Genetic Variation Underlying CSF Natural Killer T-Cell Frequency in Inflammatory CNS Diseases: A Genome-Wide Association Study

Natural killer T (NKT) cells bridge innate and adaptive immunity and are implicated in immune regulation in autoimmune diseases. In multiple sclerosis (MS), reduced CSF frequencies of NKT cells have been reported, but their role in disease pathogenesis remains unclear. Here, we investigated the genetic architecture underlying CSF NKT cell frequency variability in individuals with MS and other CNS diseases.

We conducted a genome-wide association study (GWAS) of CSF NKT cell frequencies in 456 individuals with MS, with replication in an independent cohort of 90 individuals with MS or other inflammatory CNS diseases. Functional follow-up assessed effects of the lead variant on integrin subunit beta 5 (ITGB5) gene expression in CSF CD4⁺ T cells, and Mendelian randomization (MR) analysis was used to evaluate causality. In addition, we examined associations of the lead variant and CSF NKT cell frequencies with MS disease severity as measured by the Age-Related Multiple Sclerosis Severity Score (ARMSS).

We identified and replicated a novel genome-wide significant association of rs6783734*C (joint p = 4.57 x 10^-9), an intronic variant in ITGB5 on chromosome 3, with increased CSF NKT cell frequencies. This association was absent in a control cohort of 368 individuals with other neurologic diseases (p = 1.4 × 10^-1), suggesting a context-specific effect. rs6783734 was associated with reduced ITGB5 gene expression in CSF CD4⁺ T cells, and MR supported a causal relationship between ITGB5 expression and CSF NKT cell frequencies. Although rs6783734 was not associated with disease severity, higher CSF NKT cell frequencies were associated with greater ARMSS at the ≥1-year follow-up (p = 9.33 × 10^-3).

Our findings implicate ITGB5 as a potentially context-dependent modulator of immune cell dynamics in inflammatory CNS disease, linking genetic variation to NKT cell frequencies within the CNS compartment. Given the central role of integrins in immune cell trafficking and the therapeutic success of integrin-targeting agents in MS, these results highlight integrin-mediated pathways as determinants of CNS immune responses. Although the observed association of higher CSF NKT cell frequencies with greater disease severity suggests that integrating genetic factors and immune phenotypes may ultimately prove useful for patient stratification, this finding requires confirmation in larger studies.