Two common disease-associated TYK2 variants impact exon splicing and TYK2 dosage

Abstract

TYK2 belongs to the JAK protein tyrosine kinase family and mediates signaling of numerous antiviral and immunoregulatory cytokines (type I and type III IFNs, IL-10, IL-12, IL-22, IL-23) in immune and non-immune cells. After many years of genetic association studies, TYK2 is recognized as a susceptibility gene for some inflammatory and autoimmune diseases (AID). Seven TYK2 variants have been associated with AIDs in Europeans, and establishing their causality remains challenging. Previous work showed that a protective variant (P1104A) is hypomorphic and also a risk allele for mycobacterial infection. Here, we have studied two AID-associated common TYK2 variants: rs12720270 located in intron 7 and rs2304256, a non-synonymous variant in exon 8 that causes a valine to phenylalanine substitution (c.1084 G > T, Val362Phe). We found that this amino acid substitution does not alter TYK2 expression, catalytic activity or ability to relay signaling in EBV-B cell lines or in reconstituted TYK2-null cells. Based on in silico predictions that these variants may impact splicing of exon 8, we: i) analyzed TYK2 transcripts in genotyped EBV-B cells and in CRISPR/Cas9edited cells, ii) measured splicing using minigene assays, and iii) performed eQTL (expression quantitative trait locus) analysis of TYK2 transcripts in primary monocytes and whole blood cells. Our results reveal that the two variants promote the inclusion of exon 8, which, we demonstrate, is essential for TYK2 binding to cognate receptors. In addition and in line with GTEx (Genetic Tissue Expression) data, our eQTL results show that rs2304256 mildly enhances TYK2 expression in whole blood. In all, these findings suggest that these TYK2 variants are not neutral but instead have a potential impact in AID.

Association of TYK2 polymorphisms with autoimmune diseases: A comprehensive and updated systematic review with meta-analysis

“…The A allele of the rs2304256 causes a substitution of valine to phenylalanine at position 362 in the JAK-homology 4 (JH4) region, which is a crucial domain for interaction of TYK2 with IFNAR1 and its function, maintaining the expression of IFNAR1 on cell membranes ( Tao et al, 2011 ; Marroqui et al, 2015 ). Li et al (2020 ) showed the rs2304256 A allele affects the TYK2 pre-mRNA processing since it destroys a putative exonic splicing enhancer; thus, promoting the inclusion of exon 8 in the mRNA, which is essential for TYK2 binding to cytokine receptors. Marroqui et al .…”

“…In contrast, 3 previous meta-analyses ( Tao et al., 2011 ; Lee and Bae, 2016 ; Yin et al, 2018 ), including only 3 to 5 studies with SLE patients, were not able to show any association between this SNP and SLE. This SNP is located in intron 7 of TYK2 gene, most specifically 36 nt upstream of the intron 7/exon 8 boundary ( Li et al, 2020 ). The rs12720270 SNP is in strong LD with the functional rs2304256 and the rs280519 SNPs ( Contreras-Cubas et al, 2019 ; Li et al , 2020 ).…”

“…This SNP is located in intron 7 of TYK2 gene, most specifically 36 nt upstream of the intron 7/exon 8 boundary ( Li et al, 2020 ). The rs12720270 SNP is in strong LD with the functional rs2304256 and the rs280519 SNPs ( Contreras-Cubas et al, 2019 ; Li et al , 2020 ). However, it also seems to be functional since in silico analysis and cell line experiments suggested the A allele breaks a splicing-branch point in the intron, promoting the inclusion of exon 8 in the mature TYK2 mRNA; thus, influencing TYK2 activity ( Li et al , 2020 ).…”

Genetic Susceptibility of the Host in Virus-Induced Diabetes

“…rs2304256 (V362F, C>A) is a missense variant located in exon 8 that is part of the FERM domain. It was suggested that this SNP reduces interaction between TYK2 and interferon α/β receptor 1 (IFNAR1) [59,60]. The TYK2 gene expression levels increased modestly in whole blood and adrenal gland of those carrying the A allele [60].…”

“…It was suggested that this SNP reduces interaction between TYK2 and interferon α/β receptor 1 (IFNAR1) [59,60]. The TYK2 gene expression levels increased modestly in whole blood and adrenal gland of those carrying the A allele [60]. There is evidence that the A allele of rs2304256 is a protective variant against T1D in those of European ancestry [61].…”