The dual effect of the lupus-associated polymorphism rs10516487 on BANK1 gene expression and protein localization

Abstract

Numerous loci have been found genetically associated with complex diseases, but only in a few cases has the functional variant and the molecular mechanism behind it been identified. Recently, the association of the BANK1 gene with systemic lupus erythematosus (SLE) was described. Here, we investigated the role of the associated polymorphisms on gene function and found that SNP rs17266594 located in the branch point consensus sequence has negligible effect on splicing or gene expression. The non-synonymous SNP rs10516487 located in exon 2 influenced splicing efficiency by creating an exonic splicing enhancer site for the SRp40 factor. Further, this same SNP generates protein isoforms with differential and measurable self-association properties. The full-length protein isoform containing the R61 variant forms larger protein scaffold complexes in the cell cytoplasm compared to the protective BANK1-61H variant. We also observed that, contrary to the full-length isoform, the short Δ2 isoform of BANK1 displays a homogeneous cytoplasmic distribution, underscoring the potential role of the exon 2-coded protein domain in the scaffolding function of BANK1. We provide evidence that the non-synonymous SNP rs10516487 (G<A; R61H) shows a dual nature by first, influencing mRNA splicing and consequently the quantity of protein, and, second, by producing a risk variant-containing protein isoform with increased potential for multimerization.

Genetic risk factors for sclerotic graft-versus-host disease

“…25,26 As compared with the rs10516487 C major allele, the T minor allele decreases BANK1 expression, reduces the activity of BANK1 variants with increased potential for self-association, and thereby reduces B-cell responses. 27 In several large studies, the same minor allele has been associated with decreased susceptibility to systemic sclerosis, 11,28 systemic lupus erythematosus, 25 and rheumatoid arthritis. 26 These results suggest that sclerotic GVHD shares a BANK1-mediated pathogenic mechanism with several autoimmune diseases.…”

“…HLA-matched related 374 (44) 91 (46) 283 (44) HLA-matched unrelated 326 (38) 86 (43) 240 (37) HLA-mismatched related 13 (2) 1 (1) 12 (2) HLA-mismatched unrelated 134 ( (41) 67 (34) 281 (43) #450 cGy 297 (35) 78 (39) 219 (34) .450 cGy 202 (24) 53 (27) 149 (23) Prior grade 2-4 acute GVHD, no. (%) 619 (73) 137 (69) 482 (74) CLL, chronic lymphocytic leukemia; CML, chronic myeloid leukemia; MDS, myelodysplastic syndrome; MM, multiple myeloma; MPN, myeloproliferative neoplasm.…”

“…Other demographics of the study cohort are summarized in Table 1. Male to female 153 (18) 33 (17) 120 (18) Female to male 230 (27) 42 (21) 188 (29) Female to female 192 (23) 57 (29) 135 (21) Patient race, no. (%)…”

The BANK1 SLE-risk variants are associated with alterations in peripheral B cell signaling and development in humans

“…In these studies there was no difference in total BANK1 levels in subjects with the risk genotype versus the non-risk genotype [5]. Further studies revealed that the rs10516487 R61 risk variant correlates with decreased splicing of exon 2 of BANK1 due to loss of a splice enhancer site, leading to the reduction of BANK1 Δ2 transcript levels relative to full-length transcripts [21]. Exon 2 encodes the region of BANK1 that is reported to interact with the IP3R, but the consequences of decreased levels of the Δ2 isoform in peripheral B cells are unclear.…”

Genetic Interactions Between BANK1 and BLK in Chinese Patients with Systemic Lupus Erythematosus

“…And a more recent work suggested that the kinase activity of BLK enhanced BANK1-PLCγ2 (phospholipase Cγ2) binding, further supporting the role of these 2 genes in basic B cell physiology and immune-related diseases 8 . Previous genetic studies also revealed BLK rs2736340 has an expression quantitative trait loci (eQTL) effect 9 ; and the nonsynonymous SNP rs10516487 (G>A; R61H) showed a dual nature by influencing mRNA splicing and consequently the quantity of protein, and by producing a risk variant-containing protein isoform with increased potential for multimerization 10 . However, future functional analysis focusing on combination effects of these 2 SNP are needed.…”