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Identification of Novel Key Genes and Pathways in Multiple Sclerosis Based on Weighted Gene Coexpression Network Analysis and Long Noncoding RNA-Associated Competing Endogenous RNA Network. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9328160. [PMID: 35281467 PMCID: PMC8915924 DOI: 10.1155/2022/9328160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/16/2022] [Indexed: 12/15/2022]
Abstract
Objective Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by chronic inflammation and demyelination. This study is aimed at identifying crucial genes and molecular pathways involved in MS pathogenesis. Methods Raw data in GSE52139 were collected from the Gene Expression Omnibus. The top 50% expression variants were subjected to weighted gene coexpression network analysis (WGCNA), and the key module associated with MS occurrence was identified. A long noncoding RNA- (lncRNA-) associated competing endogenous RNA (ceRNA) network was constructed in the key module. The hub gene candidates were subsequently verified in an individual database. Results Of the 18 modules obtained, the cyan module was designated as the key module. The established ceRNA network was composed of seven lncRNAs, 45 mRNAs, and 21 microRNAs (miRNAs), and the FAM13A-AS1 was the lncRNA with the highest centrality. Functional assessments indicated that the genes in the cyan module primarily gathered in ribosome-related functional terms. Interestingly, the targeted mRNAs of the ceRNA network enriched in diverse categories. Moreover, highly expressed CYBRD1, GNG12, and SMAD1, which were identified as hub genes, may be associated with “valine leucine and isoleucine degradation,” “base excision repair,” and “fatty acid metabolism,” respectively, according to the results of single gene-based genomes and gene set enrichment analysis (GSEA). Conclusions Combined with the WGCNA and ceRNA network, our findings provide novel insights into the pathogenesis of MS. The hub genes discovered herein might also serve as novel biomarkers that correlate with the development and management of MS.
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Sol N, Leurs CE, Veld SGI', Strijbis EM, Vancura A, Schweiger MW, Teunissen CE, Mateen FJ, Tannous BA, Best MG, Würdinger T, Killestein J. Blood platelet RNA enables the detection of multiple sclerosis. Mult Scler J Exp Transl Clin 2020; 6:2055217320946784. [PMID: 32843989 PMCID: PMC7418262 DOI: 10.1177/2055217320946784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/05/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Background In multiple sclerosis (MS), clinical assessment, MRI and cerebrospinal fluid are important in the diagnostic process. However, no blood biomarker has been confirmed as a useful tool in the diagnostic work-up. Objectives Blood platelets contain a rich spliced mRNA repertoire that can alter during megakaryocyte development but also during platelet formation and platelet circulation. In this proof of concept study, we evaluate the diagnostic potential of spliced blood platelet RNA for the detection of MS. Methods We isolated and sequenced platelet RNA of blood samples obtained from 57 MS patients and 66 age- and gender-matched healthy controls (HCs). 60% was used to develop a particle swarm-optimized (PSO) support vector machine classification algorithm. The remaining 40% served as an independent validation series. Results In total, 1249 RNAs with differential spliced junction expression levels were identified between platelets of MS patients as compared to HCs, including EPSTI1, IFI6, and RPS6KA3, in line with reported inflammatory signatures in the blood of MS patients. The RNAs were subsequently used as input for a MS classifier, capable of detecting MS with 80% accuracy in the independent validation series. Conclusions Spliced platelet RNA may enable the blood-based diagnosis of MS, warranting large-scale validation.
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Affiliation(s)
- Nik Sol
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Cyra E Leurs
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sjors Gjg In 't Veld
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Eva M Strijbis
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Adrienne Vancura
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Markus W Schweiger
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Charlotte E Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Neuroscience Campus Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Farrah J Mateen
- Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Bakhos A Tannous
- Department of Neurology, Massachusetts General Hospital Harvard Medical School, Boston, MA, USA
| | - Myron G Best
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Pathology, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Thomas Würdinger
- Brain Tumor Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosurgery, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
| | - Joep Killestein
- Department of Neurology, Neuroscience Amsterdam, VUmc MS Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
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D'Amico E, Zanghì A, Gastaldi M, Patti F, Zappia M, Franciotta D. Placing CD20-targeted B cell depletion in multiple sclerosis therapeutic scenario: Present and future perspectives. Autoimmun Rev 2019; 18:665-672. [PMID: 31059839 DOI: 10.1016/j.autrev.2019.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 01/18/2019] [Indexed: 12/26/2022]
Abstract
Multiple sclerosis (MS) is an acquired demyelinating disease of the central nervous system (CNS) that traditionally has been considered to be mediated primarily by T cells. Increasing evidence, however, suggests the fundamental role of B cells in the pathogenesis and development of the disease. Recently, anti-CD20 B cell-based therapies have demonstrated impressive and somewhat surprising results in MS, showing profound anti-inflammatory effects with a favorable risk-benefit ratio. Moreover, for the first time in the MS therapeutic scenario, the anti-CD20 monoclonal antibody ocrelizumab has been granted for the treatment of the primary progressive form of the disease. In this review, we provide a brief overview about anti-CD20 B cell-based therapies in MS, in the perspective of their influence on the future management of the disease, and of their possible positioning in a new wider therapeutic scenario.
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Affiliation(s)
| | - Aurora Zanghì
- Department G.F.Ingrassia, University of Catania, Italy
| | - Matteo Gastaldi
- Neuroimmunology Laboratory, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Mario Zappia
- Department G.F.Ingrassia, University of Catania, Italy
| | - Diego Franciotta
- Neuroimmunology Laboratory, IRCCS Mondino Foundation, Pavia, Italy
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Efficacy and safety of rituximab for relapsing-remitting multiple sclerosis: A systematic review and meta-analysis. Autoimmun Rev 2019; 18:542-548. [PMID: 30844555 DOI: 10.1016/j.autrev.2019.03.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 12/29/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To evaluate the efficacy and safety of rituximab for relapsing-remitting multiple sclerosis. RESULTS Fifteen studies that collectively included 946 patients were selected for the meta-analysis. Rituximab therapy was associated with the mean annualized relapse rates decreasing by 0.80 (95% confidence interval, 0.45-1.15) and the mean Expanded Disability Status Scale score decreasing by 0.46 (95% confidence interval, 0.05-0.87). The likelihood of patients experiencing a relapse after starting rituximab therapy was only 15% (95% confidence interval, 7%-26%). Although mild-to-moderate adverse events occurred in 29.6% of the patients, there were no severe adverse events. CONCLUSIONS AND RELEVANCE This systematic review and meta-analysis shows that rituximab is associated with reduced annualized relapse rates and disability levels in patients with relapsing-remitting multiple sclerosis. It is also well tolerated and is not associated with serious adverse events.
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