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Rheumatology 2001;40:662±667 Association of CTLA-4 but not CD28 gene polymorphisms with systemic lupus erythematosus in the Japanese population S. Ahmed, K. Ihara, S. Kanemitsu, H. Nakashima1, T. Otsuka1, K. Tsuzaka2, T. Takeuchi2 and T. Hara Departments of Pediatrics and 1Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, and 2 Department of Internal Medicine II, Saitama Medical Center, Saitama, Japan Abstract Objective. Systemic lupus erythematosus (SLE) in a multisystem autoimmune disorder characterized by multiorgan pathology and autoantibodies against a variety of autoantigens. The CD28 and CTLA-4 genes might be candidate genes for SLE, because costimulation signals from CD80uCD86 to CD28uCTLA-4 have been suggested to play an important role in the activation or inactivation of T lymphocytes. Methods. We investigated three polymorphic regions within the CTLA-4 gene, a CuT base exchange in the promoter region 2318 (CTLA-4 2318CuT), an AuG substitution in the exon 1 position 49 (CTLA-4 49AuG), an (AT)n repeat polymorphism in the 39 untranslated region of exon 4 wCTLA-4 39 (AT)nx, and a CD28 gene polymorphism, a TuC substitution in the intron 3 position +17 (CD28 IVS3 +17TuC), in SLE patients and controls. Results. SLE patients had signi®cantly higher frequencies of the CTLA-4 49G allele (P = 0.003) and of the CTLA-4 (AT)n 106 bp allele (P = 0.0008) than controls. We also found a strong linkage disequilibrium between the A allele of CTLA-4 49AuG and the 86 bp allele of CTLA-4 39 (AT)n. On the contrary, no association was found between SLE and CTLA-4 2318CuT or CD28 IVS3 +17TuC. Conclusion. We conclude that the CTLA-4 gene appears to play a signi®cant role in the development of SLE in the Japanese population. KEY WORDS: CTLA-4 gene, CD28 gene, Polymorphism, Systemic lupus erythematosus. Systemic lupus erythematosus (SLE) is an autoimmune multisystem disorder characterized by the production of immunoglobulin G autoantibodies. Inappropriate T-cell-dependent expansion of autoreactive B cells is considered to play a role in the production of pathogenic autoantibodies against nuclear, cytoplasmic and cell-surface autoantigens w1x. T-cell activation requires two discrete signals: a signal delivered by the T-cell receptor and an accessory signal that occurs when costimulatory receptors interact with their ligands. CD28, a major costimulatory molecule, binds to CD80uCD86 on antigen-presenting cells and delivers a potent costimulatory signal to T cells w2x. CTLA-4, a related receptor of CD28, also binds to CD80uCD86 on antigen-presenting cells but delivers negative signals to T cells, depending on both the T-cell activation state and the strength of the T-cell receptor signal w3x. Thus, CD28 and CTLA-4 molecules regulate the immune responses to self and foreign antigens by controlling antigen-speci®c T-cell activation w4x. The chromosome 2q33 region, where the CTLA-4 and CD28 genes are located w5x, is one of the potential susceptibility loci for human SLE w6, 7x. Manipulation of CD28uCTLA-4 in animal models of autoimmunity has shown that CD28 as well as CTLA-4 plays a role in the development of autoimmune disorders w8±10x. In fact, association studies have revealed that CTLA-4 gene polymorphism is genetically linked to several autoimmune diseases w11±16x. However, there have been con¯icting results as to the association between the CTLA-4 gene and SLE by the examination of a single polymorphism and there are no data on the association between the CD28 gene and SLE. The purpose of this study was to determine which of the two T-cell costimulatory molecule genes at 2q33 Submitted 5 April 2000; revised version accepted 14 December 2000. Correspondence to: K. Ihara, Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan. 662 ß 2001 British Society for Rheumatology Association of CTLA-4 with systemic lupus erythematosus is linked to the development of SLE by the analysis of all the known polymorphisms of the CTLA-4 and CD28 genes. Materials and methods Patients and controls The study population comprised 113 SLE patients. All these patients ful®lled the American College of Rheumatology 1982 revised criteria for SLE. The mean (S.D.) age at onset of SLE was 31 (13) yr. Two hundred normal individuals (104 males and 96 females) in the northern Kyushu area of Japan were recruited for the control population. Informed consent was obtained from subjects anduor their parents. DNA extraction Genomic DNA was obtained from peripheral blood lymphocytes using the QIAamp DNA extraction kit (Qiagen, Tokyo, Japan). Restriction fragment length polymorphism (RFLP) analysis of CTLA-4 promoter polymorphism To amplify the region containing the CuT polymorphism at position 2318, the following primer pairs were used: forward 59-AATGAATTGGACTGGATGG-39 and reverse 59-TTACGAGAAAGGAAGCCGTG-39. The polymerase chain reaction (PCR) was carried out in a volume of 50 ml containing 40 ng of genomic DNA, 25 pmol of each primer, 1.25 U of Taq polymerase (Promega, Madison, WI, USA) and 0.2 mM of each deoxynucleoside triphosphate. The PCR pro®le was as follows: initial denaturation at 948C for 2 min, followed by 40 cycles of 948C for 30 s, 608C for 30 s and 728C for 30 s, with ®nal extension at 728C for 7 min. The reaction products were analysed on 3% agarose gels. To screen these substitutions, the products were incubated with MseI restriction enzyme at 378C for 3 h, separated on FIG. 1. Genotyping of the CTLA-4 gene promoter 2318CuT polymorphism by MseI RFLP. M, DNA size marker (100-bp ladder). PCR fragments containing 2318 C are digested into two fragments (226, 21 bp), whereas PCR fragments containing 2318 T are digested into three fragments (21, 96, 130 bp). The 21-bp fragments are not visible on the agarose gel. 663 3.0% agarose gels and visualized by ethidium bromide staining (Fig. 1). Single-strand conformation polymorphism analysis of CTLA-4 exon 1 49 AuG polymorphism To amplify the region containing the exon 1 49AuG polymorphism, the following primer pairs were used: forward 59-GTTCAAACACATTTCAAAGCTTC-39 and reverse 59-AAATGACTGCCCTTGACTGC-39. The PCR pro®le was identical to that described above except for the annealing temperature of 558C and genomic DNA quantity of 20 ng. For genotype screening, single-strand conformation polymorphism (SSCP) analysis was carried out with GeneGel Excel 12.5u24 (Amersham Pharmacia Biotech, Uppsala, Sweden) with 25 mA at 208C, according to the manufacturer's instructions. Single-strand DNA fragments in the gel were visualized by subsequent silver staining (Fig. 2). The results of SSCP analysis were con®rmed by the direct sequencing of 20 randomly chosen samples. CTLA-4 39 (AT)n genotype using PCR and a ¯uorescence-based technique The CTLA-4 39 untranslated region (UTR) containing the (AT)n repeat was ampli®ed with the following primer pairs: forward 59-GCCAGTGATGCTAAAGGTTG-39 and reverse 59-AACATACGTGGCTCTATGCA-39. The 59 end of the forward primer was labelled with 6-carboxy¯uorescein dye. PCR was employed in a volume of 25 ml containing 20 ng of genomic DNA, 10 pmol of each primer, 0.625 U of Taq DNA polymerase and 0.2 mM of each deoxynucleoside triphosphate. The PCR conditions were the same as described above except for the cycles of 30, the annealing temperature of 558C and the extension time of 15 s. Genotyping was performed in a mixture of ampli®ed products with an internal size standard (Gene Scan 2350) by an ABI Prism 310 genetic analyser (PerkinElmer, Foster City, CA, USA). Allele-speci®c PCR and RFLP analysis of the polymorphism at position IVS3 +17 of the CD28 gene We have recently reported a CD28 gene TuC polymorphism in the intron 3 position +17 (CD28 IVS3 +17TuC) w17x. The polymorphism was determined by FIG. 2. Genotyping of CTLA-4 gene exon 1 49AuG polymorphism by SSCP analysis. Alleles with G and A polymorphisms at nucleotide position 49 show different mobility in the gels. Lane 1, GuG genotype; lane 2, AuG genotype; lane 3, AuA genotype. 664 S. Ahmed et al. (a) (b) FIG. 3. Genotype analysis of CD28 IVS3 +17TuC. (a) ASPCR analysis of CD28 IVS3 +17TuC genotype. Lanes 1 and 2, TT, TuT genotype; lanes 3 and 4, TC, TuC genotype; Lanes 5 and 6, CC, CuC genotype. (b) RFLP analysis by Eco47III of the CD28 IVS3 +17 TuC genotype. PCR fragments containing T are digested into two fragments (126 and 22 bp), whereas PCR fragments with the CuC genotype are undigested. The 22-bp fragments are not visible on the agarose gel. allele-speci®c PCR (ASPCR) using an allele-speci®c primer for C or T at position IVS3 +17 in the CD28 gene. The primers used to detect T and C alleles were 59-CTGGGTAAGAGAAGCAGCAAT-39 (T primer) and 59-CTGGGTAAGAGAAGCAGCAAC-39 (C primer) respectively and the common primer 59-CTCAATGCCTTCTGGAAATC-39 (Cm primer). A singlebase mismatch was introduced at position 2 from the 39 end of both allele-speci®c primers (shown by the underline). Each primer combination detected only the primer-speci®c allele (Fig. 3a). To con®rm the accuracy of ASPCR, 91 samples were analysed by restriction fragment length polymorphism (RFLP). To amplify the region containing the CD28 IVS3 +17TuC polymorphism, the following primer pairs were used for the PCR reaction: forward 59-TTTTCTGGGTAAGAGAAGCAGCGC-39 and reverse 59-GAACCTACTCAAGCATGGGG-39. The PCR products were then incubated with the Eco47III restriction enzyme at 378C overnight, separated on 3.0% agarose gels and visualized by ethidium bromide staining (Fig. 3b). Statistical analysis Differences between allele or genotype frequencies of groups were evaluated by x2 analysis with 2 3 2 and 2 3 3 contingency tables with Stat View J-5.0 (software for Apple Macintosh). When at least one cell number was not more than 5, Yates' correction was applied to the x2 value. A P value < 0.05 was considered to be statistically signi®cant for the CTLA-4 gene 2 318CuT, 49AuG and CD28 gene I VS3 +17TuC analyses. Because of the multiple comparisons for the microsatellite allele frequencies, a Bonferroni multiple adjustment was made to the level of signi®cance in the 39-UTR of the CTLA-4 gene, which was set at P < 0.0045 (0.05u11). The sample size was suf®cient to detect an odds ratio (OR) of 1.7 or greater with 80% power at the 5% level of signi®cance, assuming a frequency of about 50% for the G allele of the CTLA-4 49AuG polymorphism in the control population. Results Allele and genotype frequencies of CTLA-4 49AuG, 39 (AT)n and 2318CuT With respect to CTLA-4 gene 49AuG polymorphism, the frequency of the G allele was signi®cantly higher in SLE patients than in control subjects (69.5 vs 57.2%, P = 0.003) because of a signi®cant increase in the frequency of the GG genotype in SLE patients (48.7 vs 31.0%) (Table 1). Regarding the CTLA-4 39 (AT)n polymorphism, 15 discrete alleles were identi®ed in the Japanese population with sizes ranging from 86 to 132 base pairs (bp), of which the 86-bp allele was the most frequent in the control subjects. Compared with the frequency of the 86-bp allele, the frequency of the 106-bp allele was signi®cantly higher in SLE patients than in controls (OR 3.19, P = 0.0008) (Table 2). There was signi®cant linkage disequilibrium between the 86-bp allele of the 39 microsatellite polymorphism and the A allele of the 49AuG polymorphism in exon 1 of the CTLA-4 gene (Table 3). On the other hand, there were no signi®cant differences in the allele and genotype frequencies of the 2 318CuT polymorphism between SLE patients and controls (Table 1). Allele and genotype frequencies of CD28 IVS3 +17TuC No signi®cant differences were observed in the allele and genotype frequencies of this polymorphism between SLE patients and control subjects (Table 1). Discussion Multiple genetic and environmental factors are involved in the pathogenesis of SLE w18x. The genetic factors of SLE include major histocompatibility complex (MHC) class II genes w19±23x and non-MHC genes, including genes for complement components, Fc receptor IIuIII, the T-cell receptor, apoptosis (Fas, Fas-ligand, bcl-2) and cytokines w24±30x. A recent genome-wide search Association of CTLA-4 with systemic lupus erythematosus 665 TABLE 1. Comparison of genotype distributions and allelic frequencies between SLE patients and controls Genotype CTLA-4 2318CuT CC CT TT CTLA-4 49AuG GG GA AA CD28 IVS3 +17TuC TT TC CC SLE patients: number (%) Controls: number (%) P Allele SLE patients: number (%) Controls: number (%) 95 (84.1) 18 (15.9) 0 (0) 157 (78.5) 43 (21.5) 0 (0) 0.232 C T 208 (92.0) 18 (8.0) 357 (89.3) 43 (10.7) 0.26 1.39 (0.78±2.47) 55 (48.7) 47 (41.6) 11 (9.7) 62 (31.0) 105 (52.5) 33 (16.5) 0.006 G A 157 (69.5) 69 (30.5) 229 (57.2) 171 (42.8) 0.003 1.72 (1.20±2.40) 104 (92.0) 8 (7.1) 1 (0.9) 180 (90.0) 18 (9.0) 2 (1.0) 0.834 T C 216 (95.6) 10 (4.4) 378 (94.5) 22 (5.5) 0.557 1.26 (0.58±2.70) P OR (95% CI) CI, con®dence interval. TABLE 2. Allele frequencies of respective repeat number polymorphism at the 39 UTR of the CTLA-4 gene in SLE patients and controls Allele (bp) 86 102 104 106 108 110 112 116 118 120 122 124 126 128 132 Controls (n=400) 130 (32.5) 69 (17.3) 110 (27.5) 18 (4.5) 28 (7.0) 2 (0.5) 0 (0) 1 (0.3) 4 (1.0) 4 (1.0) 15 (3.8) 4 (1.0) 9 (2.3) 5 (1.3) 1 (0.3) SLE (n=226) 52 44 74 23 9 2 1 0 1 1 7 3 8 1 0 (23.0) (19.5) (32.8) (10.2) (4.0) (0.9) (0.4) (0) (0.4) (0.4) (3.1) (1.4) (3.5) (0.4) (0) OR 95% CI P 1.00 1.59 1.68 3.19 0.80 2.50 ± ± 0.63 0.63 1.17 1.88 2.22 0.50 ± ± 0.94, 2.70 1.06, 2.67 1.50, 6.82 0.31, 1.91 0.18, 35.1 ± ± 0.01, 6.53 0.01, 6.53 0.38, 3.25 0.26, 11.5 0.70, 6.86 0.01, 4.64 ± ± 0.065 0.020 0.0008a 0.599 0.706 ± ± 1.000 1.000 0.751 0.694 0.112 0.859 ± Numbers in parentheses are percentages of each allele. The most common allele (86 bp) in the control subject was chosen as the baseline allele. Each allele of the CTLA-4 gene was compared with the baseline allele. Shown are the OR and 95% con®dence intervals (CI) for the comparison of allele frequencies between SLE patients and controls. P was calculated by x2 with a 2 3 2 contingency table. a Signi®cant at the 0.0045 level after Bonferroni adjustment to control for type 1 error across multiple comparisons within a locus. for potential susceptibility loci for human SLE revealed numerous loci, including 2q33, depending on racial origin w7x. The CTLA-4 and CD28 molecules encoded at 2q33 perform critical roles in the regulation of the antigenspeci®c immune response w31x. In the present study, CTLA-4 but not CD28 gene polymorphisms were associated with the development of SLE, suggesting that the genetic factors of SLE are distinct from those of insulin-dependent diabetes mellitus (IDDM), to which CD28 gene polymorphism has also been marginally linked wK. Ihara et al., submitted for publicationx. It is worthy of note that neither CTLA-4 nor CD28 gene polymorphisms were associated with atopic asthma, in a population with the same genetic background w17x. With respect to the CTLA-4 gene, lack of association with SLE has been reported in Mexican American, British, Italian and Japanese populations w30, 32±34x, while there has been one association reported in the Slovak population w35x. The studies described TABLE 3. Linkage disequilibrium between the CTLA-4 49AuG and CTLA-4 39 (AT)n polymorphisms CTLA-4 49AuG CTLA-4 39 (AT)n AA+GA GG (without A allele) With 86-bp allele Without 86-bp allele 150 45 4 114 P < 0.0001 2 P was calculated by x with a 2 3 2 contingency table. above were done by the analysis of either the 49AuG or the 39 (AT)n polymorphism of the CTLA-4 gene. To increase the reliability of the analysis, we examined all three polymorphic sites, 49AuG, 39 (AT)n and the 2318 promoter region, and found that the former two polymorphisms were signi®cantly associated with SLE. Possible reasons for the con¯icting results might include the differences in the ethnic groups and the age at 666 S. Ahmed et al. onset of the disease in the Mexican American, British and Italian populations and a smaller sample size, as well as a minor difference in the genetic background in the Japanese population. As has been found for IDDM, Graves disease, Hashimoto's thyroiditis, multiple sclerosis and rheumatoid arthritis w11±15, 36, 37x, the G allele of the CTLA-4 49AuG polymorphism was associated with SLE in recent studies w35x and the present work. The 106-bp allele of the CTLA-4 39 (AT)n polymorphism showed a signi®cant association with SLE, consistent with results from other autoimmune disorders such as IDDM, Graves disease, Addison's disease and Wegener's granulomatosis w12, 13, 16, 38x. The CTLA-4 49AuG and 39 (AT)n polymorphisms are unlikely to affect the function of the gene because 49AuG and 39 (AT)n are located on the peptide leader and the 39 untranscribed region respectively. However, it is possible that either or both of the CTLA-4 gene polymorphisms affects CTLA-4 mRNA stability and subsequent CTLA-4 expression w11x. CTLA-4-de®cient mice develop a lethal lymphoproliferative disease by massive uncontrolled T cells w8, 9x. CTLA-4 not only counterbalances CD28 signals but also inhibits T-cell responses independently of CD28. Recent studies have suggested that CTLA-4 interacts with the CD3z chain of the T-cell receptor complex and interferes with very early T-cell receptor signalling events w39x. Thus, CTLA-4 might induce autoimmunity by the inhibiting CD3z signal because a decrease in CD3z expression was associated with SLE in a proportion of cases w40x. 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