Bioinformatics Analysis of Ataxin-3’s Transcriptional Regulation in Nervous System Inflammation, Metabolism, and Angiogenesis

Utilizing principles of bioinformatics, this study endeavors to elucidate the role of Ataxin-3 in gene expression regulation and propose novel research avenues to unravel the pathophysiological mechanisms of Spinocerebellar Ataxia Type 3 (SCA3), attributed to the functional impairment and deficiency of Ataxin-3. This study accessed the Gene Expression Omnibus (GEO) database to obtain microarray data (GSE117028) from both normal and <i>Atxn3</i> knockout Mouse embryonic fibroblasts (MEFs), aiming to identify differentially expressed genes (DEGs). Tissue expression specificity was analyzed using the BioGPS database. The DAVID 2021 analysis platform is utilized for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. A protein-protein interaction (PPI) network for DEGs was constructed with the STRING database, and PPI data visualization was achieved through the Cytoscape software, with the hub-DEGs identified using the CytoHubba plugin. Enrichment analysis of key differentially expressed proteins and transcriptional regulatory network construction were performed using DAVID 2021 and Cistrome DB databases. Our analysis identified 164 DEGs, which showed pronounced expression specificity in the nervous and immune systems. GO analysis indicated that these DEGs are extensively involved in processes such as multicellular organism development, cell adhesion, and angiogenesis. KEGG analysis highlighted the involvement of DEGs in metabolic processes, immune pathways mediated by cytokines and chemokines, and the IL-17 signaling pathway. PPI network analysis identified six hub proteins: Cxcl1, Cxcl5, Saa3, Eng, Thy1, and Lpl, playing significant roles in the immune-inflammatory pathway. Additionally, transcription factors (TFs) CEBPB, STAT5A, NR3C1, SPI1, and EP300 were found to exert regulatory functions within these pathways. The impairment of Ataxin-3's regulatory function across various signaling pathways is hypothesized to contribute to the pathogenesis of SCA3. These findings suggest that restoring Ataxin-3 function could represent a potential therapeutic strategy for SCA3.