Brief Genetics Report Association of Non-HLA Genes With Type 1 Diabetes Autoimmunity Andrea K. Steck,1 Teodorica L. Bugawan,2 Ana Maria Valdes,2 Lisa M. Emery,3 Alan Blair,2 Jill M. Norris,3 Maria J. Redondo,1 Sunanda R. Babu,1 Henry A. Erlich,2 George S. Eisenbarth,1 and Marian J. Rewers1
Approximately 50% of the genetic risk for type 1 diabetes is attributable to the HLA region. We evaluated associations between candidate genes outside the HLA region–INS, cytotoxic T-lymphocyte–associated antigen (CTLA)-4, interleukin (IL)-4, IL-4R, and IL-13 and islet autoimmunity among children participating in the Diabetes Autoimmunity Study in the Young (DAISY). Children with persistent islet autoantibody positivity (n ⴝ 102, 38 of whom have already developed diabetes) and control subjects (n ⴝ 198) were genotyped for single nucleotide polymorphisms (SNPs) in the candidate genes. The INS-23Hph1 polymorphism was significantly associated with both type 1 diabetes (OR ⴝ 0.30; 95% CI 0.13– 0.69) and persistent islet autoimmunity but in the latter, only in children with the HLA-DR3/4 genotype (0.40; 0.18 – 0.89). CTLA-4 promoter SNP was significantly associated with type 1 diabetes (3.52; 1.22– 10.17) but not with persistent islet autoimmunity. Several SNPs in the IL-4 regulatory pathway appeared to have a predisposing effect for type 1 diabetes. Associations were found between both IL-4R haplotypes and IL-4 –IL-13 haplotypes and persistent islet autoimmunity and type 1 diabetes. This study confirms the association between the INS and CTLA-4 loci and type 1 diabetes. Genes involved in the IL-4 regulatory pathway (IL-4, IL-4R, IL-13) may confer susceptibility or protection to type 1 diabetes depending on individual SNPs or specific haplotypes. Diabetes 54:2482–2486, 2005
T
ype 1 diabetes is associated with susceptibility genes in the HLA region on chromosome 6p21 that account for 50% of the familial clustering of type 1 diabetes in Caucasians (1). Candidate genes outside the HLA region are being identified. The insulin gene on chromosome 11p15 confers ⬃10% of genetic susceptibility to type 1 diabetes (2). The polymorphic, cytotoxic T-lymphocyte–associated antigen (CTLA)-4 gene on chromosome 2q33 has also been associated with susceptibility to type 1 diabetes (3), although not consistently (4). At least 10 additional susceptibility genes are under investigation (5,6). Interleukin (IL)-4 and IL-13 are multifunctional cytokines that play a critical role in the regulation of immune responses. The IL-4 and IL-13 genes have been mapped to chromosome 5q31 and the major component of their receptor, the IL-4R␣ gene, to chromosome 16p11.2–12.1 (7). IL-4R polymorphisms have been associated with immune-related diseases, including asthma, atopy (8,9), and recently type 1 diabetes (10,11). We evaluated associations between candidate genes outside the HLA region (INS, CTLA-4, IL-4, IL-4R, and IL-13) and islet autoimmunity among children participating in the Diabetes Autoimmunity Study in the Young (DAISY).
RESEARCH DESIGN AND METHODS
From the 1Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Denver, Colorado; the 2Department of Human Genetics, Roche Molecular Systems, Alameda, California; and the 3 Department of Preventive Medicine and Biometrics, University of Colorado Health Sciences Center, Denver, Colorado. Address correspondence and reprint requests to Andrea Steck, MD, Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Mail Stop A140, P.O. Box 6511, Aurora, CO 80045-6511. E-mail: andrea.
[email protected]. Received for publication 29 October 2004 and accepted in revised form 10 May 2005. Additional information for this article can be found in an online appendix at http://diabetes.diabetesjournals.org. CTLA, cytotoxic T-lymphocyte–associated antigen; DAISY, Diabetes Autoimmunity Study in the Young; IA-2, insulinoma-associated protein 2; IAA, insulin autoantibodies; IL, interleukin; NHW, non-Hispanic white; SNP, single nucleotide polymorphism. © 2005 by the American Diabetes Association. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
2482
DAISY is a prospective study that has followed, since 1993, two cohorts of young children at increased risk of type 1 diabetes (12): the siblings and offspring cohort and the general population newborn cohort, screened for diabetes high-risk HLA class II alleles. The details of the newborn screening (12) and follow-up (13) have been previously published. For this nested case-control study, all subjects were selected from the DAISY cohort. Cases included children who converted to persistent autoantibody positivity, i.e., children having one or more islet autoantibodies (insulin autoantibody [IAA], GAA, or insulinoma-associated protein 2 [IA-2] above the 99th percentile) in serum samples collected on at least two consecutive visits 3– 6 months apart (n ⫽ 102); 38 of these children have already developed type 1 diabetes. Type 1 diabetes was defined by a random blood glucose ⬎200 mg/dl and/or an HbA1c (A1C) ⬎6.2% in the presence of typical symptoms of diabetes. The average age of diagnosis in this study was 5.9 years (range 0.9 –14.7). The control subjects (n ⫽ 198) were children who have never been positive for any antibody and were selected for each case by matching on age and HLA frequency; the oldest antibody-negative–matching general population newborn cohort was selected preferentially. Most control subjects (91%) have been selected from the general population newborn cohort, whereas 60% of cases come from the siblings and offspring cohort. Sex (male-to-female ratio, 1.17) and average follow-up from birth (7.0 years) did not differ by DIABETES, VOL. 54, AUGUST 2005
A. STECK AND ASSOCIATES
TABLE 1 SNPs and allele frequencies in control subjects and cases (persistent islet autoimmunity including type 1 diabetes)
SNP CTLA (⫺318) CTLA exon 1 INS ⫺23Hph1 IL-4R ⫺3223 IL-4R ⫺1914 IL-4R 50 IL-4R 142 IL-4R 375 IL-4R 389 IL-4R 406 IL-4R 478 IL-4R 551 IL-4R 761 IL-4 ⫺524 IL-13 ⫺1512 IL-13 ⫺1112 IL-13 intron 3 IL-13 110
Allele Ref/Var C/ T A/G A/ T C/ T C/ T A/G C/ T A/C G/ T T/C T/C A/G T/C C/ T A/C C/ T C/ T G/A
DR3/DR4 heterozygotes Frequency (%) Control subjects Cases OR (n ⫽ 75) (n ⫽ 40) (95% CI) 7.3 40.7 32.7 30.0 44.0 50.7 9.3 12.0 12.0 11.3 16.0 18.7 0.7 19.3 16.0 19.3 25.3 23.3
11.2 40.0 20.0 26.2 47.5 40.0 7.5 11.2 11.2 11.2 17.5 21.2 1.2 11.2 21.2 21.2 18.7 18.7
1.60 (0.63–4.04) 0.97 (0.56–1.69) 0.51 (0.27–0.98) 0.83 (0.45–1.53) 1.15 (0.67–1.98) 0.65 (0.37–1.12) 0.79 (0.29–2.14) 0.93 (0.40–2.18) 0.93 (0.40–2.18) 0.99 (0.42–2.34) 1.11 (0.54–2.30) 1.18 (0.60–2.31) N/A 0.53 (0.24–1.18) 1.42 (0.71–2.83) 1.13 (0.58–2.20) 0.68 (0.35–1.33) 0.76 (0.38–1.49)
Other HLA genotypes Frequency (%) Control subjects Cases OR (n ⫽ 123) (n ⫽ 62) (95% CI) 9.3 43.1 25.6 26.4 50.4 43.1 11.0 11.0 11.0 11.0 17.5 26.0 0.8 17.9 16.7 17.5 21.1 19.1
9.7 40.3 23.4 38.7 36.3 54.8 9.7 14.5 14.5 12.9 18.5 23.4 0.0 23.4 17.7 18.5 19.4 17.7
1.04 (0.50–2.16) 0.89 (0.57–1.38) 0.89 (0.53–1.47) 1.76 (1.11–2.78) 0.56 (0.36–0.87) 1.60 (1.04–2.48) 0.87 (0.42–1.78) 1.38 (0.73–2.61) 1.38 (0.73–2.61) 1.20 (0.62–2.32) 1.07 (0.61–1.88) 0.87 (0.52–1.44) N/A 1.40 (0.83–2.38) 1.08 (0.61–1.91) 1.08 (0.61–1.88) 0.89 (0.52–1.54) 0.91 (0.52–1.60)
Variant allele frequencies for the SNPs are shown after stratification for HLA-DR3/4 status. Differences in allele frequencies between case and control subjects were tested by 2. ORs refer to the variant allele. Statistically significant OR values (P ⬍ 0.05) are indicated in bold. Ref, reference; Var, variant allele. affected status. The majority of the cohort (80%, n ⫽ 241) was non-Hispanic white (NHW), although this proportion was higher in cases (88%) than in control subjects (76%). Islet autoantibodies. Measurement of biochemical islet autoantibodies was performed in the laboratory of Dr. George Eisenbarth at the Barbara Davis Center, Denver, CO. We used radioimmunoassays for autoantibodies to insulin, GAD65, and IA-2. Insulin autoantibodies were measured by a microIAA assay with sensitivity of 58%, specificity of 99%, and interassay coefficient of variation (CV) 11% (14). The combined GAA (GAD65 autoantibodies) and IA-2A radioassay was done in duplicates on a 96-well filtration plate and radioactivity was counted on a TopCount 96-well plate  counter using methods previously described (15). In the 1995 Immunology of Diabetes Society Workshop, the GAA assay gave an 82% sensitivity and 99% specificity using sera from new-onset diabetic patients aged ⬍30 years. The interassay CV was 6%. The IA-2A assay gave a 73% sensitivity and 100% specificity, and the interassay CV was 10%. Based on 198 nondiabetic control subjects ages 0.4–67.5 years, the 99th percentile for IAA (0.01), GAA (0.032), and the 100th percentile (single-highest value) for IA-2A (0.07) were used as the cutoffs for positivity. Genotyping. One INS single nucleotide polymorphism (SNP) (⫺23Hph1), two CTLA-4 SNPs (the A49G site in exon 1 and the promoter C318T), ten IL-4R SNPs (including two in the promoter region), one IL-4 promoter SNP, and four IL-13 SNPs were genotyped using a linear array (immobilized probe) method essentially as described in Mirel et al. (10). Briefly, ⬃100 ng of genomic DNA was PCR amplified using 18 biotinylated primer pairs in a single PCR. The labeled amplicons were hybridized to an immobilized sequence-specific oligonucleotide probe (or SNP) array (36 probes) on a nylon membrane. The presence of bound amplicon to a specific probe is detected using streptavidin horseradish peroxidase and a soluble colorless substrate, tetramethylbenzidine, which can be converted in the presence of H2O2 to a blue precipitate. Statistical analysis. Comparisons of allele and genotype frequencies between case and control subjects were assessed by 2 test with 2 ⫻ 2 contingency tables. P values exceeding 0.05 were denoted as not significant. Since our analyses were based on a priori hypotheses, P values were not corrected for multiple testing. The strength of the association was estimated by the OR. The SNPs were in Hardy-Weinberg equilibrium for both case and control subjects. The program PHASE version 2.02 was used to assign the most likely pair of haplotypes to each individual. PHASE implements a Bayesian statistical method for reconstructing haplotypes from population genotype data using the methods described by Stephens et al. (16). Allele and genotype frequencies were also subanalyzed by ethnicity and diabetes status. As a subanalysis including only one affected member per family (i.e., excluding six siblings) gave essentially identical results, we included all cases and DIABETES, VOL. 54, AUGUST 2005
present the results of the overall group. The Colorado Multiple Institutional Review Board approved all study protocols.
RESULTS
Individual SNPs. The distributions of alleles at the individual SNPs are shown in Table 1 after stratification by high-risk HLA genotypes. Overall, there were no significant differences between allele frequencies among case and control subjects (data not shown). However, a significant association was found between the INS-23Hph1 SNP and persistent autoimmunity in the DR3/4 heterozygotes. In the other lower-risk HLA subgroup, two IL-4R SNPs (promoter ⫺3223 and the IL-4R50) had a predisposing effect, whereas the IL-4R promoter ⫺1914 had a protective effect. Results were similar in analyses restricted to NHW subjects (n ⫽ 241) (data not shown). Genotype frequencies were analyzed in the overall persistent autoimmunity group (online appendix 1 [available at http://diabetes. diabetesjournals.org]) and in the subgroup of only type 1 diabetic case and control subjects (Fig. 1). The INS23Hph1 polymorphism was significantly associated with both type 1 diabetes (OR ⫽ 0.30; 95% CI 0.13– 0.69) and persistent islet autoimmunity but in the latter only in children with the HLA-DR3/4 genotype (0.40; 0.18 – 0.89). CTLA-4 promoter SNP was significantly associated with type 1 diabetes (3.52; 1.22–10.17) but not with persistent islet autoimmunity. Several IL-4R SNPs (variant alleles) had a predisposing effect for persistent islet autoimmunity and type 1 diabetes except the promoter ⫺1914, which showed a protective effect. Results were similar in analyses restricted to NHW subjects (n ⫽ 241) (data not shown). Linkage disequilibrium patterns were computed among the DAISY Caucasian control population (16a). Pairwise linkage disequilibrium between the 10 IL-4R SNPs on 2483
ROLE OF NON-HLA GENES IN TYPE 1 DIABETES
FIG. 1. Genotype frequencies in control and case subjects (type 1 diabetes [T1D] only). The figure shows genotype frequencies for type 1 diabetes only and control and case subjects (type 1 diabetes substudy). The first column in control subjects and in type 1 diabetes (shaded in gray) refers to homozygotes dominant. The second column in control and case subjects and type 1 diabetes (in white) refers to heterozygotes and homozygotes variant (these have been combined for analysis, since several cells had values
