Multiple sclerosis (MS) is a complex neurodegenerative and autoimmune disease with a significant genetic component. A family history of MS is reported in 15%-20% of people with MS and while rare, multi-case families do occur. Such families are an opportunity to discover rare variants, segregating with disease, that may contribute to MS.
Using short-read genome sequencing from a single family of 8 siblings, where half had an MS diagnosis, we identified population rare, likely deleterious protein coding variation that segregated with disease. Based on biological plausibility for a role in MS we prioritised two missense variants for functional experiments: GRIK4-Met690Ile and NLRX1-Arg547Trp. Both variants occur on chromosome 11, 1.7Mb apart. Nanopore long-read genome sequencing confirmed that the variants occur on the same haplotype.
GRIK4 encodes a glutamate receptor subunit that is strikingly expressed in central nervous system cell types of relevance to MS, including oligodendrocytes and astrocytes. NLRX1 encodes a protein involved in anti-viral, and type I interferon signalling.
CRISPR-Cas9 edited C57BL/6 mice heterozygous for both variants were followed until 1 year of age. The variants induced a detectable motor dysfunction in vivo. Immunohistological investigation of variant carrier mouse brains identified reactive astrogliosis in the white matter. This suggests that the variants induce intrinsic astrocyte dysfunction. We explored this finding further in spatial transcriptomic experiments of mouse brains from variant carrier and control mice using spatial transcriptomics.
To examine astrocytes in vitro we generated induced pluripotent stem cell (iPSC) lines from two affected family members. iPSCs were differentiated into astrocytes. Transcriptome sequencing of iPSC-derived astrocytes from family members in comparison to unaffected unrelated controls identified dysregulated gene expression profiles.
This study has identified the first rare variants associated with MS with functional evidence in vivo, supporting the likely contribution of rare variants to MS in this family.