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British Medical Bulletin 2005 71(1):93-113; doi:10.1093/bmb/ldh032
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Published online 8 February 2005

British Medical Bulletin, Vol. 71 © The British Council 2005; all rights reserved

Genetic insights into disease mechanisms of autoimmunity

M. J. Simmonds* and S. C. L. Gough*

* Division of Medical Sciences, University of Birmingham, Institute of Biomedical Research, Birmingham B15 2TT, UK

Correspondence to: Dr S. C. L. Gough, Department of Medicine, University of Birmingham, UK. E-mail: s.c.gough{at}bham.ac.uk


   Abstract
Top
 Abstract
Introduction: distinguishing...
 Autoimmunity and disease
 General autoimmune disease...
 Disease-specific mechanisms
 Conclusions and future...
 References
 
Educating the immune system to distinguish between self and non-self is critical to ensure that an immune response is mounted against foreign antigens and not against self. A breakdown in these mechanisms can lead to the onset of autoimmune disease. Clinical and molecular data suggest that shared immunogenetic mechanisms lead to the autoimmune process. The most studied genes and molecules are the human leukocyte antigen (HLA) region and the cytotoxic T-lymphocyte-associated 4 molecule (CTLA-4). Recently progress has been achieved in narrowing down the primary variants within both gene regions, but further work is needed to determine the function and extent of the aetiological variant(s) present. Recent exciting results also suggest a role for the newly discovered lymphoid-specific phosphatase (LYP) protein. As well as these general mechanisms, disease-specific mechanisms are beginning to be elucidated, for example the role of autoimmune regulatory element 1 (AIRE1) in autoimmune polyendocrinopathy–candidiasis ectodermal dystrophy (APECED). Taken together, these data suggest that both general and disease-specific mechanisms lead to the clinical outcome of autoimmune disease and that increased understanding of these mechanisms will improve our knowledge of how autoimmune disease occurs, eventually leading to the development of novel therapeutic agents.


   Introduction: distinguishing ‘self’ from ‘non-self’
Top
 Abstract
 Introduction: distinguishing...
Autoimmunity and disease
 General autoimmune disease...
 Disease-specific mechanisms
 Conclusions and future...
 References
 
The idea that the immune system is able to detect ‘foreign’ antigens was first conceptualized in the early twentieth century. However, it was not until the early 1950s that it was widely accepted that an immune response can be mounted not only against foreign antigens but also against ‘self’-antigens. Mechanisms whereby the immune system is able to mount an immune response against foreign antigens, whilst maintaining immune tolerance towards self-antigens, have been shown to be induced via central tolerance in the thymus and peripheral tolerance in the secondary lymphoid tissues.1

Central tolerance is achieved by a two-stage process (Fig. 1). When immature T lymphocytes are released from the bone marrow they express unique T-cell receptors (TCRs) generated by random rearrangement of a variety of gene segments, leading to a population of T cells whose TCRs can recognize not only a wide variety of foreign antigens but also self-antigens. During stage 1, positive selection of the T-cell ­repertoire occurs, involving interaction of naive CD4+8+ thymocytes with major hisotocompatibility complex (MHC)–human leukocyte antigen (HLA) class I and II molecules displayed on thymic cortical epithelial cells. Naive thymocytes whose TCRs interact with MHC molecules receive a protective signal preventing them from undergoing cell death. Thymocytes whose TCR receptors have low affinity for MHC molecules do not receive the protective signal, leading to their death by apoptosis. Stage 2 involves the negative selection of the surviving population of thymocytes (containing thymocytes with both low- and high-affinity receptors for self-antigens). During negative selection antigen presenting cells (APCs), such as thymic medulla epithelial cells (MECs), dendritic cells and macrophages, only interact with thymocytes bearing high-affinity receptors for self-MHC molecules displaying self-antigens and self-MHC molecules alone, leading to their deletion by apoptosis. Only T cells that are specific for foreign antigens displayed by self-MHC ­molecules are allowed to mature into CD4+ or CD8+ cells and are then released into the immune system.



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  		Fig. 1 Diagrammatic representation of central tolerance. Thymocyte maturation: immature thymocytes from the bone marrow undergo T-cell receptor (TCR) rearrangement. Stage 1: once immature CD4+8+ thymocytes enter the thymus they undergo MHC restriction, whereby only CD4+8+ thymocytes that interact with MHC-presented antigen on ­epithelial cells receive a positive survival signal. Those that do not interact are deleted by apoptosis. Stage 2: this stage involves the negative selection of thymocytes that survive stage 1. Thymocytes with too strong an association for self-MHC and self-antigens are deleted by apoptosis, allowing the remaining thymocytes to mature into CD4+ ­­T-helper (Th) cells or CD8+ cytotoxic (Tc) cells.

 

A problem inherent with central tolerance is that not all self-antigens are expressed in the thymus. Therefore self-reactive T cells specific for self-antigens not expressed in the thymus would not be recognized as self-reactive and would not be eliminated, thus enabling them to escape into the periphery with the potential to evoke an immune response.1,2 This is prevented by employing peripheral tolerance. This involves an active mechanism of immune suppression in which CD4+ regulatory T cells (T regs), whose action is mediated by the co-stimulatory regulatory molecules CD28 and CTLA-4, suppress the activation and function of self-reactive T cells in the periphery, including those specific for antigens not expressed in the thymus.


   Autoimmunity and disease
Top
 Abstract
 Introduction: distinguishing...
 Autoimmunity and disease
General autoimmune disease...
 Disease-specific mechanisms
 Conclusions and future...
 References
 
Both peripheral and central tolerance can break down, causing certain individuals to mount a response against self, termed ‘autoimmunity’, which ultimately results in an autoimmune disease. Autoimmune ­diseases, which collectively affect 5–10% of the general population,3,4 were originally classified into two distinct groups, ‘organ-specific’ and ‘non-organ-specific’, but it now seems more appropriate to recharacterize these into a spectrum of autoimmune disease (Tables 1 and 2).


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  		Table 1 The original classification of autoimmune diseases into organ-specific and non-organ-specific

 

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  		Table 2 Reclassification of autoimmune diseases into a spectrum of disease representing the diversity of clinical features that can be observed within diseases

 

By their very nature, variations within the DNA of the genome can alter the function of genes within given physiological and immunological pathways, thereby affecting the role of the encoded protein involved in immune mechanisms, and are therefore, by definition, causal for disease. It seems likely that in the past these genomic variations have enabled ancestral human populations to adapt to and overcome numerous immune insults, most importantly the threat posed from infections. However, it would appear that the same variations that once helped us evade disease are now ‘turning against’ certain individuals.

Evidence for the role of genetic factors in autoimmune disease mechanisms has arisen from examination of disease clustering within families and concordance rates between monozygotic and dizygotic twins (reviewed by Heward and Gough5). Concordance rates for autoimmune diseases in monozygotic twins are ~30–70%5 but are <100%, implying that disease results from an interaction of genetic and environmental factors. Many environmental factors, such as diet, stress, smoking and infection, have been proposed, but, because of the difficulties in measuring and monitoring the impact of these factors on disease development, no conclusive evidence has been produced. However, the genetic component of disease susceptibility can be calculated by the sibling risk, defined as the ratio of the disease risk to a second child, where the first child has the disease, compared with the risk to the general population. Where there is no genetic component the sibling risk will be 1, whereas siblings of affected individuals with autoimmune disease have a 10–50-fold higher risk of developing the disease.3,4

The observation of clustering of multiple autoimmune diseases within individuals from the same family supports the hypothesis of involvement of common mechanisms in susceptibility to autoimmune disease. Results from the Fifth Genetic Analysis Workshop have shown that at least one case of autoimmune thyroid disease occurred in 40% of type 1 diabetic families. This has been further validated by recent data from the UK showing that 27% of parents with type 1 diabetes within the Type 1 Diabetes Warren Repository reported the presence of another autoimmune disease, compared with only 13.2% of parents without type 1 diabetes.6 In support of these clinical findings, molecular data are beginning to confirm the concept of shared determinants and mechanisms within autoimmune diseases. The treatment of multiple sclerosis patients with humanized anti-CD52 monoclonal antibody produces an alteration of the T-cell-dependent immune response, leading to the development of antibodies against the thyroid-stimulating hormone receptor and, in turn, to carbimazole-responsive autoimmune hyperthyroidism.7 Similarly, treatment of the non-obese diabetic (NOD) mouse with Mycobacterium bovis to prevent type 1 diabetes leads to the development of a lupus-like autoimmune phenomenon.8

These studies not only provide convincing evidence that genetics play a role in autoimmune disease mechanisms, but also, with the observation of clustering of multiple autoimmune diseases within families, demonstrate that shared mechanisms are involved. This review will focus on some of the major genes shown to predispose to autoimmune disease and try to elucidate the mechanism by which they contribute to disease.


   General autoimmune disease mechanisms
Top
 Abstract
 Introduction: distinguishing...
 Autoimmunity and disease
 General autoimmune disease...
Disease-specific mechanisms
 Conclusions and future...
 References
 
HLA class II encoded molecules

The HLA region on chromosome 6p21 can be split into three different parts: class I, class II and class III (Fig. 2). The class I region encodes HLA-A, HLA-B and HLA-C molecules which are expressed on the cell surface of nucleated cells involved in the presentation of endogenous antigens to CD8+ cytotoxic T (Tc) cells. The class II region encodes many membrane-bound proteins expressed on the cell surfaces of B-lymphocytes, macrophages, dendritic cells and activated T lymphocytes, which are involved in the processing and presentation of exogenous antigens to CD4+ T-helper (Th) cells. Finally, the class III region is located between the class I and class II regions and contains, amongst others, genes encoding components of the complement region (C2 and C4), the heat shock protein (HSP70) and the tumour necrosis factors (TNF).



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  		Fig. 2 A simplified map of the HLA class I and class II gene regions [transport associated with antigen-processing genes (TAP1 and TAP2) and large multifunctional protein (LMP)] and the HLA class III gene region [heat shock protein (HSP) and tumour necrosis factors (TNF{alpha} and TNFß)] is presented. A more detailed map of the HLA class II region, highlighting some of the known haplotypes protective of and predisposing to Graves’ disease (GD), type 1 diabetes (T1D) and multiple sclerosis (MS), is also shown.

 

Type 1 diabetes is probably the most studied of all the autoimmune diseases, with around 34% of familial clustering due to the MHC class II region.9 Early reports indicated a strong association of DRB1*03 and DRB1*04 alleles with type 1 diabetes.10–12 Products of the class II gene region, in particular the DRB1, DQA1 and DQB1 molecules, are highly polymorphic and play a role in both antigen presentation to CD4+ Th cells and central tolerance. The high degree of linkage disequilibrium (LD) between DRB1-DQB1-DQA1, in which genes are not inherited in a random fashion (in equilibrium), has made it difficult for the primary aetiological variants within the HLA region to be identified. Interestingly, further work on the DRB1*03 and DRB1*04 association with type 1 diabetes showed that these alleles formed part of extended haplotypes DRB1*03-DQB1*02-DQA1*0501 (DR3) and DRB1*04-DQB1*0302-DQA1*0301 (DR4) (reviewed by Tait and Gough13) associated with disease, with DR3/4 heterozygosity showing the greatest association.

Although association of these haplotypes has been reported, a stronger association with the DQB1 locus alone was reported in 1987 when an allele encoding aspartic acid (Asp) at position ß57 of DQB was found to be associated with resistance to type 1 diabetes, while an allele encoding a neutral residue at this position conferred susceptibility.14 Further work implicated the presence of Asp at position ß57 of DQB as the critical residue in peptide-binding pocket nine (P9), part of the DQB binding pocket involved in antigen presentation and TCR interaction. It has been proposed that its carboxylate group forms a salt bridge with arginine at position ß57 of the DQA chain that stabilizes the heterodimer between the DQA and DQB chains.14 Changing Asp at this position could prevent correct antigen display or thymocyte TCR docking, preventing deletion of autoreactive thymocytes during central tolerance. Even though this provides an interesting mechanism for association of the HLA class II region with type 1 diabetes, association of position ß57 of DQB was not complete. Further studies have demonstrated a potential role for other residues in DQB binding pocket P9 and DRB binding pockets P1 and P4 in disease susceptibility.14

Further studies have shown that another haplotype DR2 (DRB1*1501-DQA1*0102-DQB1*0602) is negatively associated with type 1 diabetes in all populations.15 Interestingly, when this haplotype was examined in multiple sclerosis, the presence of the same haplotype was instead shown to predispose to disease (reviewed by Giordano et al.16). This difference in the protective nature of DR2 in type 1 diabetes and predisposing nature in multiple sclerosis could help to explain why it is rare to see the clustering of multiple sclerosis in type 1 diabetes patients, and vice versa. When the amino acid sequence of the HLA-DR2 haplotype was examined more closely, these differences in the protective and predisposing nature of this haplotype were believed to be due to changes in the DRB1 binding pocket domain involved in auto-antigen binding and T-cell-receptor docking.17 The differences may be related to the processing and presentation of the different auto-antigens involved in each disease.

A group of DRB1 genes (DRB1*0101, DRB1*0102, DRB1*0401, DRB1*0404, DRB1*0405, DRB1*0408, DRB1*1001 and DRB1*1402), rather than a specific haplotype or haplotypes contributing to disease susceptibility, have been implicated in rheumatoid arthritis.18,19 Association was originally believed to be due to DRB1*04, but this hypothesis was thrown into doubt when other non-DRB1*04 alleles were found to be associated with disease. Work by Gregerson et al.18 helped to resolve this by showing that association of DRB1 alleles was due to a similarity within DRB1 peptide domain at positions ß70–ß74, with alleles containing similar sequences (QKRAA/QRRAA/RRRAA) termed the ‘shared epitope’. Amino acid changes within the shared epitope have also been postulated to differentiate the predisposing alleles from the protective DRB1*0103, DRB1*07, DRB1*1201, DRB1*1301 and DRB1*1501 alleles.20,21

Association of the DR3 extended haplotype is not unique to type 1 diabetes but appears to be a general autoimmunity haplotype. For example, it has also been associated with systemic lupus erythematosus (along with the DR15 and DR8 haplotypes22) and the autoimmune condition Graves’ disease.23 In an attempt to explain the role of DR3 in susceptibility to Graves’ disease, recent work from our own laboratory, together with that of other researchers, has shown that the predisposing DR3 haplotype can be differentiated from the protective DR7 haplotypes (DRB1*07-DQB1*03032-DQA1*0201 and DRB1*07-DQB1*02-DQA1* 0201) by the presence of different amino acids at position ß74 of the DRB1 binding pocket. Most DR3 subtypes have arginine at position ß74, whereas DR7 alleles have glutamine at this position (M. J. Simmonds et al24). However, the role of DQA1 in disease susceptibility remains to be elucidated. Association of position ß74 is also seen in type 1 diabetes, in which variation at position ß74 has been shown to differentiate between the lower-risk DRB1*0403 and DRB1*0406 alleles, containing a negatively charged glutamine, and the high-risk DRB1*0401 allele, containing a non-charged polar alanine.25–27 Interestingly, the shared epitope associated with rheumatoid arthritis also encompasses position ß74. The mechanism for involvement of position ß74, along with other positions within the DRB1 binding domain, in so many autoimmune diseases has not yet been resolved. However, it is probably due to the fact that position ß74 encompasses several binding pockets that play crucial roles in both TCR docking and antigen presentation to Th cells, suggesting that position ß74 mediates its effects on autoimmunity by altering antigen recognition. At the present time it is not known whether other, or indeed how many other, susceptibility loci are present within the HLA region. Further work is needed to exclude such effects.

The association of the HLA region with other autoimmune diseases is less clear and less consistent for diseases such as Hashimoto’s thyroiditis as most datasets studied have been relatively small (>200 cases and controls). However, it is worth noting that autoimmune hypothyroidism has been linked to DR3 and DR4 (reviewed by Simmonds and Gough28) and autoimmune Addison’s disease has been linked to DR3.29

Taken together, these data suggest that the HLA class II region contributes to most autoimmune diseases. The mechanisms by which variations lead to autoimmunity remain unknown, but are likely to be different for each disease. The clinical outcome of disease seems more likely to be the result of changes in the amino acids that compose the binding pockets of the DR and DQ molecules which enable antigen presentation and TCR interaction to occur and the subsequent effect that this has on autoreactive T-cell deletion during central tolerance and T reg production.

Additional HLA class I and class III associations?

Although there is a large body of evidence to support the involvement of HLA class II genes in autoimmune disease mechanisms, the possibility of other independent effects present within the HLA region has not been excluded. When the HLA region was originally investigated in the early 1970s much of the work focused on both the class I and class II regions. As time went on, association seemed to be stronger in the class II region, and work on the class I region ground to a halt owing to difficulties in assessing LD across the region. Recently, however, with fine mapping of the HLA region and the discovery of a large number of immune regulatory genes there has been a renewal of interest in the HLA region as encoding additional susceptibility loci. In addition to the long-established link between MHC class III encoded parts of the complement system and systemic lupus erythematosus (see later), work on type 1 diabetes has identified a DNA variant [allele 3 of microsatellite D6S2223 (4.9 kb telomeric of DQ in the extended class I region)] as being associated with a reduction in the risk of disease conferred by the HLA-DR3 extended haplotype.30 Further work has narrowed this locus to a region between the class II HLA-DOB gene and the D6S2702 micrsatellite marker within the class I region, encompassing the class III region and the HLA-B/-C gene regions.31 Studies in rheumatoid arthritis have also identified an HLA class II independent effect within the class III region, suggesting a role for lymphocyte-specific transcript, BAT1 and PG8.32 However, previous studies have suggested that association with BAT1 is due to LD with the I{kappa}BL gene,33 also in the HLA class III region (whose association with rheumatoid arthritis in the UK is believed to be due to LD with the DRB1 locus19). Studies have also suggested an independent disease-modifying effect of the lymphotoxin alpha-TNF-{alpha} gene region34 in rheumatoid arthritis, although subsequent studies suggest that this association is due to LD with DRB1*0401 and DRB1*0404.35

Although there is still controversy surrounding the presence of additional non-MHC class II susceptibility regions, it seems likely that the link between the HLA gene region and most autoimmune diseases could extend beyond the well-known associations with the class II region.

Cytotoxic T-lymphocyte-associated 4 (CTLA-4)

As stated earlier, the TCR dictates T-cell specificity and plays a central role in initiating activation of the immune response. Interaction of a naive T cell with a presented antigen alone is not sufficient for activation and a second co-stimulatory signal is required, making T-cell activation, at least, a two-step process (Fig. 3).36 Step 1 involves the generation of an initial signal (signal 1) through interaction of the antigenic peptide with the TCR–CD3 complex. Step 2 involves a subsequent antigen-non-specific co-stimulatory signal (signal 2) provided primarily by the interaction of the CD28 molecule on T cells with B7 molecules (CD80 or CD86) expressed on activated macrophages, producing a positive co-stimulatory signal to the T cells. As a means of controlling upregulation, the CTLA-4 molecule, a homologue of CD28 expressed on activated T cells, also interacts with B7 molecules to provide an inhibitory signal, leading to the downregulation of T-cell activation. Levels of CTLA-4 expression are increased by a CD28-generated co-stimulatory feedback that effectively provides braking in proportion to acceleration from CD28 (reviewed by Egen et al.37). As CTLA-4-CD28 molecules control the rate of T-cell activation, and to a large extent the fate of the immune response, they are likely to play a major role in the development of autoimmune disease.



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  		Fig. 3 The stimulatory pathway of CD28 and the antagonist effect of CTLA-4 on T-helper cell activation. T-cell activation occurs via a two-stage process. Stage 1 involves the interaction of a presented antigen with the TCR–CD3 complex, leading to the generation of an initial signal. Stage 2 involves a co-stimulatory signal from CD28 interaction with B7. This stage is regulated by downregulation of T-cell activation by CTLA-4. Owing to the negative control function of CTLA-4, functional mutations within this gene could increase susceptibility to autoimmune disease.

 

The genes encoding CD28 and CTLA-4 have been mapped to human chromosome 2q33. Until recently there were only four known polymorphisms of the CTLA-4 gene: a dinucleotide repeat microsatellite polymorphism CTLA4(AT)n in the 3’ untranslated region of exon 4; an A to G SNP (CTLA4(49)A/G) in exon 1 encoding a threonine to alanine substitution at codon 17; a C to T SNP (CTLA4(-318)C/T) in the promoter relative to the exon 1 start site; and a C to T SNP in intron 1 of CTLA-4. Numerous association studies have been carried out linking these polymorphisms with type 1 diabetes, Graves’ disease, Hashimoto’s thyroiditis, Addison’s disease and coeliac disease (reviewed by Tait and Gough13). Because of the crucial role of CTLA-4 in the inhibition of T-cell activation it seemed that this gene had important implications for the mechanisms involved in the autoimmune disease process. However, other genes in this chromosomal region, such as CD28 and Inducible Costimulator (ICOS) which are only 123 kb and 58 kb, respectively, from the CTLA-4 gene, could also be responsible for the observed genetic effect.

It is important to point out that the findings of association of a DNA variant within a gene does not imply that it is causal, or indeed that the causal variant is even within the gene of interest but is merely acting as a genetic ‘sign post’. The only way to identify the causal variant confidently is to test all variants within the region of interest, look at the most strongly associated and apply an appropriate statistical analysis such as regression modelling. This has been done for the CTLA-4 gene region (encompassing the adjacent CD28 and ICOS genes) using DNA from patients with type 1 diabetes, Graves’ disease and autoimmune hypothyroidism. CD28 and ICOS were excluded as conferring susceptibility to the autoimmune disease processing. However, disease susceptibility was mapped to a 6.1 kb 3’ region of the CTLA-4 gene, and four candidate single-nucleotide polymorphisms (SNPs), CT60, JO31, JO30 and JO27_1, were identified as primary disease-causing variants.38

The CTLA-4 molecule exists as two isoforms in humans: a full length isoform (flCTLA-4) encoded by exons 1 – 4 and a soluble form (sCTLA-4) that lacks exon 3 (transmembrane domain). In mice, the flCTLA-4 isoform and a ligand-independent form (liCTLA-4) that lacks exon 2 (essential for binding CD80 and CD86) exist. The ratio of sCTLA-4 to flCTLA-4 mRNA splice forms in unstimulated CD4+ T cells has been shown to be 50% lower in homozygotes for the disease-predisposing alleles than in the protective genotype. This suggests that the 6.1 kb region containing the candidate DNA variants determines the efficiency of splicing and production of sCTLA-4.38 Subsequent work has also shown that liCTLA-4 is a more potent regulator of T-cell inhibition than the flCTLA-4, by dephosphorylating part of the TCR chain in activated T cells and thus preventing T-cell signalling.39 Expression of liCTLA-4, but not flCTLA-4, was also found to be higher in T regs from diabetes-resistant NOD congenic mice than in susceptible NOD mice,39 suggesting that liCTLA-4 can regulate the activation status of T regs in vivo in the diabetes-prone mice. Despite the comprehensive approach adopted in these important studies, it should be noted that additional minor genetic effects, including those 5’ of the CTLA-4 gene, cannot be completely excluded. However, it can be concluded from these studies that susceptibility to autoimmune thyroid disease and type 1 diabetes, conferred by the CD28/CTLA-4/ICOS locus, is likely to be the result of polymorphism within the CTLA-4 gene itself.

Even with all these recent developments in our knowledge of CTLA-4 and its role in autoimmune disease, the mechanisms by which it functions are still poorly understood. Several potential mechanisms whereby polymorphism of the CTLA-4 gene could lead to autoimmune disease have been postulated. It has been suggested that CTLA-4 may have an effect on the counter-regulation of the CD28 co-stimulatory signal and confer susceptibility to autoimmune diseases. Competition between CTLA-4 and CD28 may exist for each of the CD80 and CD86 receptors being influenced by CTLA-4 genotype. Soluble CTLA-4 appears to be present in human serum,40–42 and binding to CD80/CD86 may inhibit T-cell proliferation via increased activation of CD28.42 It has also been suggested that as CTLA-4 is constitutively expressed by T regs43–45 and as some of their function in peripheral tolerance is mediated by CTLA-4 binding to the CD80/CD86 receptors,45–47 T-effector activity could also be determined by CTLA-4 genotype. Other potential mechanisms have been proposed, including the potential role of CTLA-4 in stimulating trytophan catabolism by dendritic cells.46 Although these hypotheses are by no means exhaustive nor mutually exclusive, the fine mapping of the CTLA-4 gene susceptibility locus has opened up a large area for future studies aimed at increasing our understanding of the autoimmune disease process.

Lymphoid-specific phosphatase (LYP)

Protein tyrosine phosphotases (PTPs) have been shown to play an important role in T-cell signal transduction pathways by dephosphorylating and inactivating TCR-associated kinases (involved in TCR activation).48 The LYP encoded by the PTPN22 gene, located on chromosome 1p13, is a 110 kDa PTP48,49 expressed in lymphocytes where it physically associates with the SH3 domain of the Csk kinase,50 an important suppressor of the Src family of kinases (Lck and Fyn) which mediate downstream T-cell activation.50 Csk kinase activity has been shown to be dependent on the SH3 and SH2 domains of Csk, implying that association with other cellular proteins is crucial for Csk function.50 LYP is believed to mediate Csk function via its interaction with the SH3 domain, causing Csk dephosphorylation of Lck and Fyn, thus making LYP one of the most powerful T-cell activation inhibitors.49

Recently, Bottini et al.49 identified an SNP at nucleotide 1858 of the PTPN22 gene, changing codon 620 from an arginine (CGG) to a tryptophan (TGG).49 Association between this SNP and type 1 diabetes was examined in a North American cohort, with an increase of 1858T observed in patients with type 1 diabetes.49 The result was replicated in a small independent Sardinian dataset, producing association but at a lower level.49 Recent work in our laboratory has replicated association of 1858T in a large Graves’ disease cohort,51 and this, together with similar data from both a rheumatoid arthritis cohort 52 and a systemic lupus erythematosus cohort,53 suggests that LYP could have a role in multiple autoimmune diseases.

The proposed mechanism of action for LYP is believed to be related to the change from arginine in codon 620 (Arg620) to a tryptophan (Trp620). Residue 620 occurs in the P1 proline-rich motif of LYP involved in binding to the SH3 domain of Csk, where Arg620 interacts with a tryptophan (Trp47) of Csk.49 Replacing Arg620 with Trp620 is believed to disrupt this interaction. Functional studies have shown that when amino acids 603–710 of LYP were expressed as a protein in Escherichia coli, only the Arg620 was precipitated by the SH3 domain of Csk; Trp620 was not precipitated.49 These results suggest that only LYP with Arg620 present can form complexes with Csk kinase, enabling Csk’s inhibition of T-cell activation. In contrast, LYP with Trp620 does not bind to Csk’s SH3 domain correctly, therefore potentially preventing LYP’s inhibitory action. Although the data surrounding this functional SNP are exciting and open up a new area of research in the field of autoimmune disease, further studies are required to determine whether the Arg620–Trp620 polymorphism is the primary disease-causing DNA variant at this locus.


   Disease-specific mechanisms
Top
 Abstract
 Introduction: distinguishing...
 Autoimmunity and disease
 General autoimmune disease...
 Disease-specific mechanisms
Conclusions and future...
 References
 
AIRE1

The autoimmune regulatory gene (AIRE1), on chromosome 21q22.3, was first identified in 1997 in an attempt to localize the gene responsible for autoimmune polyendocrinopathy–candidiasis ectodermal dystrophy (APECED).54 APECED is a monogenic autosomal recessive disorder characterized by autoimmune polyendocrinopathies, chronic mucocutaneous candidiasis and ectodermal dystrophies.54 The AIRE1 gene sequence was found to consist of 14 exons containing 45 different mutations, with a 13 bp deletion at nucleotide 964 in exon 8 accounting for more than 70% of APECED alleles in the UK.55 The predicted AIRE1 protein was found to contain several domains indicative of a transcriptional regulator protein.56 These included two cysteine-rich regions, each specifying a zinc finger motif similar to the plant homeodomain (PHD) type domain, which have been reported in a number of proteins involved in the mediation or regulation of transcription.54 As APECED is a monogenic disorder characterized by autoimmune destruction of a variety of endocrine organs, researchers surmised that identification of genetic mutations in AIRE1 would give important insights into the mechanisms of autoimmune disease.

Tolerance to self-antigens has always been believed to occur primarily via central tolerance mechanisms for antigens expressed in the thymus, with peripheral tolerance employed to maintain tolerance to tissue-restricted antigens, as discussed earlier, but recent studies have suggested that this may not be the case. RNA transcripts from numerous proteins that were previously believed to be synthesized only in peripheral tissues, including the major auto-antigens insulin, thyroglobulin and myelin basic protein, were found to be expressed by MECs57 that are involved in clonal deletion of self-reactive T cells in stage 2 of central tolerance (see Fig. 1). Anderson et al.58 have used chimeric mice to show that the underlying autoimmunity associated with APECED was due to aire-deficient stromal cells, including MECs, and went further to show that autoimmunity could be induced in naive mice by transfusing them with lymphocyte populations from aire-deficient mice.58 This confirmed that AIRE expression in the peripheral tissues is not controlling autoimmune attack and that AIRE must be expressed in thymic MECs in order to control autoimmunity in the periphery. Microarray analysis further confirmed these findings by showing that many of the potential genes regulated by AIRE were tissue specific and included thyroglobulin and insulin.58 Studies tracing the fate of autoreactive CD4+ T cells with high affinity for a pancreatic antigen in transgenic mice with an Aire-null mutation showed that AIRE deficiency causes almost complete failure to delete antigen-specific T cells in the thymus.59 Taken together, these findings suggest that the AIRE1 gene plays a vital role in expressing organ-specific antigens not normally present in the thymus for presentation to naive T cells during negative selection, thus enabling self-reactive T cells to be deleted before entering the circulatory system.

This critical role of AIRE1 in central tolerance, together with its expression in multiple immunologically relevant tissues, such as the thymus, spleen lymph nodes and bone marrow,56 and the wide variety of autoimmune polyendocrinopathies that occur as a result of APECED, suggest that AIRE1 plays a central role in controlling the immune system and preventing autoimmunity. Even though AIRE1 is critical in controlling autoimmunity, variations within this gene have not been linked with any other common autoimmune disease, including type 1 diabetes,60 Graves’ disease60 and Addison’s disease,61 suggesting that polymorphisms of the AIRE1 gene lead specifically to the development of APECED.

Insulin

The insulin gene (INS) on chromosome 11p15 was first associated with type 1 diabetes in 1984.62 Association of this region was subsequently narrowed down to a 4.1 kb region, and has been attributed to the variable number of tandem repeats (VNTR) located in the 5’ region upstream from INS (reviewed by Anjos and Polychronakos63). The INS VNTR, now referred to as IDDM2, consists of tandem repeats of a 14–15 bp consensus sequence (ACAGGGGT(G/C)(T/C)GGGG),63 tending to cluster into 30–60 repeats (class I), 60–120 repeats (class II) and 120–170 repeats (class III). Homozygosity of class I alleles was found to be associated with type 1 diabetes, and studies have shown that the INS VNTR-associated trait is inherited in a dominantly protective fashion with one dose of a class III allele providing 60–70% protection from disease.64 Other studies have reported association with neighbouring genes outside the 4.1 kb region of the INS gene including association of a SNP within the 5’ region of the tyrosine hydoxylase gene (TH),65 suggesting that the aetiological variant within this region could lie outside the INS VNTR. Resequencing of a 325 kb region encompassing the TH gene, INS and other neighbouring genes has recently been performed and 177 polymorphisms were identified.66 The strongest association was found between the –23HphI SNP within the INS gene, which is often used as a surrogate marker for the VNTR class I and class III alleles. When regression analysis was employed, it was impossible to determine whether one of the SNPs within the INS (the –23HphI SNP and the +1140A/C SNP) or the INS VNTR contained the aetiological variant.66 This study also concluded that the INS VNTR class III allele is not inherited in a dominantly protective fashion as reported previously.64,66

Although the aetiological variant within the INS region could be in the –23HphI INS SNP, the +1140A/C INS SNP or the INS VNTR,66 the INS VNTR is still believed to be the best candidate for containing the aetiological variant contributing to type 1 diabetes. The INS VNTR is believed to contribute to type 1 diabetes through regulation of INS transcription within the thymus. Levels of INS mRNA expression in the human thymus have been shown to correlate with INS allelic variation. Transcriptional activity in the thymus has been found to be ~200–300% higher in INS transcripts encoded by the resistant class III alleles compared with levels of INS transcripts produced by the class I predisposing alleles (reviewed by Pugliese67). Higher insulin levels produced by class III alleles in the thymus may induce negative selection of insulin specific T lymphocytes more efficiently (or improve selection of T regs). In contrast, homozygosity of diabetes-predisposing class I alleles, resulting in lower insulin levels, may be associated with less efficient deletion of insulin-specific autoreactive T cells (or decreased selection of T regs).67 Functional work in the mouse supports this proposed mechanism; mouse models expressing low thymic levels of insulin presented with spontaneous peripheral reactivity to insulin, whereas mice with normal insulin levels did not.68 This proposed mechanism seems to be limited to type 1 diabetes, as studies in other autoimmune diseases, including Graves’ disease and multiple sclerosis,69 have shown no evidence of association with the INS VNTR.

Complement

Normally when excess antigen is present within the body, after an immune response is elicited, antibody is released and immune complexes (composed of several sets of antibody bound antigen) are formed. The immune complexes initiate complement activation, which mediates mast cell degranulation and attracts neutrophils and other phagocytic cells to actively break down (apoptosis) and remove the antigen captured within the immune complexes. However, in some cases when there is excess antigen, phagocytic cells cannot easily clear the immune complexes formed and they are deposited and accumulate at specific sites. This leads to neutrophil recruitment to the site where the complexes have been deposited, causing granular release and consequent tissue damage. Owing to the key role played by complement in preventing immune complex build-up and subsequent tissue damage, association of the complement system with systemic lupus erythematosus has been examined.

Homozygous deficiency of complement component C1q encoded by chromosome 1p23, although extremely rare (~40 reported cases to date), has been shown to carry a 98% risk of developing systemic lupus erythematosus.70 Studies in C1q–/– knockout mice provide additional support, showing that 50% of mice produced high titres of antinuclear antibodies. Moreover, approximately 25% developed severe glomerulonephritis (with deposition and accumulation of immune complexes of numerous apoptotic cells within affected glomerules),71 characteristic of systemic lupus erythematosus. Complement genes C2 and C4, located within the MHC class III region, have also been shown to be associated with systemic lupus erythematosus, with 75% of C4 homozygous subjects and 33% of C2 homozygous subjects developing systemic lupus erythematosus.72 The hierarchy of susceptibility amongst these components is C1q>C4>C2 in disease risk order.73

Two main mechanisms have been proposed to explain the causal link between complement deficiency and the development of systemic lupus erythematosus.74 First, as complement plays such a large part in initiating the breakdown of immune complexes and the removal of apoptotic cell debris, it has been proposed that disruption of this role could cause an autoimmune response.74 As the major auto-antigens in systemic lupus erythematosus have been found to be generated against materials from apoptotic cells,75,76 incomplete removal of apoptotic cell debris, because of deficiencies within components of the complement system, could enable the apoptotic debris (consisting of parts from cells normally recognized as ‘self’) to be presented to the immune system, triggering an autoimmune response.74 Secondly, it has been proposed that complement could play a key role in determining the thresholds of B- and T-lymphocyte activation, and that complement deficiency could impair the maintenance of peripheral tolerance, causing auto-antibody production and eventually systemic lupus erythematosus. Although the role of complement has been investigated in other autoimmune diseases, mostly focusing on C2 and C4, owing to the use of small datasets and the presence of LD with components of the HLA class II region, only systemic lupus erythematosus has been consistently associated with the complement system to date.


   Conclusions and future directions
Top
 Abstract
 Introduction: distinguishing...
 Autoimmunity and disease
 General autoimmune disease...
 Disease-specific mechanisms
 Conclusions and future...
References
 
Over the past 30 years many advances have been made in our understanding of autoimmune disease and the mechanisms by which it develops. New evidence from the clustering of autoimmune diseases within families suggests that there are shared mechanisms between autoimmune diseases. Much progress has been made on both the HLA and CTLA-4 gene regions, with advances in narrowing down the aetiological variants within the CTLA-4 gene although the primary aetiological variant/s within the HLA region remain more elusive. Along with these advances, progress has also been made in identifying disease-specific genes, such as INS VNTR, AIRE1 and complement, and showing how their mechanisms are different from those that predispose to the autoimmune process in general. With the recent discovery of association of the LYP gene with the autoimmune disease process and reports of association of a myriad of other exciting candidate genes, such as the vitamin D receptor in type 1 diabetes,13 thyroglobulin in Graves’ disease28 and PADI4 in rheumatoid arthritis,77 awaiting confirmation, much excitement lies ahead in discovering new genes and enlarging upon our understanding of how these genes contribute to both general and disease-specific autoimmune mechanisms. This should lead to the development of improved diagnostic tools and treatments that directly target the underlying causes of autoimmune disease.

Accepted for publication November 22, 2004.


   References
Top
 Abstract
 Introduction: distinguishing...
 Autoimmunity and disease
 General autoimmune disease...
 Disease-specific mechanisms
 Conclusions and future...
 References
 

  1. Sprent J, Kishimoto H (2001) The thymus and central tolerance. Transplantation, 72, S25–8.[ISI][Medline]
  2. Shevach EM (2000) Regulatory T cells in autoimmmunity. Annu. Rev. Immunol., 18, 423–49.[CrossRef][ISI][Medline]
  3. Becker KG (1999) Comparative genetics of type 1 diabetes and autoimmune disease: common loci, common pathways? Diabetes, 48, 1353–8.[Abstract]
  4. Vyse TJ, Todd JA (1996) Genetic analysis of autoimmune disease. Cell, 85, 311–18.[CrossRef][ISI][Medline]
  5. Heward J, Gough SC (1997) Genetic susceptibility to the development of autoimmune disease. Clin. Sci. (Colch.), 93, 479–91.[Medline]
  6. Tait KF, Marshall T, Berman J, et al. (2004) Clustering of autoimmune disease in parents of siblings from the Type 1 Diabetes Warren Repository. Diabet. Med., 21, 358–62.[CrossRef][ISI][Medline]
  7. Coles AJ, Wing M, Smith S, et al. (1999) Pulsed monoclonal antibody treatment and autoimmune thyroid disease in multiple sclerosis. Lancet, 354, 1691–5.[CrossRef][ISI][Medline]
  8. Horsfall AC, Howson R, Silveira P, Williams DG, Baxter AG (1998) Characterization and specificity of B-cell responses in lupus induced by Mycobacterium bovis in NOD/Lt mice. Immunology, 95, 8–17.[CrossRef][ISI][Medline]
  9. Mein CA, Esposito L, Dunn MG, et al. (1998) A search for type 1 diabetes susceptibility genes in families from the United Kingdom. Nat. Genet., 19, 297–300.[CrossRef][ISI][Medline]
  10. Singal DP, Blajchman MA (1973) Histocompatibility (HL-A) antigens, lymphocytotoxic antibodies and tissue antibodies in patients with diabetes mellitus. Diabetes, 22, 429–32.[ISI][Medline]
  11. Nerup J, Platz P, Andersen OO, et al. (1974) HL-A antigens and diabetes mellitus. Lancet, ii, 864–6.
  12. Cudworth AG, Woodrow JC (1975) HL-A system and diabetes mellitus. Diabetes, 24, 345–9.[Abstract]
  13. Tait KF, Gough SC (2003) The genetics of autoimmune endocrine disease. Clin. Endocrinol. (Oxf), 59, 1–11.[CrossRef][Medline]
  14. Todd JA, Bell JI, McDevitt HO (1987) HLA-DQ beta gene contributes to susceptibility and resistance to insulin-dependent diabetes mellitus. Nature, 329, 599–604.[CrossRef][Medline]
  15. Cucca F, Lampis R, Congia M, et al. (2001) A correlation between the relative predisposition of MHC class II alleles to type 1 diabetes and the structure of their proteins. Hum. Mol. Genet., 10, 2025–37.[Abstract/Free Full Text]
  16. Giordano M, D’Alfonso S, Momigliano-Richiardi P (2002) Genetics of multiple sclerosis: linkage and association studies. Am. J. Pharmacogenom., 2, 37–58.[CrossRef][Medline]
  17. Zipp F, Windemuth C, Pankow H, et al. (2000) Multiple sclerosis associated amino acids of polymorphic regions relevant for the HLA antigen binding are confined to HLA-DR2. Hum. Immunol., 61, 1021–30.[CrossRef][ISI][Medline]
  18. Gregersen PK, Silver J, Winchester RJ (1987) The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. Arthritis Rheum., 30, 1205–13.[ISI][Medline]
  19. Newton JL, Harney SM, Wordsworth BP, Brown MA (2004) A review of the MHC genetics of rheumatoid arthritis. Genes Immun., 5, 151–7.[CrossRef][ISI][Medline]
  20. de Vries N, Tijssen H, van Riel PL, van de Putte LB (2002) Reshaping the shared epitope hypothesis: HLA-associated risk for rheumatoid arthritis is encoded by amino acid substitutions at positions 67–74 of the HLA-DRB1 molecule. Arthritis Rheum., 46, 921–8.[CrossRef][ISI][Medline]
  21. Milicic A, Lee D, Brown MA, Darke C, Wordsworth BP (2002) HLA-DR/DQ haplotype in rheumatoid arthritis: novel allelic associations in UK Caucasians. J. Rheumatol., 29, 1821–6.[ISI][Medline]
  22. Graham RR, Ortmann WA, Langefeld CD, et al. (2002) Visualizing human leukocyte antigen class II risk haplotypes in human systemic lupus erythematosus. Am. J. Hum. Genet., 71, 543–53.[CrossRef][ISI][Medline]
  23. Heward JM, Allahabadia A, Daykin J et al. (1998) Linkage disequilibrium between the human leukocyte antigen class II region of the major histocompatibility complex and Graves’ disease: replication using a population case control and family-based study. J. Clin. Endocrinol. Metab., 83, 3394–7.[Abstract/Free Full Text]
  24. Simmonds MJ, Howson JM, Heward JM, Cordell HJ, Foxall H, Carr-Smith J, Gibson SM, Walker N, Tomer Y, Franklyn JA, Todd JA, Gough SC (2005) Regression mapping of association between the human leukocyte antigen region and Graves disease. Am. J. Hum. Genet., 76(1), 157–63.
  25. Awata T, Kuzuya T, Matsuda A, Iwamoto Y, Kanazawa Y (1992) Genetic analysis of HLA class II alleles and susceptibility to type 1 (insulin-dependent) diabetes mellitus in Japanese subjects. Diabetologia, 35, 419–24.[CrossRef][ISI][Medline]
  26. Cucca F, Muntoni F, Lampis R et al. (1993) Combinations of specific DRB1, DQA1, DQB1 haplotypes are associated with insulin-dependent diabetes mellitus in Sardinia. Hum. Immunol., 37, 85–94.[ISI][Medline]
  27. Cucca F, Lampis R, Frau F et al. (1995) The distribution of DR4 haplotypes in Sardinia suggests a primary association of type I diabetes with DRB1 and DQB1 loci. Hum. Immunol., 43, 301–8.[CrossRef][ISI][Medline]
  28. Simmonds MJ, Gough SC (2004) Unravelling the genetic complexity of autoimmune thyroid disease: HLA, CTLA-4 and beyond. Clin. Exp. Immunol., 136, 1–10.[CrossRef][ISI][Medline]
  29. Weetman AP, Zhang L, Tandon N, Edwards OM (1991) HLA associations with autoimmune Addison’s disease. Tissue Antigens, 38, 31–3.[ISI][Medline]
  30. Lie BA, Todd JA, Pociot F, et al. (1999) The predisposition to type 1 diabetes linked to the human leukocyte antigen complex includes at least one non-class II gene. Am. J. Hum. Genet., 64, 793–800.[CrossRef][ISI][Medline]
  31. Johansson S, Lie BA, Todd JA, et al. (2003) Evidence of at least two type 1 diabetes susceptibility genes in the HLA complex distinct from HLA-DQB1, -DQA1 and -DRB1. Genes Immun., 4, 46–53.[CrossRef][ISI][Medline]
  32. Kilding R, Iles MM, Timms JM, Worthington J, Wilson AG (2004) Additional genetic susceptibility for rheumatoid arthritis telomeric of the DRB1 locus. Arthritis Rheum., 50, 763–9.[CrossRef][ISI][Medline]
  33. Okamoto K, Makino S, Yoshikawa Y, et al. (2003) Identification of I kappa BL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am. J. Hum. Genet., 72, 303–12.[CrossRef][ISI][Medline]
  34. Newton J, Brown MA, Milicic A, et al. (2003) The effect of HLA-DR on susceptibility to rheumatoid arthritis is influenced by the associated lymphotoxin alpha-tumor necrosis factor haplotype. Arthritis Rheum., 48, 90–6.[CrossRef][ISI][Medline]
  35. Newton JL, Harney SM, Timms AE, et al. (2004) Dissection of class III major histocompatibility complex haplotypes associated with rheumatoid arthritis. Arthritis Rheum., 50, 2122–9.[CrossRef][ISI][Medline]
  36. Mueller DL, Jenkins MK, Schwartz RH (1989) Clonal expansion versus functional clonal inactivation: a costimulatory signalling pathway determines the outcome of T cell antigen receptor occupancy. Annu. Rev. Immunol., 7, 445–80.[ISI][Medline]
  37. Egen JG, Kuhns MS, Allison JP (2002) CTLA-4: new insights into its biological function and use in tumor immunotherapy. Nat. Immunol., 3, 611–18.[CrossRef][ISI][Medline]
  38. Ueda H, Howson JM, Esposito L, et al. (2003) Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature, 423, 506–11.[CrossRef][Medline]
  39. Vijayakrishnan L, Slavik JM, Illes Z, et al. (2004) An autoimmune disease-associated CTLA-4 splice variant lacking the B7 binding domain signals negatively in T cells. Immunity, 20, 563–75.[CrossRef][ISI][Medline]
  40. Magistrelli G, Jeannin P, Herbault N, et al. (1999) A soluble form of CTLA-4 generated by alternative splicing is expressed by nonstimulated human T cells. Eur. J. Immunol., 29, 3596–602.[CrossRef][ISI][Medline]
  41. Oaks MK, Hallett KM (2000) Cutting edge: a soluble form of CTLA-4 in patients with autoimmune thyroid disease. J. Immunol., 164, 5015–18.[Abstract/Free Full Text]
  42. Oaks MK, Hallett KM, Penwell RT, Stauber EC, Warren SJ, Tector AJ (2000) A native soluble form of CTLA-4. Cell. Immunol., 201, 144–53.[CrossRef][ISI][Medline]
  43. Finger EB, Bluestone JA (2002) When ligand becomes receptor–tolerance via B7 signaling on DCs. Nat. Immunol., 3, 1056–7.[CrossRef][ISI][Medline]
  44. Asano M, Toda M, Sakaguchi N, Sakaguchi S (1996) Autoimmune disease as a consequence of developmental abnormality of a T cell subpopulation. J. Exp. Med., 184: 387–96.[Abstract/Free Full Text]
  45. Manzotti CN, Tipping H, Perry LC, et al. (2002) Inhibition of human T cell proliferation by CTLA-4 utilizes CD80 and requires CD25+ regulatory T cells. Eur. J. Immunol., 32, 2888–96.[CrossRef][ISI][Medline]
  46. Grohmann U, Orabona C, Fallarino F, et al. (2002) CTLA-4-Ig regulates tryptophan catabolism in vivo. Nat. Immunol., 3, 1097–101.
  47. Lin H, Rathmell JC, Gray GS, Thompson CB, Leiden JM, Alegre ML (1998) Cytotoxic T lymphocyte antigen 4 (CTLA4) blockade accelerates the acute rejection of cardiac allografts in CD28-deficient mice: CTLA4 can function independently of CD28. J. Exp. Med., 188, 199–204.[Abstract/Free Full Text]
  48. Gjorloff-Wingren A, Saxena M, Han S, et al. (2000) Subcellular localization of intracellular protein tyrosine phosphatases in T cells. Eur. J. Immunol., 30, 2412–21.[CrossRef][ISI][Medline]
  49. Bottini N, Musumeci L, Alonso A, et al. (2004) A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes. Nat. Genet., 36, 337–8.[CrossRef][ISI][Medline]
  50. Cloutier JF, Veillette A (1999) Cooperative inhibition of T-cell antigen receptor signaling by a complex between a kinase and a phosphatase. J. Exp. Med., 189, 111–21.[Abstract/Free Full Text]
  51. Smyth D, Cooper JD, Collins JE, et al. (2004) Replication of an association between the lymphoid tyrosine phosphatase locus (LYP/PTPN22) with type 1 diabetes, and evidence for its role as a general autoimmunity locus. Diabetes, 53, 3020–3.[Abstract/Free Full Text]
  52. Begovich AB, Carlton VE, Honigberg LA, et al. (2004) A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am. J. Hum. Genet., 75, 330–7.[CrossRef][ISI][Medline]
  53. Kyogoku C, Langefeld CD, Ortmann WA, et al. (2004) Genetic association of the R620W polymorphism of protein tyrosine phosphatase PTPN22 with human SLE. Am. J. Hum. Genet., 75, 504–7[CrossRef][ISI][Medline]
  54. Finnish-German APECED Consortium (1997) An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHD-type zinc-finger domains. Finnish-German APECED Consortium. Autoimmune Polyendocrinopathy–Candidiasis-Ectodermal Dystrophy. Nat. Genet., 17, 399–403.[CrossRef][ISI][Medline]
  55. Pearce SH, Cheetham T, Imrie H, et al. (1998) A common and recurrent 13-bp deletion in the autoimmune regulator gene in British kindreds with autoimmune polyendocrinopathy type 1. Am. J. Hum. Genet., 63, 1675–84.[CrossRef][ISI][Medline]
  56. Kumar PG, Laloraya M, She JX (2002) Population genetics and functions of the autoimmune regulator (AIRE). Endocrinol. Metab. Clin. N. Am., 31: 321–38.[CrossRef][ISI][Medline]
  57. Klein L, Kyewski B (2000) Self-antigen presentation by thymic stromal cells: a subtle division of labor. Curr. Opin. Immunol., 12, 179–86.[CrossRef][ISI][Medline]
  58. Anderson MS, Venanzi ES, Klein L, et al. (2002) Projection of an immunological self shadow within the thymus by the aire protein. Science, 298, 1395–401.[Abstract/Free Full Text]
  59. Liston A, Lesage S, Wilson J, Peltonen L, Goodnow CC (2003) Aire regulates negative selection of organ-specific T cells. Nat. Immunol., 4, 350–4.[CrossRef][ISI][Medline]
  60. Nithiyananthan R, Heward JM, Allahabadia A, Barnett AH, Franklyn JA, Gough SC (2000) A heterozygous deletion of the autoimmune regulator (AIRE1) gene, autoimmune thyroid disease, and type 1 diabetes: no evidence for association. J. Clin. Endocrinol. Metab., 85, 1320–2.[Abstract/Free Full Text]
  61. Vaidya B, Imrie H, Geatch DR, et al. (2000) Association analysis of the cytotoxic T lymphocyte antigen-4 (CTLA-4) and autoimmune regulator-1 (AIRE-1) genes in sporadic autoimmune Addison’s disease. J. Clin. Endocrinol. Metab., 85, 688–91.[Abstract/Free Full Text]
  62. Bell GI, Horita S, Karam JH (1984) A polymorphic locus near the human insulin gene is associated with insulin-dependent diabetes mellitus. Diabetes, 33, 176–83.[Abstract]
  63. Anjos S, Polychronakos C (2004) Mechanisms of genetic susceptibility to type I diabetes: beyond HLA. Mol. Genet. Metab., 81, 187–95.[CrossRef][ISI][Medline]
  64. Bennett ST, Lucassen AM, Gough SC, et al. (1995) Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus. Nat. Genet., 9, 284–92.[CrossRef][ISI][Medline]
  65. Doria A, Lee J, Warram JH, Krolewski AS (1996) Diabetes susceptibility at IDDM2 cannot be positively mapped to the VNTR locus of the insulin gene. Diabetologia, 39, 594–9.[ISI][Medline]
  66. Barratt BJ, Payne F, Lowe CE, et al. (2004) Remapping the insulin gene/IDDM2 locus in type 1 diabetes. Diabetes, 53, 1884–9.[Abstract/Free Full Text]
  67. Pugliese A (2004) Central and peripheral autoantigen presentation in immune tolerance. Immunology, 111, 138–46.[CrossRef][ISI][Medline]
  68. Chentoufi AA, Polychronakos C (2002) Insulin expression levels in the thymus modulate insulin-specific autoreactive T-cell tolerance: the mechanism by which the IDDM2 locus may predispose to diabetes. Diabetes, 51, 1383–90.[Abstract/Free Full Text]
  69. Allahabadia A, Heward J, Carr-Smith J, et al. (1999) Sharing of susceptibility loci between autoimmune diseases: lack of association of the insulin gene region with Graves’ disease. Thyroid, 9, 317–18.[ISI][Medline]
  70. Stone NM, Williams A, Wilkinson JD, Bird G (2000) Systemic lupus erythematosus with C1q deficiency. Br. J. Dermatol., 142, 521–4.[CrossRef][ISI][Medline]
  71. Botto M, Dell’Agnola C, Bygrave AE, et al. (1998) Homozygous C1q deficiency causes glomerulonephritis associated with multiple apoptotic bodies. Nat. Genet., 19, 56–9.[CrossRef][ISI][Medline]
  72. Pickering MC, Walport MJ (2000) Links between complement abnormalities and systemic lupus erythematosus. Rheumatology, 39, 133–41.[Free Full Text]
  73. Tsao BP (2003) The genetics of human systemic lupus erythematosus. Trends Immunol., 24, 595–602.[CrossRef][ISI][Medline]
  74. Manderson AP, Botto M, Walport MJ (2004) The role of complement in the development of systemic lupus erythematosus. Annu. Rev. Immunol., 22, 431–56.[CrossRef][ISI][Medline]
  75. Rosen A, Casciola-Rosen L, Ahearn J (1995) Novel packages of viral and self-antigens are generated during apoptosis. J. Exp. Med., 181: 1557–61.[Abstract/Free Full Text]
  76. Casciola-Rosen LA, Anhalt G, Rosen A (1994) Autoantigens targeted in systemic lupus erythematosus are clustered in two populations of surface structures on apoptotic keratinocytes. J. Exp. Med., 179, 1317–30.[Abstract/Free Full Text]
  77. Suzuki A, Yamada R, Chang X, et al. Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase, 4, are associated with rheumatoid arthritis. Nat. Genet., 34, 395–402.