Abstract
Introduction: The major histocompatibility complex (MHC) locus carries a significant genetic risk burden for MS, though within the MHC the structurally diverse complement component 4 (C4) alleles remain largely understudied. Objectives/Aims: To investigate C4 genetic structural variations in MS risk and better understand how the MHC region shapes disease susceptibility. Methods: We used an established protocol to impute and analyse C4 alleles based on available genotyping data from two case-control cohorts (N1= 3252 cases and 5725 controls; N2= 8978 cases and 6976 controls), a clinical MS cohort (N3= 2387 cases) and a cohort with immune cell expression data (N4= 33 cases and 33 controls). We also performed gene-level analysis to examine the shared genetic landscape between MS onset (NGWAS= 14802 cases and 26703 controls) and plasma C4 protein (NGWAS= 68716). Results: Our data showed that C4 genetic structural variants were associated with significant changes in the risk of development of MS and the progression of MS. For instance, higher C4AL copy number burden was associated with lower risk of MS onset (fixed effect meta-analysis odds ratio= 0.89, P= 5.65×10-6) and reduced hazard of reaching MS disability milestones such as Expanded Disability Status Scale 3 (hazard ratio= 0.79, P= 9.0x10-15). In downstream gene expression analysis, we found C4 alleles may also modulate C4 expression in diseaserelevant immune cell types such as CD8+ T cells. Further, we identified that candidate genes shared between MS onset risk and plasma C4 protein level were enriched in biological pathways of immune regulation, Epstein-Barr virus infection and other autoimmune diseases such as lupus. Conclusion: These findings support future investigations of the C4 genetic structural variants as potential mechanistic and therapeutic targets in MS pathogenesis and disease progression.