An Investigation of the Causal Link Between Palmoylation Genes and Epilepsy Utilising Multi-omics Mendelian Randomisation Analysis and Validation Through Single-Cell Evidence

Abstract

This work sought to examine the causal link between palmoyl-protein-modifying genes (ZDHHC family) and epilepsy by Mendelian randomisation (MR), utilising multi-level genomic data. A two-sample MR analysis was performed utilising publicly accessible blood and brain tissue expression quantitative trait locus (eQTL) data as exposure variables and epilepsy genome-wide association study (GWAS) data from the FinnGen as the outcome measure. The major analysis method utilised was inverse variance weighting (IVW), with robustness validation conducted by weighted median and MR-Egger procedures. Subsequently, summary-data-based MR (SMR) analysis confirmed signal colocalization, supplemented by single-cell transcriptomic data (GSE302285) to investigate target gene expression patterns at a cellular granularity. MR analysis indicated that heightened expression of ZDHHC3 (OR = 0.69, 95% CI: 0.57–0.84, p = 0.0002) and ZDHHC20 (OR = 0.88, 95% CI: 0.82–0.94, p = 0.0002) was significantly linked to a decreased risk of epilepsy, while increased expression of ZDHHC8 and ZDHHC18 was associated with an elevated risk. SMR analysis further corroborated the protective roles of ZDHHC3 and ZDHHC20. Layered MR analysis showed that the results are more significant in focal epilepsy. An eQTL study specific to brain cells revealed cell-type specificity in these correlations, with ZDHHC20 demonstrating the most significant protective impact in excitatory neurones (OR = 0.89, p = 0.0273). Single-cell transcriptomics demonstrated that ZDHHC20 was significantly expressed in astrocytes and neurones in the brain tissue of epilepsy patients, while ZDHHC3 was primarily concentrated in neurones. This work genetically confirms that certain palmitoylation genes, notably ZDHHC3 and ZDHHC20, may have causative protective effects against the risk of focal epilepsy, highlighting cell-type-specific processes. This establishes innovative theoretical frameworks for exploring the pathophysiology of epilepsy and formulating targeted treatments.