Autoimmune thyroid diseases (AITDs), which include hyperthyroid Graves’ disease (GD), Hashimoto’s (goitrous) thyroiditis, atrophic autoimmune hypothyroidism, postpartum thyroiditis (PPT), thyroid-associated orbitopathy (TAO), drug-induced thyroiditis, such as interferon-induced thyroiditis, thyroiditis associated with polyglandural autoimmune syndromes and the presence of thyroid antibodies (Tabs) with no apparent clinical disease, are recognized as multifactorial diseases with vital genetic background. The interaction between environmental and genetic factors cause the impairment of self-tolerance to thyroid autoantigens – cellular and humoral immune responses – directed against the thyroid gland due to AITD developing in genetically predisposed individuals. The twin studies and familial aggregation studies have shown the polygenic basis in Graves’ disease (GD) and Hashimoto’s thyroiditis (HT), the most common endocrine disorders in childhood and adolescence. Both diseases are characterized by the presence of thyroid-reactive T cells and infiltration of the thyroid gland. In GD, the majority of T cells undergo a Th2 differentiation and activate B cells to produce TSH receptor (TSHR) antibodies which stimulate the thyroid resulting in clinical hyperthyroidism. In contrast, HT involves Th1 switching of the thyroid infiltrating T cells which induces apoptosis of thyroid follicular cells and clinical hypothyroidism (1).

In recent years the genetic factors as well as epigenetic background of AITD, particularly GD and HT, have been significantly recognized. Especially, immune regulatory genes affecting the immune response, such as genes for human leukocyte antigens (HLA), cytotoxic T-lymphocyte antigen (CTLA-4), CD40, FOXP3, protein tyrosine phosphatase (PTPN-22), TSHR as well as genes for signal transducer and activator of transcription proteins (STATs) are acknowledged as predisposing to AITD (fig. 1) (2).

Moreover, the epigenetic mechanism is also observed in pathogenesis of autoimmune diseases. The recent study has shown that X chromosome inactivation (XCI) via DNA methylation, may be involved in AITD development, thus explaining the female-predominant tendency (3).

The MHC region is recognized as a large genomic area that encodes MHC molecules which play an important role in the immune system and autoimmunity. MHC genomic region consists of a complex of genes located on chromosome 6p21. The genes for MHC molecules are divided into 3 regions: (1) Class I genes encode the HLA antigens A, B, and C, (2) Class II genes encode the heterodimeric HLA-DR, DP, and DQ molecules and (3) Class III genes include genes for: complement components (e.g. C4), tumor necrosis factor alpha (TNFα), heat shock protein 70 (Hsp70), and several other genes. The MHC class II molecules are responsible for the initiation of adaptive immune responses. It has been documented that T-cells recognize and respond to antigens when they are attached to the binding groove of an HLA class II molecule (mostly DR and DQ) on the surface of antigen presenting cell. HLA region is highly polymorphic and contains several other immunoregulatory genes, therefore it has been acknowledged as a pivotal candidate locus for AITD as well as for other autoimmune diseases. Additionally, HLA region is recognized as an important chain of immunological synapse involving peptide antigen bound to HLA molecule, T cell receptor, co-stimulatory molecules, receptors on APCs, as well as integrins (4).

Initial studies based on transmission disequilibrium test (TDT) approach, conducted in a large cohort of GD families, have demonstrated strong linkage between GD and HLA. In another studies focused on the role of HMC area in AITD, tough GD association with HLA-DR3(HLA-DRB1*03) has been found. However, in a study from UK only weak evidence for linkage between GD and the HLA region has been recognized, and another study has reported linkage only when conditioning on DR3. Moreover, it has been documented that HLA-B8 and HLA-DQA1*0501 seems to be crucial in GD in Caucasians (5), Additionally, there are reports demonstrating the role of HLA polymorphisms in the clinical manifestation of GD. Interestingly, some studies have documented an association between the likelihood of relapse of GD and HLA-DR3 (5). The increased frequency of HLA-DR3 in patients with Graves’ ophthalmopathy has been observed, but it has not been confirmed by others.

The association between HLA haplotypes and HT is less definitive than in GD. Early studies failed to find an association between goitrous HT and HLA A- B- or C-antigens. Subsequently, the association of goitrous HT with HLA-DR5 and of atrophic HT with DR3 has been shown (6). The weak association of HT with HLA-DR4 (6) and DR3 (7) in Caucasians was reported in later studies. This observation has been earlier suggested by the studies on animal model in transgenic mice. Finally, HLA-DQW7 (DQB1*0301) was also reported to be associated with HT in Caucasians (8).

Detailed analysis of the HLA class II locus demonstrated that the major HLA haplotype contributing to the shared susceptibility to T1D and AITD was DR3-DQB1*0201, with DR3 conferring most of the shared risk (9).

Many studies have documented that susceptibility of HLA loci to AITD varies among populations, and no consensus has been obtained. In non-Caucasian population HLA alleles were different from those observed in Caucasian groups. Strong association of HLA-DR3 with AITD was observed in Caucasians while in Asian population (for example in Japanese) the associations between HLA-B35 and GD have been found. One study has reported that HLA-DR3, the primary HLA class II allele, predisposes to the joint susceptibility for T1D and AITDs in families in which both diseases cluster. Moreover, a significant association between DRB1*03 and early onset of polyglandular failure has been found, therefore a cooperative susceptibility genes for AITD and other autoimmune diseases have been confirmed (10).

Moreover, an increased frequency of HLA-BW46 has been reported in Chinese population. However, other class I and II HLA alleles have also been reported to be increased in Asian GD patients. The increased frequency of HLA-DRB3*0202 has been observed in African-Americans (11). Interestingly, one study of a mixed population in Brazil demonstrated an association with HLA-DR3, frequent in European group, indicating that this allele may predispose to AITD in different ethnic groups (12). Alternatively, this Brazilian population may have been comprised mostly of European ancestry.

However, two recent genomewide scans in AITD have failed to detect linkage at 6p21 markers (13). On the other hand, whole-genome linkage screening performed by testing a panel of linkage markers of HLA in AITD, has identified the AITD susceptibility gene on: 2q, 6p (HLA), 8q, 10q, 12q,14q and 20q (4).

Reassuming, the available data suggest that HLA involves immune regulatory genes modulating the gene for AITD but not a primary susceptibility gene.

HLA class II molecules are heterodimeric molecules consisting of α and β chain, which form functional highly polymorphic peptide binding pocket (14). In several autoimmune diseases, including AITD, this specific pocket amino acid sequence is recognized as associated with diseases. Moreover, the specific HLA-DR pocket variants have recently been identified as vital for the development of Graves’ disease (GD) (15) and Hashimoto’s thyroiditis (HT).

Sequencing of HLA-DQ genes have documented that arginine at position 74 of the DRβ1 chain is a critical shared amino acid for the development of both GD and HT (15). It has been claimed that a molecular marker of the HLA-DR pocket, determined by specific amino acids, confers a significant risk for the development of AITD as well as T1D – higher than the risk involving the susceptibility genes. The haplotype consisting of HLA-DR pocket amino acids Tyr-26, Leu-67, Lys-71, and Arg-74 has appeared to be strongly associated with AITD and T1D, while amino acids: Leu-26, Phe-26, Ile-67, Asp-70, Glu-71, Ala-71, and Gln-74 have been recognized as protective. Especially, arginine at position 74 of HLA-DRB1 (DRB1-Arg-74), has been shown to be the pivotal in the development of HT and GD (15). Further analysis has shown that the presence of glutamine at position 74 is protective for GD (15). According to functional mechanism of HLA polymorphism, it is hypothesized that the presence of HLA-DR allele with the appropriate amino acids peptide binding pocket, determines the binding of an autoantigenic thyroidal peptide (16). It is recognized that in pocket 4 (P4) of the DR peptide there is a cleft with position 74 of the DRb1chain. Thus, there is a real possibility that an arginine at position 74 changes the structure of the pocket and therefore has an influence on peptide binding and presentation to T-cells. Indeed, structural modeling analysis has shown that the alteration at position 74, from the common neutral amino acids (Ala or Gln) to a positively charged basic amino acid (Arg), significantly converts the three dimensional structure of the P4 peptide binding pocket. This could modify the peptide binding properties of the DR pocket during presentation to T-cells and favor antigenic peptides that induce GD (15). However, this hypothesis awaits confirmation as very few studies have examined the process of binding and presentation of thyroidal autoantigens to T-cells by different HLA-DR subtypes. Interestingly, the results of Hodge et al. (18) study have suggested the interaction at the genetic level between thyroglobulin gene variant and DRB1-Arg74 predisposing to GD. This observation indicates that the thyroglobulin/DRB1-Arg74 genetic interaction is revealed in biochemical relations, in which Arg74 implicates the presentation of thyroglobulin peptides in the initiation phase of GD. Similarly, the recent studies have identified a pocket HLA-DR amino acid signature that presents strong risk for HT.

The CTLA-4 gene, located on chromosome 2q33, encodes immunoregulatory molecule, expressed on the surface of activated T cells, which via interaction with B7 molecule downregulates immune functions mediated by T-cells activation (19). It is known that T-cells are activated by APCs that present to the T-cell receptor (TCR ) an antigenic peptide bound to an HLA class II protein on the cell surface. However, a second signal is needed for full T-cell activation, including co-stimulatory signals provided by the APCs themselves or other local cells. The CTLA-4 molecule following activation of the TCR is able to transmit signal in response to its ligation with either B7-1 or B7-2 through competition with CD28.

Human CTLA-4 gene is postulated as a major negative regulator of T-cell activity and important genetic factor responsible for susceptibility to variety of autoimmune diseases (20), including: type 1 diabetes mellitus (T1D) (21), asthma (22), Addison’s disease, myasthenia gravis, Sjogren’s syndrome (23), systemic lupus erythematosus (SLE) (24), systemic sclerosis (25), ulcerative colitis (26) and all forms of AITD (GD, HT, as well as the production of thyroid antibodies TAbs) (27).

CTLA-4 gene is highly polymorphic, that has been confirmed in many linkage and association studies in various autoimmune disorders:

1) A to G SNP substitution (49 A/G) at position 49 in exon 1 CTLA-4, resulting in threonine to alanine substitution at codon 17;

2) C to T SNP substitution in the promoter region at position _318 relative to exon 1 start site (_318 C/T);

3) microsatellite polymorphism CTLA-4(AT)n, which is a dinucleotide (AT) repeat in the 3’UTR of the CTLA-4 gene

4) A to G SNP located downstream and outside of the 3’UTR of the CTLA-4 gene (designated CT60).

Recently, it has been claimed that T-effectors activity could be determined by CTLA-4 SNPs. Especially, A49G dimorphism (Thr/Ala exchange in a peptide) leads to the expression of defective receptor, resulting in the inhibitory effect of CTLA-4 molecule on lymphocyte T-cell (28).

The association between AITDs (HT and/or GD) and CTLA-4 polymorphisms (A49G, 1822 C/T and CT60 A/G) and some other polymorphic sites has been confirmed in several studies. Microsatellite polymorphism CTLA-4(AT)n in 3’UTR region has been reported as a first one associated with autoimmune conditions and consistent in different populations (27). In some studies it has been underlined that CTLA-4(AT)n in 3’UTR region is the most powerful polymorphism associated with GD (27). However, particularly CTLA-4 A49G and CT60 polymorphisms have been correlated with susceptibility to AITD development (29). These associations have been consistent irrespective of ethnic backgrounds, and have been found characteristic in many European as well as Asian populations (30).

Among the all known polymorphism, A/G49 SNP that substitutes threonine for alanine in the signal peptide, leads to misprocessing of CTLA-4 in the ER, resulting in less efficient glycosylation and diminished surface expression of CTLA-4 protein (31). Other reports bring evidence for association between G allele and reduced control of T-cell proliferation (27). It is claimed that this association may be involved in direct effect of the A/G49 SNP or another polymorphism in linkage disequilibrium with the A/G49 SNP. However, the functional studies have revealed that there are no difference in CTLA-4 expression and/or function in case of transiently transfected T-cell line with endogenous CTLA-4 (Jurkat cells), containing a CTLA-4 construct harboring either G or A allele of the A/G49 SNP (32). This observation has suggested that A/G49 is not the causative SNP, but rather remains in linkage disequlibrium with the causative variant.

The results of association studies, focused on C/T_318 SNP of CTLA-4, are also controversial. The study of have confirmed the association of C/T_318 haplotype with CTLA-4 activity, while the results of have been contrary. Recently performed analysis of C/T_318 SNP have established that T allele is related with higher promoter activity in comparison to C allele (33). It has been accepted that the presence of T allele is associated with significantly enhanced expression of CTLA-4 on the surface of stimulated cells, and significantly increased CTLA-4 mRNA level in resting cells (34). Thus, mechanistically, the C/T_318 SNP may influence CTLA-4 levels by changing the binding of a transcription factor LEF-1 (ang. lymphoid enhancing factor 1), via changing TT(C/T)AAG site, which contains the C/T polymorphism (33).