The genetics of complex autoimmune diseases: non-MHC susceptibility genes

Susceptibility to complex autoimmune diseases (AIDs) is a multigenic phenotype affected by a variety of genetic and environmental or stochastic factors. After over a decade of linkage analyses, the identification of non-major histocompatibility complex (non-MHC) susceptibility alleles has proved to be difficult, predominantly because of extensive genetic heterogeneity and possible epistatic interactions among the multiple genes required for disease development. Despite these difficulties, progress has been made in elucidating the genetic mechanisms that influence the inheritance of susceptibility, and the pace of gene discovery is accelerating. An intriguing new finding has been the colocalization of several AID susceptibility genes in both rodent models and human linkage studies. This may indicate that several susceptibility alleles affect multiple AIDs, or alternatively that genomic organization has resulted in the clustering of many immune system genes. The completion of the human genome sequence, coupled with the imminent completion of the mouse genome, should yield key information that will dramatically enhance the rate of gene discovery in complex conditions such as AID susceptibility.     

Autoimmunity, histocompatibility, and aging.

The immunologic theory of aging proposes that the normal process of aging in man and all animals is pathogenetically related to faulty immunological processes and may be analogous to a type of autoimmune phenomena ultimately involving all body tissues. It may be said that the sharply increased incidence in elderly humans of the autoimmune and immunodeficiency "diseases of age" are thought to be greatly potentiated by the age-related decline in immune surveillance mechanisms particularly involving self/non-self discriminatory abilities. The major histocompatibility complex has emerged as a complex of "supergenes" coding for antigens whose ultimate biological function may be to serve as recognition units allowing lymphocytes to recognize self from non-self on an immunological basis. Also, recent data are consistent with our supposition that differences in age-specific peaks of various immune functional parameters in genetically homozygous mice may be influenced by genes linked to the major histocompatibility complex. These differences may account, at least in part, for the highly strain-dependent, age-specific incidence of certain diseases, including autoimmune and malignant diseases in the mouse. Heightened susceptibility to develop a particular disease in a susceptible animal occurs when a certain balance is reached between the interplay of immune functional parameters which mature, differentiate, or decline at different rates in the same animal. The age-specificity of this balance may be under partial control of H-2 or HLA-linked genes.     

Genetic aspects of rheumatoid arthritis

Summary Studies on the population of patients with rheumatoid arthritis and families with multiple cases of rheumatoid arthritis have provided definite evidence that susceptibility to the disease is determined both by genetic factors associated with alleles of the major histocompatibility complex as well as environmental factors. The development of seropositive, but not seronegative rheumatoid arthritis is associated with the presence in an individual of the la alloantigen HLA-DR4. This association is common to all major ethnic groups. Some evidence exists that this association is stronger in patients that have more severe disease but this fact requires further study. The fraction of the seropositive patients with rheumatoid arthritis that lack HLA-DR4 has not been well characterized. The occurrence of certain untoward side effects of therapy is influenced by the presence of HLA-DR2 or HLA-DR3.Family studies emphasize the association with HLA-DR4, and indicate that the disease has a dominant mode of inheritance with partial penetrance. The inheritance of susceptibility appeared, at least in some families, to be primarily associated with the inheritance of HLA-DR4 itself and not well explained by a hypothetical disease susceptibility gene present at low frequency and associated in linkage disequilibrium with a HLA-DR4 marker. However, in others different mechanisms appeared more likely. A model of two MHC genes involved in influencing disease susceptibility is postulated. Speculations concerning the primary disease mechanism are presented involving abnormalities of IR genes, general immune regulation, and factors outside of the immune system.     

The Major Histocompatibility Complex and Insulin Dependent (Type 1) Diabetes

The majority of the genetic component in insulin dependent (Type 1) diabetes mellitus can be explained by associations with genes on short arm of chromosome 6 located in the major histocompatibility complex. With the advent of cloning of the HLA Class II region genes it has been possible to refine the previous known association of HLA-DR3 and DR4 with this disease. Strong associations of IDDM have now been shown to exist with the DQB1 gene and/or linked genes, although this does not completely explain the HLA susceptibility to this disease.     

The major histocompatibility complex and insulin dependent (type 1) diabetes

The majority of the genetic component in insulin dependent (Type 1) diabetes mellitus can be explained by associations with genes on short arm of chromosome 6 located in the major histocompatibility complex. With the advent of cloning of the HLA Class II region genes it has been possible to refine the previous known association of HLA-DR3 and DR4 with this disease. Strong associations of IDDM have now been shown to exist with the DQB1 gene and/or linked genes, although this does not completely explain the HLA susceptibility to this disease.     

Complotypes in Pemhigus vulgaris: Differences between Jewish and Non-Jewish patients

Haplotypes of alleles of the major histocompatibility complex (MHC) complement genes BF, C2, C4A, and C4B are inherited as single highly polymorphic genetic units called complotypes. There are about a dozen complotypes with frequencies above about 0.01 in Caucasians. In the blistering disease pemphigus vulgaris, the complotypes SC21 and SB45 were found to be markedly elevated in patients compared with general Caucasian controls. The SC21 increase was in Ashkenazi Jewish patients exclusively (relative RISK = 17 in that population), whereas SB45 was found solely in non-Jewish Caucasians (specific population relative RISK = 57). Although there are unusually high relative risks, it is most unlikely that these complotypes represent susceptibility genes for pemphigus vulgaris. Rather, it is probable that they mark extended major histocompatibility complex haplotypes with fixed DNA so that independent examples in the population have the same alleles. It is likely that it is the class II genes on these haplotypes that confer susceptibility     

A review of the MHC genetics of rheumatoid arthritis

Rheumatoid arthritis is a common complex genetic disease, and, despite a significant genetic element, no gene other than HLA-DRB1 has been clearly demonstrated to be involved in the disease. However, this association accounts for less than half the overall genetic susceptibility. Investigation of other candidate genes, in particular those that reside within the major histocompatibility complex, are hampered by the presence of strong linkage disequilibrium and problems with study design.     

The HL-A System in Reiter's Syndrome

The HL-A phenotypes were determined in 50 patients with Reiter's syndrome. HL-A27 was found in 34 (68%) compared to 7.7% of controls. There was an association between the presence of HL-A27 and sacro-iliitis, uveitis and keratoderma blenorrhagica. Reiter's syndrome was found to have occurred in HL-A27 positive identical twins. In four sibships a brother, sharing a haplotype with the proband, was found to have spondylitis. There was evidence that in some HL-A27 positive individuals spondylitis had developed prior to the first attack of Reiter's syndrome, suggesting that spondylitis and Reiter's syndrome may be separate disease processes in the one genetically predisposed individual. When Reiter's syndrome was associated with severe keratoderma blenorrhagica and widespread psoriasiform lesions, sometimes with persisting psoriasis or recurrent uveitis, HL-A27 was present and HL-A17 absent.
There is some evidence that the HL-A phenotype itself does not determine susceptibility to disease in HL-A27 positive individuals but that linked immune response genes may be present.     

Significance of MHC class II haplotypes and IgG Fc receptors in SLE

Systemic lupus erythematosus (SLE) is a systemic antibody-mediated autoimmune disease that develops under the control of multiple susceptibility genes. Genetic studies in murine and human SLE have identified several chromosomal intervals that contain candidate susceptibility genes. However, the ultimate identification of the genes and their roles in disease process need much further investigation. Spontaneous murine SLE models provide useful tools in this respect. In this chapter, we show this line of investigation, particularly focusing on the roles of major histocompatibility complex (MHC) class II and immunoglobulin G Fc receptors (FcγRs). The existence of high-affinity autoantibodies is evidence that autoimmunity in SLE is antigen-driven. Thereby, MHC class II haplotypes have been implicated in SLE susceptibility; however, because of the linkage disequilibrium that exists among the class I, II and III genes within the MHC complex, it has been difficult to discriminate the relative contributions of individual loci. On the other hand, the extent of antibody synthesis upon antigen stimulation and associated inflammatory cascades are controlled in several ways by the balance of stimulatory and inhibitory signaling molecules on immune cells. Stimulatory/inhibitory FcγRs mediate one such mechanism, and there are reports indicating the association between polymorphic FcγRs and SLE. However, as stimulatory and inhibitory FcγRs cluster on the telomeric chromosome 1, the absolute contribution of individual genes has been difficult to dissect. In studies of genetic dissection using interval-congenic and intragenic recombinant mouse strains of SLE models, we show evidence and discuss how and to what extent MHC class II molecules and stimulatory/inhibitory FcγRs are involved in SLE susceptibility.     

Lack of association of CCR2-64I and CCR5-Delta 32 with type 1 diabetes and latent autoimmune diabetes in adults

It is well known that type 1 diabetes mellitus (T1DM) is a complex genetic disease resulting from the autoimmune destruction of pancreatic beta cells. Several genes have been associated with susceptibility and/or protection for T1DM, but the disease risk is mostly influenced by genes located in the class II region of the major histocompatibility complex. The attraction of leukocytes to tissues is essential for inflammation and the beginning of autoimmune reaction. The process is controlled by chemokines, which are chemotactic cytolines. Some studies have shown that CCR2-64I and CCR5-Delta 32 might be important for protection of susceptibility to some immunologically-mediated disorders. In the present study, we demonstrate the lack of association between CCR2-64I and CCR5-Delta 32 gene polymorphism and TIDM and we describe a new method for a simple and more precise genotyping of the CCR2 gene.     

Epistatic effects occurring among susceptibility and protective MHC genes in IgA deficiency

Immunoglobulin A deficiency (IgAD), the most prevalent primary immunodeficiency in Caucasian populations, shows strong evidence of polygenic inheritance with several associated genes being located in the major histocompatibility complex (MHC). Our aims were to determine which previously described MHC associations were primary and not secondary to a decrease or an increase in other MHC haplotype frequencies, to study the genetic interactions between all disease-associated MHC haplotypes and, finally, to ascertain the relative importance of protection vs susceptibility. A relative predispositional effect (RPE) study showed that in addition to the primary positive association of IgAD with HLA-DRB1*0102, DR3/TNFa2b3, and DR7 carrying haplotypes, DRB1*1501 was a marker of a primary protective factor in the Spanish population. Our data also indicate that the combined presence in an individual of two MHC susceptibility haplotypes notably increases the predisposition to the disease and that DRB1*1501 positive haplotypes eliminate the susceptibility conferred by any other MHC haplotype.     

Epistasis between DSG1 and HLA class II genes in pemphigus foliaceus

Pemphigus foliaceus (PF) is a rare and severe cutaneous autoimmune disease caused by autoantibodies directed against desmoglein 1 (DSG1), a desmosomal adhesion glycoprotein. We previously showed that the DSG1 gene is polymorphic and that a coding synonymous T/C single nucleotide polymorphism at position 809 is associated with PF. To determine whether the disease occurred as a consequence of complex genetic interactions, we simultaneously examined the contribution of major histocompatibility complex (MHC) class II and DSG1 polymorphisms to PF susceptibility. Our analysis performed in 31 PF patients and 84 healthy controls first confirmed the previously reported common DRB1*04 and DRB1*14 genetic background in PF and individualized DRB1*0102, DRB1*0402 and DRB1*0406, and DRB1*1404 as susceptibility MHC class II alleles in French Caucasian PF patients. It also showed that the C/C(809) genotype was associated with PF. Combined analysis of HLA class II and DSG1 polymorphisms with several distinct statistical methods including logistic regression, showed that the DRB1*04 allele and the C/C(809) genotype interact to confer a higher susceptibility to PF. These data demonstrate the role of epistasis between individual genes in PF susceptibility and illustrate the genetic complexity of organ-specific autoimmune diseases.     

A molecule basis for the HLA association in rheumatoid arthritis

Rheumatoid arthritis (RA) is a common chronic autoimmune disease that primarily affects the joints. The etiology of RA is unknown, and the pathogenesis is only poorly defined. One of the few clues to the understanding of the pathogenesis of RA is the observation that the disease is associated with genes in the major histocompatibility complex (MHC). Recent structural and functional studies provide molecular insight into the role of MHC genes in RA susceptibility. This insight provides an important basis for further understanding of the disease mechanism, generation of humanized animal models for RA, and the development of new immunomodulatory drugs with a minimum of unwanted side effects.     

Genetic control of autoimmunity in type 1 diabetes

DNA sequence analysis of major histocompatibility complex (MHC) class II genes from humans and rodents with type 1 (insulin-dependent) diabetes indicates that a portion of MHC-linked genetic susceptibility in humans is determined by the HLA-DQA1 and -DQB1 loci. In this article John Todd summarizes recent advances in these studies. The conformation of DQ molecules and their levels of expression may influence the efficiency of autoantigen presentation and the degree of pancreatic beta cells destruction during disease development. Certain DAQ1 and DQB1 alleles correlate with decreased susceptibility to disease. The penetrance of class II alleles that are correlated with positive susceptibility may be influenced by environmental factors such as bacterial and viral infections.     

Non-HLA associations with autoimmune diseases

Susceptibility to autoimmune diseases (AID) has been associated with multiple combinations of genes and environmental or stochastic factors. The strongest influence on susceptibility to autoimmunity is the major histocompatibility complex (MHC), in particular HLA; however, linkage analyses among multiple affected family members have established that non-MHC chromosomal susceptibility regions also influence the susceptibility towards AID. Besides HLA, three non-HLA genes have been convincingly associated with different AID: Citotoxic T lymphocyte-associated antigen 4 (CTLA4), Protein Tyrosine Phosphatase (PTPN22) and Tumor Necrosis Factor-alpha (TNF), indicating that autoimmune phenotypes could represent pleiotropic outcomes of non-specific diseases' genes that underline similar immunogenetic mechanisms. Identification of genes that generate susceptibility will enhance our understanding of the mechanisms that mediate these complex diseases and will allow us to predict and/or prevent them as well as to discover new therapeutic interventions.     

The haplotype structure of the human major histocompatibility complex

There is great interest in the use of single-nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD) analysis to localize human disease genes. The results suggest that the human genome, including the major histocompatibility complex (MHC), consists largely of 5- to 200-kb blocks of sequence fixity between which random recombination occurs. Direct determination of MHC haplotypes from family studies also demonstrates similar-sized blocks, but otherwise gives a very different picture, with a third to a half of Caucasian haplotypes fixed from HLA-B to HLA-DR/DQ (at least 1 Mb) as conserved extended haplotypes (CEHs), some of which encompass more than 3 Mb. These fixed haplotypes differ in frequency both in different Caucasian subpopulations and in Caucasian patients with HLA-associated diseases, complicating disease susceptibility gene localization. The inherent inability of LD analysis to "see" DNA fixity beyond three markers contributes to the failure of SNP/LD analysis to define in detail or even detect CEHs in the MHC and probably elsewhere in the genome. More importantly, the use of statistical analysis, rather than direct haplotype determination and counting, fails to reveal the details of haplotype structure essential for gene localization. Given the oversimplified picture of the MHC (and probably the rest of the genome) provided only by SNP/LD-defined blocks, it is questionable whether this approach will be of great help in disease susceptibility gene localization or identification.     

Incomplete penetrance of MHC susceptibility genes: prospective analysis of polygenic MHC-determined traits

We propose an approach to understanding incomplete penetrance of disease susceptibility genes as a method of studying the underlying mechanisms of polygenic diseases. Incomplete penetrance is the failure of genetically susceptible individuals to exhibit a trait. We define as baseline penetrance that which occurs in genetically identical (monozygotic) twins of an index subject with a major histocompatibility complex (MHC)-associated disease or trait. We consider two mechanisms for incomplete baseline penetrance: an extrinsic (environmental) trigger and an intrinsic stochastic, gene-associated process. The latter can be detected for dominant expression because susceptibility genes in homozygotes (with their two intrinsic triggers) will be up to twice as frequently penetrant as those in heterozygotes. The extent of MHC and non-MHC gene contribution determines differences between baseline penetrance and apparent penetrance in MHC-identical sib pairs, sib pairs in general and MHC-identical unrelated individuals. Inheritance patterns in families do not reveal modes of inheritance of incompletely penetrant polygenic MHC-determined traits. A method is proposed to study such traits prospectively in persons presumed to be homozygous, heterozygous or non-carrying for susceptibility genes by determining trait expression in homozygotes, heterozygotes or non-carriers of trait-associated conserved extended MHC haplotypes. The method provides direct estimates of apparent penetrance rates, modes of genetic determination, and, if the trait is dominant, the origin of penetrance. When applied to dominant MHC susceptibility gene-determined immunoglobulin deficiencies in two populations, the ratios of affected haplotype homozygotes to heterozygotes near 2.0 were consistent with an intrinsic mechanism for baseline penetrance acting on the MHC susceptibility genes.