Both environmental and genetic triggers factor into the etiology of autoimmune thyroid disease (AITD), including Graves' disease (GD) and Hashimoto's thyroiditis (HT). Although the exact pathogenesis and causative interaction between environment and genes are unknown, GD and HT share similar immune-mediated mechanisms of disease. They both are characterized by the production of thyroid autoantibodies and by thyroidal lymphocytic infiltration, despite being clinically distinct entities with thyrotoxicosis in GD and hypothyroidism in HT. Family and population studies confirm the strong genetic influence and inheritability in the development of AITD. AITD susceptibility genes can be categorized as either thyroid specific (Tg, TSHR) or immune-modulating (FOXP3, CD25, CD40, CTLA-4, HLA), with HLA-DR3 carrying the highest risk. Of the AITD susceptibility genes, FOXP3 and CD25 play critical roles in the establishment of peripheral tolerance while CD40, CTLA-4, and the HLA genes are pivotal for T lymphocyte activation and antigen presentation. Polymorphisms in these immune-modulating genes, in particular, significantly contribute to the predisposition for GD, HT and, unsurprisingly, other autoimmune diseases. Emerging evidence suggests that single nucleotide polymorphisms (SNPs) in the immunoregulatory genes may functionally hinder the proper development of central and peripheral tolerance and alter T cell interactions with antigen presenting cells (APCs) in the immunological synapse. Thus, susceptibility genes for AITD contribute directly to the key mechanism underlying the development of organ-specific autoimmunity, namely the breakdown in self-tolerance. Here we review the major immune-modulating genes that are associated with AITD and their potential functional effects on thyroidal immune dysregulation.

Hashimoto's thyroiditis (HT) is associated with HLA, but the associated allele is still controversial. We hypothesized that specific HLA-DR pocket-sequence variants are associated with HT and that similar variants in the murine I-E locus (homologous to HLA-DR) predispose to experimental autoimmune thyroiditis (EAT), a classical mouse model of HT. Therefore, we sequenced the polymorphic exon 2 of the HLA-DR gene in 94 HT patients and 149 controls. In addition, we sequenced exon 2 of the I-E gene in 22 strains of mice, 12 susceptible to EAT and 10 resistant. Using logistic regression analysis, we identified a pocket amino acid signature, Tyr-26, Tyr-30, Gln-70, Lys-71, strongly associated with HT (P ‫؍‬ 6.18 ؋ 10 ؊5 , OR ‫؍‬ 3.73). Lys-71 showed the strongest association (P ‫؍‬ 1.7 ؋ 10 ؊8 , OR ‫؍‬ 2.98). This association was seen across HLA-DR types. The 5-aa haplotype Tyr-26, Tyr-30, Gln-70, Lys-71, Arg-74 also was associated with HT (P ‫؍‬ 3.66 ؋ 10 ؊4 ). In mice, the I-E pocket amino acids Val-28, Phe-86, and Asn-88 were strongly associated with EAT. Structural modeling studies demonstrated that pocket P4 was critical for the development of HT, and pockets P1 and P4 influenced susceptibility to EAT. Surprisingly, the structures of the HTand EAT-susceptible pockets were different. We conclude that specific MHC II pocket amino acid signatures determine susceptibility to HT and EAT by causing structural changes in peptidebinding pockets that may influence peptide binding, selectivity, and presentation. Because the HT-and EAT-associated pockets are structurally different, it is likely that distinct antigenic peptides are associated with HT and EAT.gene ͉ Hashimoto's thyroiditis ͉ HLA ͉ major histocompatibility complex H ashimoto's thyroiditis (HT) is among the most common human autoimmune diseases with a population prevalence in the United States of 1-4.6% (1, 2). HT is characterized by infiltration of the thyroid by autoreactive T and B cells causing thyroid cell death and production of anti-thyroid peroxidase (TPO) and antithyroglobulin (Tg) antibodies (reviewed in ref.3). Clinically, the disease manifests by hypothyroidism requiring thyroid hormone supplementation, and most patients develop goiter. The pathogenesis of HT is believed to involve a complex interaction between inborn genetic susceptibility (reviewed in ref. 4) and an external trigger such as infection (5) or iodine (6). As a result, thyroidspecific T cells become activated and infiltrate the thyroid. The thyroid-infiltrating T cells induce thyroid cell death, causing gradual destruction of the thyroid gland, hypothyroidism, and goiter (reviewed in ref.3).The MHC gene locus encoding the HLA glycoproteins in humans consists of a complex of genes located on chromosome 6p21 (reviewed in ref. 4). Because the HLA region is highly polymorphic and contains many immune response genes, it was the first candidate genetic region to be studied for association with HT. However, in contrast to the clear association of Graves' disease (GD) with HLA-DR3, data on HL...

Significance Graves disease (GD) is an autoimmune disease caused by interactions between genetic, epigenetic, and environmental factors. The thyrotropin receptor ( TSHR ) is the major autoantigen in GD and is a key GD susceptibility gene. SNPs in intron 1 of the TSHR are associated with GD, but the causative variant and the mechanisms are unknown. By mapping epigenetic modifications induced by IFNα, a viral-induced cytokine triggering GD, we pinpointed the causative variant in intron 1 of the TSHR . We demonstrate that the disease-associated variant interacts epigenetically with a transcriptional repressor, promyelocytic leukemia zinc finger protein, and reduces thymic TSHR expression, leading to escape from tolerance and autoimmunity to the TSHR. These genetic–epigenetic interactions leading to decreased thymic self-antigen expression reveal a universal mechanism in autoimmunity.

Autoimmune thyroid diseases (AITD) arise from complex interactions between genetic, epigenetic, and environmental factors. Whole genome linkage scans and association studies have established thyroglobulin (TG) as a major AITD susceptibility gene. However, the causative TG variants and the pathogenic mechanisms are unknown. Here, we describe a genetic/ epigenetic mechanism by which a newly identified TG promoter single-nucleotide polymorphism (SNP) variant predisposes to AITD. Sequencing analyses followed by case control and familybased association studies identified an SNP (؊1623A3 G) that was associated with AITD in the Caucasian population (p ‫؍‬ 0.006). We show that the nucleotide substitution introduced by SNP (؊1623A/G) modified a binding site for interferon regulatory factor-1 (IRF-1), a major interferon-induced transcription factor. Using chromatin immunoprecipitation, we demonstrated that IRF-1 binds to the 5 TG promoter motif, and the transcription factor binding correlates with active chromatin structure and is marked by enrichment of mono-methylated Lys-4 residue of histone H3, a signature of active transcriptional enhancers. Using reporter mutations and siRNA approaches, we demonstrate that the disease-associated allele (G) conferred increased TG promoter activity through IRF-1 binding. Finally, treatment of thyroid cells with interferon ␣, a known trigger of AITD, increased TG promoter activity only when it interacted with the disease-associated variant through IRF-1 binding. These results reveal a new mechanism of interaction between environmental (IFN␣) and genetic (TG) factors to trigger AITD.Autoimmune thyroid diseases (AITD), 4 including Graves disease (GD) and Hashimoto thyroiditis (HT), are characterized by infiltration of the thyroid by T and B cells that react with local antigens leading to immune destruction of the thyroid in HT and production of thyroid-stimulating hormone receptor (TSHR) antibodies in GD. These result in the clinical manifestations of hypothyroidism in HT and hyperthyroidism in GD (1, 2). There is solid evidence that interactions between susceptibility genes and environmental triggers activate the sequence of cellular and humoral immune responses to thyroid antigens that cause AITD (1, 3, 4). Several environmental factors, including exposure to excess iodine, selenium deficiency, various infectious diseases, certain drugs, and pollutants have been associated with AITD (5, 6). Among these factors, interferon ␣ (INF␣), a therapeutic agent widely used for the treatment of chronic hepatitis C infection, has recently emerged as a major factor that triggers AITD (7,8).To date, several gene loci have been associated with AITD, including immune genes (HLA-DR, CTLA-4, CD40, FOXP3, and CD25) and thyroid-specific genes (TSHR and TG). Whole genome linkage screens, performed by our group (9) and others (10), have shown that the thyroglobulin (TG) locus on chromosome 8q24 is strongly linked with AITD. Moreover, TG has emerged as the only thyroid-specific gene that confers susceptibili...

The CD40 gene, an important immune regulatory gene, is also expressed and functional on non-myeloid derived cells, many of which are targets for tissue specific autoimmune diseases, including beta cells in type 1 diabetes, intestinal epithelial cells in Crohn’s disease, and thyroid follicular cells in Graves’ disease (GD). Whether target tissue CD40 expression plays a role in autoimmune disease etiology has yet to be determined. Here we show, that target-tissue over-expression of CD40 plays a key role in the etiology of autoimmunity. Using a murine model of GD, we demonstrated that thyroidal CD40 over-expression augmented the production of thyroid specific antibodies, resulting in more severe experimental autoimmune Graves’ disease (EAGD), whereas deletion of thyroidal CD40 suppressed disease. Using transcriptome and immune-pathway analyses we showed that in both EAGD mouse thyroids and human primary thyrocytes, CD40 mediates this effect by activating downstream cytokines and chemokines, most notably IL-6. To translate these findings into therapy, we blocked IL-6 during EAGD induction in the setting of thyroidal CD40 over-expression, and showed decreased levels of TSHR stimulating antibodies and frequency of disease. We conclude that target tissue over-expression of CD40 plays a key role in the etiology of organ specific autoimmune disease.