Multiple regulatory variants located in cell type-specific enhancers within the PKP2 locus form major risk and protective haplotypes for canine atopic dermatitis in German shepherd dogs

Background

Canine atopic dermatitis (CAD) is a chronic inflammatory skin disease triggered by allergic reactions involving IgE antibodies directed towards environmental allergens. We previously identified a ~1.5 Mb locus on canine chromosome 27 associated with CAD in German shepherd dogs (GSDs). Fine-mapping indicated association closest to the PKP2 gene encoding plakophilin 2.

Results

Additional genotyping and association analyses in GSDs combined with control dogs from five breeds with low-risk for CAD revealed the top SNP 27:19,086,778 (p = 1.4 × 10⁻⁷) and a rare ~48 kb risk haplotype overlapping the PKP2 gene and shared only with other high-risk CAD breeds. We selected altogether nine SNPs (four top-associated in GSDs and five within the ~48 kb risk haplotype) that spanned ~280 kb forming one risk haplotype carried by 35 % of the GSD cases and 10 % of the GSD controls (OR = 5.1, p = 5.9 × 10⁻⁵), and another haplotype present in 85 % of the GSD cases and 98 % of the GSD controls and conferring a protective effect against CAD in GSDs (OR = 0.14, p = 0.0032). Eight of these SNPs were analyzed for transcriptional regulation using reporter assays where all tested regions exerted regulatory effects on transcription in epithelial and/or immune cell lines, and seven SNPs showed allelic differences. The DNA fragment with the top-associated SNP 27:19,086,778 displayed the highest activity in keratinocytes with 11-fold induction of transcription by the risk allele versus 8-fold by the control allele (p_difference = 0.003), and also mapped close (~3 kb) to an ENCODE skin-specific enhancer region.

Conclusions

Our experiments indicate that multiple CAD-associated genetic variants located in cell type-specific enhancers are involved in gene regulation in different cells and tissues. No single causative variant alone, but rather multiple variants combined in a risk haplotype likely contribute to an altered expression of the PKP2 gene, and possibly nearby genes, in immune and epithelial cells, and predispose GSDs to CAD.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0404-3) contains supplementary material, which is available to authorized users.

BANK1 transgenic mice exhibit lupus-associated B cell phenotypes (BA3P.105)

BANK1 is a B-cell adaptor protein that has been implicated in SLE and systemic sclerosis. Previous studies have interpreted that the overexpression of the full length BANK1 isoform plays a pathogenic and the truncated (∆BANK1) version plays a protective role in lupus. However, there is no mechanistic evidence showing that these 2 isoforms can impact lupus development differentially. We have recently generated 2 transgenic strains on the B6 background, BANK1Tg and ∆BANK1Tg, which will be used to address this knowledge gap. The BANK1Tg mice overexpressing the full length Bank1 under the control of CD19 promoter exhibited a dramatic skewing in the splenic B cell population to MZ and B1a cells with a reduction in FO B cells. These mice also exhibited increased plasma cells along with an increased level of total IgM and anti-dsDNA IgG antibodies. Microarray analysis revealed increased transcript levels of several class switched IgG antibodies with a concomitant increase in the level of activation induced deaminase (AID), a master regulator of class switch recombination (CSR). qPCR confirmed higher level of AID and CSR. Interestingly, these phenotypes are observed only in female Tg mice. In contrast, the ∆BANK1Tg mice don’t exhibit the above phenotypes, supporting the hypothesis that the truncated isoform may play a protective role. These studies indicate that the different isoforms of BANK1 observed in humans contribute differentially to the development of B-cell autoimmunity.

NotI clones in the analysis of the human genome

Not I linking clones contain sequences flanking Not I recognition sites and were previously shown to be tightly associated with CpG islands and genes. To directly assess the value of Not I clones in genome research, high density grids with 50 000 Not I linking clones originating from six representative Not I linking libraries were constructed. Altogether, these libraries contained nearly 100 times the total number of Not I sites in the human genome. A total of 3437 sequences flanking Not I sites were generated. Analysis of 3265 unique sequences demonstrated that 51% of the clones displayed significant protein similarity to SWISSPROT and TREMBL database proteins based on MSPcrunch filtering with stringent parameters. Of the 3265 sequences, 1868 (57.2%) were new sequences, not present in the EMBL and EST databases (similarity < or =90%). Among these new sequences, 795 (24.3%) showed similarity to known proteins and 712 (21.8%) displayed an identity of >75% at the nucleotide level to sequences from EMBL or EST databases. The remaining 361 (11.1%) sequences were completely new, i.e. <75% identical. The work also showed tight, specific association of Not I sites with the first exon and suggest that the so-called 3' ESTs can actually be generated from 5'-ends of genes that contain Not I sites in their first exon.