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Schindler P, Bellmann-Strobl J, Kuhle J, Wildemann B, Jarius S, Paul F, Ruprecht K. Longitudinal change of serum NfL as disease activity biomarker candidate in MOGAD: A descriptive cohort study. Mult Scler Relat Disord 2024; 88:105729. [PMID: 38901371 DOI: 10.1016/j.msard.2024.105729] [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: 05/28/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Myelin oligodendrocyte glycoprotein antibody (MOG-IgG)-associated disease (MOGAD) is an autoinflammatory disease of the central nervous system. MOGAD often follows a relapsing course that can lead to severe disability, but monophasic disease is possible as well. Currently, there is an unmet clinical need for disease activity biomarkers in MOGAD. Serum neurofilament light chain (sNfL) is a sensitive biomarker for neuroaxonal damage. However, data on longitudinal change of sNfL as disease activity biomarker for MOGAD are scarce. OBJECTIVE To describe the longitudinal course of sNfL in adult patients with MOGAD in an active as well as a stable disease state in relation to clinical parameters and serum MOG-IgG titers. METHODS We conducted a retrospective, exploratory, monocentric cohort study of adult patients with MOGAD. Cohort 1 consisted of five patients in whom NfL was tested as part of their routine clinical workup, all of which had active disease (maximum 6 months since last attack, median 3 months). Cohort 2 comprised 13 patients, which were tested for NfL in the context of a longitudinal study at predefined time intervals, mostly during remission (median 10 months since last attack). sNfL was measured using single molecule array (Simoa) technology at least at two time points (median 3) within a median observation time of 5 months in cohort 1, and at baseline and after a median duration of 12 months in cohort 2. MOG-IgG titers were measured by a fixed cell-based assay. RESULTS Change in sNfL correlated positively with change in MOG-IgG titers (rho=0.59, p = 0.027). The variability of sNfL (difference between highest and lowest level) during the observation period was higher in patients who had an attack within six months before baseline (median 37 [interquartile range [IQR] 10-64] pg/ml vs. 2.3 [IQR 1-5] pg/ml, p = 0.006). sNfL increased in patients with an attack during the observation period. Patients with baseline sNfL measurement within two weeks after attack symptom onset displayed relatively low initial sNfL with an increase afterwards. CONCLUSIONS Longitudinal sNfL change correlates with MOG-IgG titer change and may be a promising biomarker candidate for disease activity in MOGAD. Increasing sNfL levels might be utilized to adjudicate suspected attacks. In acute attacks, sNfL increase may occur with a delay after symptom onset.
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Affiliation(s)
- Patrick Schindler
- Department of Neurology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany; Neuroscience Clinical Research Center, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.
| | - Judith Bellmann-Strobl
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany; Neuroscience Clinical Research Center, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Jens Kuhle
- Multiple Sclerosis Centre and Research Center for Clinical Neuroimmunology and Neuroscience (RC2NB), Departments of Biomedicine and Clinical Research, University Hospital and University of Basel, Basel, Switzerland; Department of Neurology, University Hospital and University of Basel, Basel, Switzerland
| | - Brigitte Wildemann
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Sven Jarius
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Friedemann Paul
- Department of Neurology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany; Neuroscience Clinical Research Center, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Klemens Ruprecht
- Department of Neurology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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Ma F, Cao D, Liu Z, Li Y, Ouyang S, Wu J. Identification of novel circulating miRNAs biomarkers for healthy obese and lean children. BMC Endocr Disord 2023; 23:238. [PMID: 37904219 PMCID: PMC10614305 DOI: 10.1186/s12902-023-01498-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/25/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The prevalence of childhood obesity and overweight has risen globally, leading to increased rates of metabolic disorders. Various factors, including genetic, epigenetic, and environmental influences such as diet and physical activity, contribute to pediatric obesity. This study aimed to identify specific circulating miRNAs as potential biomarkers for assessing obesity in children. METHODS Thirty children, including 15 obese and 15 extremely thin individuals, were selected for this study. MiRNA expression in circulating plasma was assessed using miRNA microarrays. The reliability of differential miRNA expression was confirmed using TaqMan qPCR. The correlation between miRNAs and obesity was analyzed through multiple linear regression, receiver operator characteristic (ROC) curve analysis, and odds ratio (OR) calculations. Bioinformatics tools were utilized to identify target genes for the selected miRNAs, and a functional network map was constructed. RESULTS A total of 36 differentially expressed miRNAs were identified through gene chip analysis, and TaqMan qPCR validation confirmed the upregulation of seven miRNAs: hsa-miR-126-3p, hsa-miR-15b-5p, hsa-miR-199a-3p, hsa-miR-20a-5p, hsa-miR-223-3p, hsa-miR-23a-3p, and hsa-miR-24-3p. Among these, hsa-miR-15b-5p and hsa-miR-223-3p exhibited a statistically significant difference except for hsa-miR-23a-3p. These two miRNAs showed more predicted target genes related to obesity than others. Multiple linear regression analysis revealed an association between obesity and hsa-miR-15b-5p and hsa-miR-223-3p [10.529 (4.974-16.084), -10.225 (-17.852~ -2.657)]. Even after adjusting for age and sex, these two miRNAs remained associated with obesity [8.936 (3.572-14.301), -8.449(-15.634~ -1.303)]. The area under the ROC curve (AUC) reached values of 0.816, 0.711, and 0.929, respectively. Odds ratio analysis demonstrated a significant correlation between obesity and hsa-miR-15b-5p (OR = 143, 95% CI 5.80 to 56,313, p = 0.024) and between obesity and hsa-miR-223-3p (OR = 0.01, 95% CI 0.00 to 0.23, p = 0.037). Importantly, hsa-miR-15b-5p was found to have numerous target genes associated with the FoxO, insulin, Ras, and AMPK signaling pathways. CONCLUSIONS Differential miRNA expression profiles in the circulation of obese children compared to controls suggest underlying metabolic abnormalities. Hsa-miR-15b-5p and hsa-miR-223-3p may be considered as molecular markers for the screening of obese children and populations at risk of developing metabolic syndrome.
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Affiliation(s)
- Feifei Ma
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, 2 Yabao street, Beijing, 100020, People's Republic of China
- Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, 5 Dongdansantiao, Beijing, 100005, People's Republic of China
| | - Dingding Cao
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, 2 Yabao street, Beijing, 100020, People's Republic of China
| | - Zhuo Liu
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, 2 Yabao street, Beijing, 100020, People's Republic of China
| | - Yuanyuan Li
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, 2 Yabao street, Beijing, 100020, People's Republic of China
| | - Shengrong Ouyang
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, 2 Yabao street, Beijing, 100020, People's Republic of China.
| | - Jianxin Wu
- Department of Biochemistry and Immunology, Capital Institute of Pediatrics, 2 Yabao street, Beijing, 100020, People's Republic of China.
- Beijing TongRen Hospital, Capital Medical University, 17 Hougou Street, Chong Wen Men, Beijing, 100730, People's Republic of China.
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Ramanathan S, Brilot F, Irani SR, Dale RC. Origins and immunopathogenesis of autoimmune central nervous system disorders. Nat Rev Neurol 2023; 19:172-190. [PMID: 36788293 DOI: 10.1038/s41582-023-00776-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2023] [Indexed: 02/16/2023]
Abstract
The field of autoimmune neurology is rapidly evolving, and recent discoveries have advanced our understanding of disease aetiologies. In this article, we review the key pathogenic mechanisms underlying the development of CNS autoimmunity. First, we review non-modifiable risk factors, such as age, sex and ethnicity, as well as genetic factors such as monogenic variants, common variants in vulnerability genes and emerging HLA associations. Second, we highlight how interactions between environmental factors and epigenetics can modify disease onset and severity. Third, we review possible disease mechanisms underlying triggers that are associated with the loss of immune tolerance with consequent recognition of self-antigens; these triggers include infections, tumours and immune-checkpoint inhibitor therapies. Fourth, we outline how advances in our understanding of the anatomy of lymphatic drainage and neuroimmune interfaces are challenging long-held notions of CNS immune privilege, with direct relevance to CNS autoimmunity, and how disruption of B cell and T cell tolerance and the passage of immune cells between the peripheral and intrathecal compartments have key roles in initiating disease activity. Last, we consider novel therapeutic approaches based on our knowledge of the immunopathogenesis of autoimmune CNS disorders.
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Affiliation(s)
- Sudarshini Ramanathan
- Translational Neuroimmunology Group, Kids Neuroscience Centre, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Medical School, Faculty of Medicine and Health and Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
- Department of Neurology, Concord Hospital, Sydney, New South Wales, Australia
| | - Fabienne Brilot
- Translational Neuroimmunology Group, Kids Neuroscience Centre, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- School of Medical Science, Faculty of Medicine and Health and Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Russell C Dale
- Translational Neuroimmunology Group, Kids Neuroscience Centre, Children's Hospital at Westmead, Sydney, New South Wales, Australia.
- Sydney Medical School, Faculty of Medicine and Health and Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia.
- TY Nelson Department of Paediatric Neurology, Children's Hospital Westmead, Sydney, New South Wales, Australia.
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Ay A, Alkanli N, Atli E, Gurkan H, Gulyasar T, Guler S, Sipahi T, Sut N. Investigation of Relationship Between Small Noncoding RNA (sncRNA) Expression Levels and Serum Iron, Copper, and Zinc Levels in Clinical Diagnosed Multiple Sclerosis Patients. Mol Neurobiol 2023; 60:875-883. [PMID: 36383327 DOI: 10.1007/s12035-022-03135-4] [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: 09/17/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
In our study, we aimed to investigate the relationship between microRNA (miRNA) expression levels and serum iron (Fe), copper (Cu), and zinc (Zn) levels in Multiple sclerosis (MS) patients. Total RNA was isolated from peripheral venous blood containing ethylenediaminetetraacetic acid (EDTA) of MS patients and controls. Total RNA was labeled with Cy3-CTP fluorescent dye. Hybridization of samples was performed on microarray slides and arrays were scanned. Data argument and bioinformatics analysis were performed. Atomic absorption spectrophotometer method was used to measure serum Fe, Cu, and Zn levels. In our study, in bioinformatics analysis, although differently expressed miRNAs were not detected between 16 MS patients and 16 controls, hsa-miR-744-5p upregulation was detected between 4 MS patients and 4 controls. This may be stem from the patient group consisting of MS patients who have never had an attack for 1 year. Serum iron levels were detected significantly higher in the 16 MS patients compared to the 16 controls. This may be stem from the increase in iron accumulation based on inflammation in MS disease. According to the findings in our study, hsa-miR-744-5p upregulation has been determined as an early diagnostic biomarker for the development together of insulin resistance, diabetes mellitus associated with insulin signaling, and Alzheimer's diseases. Therefore, hsa-miR-744-5p is recommended as an important biomarker for the development together of diabetes mellitus, Alzheimer's disease, and MS disease. In addition, increased serum Fe levels may be suggested as an important biomarker for neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, and MS disease.
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Affiliation(s)
- Arzu Ay
- Department of Biophysics, Faculty of Medicine, Trakya University, Edirne, 22030, Turkey.
| | - Nevra Alkanli
- Department of Biophysics, Faculty of Medicine, Haliç University, Istanbul, 34060, Turkey
| | - Engin Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, 22030, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, 22030, Turkey
| | - Tevfik Gulyasar
- Department of Biophysics, Faculty of Medicine, Trakya University, Edirne, 22030, Turkey
| | - Sibel Guler
- Department of Neurology, Faculty of Medicine, Trakya University, Edirne, 22030, Turkey
| | - Tammam Sipahi
- Department of Biophysics, Faculty of Medicine, Trakya University, Edirne, 22030, Turkey
| | - Necdet Sut
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Trakya University, Edirne, 22030, Turkey
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5
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Chen J, Zhang L, Lin J, Wang Z, Lin A. Excessive MALAT1 promotes the immunologic process of neuromyelitis optica spectrum disorder by upregulating BAFF expression. Transl Neurosci 2023; 14:20220306. [PMID: 37873058 PMCID: PMC10590614 DOI: 10.1515/tnsci-2022-0306] [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: 04/02/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 10/25/2023] Open
Abstract
Increased B cell activating factor (BAFF) expression in patients with neuromyelitis optica spectrum disorder (NMOSD) is associated with B cell overstimulation, but the underlying mechanism remains unclear. This study aimed to reveal the emerging mechanisms that regulate BAFF expression in the inflammatory process of NMOSD. The results showed that the expression of miR-30b-5p was significantly decreased in NMOSD CD14+ monocytes compared with the normal control. Furthermore, we confirmed that metastasis-associated lung adenocarcinoma transcription 1 (MALAT1) is an upstream target of miR-30b-5p, and it could act as a ceRNA and absorb miR-30b-5p with reduced expression of miR-30b-5p. The low expression of miR-30b-5p could not bind to BAFF messenger RNA (mRNA), which resulted in the overexpression of both BAFF mRNA and protein expression. Overexpression of BAFF could bind to the corresponding receptors on B cells, which may initiate activation and proliferation of B cells and increase their production of autoantibodies. Therefore, these findings interpreted that excessive MALAT1 expression in NMOSD mononuclear macrophages led to increased BAFF expression by targeting miR-30b-5p, which caused B cell autoimmune reaction and autoantibodies production, aggravated the disease progression of NMOSD.
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Affiliation(s)
- Jing Chen
- Department of Neurology and Institute of Neurology of the First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou350005, China
- Department of Neurology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, 363000, Fujian, China
| | - Lijie Zhang
- Department of Neurology and Institute of Neurology of the First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou350212, China
| | - Jingyu Lin
- Department of Neurology and Institute of Neurology of the First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou350005, China
| | - Zeng Wang
- Central Research Lab, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, Fujian, China
| | - Aiyu Lin
- Department of Neurology and Institute of Neurology of the First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou350212, Fujian, China
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Mesenchymal Stem Cell-Derived Extracellular Vesicles and Their Therapeutic Use in Central Nervous System Demyelinating Disorders. Int J Mol Sci 2022; 23:ijms23073829. [PMID: 35409188 PMCID: PMC8998258 DOI: 10.3390/ijms23073829] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Autoimmune demyelinating diseases-including multiple sclerosis, neuromyelitis optica spectrum disorder, anti-myelin oligodendrocyte glycoprotein-associated disease, acute disseminated encephalomyelitis, and glial fibrillary acidic protein (GFAP)-associated meningoencephalomyelitis-are a heterogeneous group of diseases even though their common pathology is characterized by neuroinflammation, loss of myelin, and reactive astrogliosis. The lack of safe pharmacological therapies has purported the notion that cell-based treatments could be introduced to cure these patients. Among stem cells, mesenchymal stem cells (MSCs), obtained from various sources, are considered to be the ones with more interesting features in the context of demyelinating disorders, given that their secretome is fully equipped with an array of anti-inflammatory and neuroprotective molecules, such as mRNAs, miRNAs, lipids, and proteins with multiple functions. In this review, we discuss the potential of cell-free therapeutics utilizing MSC secretome-derived extracellular vesicles-and in particular exosomes-in the treatment of autoimmune demyelinating diseases, and provide an outlook for studies of their future applications.
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Saha S, Mukherjee S, Guha G, Mukhopadhyay D. Dynamics of AQP4 upon exposure to seropositive patient serum before and after Rituximab therapy in Neuromyelitis Optica: A cell-based study. J Neuroimmunol 2021; 361:577752. [PMID: 34715591 DOI: 10.1016/j.jneuroim.2021.577752] [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: 04/28/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Neuromyelitis Optica (NMO) is an autoimmune inflammatory disease that affects the optic nerves and spinal cord. The autoantibody is generated against the abundant water channel protein of the brain, Aquaporin 4 (AQP4). Of the two isoforms of AQP4, the shorter one (M23) often exists as a supramolecular assembly known as an orthogonal array of particles (OAPs). There have been debates about the fate of these AQP4 clusters upon binding to the antibody, the exact mechanism of its turnover, and the proteins associated with the process. Recently several clinical cases of NMO were reported delineating the effect of Rituximab (RTX) therapy. Extending these reports at the cell signaling level, we developed a glioma based cellular model that mimicked antibody binding and helped us track the subsequent events including a variation of AQP4 levels, alterations in cellular morphology, and the changes in downstream signaling cascades. Our results revealed the extent of perturbations in the signaling pathways related to stress involving ERK, JNK, and AKT1 together with markers for cell death. We could also decipher the possible routes of degradation of AQP4, post-exposure to antibody. We further investigated the effect of autoantibody on AQP4 transcriptional level and involvement of FOXO3a and miRNA-145 in the regulation of transcription. This study highlights the differential outcome at the cellular level when treated with the serum of the same patient pre and post RTX therapy and for the first time mechanistically describes the effect of RTX.
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Affiliation(s)
- Suparna Saha
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, HBNI.Sector - 1, Block - AF Bidhannagar, Kolkata 700064, India.
| | - Soumava Mukherjee
- Department of Neurology, Nil Ratan Sircar Medical College and Hospital, West Bengal University of Health Sciences, Kolkata, West Bengal, India
| | - Gautam Guha
- Department of Neurology, Nil Ratan Sircar Medical College and Hospital, West Bengal University of Health Sciences, Kolkata, West Bengal, India
| | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, HBNI.Sector - 1, Block - AF Bidhannagar, Kolkata 700064, India.
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8
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miRNome profiling in Duchenne muscular dystrophy; identification of asymptomatic and manifesting female carriers. Biosci Rep 2021; 41:229711. [PMID: 34472584 PMCID: PMC8450315 DOI: 10.1042/bsr20211325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal neuromuscular disorder that occurs due to inactivating mutations in DMD gene, leading to muscular dystrophy. Prediction of pathological complications of DMD and the identification of female carriers are important research points that aim to reduce disease burden. Herein, we describe a case of a late DMD patient and his immediate female family members, who all carry same DMD mutation and exhibited varied degrees of symptoms. In our study, we sequenced the whole miRNome in leukocytes and plasma of the family members and results were validated using real-time PCR. Our results highlighted the role of miR-409-3p, miR-424-5p, miR-144-3p as microRNAs that show correlation with the extent of severity of muscular weakness and can be used for detection of asymptomatic carriers. Cellular and circulating levels of miR-494-3p had shown significant increase in symptomatic carriers, which may indicate significant roles played by this miRNA in the onset of muscular weakness. Interestingly, circulating levels of miR-206 and miR-410-3p were significantly increased only in the severely symptomatic carrier. In conclusion, our study highlighted several miRNA species, which could be used in predicting the onset of muscle and/or neurological complications in DMD carriers.
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Wang J, Cao Y, Lu X, Wang T, Li S, Kong X, Bo C, Li J, Wang X, Ma H, Li L, Zhang H, Ning S, Wang L. MicroRNAs and nervous system diseases: network insights and computational challenges. Brief Bioinform 2021; 21:863-875. [PMID: 30953059 DOI: 10.1093/bib/bbz032] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/12/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
The nervous system is one of the most complex biological systems, and nervous system disease (NSD) is a major cause of disability and mortality. Extensive evidence indicates that numerous dysregulated microRNAs (miRNAs) are involved in a broad spectrum of NSDs. A comprehensive review of miRNA-mediated regulatory will facilitate our understanding of miRNA dysregulation mechanisms in NSDs. In this work, we summarized currently available databases on miRNAs and NSDs, star NSD miRNAs, NSD spectrum width, miRNA spectrum width and the distribution of miRNAs in NSD sub-categories by reviewing approximately 1000 studies. In addition, we characterized miRNA-miRNA and NSD-NSD interactions from a network perspective based on miRNA-NSD benchmarking data sets. Furthermore, we summarized the regulatory principles of miRNAs in NSDs, including miRNA synergistic regulation in NSDs, miRNA modules and NSD modules. We also discussed computational challenges for identifying novel miRNAs in NSDs. Elucidating the roles of miRNAs in NSDs from a network perspective would not only improve our understanding of the precise mechanism underlying these complex diseases, but also provide novel insight into the development, diagnosis and treatment of NSDs.
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Affiliation(s)
- Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuze Cao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jie Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaolong Wang
- Department of Orthopedics, Harbin Medical University Cancer Hospital, Harbin, China
| | - Heping Ma
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lei Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Li W, Liu J, Tan W, Zhou Y. The role and mechanisms of Microglia in Neuromyelitis Optica Spectrum Disorders. Int J Med Sci 2021; 18:3059-3065. [PMID: 34400876 PMCID: PMC8364446 DOI: 10.7150/ijms.61153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022] Open
Abstract
Neuromyelitis optica spectrum disorder (NMOSD) is an autoimmune neurological disease that can cause blindness and disability. As the major mediators in the central nervous system, microglia plays key roles in immunological regulation in neuroinflammatory diseases, including NMOSD. Microglia can be activated by interleukin (IL)-6 and type I interferons (IFN-Is) during NMOSD, leading to signal transducer and activator of transcription (STAT) activation. Moreover, complement C3a secreted from activated astrocytes may induce the secretion of complement C1q, inflammatory cytokines and progranulin (PGRN) by microglia, facilitating injury to microglia, neurons, astrocytes and oligodendrocytes in an autocrine or paracrine manner. These processes involving activated microglia ultimately promote the pathological course of NMOSD. In this review, recent research progress on the roles of microglia in NMOSD pathogenesis is summarized, and the mechanisms of microglial activation and microglial-mediated inflammation, and the potential research prospects associated with microglial activation are also discussed.
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Affiliation(s)
- Wenqun Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Institute of Clinical Pharmacy, Central South University, Changsha, 410011, Hunan, China
| | - Jiaqin Liu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Institute of Clinical Pharmacy, Central South University, Changsha, 410011, Hunan, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan 410011, China
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan 410011, China
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11
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Chen C, Wu Y, Li M, Cui C, Zhao Y, Sun X, Wang Y, Liu C, Wu H, Zhong X, Kermode AG, Peng L, Qiu W. Different Exosomal microRNA Profile in Aquaporin-4 Antibody Positive Neuromyelitis Optica Spectrum Disorders. Front Immunol 2020; 11:1064. [PMID: 32547558 PMCID: PMC7274160 DOI: 10.3389/fimmu.2020.01064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/04/2020] [Indexed: 12/29/2022] Open
Abstract
Neuromyelitis optica spectrum disorders (NMOSD) and multiple sclerosis (MS) are inflammatory demyelinating diseases of the central nervous system. Exosomal microRNAs (miRNAs) are emerging biomarkers for demyelinating diseases. In this study, 52 aquaporin-4 antibody serum-positive NMOSD patients, 18 relapsing-remitting multiple sclerosis (RRMS) patients and 17 healthy controls (HCs) were included for the next-generation sequencing (NGS). To validate the NGS results, the valuable miRNAs were selected for validation by real-time quantitative polymerase chain reaction in another cohort of patients, comprising 31 NMOSD patients and 14 HCs. In addition, these miRNAs were also validated in a longitudinal study. NGS data revealed the exosomal miRNAs profile in NMOSD patients was different from HCs. Among those potential exosomal miRNAs which can distinguish NMOSD status, hsa-miR-122-3p and hsa-miR-200a-5p were the most abundant miRNAs. In addition, hsa-miR-122-3p and hsa-miR-200a-5p were significantly upregulated in the serum exosome of relapsing NMOSD compared with that in remitting NMOSD. Hsa-miR-122-3p and hsa-miR-200a-5p had positive correlations with disease severity in NMOSD patients. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the MAPK, Wnt and Ras signaling pathways were enriched. Further biological function analysis demonstrated that these two miRNAs might be involved in the immunoregulation of NMOSD pathogenesis. Our results indicated that miRNAs delivered by exosomes could be applied as potential biomarkers for NMOSD.
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Affiliation(s)
- Chen Chen
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yunting Wu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Miaochang Li
- Department of Neurology, Zhaoqing No. 1 People's Hospital, Zhaoqing, China
| | - Chunping Cui
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yipeng Zhao
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaobo Sun
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuge Wang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chunxin Liu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haotian Wu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaonan Zhong
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Allan G Kermode
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Perth, WA, Australia.,Department of Neurology, Sir Charles Gairdner Hospital, Queen Elizabeth II Medical Centre, Perth, WA, Australia.,Institute of Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Lisheng Peng
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Qiu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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12
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Identifying the culprits in neurological autoimmune diseases. J Transl Autoimmun 2019; 2:100015. [PMID: 32743503 PMCID: PMC7388404 DOI: 10.1016/j.jtauto.2019.100015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022] Open
Abstract
The target organ of neurological autoimmune diseases (NADs) is the central or peripheral nervous system. Multiple sclerosis (MS) is the most common NAD, whereas Guillain-Barré syndrome (GBS), myasthenia gravis (MG), and neuromyelitis optica (NMO) are less common NADs, but the incidence of these diseases has increased exponentially in the last few years. The identification of a specific culprit in NADs is challenging since a myriad of triggering factors interplay with each other to cause an autoimmune response. Among the factors that have been associated with NADs are genetic susceptibility, epigenetic mechanisms, and environmental factors such as infection, microbiota, vitamins, etc. This review focuses on the most studied culprits as well as the mechanisms used by these to trigger NADs. Neurological autoimmune diseases are caused by a complex interaction between genes, environmental factors, and epigenetic deregulation. Infectious agents can cause an autoimmune reaction to myelin epitopes through molecular mimicry and/or bystander activation. Gut microbiota dysbiosis contributes to neurological autoimmune diseases. Smoking increases the risk of NADs through inflammatory signaling pathways, oxidative stress, and Th17 differentiation. Deficiency in vitamin D favors NAD development through direct damage to the central and peripheral nervous system.
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13
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Baulina N, Osmak G, Kiselev I, Popova E, Boyko A, Kulakova O, Favorova O. MiRNAs from DLK1-DIO3 Imprinted Locus at 14q32 are Associated with Multiple Sclerosis: Gender-Specific Expression and Regulation of Receptor Tyrosine Kinases Signaling. Cells 2019; 8:cells8020133. [PMID: 30743997 PMCID: PMC6406543 DOI: 10.3390/cells8020133] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/01/2019] [Accepted: 02/07/2019] [Indexed: 02/07/2023] Open
Abstract
Relapsing-remitting multiple sclerosis (RRMS) is the most prevalent course of multiple sclerosis. It is an autoimmune inflammatory disease of the central nervous system. To investigate the gender-specific involvement of microRNAs (miRNAs) in RRMS pathogenesis, we compared miRNA profiles in peripheral blood mononuclear cells separately in men and women (eight RRMS patients versus four healthy controls of each gender) using high-throughput sequencing. In contrast to women, six downregulated and 26 upregulated miRNAs (padj < 0.05) were identified in men with RRMS. Genes encoding upregulated miRNAs are co-localized in DLK1-DIO3 imprinted locus on human chromosome 14q32. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis was performed in independent groups of men (16 RRMS patients and 10 healthy controls) and women (20 RRMS patients and 10 healthy controls). Increased expression of miR-431, miR-127-3p, miR-379, miR-376c, miR-381, miR-410 and miR-656 was again demonstrated in male (padj < 0.05), but not in female RRMS patients. At the same time, the expression levels of these miRNAs were lower in healthy men than in healthy women, whereas in RRMS men they increased and reached or exceeded levels in RRMS women. In general, we demonstrated that expression levels of these miRNAs depend both on “health–disease” status and gender. Network-based enrichment analysis identified that receptor tyrosine kinases-activated pathways were enriched with products of genes targeted by miRNAs from DLK1-DIO3 locus. These results suggest the male-specific involvement of these miRNAs in RRMS pathogenesis via regulation of PI3K/Akt signaling.
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Affiliation(s)
- Natalia Baulina
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
| | - German Osmak
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
| | - Ivan Kiselev
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
| | - Ekaterina Popova
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
| | - Alexey Boyko
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
| | - Olga Kulakova
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
| | - Olga Favorova
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
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14
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MicroRNA in diagnosis and therapy monitoring of early-stage triple-negative breast cancer. Sci Rep 2018; 8:11584. [PMID: 30072748 PMCID: PMC6072710 DOI: 10.1038/s41598-018-29917-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/09/2018] [Indexed: 11/12/2022] Open
Abstract
Breast cancer is a heterogeneous disease with distinct molecular subtypes including the aggressive subtype triple-negative breast cancer (TNBC). We compared blood-borne miRNA signatures of early-stage basal-like (cytokeratin-CK5-positive) TNBC patients to age-matched controls. The miRNAs of TNBC patients were assessed prior to and following platinum-based neoadjuvant chemotherapy (NCT). After an exploratory genome-wide study on 21 cases and 21 controls using microarrays, the identified signatures were verified independently in two laboratories on the same and a new cohort by RT-qPCR. We differentiated the blood of TNBC patients before NCT from controls with 84% sensitivity. The most significant miRNA for this diagnostic classification was miR-126-5p (two tailed t-test p-value of 1.4 × 10−5). Validation confirmed the microarray results for all tested miRNAs. Comparing cancer patients prior to and post NCT highlighted 321 significant miRNAs (among them miR-34a, p-value of 1.2 × 10−23). Our results also suggest that changes in miRNA expression during NCT may have predictive potential to predict pathological complete response (pCR). In conclusion we report that miRNA expression measured from blood facilitates early and minimally-invasive diagnosis of basal-like TNBC. We also demonstrate that NCT has a significant influence on miRNA expression. Finally, we show that blood-borne miRNA profiles monitored over time have potential to predict pCR.
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15
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Gomes A, da Silva IV, Rodrigues CMP, Castro RE, Soveral G. The Emerging Role of microRNAs in Aquaporin Regulation. Front Chem 2018; 6:238. [PMID: 29977890 PMCID: PMC6021494 DOI: 10.3389/fchem.2018.00238] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022] Open
Abstract
Aquaporins (AQPs) are membrane channels widely distributed in human tissues. AQPs are essential for water and energy homeostasis being involved in a broad range of pathophysiological processes such as edema, brain injury, glaucoma, nephrogenic diabetes insipidus, salivary and lacrimal gland dysfunction, cancer, obesity and related metabolic complications. Compelling evidence indicates that AQPs are targets for therapeutic intervention with potential broad application. Nevertheless, efficient AQP modulators have been difficult to find due to either lack of selectivity and stability, or associated toxicity that hamper in vivo studies. MicroRNAs (miRNAs) are naturally occurring small non-coding RNAs that regulate post-transcriptional gene expression and are involved in several diseases. Recent identification of miRNAs as endogenous modulators of AQP expression provides an alternative approach to target these proteins and opens new perspectives for therapeutic applications. This mini-review compiles the current knowledge of miRNA interaction with AQPs highlighting miRNA potential for regulation of AQP-based disorders.
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Affiliation(s)
- André Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.,Department Bioquimica e Biologia Humana, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Inês V da Silva
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.,Department Bioquimica e Biologia Humana, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Cecília M P Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.,Department Bioquimica e Biologia Humana, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.,Department Bioquimica e Biologia Humana, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Graça Soveral
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.,Department Bioquimica e Biologia Humana, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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16
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Groen K, Maltby VE, Lea RA, Sanders KA, Fink JL, Scott RJ, Tajouri L, Lechner-Scott J. Erythrocyte microRNA sequencing reveals differential expression in relapsing-remitting multiple sclerosis. BMC Med Genomics 2018; 11:48. [PMID: 29783973 PMCID: PMC5963124 DOI: 10.1186/s12920-018-0365-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/01/2018] [Indexed: 02/06/2023] Open
Abstract
Background There is a paucity of knowledge concerning erythrocytes in the aetiology of Multiple Sclerosis (MS) despite their potential to contribute to disease through impaired antioxidant capacity and altered haemorheological features. Several studies have identified an abundance of erythrocyte miRNAs and variable profiles associated with disease states, such as sickle cell disease and malaria. The aim of this study was to compare the erythrocyte miRNA profile of relapsing-remitting MS (RRMS) patients to healthy sex- and age-matched controls. Methods Erythrocytes were purified by density-gradient centrifugation and RNA was extracted. Following library preparation, samples were run on a HiSeq4000 Illumina instrument (paired-end 100 bp sequencing). Sequenced erythrocyte miRNA profiles (9 patients and 9 controls) were analysed by DESeq2. Differentially expressed miRNAs were validated by RT-qPCR using miR-152-3p as an endogenous control and replicated in a larger cohort (20 patients and 18 controls). After logarithmic transformation, differential expression was determined by two-tailed unpaired t-tests. Logistic regression analysis was carried out and receiver operating characteristic (ROC) curves were generated to determine biomarker potential. Results A total of 236 erythrocyte miRNAs were identified. Of twelve differentially expressed miRNAs in RRMS two showed increased expression (adj. p < 0.05). Only modest fold-changes were evident across differentially expressed miRNAs. RT-qPCR confirmed differential expression of miR-30b-5p (0.61 fold, p < 0.05) and miR-3200-3p (0.36 fold, p < 0.01) in RRMS compared to healthy controls. Relative expression of miR-3200-5p (0.66 fold, NS p = 0.096) also approached significance. MiR-3200-5p was positively correlated with cognition measured by audio-recorded cognitive screen (r = 0.60; p < 0.01). MiR-3200-3p showed greatest biomarker potential as a single miRNA (accuracy = 75.5%, p < 0.01, sensitivity = 72.7%, specificity = 84.0%). Combining miR-3200-3p, miR-3200-5p, and miR-30b-5p into a composite biomarker increased accuracy to 83.0% (p < 0.05), sensitivity to 77.3%, and specificity to 88.0%. Conclusions This is the first study to report differences in erythrocyte miRNAs in RRMS. While the role of miRNAs in erythrocytes remains to be elucidated, differential expression of erythrocyte miRNAs may be exploited as biomarkers and their potential contribution to MS pathology and cognition should be further investigated. Electronic supplementary material The online version of this article (10.1186/s12920-018-0365-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kira Groen
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia.,Centre for Information Based Medicine, Level 3 West, Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia
| | - Vicki E Maltby
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia.,Centre for Information Based Medicine, Level 3 West, Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia
| | - Rodney A Lea
- Centre for Information Based Medicine, Level 3 West, Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia.,Institute of Health and Biomedical Innovations, Genomics Research Centre, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia
| | - Katherine A Sanders
- Centre for Anatomical and Human Sciences, Hull York Medical School, Hull, HU6 7RX, UK
| | - J Lynn Fink
- Diamantina Institute, University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Rodney J Scott
- Centre for Information Based Medicine, Level 3 West, Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia.,Division of Molecular Genetics, Pathology North, John Hunter Hospital, New Lambton Heights, NSW, 2305, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Lotti Tajouri
- Faculty of Health Sciences and Medicine, Bond University, QLD, Robina, 4229, Australia
| | - Jeannette Lechner-Scott
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia. .,Centre for Information Based Medicine, Level 3 West, Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia. .,Department of Neurology, John Hunter Hospital, New Lambton Heights, NSW, 2305, Australia.
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17
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Immune-related miRNA expression patterns in peripheral blood mononuclear cells differ in multiple sclerosis relapse and remission. J Neuroimmunol 2018; 317:67-76. [DOI: 10.1016/j.jneuroim.2018.01.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/28/2017] [Accepted: 01/04/2018] [Indexed: 01/21/2023]
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18
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Sharaf-Eldin WE, Kishk NA, Gad YZ, Hassan H, Ali MAM, Zaki MS, Mohamed MR, Essawi ML. Extracellular miR-145, miR-223 and miR-326 expression signature allow for differential diagnosis of immune-mediated neuroinflammatory diseases. J Neurol Sci 2017; 383:188-198. [PMID: 29246612 DOI: 10.1016/j.jns.2017.11.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/17/2017] [Accepted: 11/14/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND Although misdiagnosis of neuromyelitis optica spectrum disorder (NMOSD) with neuropsychiatric systemic lupus erythematosus (NPSLE) or multiple sclerosis (MS) is not infrequent, reliable biomarkers remains an unmet need. Extracellular microRNAs (miRNAs) represent a worthy avenue to identify biomarkers for differential diagnosis. We aimed to explore the potential role of some selected circulating miRNAs as biomarkers for the differential diagnosis in immune-mediated neuroinflammatory diseases. METHODS A total of 80 subjects were enrolled in the present study, including 37 patients with MS (relapsing-remitting MS [RRMS; n=18] and secondary progressive MS [SPMS; n=19]), 10 patients with NMOSD and 10 patients with NPSLE as well as 23 healthy subjects. Serum expression levels of three selected miRNAs (miR-145, miR-223 and miR-326) were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Whole blood expression levels of cellular immune response-relevant target genes, including signaling mother against decapentaplegic peptide 3 (SMAD3) and specificity protein 1 (SP1), were also measured using qRT-PCR. RESULTS In comparison to healthy subjects, only miR-145 and miR-223 were significantly up-regulated in MS patients, whereas, all the analyzed miRNAs revealed insignificant upregulation in NMOSD patients. All the examined miRNAs were significantly down-regulated in NPSLE patients compared to healthy subjects. miR-145, miR-223 and miR-326 expression profile is a promising diagnostic biomarker for MS and NPSLE, but not for NMOSD. This expression profile is capable of differentiating not only among MS, NMOSD and NPSLE, but also between RRMS and SPMS. CONCLUSION Specific circulating miRNAs expression signature may have the potential to differentially diagnose immune-mediated neuroinflammatory diseases.
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Affiliation(s)
| | - Nirmeen A Kishk
- Neurology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yehia Z Gad
- Medical Molecular Genetics Department, National Research Centre, Cairo, Egypt
| | - Heba Hassan
- Medical Molecular Genetics Department, National Research Centre, Cairo, Egypt
| | - Mohamed A M Ali
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt.
| | - Maha S Zaki
- Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Mohamed R Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mona L Essawi
- Medical Molecular Genetics Department, National Research Centre, Cairo, Egypt
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19
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Fehlmann T, Backes C, Kahraman M, Haas J, Ludwig N, Posch AE, Würstle ML, Hübenthal M, Franke A, Meder B, Meese E, Keller A. Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs. Nucleic Acids Res 2017; 45:8731-8744. [PMID: 28911107 PMCID: PMC5587802 DOI: 10.1093/nar/gkx595] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/04/2017] [Indexed: 01/21/2023] Open
Abstract
The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, our analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, we designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction. MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, our predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | - Jan Haas
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany.,Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | | | | | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany.,Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
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20
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Daniel R, Wu Q, Williams V, Clark G, Guruli G, Zehner Z. A Panel of MicroRNAs as Diagnostic Biomarkers for the Identification of Prostate Cancer. Int J Mol Sci 2017. [PMID: 28621736 PMCID: PMC5486103 DOI: 10.3390/ijms18061281] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is the most common non-cutaneous cancer among men; yet, current diagnostic methods are insufficient, and more reliable diagnostic markers need to be developed. One answer that can bridge this gap may lie in microRNAs. These small RNA molecules impact protein expression at the translational level, regulating important cellular pathways, the dysregulation of which can exert tumorigenic effects contributing to cancer. In this study, high throughput sequencing of small RNAs extracted from blood from 28 prostate cancer patients at initial stages of diagnosis and prior to treatment was used to identify microRNAs that could be utilized as diagnostic biomarkers for prostate cancer compared to 12 healthy controls. In addition, a group of four microRNAs (miR-1468-3p, miR-146a-5p, miR-1538 and miR-197-3p) was identified as normalization standards for subsequent qRT-PCR confirmation. qRT-PCR analysis corroborated microRNA sequencing results for the seven top dysregulated microRNAs. The abundance of four microRNAs (miR-127-3p, miR-204-5p, miR-329-3p and miR-487b-3p) was upregulated in blood, whereas the levels of three microRNAs (miR-32-5p, miR-20a-5p and miR-454-3p) were downregulated. Data analysis of the receiver operating curves for these selected microRNAs exhibited a better correlation with prostate cancer than PSA (prostate-specific antigen), the current gold standard for prostate cancer detection. In summary, a panel of seven microRNAs is proposed, many of which have prostate-specific targets, which may represent a significant improvement over current testing methods.
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Affiliation(s)
- Rhonda Daniel
- Department of Biochemistry and Molecular Biology, VCU Medical Center and the Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298-0614, USA.
| | - Qianni Wu
- Department of Biochemistry and Molecular Biology, VCU Medical Center and the Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298-0614, USA.
| | - Vernell Williams
- Molecular Diagnostic Laboratory, Department of Pathology, VCU Health System, Virginia Commonwealth University, Richmond, VA 23298-0248, USA.
| | - Gene Clark
- Department of Biochemistry and Molecular Biology, VCU Medical Center and the Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298-0614, USA.
| | - Georgi Guruli
- Division of Urology, VCU Medical Center and the Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298-0037, USA.
| | - Zendra Zehner
- Department of Biochemistry and Molecular Biology, VCU Medical Center and the Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298-0614, USA.
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21
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Chen J, Zhu J, Wang Z, Yao X, Wu X, Liu F, Zheng W, Li Z, Lin A. MicroRNAs Correlate with Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder in a Chinese Population. Med Sci Monit 2017; 23:2565-2583. [PMID: 28550707 PMCID: PMC5458669 DOI: 10.12659/msm.904642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Recent studies identified a set of differentially expressed miRNAs in whole blood that may discriminate neuromyelitis optica spectrum disorders (NMOSD) from relapsing-remitting multiple sclerosis (RRMS). This study invalidated 9 known miRNAs in Chinese patients. Material/Methods The levels of miRNAs in whole blood were assayed in healthy controls (n=20) and patients with NMOSD (n=45), RRMS (n=17) by quantitative real-time polymerase chain reaction (qRT-PCR), and pairwise-compared between groups. They were further analyzed for association with clinical features and MRI findings of the diseases. Results Compared with healthy controls, miR-22b-5p, miR-30b-5p and miR-126-5p were down-regulated in NMOSD, in contrast, both miR-101-5p and miR-126-5p were up-regulated in RRMS. Moreover, the levels of miR-101-5p, miR-126-5p and miR-660-5p, were significantly higher in RRMS than in NMOSD (P=0.04, 0.01 and 0.02, respectively). The level of miR-576-5p was significantly higher in patients underwent relapse for ≤3 times than those for ≥4 times. In addition, its level was significantly higher in patients suffered from a severe visual impairment (visual sight ≤0.1). Moreover, the levels of each of the 9 miRNAs were lower in NMOSD patients with intracranial lesions (NMOSD-IC) than those without (NMOSD-non-IC). Despite correlations of miRNAs with these disease subtypes, all AUCs of ROC generated to discriminate patients and controls, as well as intracranial lesions, were <0.8. Conclusions Certain miRNAs are associated with RRMS and NMOSD. They are also related to the clinical features, especially intracranial lesions of NMOSD. However, none of the miRNAs alone or in combination was powerful to ensure the diagnosis and differentiation of the 2 disease subtypes.
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Affiliation(s)
- Jianglong Chen
- Department of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China (mainland).,Department of Neurology, Jinjiang Hospital of traditional Chinese Medicine, Jinjiang, Fujian, China (mainland)
| | - Jiting Zhu
- Department of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Zeng Wang
- Department of Neurology, The Third Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Xiaoping Yao
- Department of Neurology, Jinjiang Hospital of traditional Chinese Medicine, Jinjiang, Fujian, China (mainland)
| | - Xuan Wu
- Department of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Fang Liu
- Department of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Weidong Zheng
- Department of Ophthalmology, Jinjiang Hospital of Traditional Chinese Medicine, Fuzhou, Fujian, China (mainland)
| | - Zhiwen Li
- Department of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Aiyu Lin
- Department of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China (mainland)
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22
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Alles J, Ludwig N, Rheinheimer S, Leidinger P, Grässer FA, Keller A, Meese E. MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins. Oncotarget 2017; 8:56417-56427. [PMID: 28915601 PMCID: PMC5593572 DOI: 10.18632/oncotarget.17662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 12/12/2022] Open
Abstract
Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3′UTR of either SOS1 or SOS2. Each of the 3′UTRs of SOS1 and SOS2 contained two binding sites for miR-148a both of which were necessary for the decreased luciferase activity. MiR-148a overexpression in HEK-293T lead to significantly reduced levels of both endogenous SOS1 and SOS2 proteins. Likewise, reduced levels of SOS proteins were found in two B cell lines that were transfected with miR-148a. The level of ERK1/2 phosphorylation as one of the most relevant downstream members of the Ras/ERK signaling pathway was also reduced in cells with miR-148a overexpression. The data show that miR-148a impairs the Ras/ERK signaling pathway via SOS1 and SOS2 proteins in B cells.
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Affiliation(s)
- Julia Alles
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Petra Leidinger
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
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23
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Serum Compounds of Energy Metabolism Impairment Are Related to Disability, Disease Course and Neuroimaging in Multiple Sclerosis. Mol Neurobiol 2016; 54:7520-7533. [DOI: 10.1007/s12035-016-0257-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/24/2016] [Indexed: 12/15/2022]
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24
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Sanders KA, Benton MC, Lea RA, Maltby VE, Agland S, Griffin N, Scott RJ, Tajouri L, Lechner-Scott J. Next-generation sequencing reveals broad down-regulation of microRNAs in secondary progressive multiple sclerosis CD4+ T cells. Clin Epigenetics 2016; 8:87. [PMID: 27570566 PMCID: PMC5002332 DOI: 10.1186/s13148-016-0253-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/09/2016] [Indexed: 01/06/2023] Open
Abstract
Background Immunoactivation is less evident in secondary progressive MS (SPMS) compared to relapsing-remitting disease. MicroRNA (miRNA) expression is integral to the regulation of gene expression; determining their impact on immune-related cell functions, especially CD4+ T cells, during disease progression will advance our understanding of MS pathophysiology. This study aimed to compare miRNA profiles of CD4+ T cells from SPMS patients to healthy controls (HC) using whole miRNA transcriptome next-generation sequencing (NGS). Total RNA was extracted from CD4+ T cells and miRNA expression patterns analyzed using Illumina-based small-RNA NGS in 12 SPMS and 12 HC samples. Results were validated in a further cohort of 12 SPMS and 10 HC by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Results The ten most dysregulated miRNAs identified by NGS were selected for qPCR confirmation; five (miR-21-5p, miR-26b-5p, miR-29b-3p, miR-142-3p, and miR-155-5p) were confirmed to be down-regulated in SPMS (p < 0.05). SOCS6 is targeted by eight of these ten miRNAs. Consistent with this, SOCS6 expression is up-regulated in SPMS CD4+ T cells (p < 0.05). This is of particular interest as SOCS6 has previously been shown to act as a negative regulator of T cell activation. Conclusions Ninety-seven percent of miRNA candidates identified by NGS were down-regulated in SPMS. The down-regulation of miRNAs and increased expression of SOCS6 in SPMS CD4+ T cells may contribute to reduced immune system activity in progressive MS. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0253-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine A Sanders
- Faculty of Health Sciences and Medicine, Bond University, Robina, Queensland 4226 Australia ; Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales 2305 Australia ; School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales 2308 Australia
| | - Miles C Benton
- Institute of Health and Biomedical Innovation, Genomics Research Centre, Brisbane, Queensland 4059 Australia
| | - Rod A Lea
- Institute of Health and Biomedical Innovation, Genomics Research Centre, Brisbane, Queensland 4059 Australia ; Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales 2305 Australia
| | - Vicki E Maltby
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales 2305 Australia ; School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales 2308 Australia
| | - Susan Agland
- Department of Neurology, Division of Medicine, John Hunter Hospital, Locked Bag 1, Hunter Region Mail Centre, Newcastle, NSW 2310 Australia
| | - Nathan Griffin
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales 2305 Australia ; School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales 2308 Australia
| | - Rodney J Scott
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales 2305 Australia ; School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales 2308 Australia ; Division of Molecular Genetics, Pathology North, Newcastle, New South Wales 2305 Australia
| | - Lotti Tajouri
- Faculty of Health Sciences and Medicine, Bond University, Robina, Queensland 4226 Australia
| | - Jeannette Lechner-Scott
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, New South Wales 2305 Australia ; Department of Neurology, Division of Medicine, John Hunter Hospital, Locked Bag 1, Hunter Region Mail Centre, Newcastle, NSW 2310 Australia ; School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales 2308 Australia
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25
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Vaknin-Dembinsky A, Charbit H, Brill L, Abramsky O, Gur-Wahnon D, Ben-Dov IZ, Lavon I. Circulating microRNAs as biomarkers for rituximab therapy, in neuromyelitis optica (NMO). J Neuroinflammation 2016; 13:179. [PMID: 27393339 PMCID: PMC4939003 DOI: 10.1186/s12974-016-0648-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/29/2016] [Indexed: 12/23/2022] Open
Abstract
Background Neuromyelitis optica (NMO) is a chronic autoimmune disease of the central nervous system (CNS). The main immunological feature of the disease is the presence of autoantibodies to Aquaporin 4 (AQP4+), identified in about 82 % of cases. Currently, there are no reliable biomarkers for monitoring treatment response in patients with NMO. In an effort to identify biomarkers, we analyzed microRNAs (miRNAs) in the blood of rituximab-treated NMO patients before and after therapy. Methods Total RNA extracted from whole blood of nine rituximab-responsive NMO patients before and 6 months following treatment was subjected to small RNAseq analysis. The study included an additional group of seven untreated AQP4+ seropositive NMO patients and 15 healthy controls (HCs). Results Fourteen miRNAs were up regulated and 32 were downregulated significantly in the blood of NMO patients following effective therapy with rituximab (all p < 0.05). Furthermore, we show that expression of 17 miRNAs was significantly higher and of 25 miRNAs was significantly lower in untreated NMO patients compared with HCs (all p < 0.05). Following rituximab treatment, the expression levels of 10 of the 17 miRNAs that show increased expression in NMO reverted to the levels seen in HCs. Six of these “normalized” miRNAs are known as brain-specific/enriched miRNAs. Conclusions Specific miRNA signatures in whole blood of patients with NMO might serve as biomarkers for therapy response. Furthermore, monitoring the levels of brain-specific/enriched miRNAs in the blood might reflect the degree of disease activity in the CNS of inflammatory demyelinating disorders. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0648-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adi Vaknin-Dembinsky
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel.
| | - Hanna Charbit
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Livnat Brill
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Oded Abramsky
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Devorah Gur-Wahnon
- Nephrology and Hypertension Services, Internal Medicine Wing, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Iddo Z Ben-Dov
- Nephrology and Hypertension Services, Internal Medicine Wing, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
| | - Iris Lavon
- Department of Neurology, Multiple Sclerosis Center and Laboratory of Neuroimmunology, and the Agnes-Ginges Center for Neurogenetics, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel.,Department of Neurology, the Agnes-Ginges Center for Neurogenetics and Leslie and Michel Gaffin Center for Neuro-Oncology, Hadassah Hebrew University Medical Center, Ein-Karem, Jerusalem, 91120, Israel
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26
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Specific miRNA Disease Biomarkers in Blood, Serum and Plasma: Challenges and Prospects. Mol Diagn Ther 2016; 20:509-518. [DOI: 10.1007/s40291-016-0221-4] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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28
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Backes C, Sedaghat-Hamedani F, Frese K, Hart M, Ludwig N, Meder B, Meese E, Keller A. Bias in High-Throughput Analysis of miRNAs and Implications for Biomarker Studies. Anal Chem 2016; 88:2088-95. [PMID: 26760198 DOI: 10.1021/acs.analchem.5b03376] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A certain degree of bias in high-throughput molecular technologies including microarrays and next-generation sequencing (NGS) is known. To quantify the actual impact of the biomarker discovery platform on miRNA profiles, we first performed a meta-analysis: raw data of 1 539 microarrays and 705 NGS blood-borne miRNomes were statistically evaluated, suggesting a substantial influence of the technology on biomarker profiles. We observed highly significant dependency of the miRNA nucleotide composition on the expression level. Higher expression in NGS was discovered for uracil-rich miRNAs (p = 7 × 10(-37)), while high expression in microarrays was found predominantly for guanine-rich miRNAs (p = 3 × 10(-33)). To verify the findings, 10 identical replicates of one individual were measured using NGS and microarrays (2 525 miRNAs from miRBase version 21). Overall, we calculated a correlation coefficient of 0.414 for both technologies. Detailed analysis however revealed that the correlation was observed only for miRNAs in the early miRBase versions (<8). The majority of miRNAs (2 013 from miRBase version 8 onward) was not correlated between microarray and NGS. Specifically, we observed 67 miRNAs with a median read count above 10 in NGS, while they were not detected in any of the 10 replicated array experiments. In contrast, 234 miRNAs were discovered in all 10 replicated array measurements but were not found in any of the NGS experiments of the same individual. While the first group had average guanine content of 22%, the latter group consisted of 41% of this nucleotide. Selected concordant and discordant miRNAs were tested in quantitative real-time-polymerase chain reaction (RT-qPCR) experiments again of the same individual, providing further evidence for the substantial bias depending on the base composition. As a consequence, biomarkers that have been discovered by specific high-throughout technologies have to be carefully considered. Especially for validation of the platform, the selection of reasonable candidates is essential.
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Affiliation(s)
- Christina Backes
- Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbrücken, Germany
| | - Farbod Sedaghat-Hamedani
- Department of Internal Medicine III, University Hospital Heidelberg , 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK) , 69120 Heidelberg, Germany.,Klaus Tschira Institute for Integrative Computational Cardiology , D-69118 Heidelberg, Germany
| | - Karen Frese
- Department of Internal Medicine III, University Hospital Heidelberg , 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK) , 69120 Heidelberg, Germany.,Klaus Tschira Institute for Integrative Computational Cardiology , D-69118 Heidelberg, Germany
| | - Martin Hart
- Department of Human Genetics, Saarland University , 66421, Homburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University , 66421, Homburg, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University Hospital Heidelberg , 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK) , 69120 Heidelberg, Germany.,Klaus Tschira Institute for Integrative Computational Cardiology , D-69118 Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University , 66421, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University , 66123 Saarbrücken, Germany
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