Identification of a novel locus on chromosome 2q13, which predisposes to clinical vertebral fractures independently of bone density

OBJECTIVES

To identify genetic determinants of susceptibility to clinical vertebral fractures, which is an important complication of osteoporosis.

METHODS

Here we conduct a genome-wide association study in 1553 postmenopausal women with clinical vertebral fractures and 4340 controls, with a two-stage replication involving 1028 cases and 3762 controls. Potentially causal variants were identified using expression quantitative trait loci (eQTL) data from transiliac bone biopsies and bioinformatic studies.

RESULTS

A locus tagged by rs10190845 was identified on chromosome 2q13, which was significantly associated with clinical vertebral fracture (P=1.04×10-9) with a large effect size (OR 1.74, 95% CI 1.06 to 2.6). Bioinformatic analysis of this locus identified several potentially functional SNPs that are associated with expression of the positional candidate genes TTL (tubulin tyrosine ligase) and SLC20A1 (solute carrier family 20 member 1). Three other suggestive loci were identified on chromosomes 1p31, 11q12 and 15q11. All these loci were novel and had not previously been associated with bone mineral density or clinical fractures.

CONCLUSION

We have identified a novel genetic variant that is associated with clinical vertebral fractures by mechanisms that are independent of BMD. Further studies are now in progress to validate this association and evaluate the underlying mechanism.

Assessment of gene-by-sex interaction effect on bone mineral density

Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however, the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed expression quantitative trait loci (eQTL) analysis and bioinformatics network analysis. We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS) and femoral neck (FN) BMD in 25,353 individuals from 8 cohorts. In a second stage, we followed up the 12 top single-nucleotide polymorphisms (SNPs; p < 1 × 10(-5) ) in an additional set of 24,763 individuals. Gene-by-sex interaction and sex-specific effects were examined in these 12 SNPs. We detected one novel genome-wide significant interaction associated with LS-BMD at the Chr3p26.1-p25.1 locus, near the GRM7 gene (male effect = 0.02 and p = 3.0 × 10(-5) ; female effect = -0.007 and p = 3.3 × 10(-2) ), and 11 suggestive loci associated with either FN- or LS-BMD in discovery cohorts. However, there was no evidence for genome-wide significant (p < 5 × 10(-8) ) gene-by-sex interaction in the joint analysis of discovery and replication cohorts. Despite the large collaborative effort, no genome-wide significant evidence for gene-by-sex interaction was found to influence BMD variation in this screen of autosomal markers. If they exist, gene-by-sex interactions for BMD probably have weak effects, accounting for less than 0.08% of the variation in these traits per implicated SNP. © 2012 American Society for Bone and Mineral Research.

Gene-gene interactions in RANK/RANKL/OPG system influence bone mineral density in postmenopausal women

Receptor activator of nuclear factor kappaB (RANK) is one of the proteins in regulation of osteoclastogenesis via RANK/RANKL/OPG. Gene that codes for RANK protein (TNFRSF11A) was associated with osteoporotic fractures in a recent genome-wide association study. As variations in the RANK gene could alter its expression and activity, the aim of our study was to evaluate the influence of four RANK gene polymorphisms on bone mineral density (BMD) and biochemical markers. We evaluated 467 postmenopausal women and 117 elderly men. All subjects were genotyped for the presence of RANK polymorphisms -670G>C, +34694C>T, +34901G>A and +35966insdelC. BMD and biochemical markers were measured. Significant associations of +35966insdelC with BMD at lumbar spine (BMD-ls), total hip (BMD-th) and femoral neck (BMD-fn) were found in postmenopausal women (p=0.020, 0.024 and 0.034), but not in men. Significant gene-gene interaction was proved for two RANK polymorphisms in combination with OPG and RANKL polymorphisms studied previously in postmenopausal women. Firstly, RANK/RANKL (+34901G>A/-290C>T) combination was associated with BMD-fn, BMD-th and BMD-ls (p=0.034, 0.016 and 0.050), and secondly, RANK/OPG combination (+35966insdelC/K3N) showed influence on BMD-fn and BMD-ls (p=0.043 and 0.039). Our results suggest that gene-gene interactions between RANK and OPG, and RANK and RANKL influence BMD in postmenopausal women.

Analysis of association of LRP5, LRP6, SOST, DKK1, and CTNNB1 genes with bone mineral density in a Slovenian population

The Wnt pathway has a bifunctional role in bone mass regulation, influencing osteoblasts and osteoclasts. The Wnt pathway genes are therefore candidate genes for susceptibility to osteoporosis. In our study, we focused on the effects of polymorphisms in selected Wnt pathway genes: low-density lipoprotein receptor-related proteins 5 and 6 (LRP5 and LRP6), Dickkopf1 (DKK1), sclerostin (SOST), and beta-catenin (CTNNB1). We genotyped 652 subjects for the following polymorphisms: A1330V in LRP5; I1062V in LRP6; E232K in DKK1; D32Y, G34V, and N287S in CTNNB1; and -1397_-1396insGGA in SOST. Bone mineral density (BMD) was also measured. The allele frequencies were as follows: for A1330V C:T = 87%:13%, for I1062V C:T = 20%:80%, and for -1397_-1396insGGA-:GGA = 64%:36%. The studied nucleotide changes in the DKK1 and CTNNB1 genes were shown not to be polymorphic. In a Slovenian population, no association was shown between lumbar spine and femoral neck BMD in A1330V (P = 0.151 and 0.243) and in I1062V (P = 0.209 and 0.405). We observed a difference between SOST genotypes, corresponding to an allele dose effect, which was borderline significant for lumbar spine and femoral neck BMD (P = 0.047 and 0.085); but this did not survive the adjustment for multiple testing. These results indicate that a larger sample size would be necessary to detect these subtle effects. Our results suggest that A1330V in LRP5, I1062V in LRP6, and -1397_-1396insGGA in SOST are not associated with BMD in the Slovenian population.

The combinations of polymorphisms in vitamin D receptor, osteoprotegerin and tumour necrosis factor superfamily member 11 genes are associated with bone mineral density

1alpha,25-dihydroxyvitamin D(3) upregulates tumour necrosis factor superfamily member 11 (TNFSF11) that codes for the receptor activator of nuclear factor kappaB ligand (RANKL), and downregulates osteoprotegerin (OPG) expression. We have analyzed the individual effects of polymorphisms in the vitamin D receptor gene (VDR), OPG and TNFSF11, and searched for interactions between them. Six hundred and forty one subjects were evaluated: 239 osteoporotic and 228 non-osteoporotic post-menopausal, 57 pre-menopausal women and 117 elderly men. The subjects were genotyped for BsmI, FokI and Cdx2 in VDR, K3N in OPG and -290C>T, -643C>T and -693G>C in TNFSF11 gene. Bone mineral density (BMD) and biochemical markers were measured. In the osteoporotic women, femoral neck BMD (BMD-fn) showed associations with BsmI(VDR) and Cdx2(VDR) (P=0.015 and 0.047 respectively), and lumbar spine BMD (BMD-ls) with K3N(OPG) and -290C>T(TNFSF11) (P=0.021 and 0.017). No association with BMD was found in the non-osteoporotic women. In the pre-menopausal women, the Cdx2(VDR) polymorphism was associated with BMD-fn and total hip BMD (P=0.011 and 0.011). In elderly men, FokI(VDR) was associated with BMD-fn and BMD-ls (P=0.040 and 0.036). Interestingly, the -290C>T(TNFSF11)-K3N(OPG) combination was associated with BMD-th (P=0.041) in the osteoporotic women. In the non-osteoporotic women, the combination K3N(OPG)-Cdx2(VDR) was associated with BMD-ls, BMD-th and BMD-fn (P=0.032, 0.049 and 0.022), and the combination -290C>T(TNFSF11)-K3N(OPG) with BMD-fn (P=0.029). For the first time, the presence of gene-gene interactions between VDR, OPG and TNFSF11 genes was studied. Our results strongly suggest further confirmation of their combined influence on larger cohorts.