Variants within the CBLB gene are associated with multiple sclerosis

Multiple sclerosis (MS) is a multi-factorial neuroinflammatory and autoimmune
disorder. A primary cause of disability in young adults, it results from
interactions between unknown environmental factors and alleles of many
susceptibility loci across the genome. Recent investigations of the genetics
of MS have resulted in important advances, driven largely by completion of
the first genome-wide association scans (GWAS). To detect additional loci,
we performed a GWAS in 882 Sardinian Multiple Sclerosis (MS) cases and
872 controls genotyped with the Affymetrix 6.0 chip, using 575,678 SNPs
that passed quality checks. We then successfully imputed 6,031,588 SNPs
using haplotypes available from HapMap II, HapMap III and 1000 Genomes
projects, and tested for association ~6.6 million variants. The strongest
signal (OR=2.05, p=1.45x10-20) was observed at a SNP tag for the HLADRB1*
0301-DQB1*0201 allele. We then selected 9 SNPs outside of the
HLA locus for validation and follow-up, based on their level of significance,
proximity to functional candidate genes, and quality of imputation. Of those,
SNP rs9657904 on chr3q13 was successfully confirmed in the GWAS samples
and replicated in an independent set of 1,775 MS cases and 2,005
controls (p=9.4x10-6). Notably, this variant is absent from the HapMap II
reference panel, and we were able to fully assess it only after imputation
with HapMap III and 1000 Genomes haplotypes. Combining all available
genotypes, the observed pvalue was 1.6x10-10 (OR=1.40). The most associated
variants at this locus fall in the promoter of a gene, CBLB, which
encodes a negative regulator of adaptive immune responses. In support of
its involvement in MS, mice lacking the ortholog are prone to experimental
autoimmune encephalomyelitis, the animal model of multiple sclerosis. The
strongest associated variant was also replicated in 1,441 cases and 1,465
controls from central-northern Italy with a similar effect size, hence confirming
the role of this marker in increased risk for multiple sclerosis in another
southern European population. Finally, we sequenced by the Sanger method
the coding regions and promoter of the gene in 96 patients, observing novel
variants that are potentially causative, and will now be assessed with focused
biological studies.