -208b, -21, -1, -34a, -150, and -423, shown to be involved in cell differentiation, apoptosis, and angiogenesis. Barriers to the use of miRNAs as prognostic markers include bias in miRNA selection, small sample size, variable normalization of data, and adjustment for confounders. Therefore, findings from this systematic review do not support the use of miRNAs for prognostication post-ACS beyond traditional cardiovascular risk factors, existing risk scores, and stratifications tools.
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Affiliation(s)
- Jennifer Y Barraclough
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney 2050, Australia
- Sydney Medical School, The University of Sydney, Sydney 2050, Australia
- Heart Research Institute, Sydney 2042, Australia
| | - Michelyn Joan
- Sydney Medical School, The University of Sydney, Sydney 2050, Australia
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney 2050, Australia
| | - Anandwardhan A Hardikar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney 2050, Australia
| | - Sanjay Patel
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney 2050, Australia
- Sydney Medical School, The University of Sydney, Sydney 2050, Australia
- Heart Research Institute, Sydney 2042, Australia
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18
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Chen IH, Chou LS, Chou SJ, Wang JH, Stott J, Blanchard M, Jen IF, Yang WC. Sound exposure-induced cytokine gene transcript profile changes in captive bottlenose dolphin (Tursiops truncatus) blood identified by a probe-based qRT-PCR. J Vet Med Sci 2018; 80:601-605. [PMID: 29479043 PMCID: PMC5938186 DOI: 10.1292/jvms.17-0548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cetacean health may be potentially affected by anthropogenic sound. We have initiated investigations on the effect of low-frequency underwater sound on immunological gene transcript profiles of captive bottlenose dolphins (Tursiops truncatus) using a probe-based quantitative gene expression assay. Six immunologic genes (IL-2Rα, -4, -10, -12, TNFα and IFNγ) were selected for analysis using two validated housekeeping genes (PGK1 and HPRT1) as reference genes. Twenty-four blood samples from six clinically healthy individuals and six blood samples from individuals after sound exposures were available. The gene transcript profile of sound-exposed dolphins was consistent with a stress-induced TH2 shift profile as compared to controls. This study may lead to better understanding of the effects of anthropogenic sound on immune responses of cetaceans.
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Affiliation(s)
- I-Hua Chen
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Lien-Siang Chou
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan (R.O.C.)
| | - Shih-Jen Chou
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Jiann-Hsiung Wang
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
| | - Jeffrey Stott
- School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A
| | - Myra Blanchard
- School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A
| | - I-Fan Jen
- Farglory Ocean Park, No.189, Yenliao Village, Shoufong, Hualien, Taiwan (R.O.C.)
| | - Wei-Cheng Yang
- Department of Veterinary Medicine, National Chiayi University, No. 580, Xinmin Rd., Chiayi, Taiwan (R.O.C.)
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19
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Andrea Hernández-Castañeda M, Mbagwu S, Babatunde KA, Walch M, Filgueira L, Mantel PY. Evaluation of Extracellular Vesicle Function During Malaria Infection. J Vis Exp 2018. [PMID: 29553510 DOI: 10.3791/57067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Malaria is a life-threatening disease caused by Plasmodium parasites, with P. falciparum being the most prevalent on the African continent and responsible for most malaria-related deaths globally. Several factors including parasite sequestration in tissues, vascular dysfunction, and inflammatory responses influence the evolution of the disease in malaria-infected people. P. falciparum-infected red blood cells (iRBCs) release small extracellular vesicles (EVs) containing different kinds of cargo molecules that mediate pathogenesis and cellular communication between parasites and host. EVs are efficiently taken up by cells in which they modulate their function. Here we discuss strategies to address the role of EVs in parasite-host interactions. First, we describe a straightforward method for labeling and tracking EV internalization by endothelial cells, using a green cell linker dye. Second, we report a simple way to measure permeability across an endothelial cell monolayer by using a fluorescently labeled dextran. Finally, we show how to investigate the role of small non-coding RNA molecules in endothelial cell function.
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20
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Tsai MA, Chen IH, Wang JH, Chou SJ, Li TH, Leu MY, Ho HK, Yang WC. A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales ( Delphinapterus leucas). PeerJ 2017; 5:e3840. [PMID: 28970970 PMCID: PMC5622604 DOI: 10.7717/peerj.3840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 09/01/2017] [Indexed: 12/20/2022] Open
Abstract
Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.
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Affiliation(s)
- Ming-An Tsai
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - I-Hua Chen
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Jiann-Hsiung Wang
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Shih-Jen Chou
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Tsung-Hsien Li
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Ming-Yih Leu
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Hsiao-Kuan Ho
- Department of Biology, Hi-Scene World Enterprise Co. Ltd., Pingtung, Taiwan
| | - Wei Cheng Yang
- College of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
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21
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Kim KW, Ho A, Alshabee-Akil A, Hardikar AA, Kay TWH, Rawlinson WD, Craig ME. Coxsackievirus B5 Infection Induces Dysregulation of microRNAs Predicted to Target Known Type 1 Diabetes Risk Genes in Human Pancreatic Islets. Diabetes 2016; 65:996-1003. [PMID: 26558682 DOI: 10.2337/db15-0956] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 11/05/2015] [Indexed: 12/15/2022]
Abstract
Extensive research has identified enterovirus (EV) infections as key environmental triggers of type 1 diabetes. However, the underlying molecular mechanisms via which EVs contribute to the pathogenesis of type 1 diabetes remain unclear. Given that EVs dysregulate host microRNAs (miRNAs), which function as key regulators of β-cell biology, we investigated the impact of coxsackievirus B5 (CVB5) infection on the cellular expression of miRNAs within human islets. Using high-throughput quantitative PCR nanofluidics arrays, the expression of 754 miRNAs was examined in CVB5-infected human pancreatic islets. In total, 33 miRNAs were significantly dysregulated (≥ threefold difference) in the infected compared with control islets (P < 0.05). Subsequently, these differentially expressed miRNAs were predicted to target mRNAs of 57 known type 1 diabetes risk genes that collectively mediate various biological processes, including the regulation of cell proliferation, cytokine production, the innate immune response, and apoptosis. In conclusion, we report the first global miRNA expression profiling of CVB5-infected human pancreatic islets. We propose that EVs disrupt the miRNA-directed suppression of proinflammatory factors within β-cells, thereby resulting in an exacerbated antiviral immune response that promotes β-cell destruction and eventual type 1 diabetes.
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Affiliation(s)
- Ki Wook Kim
- Faculty of Medicine, University of New South Wales, Sydney, Australia School of Women's and Children's Health, University of New South Wales, Sydney, Australia Prince of Wales Hospital, Virology Research Laboratory, Sydney, Australia
| | - Andy Ho
- Faculty of Medicine, University of New South Wales, Sydney, Australia Prince of Wales Hospital, Virology Research Laboratory, Sydney, Australia
| | - Ammira Alshabee-Akil
- Faculty of Medicine, University of New South Wales, Sydney, Australia School of Women's and Children's Health, University of New South Wales, Sydney, Australia Prince of Wales Hospital, Virology Research Laboratory, Sydney, Australia
| | | | - Thomas W H Kay
- St Vincent's Institute of Medical Research, Melbourne, Australia Department of Medicine, St Vincent's Hospital, The University of Melbourne, Melbourne, Australia
| | - William D Rawlinson
- Faculty of Medicine, University of New South Wales, Sydney, Australia Prince of Wales Hospital, Virology Research Laboratory, Sydney, Australia School of Medical Sciences, University of New South Wales, Sydney, Australia School of Biotechnology and Biomolecular Science, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Maria E Craig
- Faculty of Medicine, University of New South Wales, Sydney, Australia School of Women's and Children's Health, University of New South Wales, Sydney, Australia Prince of Wales Hospital, Virology Research Laboratory, Sydney, Australia Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, Australia Discipline of Pediatrics and Child Health, The Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, Australia
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22
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Farr RJ, Januszewski AS, Joglekar MV, Liang H, McAulley AK, Hewitt AW, Thomas HE, Loudovaris T, Kay TWH, Jenkins A, Hardikar AA. A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy. Sci Rep 2015; 5:10375. [PMID: 26035063 PMCID: PMC4649912 DOI: 10.1038/srep10375] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/01/2015] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs are now increasingly recognized as biomarkers of disease progression. Several quantitative real-time PCR (qPCR) platforms have been developed to determine the relative levels of microRNAs in biological fluids. We systematically compared the detection of cellular and circulating microRNA using a standard 96-well platform, a high-content microfluidics platform and two ultra-high content platforms. We used extensive analytical tools to compute inter- and intra-run variability and concordance measured using fidelity scoring, coefficient of variation and cluster analysis. We carried out unprejudiced next generation sequencing to identify a microRNA signature for Diabetic Retinopathy (DR) and systematically assessed the validation of this signature on clinical samples using each of the above four qPCR platforms. The results indicate that sensitivity to measure low copy number microRNAs is inversely related to qPCR reaction volume and that the choice of platform for microRNA biomarker validation should be made based on the abundance of miRNAs of interest.
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Affiliation(s)
- Ryan J Farr
- Diabetes and Islet biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Andrzej S Januszewski
- Biomarkers Laboratory, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Mugdha V Joglekar
- Diabetes and Islet biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Helena Liang
- Clinical Genetics Unit, Center for Eye Research Australia (CERA), The University of Melbourne, Royal Victorian Eye and Ear Hospital, Peter Howson Wing, Level 1, 32 Gisborne Street, Melbourne, VIC 3002, Australia
| | - Annie K McAulley
- Clinical Genetics Unit, Center for Eye Research Australia (CERA), The University of Melbourne, Royal Victorian Eye and Ear Hospital, Peter Howson Wing, Level 1, 32 Gisborne Street, Melbourne, VIC 3002, Australia
| | - Alex W Hewitt
- Clinical Genetics Unit, Center for Eye Research Australia (CERA), The University of Melbourne, Royal Victorian Eye and Ear Hospital, Peter Howson Wing, Level 1, 32 Gisborne Street, Melbourne, VIC 3002, Australia
| | - Helen E Thomas
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Tom Loudovaris
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Thomas W H Kay
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Alicia Jenkins
- Biomarkers Laboratory, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW 2050, Australia
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