Novel Genetic Variants Associated With Increased Vertebral Volumetric BMD, Reduced Vertebral Fracture Risk, and Increased Expression of SLC1A3 and EPHB2

Abstract

Genome-wide association studies (GWASs) have revealed numerous loci for areal bone mineral density (aBMD). We completed the first GWAS meta-analysis (n = 15,275) of lumbar spine volumetric BMD (vBMD) measured by quantitative computed tomography (QCT), allowing for examination of the trabecular bone compartment. SNPs that were significantly associated with vBMD were also examined in two GWAS meta-analyses to determine associations with morphometric vertebral fracture (n = 21,701) and clinical vertebral fracture (n = 5893). Expression quantitative trait locus (eQTL) analyses of iliac crest biopsies were performed in 84 postmenopausal women, and murine osteoblast expression of genes implicated by eQTL or by proximity to vBMD-associated SNPs was examined. We identified significant vBMD associations with five loci, including: 1p36.12, containing WNT4 and ZBTB40; 8q24, containing TNFRSF11B; and 13q14, containing AKAP11 and TNFSF11. Two loci (5p13 and 1p36.12) also contained associations with radiographic and clinical vertebral fracture, respectively. In 5p13, rs2468531 (minor allele frequency [MAF] = 3%) was associated with higher vBMD (β = 0.22, p = 1.9 × 10−8) and decreased risk of radiographic vertebral fracture (odds ratio [OR] = 0.75; false discovery rate [FDR] p = 0.01). In 1p36.12, rs12742784 (MAF = 21%) was associated with higher vBMD (β = 0.09, p = 1.2 × 10−10) and decreased risk of clinical vertebral fracture (OR = 0.82; FDR p = 7.4 × 10−4). Both SNPs are noncoding and were associated with increased mRNA expression levels in human bone biopsies: rs2468531 with SLC1A3 (β = 0.28, FDR p = 0.01, involved in glutamate signaling and osteogenic response to mechanical loading) and rs12742784 with EPHB2 (β = 0.12, FDR p = 1.7 × 10−3, functions in bone-related ephrin signaling). Both genes are expressed in murine osteoblasts. This is the first study to linkSLC1A3 and EPHB2 to clinically relevant vertebral osteoporosis phenotypes. These results may help elucidate vertebral bone biology and novel approaches to reducing vertebral fracture incidence. © 2016 American Society for Bone and Mineral Research.

Quantitative imaging methods in osteoporosis

“…Simply measuring X-ray attenuation expressed as Hounsfield units (HU) to derive BMD has been evaluated (62,63), but ideally the tissue density of the analyzed volume is calibrated to units of equivalent concentration of a hydroxyapatite phantom in g/cm 3 yielding the BMD values (64). Volumes of interest are defined and a distinction is made between cortical, trabecular and integral volumes (65).…”

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

“…rs17040773 is not in linkage disequilibrium with rs10190845 in our population (r 2 =0.006), and in keeping with this, when we performed conditional analysis on rs17040773, we confirmed that rs10190845 remained significantly associated with clinical vertebral fractures (P=2.09×10 −8 ; OR 1.73 (95% CI 1.43 to 2.09)). In order to test whether the variants associated with clinical vertebral fractures played a role in BMD, we tested the rs10190845 variant for association with volumetric vertebral BMD in females on the dataset from Nielson and colleagues 27. We did not find any association for the variant and BMD (P=0.23).…”

“…We also analysed 15 variants previously associated with clinical fracture,13 of which three were associated with clinical vertebral fractures in this study. We also analysed the SNPs identified by Nielson and colleagues27 as genome-wide significant predictors of volumetric vertebral BMD for association with clinical vertebral fractures in our dataset. Of the six genome-wide significant SNPs identified by Nielson et al , we found that one was significantly associated with clinical vertebral fractures after Bonferroni correction (rs12742784, P=6.24×10 −5 ).…”

Genetic Studies of Endophenotypes From Spine CT Scans Provide Novel Insights Into the Contribution of Mechanosensory Pathways to Vertebral Fractures and Spinal Curvature

“…Nielson and colleagues took a different approach to exploring the genetics of spinal endophenotypes (5) . They performed a classical GWAS using CT quantification of lumbar spine vBMD, with specific focus on 'pure' trabecular bone, adjusting for age, gender and weight.…”

“…Though the sample size (around 2000) was insufficient to perform a GWAS, they were able to gain important insights into genetic influences by examining the heritability of spinal curvature, and its genetic correlation with other traits (4) . In contrast, Nielson et al, assembled over 15,000 participates, making it feasible to perform a GWAS, from which novel loci were identified which have not previously been found in GWAS of DXA-derived lumbar BMD (5) .…”