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Article

Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes

by
Elvezia Maria Paraboschi
1,
Giulia Cardamone
1,
Valeria Rimoldi
2,3,
Donato Gemmati
4,
Marta Spreafico
5,
Stefano Duga
2,3,
Giulia Soldà
2,3,* and
Rosanna Asselta
2,3
1
Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, Milan 20133, Italy
2
Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy
3
Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy
4
Center Haemostasis & Thrombosis, Department of Medical Sciences, Corso Giovecca 203, University of Ferrara, Ferrara 44121, Italy
5
Department of Transfusion Medicine and Hematology, Azienda Ospedaliera della Provincia di Lecco, Alessandro Manzoni Hospital, Via dell'Eremo 9/11, Lecco 23900, Italy
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2015, 16(10), 23463-23481; https://doi.org/10.3390/ijms161023463
Submission received: 22 July 2015 / Revised: 8 September 2015 / Accepted: 14 September 2015 / Published: 30 September 2015
(This article belongs to the Special Issue Pre-mRNA Splicing 2015)
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Abstract

Abnormalities in RNA metabolism and alternative splicing (AS) are emerging as important players in complex disease phenotypes. In particular, accumulating evidence suggests the existence of pathogenic links between multiple sclerosis (MS) and altered AS, including functional studies showing that an imbalance in alternatively-spliced isoforms may contribute to disease etiology. Here, we tested whether the altered expression of AS-related genes represents a MS-specific signature. A comprehensive comparative analysis of gene expression profiles of publicly-available microarray datasets (190 MS cases, 182 controls), followed by gene-ontology enrichment analysis, highlighted a significant enrichment for differentially-expressed genes involved in RNA metabolism/AS. In detail, a total of 17 genes were found to be differentially expressed in MS in multiple datasets, with CELF1 being dysregulated in five out of seven studies. We confirmed CELF1 downregulation in MS (p = 0.0015) by real-time RT-PCRs on RNA extracted from blood cells of 30 cases and 30 controls. As a proof of concept, we experimentally verified the unbalance in alternatively-spliced isoforms in MS of the NFAT5 gene, a putative CELF1 target. In conclusion, for the first time we provide evidence of a consistent dysregulation of splicing-related genes in MS and we discuss its possible implications in modulating specific AS events in MS susceptibility genes.
Keywords: alternative splicing; microarray; peripheral blood mononuclear cells; autoimmune neurodegenerative disorder; multiple sclerosis alternative splicing; microarray; peripheral blood mononuclear cells; autoimmune neurodegenerative disorder; multiple sclerosis

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MDPI and ACS Style

Paraboschi, E.M.; Cardamone, G.; Rimoldi, V.; Gemmati, D.; Spreafico, M.; Duga, S.; Soldà, G.; Asselta, R. Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes. Int. J. Mol. Sci. 2015, 16, 23463-23481. https://doi.org/10.3390/ijms161023463

AMA Style

Paraboschi EM, Cardamone G, Rimoldi V, Gemmati D, Spreafico M, Duga S, Soldà G, Asselta R. Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes. International Journal of Molecular Sciences. 2015; 16(10):23463-23481. https://doi.org/10.3390/ijms161023463

Chicago/Turabian Style

Paraboschi, Elvezia Maria, Giulia Cardamone, Valeria Rimoldi, Donato Gemmati, Marta Spreafico, Stefano Duga, Giulia Soldà, and Rosanna Asselta. 2015. "Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes" International Journal of Molecular Sciences 16, no. 10: 23463-23481. https://doi.org/10.3390/ijms161023463

APA Style

Paraboschi, E. M., Cardamone, G., Rimoldi, V., Gemmati, D., Spreafico, M., Duga, S., Soldà, G., & Asselta, R. (2015). Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes. International Journal of Molecular Sciences, 16(10), 23463-23481. https://doi.org/10.3390/ijms161023463

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