Genome wide association studies (GWAS) have been successful in uncovering loci that are robustly associated with many complex traits. BMI is one such phenotype, with increasing numbers of variants being revealed with increasing sample size (1,2,3,4,5,6). Ultimately, researchers have combined their datasets to carry out meta-analyses, in order to elucidate additional genetic contributors to a trait. These latest signals yield relatively modest strengths of association compared to the initial “low-hanging fruit” variants in genes such as FTO (2).
Building on previous discoveries, 22 additional loci were reported by the GIANT consortium in the past year to be associated with BMI, primarily in adults, from a GWAS meta-analysis of 249,796 individuals (3). A total of 32 loci actually reached genome wide significance but ten were already known, namely FTO, TMEM18, MC4R, GNPDA2, BDNF, NEGR1, SH2B1, ETV5, MTCH2, and KCTD15. Of the novel loci, four had been previously reported to be associated with either weight and waist-hip ratio, namely SEC16B, TFAP2B, FAIM2, and NRXN3, while 18 had never been implicated in a GWAS of BMI-related traits previously, consisting of RBJ-ADCY3-POMC, GPRC5B-IQCK, MAP2K5-LBXCOR1, QPCTL-GIPR, TNNI3K, SLC39A8, FLJ35779-HMGCR, LRRN6C, TMEM160-ZC3H4, FANCL, CADM2, PRKD1, LRP1B, PTBP2, MTIF3-GTF3A, ZNF608, RPL27A-TUB, and NUDT3-HMGA1. The same study also tested these variants in the context of extreme obesity in children, where 30 of the 32 loci also showed directionally consistent effects to that of adult BMI.
It is important to determine which variants previously uncovered in GWAS analyses of adult traits are exerting an effect early on in life to shed light on mechanisms of action. In this study, we aimed at examining the BMI loci reported from the GIANT meta-analysis in the context of a large cohort of subjects presenting with common childhood obesity, where we specifically excluded extreme cases in order to determine the relative impact of these variants in the pathogenesis of this pediatric trait. To achieve this goal, we leveraged genotyping data generated on the Human Hap550 BeadChip (Illumina, San Diego, CA) in our pediatric cohort.
Our case-control design consisted of 1,097 European American children with common obesity (defined as BMI ≥95th percentile) and 2,760 lean controls (defined as BMI <50th percentile) of the same ethnicity (based on principal components analysis). The age-range was restricted to subjects between 2 and 18 years of age due to the age-range limit of the BMI reference range. All individuals were drawn from a conservatively defined cohort, where outliers were excluded to avoid the consequences of potential measurement error or Mendelian causes of extreme obesity.
We examined the 32 single nucleotide polymorphisms (SNPs) corresponding to the loci uncovered in the GIANT BMI meta-analysis in the context of common childhood obesity. Nine of these SNPs yielded at least nominal evidence for association to childhood obesity (P < 0.05) (Table 1).
Variation at the loci harboring FTO, TMEM18, NRXN3, and MC4R yielded the strongest associations and survived correction for the number of tests applied, namely rs1558902 (P = 1.42 × 10−8; odds ratio (OR) = 1.34), rs2867125 (P = 2.03 × 10−4; OR = 0.78), rs10150332 (P = 7.97 × 10−4; OR = 1.23), and rs571312 (P = 0.001; OR = 1.21), respectively.
Next, with a lower magnitude of association, came SEC16B, GNPDA2, and TNNI3K, with rs543874 yielding an OR = 1.21 (P = 0.0038), rs10938397 yielding an OR = 1.14 (P = 0.0097), and rs1514175 yielding an OR = 1.14 (P = 0.011), respectively. Lastly was the QPCTL and BDNF loci, with rs2287019 yielding an OR = 1.17 (P = 0.015) and rs10767664 yielding an OR = 0.87 (P = 0.03), respectively.
SNPs residing at the RBJ, SDCCAG8, ZNF608, MTIF3, KCTD15, TFAP2B, FAIM2, NPC1, TNKS/MSRA, PTBP2, LRP1B, NUDT3, PTER, CADM2, RPL27A, SH2B1, SLC39A8, TMEM160, MTCH2, MAF, MAP2K5, FANCL, GPRC5B, FLJ35779, LRRN6C, PRKD1, NEGR1, and ETV5 loci did not reveal statistically significant evidence of association in our childhood obesity cohort. However, overall 28 of the 32 loci yielded directionally consistent effects to that of the adult BMI meta-analysis (Table 1), with only TMEM160 being inconsistent with the extreme childhood obesity investigation in the same study. In addition, there were no significant differences between genders (Supplementary Table S1 online).
Two loci were previously described in a French/German GWAS of extreme childhood obesity (7) and were specifically tested in the GIANT meta-analysis (3). Although not statistically significant, we observed evidence for consistency of direction of association with variants at the TNKS/MSRA and SDCCAG8 loci. Similarly, we see comparable directions of effect for variants at two of the three loci previously reported to be associated with early-onset obesity (8), namely PTER, and MAF but not NPC1.
From this analysis of genotype data generated in our cohort of common pediatric obesity in European Americans, it is clear that a number of loci detected in the GIANT meta-analysis of adult BMI also play a role in our phenotype of interest.
The neuronal control on various aspect of energy consumption and energy balance, in particular, the hypothalamus has been well recognized (9); indeed the knockout mouse for FTO supports this fact (10). NRXN3, the most strongly associated novel locus of these reported regions (i.e., the GIANT meta-analysis was the first to implicate it in BMI) in our cohort, encodes a cell adhesion molecule and receptor which is highly expressed in the central nervous system (11). Prior studies on NRNX3 function have suggested it plays an important role in alcohol dependence, cocaine addiction, and illegal substance abuse (12,13). The association of NRNX3 with BMI has lead to suggestions that obesity results partly as a consequence of food addiction controlled by the central nervous system (11). The association of this locus in our pediatric cohort, further refines the association of NRNX3 locus with respect to obesity-related traits and suggests that it exerts its influence in early life. Indeed, the same conclusion of an early age effect can be drawn for the loci harboring FTO, TMEM18, NRXN3, MC4R, SEC16B, GNPDA2, TNNI3K, QPCTL, and BDNF. Interestingly, NRNX3, GNPDA2, and QPCTL were not significantly associated with extreme obesity in children in the GIANT study (3).
We have followed up older GWAS reports for BMI in this same cohort (14), albeit when our collection was substantially smaller in scale. However, with relatively modest novel signals derived form the most recent meta-analysis, we elected to use a leaner control set in this instance to enhance the contrast between patients and controls in order to increase sensitivity for the newest loci in this pediatric setting.
For the loci that did not yield significant evidence for association could be as a consequence of power issues, but could also suggest that these particular loci play a smaller role in the pathogenesis of common childhood obesity.
We conclude that among 32 loci that have been reported to associate with adult BMI in a recent meta-analysis of GWAS data, at least nine also contribute to the pathogenesis of common childhood obesity in European Americans.