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Guo HQ, Xue R, Wan G. Identification of biomarkers associated with ferroptosis in diabetic retinopathy based on WGCNA and machine learning. Front Genet 2024; 15:1376771. [PMID: 38863444 PMCID: PMC11165058 DOI: 10.3389/fgene.2024.1376771] [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: 01/26/2024] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
Objective: Diabetic retinopathy (DR) is a chronic progressive eye disease that affects millions of diabetic patients worldwide, and ferroptosis may contribute to the underlying mechanisms of DR. The main objective of this work is to explore key genes associated with ferroptosis in DR and to determine their feasibility as diagnostic markers. Methods: WGCNA identify the most relevant signature modules in DR. Machine learning methods were used to de-screen the feature genes. ssGSEA calculated the scoring of immune cells in the DR versus control samples and compared the associations with the core genes by Spearman correlation. Results: We identified 2,897 differential genes in DR versus normal samples. WGCNA found tan module to have the highest correlation with DR patients. Finally, 20 intersecting genes were obtained from differential genes, tan module and iron death genes, which were screened by LASSO and SVM-RFE method, and together identified 6 genes as potential diagnostic markers. qPCR verified the expression and ROC curves confirmed the diagnostic accuracy of the 6 genes. In addition, our ssGSEA scoring identified these 6 core genes as closely associated with immune infiltrating cells. Conclusion: In conclusion, we analyzed for the first time the potential link of iron death in the pathogenesis of DR. This has important implications for future studies of iron death-mediated pro-inflammatory immune mechanisms.
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Affiliation(s)
| | | | - Guangming Wan
- Department of Ophthalmology, First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Zhengzhou, China
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2
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Yu G, Tam HCH, Huang C, Shi M, Lim CKP, Chan JCN, Ma RCW. Lessons and Applications of Omics Research in Diabetes Epidemiology. Curr Diab Rep 2024; 24:27-44. [PMID: 38294727 PMCID: PMC10874344 DOI: 10.1007/s11892-024-01533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
PURPOSE OF REVIEW Recent advances in genomic technology and molecular techniques have greatly facilitated the identification of disease biomarkers, advanced understanding of pathogenesis of different common diseases, and heralded the dawn of precision medicine. Much of these advances in the area of diabetes have been made possible through deep phenotyping of epidemiological cohorts, and analysis of the different omics data in relation to detailed clinical information. In this review, we aim to provide an overview on how omics research could be incorporated into the design of current and future epidemiological studies. RECENT FINDINGS We provide an up-to-date review of the current understanding in the area of genetic, epigenetic, proteomic and metabolomic markers for diabetes and related outcomes, including polygenic risk scores. We have drawn on key examples from the literature, as well as our own experience of conducting omics research using the Hong Kong Diabetes Register and Hong Kong Diabetes Biobank, as well as other cohorts, to illustrate the potential of omics research in diabetes. Recent studies highlight the opportunity, as well as potential benefit, to incorporate molecular profiling in the design and set-up of diabetes epidemiology studies, which can also advance understanding on the heterogeneity of diabetes. Learnings from these examples should facilitate other researchers to consider incorporating research on omics technologies into their work to advance the field and our understanding of diabetes and its related co-morbidities. Insights from these studies would be important for future development of precision medicine in diabetes.
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Affiliation(s)
- Gechang Yu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Henry C H Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Cadmon K P Lim
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
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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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Wong WKM, Polkamp M, Farr RJ, Kunte PS, Hardikar HP, Yajnik CS, Hardikar AA, Joglekar MV. MicroRNA Profiling from Tears as a Potential Non-invasive Method for Early Detection of Diabetic Retinopathy. Methods Mol Biol 2023; 2678:117-134. [PMID: 37326708 DOI: 10.1007/978-1-0716-3255-0_8] [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: 06/17/2023]
Abstract
Diabetic retinopathy (DR) is a vascular complication of diabetes that can lead to partial or complete loss of vision. Early detection and treatment of DR can prevent blindness. Regular clinical examination is recommended for DR diagnosis; however, it is not always possible or feasible due to limited resources, expertise, time, and infrastructure. Several clinical and molecular biomarkers are proposed for the prediction of DR including microRNAs. MicroRNAs are a class of small non-coding RNAs that are found in biofluids and can be measured using reliable and sensitive methods. The most commonly used biofluid for microRNA profiling is plasma or serum; however, tear fluid (tears) is also demonstrated to contain microRNAs. MicroRNAs isolated from tears present a non-invasive source for DR detection. Different methods of microRNA profiling are available including digital PCR-based methods that can detect up to a single copy of microRNA in the biofluids. Here, we describe microRNA isolation from tears using manual method as well as using a high-throughput automated platform followed by microRNA profiling using digital PCR system.
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Affiliation(s)
- Wilson K M Wong
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Mya Polkamp
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Ryan J Farr
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
- Health and Biosecurity (H&B) at the Australian Centre for Disease Preparedness (ACDP), CSIRO, Geelong, VIC, Australia
| | - Pooja S Kunte
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
- Diabetes Unit, KEM Hospital and Research Centre, Pune, India
| | - Hrishikesh P Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | | | - Anandwardhan A Hardikar
- 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.
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5
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Circulating microRNAs from early childhood and adolescence are associated with pre-diabetes at 18 years of age in women from the PMNS cohort. J Dev Orig Health Dis 2022; 13:806-811. [PMID: 35450554 DOI: 10.1017/s2040174422000137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
With type 2 diabetes presenting at younger ages, there is a growing need to identify biomarkers of future glucose intolerance. A high (20%) prevalence of glucose intolerance at 18 years was seen in women from the Pune Maternal Nutrition Study (PMNS) birth cohort. We investigated the potential of circulating microRNAs in risk stratification for future pre-diabetes in these women. Here, we provide preliminary longitudinal analyses of circulating microRNAs in normal glucose tolerant (NGT@18y, N = 10) and glucose intolerant (N = 8) women (ADA criteria) at 6, 12 and 17 years of their age using discovery analysis (OpenArray™ platform). Machine-learning workflows involving Lasso with bootstrapping/leave-one-out cross-validation identified microRNAs associated with glucose intolerance at 18 years of age. Several microRNAs, including miR-212-3p, miR-30e-3p and miR-638, stratified glucose-intolerant women from NGT at childhood. Our results suggest that circulating microRNAs, longitudinally assessed over 17 years of life, are dynamic biomarkers associated with and predictive of pre-diabetes at 18 years of age. Validation of these findings in males and remaining participants from the PMNS birth cohort will provide a unique opportunity to study novel epigenetic mechanisms in the life-course progression of glucose intolerance and enhance current clinical risk prediction of pre-diabetes and progression to type 2 diabetes.
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6
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Gargiuli C, De Cecco L, Mariancini A, Iannò MF, Micali A, Mancinelli E, Boeri M, Sozzi G, Dugo M, Sensi M. A Cross-Comparison of High-Throughput Platforms for Circulating MicroRNA Quantification, Agreement in Risk Classification, and Biomarker Discovery in Non-Small Cell Lung Cancer. Front Oncol 2022; 12:911613. [PMID: 35928879 PMCID: PMC9343840 DOI: 10.3389/fonc.2022.911613] [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: 04/02/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundCirculating microRNAs (ct-miRs) are promising cancer biomarkers. This study focuses on platform comparison to assess performance variability, agreement in the assignment of a miR signature classifier (MSC), and concordance for the identification of cancer-associated miRs in plasma samples from non‐small cell lung cancer (NSCLC) patients.MethodsA plasma cohort of 10 NSCLC patients and 10 healthy donors matched for clinical features and MSC risk level was profiled for miR expression using two sequencing-based and three quantitative reverse transcription PCR (qPCR)-based platforms. Intra- and inter-platform variations were examined by correlation and concordance analysis. The MSC risk levels were compared with those estimated using a reference method. Differentially expressed ct-miRs were identified among NSCLC patients and donors, and the diagnostic value of those dysregulated in patients was assessed by receiver operating characteristic curve analysis. The downregulation of miR-150-5p was verified by qPCR. The Cancer Genome Atlas (TCGA) lung carcinoma dataset was used for validation at the tissue level.ResultsThe intra-platform reproducibility was consistent, whereas the highest values of inter-platform correlations were among qPCR-based platforms. MSC classification concordance was >80% for four platforms. The dysregulation and discriminatory power of miR-150-5p and miR-210-3p were documented. Both were significantly dysregulated also on TCGA tissue-originated profiles from lung cell carcinoma in comparison with normal samples.ConclusionOverall, our studies provide a large performance analysis between five different platforms for miR quantification, indicate the solidity of MSC classifier, and identify two noninvasive biomarkers for NSCLC.
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Affiliation(s)
- Chiara Gargiuli
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- *Correspondence: Marialuisa Sensi, ; Loris De Cecco,
| | - Andrea Mariancini
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maria Federica Iannò
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Arianna Micali
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elisa Mancinelli
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mattia Boeri
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabriella Sozzi
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marialuisa Sensi
- Platform of Integrated Biology Unit, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- *Correspondence: Marialuisa Sensi, ; Loris De Cecco,
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7
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Viral Encoded miRNAs in Tumorigenesis: Theranostic Opportunities in Precision Oncology. Microorganisms 2022; 10:microorganisms10071448. [PMID: 35889167 PMCID: PMC9321719 DOI: 10.3390/microorganisms10071448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
About 15% of all human cancers have a viral etiology. Although progress has been made, understanding the viral oncogenesis and associated molecular mechanisms remain complex. The discovery of cellular miRNAs has led to major breakthroughs. Interestingly, viruses have also been discovered to encode their own miRNAs. These viral, small, non-coding miRNAs are also known as viral-miRNAs (v-miRNAs). Although the function of v-miRNAs largely remains to be elucidated, their role in tumorigenesis cannot be ignored. V-miRNAs have also been shown to exploit the cellular machinery to benefit viral replication and survival. Although the discovery of Hepatitis C virus (HCV), and its viral miRNAs, is a work in progress, the existence of HPV-, EBV-, HBV-, MCPyV- and KSHV-encoded miRNA has been documented. V-miRNAs have been shown to target host factors to advance tumorigenesis, evade and suppress the immune system, and deregulate both the cell cycle and the apoptotic machinery. Although the exact mechanisms of v-miRNAs-induced tumorigenesis are still unclear, v-miRNAs are active role-players in tumorigenesis, viral latency and cell transformation. Furthermore, v-miRNAs can function as posttranscriptional gene regulators of both viral and host genes. Thus, it has been proposed that v-miRNAs may serve as diagnostic biomarkers and therapeutic targets for cancers with a viral etiology. Although significant challenges exist in their clinical application, emerging reports demonstrate their potent role in precision medicine. This review will focus on the roles of HPV-, HCV-, EBV-, HBV-, MCPyV-, and KSHV-produced v-miRNAs in tumorigenesis, as effectors in immune evasion, as diagnostic biomarkers and as novel anti-cancer therapeutic targets. Finally, it will discuss the challenges and opportunities associated with v-miRNAs theranostics in precision oncology.
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8
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Bozack AK, Colicino E, Rodosthenous RS, Bloomquist TR, Baccarelli AA, Wright RO, Wright RJ, Lee AG. Breast milk-derived extracellular vesicle miRNAs are associated with maternal asthma and atopy. Epigenomics 2022; 14:727-739. [PMID: 35638388 PMCID: PMC9280402 DOI: 10.2217/epi-2022-0090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Breast milk-derived extracellular vesicle (EV) miRNAs may program child health outcomes associated with maternal asthma and atopy. The authors investigated associations between maternal asthma/atopy and EV miRNAs in the Programming of Intergenerational Stress Mechanisms cohort. Methods: Breast milk-derived EV miRNAs collected 6.1 ± 5.9 weeks postnatally (n = 80 mothers) were profiled using the TaqMan OpenArray Human MicroRNA Panel. The authors assessed associations using adjusted robust regression. Results: Nine EV miRNAs were associated with asthma during pregnancy (a priori criteria: nominal p < 0.05; |Bregression| >0.2). miR-1290 was associated with asthma and atopy during pregnancy (p < 0.05; |Bregression| >0.2). Enriched Kyoto Encyclopedia of Genes and Genomes pathways included TGF-β signaling and extracellular matrix-receptor interaction (false discovery rate <0.05). Conclusion: In this study, maternal asthma and atopy were associated with breast milk-derived EV miRNAs. Additional studies are needed to understand whether EV miRNAs have direct effects on infant and child health.
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Affiliation(s)
- Anne K Bozack
- Department of Internal Medicine, Division of Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rodosthenis S Rodosthenous
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tessa R Bloomquist
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rosalind J Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison G Lee
- Department of Internal Medicine, Division of Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Shultz SR, Taylor CJ, Aggio-Bruce R, O’Brien WT, Sun M, Cioanca AV, Neocleous G, Symons GF, Brady RD, Hardikar AA, Joglekar MV, Costello DM, O’Brien TJ, Natoli R, McDonald SJ. Decrease in Plasma miR-27a and miR-221 After Concussion in Australian Football Players. Biomark Insights 2022; 17:11772719221081318. [PMID: 35250259 PMCID: PMC8891921 DOI: 10.1177/11772719221081318] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/31/2022] [Indexed: 12/16/2022] Open
Abstract
Introduction: Sports-related concussion (SRC) is a common form of brain injury that lacks reliable methods to guide clinical decisions. MicroRNAs (miRNAs) can influence biological processes involved in SRC, and measurement of miRNAs in biological fluids may provide objective diagnostic and return to play/recovery biomarkers. Therefore, this prospective study investigated the temporal profile of circulating miRNA levels in concussed male and female athletes. Methods: Pre-season baseline blood samples were collected from amateur Australian rules football players (82 males, 45 females). Of these, 20 males and 8 females sustained an SRC during the subsequent season and underwent blood sampling at 2-, 6- and 13-days post-injury. A miRNA discovery Open Array was conducted on plasma to assess the expression of 754 known/validated miRNAs. miRNA target identified were further investigated with quantitative real-time PCR (qRT-PCR) in a validation study. Data pertaining to SRC symptoms, demographics, sporting history, education history and concussion history were also collected. Results: Discovery analysis identified 18 candidate miRNA. The consequent validation study found that plasma miR-221-3p levels were decreased at 6d and 13d, and that miR-27a-3p levels were decreased at 6d, when compared to baseline. Moreover, miR-27a and miR-221-3p levels were inversely correlated with SRC symptom severity. Conclusion: Circulating levels of miR-27a-3p and miR-221-3p were decreased in the sub-acute stages after SRC, and were inversely correlated with SRC symptom severity. Although further studies are required, these analyses have identified miRNA biomarker candidates of SRC severity and recovery that may one day assist in its clinical management.
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Affiliation(s)
- Sandy R Shultz
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Caroline J Taylor
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Riemke Aggio-Bruce
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - William T O’Brien
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Mujun Sun
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Adrian V Cioanca
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - George Neocleous
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Georgia F Symons
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Rhys D Brady
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | | | - Mugdha V Joglekar
- School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Daniel M Costello
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Terence J O’Brien
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Riccardo Natoli
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Stuart J McDonald
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, VIC, Australia
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10
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Lee G, Yoo K. A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods. RE/VIEWS IN ENVIRONMENTAL SCIENCE AND BIO/TECHNOLOGY 2022; 21:799-827. [PMID: 35694630 PMCID: PMC9169023 DOI: 10.1007/s11157-022-09622-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/30/2022] [Indexed: 04/18/2023]
Abstract
Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.
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Affiliation(s)
- Gihan Lee
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112 South Korea
- Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, Busan, 49112 South Korea
| | - Keunje Yoo
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112 South Korea
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11
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Nakagawa A, Nakajima T, Azuma M. Tear miRNA expression analysis reveals miR-203 as a potential regulator of corneal epithelial cells. BMC Ophthalmol 2021; 21:377. [PMID: 34696757 PMCID: PMC8543880 DOI: 10.1186/s12886-021-02141-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 10/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background microRNAs (miRNAs) are small noncoding RNAs that negatively regulate gene expression. They are found within cells and in body fluids. Extracellular miRNAs have been shown to associate with the surrounding tissues. Therefore, we predicted that miRNAs in tears may contribute to regulate corneal epithelial cell function. However, information on the miRNA expression profile of tears is limited and the specific functions of tear miRNAs for corneal epithelial cells are still unknown. To study the role of tear miRNAs, we determined which miRNAs are highly expressed in tears and examined the involvement of miRNAs in corneal epithelial cell viability. Methods miRNAs extracted from monkey tears and sera were subjected to microarray analysis. miRNAs of which expression levels were higher in tears than in sera were selected, and their expression levels were quantified by quantitative polymerase chain reaction (qPCR). To examine miRNA function, mimics and inhibitors of miRNAs were transfected into human corneal epithelial (HCE-T) cells and incubated for 24 or 48 h. After transfection of miRNA mimics and inhibitors, the viability of HCE-T cells was measured using the water soluble tetrazolium salt (WST) assay, and microarray analysis and qPCR were performed using total RNA extracted from HCE-T cells. siRNAs of the candidate targets for miR-203 were transfected into HCE-T cells and the WST assay was performed. To determine a direct target gene for miR-203, a dual luciferase reporter assay was performed in HCE-T cells using a luciferase reporter plasmid containing 3′-UTR of human IGFBP5. Results Microarray and qPCR analyses showed that miR-184 and miR-203 were expressed significantly more highly in tears than in sera (165,542.8- and 567.8-fold, respectively, p < 0.05). Of these two miRNAs, transfection of a miR-203 mimic significantly reduced the viability of HCE-T cells (p < 0.05), while a miR-203 inhibitor significantly increased this viability (p < 0.05). miR-203 mimic downregulated insulin-like growth factor-binding protein 5 (IGFBP5) and nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1), while miR-203 inhibitor upregulated these two genes. Transfection of IGFBP5-siRNA decreased the viability of HCE-T cells. miR-203 mimic significantly diminished the luciferase reporter activity. Conclusions In this study, we identified miRNAs that are highly expressed in tears, and the inhibition of miR-203 increases the viability of corneal epithelial cells. Our results suggest that miR-203 contributes to regulating the homeostasis of corneal epithelial cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-021-02141-9.
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Affiliation(s)
- Ayumi Nakagawa
- Central Research Laboratories, Research and Development Division, Senju Pharmaceutical Co., Ltd., 6-4-3, Minatojima-Minamimachi, Chuo-Ku, Kobe, Hyogo, 650-0047, Japan
| | - Takeshi Nakajima
- Senju Laboratory of Ocular Sciences, Senju Pharmaceutical Co., Ltd., 6-4-3, Minatojima-Minamimachi, Chuo-Ku, Kobe, Hyogo, 650-0047, Japan
| | - Mitsuyoshi Azuma
- Senju Laboratory of Ocular Sciences, Senju Pharmaceutical Co., Ltd., 6-4-3, Minatojima-Minamimachi, Chuo-Ku, Kobe, Hyogo, 650-0047, Japan.
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12
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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: 16] [Impact Index Per Article: 5.3] [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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13
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Description of a CSF-Enriched miRNA Panel for the Study of Neurological Diseases. Life (Basel) 2021; 11:life11070594. [PMID: 34206241 PMCID: PMC8305419 DOI: 10.3390/life11070594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/18/2022] Open
Abstract
Background: The study of circulating miRNAs in CSF has gained tremendous attention during the last years, as these molecules might be promising candidates to be used as biomarkers and provide new insights into the disease pathology of neurological disorders. Objective: The main aim of this study was to describe an OpenArray panel of CSF-enriched miRNAs to offer a suitable tool to identify and characterize new molecular signatures in different neurological diseases. Methods: Two hundred and fifteen human miRNAs were selected to be included in the panel, and their expression and abundance in CSF samples were analyzed. In addition, their stability was studied in order to propose suitable endogenous controls for CSF miRNA studies. Results: miR-143-3p and miR-23a-3p were detected in all CSF samples, while another 80 miRNAs were detected in at least 70% of samples. miR-770-5p was the most abundant miRNA in CSF, presenting the lowest mean Cq value. In addition, miR-26b-5p, miR-335-5p and miR-92b-3p were the most stable miRNAs and could be suitable endogenous normalizers for CSF miRNA studies. Conclusions: These OpenArray plates might be a suitable and efficient tool to identify and characterize new molecular signatures in different neurological diseases and would improve the yield of miRNA detection in CSF.
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14
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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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15
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Plasma miR-26a-5p is a biomarker for retinal neurodegeneration of early diabetic retinopathy. Eye (Lond) 2021; 35:1587-1599. [PMID: 33931763 DOI: 10.1038/s41433-021-01393-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/24/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Retinal neurodegeneration is an early pathological change in diabetic retinopathy (DR). Early-stage retinal neurodegeneration is usually asymptomatic. This study aims to identify circulating microRNAs (miRNAs) as sensitive biomarkers for early retinal neurodegeneration. METHODS We profiled the plasma miRNA expression in three mild nonproliferative diabetic retinopathy (NPDR) cases and three matched non-DR patients using RNA sequencing. The differential miRNAs were validated with qRT-PCR. The retinal nerve fibre layer (RNFL) thickness of the eyes was measured using spectral-domain Optical coherence tomography (SD-OCT). The association between differential miRNAs and RNFL thickness was analysed using the Pearson correlation analysis. Bioinformatics tools were used to predict potential targets of miRNA associated with RNFL thickness and investigate the functions of the potential target genes. RESULTS RNA sequencing identified 69 differential miRNAs and eight of them were reported to be associated with DR. The qRT-PCR for these eight miRNAs validated the down-regulation of circulating miR-26a-5p and miR-126-5p in a larger validating cohort. A positive correlation between plasma miR-26a-5p level and the RNFL thickness of the superior quadrant of both eyes was identified in another cohort, including 33 mild NPDR cases, 33 matched non-DR patients and 20 healthy controls. Furthermore, 367 candidate targets of miR-26a-5p were predicted. The functional studies revealed that these target genes are profoundly involved in various cellular functions and signalling pathways. CONCLUSIONS Circulating miR-26a-5p is a potential biomarker for early-stage retinal neurodegeneration and it may be involved in the development of DR via profoundly influencing the functions of retinal cells.
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16
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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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17
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Bozack AK, Colicino E, Rodosthenous R, Bloomquist TR, Baccarelli AA, Wright RO, Wright RJ, Lee AG. Associations between maternal lifetime stressors and negative events in pregnancy and breast milk-derived extracellular vesicle microRNAs in the programming of intergenerational stress mechanisms (PRISM) pregnancy cohort. Epigenetics 2021; 16:389-404. [PMID: 32777999 PMCID: PMC7996083 DOI: 10.1080/15592294.2020.1805677] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 01/02/2023] Open
Abstract
Maternal stress is associated with adverse child health. Breast milk microRNAs encapsulated in extracellular vesicles (EVs) are involved in mother-infant biochemical communication during early-life programming. We leverage the PRogramming of Intergenerational Stress Mechanisms (PRISM) pregnancy cohort to investigate associations between maternal stress and breast milk EV-microRNAs. Lifetime stress and negative life events (NLEs) during pregnancy were assessed using the Life Stressor Checklist-Revised (LSCR) and the Crisis in Family Systems-Revised surveys, respectively. RNA was extracted from breast milk EVs (N = 80; collected 6.1 ± 5.9 weeks postnatally), and microRNAs were profiled using the TaqMan OpenArray Human miRNA panel. Associations between stress scores and detection (yes/no) of 173 microRNAs identified in 20-80% of samples were assessed using logistic regression; associations with expression levels of 205 EV-microRNAs identified in >50% of samples were assessed using linear regression. In adjusted models, detection of 60 and 44 EV-microRNAs was associated with higher LSCR and NLE scores, respectively (p < 0.05). Expression level of 8 and 17 EV-microRNAs was associated with LSCR and NLE scores, respectively, at our a priori criteria of p < 0.05 and |Bregression|>0.2. Enriched KEGG pathways for microRNAs associated with stress scores included fatty acid metabolism and the Hippo signaling pathway. Maternal lifetime stress and NLEs during pregnancy were both associated with detection and expression level of breast milk EV-microRNAs, although associations with microRNA profiles differed between stress measures. Further research is needed to identify biological pathways impacted by associated microRNAs and investigate relationships with child health outcomes.Abbreviations: EV: extracellular vesicle; PRISM: PRogramming of Intergenerational Stress Mechanisms pregnancy cohort; LSCR: Life Stressor Checklist-Revised survey; NLE: negative life event; CRISYS-R: Crisis in Family Systems-Revised survey; KEGG: Kyoto Encyclopaedia of Genes and Genomes; NYC: New York City; SD: standard deviation; IQR: interquartile range; Cq: relative cycle threshold values; PCA: principal component analysis.
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Affiliation(s)
- Anne K. Bozack
- Division of Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, New York, NY, USA
| | | | - Tessa R. Bloomquist
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Robert O. Wright
- Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Rosalind J. Wright
- Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Alison G. Lee
- Division of Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
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18
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Shihana F, Mohamed F, Joglekar MV, Hardikar AA, Seth D, Buckley NA. Urinary versus serum microRNAs in human oxalic acid poisoning: Contrasting signals and performance. Toxicol Lett 2020; 334:21-26. [PMID: 32910981 DOI: 10.1016/j.toxlet.2020.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/25/2020] [Accepted: 09/03/2020] [Indexed: 11/28/2022]
Abstract
MicroRNAs are key regulators of the normal kidney function and development, and altered in acute kidney injury (AKI). However, there is a lack of studies comparing serum and urine miRNA expression in toxic AKI in humans. We aimed to compare the global signature of urinary and serum microRNAs, with and without kidney injury, after human oxalic acid poisoning. We profiled urinary microRNAs in patients who ingested oxalic acid and developed no injury (No AKI n = 3), moderate injury (AKIN2 n = 3) or severe injury (AKIN3 n = 3) and healthy controls (n = 3). We validated a signature of 30 urinary microRNAs identified in the discovery profiling, in a second cohort of individuals exposed to oxalic acid (No AKI n = 15, AKIN2 n=11 & AKIN3 n= 18) and healthy controls (n=-27) and we compared the results with previously published serum data. Global profiling in toxic AKI patients showed a higher expression of urinary microRNAs and lower expression of serum microRNAs. Most urine microRNA in the validation cohort were significantly upregulated (25/30, fold change >2.8 and p < 0.05) in AKIN2/3 patients compared to No AKI. Four urinary microRNAs (miR-191, miR-19b, miR-20a and miR-30b) had good diagnostic performance (AUC greater than 0.8) to predict AKIN2/3 between 4-8 hours post ingestion. Poisoning irrespective of AKI led to significantly lower expression of many microRNAs in serum but relatively few changes in urinary miRNA expression. In conclusion, urinary microRNA signature provides a stronger measure of AKI in oxalic acid poisoning compared to serum microRNA. Kidney injury has the greatest impact on urinary microRNA, while poisoning itself was better reflected in serum miRNA. Plasma and urinary microRNAs signatures provide complementary information in toxic kidney injury.
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Affiliation(s)
- Fathima Shihana
- The University of Sydney, Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, Sydney, NSW, Australia; University of Peradeniya, South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, Peradeniya, Sri Lanka.
| | - Fahim Mohamed
- The University of Sydney, Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, Sydney, NSW, Australia; University of Peradeniya, South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, Peradeniya, Sri Lanka; University of Peradeniya, Faculty of Allied Health Sciences, Department of Pharmacy, Peradeniya, Sri Lanka
| | - Mugdha V Joglekar
- The University of Sydney, Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine & Health, NSW, Australia
| | - Anandwardhan A Hardikar
- The University of Sydney, Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine & Health, NSW, Australia.
| | - Devanshi Seth
- The University of Sydney, Discipline of Clinical Medicine & Addiction Medicine, Faculty of Medicine & Health, NSW, Australia; Drug Health Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; The University of Sydney The Centenary Institute of Cancer Medicine & Cell Biology, NSW, Australia
| | - Nicholas A Buckley
- The University of Sydney, Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, Sydney, NSW, Australia; University of Peradeniya, South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, Peradeniya, Sri Lanka
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19
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The crucial choice of reference genes: identification of miR-191-5p for normalization of miRNAs expression in bone marrow mesenchymal stromal cell and HS27a/HS5 cell lines. Sci Rep 2020; 10:17728. [PMID: 33082452 PMCID: PMC7576785 DOI: 10.1038/s41598-020-74685-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
Bone marrow mesenchymal stromal cells (BM-MSCs) have a critical role in tissue regeneration and in the hematopoietic niche due to their differentiation and self-renewal capacities. These mechanisms are finely tuned partly by small non-coding microRNA implicated in post-transcriptional regulation. The easiest way to quantify them is RT-qPCR followed by normalization on validated reference genes (RGs). This study identified appropriate RG for normalization of miRNA expression in BM-MSCs and HS27a and HS5 cell lines in various conditions including normoxia, hypoxia, co-culture, as model for the hematopoietic niche and after induced differentiation as model for regenerative medicine. Six candidates, namely miR-16-5p, miR-34b-3p, miR-103a-3p, miR-191-5p, let-7a-5p and RNU6A were selected and their expression verified by RT-qPCR. Next, a ranking on stability of the RG candidates were performed with two algorithms geNorm and RefFinder and the optimal number of RGs needed to normalize was determined. Our results indicate miR-191-5p as the most stable miRNA in all conditions but also that RNU6a, usually used as RG is the less stable gene. This study demonstrates the interest of rigorously evaluating candidate miRNAs as reference genes and the importance of the normalization process to study the expression of miRNAs in BM-MSCs or derived cell lines.
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20
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Thangavelu B, Wilfred BS, Johnson D, Gilsdorf JS, Shear DA, Boutté AM. Penetrating Ballistic-Like Brain Injury Leads to MicroRNA Dysregulation, BACE1 Upregulation, and Amyloid Precursor Protein Loss in Lesioned Rat Brain Tissues. Front Neurosci 2020; 14:915. [PMID: 33071724 PMCID: PMC7530327 DOI: 10.3389/fnins.2020.00915] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/07/2020] [Indexed: 12/22/2022] Open
Abstract
Severe traumatic brain injury (TBI) is a risk factor for neurodegenerative diseases. Yet, the molecular events involving dysregulated miRNAs that may be associated with protein degradation in the brain remains elusive. Quantitation of more than 800 miRNAs was conducted using rat ipsilateral coronal brain tissues collected 1, 3, or 7 days after penetrating ballistic-like brain injury (PBBI). As a control for each time-point, Sham-operated animals received craniotomy alone. Microarray and systems biology analysis indicated that the amplitude and complexity of miRNAs affected were greatest 7 day after PBBI. Arrays and Q-PCR inferred that dysregulation of miR-135a, miR-328, miR-29c, and miR-21 were associated with altered levels of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), PSEN1, PSEN2, and amyloid precursor protein (APP) genes. These events were followed by increased levels of mature BACE1 protein and concomitant loss of full length APP within 3–7 days, then elevation of amyloid beta (Aβ)-40 7 days after PBBI. This study indicates that miRNA arrays, coupled with systems biology, may be used to guide study design prior validation of miRNA dysregulation. Associative analysis of miRNAs, mRNAs, and proteins within a proposed pathway are poised for further validation as biomarkers and therapeutic targets relevant to TBI-induced APP loss and subsequent Aβ peptide generation during neurodegeneration.
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Affiliation(s)
- Bharani Thangavelu
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Bernard S Wilfred
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - David Johnson
- Department of Pathology and Area Laboratory Services, Landstuhl Regional Medical Center, Landstuhl, Germany
| | - Janice S Gilsdorf
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Deborah A Shear
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Angela M Boutté
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
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21
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Torres-Do Rego A, Barrientos M, Ortega-Hernández A, Modrego J, Gómez-Gordo R, Álvarez-Sala LA, Cachofeiro V, Gómez-Garre D. Identification of a Plasma Microrna Signature as Biomarker of Subaneurysmal Aortic Dilation in Patients with High Cardiovascular Risk. J Clin Med 2020; 9:jcm9092783. [PMID: 32872191 PMCID: PMC7565169 DOI: 10.3390/jcm9092783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/25/2022] Open
Abstract
Patients with subaneurysmal aortic dilation (SAD; 25–29 mm diameter) are likely to progress to true abdominal aortic aneurysm (AAA). Despite these patients having a higher risk of all-cause mortality than subjects with aortic size <24 mm, early diagnostic biomarkers are lacking. MicroRNAs (miRs) are well-recognized potential biomarkers due to their differential expression in different tissues and their stability in blood. We have investigated whether a plasma miRs profile could identify the presence of SAD in high cardiovascular risk patients. Using qRT-PCR arrays in plasma samples, we determined miRs differentially expressed between SAD patients and patients with normal aortic diameter. We then selected 12 miRs to be investigated as biomarkers by construction of ROC curves. A total of 82 significantly differentially expressed miRs were found by qPCR array, and 12 were validated by qRT-PCR. ROC curve analyses showed that seven selected miRs (miR-28-3p, miR-29a-3p, miR-93-3p, miR-150-5p, miR-338-3p, miR-339-3p, and miR-378a-3p) could be valuable biomarkers for distinguishing SAD patients. MiR-339-3p showed the best sensitivity and specificity, even after combination with other miRs. Decreased miR-339-3p expression was associated with increased aortic abdominal diameter. MiR-339-3p, alone or in combination with other miRs, could be used for SAD screening in high cardiovascular risk patients, helping to the early diagnosis of asymptomatic AAA.
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Affiliation(s)
- Ana Torres-Do Rego
- Internal Medicine Service, HGU Gregorio Marañón, Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), 28007 Madrid, Spain; (A.T.-D.R.); (M.B.); (L.A.Á.-S.)
| | - María Barrientos
- Internal Medicine Service, HGU Gregorio Marañón, Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), 28007 Madrid, Spain; (A.T.-D.R.); (M.B.); (L.A.Á.-S.)
| | - Adriana Ortega-Hernández
- Vascular Biology Research Laboratory, Hospital Clínico San Carlos-Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.O.-H.); (J.M.); (R.G.-G.)
| | - Javier Modrego
- Vascular Biology Research Laboratory, Hospital Clínico San Carlos-Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.O.-H.); (J.M.); (R.G.-G.)
- Biomedical Research Networking Center in Cardiovascular Diseases (CIBERCV), 28029 Madrid, Spain;
| | - Rubén Gómez-Gordo
- Vascular Biology Research Laboratory, Hospital Clínico San Carlos-Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.O.-H.); (J.M.); (R.G.-G.)
| | - Luis A. Álvarez-Sala
- Internal Medicine Service, HGU Gregorio Marañón, Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), 28007 Madrid, Spain; (A.T.-D.R.); (M.B.); (L.A.Á.-S.)
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
| | - Victoria Cachofeiro
- Biomedical Research Networking Center in Cardiovascular Diseases (CIBERCV), 28029 Madrid, Spain;
- Department of Physiology, School of Medicine, Universidad Complutense and Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), 28040 Madrid, Spain
| | - Dulcenombre Gómez-Garre
- Vascular Biology Research Laboratory, Hospital Clínico San Carlos-Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.O.-H.); (J.M.); (R.G.-G.)
- Biomedical Research Networking Center in Cardiovascular Diseases (CIBERCV), 28029 Madrid, Spain;
- Correspondence: ; Tel.: +34-91-330-3000 (ext. 7769)
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22
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Conte G, Nguyen NT, Alves M, de Diego-Garcia L, Kenny A, Nicke A, Henshall DC, Jimenez-Mateos EM, Engel T. P2X7 Receptor-Dependent microRNA Expression Profile in the Brain Following Status Epilepticus in Mice. Front Mol Neurosci 2020; 13:127. [PMID: 32982684 PMCID: PMC7485385 DOI: 10.3389/fnmol.2020.00127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022] Open
Abstract
The ionotropic ATP-gated P2X7 receptor is an important contributor to inflammatory signaling cascades via the release of Interleukin-1β, as well as having roles in cell death, neuronal plasticity and the release of neurotransmitters. Accordingly, there is interest in targeting the P2X7 receptor for the treatment of epilepsy. However, the signaling pathways downstream of P2X7 receptor activation remain incompletely understood. Notably, recent studies showed that P2X7 receptor expression is controlled, in part, by microRNAs (miRNAs). Here, we explored P2X7 receptor-dependent microRNA expression by comparing microRNA expression profiles of wild-type (wt) and P2X7 receptor knockout mice before and after status epilepticus. Genome-wide microRNA profiling was performed using hippocampi from wt and P2X7 receptor knockout mice following status epilepticus induced by intra-amygdala kainic acid. This revealed that the genetic deletion of the P2X7 receptor results in distinct patterns of microRNA expression. Specifically, we found that in vehicle-injected control mice, the lack of the P2X7 receptor resulted in the up-regulation of 50 microRNAs and down-regulation of 35 microRNAs. Post-status epilepticus, P2X7 receptor deficiency led to the up-regulation of 44 microRNAs while 13 microRNAs were down-regulated. Moreover, there was only limited overlap among identified P2X7 receptor-dependent microRNAs between control conditions and post-status epilepticus, suggesting that the P2X7 receptor regulates the expression of different microRNAs during normal physiology and pathology. Bioinformatic analysis revealed that genes targeted by P2X7 receptor-dependent microRNAs were particularly overrepresented in pathways involved in intracellular signaling, inflammation, and cell death; processes that have been repeatedly associated with P2X7 receptor activation. Moreover, whereas genes involved in signaling pathways and inflammation were common among up- and down-regulated P2X7 receptor-dependent microRNAs during physiological and pathological conditions, genes associated with cell death seemed to be restricted to up-regulated microRNAs during both physiological conditions and post-status epilepticus. Taken together, our results demonstrate that the P2X7 receptor impacts on the expression profile of microRNAs in the brain, thereby possibly contributing to both the maintenance of normal cellular homeostasis and pathological processes.
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Affiliation(s)
- Giorgia Conte
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Ngoc T Nguyen
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland.,FutureNeuro, Science Foundation Ireland (SFI) Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Mariana Alves
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Laura de Diego-Garcia
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Aidan Kenny
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - David C Henshall
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland.,FutureNeuro, Science Foundation Ireland (SFI) Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Eva M Jimenez-Mateos
- Discipline of Physiology, School of Medicine, Trinity College Ireland, The University of Dublin, Dublin, Ireland
| | - Tobias Engel
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland.,FutureNeuro, Science Foundation Ireland (SFI) Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
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23
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Martins B, Amorim M, Reis F, Ambrósio AF, Fernandes R. Extracellular Vesicles and MicroRNA: Putative Role in Diagnosis and Treatment of Diabetic Retinopathy. Antioxidants (Basel) 2020; 9:antiox9080705. [PMID: 32759750 PMCID: PMC7463887 DOI: 10.3390/antiox9080705] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/01/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023] Open
Abstract
Diabetic retinopathy (DR) is a complex, progressive, and heterogenous retinal degenerative disease associated with diabetes duration. It is characterized by glial, neural, and microvascular dysfunction, being the blood-retinal barrier (BRB) breakdown a hallmark of the early stages. In advanced stages, there is formation of new blood vessels, which are fragile and prone to leaking. This disease, if left untreated, may result in severe vision loss and eventually legal blindness. Although there are some available treatment options for DR, most of them are targeted to the advanced stages of the disease, have some adverse effects, and many patients do not adequately respond to the treatment, which demands further research. Oxidative stress and low-grade inflammation are closely associated processes that play a critical role in the development of DR. Retinal cells communicate with each other or with another one, using cell junctions, adhesion contacts, and secreted soluble factors that can act in neighboring or long-distance cells. Another mechanism of cell communication is via secreted extracellular vesicles (EVs), through exchange of material. Here, we review the current knowledge on deregulation of cell-to-cell communication through EVs, discussing the changes in miRNA expression profiling in body fluids and their role in the development of DR. Thereafter, current and promising therapeutic agents for preventing the progression of DR will be discussed.
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Affiliation(s)
- Beatriz Martins
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (B.M.); (M.A.); (F.R.); (A.F.A.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Madania Amorim
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (B.M.); (M.A.); (F.R.); (A.F.A.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Flávio Reis
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (B.M.); (M.A.); (F.R.); (A.F.A.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
| | - António Francisco Ambrósio
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (B.M.); (M.A.); (F.R.); (A.F.A.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
- Association for Innovation and Biomedical Research on Light and Image (AIBILI), 3000-548 Coimbra, Portugal
| | - Rosa Fernandes
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (B.M.); (M.A.); (F.R.); (A.F.A.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
- Association for Innovation and Biomedical Research on Light and Image (AIBILI), 3000-548 Coimbra, Portugal
- Correspondence: ; Tel.: +351-239480072
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24
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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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25
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Barraclough JY, Joglekar MV, Januszewski AS, Martínez G, Celermajer DS, Keech AC, Hardikar AA, Patel S. A MicroRNA Signature in Acute Coronary Syndrome Patients and Modulation by Colchicine. J Cardiovasc Pharmacol Ther 2020; 25:444-455. [PMID: 32356454 DOI: 10.1177/1074248420922793] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Circulating microRNAs (miRNAs) may play a pathogenic role in acute coronary syndromes (ACS). It is not yet known if miRNAs dysregulated in ACS are modulated by colchicine. We profiled miRNAs in plasma samples simultaneously collected from the aorta, coronary sinus, and right atrium in patients with ACS. METHODS A total of 396 of 754 miRNAs were detected by TaqMan real-time polymerase chain reaction from EDTA-plasma in a discovery cohort of 15 patients (n = 3 controls, n = 6 ACS standard therapy, n = 6 ACS standard therapy plus colchicine). Fifty-one significantly different miRNAs were then measured in a verification cohort of 92 patients (n = 13 controls, n = 40 ACS standard therapy, n = 39 ACS standard therapy plus colchicine). Samples were simultaneously obtained from the coronary sinus, aortic root, and right atrium. RESULTS Circulating levels of 30 of 51 measured miRNAs were higher in ACS standard therapy patients compared to controls. In patients with ACS, levels of 12 miRNAs (miR-17, -106b-3p, -191, -106a, -146a, -130a, -223, -484, -889, -425-3p, -629, -142-5p) were lower with colchicine treatment. Levels of 7 of these 12 miRNA were higher in ACS standard therapy patients compared to controls and returned to levels seen in control individuals after colchicine treatment. Three miRNAs suppressed by colchicine (miR-146a, miR-17, miR-130a) were identified as regulators of inflammatory pathways. MicroRNAs were comparable across sampling sites with select differences in the transcoronary gradient of 4 miRNA. CONCLUSION The levels of specific miRNAs elevated in ACS returned to levels similar to control individuals following colchicine. These miRNAs may mediate ACS (via inflammatory pathways) or increase post-ACS risk, and could be potentially used as biomarkers of treatment efficacy.
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Affiliation(s)
- Jennifer Y Barraclough
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia.,Sydney Medical School, The University of Sydney, Australia.,Heart Research Institute Sydney, Australia
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Australia
| | - Andrzej S Januszewski
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Australia
| | - Gonzalo Martínez
- Heart Research Institute Sydney, Australia.,Division of Cardiovascular Diseases, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - David S Celermajer
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia.,Sydney Medical School, The University of Sydney, Australia.,Heart Research Institute Sydney, Australia
| | - Anthony C Keech
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia.,NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Australia
| | - Anandwardhan A Hardikar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Australia
| | - Sanjay Patel
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia.,Sydney Medical School, The University of Sydney, Australia.,Heart Research Institute Sydney, Australia
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26
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Shao D, He S, Ye Z, Zhu X, Sun W, Fu W, Ma T, Li Z. Identification of potential molecular targets associated with proliferative diabetic retinopathy. BMC Ophthalmol 2020; 20:143. [PMID: 32290826 PMCID: PMC7155274 DOI: 10.1186/s12886-020-01381-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/10/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND This study aimed to identify and evaluate potential molecular targets associated with the development of proliferative diabetic retinopathy (DR). METHODS The microarray dataset "GSE60436" generated from fibrovascular membranes (FVMs) associated with proliferative DR was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) from the active FVMs and control or inactive FVMs and control were evaluated and co-DEGs were identified using VEEN analysis. Functional enrichment analysis, and protein-protein interactions (PPI) network and module analyses were performed on the upregulated and downregulated coDEGs. Finally, several predictions regarding microRNAs (miRNAs) and transcription factors (TFs) were made to construct a putative TF-miRNA-target network. RESULTS A total of 1475 co-DEGs were screened in active/inactive FVM samples, including 461 upregulated and 1014 downregulated genes, which were enriched for angiogenesis [Hypoxia Inducible Factor 1 Subunit Alpha (HIF1A) and Placental Growth Factor (PGF)] and visual perception, respectively. In the case of the upregulated co-DEGs, Kinesin Family Member 11 (KIF11), and BUB1 Mitotic Checkpoint Serine/Threonine Kinase (BUB1) exhibited the highest values in both the PPI network and module analyses, as well as the genes related to mitosis. In the case of downregulated co-DEGs, several G protein subunits, including G Protein Subunit Beta 3 (GNB3), exhibited the highest values in both the PPI network and module analyses. The genes identified in the module analysis were found to be from the signal transduction-related pathways. In addition, we were able to identify four miRNAs and five TFs, including miR-136 and miR-374. CONCLUSIONS In brief, HIF1A, PGF, KIF11, G protein subunits, and miR-136, miR-374 may all be involved in angiogenesis, retinal endothelial cell proliferation, and visual signal transduction in proliferative DR. This study provides a number of novel insights that may aid the development of future studies dedicated to discovering novel therapeutic targets in proliferative DR.
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Affiliation(s)
- Dewang Shao
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China. .,Department of Ophthalmology, Air Force Medical Center, PLA, No.15 Chang Yun Gong, Haidian District, Beijing, 100089, China.
| | - Shouzhi He
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zi Ye
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Xiaoquan Zhu
- Department of Ophthalmology, Air Force Medical Center, PLA, No.15 Chang Yun Gong, Haidian District, Beijing, 100089, China
| | - Wei Sun
- Department of Ophthalmology, Air Force Medical Center, PLA, No.15 Chang Yun Gong, Haidian District, Beijing, 100089, China
| | - Wei Fu
- Department of Ophthalmology, Air Force Medical Center, PLA, No.15 Chang Yun Gong, Haidian District, Beijing, 100089, China
| | - Tianju Ma
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhaohui Li
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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27
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Fontes PK, Castilho ACS, Razza EM, Nogueira MFG. Bona fide gene expression analysis of samples from the bovine reproductive system by microfluidic platform. Anal Biochem 2020; 596:113641. [PMID: 32087128 DOI: 10.1016/j.ab.2020.113641] [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] [Received: 11/21/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 10/25/2022]
Abstract
Sample types such as those from reproductive systems often yield scarce material, which limits RT-qPCR analysis to only a few targets. Recently developed high-throughput systems can potentially change this scenario, however, the nanoliter scale of such platforms requires extra processing, e.g., preamplification, which needs to be defined through observation and experience. In order to establish best practices in high-throughput PCR approaches using samples from reproductive systems, we evaluated the Biomark™ HD performance using 11 different sample types from the bovine reproductive system: blastocyst (single/pool), oocyte (pool), cumulus, granulosa, and theca cells, oviduct tissue, fetal ovary, testicle (adult/fetal), and uterine horn. We observed that the preamplification step is not just reliable, but mandatory. Our results indicated that 14-preamplification cycles associated to 5- and 7-fold-dilution is the best approach for those samples. Additionally, the Biomark™ HD system has a high intra and inter reproducibility, therefore its performance in duplicate is unnecessary for the ΔCq analysis, taking in consideration the cutoff value 4 < Cq < 22. In summary, this high-throughput approach is a reliable and excellent tool for studying the bovine reproductive system, especially using quantitatively-limited samples, as a larger number of target genes can be assessed from a very low amount of starting material.
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Affiliation(s)
- Patricia Kubo Fontes
- Laboratory of Phytomedicines, Pharmacology and Biotechnology, Department of Pharmacology, Institute of Biosciences, University of São Paulo State (Unesp), Campus of Botucatu, São Paulo, Brazil.
| | - Anthony César Souza Castilho
- Laboratory of Phytomedicines, Pharmacology and Biotechnology, Department of Pharmacology, Institute of Biosciences, University of São Paulo State (Unesp), Campus of Botucatu, São Paulo, Brazil; University of Western São Paulo (Unoeste), Campus of Presidente Prudente, São Paulo, Brazil.
| | - Eduardo Montanari Razza
- Laboratory of Phytomedicines, Pharmacology and Biotechnology, Department of Pharmacology, Institute of Biosciences, University of São Paulo State (Unesp), Campus of Botucatu, São Paulo, Brazil.
| | - Marcelo Fábio Gouveia Nogueira
- Laboratory of Phytomedicines, Pharmacology and Biotechnology, Department of Pharmacology, Institute of Biosciences, University of São Paulo State (Unesp), Campus of Botucatu, São Paulo, Brazil; Department of Biological Sciences, School of Sciences and Languages, São Paulo State University (Unesp), Campus of Assis, São Paulo, Brazil.
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28
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Broccanello C, Gerace L, Stevanato P. QuantStudio ™ 12K Flex OpenArray ® System as a Tool for High-Throughput Genotyping and Gene Expression Analysis. Methods Mol Biol 2020; 2065:199-208. [PMID: 31578697 DOI: 10.1007/978-1-4939-9833-3_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Real time technology provides great advancements over PCR-based methods for a broad range of applications. With the increased availability of sequencing information, there is a need for the development and application of high-throughput real time PCR genotyping and gene expression methods that significantly broaden the current screening capabilities. Thermo Fisher Scientific (USA) has released a platform (QuantStudio™ 12K Flex system coupled with OpenArray® technology) with key elements required for high-throughput SNP genotyping and gene expression analysis. This allows for a rapid screening of large numbers of TaqMan® assays (up to 256) in many samples (up to 480) per run. This advanced real-time method involves the use of an array composed of 3,000 through-holes running on the QuantStudio™ 12K with OpenArray® block. The aim of this chapter is to outline the OpenArray® approach while providing a comprehensive in-depth review of the scientific literature on this topic. In agreement with a large number of independent studies, we conclude that the use of OpenArray® technology is a rapid and accurate method for high-throughput and large-scale systems biology studies with high specificity and sensitivity.
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Affiliation(s)
| | - Letizia Gerace
- Thermo Fisher Scientific, Life Sciences Solutions, Monza (MB), Italy
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29
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MicroRNA-423 may regulate diabetic vasculopathy. Clin Exp Med 2019; 19:469-477. [PMID: 31422516 DOI: 10.1007/s10238-019-00573-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/03/2019] [Indexed: 02/07/2023]
Abstract
To test the hypothesis that microRNAs may play a role in diabetic retinopathy, we measured the levels of different markers [microRNAs, vascular endothelial growth factor (VEGF), nitric oxide (NO), and total antioxidant capacity (TAO)] in patients with type 2 diabetes mellitus (T2DM) and microvascular complications. Sixty-nine patients were recruited: 22 healthy subjects, ten T2DM patients without retinopathy, 22 with nonproliferative diabetic retinopathy, and 15 with proliferative diabetic retinopathy (PDR). Serum levels of NO, VEGF, TAO and 16 candidate microRNAs were measured. Additionally, the mRNA levels of endothelial nitric oxide synthase (eNOS), induced NOS (iNOS), C reactive protein (CRP), VEGF, tumor necrosis factor α (TNFα), PON2, p22, and SOD2 were measured in human vascular endothelial cells cultured in the presence of pooled sera from the subject groups. Plasma miR-423 levels showed a significant ~ twofold decrease in patients with PDR compared to controls. P lasma NO levels were significantly higher in retinopathy, VEGF levels were significantly lower, and TAO was significantly decreased. eNOS mRNA levels were lower in the cells of T2DM patients without retinopathy, but higher in PDR. PON2, p22, and SOD2 mRNA levels were all significantly lower in PDR. CRP, TNFα, iNOS, and VEGF mRNA levels showed no significant association with disease status. Lowered miR-423 levels in diabetic patients showed a correlation with VEGF and an inverse correlation between NO and eNOS expression. Our findings suggest a cross talk between miR-423 and VEGF signaling, affecting eNOS function. miR-423 may be involved in the regulation of diabetic vascular retinal proliferation.
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30
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Farr RJ, Wong WKM, Maynard CL, Tersey SA, Mirmira RG, Hardikar AA, Joglekar MV. Comparative analysis of diagnostic platforms for measurement of differentially methylated insulin DNA. J Biol Methods 2019; 6. [PMID: 31328130 PMCID: PMC6641562 DOI: 10.14440/jbm.2019.280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has been intensively investigated as a diagnostic and prognostic marker for various cancers. In recent years, presence of unmethylated insulin cfDNA in the circulation has been correlated with pancreatic β-cell death and risk of developing type 1 diabetes. Digital (d)PCR is an increasingly popular method of quantifying insulin cfDNA due to its ability to determine absolute copy numbers, and its increased sensitivity when compared to the more routinely used quantitative PCR. Multiple platforms have been developed to carry out dPCR. However, not all technologies perform comparably, thereby necessitating evaluation of each platform. Here, we compare two dPCR platforms: the QuantStudio 3D (QS3D, Applied Biosystems) and the QX200 (Bio-Rad), to measure copies of unmethylated/methylated insulin plasmids. The QS3D detected greater copy numbers of the plasmids than the QX200 (manual mode), whereas QX200 demonstrated minimal replicate variability, increased throughput, ease of use and the potential for automation. Overall, the performance of QX200, in our hands, was better suited to measure differentially methylated insulin cfDNA.
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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
| | - Wilson K M Wong
- 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
| | - Cody-Lee Maynard
- 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
| | - Sarah A Tersey
- Herman B Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, and Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Raghavendra G Mirmira
- Herman B Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, and Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - 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
| | - 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
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Abstract
Diabetes mellitus, together with its complications, has been increasing in prevalence worldwide. Its complications include cardiovascular disease (e.g., myocardial infarction, stroke), neuropathy, nephropathy, and eye complications (e.g., glaucoma, cataracts, retinopathy, and macular edema). In patients with either type 1 or type 2 diabetes mellitus, diabetic retinopathy is the leading cause of visual impairment or blindness. It is characterized by progressive changes in the retinal microvasculature. The progression from nonproliferative diabetic retinopathy to a more advanced stage of moderate to severe nonproliferative diabetic retinopathy and proliferative diabetic retinopathy occurs very quickly after diagnosis of mild nonproliferative diabetic retinopathy. The etiology of diabetic retinopathy is unclear, and present treatments have limited effectiveness. Currently diabetic retinopathy can only be diagnosed by a trained specialist, which reduces the population that can be examined. A screening biomarker of diabetic retinopathy with high sensitivity and specificity would aid considerably in identifying those individuals in need of clinical assessment and treatment. The majority of the studies reviewed identified specific microRNAs in blood serum/plasma able to distinguish diabetic patients with retinopathy from those without retinopathy and for the progresion of the disease from nonproliferative diabetic retinopathy to proliferative diabetic retinopathy. In addition, certain microRNAs in vitreous humor were dysregulated in proliferative diabetic retinopathy compared to controls. A very high percentage of patients with diabetic retinopathy develop Alzheimer’s disease. Thus, identifying diabetic retinopathy by measurement of suitable biomarkers would also enable better screening and treatment of those individuals at risk of Alzheimer’s disease.
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Affiliation(s)
- Bridget Martinez
- Department of Molecular & Cellular Biology, University of California, Merced, Merced, California, USA; Department of Medicine, St. Georges University School of Medicine, Grenada; Department of Physics and Engineering, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Philip V Peplow
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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Kenny A, Hernández F, Avila J, Lucas JJ, Henshall DC, Prehn JHM, Jiménez-Mateos EM, Engel T. Profiling of Argonaute-2-loaded microRNAs in a mouse model of frontotemporal dementia with parkinsonism-17. INTERNATIONAL JOURNAL OF PHYSIOLOGY, PATHOPHYSIOLOGY AND PHARMACOLOGY 2018; 10:172-183. [PMID: 30697364 PMCID: PMC6334219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Tauopathies are a group of neurodegenerative diseases characterized by the pathological aggregation of the microtubule-associated protein tau. These include more than 20 diseases, with Alzheimer's disease being the most frequent. While pathological and neurotoxic effects of tau are well documented, the mechanisms by which tau can promote neurodegeneration are less clear. Increasing evidence suggests a functional role for microRNAs in the pathogenesis of tauopathies, with altered expression and function of microRNAs in experimental models and patient brain. To determine whether a pathological expression of tau leads to altered microRNA expression, we investigated a mouse model (VLW), which overexpresses tau carrying three mutations identified in patients suffering from frontotemporal dementia with parkinsonism-17. Argonaute-2-bound microRNAs were co-immunoprecipitated using hippocampal tissue to identify active microRNAs within the model and quantified using a genome-wide high-throughput qPCR-based microRNA platform. While similar numbers of microRNAs are present between wild-type and VLW mice, a prominent increase in Argonaute-2-bound levels of microRNAs could be observed in VLW mice. This included microRNA-134, microRNA-99a and microRNA-101. Subsequent experiments revealed this increase in Argonaute-2 loading of microRNAs to correlate with increased microRNA expression. Our in vivo study suggests that a pathological tau overexpression may lead to an increase in active microRNAs, possibly contributing to dysregulation of gene expression and tau-induced pathology.
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Affiliation(s)
- Aidan Kenny
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
| | - Félix Hernández
- Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - Jesús Avila
- Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - José J Lucas
- Department of Molecular Neuropathology, Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- FutureNeuro Research CentreDublin 2, Ireland
| | - Jochen HM Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- FutureNeuro Research CentreDublin 2, Ireland
| | - Eva M Jiménez-Mateos
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- Discipline of Physiology, School of Medicine, Trinity College Dublin, The University of DublinDublin 2, Ireland
| | - Tobias Engel
- Department of Physiology and Medical Physics, Royal College of Surgeons in IrelandDublin 2, Ireland
- FutureNeuro Research CentreDublin 2, Ireland
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33
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Joglekar MV, Wong WKM, Maynard CL, Umrani MR, Martin D, Loudovaris T, Thomas HE, Dalgaard LT, Hardikar AA. Expression of miR-206 in human islets and its role in glucokinase regulation. Am J Physiol Endocrinol Metab 2018; 315:E634-E637. [PMID: 29989852 DOI: 10.1152/ajpendo.00152.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Inappropriate insulin secretion from β-cells is considered as an early sign of impaired glucose tolerance and type 2 diabetes (T2D). Glucokinase (GCK) is an important enzyme that regulates glucose metabolism and ensures that the normal circulating glucose concentrations are maintained. GCK expression is induced by glucose and regulated via transcription factors and regulatory proteins. Recently, microRNA-206 (miR-206) was reported to regulate GCK and alter glucose tolerance in normal and high-fat diet-fed mice. Although the study findings have implications for human diabetes, studies in human islets are lacking. Here, we analyze human islets from individuals without or with T2D, using TaqMan-based real-time qPCR at the tissue (isolated islet) level as well as at single cell resolution, to assess the relationship between miR-206 and GCK expression in normal and T2D human islets. Our data suggest that, unlike mouse islets, human islets do not exhibit any correlation between miR-206 and GCK transcripts. These data implicate the need for further studies aimed toward exploring its potential role(s) in human islets.
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Affiliation(s)
- Mugdha V Joglekar
- NHMRC Clinical Trials Centre, The University of Sydney , New South Wales , Australia
| | - Wilson K M Wong
- NHMRC Clinical Trials Centre, The University of Sydney , New South Wales , Australia
| | - Cody-Lee Maynard
- NHMRC Clinical Trials Centre, The University of Sydney , New South Wales , Australia
| | - Malati R Umrani
- NHMRC Clinical Trials Centre, The University of Sydney , New South Wales , Australia
| | - David Martin
- Department of Gastrointestinal surgery, Strathfield Private Hospital , New South Wales , Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Laboratory, St. Vincent's Institute , Fitzroy, Victoria , Australia
| | - Helen E Thomas
- Immunology and Diabetes Laboratory, St. Vincent's Institute , Fitzroy, Victoria , Australia
| | - Louise T Dalgaard
- Department of Science and Environment, Roskilde University , Roskilde , Denmark
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34
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Drobna M, Szarzyńska-Zawadzka B, Daca-Roszak P, Kosmalska M, Jaksik R, Witt M, Dawidowska M. Identification of Endogenous Control miRNAs for RT-qPCR in T-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2018; 19:ijms19102858. [PMID: 30241379 PMCID: PMC6212946 DOI: 10.3390/ijms19102858] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023] Open
Abstract
Optimal endogenous controls enable reliable normalization of microRNA (miRNA) expression in reverse-transcription quantitative PCR (RT-qPCR). This is particularly important when miRNAs are considered as candidate diagnostic or prognostic biomarkers. Universal endogenous controls are lacking, thus candidate normalizers must be evaluated individually for each experiment. Here we present a strategy that we applied to the identification of optimal control miRNAs for RT-qPCR profiling of miRNA expression in T-cell acute lymphoblastic leukemia (T-ALL) and in normal cells of T-lineage. First, using NormFinder for an iterative analysis of miRNA stability in our miRNA-seq data, we established the number of control miRNAs to be used in RT-qPCR. Then, we identified optimal control miRNAs by a comprehensive analysis of miRNA stability in miRNA-seq data and in RT-qPCR by analysis of RT-qPCR amplification efficiency and expression across a variety of T-lineage samples and T-ALL cell line culture conditions. We then showed the utility of the combination of three miRNAs as endogenous normalizers (hsa-miR-16-5p, hsa-miR-25-3p, and hsa-let-7a-5p). These miRNAs might serve as first-line candidate endogenous controls for RT-qPCR analysis of miRNAs in different types of T-lineage samples: T-ALL patient samples, T-ALL cell lines, normal immature thymocytes, and mature T-lymphocytes. The strategy we present is universal and can be transferred to other RT-qPCR experiments.
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Affiliation(s)
- Monika Drobna
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | | | | | - Maria Kosmalska
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Roman Jaksik
- Department, Silesian University of Technology, 44-100 Gliwice, Poland.
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
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35
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Kang ST, Hsieh YS, Feng CT, Chen YT, Yang PE, Chen WM. miPrimer: an empirical-based qPCR primer design method for small noncoding microRNA. RNA (NEW YORK, N.Y.) 2018; 24:304-312. [PMID: 29208706 PMCID: PMC5824350 DOI: 10.1261/rna.061150.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/29/2017] [Indexed: 05/05/2023]
Abstract
MicroRNAs (miRNAs) are 18-25 nucleotides (nt) of highly conserved, noncoding RNAs involved in gene regulation. Because of miRNAs' short length, the design of miRNA primers for PCR amplification remains a significant challenge. Adding to the challenge are miRNAs similar in sequence and miRNA family members that often only differ in sequences by 1 nt. Here, we describe a novel empirical-based method, miPrimer, which greatly reduces primer dimerization and increases primer specificity by factoring various intrinsic primer properties and employing four primer design strategies. The resulting primer pairs displayed an acceptable qPCR efficiency of between 90% and 110%. When tested on miRNA families, miPrimer-designed primers are capable of discriminating among members of miRNA families, as validated by qPCR assays using Quark Biosciences' platform. Of the 120 miRNA primer pairs tested, 95.6% and 93.3% were successful in amplifying specifically non-family and family miRNA members, respectively, after only one design trial. In summary, miPrimer provides a cost-effective and valuable tool for designing miRNA primers.
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Affiliation(s)
| | | | | | - Yu-Ting Chen
- Quark Biosciences, Zhubei, Hsinchu, 30261, Taiwan
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36
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Ivanov MK, Titov SE, Glushkov SA, Dzyubenko VV, Malek AV, Arkhangelskaya PA, Samsonov RB, Mikhetko AA, Bakhidze EV, Berlev IV, Kolesnikov NN. Detection of high-grade neoplasia in air-dried cervical PAP smears by a microRNA-based classifier. Oncol Rep 2018; 39:1099-1111. [PMID: 29328473 PMCID: PMC5802032 DOI: 10.3892/or.2018.6214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/29/2017] [Indexed: 01/17/2023] Open
Abstract
Recent studies have shown that changes in the expression levels of certain microRNAs correlate with the degree of severity of cervical lesions. The aim of the present study was to develop a microRNA-based classifier for the detection of high-grade cervical intraepithelial neoplasia (CIN ≥2) in cytological samples from patients with different high-risk human papillomavirus (HR-HPV) viral loads. For this purpose, raw RT-qPCR data for 25 candidate microRNAs, U6 snRNA and human DNA in air-dried PAP smears from 174 women with different cervical cytological diagnoses, 144 of which were HR-HPV-positive [40 negative for intraepithelial lesion or malignancy (NILM), 34 low-grade squamous intraepithelial lesions (L-SIL), 57 high-grade squamous intraepithelial lesions (H-SIL), 43 invasive cancers], were statistically processed. The expression level changes of various individual microRNAs were found to be significantly correlated with the cytological diagnosis but the statistical significance of this correlation was critically dependent on the normalization strategy. We developed a linear classifier based on the paired ratios of 8 microRNA concentrations and cellular DNA content. The classifier determines the dimensionless coefficient (DF value), which increases with the severity of cervical lesion. The high- and low-grade CINs were better distinguished by the microRNA classifier than by the measurement of individual microRNA levels with the use of traditional normalization methods. The diagnostic sensitivity of detecting high-grade lesions (CIN ≥2) with the developed microRNA classifier was 83.4%, diagnostic specificity 81.2%, ROC AUC=0.913. The analysis can be performed with the same nucleic acid preparation as used for HPV testing. No statistically significant correlation of the DF value and HR-HPV DNA load was found. The DF value and the HR HPV presence and viral DNA load may be regarded as independent criteria that can complement each other in molecular screening for high-grade cervical intraepithelial neoplasia. Although it has several limitations, the present study showed that the small-scale analysis of microRNA signatures performed by simple PCR-based methods may be useful for improving the diagnostic/prognostic value of cervical screening.
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Affiliation(s)
| | | | | | | | - Anastasia V Malek
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | | | - Roman B Samsonov
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Andrey A Mikhetko
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Elena V Bakhidze
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Igor V Berlev
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Nikolay N Kolesnikov
- Institute of Molecular and Cellular Biology, Siberian Branch of The Russian Academy of Sciences, 630090 Novosibirsk, Russia
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37
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Darvasi O, Szabo PM, Nemeth K, Szabo K, Spisak S, Liko I, Czirjak S, Racz K, Igaz P, Patocs A, Butz H. Limitations of high throughput methods for miRNA expression profiles in non-functioning pituitary adenomas. Pathol Oncol Res 2017; 25:169-182. [PMID: 29043608 DOI: 10.1007/s12253-017-0330-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 10/02/2017] [Indexed: 12/24/2022]
Abstract
Microarray, RT-qPCR based arrays and next-generation-sequencing (NGS) are available high-throughput methods for miRNA profiling (miRNome). Analytical and biological performance of these methods were tested in identification of biologically relevant miRNAs in non-functioning pituitary adenomas (NFPA). miRNome of 4 normal pituitary (NP) and 8 NFPA samples was determined by these platforms and expression of 21 individual miRNAs was measured on 30 (20 NFPA and 10 NP) independent samples. Complex bioinformatics was used. 132 and 137 miRNAs were detected by all three platforms in NP and NFPA, respectively, of which 25 were differentially expressed (fold change > 2). The strongest correlation was observed between microarray and TaqMan-array, while the data obtained by NGS were the most discordant despite of various bioinformatics settings. As a technical validation we measured the expression of 21 selected miRNAs by individual RT-qPCR and we were able to validate 35.1%, 76.2% and 71.4% of the miRNAs revealed by SOLiD, TLDA and microarray result, respectively. We performed biological validation using an extended number of samples (20 NFPAs and 8 NPs). Technical and biological validation showed high correlation (p < 0.001; R = 0.96). Pathway and network analysis revealed several common pathways but no pathway showed the same activation score. Using the 25 platform-independent miRNAs developmental pathways were the top functional categories relevant for NFPA genesis. The difference among high-throughput platforms is of great importance and selection of screening method can influence experimental results. Validation by another platform is essential in order to avoid or to minimalize the platform specific errors.
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Affiliation(s)
- O Darvasi
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - P M Szabo
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - K Nemeth
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - K Szabo
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - S Spisak
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - I Liko
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - S Czirjak
- National Institute of Neurosurgery, Budapest, Hungary
| | - K Racz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - P Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - A Patocs
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
- Semmelweis University, Department of Laboratory Medicine, 46 Szentkirályi Str, Budapest, H-1088, Hungary
| | - Henriett Butz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.
- Semmelweis University, Department of Laboratory Medicine, 46 Szentkirályi Str, Budapest, H-1088, Hungary.
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38
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Umrani MR, Joglekar MV, Somerville Glover E, Wong W, Hardikar AA. Connexins and microRNAs: Interlinked players in regulating islet function? Islets 2017; 9:99-108. [PMID: 28686518 PMCID: PMC5624287 DOI: 10.1080/19382014.2017.1331192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 02/09/2023] Open
Abstract
Pancreatic β-cells are connected to neighboring endocrine cells through the adherin proteins and gap junctions. Connexin 36 (Cx36) is one of the most well-studied and abundantly expressed gap-junction proteins within rodent islets, which is important in coordinated insulin secretion. The expression of connexins is regulated at various levels and by several mechanisms; one of which is via microRNAs. In past 2 decades, microRNAs (miRNAs) have emerged as key molecules in developmental, physiologic and pathological processes. However, very few studies have demonstrated miRNA-mediated regulation of connexins. Even though there are no reports yet on miRNAs and Cx36; we envisage that considering the important role of connexins and microRNAs in insulin secretion, there would be common pathways interlinking these biomolecules. Here, we discuss the current literature on connexins and miRNAs specifically with reference to islet function.
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Affiliation(s)
- Malati R. Umrani
- National centre for cell science, Ganeshkhind, Pune University Campus, Pune, India
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Mugdha V. Joglekar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Ella Somerville Glover
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Wilson Wong
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Anandwardhan A. Hardikar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, University of Sydney, Sydney, Australia
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39
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Zhang X, Zhao L, Hambly B, Bao S, Wang K. Diabetic retinopathy: reversibility of epigenetic modifications and new therapeutic targets. Cell Biosci 2017; 7:42. [PMID: 28815013 PMCID: PMC5557533 DOI: 10.1186/s13578-017-0167-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022] Open
Abstract
In recent years, considerable progress has been made in the molecular mechanisms of epigenetics in disease development and progression, the reversible characteristics of epigenetic modification provide new insights for the treatment of such diseases. The pathogenesis of diabetic retinopathy (DR) has not yet been fully understood, treatment of refractory and recurrent diabetic macular edema remains a big change in clinical practice. This review emphasizes that reversibility of epigenetic modification could provide a new strategy for the prevention and treatment of diseases.
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Affiliation(s)
- Xinyuan Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, 100730 People’s Republic of China
| | - Lin Zhao
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, 100730 People’s Republic of China
| | - Brett Hambly
- Charles Perkins Centre, The University of Sydney, Level 4 West, D17, Camperdown, NSW 2006 Australia
| | - Shisan Bao
- Charles Perkins Centre, The University of Sydney, Level 4 West, D17, Camperdown, NSW 2006 Australia
| | - Kaiyue Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Lab, Capital Medical University, Beijing, 100730 People’s Republic of China
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40
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Sebastiani G, Nigi L, Grieco GE, Mancarella F, Ventriglia G, Dotta F. Circulating microRNAs and diabetes mellitus: a novel tool for disease prediction, diagnosis, and staging? J Endocrinol Invest 2017; 40:591-610. [PMID: 28213644 DOI: 10.1007/s40618-017-0611-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/03/2017] [Indexed: 12/19/2022]
Abstract
Diabetes is a complex, multifactorial group of metabolic diseases characterized by chronic hyperglycaemia due to pancreatic beta-cell dysfunction and/or loss. It is characterized by an asymptomatic and highly variable prodromic phase, which renders diabetes mellitus difficult to be predicted with sufficient accuracy. Despite several efforts in the identification and standardization of newly trustable. Biomarkers able to predict and follow-up diabetes and to specifically subtype its different forms, few of them have proven of clinical utility. Recently, a new class of endogenous non-coding small RNAs, namely microRNAs, have been indicated as putative biomarkers, being released by cells and tissues and found in a cell-free circulating form in many biological fluids, including serum and/or plasma. MicroRNAs have been initially identified as promising biomarkers in cancer, and nowadays their application has been extended to other diseases, including diabetes. Although an increasing number of studies focused on the evaluation of circulating microRNAs in diabetes, few reproducibly identified microRNAs as biomarkers for disease prediction or follow-up. Technological problems as well as the need to obtain highly standardized operating procedures and methods are still an issue in such research field. In this review, we comprehensively resume the main and most recent findings on circulating microRNAs, and their possible use as biomarkers to predict and follow-up diabetes and its complications, as well as the methodological challenges to standardize accurate operating procedures for their analysis.
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Affiliation(s)
- G Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - L Nigi
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - G E Grieco
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - F Mancarella
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - G Ventriglia
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy
| | - F Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy.
- Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, Siena, Italy.
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41
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Lee I, Baxter D, Lee MY, Scherler K, Wang K. The Importance of Standardization on Analyzing Circulating RNA. Mol Diagn Ther 2017; 21:259-268. [PMID: 28039578 PMCID: PMC5426982 DOI: 10.1007/s40291-016-0251-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Circulating RNAs, especially microRNAs (miRNAs), have recently emerged as non-invasive disease biomarkers. Despite enthusiasm and numerous reports on disease-associated circulating miRNAs, currently there is no circulating miRNA-based diagnostic in use. In addition, there are many contradictory reports on the concentration changes of specific miRNA in circulation. Here we review the impact of various technical and non-technical factors related to circulating miRNA measurement and elucidate the importance of having a general guideline for sample preparation and concentration measurement in studying circulating RNA.
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Affiliation(s)
- Inyoul Lee
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - David Baxter
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - Min Young Lee
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - Kelsey Scherler
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - Kai Wang
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA.
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42
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Wang J, Huang W, Thibault S, Brown TP, Bobrowski W, Gukasyan HJ, Evering W, Hu W, John-Baptiste A, Vitsky A. Evaluation of miR-216a and miR-217 as Potential Biomarkers of Acute Exocrine Pancreatic Toxicity in Rats. Toxicol Pathol 2016; 45:321-334. [DOI: 10.1177/0192623316678090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Detecting and monitoring exocrine pancreatic damage during nonclinical and clinical testing is challenging because classical biomarkers amylase and lipase have limited sensitivity and specificity. Novel biomarkers for drug-induced pancreatic injury are needed to improve safety assessment and reduce late-stage attrition rates. In a series of studies, miR-216a and miR-217 were evaluated as potential biomarkers of acute exocrine pancreatic toxicity in rats. Our results revealed that miR-216a and miR-217 were almost exclusively expressed in rat pancreas and that circulating miR-216a and miR-217 were significantly increased in rats following administration of established exocrine pancreatic toxicants caerulein (CL) and 1-cyano-2-hydroxy-3-butene (CHB) as well as in rats administered a proprietary molecule known to primarily affect the exocrine pancreas. Conversely, neither microRNA was increased in rats administered a proprietary molecule known to cause a lesion at the pancreatic endocrine–exocrine interface (EEI) or in rats administered an established renal toxicant. Compared with amylase and lipase, increases in miR-216a and miR-217 were of greater magnitude, persisted longer, and/or correlated better with microscopic findings within the exocrine pancreas. Our findings demonstrate that in rats, miR-216a and miR-217 are sensitive and specific biomarkers of acute exocrine pancreatic toxicity that may add value to the measurement of classical pancreatic biomarkers.
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Affiliation(s)
- Jianying Wang
- Drug Safety R&D, Pfizer Inc., San Diego, California, USA
| | - Wenhu Huang
- Drug Safety R&D, Pfizer Inc., San Diego, California, USA
| | | | | | | | | | | | - Wenyue Hu
- Drug Safety R&D, Pfizer Inc., San Diego, California, USA
| | | | - Allison Vitsky
- Drug Safety R&D, Pfizer Inc., San Diego, California, USA
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43
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Abstract
Incidence of diabetes and other metabolic disorders is increasing worldwide, with almost half the cases remaining undiagnosed. This is cause for concern as poor management of glucose or lipid levels causes tissue damage that may result in micro- or macrovascular complications. Current methods of diagnosing metabolic disorders do not provide any clues on disease aetiology or their posterior evolution and incidence of complications, which are the main cause of disease-associated morbidity. Circulating microRNAs found in blood change with the physiological condition of the organism and may help to: (1) identify people at risk of developing metabolic disease, (2) diagnose diabetes or other metabolic disorders on the basis of their aetiology, (3) predict the development of complications, and (4) monitor response to treatment. Results published to date show promise in this direction but technical issues must still be honed in order to warrant their application in the clinical practice.
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Affiliation(s)
- Marcelina Párrizas
- Laboratory of Diabetes and Obesity, CIBERDEM, IDIBAPS, Rosselló 149-153, pl.5, Barcelona, 08036, Spain.
| | - Anna Novials
- Laboratory of Diabetes and Obesity, CIBERDEM, IDIBAPS, Rosselló 149-153, pl.5, Barcelona, 08036, Spain.
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44
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Cuppen BVJ, Rossato M, Fritsch-Stork RDE, Concepcion AN, Schenk Y, Bijlsma JWJ, Radstake TRDJ, Lafeber FPJG. Can baseline serum microRNAs predict response to TNF-alpha inhibitors in rheumatoid arthritis? Arthritis Res Ther 2016; 18:189. [PMID: 27558398 PMCID: PMC4997731 DOI: 10.1186/s13075-016-1085-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND In rheumatoid arthritis, prediction of response to TNF-alpha inhibitor (TNFi) treatment would be of clinical value. This study aims to discover miRNAs that predict response and aims to replicate results of two previous studies addressing this topic. METHODS From the observational BiOCURA cohort, 40 adalimumab- (ADA) and 40 etanercept- (ETN) treated patients were selected to enter the discovery cohort and baseline serum profiling on 758 miRNAs was performed. The added value of univariately selected miRNAs (p < 0.05) over clinical parameters in prediction of response was determined by means of the area under the receiver operating characteristic curve (AUC-ROC). Validation was performed by TaqMan single qPCR assays in 40 new patients. RESULTS Expression of miR-99a and miR-143 predicted response to ADA, and miR-23a and miR-197 predicted response to ETN. The addition of miRNAs increased the AUC-ROC of a model containing only clinical parameters for ADA (0.75 to 0.97) and ETN (0.68 to 0.78). In validation, none of the selected miRNAs significantly predicted response. miR-23a was the only overlapping miRNA compared to the two previous studies, however inversely related with response in one of these studies. The reasons for the inability to replicate previously proposed miRNAs predicting response to TNFi and replicate those from the discovery cohort were investigated and discussed. CONCLUSIONS To date, no miRNA consistently predicting response to TNFi therapy in RA has been identified. Future studies on this topic should meet a minimum of standards in design that are addressed in this study, in order to increase the reproducibility.
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Affiliation(s)
- Bart V J Cuppen
- Rheumatology and Clinical Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Marzia Rossato
- Rheumatology and Clinical Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,Laboratory of Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Ruth D E Fritsch-Stork
- Rheumatology and Clinical Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,1st Medical Department & Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, Hanusch Hospital, Heinrich-Collin-Straße 30, 1140, Vienna, Austria.,Sigmund Freud University, Freudplatz 1, 1020, Vienna, Austria
| | - Arno N Concepcion
- Rheumatology and Clinical Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Yolande Schenk
- Rheumatology, Diakonessen Hospital, Bosboomstraat 1, 3582 KE, Utrecht, The Netherlands
| | - Johannes W J Bijlsma
- Rheumatology and Clinical Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Timothy R D J Radstake
- Rheumatology and Clinical Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.,Laboratory of Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Floris P J G Lafeber
- Rheumatology and Clinical Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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45
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Tanriverdi K, Kucukural A, Mikhalev E, Tanriverdi SE, Lee R, Ambros VR, Freedman JE. Comparison of RNA isolation and associated methods for extracellular RNA detection by high-throughput quantitative polymerase chain reaction. Anal Biochem 2016; 501:66-74. [PMID: 26969789 DOI: 10.1016/j.ab.2016.02.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 01/23/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that function in RNA silencing and posttranscriptional regulation of gene expression. miRNAs in biofluids are being used for clinical diagnosis as well as disease prediction. Efficient and reproducible isolation methods are crucial for extracellular RNA detection. To determine the best methodologies for miRNA detection from plasma, the performance of four RNA extraction kits, including an in-house kit, were determined with miScript miRNA assay technology; all were measured using a high-throughput quantitative polymerase chain reaction (qPCR) platform (BioMark System) with 90 human miRNA assays. In addition, the performances of complementary DNA (cDNA) and preamplification kits for TaqMan miRNA assays and miScript miRNA assays were compared using the same 90 miRNAs on the BioMark System. There were significant quantification cycle (Cq) value differences for the detection of miRNA targets between isolation kits. cDNA, preamplification, and qPCR performances were also varied. In summary, this study demonstrates differences among RNA isolation methods as measured by reverse transcription (RT)-qPCR. Importantly, differences were also noted in cDNA and preamplification performance using TaqMan and miScript. The in-house kit performed better than the other three kits. These findings demonstrate significant variability between isolation and detection methods for low-abundant miRNA detection from biofluids.
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Affiliation(s)
- Kahraman Tanriverdi
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ekaterina Mikhalev
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Selim E Tanriverdi
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rosalind Lee
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor R Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jane E Freedman
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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46
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Joglekar MV, Januszewski AS, Jenkins AJ, Hardikar AA. Circulating microRNA Biomarkers of Diabetic Retinopathy. Diabetes 2016; 65:22-4. [PMID: 26696637 DOI: 10.2337/dbi15-0028] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mugdha V Joglekar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Andrzej S Januszewski
- Vascular Biology and Biomarker Laboratory, NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Alicia J Jenkins
- Vascular Biology and Biomarker Laboratory, NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
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47
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McKiernan PJ, Greene CM. High-throughput profiling for discovery of non-coding RNA biomarkers of lung disease. Expert Rev Mol Diagn 2015; 16:173-85. [PMID: 26581119 DOI: 10.1586/14737159.2016.1122526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In respiratory medicine there is a need for clinical biomarkers for diagnosis, prognosis and assessment of response to therapy. Noncoding RNA (ncRNA) is expressed in all human cells; two major classes--long ncRNA and microRNA--are detectable extracellularly in the circulation and other biofluids. Altered ncRNA expression is associated with lung disease; collectively this indicates that ncRNA represents a potential biomarker class. This article presents and compares existing platforms for detection and quantification of ncRNA, specifically hybridization, qRT-PCR and RNA sequencing, and outlines methods for data interpretation and normalization. Each approach has merits and shortcomings, which can affect the choice of method when embarking on a biomarker study. Biomarker properties and pre-analytical considerations for ncRNA profiling are also presented. Since a variety of profiling approaches are available, careful study and experimental design are important. Finally, challenges and goals for reliable, standardized high-throughput ncRNA profiling in biofluids as lung disease biomarkers are reviewed.
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Affiliation(s)
- Paul J McKiernan
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
| | - Catherine M Greene
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
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48
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Jenkins AJ, Joglekar MV, Hardikar AA, Keech AC, O'Neal DN, Januszewski AS. Biomarkers in Diabetic Retinopathy. Rev Diabet Stud 2015; 12:159-95. [PMID: 26676667 DOI: 10.1900/rds.2015.12.159] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is a global diabetes epidemic correlating with an increase in obesity. This coincidence may lead to a rise in the prevalence of type 2 diabetes. There is also an as yet unexplained increase in the incidence of type 1 diabetes, which is not related to adiposity. Whilst improved diabetes care has substantially improved diabetes outcomes, the disease remains a common cause of working age adult-onset blindness. Diabetic retinopathy is the most frequently occurring complication of diabetes; it is greatly feared by many diabetes patients. There are multiple risk factors and markers for the onset and progression of diabetic retinopathy, yet residual risk remains. Screening for diabetic retinopathy is recommended to facilitate early detection and treatment. Common biomarkers of diabetic retinopathy and its risk in clinical practice today relate to the visualization of the retinal vasculature and measures of glycemia, lipids, blood pressure, body weight, smoking, and pregnancy status. Greater knowledge of novel biomarkers and mediators of diabetic retinopathy, such as those related to inflammation and angiogenesis, has contributed to the development of additional therapeutics, in particular for late-stage retinopathy, including intra-ocular corticosteroids and intravitreal vascular endothelial growth factor inhibitors ('anti-VEGFs') agents. Unfortunately, in spite of a range of treatments (including laser photocoagulation, intraocular steroids, and anti-VEGF agents, and more recently oral fenofibrate, a PPAR-alpha agonist lipid-lowering drug), many patients with diabetic retinopathy do not respond well to current therapeutics. Therefore, more effective treatments for diabetic retinopathy are necessary. New analytical techniques, in particular those related to molecular markers, are accelerating progress in diabetic retinopathy research. Given the increasing incidence and prevalence of diabetes, and the limited capacity of healthcare systems to screen and treat diabetic retinopathy, there is need to reliably identify and triage people with diabetes. Biomarkers may facilitate a better understanding of diabetic retinopathy, and contribute to the development of novel treatments and new clinical strategies to prevent vision loss in people with diabetes. This article reviews key aspects related to biomarker research, and focuses on some specific biomarkers relevant to diabetic retinopathy.
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Affiliation(s)
- Alicia J Jenkins
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Sydney, Australia
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Sydney, Australia
| | | | - Anthony C Keech
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Sydney, Australia
| | - David N O'Neal
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Sydney, Australia
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