A spotter’s guide to SNPtic exons: The common splice variants underlying some SNP–phenotype correlations

Keegan, Niall; Fletcher, Sue

doi:10.1002/mgg3.1840

Cited by 2 publications

(1 citation statement)

References 104 publications

(87 reference statements)

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“…However, they only studied a small study cohort of eight individuals per genotype. In a recently published report, which focused exclusively on the identification of potential cryptic exons based on literature reports and the dbSNP database, a genotype-dependent splicing of TSFM exon 3 was also postulated ( 90 ). Moreover, an sQTL that links the skipping of TSFM exon 3 and 4 with SNP rs2014886 is listed for EBV-transformed lymphocytes in the GTEx portal ( 34 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic risk variants for multiple sclerosis are linked to differences in alternative pre-mRNA splicing

Putscher

Hecker²,

Fitzner³

et al. 2022

Front. Immunol.

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BackgroundMultiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system to which a genetic predisposition contributes. Over 200 genetic regions have been associated with increased disease risk, but the disease-causing variants and their functional impact at the molecular level are mostly poorly defined. We hypothesized that single-nucleotide polymorphisms (SNPs) have an impact on pre-mRNA splicing in MS.MethodsOur study focused on 10 bioinformatically prioritized SNP–gene pairs, in which the SNP has a high potential to alter alternative splicing events (ASEs). We tested for differential gene expression and differential alternative splicing in B cells from MS patients and healthy controls. We further examined the impact of the SNP genotypes on ASEs and on splice isoform expression levels. Novel genotype-dependent effects on splicing were verified with splicing reporter minigene assays.ResultsWe were able to confirm previously described findings regarding the relation of MS-associated SNPs with the ASEs of the pre-mRNAs from GSDMB and SP140. We also observed an increased IL7R exon 6 skipping when comparing relapsing and progressive MS patients to healthy subjects. Moreover, we found evidence that the MS risk alleles of the SNPs rs3851808 (EFCAB13), rs1131123 (HLA-C), rs10783847 (TSFM), and rs2014886 (TSFM) may contribute to a differential splicing pattern. Of particular interest is the genotype-dependent exon skipping of TSFM due to the SNP rs2014886. The minor allele T creates a donor splice site, resulting in the expression of the exon 3 and 4 of a short TSFM transcript isoform, whereas in the presence of the MS risk allele C, this donor site is absent, and thus the short transcript isoform is not expressed.ConclusionIn summary, we found that genetic variants from MS risk loci affect pre-mRNA splicing. Our findings substantiate the role of ASEs with respect to the genetics of MS. Further studies on how disease-causing genetic variants may modify the interactions between splicing regulatory sequence elements and RNA-binding proteins can help to deepen our understanding of the genetic susceptibility to MS.

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