Genome wide identification of new genes and pathways in patients with both autoimmune thyroiditis and type 1 diabetes

Abstract

Autoimmune thyroid diseases (AITD) and Type 1 diabetes (T1D) frequently occur in the same individual pointing to a strong shared genetic susceptibility. Indeed, the co-occurrence of T1D and AITD in the same individual is classified as a variant of the autoimmune polyglandular syndrome type 3 (designated APS3v). Our aim was to identify new genes and mechanisms causing the co-occurrence of T1D + AITD (APS3v) in the same individual using a genome-wide approach. For our discovery set we analyzed 346 Caucasian APS3v patients and 727 gender and ethnicity matched healthy controls. Genotyping was performed using the Illumina Human660W-Quad.v1. The replication set included 185 APS3v patients and 340 controls. Association analyses were performed using the PLINK program, and pathway analyses were performed using the MAGENTA software. We identified multiple signals within the HLA region and conditioning studies suggested that a few of them contributed independently to the strong association of the HLA locus with APS3v. Outside the HLA region, variants in GPR103, a gene not suggested by previous studies of APS3v, T1D, or AITD, showed genome-wide significance (p < 5 × 10(-8)). In addition, a locus on 1p13 containing the PTPN22 gene showed genome-wide significant associations. Pathway analysis demonstrated that cell cycle, B-cell development, CD40, and CTLA-4 signaling were the major pathways contributing to the pathogenesis of APS3v. These findings suggest that complex mechanisms involving T-cell and B-cell pathways are involved in the strong genetic association between AITD and T1D.

Keywords: Gene; Graves' disease; HLA; Hashimoto's thyroiditis; Type 1 diabetes.

Figure 1

Manhattan plot showing the results of the association analysis in the Discovery set. The X-axis shows the chromosomal location of the analyzed SNPs and the Y-axis shows the – log(p-value). As expected the strongest association was seen on chromosome 6 at the MHC (HLA) locus with many SNPs in this locus showing genome wide significance (p < 5×10⁻⁸); however, other non-MHC loci also showed significant associations.

Figure 2

Schematic diagram of the MHC region showing non-HLA genes within the MHC locus found to be associated with T1D+AITD (APS3v). Of 21 replicated genes 16 were located within the MHC locus on chromosome 6p but are not HLA genes. Shown are HLA-A, HLA-C, and HLA-DQB1 (gray boxes), as well as 9 of the 16 genes within the MHC region that were replicated. Gene names are indicated below the line representing chromosome 6p and their chromosomal location in bp is indicated above the line.

Figure 3

(A) Linkage disequilibrium (LD) analysis of SNPs within 16 MHC genes that were replicated. LD analysis showed that the MHC region, where the replicated genes are located, consisted of 4 LD blocks. These results suggested that while some genes that are located within the same LD block (e.g. HCP5 and MICA) may show association with APS3v because of LD, others that are outside these blocks may have independent contributions. (B) LD analysis of the 1p13 locus. The PHTF1 and PTPN22 genes show tight LD with a D’ of 0.99 while the BCL2L15 gene was in weaker LD with PTPN22 (D’=0.85) and PHTF1 (D’=0.93). In contrast, MAGI3 was not in LD with the other 3 genes at the locus showing D’<0.80 with all 3 genes.

Figure 3

(A) Linkage disequilibrium (LD) analysis of SNPs within 16 MHC genes that were replicated. LD analysis showed that the MHC region, where the replicated genes are located, consisted of 4 LD blocks. These results suggested that while some genes that are located within the same LD block (e.g. HCP5 and MICA) may show association with APS3v because of LD, others that are outside these blocks may have independent contributions. (B) LD analysis of the 1p13 locus. The PHTF1 and PTPN22 genes show tight LD with a D’ of 0.99 while the BCL2L15 gene was in weaker LD with PTPN22 (D’=0.85) and PHTF1 (D’=0.93). In contrast, MAGI3 was not in LD with the other 3 genes at the locus showing D’<0.80 with all 3 genes.