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Akbarzadeh A, Gerami MH, Farrokhi MR, Shapoori S, Jafarinia M. Therapeutic prospects of microRNAs derived from mesenchymal stem cell extracellular vesicles in rheumatoid arthritis: a comprehensive overview. Mol Cell Biochem 2024:10.1007/s11010-024-05082-1. [PMID: 39105963 DOI: 10.1007/s11010-024-05082-1] [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: 04/17/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by inflammatory joint damage. Recent studies have focused on the significance of microRNAs (miRNAs) in the pathogenesis of RA. Mesenchymal stem cells (MSCs) have emerged as a potential therapeutic option for RA based on their regenerative and immunomodulatory properties. MSCs release extracellular vesicles (EVs) containing miRNAs that can modulate immune and inflammatory responses. This article provides a comprehensive overview of the current evidence on the existence of various MSCs-derived miRNAs involved in the pathophysiology, characterization, and treatment of RA. An overview of the miRNA profiles in MSC-EVs is provided, along with an examination of their impact on various cell types implicated in RA pathogenesis, including synovial fibroblasts, macrophages, and T cells. Furthermore, the therapeutic capability of MSC-EVs for miRNA-based therapies in RA is discussed. In total, this review can present an extensive view of the complex interaction between EVs and MSC-derived miRNAs in RA and thus suggest valuable strategies for developing new therapeutic approaches to target this debilitating disease.
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Affiliation(s)
- Armin Akbarzadeh
- Department of Orthopedic Surgery, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hadi Gerami
- Department of Orthopedic Surgery, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Reza Farrokhi
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Shapoori
- Center for Research in Medical Devices (CÚRAM), University of Galway, Galway, Ireland
| | - Morteza Jafarinia
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Zhang Z, Liu T, Dong M, Ahamed MA, Guan W. Sample-to-answer salivary miRNA testing: New frontiers in point-of-care diagnostic technologies. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1969. [PMID: 38783564 PMCID: PMC11141732 DOI: 10.1002/wnan.1969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/10/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
MicroRNA (miRNA), crucial non-coding RNAs, have emerged as key biomarkers in molecular diagnostics, prognosis, and personalized medicine due to their significant role in gene expression regulation. Salivary miRNA, in particular, stands out for its non-invasive collection method and ease of accessibility, offering promising avenues for the development of point-of-care diagnostics for a spectrum of diseases, including cancer, neurodegenerative disorders, and infectious diseases. Such development promises rapid and precise diagnosis, enabling timely treatment. Despite significant advancements in salivary miRNA-based testing, challenges persist in the quantification, multiplexing, sensitivity, and specificity, particularly for miRNA at low concentrations in complex biological mixtures. This work delves into these challenges, focusing on the development and application of salivary miRNA tests for point-of-care use. We explore the biogenesis of salivary miRNA and analyze their quantitative expression and their disease relevance in cancer, infection, and neurodegenerative disorders. We also examined recent progress in miRNA extraction, amplification, and multiplexed detection methods. This study offers a comprehensive view of the development of salivary miRNA-based point-of-care testing (POCT). Its successful advancement could revolutionize the early detection, monitoring, and management of various conditions, enhancing healthcare outcomes. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.
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Affiliation(s)
- Zhikun Zhang
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Md. Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
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McGurran H, Kumbol V, Krüger C, Wallach T, Lehnardt S. miR-154-5p Is a Novel Endogenous Ligand for TLR7 Inducing Microglial Activation and Neuronal Injury. Cells 2024; 13:407. [PMID: 38474371 DOI: 10.3390/cells13050407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Toll-like receptors (TLRs) are a collection of pattern recognition sensors that form a first line of defence by detecting pathogen- or damage-associated molecular patterns and initiating an inflammatory response. TLR activation in microglia, the major immune cells in the brain, can trigger the release of inflammatory molecules, which may contribute to various CNS diseases including Alzheimer's disease. Recently, some microRNAs were shown to serve as signalling molecules for TLRs. Here, we present miR-154-5p as a novel TLR7 ligand. Exposing microglia to miR-154-5p results in cytokine release and alters expression of the TLR signalling pathway dependent on TLR7. Additionally, miR-154-5p causes neuronal injury in enriched cortical neuron cultures and additive toxicity in the presence of microglia. Finally, intrathecal injection of miR-154-5p into mice leads to neuronal injury and accumulation of microglia in the cerebral cortex dependent on TLR7 expression. In conclusion, this study establishes miR-154-5p as a direct activator of TLR7 that can cause neuroinflammation and neuronal injury, which may contribute to CNS disease.
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Affiliation(s)
- Hugo McGurran
- Charité-Universitätsmedizin Berlin, Einstein Center for Neurosciences Berlin, 10117 Berlin, Germany
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Victor Kumbol
- Charité-Universitätsmedizin Berlin, Einstein Center for Neurosciences Berlin, 10117 Berlin, Germany
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Christina Krüger
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Thomas Wallach
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Seija Lehnardt
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
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4
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Ock J, Liu FY, Fridayana FR, Niloofar L, Vo MN, Huang Y, Piao S, Zhou T, Guonan Y. MicroRNA-148a-3p in pericyte-derived extracellular vesicles improves erectile function in diabetic mice by promoting cavernous neurovascular regeneration. BMC Urol 2023; 23:209. [PMID: 38104056 PMCID: PMC10725581 DOI: 10.1186/s12894-023-01378-4] [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] [Received: 01/06/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND To investigate the regulatory role of microRNA (miR)-148a-3p in mouse corpus cavernous pericyte (MCPs)-derived extracellular vesicles (EVs) in the treatment of diabetes-induced erectile dysfunction (ED). METHODS Mouse corpus cavernous tissue was used for MCP primary culture and EV isolation. Small-RNA sequencing analysis was performed to assess the type and content of miRs in MCPs-EVs. Four groups of mice were used: control nondiabetic mice and streptozotocin-induced diabetic mice receiving two intracavernous injections (days - 3 and 0) of phosphate buffered saline, MCPs-EVs transfected with reagent control, or MCPs-EVs transfected with a miR-148a-3p inhibitor. miR-148a-3p function in MCPs-EVs was evaluated by tube-formation assay, migration assay, TUNEL assay, intracavernous pressure, immunofluorescence staining, and Western blotting. RESULTS We extracted EVs from MCPs, and small-RNA sequencing analysis showed miR-148a-3p enrichment in MCPs-EVs. Exogenous MCPs-EV administration effectively promoted mouse cavernous endothelial cell (MCECs) tube formation, migration, and proliferation, and reduced MCECs apoptosis under high-glucose conditions. These effects were significantly attenuated in miR-148a-3p-depleted MCPs-EVs, which were extracted after inhibiting miR-148a-3p expression in MCPs. Repetitive intracavernous injections of MCPs-EVs improved erectile function by inducing cavernous neurovascular regeneration in diabetic mice. Using online bioinformatics databases and luciferase report assays, we predicted that pyruvate dehydrogenase kinase-4 (PDK4) is a potential target gene of miR-148a-3p. CONCLUSIONS Our findings provide new and reliable evidence that miR-148a-3p in MCPs-EVs significantly enhances cavernous neurovascular regeneration by inhibiting PDK4 expression in diabetic mice.
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Affiliation(s)
- Jiyeon Ock
- Department of Urology and National Research Center for Sexual Medicine, Inha University School of Medicine, 7-206, 3rd ST, Shinheung-Dong, Jung-Gu, Incheon, 22332, Republic of Korea
| | - Fang-Yuan Liu
- Department of Urology and National Research Center for Sexual Medicine, Inha University School of Medicine, 7-206, 3rd ST, Shinheung-Dong, Jung-Gu, Incheon, 22332, Republic of Korea
| | - Fitri Rahma Fridayana
- Department of Urology and National Research Center for Sexual Medicine, Inha University School of Medicine, 7-206, 3rd ST, Shinheung-Dong, Jung-Gu, Incheon, 22332, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, South Korea
| | - Lashkari Niloofar
- Department of Urology and National Research Center for Sexual Medicine, Inha University School of Medicine, 7-206, 3rd ST, Shinheung-Dong, Jung-Gu, Incheon, 22332, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, South Korea
| | - Minh Nhat Vo
- Department of Urology and National Research Center for Sexual Medicine, Inha University School of Medicine, 7-206, 3rd ST, Shinheung-Dong, Jung-Gu, Incheon, 22332, Republic of Korea
| | - Yan Huang
- Department of Urology and National Research Center for Sexual Medicine, Inha University School of Medicine, 7-206, 3rd ST, Shinheung-Dong, Jung-Gu, Incheon, 22332, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, South Korea
| | - Shuguang Piao
- Department of Urology, Changhai Hospital Affiliated with the Naval Medicine University, Shanghai, 200433, People's Republic of China.
| | - Tie Zhou
- Department of Urology, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, No. 1279 Sanmen Road, Shanghai, 200434, China.
| | - Yin Guonan
- Department of Urology and National Research Center for Sexual Medicine, Inha University School of Medicine, 7-206, 3rd ST, Shinheung-Dong, Jung-Gu, Incheon, 22332, Republic of Korea.
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Grodzka O, Słyk S, Domitrz I. The Role of MicroRNA in Migraine: A Systemic Literature Review. Cell Mol Neurobiol 2023; 43:3315-3327. [PMID: 37432603 PMCID: PMC10477106 DOI: 10.1007/s10571-023-01387-9] [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] [Received: 05/17/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023]
Abstract
Migraine is a common primary headache disorder, affecting about 14% of the population. Importantly, it was indicated as the second cause of disability globally and the leading cause among young women. Despite the widespread prevalence, migraine remains underdiagnosed and undertreated. The possible solution may be microRNAs-small, non-coding molecules. Until now, multiple studies have shown the great value of microRNA in both the diagnosis and treatment of different human diseases. Furthermore, a significant role in neurological disorders has been suggested. Little research regarding the utility of microRNA in migraine has been conducted, however, the results so far appear to be promising. We performed an electronic article search through PubMed and Embase Database to further explore the topic. After the analysis, according to PRISMA 2020 guidelines, we included 21 studies. The dysregulation was observed in migraine in general, as well as in different types and phases; thus, miRNAs emerge as promising diagnostic biomarkers. Additionally, some studies showed the influence of the intervention with miRNA levels on neuroinflammation and the expression of peptides, which are crucial in migraine pathogenesis. This review aims to summarize the current knowledge about the role of miRNAs in migraine and encourage to further research in this field.Kindly check and confirm the edit made in the title.I checked and confirm.
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Affiliation(s)
- Olga Grodzka
- Department of Neurology, Faculty of Medicine and Dentistry, Medical University of Warsaw, Ceglowska 80, 01-809, Warsaw, Poland.
| | - Stanisław Słyk
- Department of Neurology, Faculty of Medicine and Dentistry, Medical University of Warsaw, Ceglowska 80, 01-809, Warsaw, Poland
- Doctoral School, Medical University of Warsaw, Banacha 1A, 02-097, Warsaw, Poland
| | - Izabela Domitrz
- Department of Neurology, Faculty of Medicine and Dentistry, Medical University of Warsaw, Ceglowska 80, 01-809, Warsaw, Poland
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Martino S, Tammaro C, Misso G, Falco M, Scrima M, Bocchetti M, Rea I, De Stefano L, Caraglia M. microRNA Detection via Nanostructured Biochips for Early Cancer Diagnostics. Int J Mol Sci 2023; 24:7762. [PMID: 37175469 PMCID: PMC10178165 DOI: 10.3390/ijms24097762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNA (miRNA) are constituted of approximately 22 nucleotides and play an important role in the regulation of many physiological functions and diseases. In the last 10 years, an increasing interest has been recorded in studying the expression profile of miRNAs in cancer. Real time-quantitative polymerase chain reaction (RT-qPCR), microarrays, and small RNA sequencing represent the gold standard techniques used in the last 30 years as detection methods. The advent of nanotechnology has allowed the fabrication of nanostructured biosensors which are widely exploited in the diagnostic field. Nanostructured biosensors offer many advantages: (i) their small size allows the construction of portable, wearable, and low-cost products; (ii) the large surface-volume ratio enables the loading of a great number of biorecognition elements (e.g., probes, receptors); and (iii) direct contact of the recognition element with the analyte increases the sensitivity and specificity inducing low limits of detection (LOD). In this review, the role of nanostructured biosensors in miRNA detection is explored, focusing on electrochemical and optical sensing. In particular, four types of nanomaterials (metallic nanoparticles, graphene oxide, quantum dots, and nanostructured polymers) are reported for both detection strategies with the aim to show their distinct properties and applications.
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Affiliation(s)
- Sara Martino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Unit of Naples, National Research Council, Institute of Applied Sciences and Intelligent Systems, 80138 Naples, Italy;
| | - Chiara Tammaro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
| | - Gabriella Misso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
| | - Michela Falco
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Marianna Scrima
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
| | - Ilaria Rea
- Unit of Naples, National Research Council, Institute of Applied Sciences and Intelligent Systems, 80138 Naples, Italy;
| | - Luca De Stefano
- Unit of Naples, National Research Council, Institute of Applied Sciences and Intelligent Systems, 80138 Naples, Italy;
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.M.); (C.T.); (M.F.); (M.B.); (M.C.)
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Institute of Genetic Research, 83031 Ariano Irpino, Italy;
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Fernandes J, Uppal K, Liu KH, Hu X, Orr M, Tran V, Go YM, Jones DP. Antagonistic Interactions in Mitochondria ROS Signaling Responses to Manganese. Antioxidants (Basel) 2023; 12:804. [PMID: 37107179 PMCID: PMC10134992 DOI: 10.3390/antiox12040804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Antagonistic interaction refers to opposing beneficial and adverse signaling by a single agent. Understanding opposing signaling is important because pathologic outcomes can result from adverse causative agents or the failure of beneficial mechanisms. To test for opposing responses at a systems level, we used a transcriptome-metabolome-wide association study (TMWAS) with the rationale that metabolite changes provide a phenotypic readout of gene expression, and gene expression provides a phenotypic readout of signaling metabolites. We incorporated measures of mitochondrial oxidative stress (mtOx) and oxygen consumption rate (mtOCR) with TMWAS of cells with varied manganese (Mn) concentration and found that adverse neuroinflammatory signaling and fatty acid metabolism were connected to mtOx, while beneficial ion transport and neurotransmitter metabolism were connected to mtOCR. Each community contained opposing transcriptome-metabolome interactions, which were linked to biologic functions. The results show that antagonistic interaction is a generalized cell systems response to mitochondrial ROS signaling.
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Affiliation(s)
- Jolyn Fernandes
- Section of Neonatal-Perinatal Medicine, Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ken H. Liu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Orr
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Dean P. Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
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Li K, Chi R, Liu L, Feng M, Su K, Li X, He G, Shi Y. 3D genome-selected microRNAs to improve Alzheimer's disease prediction. Front Neurol 2023; 14:1059492. [PMID: 36860572 PMCID: PMC9968804 DOI: 10.3389/fneur.2023.1059492] [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: 10/01/2022] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
Introduction Alzheimer's disease (AD) is a type of neurodegenerative disease that has no effective treatment in its late stage, making the early prediction of AD critical. There have been an increase in the number of studies indicating that miRNAs play an important role in neurodegenerative diseases including Alzheimer's disease via epigenetic modifications including DNA methylation. Therefore, miRNAs may serve as excellent biomarkers in early AD prediction. Methods Considering that the non-coding RNAs' activity may be linked to their corresponding DNA loci in the 3D genome, we collected the existing AD-related miRNAs combined with 3D genomic data in this study. We investigated three machine learning models in this work under leave-one-out cross-validation (LOOCV): support vector classification (SVC), support vector regression (SVR), and knearest neighbors (KNNs). Results The prediction results of different models demonstrated the effectiveness of incorporating 3D genome information into the AD prediction models. Discussion With the assistance of the 3D genome, we were able to train more accurate models by selecting fewer but more discriminatory miRNAs, as witnessed by several ML models. These interesting findings indicate that the 3D genome has great potential to play an important role in future AD research.
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Affiliation(s)
- Keyi Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Runqiu Chi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Liangjie Liu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Mofan Feng
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Su
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Li
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang He
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Guang He ✉
| | - Yi Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China,Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China,Yi Shi ✉
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Gelisin O, Susgun S, Toruntay C, Yabaci A, Baran G, Gursoy AEB, Yildiz GB, Yucesan E. Evaluation of miR-526b-3p, miR-1179, miR-3529-3p, miR-5011-5p as potential diagnostic biomarkers in isolated cervical dystonia. Rev Neurol (Paris) 2023:S0035-3787(23)00753-1. [PMID: 36759300 DOI: 10.1016/j.neurol.2022.10.008] [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: 01/13/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 02/10/2023]
Abstract
BACKGROUND Cervical dystonia (CD) also named spasmodic torticollis is the most common type of focal dystonias and characterized by abnormal head, neck, and shoulder movements due to involuntary muscular spasm. Although CD is mostly idiopathic, to date, several genes have been associated with CD. However, to the best of our knowledge, microRNAs (miRNAs) which are interacted with CD-associated genes have been not evaluated yet. miRNAs are regulatory small non-coding RNAs and are suggested as potential biomarkers for many diseases through their stability in clinical samples. Therefore, we aimed to assess the expression levels of miRNAs (miR-526b-3p, miR-1179, miR-3529-3p, miR-5011-5p) which are targeted the CD-associated genes, and evaluate their performance as diagnostic biomarkers. METHODS Peripheral blood samples were obtained from 30 patients with isolated CD (ICD) and 25 healthy controls. The expression levels of miR-526b-3p, miR-1179, miR-3529-3p, and miR-5011-5p were analyzed via quantitative real-time PCR (qRT-PCR), and receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic values. RESULTS miR-526b-3p, miR-1179, and miR-3529-3p were significantly up-regulated while miR-5011-5p was significantly down-regulated in ICD patients compared to healthy controls. ROC analysis revealed that all miRNAs, especially miR-1179 and miR-3529-3p were statistically significant with the area under the curve (AUC) of 0.905 and 0.933, respectively. CONCLUSION Altered expression levels of aforementioned miRNAs may be associated with CD pathogenesis. Our findings suggest using these four miRNAs as remarkable biomarkers in the diagnosis of ICD.
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Affiliation(s)
- O Gelisin
- Department of Neurology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - S Susgun
- Department of Genetics, Istanbul University, Aziz Sancar Institute of Experimental Research, Istanbul, Turkey; Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Turkey
| | - C Toruntay
- Department of Molecular Biology and Genetics, Yildiz Technical University, Graduate School of Science and Engineering, Istanbul, Turkey
| | - A Yabaci
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - G Baran
- Department of Neurology, Marmara University, Pendik Training and Research Hospital, Istanbul, Turkey
| | - A E B Gursoy
- Department of Neurology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - G B Yildiz
- Department of Neurology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - E Yucesan
- Department of Neurogenetics, Institute of Neurological Sciences , Istanbul University-Cerrahpasa, Istanbul, Turkey.
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Elangovan A, Venkatesan D, Selvaraj P, Pasha MY, Babu HWS, Iyer M, Narayanasamy A, Subramaniam MD, Valsala Gopalakrishnan A, Kumar NS, Vellingiri B. miRNA in Parkinson's disease: From pathogenesis to theranostic approaches. J Cell Physiol 2023; 238:329-354. [PMID: 36502506 DOI: 10.1002/jcp.30932] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/22/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Parkinson's disease (PD) is an age associated neurological disorder which is specified by cardinal motor symptoms such as tremor, stiffness, bradykinesia, postural instability, and non-motor symptoms. Dopaminergic neurons degradation in substantia nigra region and aggregation of αSyn are the classic signs of molecular defects noticed in PD pathogenesis. The discovery of microRNAs (miRNA) predicted to have a pivotal part in various processes regarding regularizing the cellular functions. Studies on dysregulation of miRNA in PD pathogenesis has recently gained the concern where our review unravels the role of miRNA expression in PD and its necessity in clinical validation for therapeutic development in PD. Here, we discussed how miRNA associated with ageing process in PD through molecular mechanistic approach of miRNAs on sirtuins, tumor necrosis factor-alpha and interleukin-6, dopamine loss, oxidative stress and autophagic dysregulation. Further we have also conferred the expression of miRNAs affected by SNCA gene expression, neuronal differentiation and its therapeutic potential with PD. In conclusion, we suggest more rigorous studies should be conducted on understanding the mechanisms and functions of miRNA in PD which will eventually lead to discovery of novel and promising therapeutics for PD.
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Affiliation(s)
- Ajay Elangovan
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Dhivya Venkatesan
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Priyanka Selvaraj
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Md Younus Pasha
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Harysh Winster Suresh Babu
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India.,Department of Zoology, Disease Proteomics Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Mahalaxmi Iyer
- Livestock Farming, & Bioresources Technology, Tamil Nadu, India
| | - Arul Narayanasamy
- Department of Zoology, Disease Proteomics Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India
| | - Mohana Devi Subramaniam
- Department of Genetics and Molecular Biology, Vision Research Foundation, Tamil Nadu, Chennai, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bioscience and Technology, Vellore Institute of Technology (VIT), Tamil Nadu, Vellore, India
| | | | - Balachandar Vellingiri
- Department of Human Genetics and Molecular Biology, Human Molecular Cytogenetics and Stem Cell Laboratory, Bharathiar University, Tamil Nadu, Coimbatore, India.,Stem cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab, Punjab, Bathinda, India
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11
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Ma M, Na S, Zhang X, Chen C, Xu J. SFGAE: a self-feature-based graph autoencoder model for miRNA-disease associations prediction. Brief Bioinform 2022; 23:6678419. [PMID: 36037084 DOI: 10.1093/bib/bbac340] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence has suggested that microRNAs (miRNAs) are important biomarkers of various diseases. Numerous graph neural network (GNN) models have been proposed for predicting miRNA-disease associations. However, the existing GNN-based methods have over-smoothing issue-the learned feature embeddings of miRNA nodes and disease nodes are indistinguishable when stacking multiple GNN layers. This issue makes the performance of the methods sensitive to the number of layers, and significantly hurts the performance when more layers are employed. In this study, we resolve this issue by a novel self-feature-based graph autoencoder model, shortened as SFGAE. The key novelty of SFGAE is to construct miRNA-self embeddings and disease-self embeddings, and let them be independent of graph interactions between two types of nodes. The novel self-feature embeddings enrich the information of typical aggregated feature embeddings, which aggregate the information from direct neighbors and hence heavily rely on graph interactions. SFGAE adopts a graph encoder with attention mechanism to concatenate aggregated feature embeddings and self-feature embeddings, and adopts a bilinear decoder to predict links. Our experiments show that SFGAE achieves state-of-the-art performance. In particular, SFGAE improves the average AUC upon recent GAEMDA [1] on the benchmark datasets HMDD v2.0 and HMDD v3.2, and consistently performs better when less (e.g. 10%) training samples are used. Furthermore, SFGAE effectively overcomes the over-smoothing issue and performs stably well on deeper models (e.g. eight layers). Finally, we carry out case studies on three human diseases, colon neoplasms, esophageal neoplasms and kidney neoplasms, and perform a survival analysis using kidney neoplasm as an example. The results suggest that SFGAE is a reliable tool for predicting potential miRNA-disease associations.
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Affiliation(s)
- Mingyuan Ma
- Key Laboratory of High Confidence Software Technologies of Ministry of Education, School of Computer Science, Peking University, Beijing, China
| | - Sen Na
- International Computer Science Institute and Department of Statistics, University of California, Berkeley, Berkeley CA, USA
| | - Xiaolu Zhang
- Department of Information Systems, City University of Hong Kong, Hong Kong, China
| | - Congzhou Chen
- Key Laboratory of High Confidence Software Technologies of Ministry of Education, School of Computer Science, Peking University, Beijing, China
| | - Jin Xu
- Key Laboratory of High Confidence Software Technologies of Ministry of Education, School of Computer Science, Peking University, Beijing, China
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12
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Mukherjee S, Murata A, Ishida R, Sugai A, Dohno C, Hamada M, Krishna S, Nakatani K. HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:165-174. [PMID: 34976435 PMCID: PMC8685993 DOI: 10.1016/j.omtn.2021.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022]
Abstract
Selective targeting of biologically relevant RNAs with small molecules is a long-standing challenge due to the lack of clear understanding of the binding RNA motifs for small molecules. The standard SELEX procedure allows the identification of specific RNA binders (aptamers) for the target of interest. However, more effort is needed to identify and characterize the sequence-structure motifs in the aptamers important for binding to the target. Herein, we described a strategy integrating high-throughput (HT) sequencing with conventional SELEX followed by bioinformatic analysis to identify aptamers with high binding affinity and target specificity to unravel the sequence-structure motifs of pre-miRNA, which is essential for binding to the recently developed new water-soluble small-molecule CMBL3aL. To confirm the fidelity of this approach, we investigated the binding of CMBL3aL to the identified motifs by surface plasmon resonance (SPR) spectroscopy and its potential regulatory activity on dicer-mediated cleavage of the obtained aptamers and endogenous pre-miRNAs comprising the identified motif in its hairpin loop. This new approach would significantly accelerate the identification process of binding sequence-structure motifs of pre-miRNA for the compound of interest and would contribute to increase the spectrum of biomedical application.
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Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bellary Road, Bangalore 560065, India
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Ryoga Ishida
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Ayako Sugai
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Sudhir Krishna
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bellary Road, Bangalore 560065, India
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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13
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Belkozhayev AM, Al-Yozbaki M, George A, Niyazova RY, Sharipov KO, Byrne LJ, Wilson CM. Extracellular Vesicles, Stem Cells and the Role of miRNAs in Neurodegeneration. Curr Neuropharmacol 2022; 20:1450-1478. [PMID: 34414870 PMCID: PMC9881087 DOI: 10.2174/1570159x19666210817150141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/16/2021] [Accepted: 06/14/2021] [Indexed: 11/22/2022] Open
Abstract
There are different modalities of intercellular communication governed by cellular homeostasis. In this review, we will explore one of these forms of communication called extracellular vesicles (EVs). These vesicles are released by all cells in the body and are heterogeneous in nature. The primary function of EVs is to share information through their cargo consisting of proteins, lipids and nucleic acids (mRNA, miRNA, dsDNA etc.) with other cells, which have a direct consequence on their microenvironment. We will focus on the role of EVs of mesenchymal stem cells (MSCs) in the nervous system and how these participate in intercellular communication to maintain physiological function and provide neuroprotection. However, deregulation of this same communication system could play a role in several neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, multiple sclerosis, prion disease and Huntington's disease. The release of EVs from a cell provides crucial information to what is happening inside the cell and thus could be used in diagnostics and therapy. We will discuss and explore new avenues for the clinical applications of using engineered MSC-EVs and their potential therapeutic benefit in treating neurodegenerative diseases.
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Affiliation(s)
- Ayaz M. Belkozhayev
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Almaty, Republic of Kazakhstan
- Structural and Functional Genomics Laboratory of M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Minnatallah Al-Yozbaki
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Alex George
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
- Jubilee Centre for Medical Research, Jubilee Mission Medical College & Research Institute, Thrissur, Kerala, India
| | - Raigul Ye Niyazova
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Almaty, Republic of Kazakhstan
| | - Kamalidin O. Sharipov
- Structural and Functional Genomics Laboratory of M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Lee J. Byrne
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Cornelia M. Wilson
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
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14
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Church VA, Yoo AS. MiR-218 steps down to a threshold of motor impairment. Neuron 2021; 109:3233-3235. [PMID: 34672981 DOI: 10.1016/j.neuron.2021.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue of Neuron, Amin et al. (2021) generate genetic tools to titrate down levels of miR-218, a motor neuron-enriched microRNA, in vivo. Varying miR-218 dose alters target selection, results in distinct dose-response curves reflecting 3' UTR features, and reveals a miR-218 threshold below which motor neuron deficits emerge.
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Affiliation(s)
- Victoria A Church
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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15
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Amin ND, Senturk G, Costaguta G, Driscoll S, O'Leary B, Bonanomi D, Pfaff SL. A hidden threshold in motor neuron gene networks revealed by modulation of miR-218 dose. Neuron 2021; 109:3252-3267.e6. [PMID: 34450025 DOI: 10.1016/j.neuron.2021.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/01/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
Disruption of homeostatic microRNA (miRNA) expression levels is known to cause human neuropathology. However, the gene regulatory and phenotypic effects of altering a miRNA's in vivo abundance (rather than its binary gain or loss) are not well understood. By genetic combination, we generated an allelic series of mice expressing varying levels of miR-218, a motor neuron-selective gene regulator associated with motor neuron disease. Titration of miR-218 cellular dose unexpectedly revealed complex, non-ratiometric target mRNA dose responses and distinct gene network outputs. A non-linearly responsive regulon exhibited a steep miR-218 dose-dependent threshold in repression that, when crossed, resulted in severe motor neuron synaptic failure and death. This work demonstrates that a miRNA can govern distinct gene network outputs at different expression levels and that miRNA-dependent phenotypes emerge at particular dose ranges because of hidden regulatory inflection points of their underlying gene networks.
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Affiliation(s)
- Neal D Amin
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Gokhan Senturk
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Giancarlo Costaguta
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shawn Driscoll
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Brendan O'Leary
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dario Bonanomi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Samuel L Pfaff
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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16
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Alamdari AF, Rahnemayan S, Rajabi H, Vahed N, Kashani HRK, Rezabakhsh A, Sanaie S. Melatonin as a promising modulator of aging related neurodegenerative disorders: Role of microRNAs. Pharmacol Res 2021; 173:105839. [PMID: 34418564 DOI: 10.1016/j.phrs.2021.105839] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/02/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023]
Abstract
One of the host risk factors involved in aging-related diseases is coupled with the reduction of endogenous melatonin (MLT) synthesis in the pineal gland. MLT is considered a well-known pleiotropic regulatory hormone to modulate a multitude of biological processes such as the regulation of circadian rhythm attended by potent anti-oxidant, anti-inflammatory, and anti-cancer properties. It has also been established that the microRNAs family, as non-coding mRNAs regulating post-transcriptional processes, also serve a crucial role to promote MLT-related advantageous effects in both experimental and clinical settings. Moreover, the anti-aging impact of MLT and miRNAs participation jointly are of particular interest, recently. In this review, we aimed to scrutinize recent advances concerning the therapeutic implications of MLT, particularly in the brain tissue in the face of aging. We also assessed the possible interplay between microRNAs and MLT, which could be considered a therapeutic strategy to slow down the aging process in the nervous system.
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Affiliation(s)
- Arezoo Fathalizadeh Alamdari
- Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sama Rahnemayan
- Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Rajabi
- Research Center for Translational Medicine, School of Medicine, Koç University, Istanbul, Turkey
| | - Nafiseh Vahed
- Research Center for Evidence-Based Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Reza Khayat Kashani
- Department of Neurosurgery, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aysa Rezabakhsh
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Emergency Medicine Research Team, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Sarvin Sanaie
- Neurosciences Research Center, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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17
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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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18
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Akbari Dilmaghani N, Hussen BM, Nateghinia S, Taheri M, Ghafouri-Fard S. Emerging role of microRNAs in the pathogenesis of amyotrophic lateral sclerosis. Metab Brain Dis 2021; 36:737-749. [PMID: 33604874 DOI: 10.1007/s11011-021-00697-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a deadly motor neuron disease (MND) and the most frequent MND in adults. ALS is recognized by degenerative alterations in both upper and lower motor neurons. This disorder is classified to familial and sporadic classes. Disease-causing mutations in SOD1, C9ORF72, FUS, and TARDBP have been recognized in familial ALS cases. However, in spite of conduction of several genetic association studies, heritable genetic risk elements in sporadic have not been identified completely. Several miRNAs have been dysregulated in the serum samples or brain tissues of ALS patients. Moreover, a number of miRNAs have been suggested as putative biomarkers for sporadic ALS. In the current manuscript, we review of miRNAs in the development of ALS.
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Affiliation(s)
- Nader Akbari Dilmaghani
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Pharmacognosy Department, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Saeedeh Nateghinia
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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19
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miR-499-5p suppresses C-reactive protein and provides neuroprotection in hypoxic-ischemic encephalopathy in neonatal rat. Neurosci Res 2020; 161:44-50. [DOI: 10.1016/j.neures.2019.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/16/2022]
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20
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Emon MA, Heinson A, Wu P, Domingo-Fernández D, Sood M, Vrooman H, Corvol JC, Scordis P, Hofmann-Apitius M, Fröhlich H. Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms. Sci Rep 2020; 10:19097. [PMID: 33154531 PMCID: PMC7645798 DOI: 10.1038/s41598-020-76200-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/23/2020] [Indexed: 02/07/2023] Open
Abstract
One of the visions of precision medicine has been to re-define disease taxonomies based on molecular characteristics rather than on phenotypic evidence. However, achieving this goal is highly challenging, specifically in neurology. Our contribution is a machine-learning based joint molecular subtyping of Alzheimer's (AD) and Parkinson's Disease (PD), based on the genetic burden of 15 molecular mechanisms comprising 27 proteins (e.g. APOE) that have been described in both diseases. We demonstrate that our joint AD/PD clustering using a combination of sparse autoencoders and sparse non-negative matrix factorization is reproducible and can be associated with significant differences of AD and PD patient subgroups on a clinical, pathophysiological and molecular level. Hence, clusters are disease-associated. To our knowledge this work is the first demonstration of a mechanism based stratification in the field of neurodegenerative diseases. Overall, we thus see this work as an important step towards a molecular mechanism-based taxonomy of neurological disorders, which could help in developing better targeted therapies in the future by going beyond classical phenotype based disease definitions.
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Affiliation(s)
- Mohammad Asif Emon
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, University of Bonn, Endenicher Allee 19c, 53115, Bonn, Germany
| | - Ashley Heinson
- UCB Pharma (UCB Celltech Ltd.), 208 Bath Road, Slough, SL1 3WE, Berkshire, UK
| | - Ping Wu
- UCB Pharma (UCB Celltech Ltd.), 208 Bath Road, Slough, SL1 3WE, Berkshire, UK
| | - Daniel Domingo-Fernández
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, University of Bonn, Endenicher Allee 19c, 53115, Bonn, Germany
| | - Meemansa Sood
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, University of Bonn, Endenicher Allee 19c, 53115, Bonn, Germany
| | - Henri Vrooman
- Department of Radiology and Nuclear Medicine, Department of Medical Informatics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | | | - Phil Scordis
- UCB Pharma (UCB Celltech Ltd.), 208 Bath Road, Slough, SL1 3WE, Berkshire, UK
| | - Martin Hofmann-Apitius
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, University of Bonn, Endenicher Allee 19c, 53115, Bonn, Germany
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754, Sankt Augustin, Germany.
- Bonn-Aachen International Center for IT, University of Bonn, Endenicher Allee 19c, 53115, Bonn, Germany.
- UCB Pharma (UCB Biosciences GmbH), Alfred-Nobel-Str. 10, 40789, Monheim, Germany.
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21
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Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs that are evolutionarily conserved across many different species. miRNA regulation of gene expression, specifically in the context of the mammalian brain, has been well characterized; however, the regulation of miRNA degradation is still a focus of ongoing research. This review focuses on recent findings concerning the cellular mechanisms that govern miRNA degradation, with an emphasis on target-mediated miRNA degradation and how this phenomenon is uniquely poised to maintain homeostasis in neuronal systems.
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Affiliation(s)
- Chun K Kim
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois
| | - Toni R Pak
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois
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22
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Li L, Wang P, Zhao H, Luo Y. Noncoding RNAs and Intracerebral Hemorrhage. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2020; 18:205-211. [PMID: 30714535 DOI: 10.2174/1871527318666190204102604] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/20/2018] [Accepted: 01/21/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND & OBJECTIVE Intracerebral hemorrhage (ICH) is the most devastating subtype of stroke, for which there are few effective interventions. Computed tomography is accepted as the gold standard for diagnosis, whereas surgical evacuation is the main treatment for ICH. However, in emergency rooms, time is limited and information regarding a patient's clinical status or tolerance is typically not available. Many studies over the last decade have investigated the fundamental mechanisms of ICH and especially hematoma, which not only cause physical damage but also release toxins that have detrimental effects. However, there remain many gaps in our understanding of ICH. Compared to ischemic stroke, there is little known about the ICH pathogenesis and treatment options, and few specific biomarkers are available for monitoring disease progression, which include hematoma enlargement and perihematoma edema. Noncoding RNAs (ncRNAs) are involved in various biological processes and are potential biomarkers and therapeutic tools in central nervous system diseases. Recent studies have examined the role of ncRNAs including microRNAs, long noncoding RNAs, and circular RNAs-the three main subgroups associated with stroke-in ICH models. A deeper understanding of the functions of ncRNAs in different biological processes can provide a basis for developing more effective therapeutic strategies to prevent neuronal damage following ICH. In clinical settings, ncRNAs can serve as biomarkers for predicting the degree of injury resulting from ICH. CONCLUSION In this review, we discuss the current state of knowledge of the role of ncRNAs in ICH.
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Affiliation(s)
- Lingzhi Li
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Pingping Wang
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Haiping Zhao
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China
| | - Yumin Luo
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing, China.,Beijing Institute for Brain Disorders, Beijing, China
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23
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Das Gupta S, Ndode-Ekane XE, Puhakka N, Pitkänen A. Droplet digital polymerase chain reaction-based quantification of circulating microRNAs using small RNA concentration normalization. Sci Rep 2020; 10:9012. [PMID: 32488181 PMCID: PMC7265372 DOI: 10.1038/s41598-020-66072-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022] Open
Abstract
Quantification of plasma microRNAs (miRNAs) as non-invasive disease biomarkers is subject to multiple technical variabilities. This study aimed to develop an optimized protocol for miRNA quantification from rodent plasma. We hypothesized that a fixed small RNA concentration input for reverse transcription (RT) reaction will provide better miRNA quantification than a fixed RNA volume input. For this, tail-vein plasma was collected from 30 naïve, adult male Sprague-Dawley rats. Plasma hemolysis was measured with NanoDrop-1000 and Denovix DS-11 spectrophotometers. Plasma was then pooled, and RNA was extracted from 50-μl, 100-μl or 200-μl pool aliquots. Small RNA concentration was measured with Qubit miRNA assay. A fixed RNA volume (un-normalized) or a fixed small RNA concentration was used for RT (concentration-normalized). The method was setup with miR-23a-3p and validated with miR-103a-3p and miR-451a. Hemolysis measurements from Denovix and NanoDrop strongly correlated. Qubit revealed increased small RNA concentrations with increasing starting plasma volumes. With concentration-normalization, miRNA levels from 100-µl and 200-µl plasma volume groups mostly normalized to the level of the 50-µl in ddPCR. Our results indicate that miRNA quantification with ddPCR should be performed with small RNA concentration-normalization to minimize variations in eluted RNA concentrations occuring during RNA extraction.
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Affiliation(s)
- Shalini Das Gupta
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211, Kuopio, Finland
| | - Xavier Ekolle Ndode-Ekane
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211, Kuopio, Finland
| | - Noora Puhakka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211, Kuopio, Finland.
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211, Kuopio, Finland
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24
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Hu X, Mao C, Fan L, Luo H, Hu Z, Zhang S, Yang Z, Zheng H, Sun H, Fan Y, Yang J, Shi C, Xu Y. Modeling Parkinson's Disease Using Induced Pluripotent Stem Cells. Stem Cells Int 2020; 2020:1061470. [PMID: 32256606 PMCID: PMC7091557 DOI: 10.1155/2020/1061470] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/08/2020] [Accepted: 02/15/2020] [Indexed: 02/06/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. The molecular mechanisms of PD at the cellular level involve oxidative stress, mitochondrial dysfunction, autophagy, axonal transport, and neuroinflammation. Induced pluripotent stem cells (iPSCs) with patient-specific genetic background are capable of directed differentiation into dopaminergic neurons. Cell models based on iPSCs are powerful tools for studying the molecular mechanisms of PD. The iPSCs used for PD studies were mainly from patients carrying mutations in synuclein alpha (SNCA), leucine-rich repeat kinase 2 (LRRK2), PTEN-induced putative kinase 1 (PINK1), parkin RBR E3 ubiquitin protein ligase (PARK2), cytoplasmic protein sorting 35 (VPS35), and variants in glucosidase beta acid (GBA). In this review, we summarized the advances in molecular mechanisms of Parkinson's disease using iPSC models.
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Affiliation(s)
- Xinchao Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Liyuan Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Haiyang Luo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Shuo Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Zhihua Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Huimin Zheng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Huifang Sun
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Yu Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000 Henan, China
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25
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Goh SY, Chao YX, Dheen ST, Tan EK, Tay SSW. Role of MicroRNAs in Parkinson's Disease. Int J Mol Sci 2019; 20:E5649. [PMID: 31718095 PMCID: PMC6888719 DOI: 10.3390/ijms20225649] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/08/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is a disabling neurodegenerative disease that manifests with resting tremor, bradykinesia, rigidity and postural instability. Since the discovery of microRNAs (miRNAs) in 1993, miRNAs have been shown to be important biological molecules involved in diverse processes to maintain normal cellular functions. Over the past decade, many studies have reported dysregulation of miRNA expressions in PD. Here, we identified 15 miRNAs from 34 reported screening studies that demonstrated dysregulation in the brain and/or neuronal models, cerebrospinal fluid (CSF) and blood. Specific miRNAs-of-interest that have been implicated in PD pathogenesis include miR-30, miR-29, let-7, miR-485 and miR-26. However, there are several challenges and limitations in drawing definitive conclusions due to the small sample size in clinical studies, varied laboratory techniques and methodologies and their incomplete penetrance of the blood-brain barrier. Developing an optimal delivery system and unravelling druggable targets of miRNAs in both experimental and human models and clinical validation of the results may pave way for novel therapeutics in PD.
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Affiliation(s)
- Suh Yee Goh
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore 117594, Singapore; (S.Y.G.); (S.T.D.)
| | - Yin Xia Chao
- National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
- Department of Neurology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
- Medical Education, Research and Evaluation (MERE) department, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Shaikali Thameem Dheen
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore 117594, Singapore; (S.Y.G.); (S.T.D.)
| | - Eng-King Tan
- National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
- Department of Neurology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
- Neuroscience and Behavioral Disorders (NBD) department, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Samuel Sam-Wah Tay
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore 117594, Singapore; (S.Y.G.); (S.T.D.)
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26
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Wang Q, Yu H, Yu H, Ma M, Ma Y, Li R. miR‑223‑3p/TIAL1 interaction is involved in the mechanisms associated with the neuroprotective effects of dexmedetomidine on hippocampal neuronal cells in vitro. Mol Med Rep 2018; 19:805-812. [PMID: 30569136 PMCID: PMC6323261 DOI: 10.3892/mmr.2018.9742] [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: 03/10/2017] [Accepted: 05/15/2018] [Indexed: 11/09/2022] Open
Abstract
Dexmedetomidine (DEX), an α2 adrenoceptor agonist, is a commonly used anesthetic drug in surgical procedures. Previous studies have indicated that DEX exerts neuroprotective effects. However, the molecular mechanism underlying this process remains to be elucidated. The present study investigated a potential implication of microRNA (miR)-223-3p in the DEX-induced anti-oxidative effect on neuronal cells. The results indicated that following hydrogen peroxide (H2O2)-mediated induction of oxidative stress, the viability of human hippocampal neuronal cells was markedly decreased, as determined by an MTT assay. In addition, treatment with H2O2 induced cell apoptosis, the release of lactate dehydrogenase, accumulation of intracellular calcium, phosphorylation of calmodulin-2, and production of malondialdehyde and reactive oxygen species. Furthermore, treatment with H2O2 inhibited the expression of mir-223-3p and enhanced the expression of its target cytotoxic granule associated RNA binding protein like 1 (TIAL1), and these effects were reversed by treatment with DEX. Mechanistic studies demonstrated that the 3′-untranslated region of TIAL1 is a direct target of mir-223-3p. The results of the present study demonstrated that DEX may induce its neuroprotective effects by regulating the interaction between miR-223-3p and TIAL1. Therefore, the manipulation of miR-223-3p/TIAL1 interaction may be involved in the neuroprotective effects of DEX.
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Affiliation(s)
- Qi Wang
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Hongmei Yu
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Hong Yu
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Meina Ma
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Yali Ma
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
| | - Rui Li
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061001, P.R. China
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Jin L, Wan W, Wang L, Wang C, Xiao J, Zhang F, Zhao J, Wang J, Zhan C, Zhong C. Elevated microRNA-520d-5p in the serum of patients with Parkinson's disease, possibly through regulation of cereloplasmin expression. Neurosci Lett 2018; 687:88-93. [PMID: 30243884 DOI: 10.1016/j.neulet.2018.09.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 12/21/2022]
Abstract
Iron metabolism dysfunction and redox-active iron-induced oxidative stress in the brain may contribute to the pathogenesis of Parkinson's disease. We have previously demonstrated that reduced serum ceruloplasmin level exacerbates nigral iron deposition in Parkinson's disease, although the underlying cause of the low serum ceruloplasmin level in Parkinson's disease remains unknown. Fluorescent quantitative real-time polymerase chain reaction analysis revealed that patients with Parkinson's disease had higher serum levels of microRNA (miR)-520d-5p than controls (p = 0.0011). Patients with Alzheimer's disease or multiple system atrophy did not have significantly elevated miR-520d-5p levels. Expression of miR-520d-5p did not correlate with disease severity or the motor phenotype of Parkinson's disease. Luciferase assays confirmed that miR-520d-5p was associated with ceruloplasmin gene expression, as predicted by the TargetScan tool and miRBase. In vitro experiments showed that miR-520d-5p reduced ceruloplasmin gene expression in the U251 astrocyte cell line. Our data suggest that miR-520d-5p may be a potential regulator of ceruloplasmin gene expression in vitro.
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Affiliation(s)
- Lirong Jin
- Department of Neurology, Zhongshan Hospital, Fudan University, China.
| | - Wenbin Wan
- Department of Neurology, Zhongshan Hospital, Fudan University, China
| | - Lingyan Wang
- Biomedical Research Center, Zhongshan Hospital, Fudan University, China
| | - Changpeng Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, China
| | - Jianqiu Xiao
- School of Life Sciences, Fudan University, China
| | - Feng Zhang
- School of Life Sciences, Fudan University, China
| | - Jue Zhao
- Department of Neurology, Huashan Hospital, Fudan University, China
| | - Jian Wang
- Department of Neurology, Huashan Hospital, Fudan University, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Chunjiu Zhong
- Department of Neurology, Zhongshan Hospital, Fudan University, China.
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28
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He BS, Qu J, Zhao Q. Identifying and Exploiting Potential miRNA-Disease Associations With Neighborhood Regularized Logistic Matrix Factorization. Front Genet 2018; 9:303. [PMID: 30131824 PMCID: PMC6090164 DOI: 10.3389/fgene.2018.00303] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
Abstract
With the rapid development of biological research, microRNAs (miRNA) have become an attractive topic because lots of experimental studies have revealed the significant associations between miRNAs and diseases. However, considering that experiments are expensive and time-consuming, computational methods for predicting associations between miRNAs and diseases have become increasingly crucial. In this study, we proposed a neighborhood regularized logistic matrix factorization method for miRNA-disease association prediction (NRLMFMDA) by integrating miRNA functional similarity, disease semantic similarity, Gaussian interaction profile kernel similarity, and experimentally validation of disease-miRNA association. We used Gaussian interaction profile kernel similarity to cover the shortage of the traditional similarity to make it more reasonable and complete. Furthermore, NRLMFMDA also considered the important influences of the neighborhood information and took full advantage of them to improve the accuracy of the miRNA-disease association prediction. We also improved the accuracy by giving higher weights to the known association data in the process of calculating the potential association probabilities. In the global and the local leave-one-out cross validation, NRLMFMDA got the AUCs of 0.9068 and 0.8239, respectively. Moreover, the average AUC of NRLMFMDA in 5-fold cross validation was 0.8976 ± 0.0034. All the three kinds of cross validations have shown significant advantages to a number of previous models. In the case studies of breast neoplasms, esophageal neoplasms and lymphoma according to known miRNA-disease associations in the recent version of HMDD database, there were 78, 80, and 74% of top 50 predicted related miRNAs verified to have associations with these three diseases, respectively. In the further case studies for new disease without any known related miRNAs and the previous version of HMDD database, there were also high proportions of the predicted miRNAs verified by experimental reports. All the validation experiment results have demonstrated the effectiveness and practicability of NRLFMDA to predict the potential miRNA-disease associations.
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Affiliation(s)
- Bin-Sheng He
- The First Affiliated Hospital, Changsha Medical University, Changsha, China
| | - Jia Qu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Qi Zhao
- School of Mathematics, Liaoning University, Shenyang, China.,Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang, China
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29
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Chen X, Qu J, Yin J. TLHNMDA: Triple Layer Heterogeneous Network Based Inference for MiRNA-Disease Association Prediction. Front Genet 2018; 9:234. [PMID: 30018632 PMCID: PMC6038677 DOI: 10.3389/fgene.2018.00234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 06/12/2018] [Indexed: 12/12/2022] Open
Abstract
In recent years, microRNAs (miRNAs) have been confirmed to be involved in many important biological processes and associated with various kinds of human complex diseases. Therefore, predicting potential associations between miRNAs and diseases with the huge number of verified heterogeneous biological datasets will provide a new perspective for disease therapy. In this article, we developed a novel computational model of Triple Layer Heterogeneous Network based inference for MiRNA-Disease Association prediction (TLHNMDA) by using the experimentally verified miRNA-disease associations, miRNA-long noncoding RNA (lncRNA) interactions, miRNA function similarity information, disease semantic similarity information and Gaussian interaction profile kernel similarity for lncRNAs into an triple layer heterogeneous network to predict new miRNA-disease associations. As a result, the AUCs of TLHNMDA are 0.8795 and 0.8795 ± 0.0010 based on leave-one-out cross validation (LOOCV) and 5-fold cross validation, respectively. Furthermore, TLHNMDA was implemented on three complex human diseases to evaluate predictive ability. As a result, 84% (kidney neoplasms), 78% (lymphoma) and 76% (prostate neoplasms) of top 50 predicted miRNAs for the three complex diseases can be verified by biological experiments. In addition, based on the HMDD v1.0 database, 98% of top 50 potential esophageal neoplasms-associated miRNAs were confirmed by experimental reports. It is expected that TLHNMDA could be a useful model to predict potential miRNA-disease associations with high prediction accuracy and stability.
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Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Jia Qu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Jun Yin
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
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30
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Ahmad K, Baig MH, Mushtaq G, Kamal MA, Greig NH, Choi I. Commonalities in Biological Pathways, Genetics, and Cellular Mechanism between Alzheimer Disease and Other Neurodegenerative Diseases: An In Silico-Updated Overview. Curr Alzheimer Res 2018; 14:1190-1197. [PMID: 28164765 DOI: 10.2174/1567205014666170203141151] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/07/2016] [Accepted: 01/30/2016] [Indexed: 12/29/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common and well-studied neurodegenerative disease (ND). Biological pathways, pathophysiology and genetics of AD show commonalities with other NDs viz. Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), Prion disease and Dentatorubral-pallidoluysian atrophy (DRPLA). Many of the NDs, sharing the common features and molecular mechanisms suggest that pathology may be directly comparable and be implicated in disease prevention and development of highly effective therapies. METHOD In this review, a brief description of pathophysiology, clinical symptoms and available treatment of various NDs have been explored with special emphasis on AD. Commonalities in these fatal NDs provide support for therapeutic advancements and enhance the understanding of disease manifestation. CONCLUSION The studies concentrating on the commonalities in biological pathways, cellular mechanisms and genetics may provide the scope to researchers to identify few novel common target(s) for disease prevention and development of effective common drugs for multi-neurodegenerative diseases.
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Affiliation(s)
- Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan. Korea
| | - Mohammad Hassan Baig
- Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 712-749. Korea
| | - Gohar Mushtaq
- Department of Biochemistry, College of Science, King Abdulaziz University, Jeddah 21589. Saudi Arabia
| | - Mohammad Amjad Kamal
- King Fahd Medical Research Centre, King Abdulaziz University, P.O. Box 80216, Jeddah 21589. Saudi Arabia
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National, Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224. United States
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 712-749. Korea
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31
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More SV, Choi DK. Emerging preclinical pharmacological targets for Parkinson's disease. Oncotarget 2018; 7:29835-63. [PMID: 26988916 PMCID: PMC5045437 DOI: 10.18632/oncotarget.8104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurological condition caused by the degeneration of dopaminergic neurons in the basal ganglia. It is the most prevalent form of Parkinsonism, categorized by cardinal features such as bradykinesia, rigidity, tremors, and postural instability. Due to the multicentric pathology of PD involving inflammation, oxidative stress, excitotoxicity, apoptosis, and protein aggregation, it has become difficult to pin-point a single therapeutic target and evaluate its potential application. Currently available drugs for treating PD provide only symptomatic relief and do not decrease or avert disease progression resulting in poor patient satisfaction and compliance. Significant amount of understanding concerning the pathophysiology of PD has offered a range of potential targets for PD. Several emerging targets including AAV-hAADC gene therapy, phosphodiesterase-4, potassium channels, myeloperoxidase, acetylcholinesterase, MAO-B, dopamine, A2A, mGlu5, and 5-HT-1A/1B receptors are in different stages of clinical development. Additionally, alternative interventions such as deep brain stimulation, thalamotomy, transcranial magnetic stimulation, and gamma knife surgery, are also being developed for patients with advanced PD. As much as these therapeutic targets hold potential to delay the onset and reverse the disease, more targets and alternative interventions need to be examined in different stages of PD. In this review, we discuss various emerging preclinical pharmacological targets that may serve as a new promising neuroprotective strategy that could actually help alleviate PD and its symptoms.
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Affiliation(s)
- Sandeep Vasant More
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju, South Korea
| | - Dong-Kug Choi
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju, South Korea
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32
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Cruz LO, Hashemifar SS, Wu CJ, Cho S, Nguyen DT, Lin LL, Khan AA, Lu LF. Excessive expression of miR-27 impairs Treg-mediated immunological tolerance. J Clin Invest 2017; 127:530-542. [PMID: 28067667 DOI: 10.1172/jci88415] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/10/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRs) are tightly regulated in the immune system, and aberrant expression of miRs often results in hematopoietic malignancies and autoimmune diseases. Previously, it was suggested that elevated levels of miR-27 in T cells isolated from patients with multiple sclerosis facilitate disease progression by inhibiting Th2 immunity and promoting pathogenic Th1 responses. Here we have demonstrated that, although mice with T cell-specific overexpression of miR-27 harbor dysregulated Th1 responses and develop autoimmune pathology, these disease phenotypes are not driven by miR-27 in effector T cells in a cell-autonomous manner. Rather, dysregulation of Th1 responses and autoimmunity resulted from a perturbed Treg compartment. Excessive miR-27 expression in murine T cells severely impaired Treg differentiation. Moreover, Tregs with exaggerated miR-27-mediated gene regulation exhibited diminished homeostasis and suppressor function in vivo. Mechanistically, we determined that miR-27 represses several known as well as previously uncharacterized targets that play critical roles in controlling multiple aspects of Treg biology. Collectively, our data show that miR-27 functions as a key regulator in Treg development and function and suggest that proper regulation of miR-27 is pivotal to safeguarding Treg-mediated immunological tolerance.
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33
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Mushtaq G, Greig NH, Anwar F, Zamzami MA, Choudhry H, Shaik MM, Tamargo IA, Kamal MA. miRNAs as Circulating Biomarkers for Alzheimer's Disease and Parkinson's Disease. Med Chem 2016; 12:217-25. [PMID: 26527155 PMCID: PMC6138249 DOI: 10.2174/1573406411666151030112140] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022]
Abstract
Detection of biomarkers for neurodegenerative disorders (NDDs) within brain tissues of Alzheimer's disease (AD) and Parkinson's disease (PD) patients has always been hampered by our inability to access and biopsy tissue of key brain regions implicated in disease occurrence and progression. Currently, diagnosis of NDDs is principally based on clinical observations of symptoms that present at later stages of disease progression, followed by neuroimaging and, possibly, CSF evaluation. One way to potentially detect and diagnose NDDs at a far earlier stage is to screen for abnormal levels of specific disease markers within the peripheral circulation of patients with NDDs. Increasing evidence suggests that there is dysregulation of microRNAs (miRNAs) in NDDs. Peripheral blood mononuclear cells, as well as biofluids, such as plasma, serum, urine and cerebrospinal fluid, contain miRNAs that can be identified and quantified. Circulating miRNAs within blood and other biofluids may thus be characterized and used as non-invasive, diagnostic biomarkers that facilitate the early detection of disease and potentially the continual monitoring of disease progression for NDDs such as AD and PD. Plainly, such a screen is only possible with a clear understanding of which miRNAs change with disease, and when these changes occur during the progression of AD and PD. Such information is becoming increasingly available and, in the near future, may not only support disease diagnosis, but provide the opportunity to evaluate therapeutic interventions earlier in the disease process.
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Affiliation(s)
| | - Nigel H Greig
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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34
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Wang Y, Liu Z, Zou W, Hong H, Fang H, Tong W. Molecular regulation of miRNAs and potential biomarkers in the progression of hepatic steatosis to NASH. Biomark Med 2015; 9:1189-200. [DOI: 10.2217/bmm.15.70] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence suggests that microRNAs regulate diverse biological functions in the liver and play a very important function in metabolic-related disorders such as nonalcoholic fatty liver disease via regulating their target genes expression. In this review, we summarized the most recent progress in identification of miRNAs involving in the progression of liver steatosis and discussed the possible mechanisms by which miRNAs contribute to the diverse pathogenic liver injuries. We provide insights into the functional network of miRNAs by connecting miRNAs, their targets and biological pathways associated to hepatic steatosis and fibrosis, with important implications for our understanding of phenotypic-based disease pathogenesis. We also discuss the possible roles and challenges of miRNAs as biomarkers for drug-induced liver injury.
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Affiliation(s)
- Yuping Wang
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Zhichao Liu
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Wen Zou
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Hong Fang
- Office of Scientific Coordination, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Weida Tong
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
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