A Bioinformatics Approach to Identifying Differentially Expressed Genes in Multiple Sclerosis Subtypes

Multiple sclerosis (MS) is a chronic autoimmune disorder of the central nervous system characterized by the loss of myelin (demyelination), which disrupts nerve signal transmission and can lead to lasting neurological damage. Clinically, MS presents with a range of symptoms such as numbness, muscle weakness, impaired coordination, and visual disturbances, and it manifests in several forms including primary progressive (PPMS), relapsing-remitting (RRMS), and secondary progressive MS (SPMS). In this study, we analyzed gene expression profiles from 16 individuals (including PPMS, RRMS, SPMS patients and healthy controls) to identify genes differentially expressed in each MS subtype. Several genes exhibited subtype-specific dysregulation. Notably, RRMS samples showed strong upregulation of IFNA14 and two long intergenic non-coding RNAs (LINC01994 and LINC01995), along with significant downregulation of LINC01478 and NEUROD1, whereas SPMS samples were marked by reduced expression of PKP4. IFNA14 encodes a type I interferon cytokine involved in lymphocyte activation during immune responses. NEUROD1 is a neurogenic transcription factor that regulates insulin gene expression and contributes to neuronal differentiation and repair. PKP4 (plakophilin-4) is a junctional plaque protein involved in organizing cell–cell junctions and cadherin-mediated adhesion. The differential regulation of these genes highlights potential molecular markers and pathways underlying MS progression, suggesting new targets for further investigation.