Genetic modifiers of cystic fibrosis-related diabetes

Abstract

Diabetes is a common age-dependent complication of cystic fibrosis (CF) that is strongly influenced by modifier genes. We conducted a genome-wide association study in 3,059 individuals with CF (644 with CF-related diabetes [CFRD]) and identified single nucleotide polymorphisms (SNPs) within and 5' to the SLC26A9 gene that associated with CFRD (hazard ratio [HR] 1.38; P = 3.6 × 10(-8)). Replication was demonstrated in 694 individuals (124 with CFRD) (HR, 1.47; P = 0.007), with combined analysis significant at P = 9.8 × 10(-10). SLC26A9 is an epithelial chloride/bicarbonate channel that can interact with the CF transmembrane regulator (CFTR), the protein mutated in CF. We also hypothesized that common SNPs associated with type 2 diabetes also might affect risk for CFRD. A previous association of CFRD with SNPs in TCF7L2 was replicated in this study (P = 0.004; combined analysis P = 3.8 × 10(-6)), and type 2 diabetes SNPs at or near CDKAL1, CDKN2A/B, and IGF2BP2 were associated with CFRD (P < 0.004). These five loci accounted for 8.3% of the phenotypic variance in CFRD onset and had a combined population-attributable risk of 68%. Diabetes is a highly prevalent complication of CF, for which susceptibility is determined in part by variants at SLC26A9 (which mediates processes proximate to the CF disease-causing gene) and at four susceptibility loci for type 2 diabetes in the general population.

FIG. 1.

Manhattan plot of the association P values for CFRD meta-analysis in the discovery sample (n = 3,059). Log-transformed P values are plotted as a function of genome position (National Center for Biotechnology Information build 36.3 coordinates; even chromosomes = blue; odd chromosomes = black). CFRD onset was analyzed as a censored trait (time of event = CFRD diagnosis; time of censoring = last normal diabetes screening test); analysis includes adjustment for principal components. The dashed and dotted lines denote genome-wide significant (P < 9.1 × 10⁻⁸) and suggestive (P < 1.8 × 10⁻⁶) thresholds, respectively.

FIG. 2.

Regional plot of negative log P values for SNPs at or near SLC26A9 gene. A: Three-study meta-analysis illustrating maximum evidence for association at rs4077468 and rs4077469 (♦). B: Three-study meta-analysis performed while conditioning the number of minor alleles at rs4077468, demonstrating no evidence for locus heterogeneity (all P > 0.05).

FIG. 3.

Cumulative incidence of CFRD as a function of SNP genotype rs4077468. A: Discovery sample. Data from 3,059 individuals (644 with CFRD) in the TSS + CGS + GMS discovery sample were analyzed. Each “A” allele associated with increased risk of CFRD (HR, 1.38; 95% CI, 1.23–1.54; P = 3.6 × 10⁻⁸). B: Replication sample. Data from 694 individuals (124 with CFRD) in the CGS + GMS replication sample were analyzed. Each “A” allele associated with increased risk of CFRD (HR, 1.47; 95% CI, 1.11–1.94; P = 0.007).

FIG. 4.

Location of SNPs associated with CFRD relative to the SLC26A9 gene. Genotyped SNPs reaching genome-wide significance are in bold. Locations of imputed (i) and genotyped (g) SNPs are indicated along with their −log₁₀ P values; kb distances are calculated relative to the transcription start. Because SLC26A9 is on the negative strand of chromosome 1, the orientation of SLC26A9 has been reversed in this figure so that it can be viewed from the 5′ end on the left to the 3′ end on the right. Boxes indicate positions of exons that are numbered from 1 through 21. The region of the gene spanning from 5 kb upstream of the SLC26A9 transcription start site through the second exon has been magnified.

FIG. 5.

Combined effect on CFRD prevalence of modifier alleles at five loci: TCF7L2 (rs7901695), CDKAL1 (rs7756992), CDKN2A/B (rs1412829), IGF2BP2 (rs1470579), and SLC26A9 (rs4077468). A risk score was generated by adding the number of high-risk alleles (0, 1, or 2) for each SNP for the 3,058 discovery subjects with genotypes for all 5 SNPs. The 644 with CFRD had higher mean risk score (4.62; SD, 1.51) than the 2,414 individuals without CFRD (4.09; SD, 1.53; P = 3 × 10⁻¹⁵). The CFRD risk score associated with CFRD onset (HR, 1.26 per high-risk allele; 95% CI, 1.20–1.33; P = 2 × 10⁻²⁰) that predicts a 10.4-fold variation in risk attributable to these 5 SNPs. Essentially identical results were obtained when adjusting for age, sex, and liver disease (not shown). ◇, CFRD prevalence within each risk group. Error bars represent SD calculated by modeling the counts as a Poisson distribution.