Genetic associations with 25-hydroxyvitamin D deficiency in HIV-1-infected youth: fine-mapping for the GC/DBP gene that encodes the vitamin D-binding protein

Abstract

Serum 25-hydroxyvitamin D [25(OH)D] is often deficient (<12 ng/ml) or insufficient (<20 ng/ml) in youth living with human immunodeficiency virus type 1 infection (YLH). Based on evidence from multiple genome-wide association studies, we hypothesized that genetic factors associated with 25(OH)D deficiency should be readily detectable in YLH even when controlling for other known factors, including use of the antiretroviral drug efavirenz (EFV). Genotyping by bi-directional sequencing targeted 15 single nucleotide polymorphisms (SNPs) at the GC/DBP locus, with a focus on coding and regulatory variants, as well as those repeatedly reported in the literature. Three intronic SNPs (rs222016, rs222020, and rs222029) in a conserved haplotype block had unequivocal association signals (false discovery rate ≤ 0.006). In particular, the minor allele G for rs222020 was highly unfavorable among 192 YLH (99 African-Americans and 93 others), as gauged by relatively low likelihood for 25(OH)D sufficiency at enrollment (odds ratio = 0.31, p = 9.0 × 10(-4)). In a reduced multivariable model, race, season, latitude, body mass index, exposure to EFV, and rs222020-G were independent factors that collectively accounted for 38% of variance in the log10-transformed 25(OH)D concentration (p < 0.0001). Interaction terms were evident for rs222020-G × season (p < 0.001), latitude × season (especially fall and winter; p < 0.01), and race × EFV use (p = 0.024). Overall, variance in serum 25(OH)D is substantially attributable to multiple factors, but the exact contribution of genetic and non-genetic factors can be obscured by partial overlaps and frequent interactions.

Keywords: HIV-1; antiretroviral; genetics; race; vitamin D; youth.

FIGURE 1

Stability of serum 25-hydroxyvitamin D [25(OH)D] concentration (ng/ml) in 88 HIV-1-infected youth who did not receive randomized vitamin D supplementation over a 12-week period. Measurements at baseline (week 0) and at study week 12 are shown for 46 African–Americans (AAs) and 42 non-AA subjects (others). The predicted slope and its 95% confidence intervals in each subgroup are represented by sold and dotted lines, respectively. Six subjects (four AAs and two others) with missing data at week 12 are excluded.

FIGURE 2

Patterns of pairwise linkage disequilibrium (LD) among 15 GC SNPs used for screening and estimating statistical power. Each pairwise comparison of SNP genotypes (defined by direct sequencing) is captured by an r² value (×100). Similar results are obtained from analyses of SNP genotypes in AAs and other races (excluding SNPs rs112205706 and rs115617005). By default, absolute LD (r² = 1.00) is indicated by a dark square.

FIGURE 3

Season-dependent association of GC genotypes with serum 25-hydroxyvitamin D [25(OH)D] concentration. The log₁₀-transformed 25(OH)D (ng/ml) values in 192 HIV-1-infected youth are plotted according to four enrollment seasons and three genotypes defined by the GC SNP, rs222020 (major allele A and minor allele G). For each stratum, the horizontal bars connected by a vertical line correspond to the mean ± standard deviation (SD). The nominal p values are based on Student’s t-test, assuming a dominant effect of allele G (see Table 6 for full analyses of interactions between rs222020-G and enrollment season).