| Literature DB >> 30127800 |
Xueya Zhou1,2, Ching-Lung Cheung3,4, Tatsuki Karasugi5, Jaro Karppinen6, Dino Samartzis7, Yi-Hsiang Hsu8,9,10, Timothy Shin-Heng Mak4, You-Qiang Song4,11, Kazuhiro Chiba12, Yoshiharu Kawaguchi13, Yan Li1, Danny Chan11, Kenneth Man-Chee Cheung7, Shiro Ikegawa14, Kathryn Song-Eng Cheah11, Pak Chung Sham1,4.
Abstract
Lumbar disc degeneration (LDD) is age-related break-down in the fibrocartilaginous joints between lumbar vertebrae. It is a major cause of low back pain and is conventionally assessed by magnetic resonance imaging (MRI). Like most other complex traits, LDD is likely polygenic and influenced by both genetic and environmental factors. However, genome-wide association studies (GWASs) of LDD have uncovered few susceptibility loci due to the limited sample size. Previous epidemiology studies of LDD also reported multiple heritable risk factors, including height, body mass index (BMI), bone mineral density (BMD), lipid levels, etc. Genetics can help elucidate causality between traits and suggest loci with pleiotropic effects. One such approach is polygenic score (PGS) which summarizes the effect of multiple variants by the summation of alleles weighted by estimated effects from GWAS. To investigate genetic overlaps of LDD and related heritable risk factors, we calculated the PGS of height, BMI, BMD and lipid levels in a Chinese population-based cohort with spine MRI examination and a Japanese case-control cohort of lumbar disc herniation (LDH) requiring surgery. Because most large-scale GWASs were done in European populations, PGS of corresponding traits were created using weights from European GWASs. We calibrated their prediction performance in independent Chinese samples, then tested associations with MRI-derived LDD scores and LDH affection status. The PGS of height, BMI, BMD and lipid levels were strongly associated with respective phenotypes in Chinese, but phenotype variances explained were lower than in Europeans which would reduce the power to detect genetic overlaps. Despite of this, the PGS of BMI and lumbar spine BMD were significantly associated with LDD scores; and the PGS of height was associated with the increased the liability of LDH. Furthermore, linkage disequilibrium score regression suggested that, osteoarthritis, another degenerative disorder that shares common features with LDD, also showed genetic correlations with height, BMI and BMD. The findings suggest a common key contribution of biomechanical stress to the pathogenesis of LDD and will direct the future search for pleiotropic genes.Entities:
Keywords: causality; genetic correlation; lumbar disc degeneration; osteoarthritis; pleiotropy; polygenic score
Year: 2018 PMID: 30127800 PMCID: PMC6088183 DOI: 10.3389/fgene.2018.00267
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Figure 1The analysis framework. GWAS summary statistics of base phenotypes were obtained from published studies in European populations. The polygenic score (PGS) in a testing sample of East Asian population was calculated by weighted summation of alleles at approximately independent SNPs whose association p-values fall below some threshold in the discovery GWAS done in European populations. The performance of PGS to predict the base phenotype in East Asians was first evaluated in a validation sample. Then the best performing PGS of the base phenotype was used to test genetic overlap with lumbar disc degeneration (LDD) in the testing samples. In this study, we selected height, body mass index (BMI), bone mineral density (BMD) and lipid levels as base phenotypes. The prediction performance of PGS was evaluated in the HKDD cohort for height, BMI, and lipid levels, and in the HKOS cohort for BMD. Three LDD phenotypes were used as target phenotypes, including disc displacement and disc degeneration scores in the HKDD cohort and affection status of lumbar disc herniation (LDH) in the Japanese LDH case-control cohort.
Figure 2Summary of phenotypes in the HKDD cohort. (a) Examples of magnetic resonance imaging show two major aspects of LDD. Disc displacement (left) is shown as bulging of disc material beyond confine of annulus fibrosus. The loss of proteoglycan and water content (right) within nucleus pulposus is reflected by the signal intensity loss. The lumbar spine has 5 intervertebral segments, termed L1 through L5. S1 stands for the first segment of sacral that is intermediately below the lumbar spine. (b) The prevalence of signal intensity loss and disc displacement at different levels of lumbar spine discs. Two ordinal grades (0–3 for signal intensity loss, 0–2 for disc displacement) were assigned to each lumbar disc to indicate the presence and severity of LDD, where 0 indicated normal and higher scores indicated increased severity. (c) The distribution of two LDD scores. The disc degeneration score and displacement score were defined by the summation of grades over all disc levels for signal intensity loss and disc displacement respectively. The two LDD scores are correlated in the population. The age threshold divides the HKDD cohort in two parts with roughly equal sample sizes. The older subjects tend to have higher disc degeneration scores and disc displacement scores. (d) Pairwise Pearson correlations between original phenotypes (upper triangle) and between residual phenotypes after adjusting for age and gender (lower triangle).
GWAS summary statistics used in this study.
| Height | GIANT Consortium | Wood et al. ( | 253,000 | European | Public |
| BMI | Locke et al. ( | 234,000~322,000 | European | Public | |
| Serum lipids | GLGC | Willer et al. ( | 95,000~189,000 | European | Public |
| BMD | GEFOS Consortium | Estrada et al. ( | 33,000 | European | Application to the consortium |
| HKOS | Kung et al. ( | 780 | Chinese | Contributed by the collaborator | |
| OA | arcOGEN Consortium | Zeggini et al. ( | 7,400 cases, 11,000 population controls | European | Application to the consortium |
| Hospitalized LDH | Japan LDH | Song et al. ( | 366 cases, 3,331 population controls | Japanese | Contributed by the collaborator |
BMI, body mass index; BMD, bone mineral density; OA, osteoarthritis; LDH, lumbar disc herniation; GLGC, Global Lipids Genetics Consortium; HKOS, Hong Kong Osteoporosis Study.
The GIANT consortium's BMI GWAS included samples from multiple ethnicities; only the result of the European samples was used.
BMI and lipids summary data were generated from GWAS+Metabochip joint analysis, so sample sizes can vary across different SNPs.
The HKOS GWAS was part of the GEFOS meta-analysis and was the only study of non-European population in that study.
SNP heritability estimates of phenotypes analyzed in the HKDD cohort.
| Height | Age, sex; inverse normal transformation | 0.533 (0.170) | 6.75E-05 |
| Age, sex, first two PCs; inverse normal transform | 0.383 (0.182) | 1.67E-02 | |
| BMI | Age, age2, sex; inverse normal transformation | 0.285 (0.171) | 2.97E-02 |
| Age, age2, sex, first PC; inverse normal transformation | 0.249 (0.174) | 6.03E-02 | |
| Disc degeneration score | Age, sex, lumbar injury | 0.218 (0.163) | 6.50E-02 |
| Age, sex, lumbar injury, height | 0.232 (0.169) | 6.43E-02 | |
| Age, sex, lumbar injury, BMI | 0.226 (0.170) | 7.26E-02 | |
| Age, sex, lumbar injury, height, BMI | 0.219 (0.171) | 8.40E-02 | |
| Age, sex, lumbar injury, weight | 0.225 (0.171) | 7.80E-02 | |
| Disc displacement score | Age, sex, lumbar injury | 0.291 (0.176) | 4.26E-02 |
| Age, sex, lumbar injury, height | 0.269 (0.180) | 6.20E-02 | |
| Age, sex, lumbar injury, BMI | 0.238 (0.181) | 9.17E-02 | |
| Age, sex, lumbar injury, height, BMI | 0.216 (0.182) | 1.21E-01 | |
| Age, sex, lumbar injury, weight | 0.213 (0.182) | 1.22E-01 |
Figure 3Prediction performance of polygenic scores (PGS) on four base phenotypes in Chinese population. Phenotype variances explained (R2) are shown at different p-value thresholds. The gray lines are the predicted R2 based on the theoretical model of Dudbridge (2013) with parameters given in Table S4. Different parameter sets of each model give similar results. PGS of height (A) and BMI (B) were tested on HKDD cohort; PGS of bone mineral density at the lumbar spine (LS-BMD, C), and femoral neck (FN-BMD, D), were evaluated on HKOS sample.
Genetic overlap of lumbar disc degeneration with anthropometric traits.
| Height (Wood et al., | Known loci | 253,000 | 622 | 5.76% | + | 0.003% | 8.04E-01 | + | 0.135% | 9.40E-02 | + | 0.351% | 7.73E-03 |
| PGS | 3,933 | 6.69% | + | 0.023% | 4.88E-01 | + | 0.162% | 6.95E-02 | + | ||||
| BMI (Locke et al., | Known loci | 234,000~322,000 | 92 | 1.24% | + | 0.016% | 5.46E-01 | + | 0.053% | 2.94E-01 | − | 0.000% | 9.80E-01 |
| PGS | 4,238 | 2.64% | + | + | + | 0.011% | 6.44E-01 | ||||||
| Lumbar Spine BMD (Estrada et al., | Known loci | 46,000 | 60 | 9.33% | + | + | 0.000% | 9.92E-01 | + | 0.093% | 1.71E-01 | ||
| PGS | 32,000 | 109 | 7.53% | + | 0.200% | 4.10E-02 | + | 0.009% | 6.66E-01 | + | 0.136% | 9.80E-02 | |
| Femoral Neck BMD (Estrada et al., | Known loci | 51,000 | 60 | 7.78% | + | 0.062% | 2.55E-01 | − | 0.017% | 5.51E-01 | + | 0.073% | 2.24E-01 |
| PGS | 33,000 | 563 | 8.88% | + | 0.153% | 7.43E-02 | + | 0.044% | 3.36E-01 | + | 0.187% | 5.27E-02 | |
For the four base phenotypes, we adopted two strategies to create polygenic profiles to predict target phenotypes: using known trait-associated SNPs and their effect size estimates or using independent SNPs of GWAS summary statistics selected based on the optimal p-value threshold for predicting the base phenotype. Nominally significant associations with LDD phenotypes are shown in bold for PGS with best prediction performance for the base phenotype.
Sample size of discovery sample GWAS. For known BMD-associated loci, shown are the sample size of second stage replication cohort.
Number of SNPs in the HKDD cohort that passed QC and have minor allele frequency ≥0.01.
Variance of base phenotype in Chinese population explained by the PGS. For height and BMI, R.
Association with disc displacement and degeneration scores were evaluated by inclusion of polygenic profile score as a covariate to the multiple linear regression model of target phenotype that adjusted for age, sex and lumbar spine injury.
For LDH, R.
The HKOS GWAS sample were selected from extreme ends of BMD distribution. After correcting for extreme-selection (Appendix .
Figure 4Power to detect association with polygenic score (PGS) in two testing samples. (A) For the HKDD cohort (N = 2,054), given significance level (at α = 0.01 or 0.05), the power is determined by the phenotype variance explained by PGS. (B) For the Japanese case-control cohort (366 cases, 3,331 controls), assuming the disease prevalence of 0.02, the power is a function of the disease liability explained by PGS.
Association of rs4733724-A allele with lumbar disc degeneration and height in East Asian samples.
| Disc displacement score ( | Age, sex, lumbar injury | 0.078 (0.032) | 1.61E-02 |
| Age, sex, lumbar injury, BMI | 0.074 (0.033) | 2.28E-02 | |
| Age, sex, lumbar injury, height | 0.074 (0.033) | 2.43E-02 | |
| Age, sex, lumbar injury, weight | 0.072 (0.032) | 2.68E-02 | |
| Age, sex, lumbar injury, height, BMI | 0.071 (0.032) | 2.91E-02 | |
| Disc degeneration score ( | Age, sex, lumbar injury | 0.182 (0.089) | 4.16E-02 |
| Age, sex, lumbar injury, BMI | 0.187 (0.090) | 3.73E-02 | |
| Age, sex, lumbar injury, height | 0.183 (0.090) | 4.16E-02 | |
| Age, sex, lumbar injury, weight | 0.180 (0.089) | 4.33E-02 | |
| Age, sex, lumbar injury, height, BMI | 0.176 (0.089) | 4.83E-02 | |
| Hospitalized LDH (366 cases, 3,331 controls) | NA | 0.105 | 1.96E-01 |
| Height ( | Age, sex, PC1, PC2 | 0.032 (0.035) | 3.59E-01 |
The SNP rs4733724 was genotyped in the HKDD cohort and reliably imputed in the Japanese LDH case-control cohort. The A allele was previously reported to be associated with increased height in Europeans (Wood et al., 2014). The rs4733724-A allele is coupled to rs6651255-T, the latter of which was recently found to increase the risk (odds ratio = 1.23) of LDH requiring surgery in Icelanders (Bjornsdottir et al., 2017). The frequency of rs4733724-A allele is 0.72 in East Asians and 0.23 in Europeans.
Odds ratio = 1.11.
Genetic correlations estimated by LD-score regression.
| Height | BMI | −0.055 (0.022) | 1.36E-02 |
| Height | LS-BMD | 0.071 (0.032) | 2.72E-02 |
| Height | FN-BMD | 0.036 (0.033) | 2.83E-01 |
| BMI | LS-BMD | 0.067 (0.028) | 1.75E-02 |
| BMI | FN-BMD | 0.071 (0.028) | 9.90E-03 |
| LS-BMD | FN-BMD | 0.669 (0.032) | 4.64E-96 |
| OA | BMI | 0.255 (0.050) | 4.02E-07 |
| OA | Height | 0.117 (0.045) | 9.50E-03 |
| OA | LS-BMD | 0.192 (0.076) | 1.18E-02 |
| OA | FN-BMD | 0.094 (0.068) | 1.63E-01 |
BMI, body mass index; BMD, bone mineral density; LS, lumbar spine; FN, femoral neck; OA, osteoarthritis.
Figure 5Comparing the prediction performance of polygenic score (PGS) in Chinese sample using GWAS of European and East Asian. Expected phenotype variances explained by PGS (R2) were calculated using the theoretical model of Dudbridge (2013) with parameters compatible with the observed PGS results of height and BMI. (A) For height, the latest European GWAS has sample size 252K. Assuming SNP heritability of 0.42 in both populations, expected R2 in Chinese population (red line) was calculated using the parameters best fit to Figure 3. In comparison, the latest East Asian GWAS has sample size only 36K, expected R2 was calculated using the same set of parameters except that we assumed no heterogeneity in effect sizes (i.e., genetic correlation = 1) between discovery and testing sample (blue line). To predict the gain in R2 when using even larger European GWAS in the future, we further increased the discovery GWAS sample size by 500K (red dashed line). We also relaxed the assumption of no heterogeneity within East Asian and calculate expected R2 assuming genetic correlation of 0.9 (blue dashed line). (B) For BMI, European GWAS has sample size 234K; East Asian GWAS has sample size 87K. Expected R2 were calculated similarly as height, assuming SNP heritability of 0.22.