Transcriptomic Analysis and Multiple Machine Learning Approaches Identify ZDHHC20 and Its Highly Correlated Gene AK5 as Diagnostic Markers in Multiple System Atrophy

Background Multiple system atrophy (MSA) is a fatal neurodegenerative disorder lacking effective diagnostic tools. While protein palmitoylation is crucial for neuronal function, its specific role in MSA pathogenesis remains unexplored. Methods We integrated bulk and single-nucleus RNA sequencing (snRNA-seq) data from postmortem MSA brain tissues. Eight machine learning algorithms were utilized to screen palmitoylation-related genes. Downstream analyses, including functional enrichment, cellular deconvolution, and pseudotime trajectory inference, were then conducted. Results ZDHHC20 and its highly correlated gene, AK5, were identified as hub genes. Both demonstrated significant downregulation in MSA, particularly within the cerebellar white matter. Functional enrichment analysis linked this expression pattern to mitochondrial dysfunction and impaired energy metabolism. Furthermore, snRNA-seq revealed that ZDHHC20 and AK5 are predominantly expressed in oligodendrocytes and are progressively suppressed during the abnormal terminal differentiation trajectory observed in MSA. Conclusions ZDHHC20 and AK5 represent promising diagnostic biomarkers for MSA. These findings highlight the potential role of palmitoylation in MSA pathogenesis, providing new insights into the diagnosis and treatment of MSA.