FTO and ABCA1 risk allele frequencies were 20.3 and 10.0% in the overall population, respectively. In order to avoid potential population stratification, all individuals included in the analysis were from Central Mexico.
In the overall analysis and under additive inheritance models, the FTO “A” risk allele was not significantly associated with higher BMI (β = 0.187, P = 0.143) or higher WC (β = 0.409, P = 0.208), nor was the ABCA1 “T” risk allele associated with BMI or WC (β = 0.247, P = 0.154 and β = 0.369, P = 0.403, respectively). Furthermore, although HDL-C levels were higher in FTO “A” homozygous individuals, the association did not reach statistical significance (β = 0.005, P = 0.097). As expected, the ABCA1 “T” allele was strongly associated with lower HDL-C levels (β = −0.03, P = 2.37 × 10−12) (Fig. 1).
In order to assess a possible FTO-ABCA1 gene interaction, we sought associations between the FTO risk variant and BMI, WC and HDL-C, stratified by the absence or presence of the ABCA1 risk allele (“CC” and “CT/TT” genotypes, respectively). Interestingly, in the absence of the ABCA1 risk “T” allele, the FTO risk variant was significantly associated with higher BMI (β = 0.284, P = 0.042, n = 3191) and marginally associated with higher WC (β = 0.650, P = 0.063, n = 3191). In contrast, in the presence of the ABCA1 risk allele, the FTO risk variant was not associated with BMI (P = 0.421, n = 747) or WC (P = 0.376, n = 747). The interaction analyses between FTO rs9939609 and ABCA1 rs9282541 affecting BMI and WC were statistically significant (P = 0.040 and P = 0.045, respectively). ABCA1 and FTO gene variants showed no significant interaction affecting HDL-C levels (P = 0.856) (Fig. 1).
Individual ancestry estimates were available in 60% of the samples. After adjusting for Native American ancestry, the statistical significance of interactions between FTO rs9939609 and ABCA1 rs9282541 affecting BMI and WC was borderline significant (P = 0.054 and P = 0.063, respectively). This drop of significance is probably due to the lower sample size. Figure 2 shows the mean proportion of Native American component according to FTO genotype, stratified by the absence or presence of the ABCA1 risk allele (“CC” and “CT/TT” genotypes). As expected, the Native American component was lower in individuals with 1 and 2 FTO risk alleles, regardless of the presence of the ABCA1 risk allele. This suggests that the interactions are not confounded by ancestry.
We sought to evaluate this finding in an independent cohort of 636 children. As observed in adults, in the overall analysis using an additive inheritance model, the association of FTO “A” and the ABCA1 “T” risk alleles with BMI percentile did not reach statistical significance (β = 3.116, P = 0.084 and β = 4.002, P = 0.058, respectively). However, in the absence of the ABCA1 “T” risk variant, the effect of FTO risk allele over the BMI was higher and significant (β = 4.20, P = 0.043, n = 505), although the interaction did not reach significance (P = 0.356).
We further explored whether FTO mRNA expression is affected by ABCA1 genotypes. Figure 3 shows differences in relative FTO mRNA expression levels in human adipose tissue biopsies according to FTO rs9939609 genotypes under a dominant model. In the overall analysis of SAT biopsies, while FTO mRNA expression was higher for “TA/AA” than those with “TT” genotypes, the difference did not reach statistical significance (9.084 vs 8.961 AU, respectively; P = 0.068). However, considering only biopsies of individuals not bearing the ABCA1 risk allele (wild-type), FTO “TA/AA” SAT biopsies showed significantly higher FTO mRNA expression than those with “TT” genotypes (9.112 vs 8.943 AU, respectively; P = 0.003). Comparisons of FTO mRNA expression according to genotype in individuals bearing the ABCA1 risk variant were limited because only one individual carried the FTO “TT” genotype. However, the FTO “TA/AA” SAT biopsies showed significantly lower FTO mRNA expression levels in the presence of the ABCA1 risk allele (9.043 vs 9.112, P = 0.045). In VAT biopsies, FTO mRNA expression did not differ significantly according to genotype in the overall population (TT: 8.879 vs TA/AA: 8.975, P = 0.857), or in absence of the R230C risk allele (TT: 8.942; TA/AA: 8.965, P = 0.371). ABCA1 expression was not significantly affected by FTO rs9939609 genotypes (data not shown).