Polymorphic markers of human T-cell receptor alpha and beta genes. Family studies and comparison of frequencies in healthy individuals and patients with multiple sclerosis and myasthenia gravis

Revisiting the T-cell receptor alpha/delta locus and possible associations with multiple sclerosis

A role for T cells in the pathogenesis of multiple sclerosis (MS) is well supported, evidenced by myriad immunological studies, as well as the unequivocal genetic influence of the major histocompatibility complex (MHC). Despite many attempts, no convincing genetic associations have been made between T-cell receptor (TCR) gene loci and MS. However, these studies may not be definitive because of small sample sizes and under-representative marker coverage of the chromosomal regions being investigated. To explore potential roles between the TCR alpha locus and MS, we have genotyped a large family-based cohort, including 1360 affected individuals and 1659 of their unaffected first-degree relatives, at 40 single-nucleotide polymorphism (SNP) markers within the TCR alpha/delta locus. This represents the largest TCR alpha-MS study to date. From this screen, we identified three potential loci of interest in TCR alpha variable and constant gene regions using the transmission disequilibrium test. Although SNPs implicating each of these regions of interest will require genotyping in independent replication cohorts, these findings suggest a role for TCR gene polymorphisms in MS susceptibility. In the context of these findings we review the evidence.

Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus

T cell receptors (TR), through their interaction with the major histocompatibility complex, play a central role in immune responsiveness and potentially immune-related disorders. We resequenced all 57 variable (V) genes in the human T cell receptor alpha and delta (TRA/TRD) locus in 40 individuals of Northern European, Mexican, African-American and Chinese descent. Two hundred and eighty-four single nucleotide polymorphisms (SNPs) were identified. The distribution of SNPs between V genes was heterogeneous, with an average of five SNPs per gene and a range of zero to 15. We describe the patterns of linkage disequilibrium for these newly discovered SNPs and compare these patterns with other emerging large-scale datasets (e.g. Perlegen and HapMap projects) to place our findings into a framework for future analysis of genotype-phenotype associations across this locus. Furthermore, we explore signatures of natural selection across V genes. We find evidence of strong directional selection at this locus as evidenced by unusually high values of Fst.

Multiple Sclerosis

This chapter provides information on the epidemiology of multiple sclerosis (MS), the most common disabling neurological disease in young adults. It describes the clinical and pathologic features of MS and how these features pose challenges for clinical diagnosis and case definition criteria. Information is provided regarding the descriptive epidemiology of MS, including studies of incidence, prevalence, and temporal trends in MS frequency. Also included is a discussion of the interesting geographical features of the MS distribution, including MS disease clusters, the latitude gradient in disease risk, and migrant studies of individuals who move from high-risk to low-risk regions. Other sections of the chapter cover evidence regarding the infectious etiology of MS, including the important role that Epstein-Barr virus appears to play in disease susceptibility. The role of lifestyle factors is receiving increasing emphasis in MS epidemiologic studies, and evidence is summarized regarding the potential role of cigarette smoking, diet, and hormonal factors.

Genetics of autoimmune myasthenia gravis, a model for antibody-mediated autoimmunity in man

Autoimmune myasthenia gravis is an antibody-mediated autoimmune disease of the neuromuscular junction aimed at the muscle acetylcholine receptor. Recent genetic analyses focusing on a nonclass II HLA-linked locus, MYAS1, and on one of the genes encoding the AChR self-antigen, CHRNA1, are discussed.

Sequence variation in the human T-cell receptor loci

Identifying common sequence variations known as single nucleotide polymorphisms (SNPs) in human populations is one of the current objectives of the human genome project. Nearly 3 million SNPs have been identified. Analysis of the relative allele frequency of these markers in human populations and the genetic associations between these markers, known as linkage disequilibrium, is now underway to generate a high-density genetic map. Because of the central role T cells play in immune reactivity, the T-cell receptor (TCR) loci have long been considered important candidates for common disease susceptibility within the immune system (e.g., asthma, atopy and autoimmunity). Over the past two decades, hundreds of SNPs in the TCR loci have been identified. Most studies have focused on defining SNPs in the variable gene segments which are involved in antigenic recognition. On average, the coding sequence of each TCR variable gene segment contains two SNPs, with many more found in the 5', 3' and intronic sequences of these segments. Therefore, a potentially large repertoire of functional variants exists in these loci. Association between SNPs (linkage disequilibrium) extends approximately 30 kb in the TCR loci, although a few larger regions of disequilibrium have been identified. Therefore, the SNPs found in one variable gene segment may or may not be associated with SNPs in other surrounding variable gene segments. This suggests that meaningful association studies in the TCR loci will require the analysis and typing of large marker sets to fully evaluate the role of TCR loci in common disease susceptibility in human populations.

Insights into the immunopathogenesis of multiple sclerosis

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). Significant progress has been made in our understanding of the etiology of MS. MS is widely believed to be an autoimmune disease that results from aberrant immune responses to CNS antigens. T cells are considered to be crucial in orchestrating an immunopathological cascade that results in damage to the myelin sheath. This review summarizes the currently available data supporting the idea that myelin reactive T cells are actively involved in the immunopathogenesis of MS. Some of the therapeutic strategies for MS are discussed with a focus on immunotherapies that aim to specifically target the myelin reactive T cells.

Structure and diversity of the T-cell receptor alpha chain in rhesus macaque and chimpanzee

We cloned and sequenced cDNA for the TCRAC1 of a healthy rhesus monkey and chimpanzee. TCRAC1 from both nonhuman primates show extensive conservation compared to the human sequence and to other mammals. A possible primate-specific insertion near the hinge region of the TCRAC1 region is described. Characterization of 18 rhesus macaque and eight chimpanzee TCRA chain cDNA clones derived from inverse PCR revealed 12 different TCRAV and 16 different TCRAJ regions which corresponded closely to known human counterparts. One functional rhesus macaque TCRDV-TCRAJ rearrangement was detected, suggesting a genomic organization of the macaque TCRD locus which is similar to humans. At the genomic level, a single TCRAC1 gene segment was detected in rhesus macaque and chimpanzee. The close phylogenetic relationship between primates shown here for TCRA chain components supports the use of these species as animal models of human immune-mediated disease.

No linkage between multiple sclerosis and the T cell receptor alpha chain locus

Susceptibility to multiple sclerosis (MS) is genetically determined but it is thought that more than one gene contributes to development of the disease. We report a study of linkage to one candidate, the T cell receptor alpha chain locus, on chromosome 14, in affected sibling pairs. Markers with high polymorphism information contents were used to assign haplotypes identical by descent and state. Forty nine pairs were studied using restriction fragment length polymorphisms (RFLP) and 82 pairs were investigated using a microsatellite repeat polymorphism. In neither case did genotype or haplotype sharing differ significantly from expected rates. Stratification of patients according to DR15 status did not alter the distribution of haplotypes in affected siblings. We conclude that the T cell receptor alpha locus is not linked to susceptibility in patients with MS from the United Kingdom.

T-cell receptor constant beta germline gene polymorphisms and susceptibility to autoimmune hepatitis

BACKGROUND/AIMS

Susceptibility to autoimmune hepatitis is associated with HLA A1-B8-DR3 and DR4. T-Cell antigen receptors (TCR) are candidates for genetic susceptibility to autoimmune diseases because they recognize peptide antigens in the context of HLA molecules. The aim of this study was to investigate the possible role of TCR germline polymorphisms in susceptibility to autoimmune hepatitis.

METHODS

TCR constant beta (C beta) region polymorphisms were investigated using restriction fragment length polymorphism analysis in 60 unrelated northern European White patients with autoimmune hepatitis and 190 racially and geographically matched healthy controls.

RESULTS

A significant increase in the frequency of homozygous status for the 10-kilobase/Bgl II of the TCR C beta was found in the patients compared with controls (42% vs. 21%; corrected P value [Pc] < 0.0075; relative risk [RR] = 2.8). This difference was more pronounced in patients without HLA-DR3 and DR4 (50% vs. 14%; Pc < 0.015; RR = 6.1). Furthermore, heterozygosity for TCR C beta was significantly decreased in early-onset patients presenting with HLA-DR3 before 30 years of age (12% vs. 48%; Pc < 0.03; RR = 0.16).

CONCLUSIONS

The present findings provide evidence that genetic susceptibility to AIH may be determined by both the TCR C beta genes and HLA genes and that the genotype of the TCR C beta may be one of the factors in influencing the age at onset of disease.

Identification and physical mapping of a polymorphic human T cell receptor V beta gene with a frequent null allele

Germline variation in genes that encode the human T cell receptors (TCRs) may have an important influence in shaping the immune T cell repertoire. In this report we describe a frequent null allele of the human V beta 18 gene, resulting from a nucleotide substitution that creates a stop codon (CGA<-->TGA). Approximately 11% of the population tested was homozygous for this null allele, indicating that this is a frequent "hole in the repertoire." We confirmed that there is a greatly reduced (undetectable) level of V beta 18 mRNA in peripheral blood lymphocytes from an individual homozygous for this null allele. In addition, all heterozygous individuals expressed detectable levels of only the functional V beta 18 allele in their peripheral blood lymphocytes. Two other DNA polymorphisms were identified in V beta 18, one of which would result in an amino acid substitution in an expressed V beta 18 gene. Genotypes for all three of these V beta 18 DNA polymorphisms were determined in a group of unrelated individuals. Statistical analyses of the associations between alleles of the V beta 18 polymorphisms and those of other DNA polymorphisms in the TCR beta locus suggested a close physical proximity between the V beta 18 gene and the 3' end of the C beta 2 region. This localization of human V beta 18 had been previously predicted by the sequence homology between human V beta 18 and mouse V beta 14, a V gene segment previously mapped to 3' of the mouse C beta genes. We confirmed this localization of the human V beta 18 gene by isolating a cosmid clone that contains both the V beta 18 and C beta 2 segments. Mapping by restriction enzyme digestion and by the polymerase chain reaction indicated that the V beta 18 gene segment is approximately 9 kb 3' of the C beta 2 gene, making this the only known human V beta gene 3' of the C beta region.

T-cell receptor constant beta chain polymorphisms and susceptibility to type 1 diabetes

Several groups have previously shown that the T-cell receptor (TCR) constant-beta (C beta) chain locus is associated with susceptibility to Type 1 diabetes, although other studies have failed to show this. We have extended these studies by investigating 125 individuals with Type 1 diabetes and failed to confirm the significantly increased frequency of the 10;9.2 kb TCR-C beta/Bgl-II genotype in our patient population. However, further analysis showed that the 10;9.2 kb TCR-C beta genotype was significantly increased in those patients with no microvascular complications after 20 years of diabetes compared to those patients with complications (proteinuria, overt neuropathy, and moderate or severe retinopathy) 69.2% vs 31.7%, respectively, p < 0.005 Pc = 0.025). Similar results were also found in a second group of 74 patients who were analysed in the same way. Hence, the failure of some investigators to confirm the association between TCR-C beta and Type I diabetes may be due to heterogeneity in the patient populations being studied.

Molecular aspects of autoimmunity: a review

Molecular genetic techniques are being widely applied to the study of autoimmune diseases. Major advances have been made in diabetes, rheumatoid arthritis and coeliac disease. Work on experimental models of autoimmune uveitis suggests that similar advances will follow in this field. The application of molecular genetics to the study of immunology has lead to great advances in our understanding of the anatomy of antigen recognition. This work has lead to the identification of some of the structural determinants of antigen binding by MHC molecules and is helping to explain some MHC-disease associations. More recently, molecular studies of the T cell receptor have characterized patterns of T cell receptor expression in humans and have lead to the identification of regions of the T cell receptor critical for antigen recognition. These techniques will hopefully provide insights into the nature of autoimmunity and permit the identification of targets for disease specific immunotherapies. This review describes attempts to corelate MHC structure and function in the context of autoimmunity and discusses some of the strategies for analyzing T cell receptor usage in autoimmune disease.

The contribution of non-MHC genes to susceptibility to autoimmune diseases

Genetic studies of experimental models of autoimmune diseases, including systemic lupus-like syndromes and organ-specific autoimmunity, provide major information on genetic control of autoimmune diseases. In addition to genes known to be linked to the major histocompatibility complex (MHC), these studies point to multiple genes located outside the MHC that influence the onset and the progression of autoimmune diseases. Identification of these genes and of their interrelationships is now a major task that will be facilitated by recent progress in molecular biology and gene mapping. Among candidate genes, antigen-receptor genes (i.e., immunoglobulin- and T-cell receptor genes) most likely contribute an important part of the autoimmune susceptibility in several of these animal models. Available linkage data suggest a similar involvement of these antigen-receptor genes in several human autoimmune diseases. In addition to a better understanding of pathogenic mechanisms associated with autoimmunity, the knowledge of these disease-predisposing genes is expected to permit a better classification of often complex syndromes as well as the design of new treatments.

Further localization of a multiple sclerosis susceptibility gene on chromosome 7q using a new T cell receptor beta-chain DNA polymorphism

Multiple sclerosis (MS) has been associated with particular HLA haplotypes and has recently been reported to also be associated with the T cell receptor (TCR) beta-chain complex. We have tried to determine the source of the TCR-beta/MS association by exploiting the pattern of linkage disequilibrium within the TCR-beta complex. We describe a new DNA polymorphism with the TCR variable region gene segment V beta 15 which appears to localize between the constant region and V beta 11. When the distribution of V beta 11-V beta 15 haplotypes in MS patients was compared to healthy controls, the strength of the V beta 11-V beta 15 MS association (p = 0.107) was much less than the MS association with the adjacent V beta 8-V beta 11 haplotype (p = 0.0010). On the basis we exclude an MS susceptibility gene telomeric to V beta 11. The reported MS association with the TCR-beta gene complex therefore does not appear to be due to genes within the diversity, joining, or constant region but more likely involves a specific gene(s) within the variable region.

Genomic, phenotypic, and functional analyses of T cells in patients with psoriasis undergoing systemic cyclosporin A treatment

Recent studies have demonstrated that cyclosporin A (CyA) exerts a beneficial effect on psoriasis. It remains unclear, however, whether T-cell immune responses are definitely impaired in psoriasis and whether the anti-psoriatic effect of CyA is mediated by interference with T-cell activation. To study these questions, 20 patients with severe psoriasis were treated with oral CyA (5 mg/kg/d) for 12 weeks and examined for several phenotypic and functional properties of peripheral blood T cells before and after therapy. The analyses included CD3, CD4, and CD8 phenotypes, IL-2 production and IL-2 receptor expression following Con A stimulation, proliferative responses to PHA, and in vivo responsiveness to a foreign antigen, PPD. When the values of patients before therapy and healthy individuals were compared, no statistically significant differences were detected in any of these analyses. Furthermore, none of these T-cell properties were changed after 12 weeks of treatment. To assess possible minor mutations in T-cell-related genes in psoriasis, the T-cell receptor beta-chain locus was analyzed by Southern hybridization. With a cDNA probe for C beta 1, a polymorphic fragment of congruent to 9 kb was detected in Eco RI digests in one of 20 patients and in four of 10 healthy individuals examined. No polymorphism was detected in Bam HI digests in any individual. These results fail to support the hypothesis that a general or "systemic" alteration in T-cell immunity plays a central role in the pathogenesis of psoriasis and in the action of CyA against this skin disorder.

Association between a T cell receptor restriction fragment length polymorphism and systemic lupus erythematosus

The present study was designed to test the possibility that T cell receptor genes are associated/linked to those involved in systemic lupus erythematosus (SLE). Genomic DNA was isolated from 31 unrelated Caucasian SLE patients, 34 unrelated Caucasian normals, 5 multiplex American Caucasian SLE families, 9 multiplex Mexican SLE families, and 13 unrelated Mexican normals. The DNA was digested with Pst I, electrophoresed, and transferred to membranes by the Southern blot method. The blots were probed with a cDNA probe for the alpha chain of the T cell receptor. 13 polymorphic RFLP patterns were recognized. 1.3- and 3.0-kb band pairs were observed in 15 of 31 of American Caucasian patients and 4 of 34 American Caucasian controls (chi square, 8.81; P less than 0.002; relative risk, 7); there was no association of any RFLP pattern with Mexican SLE. The cDNA probe was cut with Rsa I, EcoR I, and Ava II into fragments corresponding to the V, J, C, and 3'UT regions. Only the fragment corresponding to the constant region reacted with the 1.3/3.0-kb band pair. These observations suggest that a genetic marker of the constant region of the alpha chain of the T cell receptor is associated with genes involved in SLE.

Lack of association of T cell receptor beta-chain constant region polymorphism with insulin-dependent diabetes mellitus in Finland

Allelic polymorphism in the T cell receptor constant beta-chain gene region has been reported to be associated with autoimmune diseases, including insulin-dependent diabetes mellitus (IDDM). The present analysis of 164 children and adolescents with IDDM and 193 controls for BqlII polymorphism using a TcR-C beta cDNA probe revealed two allelic restriction fragments with sizes of 10.5 kb (U) and 9.6 kb (L). No particular association was observed between the RFLP genotypes and IDDM (UU 27% versus 31%; UL 53% versus 52%; and LL 20% versus 17%, in diabetic subjects and controls, respectively), nor were any differences found between patients with various HLA risk antigens. The frequency of heterozygotes was 52% in 63 DR3-positive diabetic subjects and 53% in 73 DR3-negative ones. The results do not support any involvement of the TcR constant region genes in susceptibility to IDDM.

Increased incidence of certain TCR and HLA genes associated with myasthenia gravis in Italians

In order to study the immunogenetics of myasthenia gravis (MG), we analysed the TCR and HLA-class II genes from Italian and Californian myasthenic patients. We investigated polymorphisms of the TCR using the full length cDNA probes pGA5 and the pT10 for the alpha and beta chains, respectively. The 6.3 kb and 2.0 kb polymorphic markers, revealed by the PssI enzyme and the alpha chain probe, were shown to be significantly associated with MG. Italian MG patients were HLA typed, and allele frequencies showed a significant association of DR3 and DQw2 with MG. The relative risk calculated for DR3 was 7.4. T-cell proliferative responses to peptides of the AchR alpha chain were also studied and no associations with TCR RFLP analysis or HLA-class II typing were observed.

Autoimmune diseases: the failure of self tolerance

The ability to discriminate between self and nonself antigens is vital to the functioning of the immune system as a specific defense against invading microorganisms. Failure of the immune system to "tolerate" self tissues can result in pathological autoimmune states leading to debilitating illness and sometimes death. The induction of autoimmunity involves genetic and environmental factors that have focused the attention of researchers on the trimolecular complex formed by major histocompatibility complex molecules, antigen, and T cell receptors. Detailed molecular characterization of these components points to potential strategies for disease intervention.

T-cell receptor beta-chain DNA polymorphism frequencies in healthy HLA-DR homozygotes

In view of numerous recent reports of T-cell receptor (TCR) beta-chain/disease associations with HLA-associated diseases, we tested the possibilities that associations might exist directly between these two gene complexes at the level of the germline DNA. We determined frequencies of five TCR-beta DNA polymorphisms in 33 HLA-DR2/2 homozygotes, 29 HLA-DR3/3 homozygotes and 42 HLA-DR4/4 homozygotes. The control population (n = 74) was chosen without "bias toward" their HLA-DR genes. We selected DR2, DR3 and DR4 homozygotes because they have been the most frequently involved in HLA-DR associated diseases. Our results indicate that the recent reports in the literature of TCR-beta/disease associations can not be explained by a significantly different distribution of TCR-beta genes in HLA-DR2+, -DR3+, or -DR4+ subpopulations. Our results also suggest that if co-evolution between TCR-beta and MHC haplotypes does exist, the selective pressures in recent generations have not been strong enough to significantly alter the germline TCR-beta gene frequencies in HLA-DR2+, -DR3+, or -DR4+ subpopulations.

Anti-Ro(SSA) autoantibodies are associated with T cell receptor beta genes in systemic lupus erythematosus patients

Several of the heterogeneous clinical manifestations of systemic lupus erythematosus have been associated with specific autoantibodies. Associations between HLA class II antigens and autoantibodies to the ribonucleoproteins Ro(SSA) and La(SSB) have been reported in these patients. Because HLA class II molecules present antigen to T cell receptors (TCRs), we have searched for a TCR gene associated with the production of anti-Ro(SSA) antibodies. A pair of restriction fragment length polymorphisms (RFLPs), one of which hybridizes to the TCR constant region C beta 1 and the other to the C beta 2 gene, has been identified, suggesting these may be genotypic markers for an extended region of the TCR beta locus. This RFLP pair occurs in 76% of patients with Ro(SSA) precipitins, 84% of anti-Ro(SSA)-positive patients lacking La(SSB) precipitins, but only 41% of the patients lacking both precipitins (P = 0.0004). This disproportionate occurrence in a subset of lupus patients indicates that these RFLPs are not disease susceptibility markers, but rather are important markers for TCR genes whose products are involved in the production of anti-Ro(SSA) antibodies. The majority of patients who have these RFLPs and HLA class II antigens previously associated with the anti-Ro(SSA) response make this antibody, suggesting that interactions between products of these loci occur in response to Ro(SSA).

Allelic T-cell receptor alpha complexes have little or no influence on susceptibility to type 1 diabetes

We performed a multiple-affected-sib study to determine if T-cell receptor alpha-chain alleles affect susceptibility to insulin-dependent diabetes mellitus. Restriction fragment length polymorphisms were used to follow the segregation of allelic T-cell receptor alpha complexes within the families. The segregation of T-cell receptor alpha alleles in 29 multiplex families revealed no significant tendency for affected sibs to share T-cell receptor alpha-chain alleles more often than would be expected by chance alone (p greater than 0.2). In contrast, the same type of analysis for HLA alleles easily detected the well-known linkage of insulin-dependent diabetes mellitus susceptibility to the HLA complex (p = 0.003). We suggest that the importance of HLA alleles in insulin-dependent diabetes mellitus susceptibility and the lack of importance of T-cell receptor alpha alleles result from the different strategies by which HLA and T-cell receptor molecules achieve antigen-binding diversity: multiple loci and allelic diversity in the case of HLA; combinatorial, junctional, and N-region diversity in the case of the T-cell receptor. In this paper we also describe three new restriction fragment length polymorphisms of the T-cell receptor alpha complex and a new method for testing the significance of linkage in multiple-affected-sib studies.

T-cell receptor V alpha and C alpha alleles associated with multiple and myasthenia gravis

Polymorphic markers in genes encoding that alpha chain of the human T-cell receptor (TcR) have been detected by Southern blot analysis in Pss I digests. Polymorphic bands were observed at 6.3 and 2.0 kilobases (kb) with frequencies of 0.30 and 0.44, respectively, in the general population. Using the polymerase chain reaction (PCR) method, we amplified selected sequences derived from the full-length TcR alpha cDNA probe. These PCR products were used as specific probes to demonstrate that the 6.3-kb polymorphic fragment hybridizes to the variable (V)-region probe and the 2.0-kb fragment hybridizes to the constant (C)-region probe. Segregation of the polymorphic bands was analyzed in family studies. To look for associations between these markers and autoimmune diseases, we have studied the restriction fragment length polymorphism distribution of the Pss I markers in patients with multiple sclerosis, myasthenia gravis, and Graves disease. Significant differences in the frequency of the polymorphic V alpha and C alpha markers were identified between patients and healthy individuals.