Unveiling alterative splice diversity from human oligodendrocyte proteome data

Publication date: Available online 21 May 2016
Source:Journal of Proteomics
Author(s): Raphael Tavares, Gabriel Wajnberg, Nicole de Miranda Scherer, Bianca Alves Pauletti, Juliana S. Cassoli, Carlos Gil Ferreira, Adriana Franco Paes Leme, Patricia Savio de Araujo-Souza, Daniel Martins-de-Souza, Fabio Passetti
Oligodendrocytes produce and maintain the myelin sheath of axons in the central nervous system. Because misassembled myelin sheaths have been associated with brain disorders such as multiple sclerosis and schizophrenia, recent advances have been made towards the description of the oligodendrocyte proteome. The identification of splice variants represented in the proteome is as important as determining the level of oligodendrocyte-associated proteins. Here, we used an oligodendrocyte proteome dataset deposited in ProteomeXchange to search against a customized protein sequence file containing computationally predicted splice variants. Our approach resulted in the identification of 39 splice variants, including one variant from the GTPase KRAS gene and another from the human glutaminase gene family. We also detected the mRNA expression of five selected splice variants and demonstrated that a fraction of these have canonical proteins that may participate in direct protein-protein interactions. In conclusion, we believe our findings contribute to the molecular characterization of oligodendrocytes and may encourage other research groups working with central nervous system disorders to investigate the biological significance of these splice variants. The splice variants identified in this study may encode proteins that could be targeted in novel treatment strategies and diagnostic methods.SignificanceSeveral disorders of the central nervous system (CNS) are associated with misassembled myelin sheaths, which are produced and maintained by oligodendrocytes (OL). Recently, the OL proteome has been explored to identify key proteins and molecular functions associated with CNS disorders. We developed an innovative approach to select, with a higher level of confidence, a relevant list of splice variants from a proteome dataset and detected the mRNA expression of five selected variants: EEF1D, KRAS, MFF, SDR39U1, and SUGT1. We also described splice variants extracted from OL proteome data. Among the splice variants identified, some are from genes previously linked to CNS and related disorders. Our findings may contribute to oligodendrocyte characterization and encourage other research groups to investigate the biological role of splice variants and to improve current treatments and diagnostic methods for CNS disorders.Hightlights• Oligodendrocyte splice variants were investigated using a combined approach of proteogenomics and Mass Spectrometry• A customized protein repository identified 39 alternative splicing variants in the human oligodendrocyte proteome.• Five of those splice variants were confirmed at the transcriptome level in the MO3.13 cell line• Protein-protein network interactions were investigated



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