Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects

Ethnic disparities in fracture risk assessment using polygenic scores

Whether the PGS developed using data from European ancestry is predictive of fracture risk for minorities remains unclear. This study demonstrated that PGSs based on common BMD-related genetic variants discovered in the European ancestry cohort are predictive of fracture risk in people of Asian but not African ancestry.

PURPOSE

Large-scale genome-wide association studies (GWAS) on bone mineral density (BMD) have been conducted predominantly in European cohorts. Genetic models based on common variants associated with BMD have been evaluated using almost exclusively European data, which could potentially exacerbate health disparities due to different linkage disequilibrium among different ethnic groups.

METHODS

UK Biobank (UKB) is a large-scale population-based observational study starting in 2006 that recruited 502,617 individuals aged between 40 and 69 years with genotypic and phenotypic data available. Based on the summary statistics of two GWAS studies of femoral neck BMD and total body BMD, we derived four PGSs and assessed the association between each PGS and prevalent/incident fractures within each ethnic group separately using Multivariate logistic regressions and Cox proportional hazard models. All models were adjusted for age, sex, and the first four principal components.

RESULTS

We assessed four PGSs derived from European cohorts. Significant associations were observed between PGSs and fracture in European and Asian cohorts but not in the African cohort. Of all four PGSs, [Formula: see text] performed the best. A standard deviation decreases in [Formula: see text] were associated with an increased hazard ratio (HR) of 1.24 (1.22-1.27), 1.28 (0.83-1.99), and 1.34 (1.10-1.64) in European, African, and Asian ancestry, respectively. A low BMD-related PGS is associated with up to 2.35- and 4.31-fold increased fracture risk in European and Asian populations.

CONCLUSIONS

These results showed that PGSs based on common BMD-related genetic variants discovered in the European ancestry cohort are predictive of fracture risk in people of Asian but not African ancestry.

The clinical utility of the BMD-related comprehensive genome-wide polygenic score in identifying individuals with a high risk of osteoporotic fractures

The potential of bone mineral density (BMD)-related genome-wide polygenic score (PGS) in identifying individuals with a high risk of fractures remains unclear. This study suggests that an efficient PGS enables the identification of strata with up to a 1.5-fold difference in fracture incidence. Incorporating PGS into clinical diagnosis is anticipated to increase the population-level screening benefits.

PURPOSE

This study sought to construct genome-wide polygenic scores for femoral neck and total body BMD and to estimate their potential in identifying individuals with a high risk of osteoporotic fractures.

METHODS

Genome-wide polygenic scores were developed and validated for femoral neck and total body BMD. We externally tested the PGSs, both by themselves and in combination with available clinical risk factors, in 455,663 European ancestry individuals from the UK Biobank. The predictive accuracy of the developed genome-wide PGS was also compared with previously published restricted PGS employed in fracture risk assessment.

RESULTS

For each unit decrease in PGSs, the genome-wide PGSs were associated with up to 1.17-fold increased fracture risk. Out of four studied PGSs, [Formula: see text] (HR: 1.03; 95%CI 1.01-1.05, p = 0.001) had the weakest and the [Formula: see text] (HR: 1.17; 95%CI 1.15-1.19, p < 0.0001) had the strongest association with an incident fracture. In the reclassification analysis, compared to the FRAX base model, the models with [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] improved the reclassification of fracture by 1.2% (95% CI, 1.0 to 1.3%), 0.2% (95% CI, 0.1 to 0.3%), 1.4% (95% CI, 1.3 to 1.5%), and 2.2% (95% CI, 2.1 to 2.4%), respectively.

CONCLUSIONS

Our findings suggested that an efficient PGS estimate enables the identification of strata with up to a 1.7-fold difference in fracture incidence. Incorporating PGS information into clinical diagnosis is anticipated to increase the benefits of screening programs at the population level.

Phenome-wide Mendelian randomization study evaluating the association of circulating vitamin D with complex diseases

Background

Circulating vitamin D has been associated with multiple clinical diseases in observational studies, but the association was inconsistent due to the presence of confounders. We conducted a bidirectional Mendelian randomization (MR) study to explore the healthy atlas of vitamin D in many clinical traits and evaluate their causal association.

Methods

Based on a large-scale genome-wide association study (GWAS), the single nucleotide polymorphism (SNPs) instruments of circulating 25-hydroxyvitamin D (25OHD) from 443,734 Europeans and the corresponding effects of 10 clinical diseases and 42 clinical traits in the European population were recruited to conduct a bidirectional two-sample Mendelian randomization study. Under the network of Mendelian randomization analysis, inverse-variance weighting (IVW), weighted median, weighted mode, and Mendelian randomization (MR)–Egger regression were performed to explore the causal effects and pleiotropy. Mendelian randomization pleiotropy RESidual Sum and Outlier (MR-PRESSO) was conducted to uncover and exclude pleiotropic SNPs.

Results

The results revealed that genetically decreased vitamin D was inversely related to the estimated BMD (β = −0.029 g/cm2, p = 0.027), TC (β = −0.269 mmol/L, p = 0.006), TG (β = −0.208 mmol/L, p = 0.002), and pulse pressure (β = −0.241 mmHg, p = 0.043), while positively associated with lymphocyte count (β = 0.037%, p = 0.015). The results did not reveal any causal association of vitamin D with clinical diseases. On the contrary, genetically protected CKD was significantly associated with increased vitamin D (β = 0.056, p = 2.361 × 10−26).

Conclusion

The putative causal effects of circulating vitamin D on estimated bone mass, plasma triglyceride, and total cholesterol were uncovered, but not on clinical diseases. Vitamin D may be linked to clinical disease by affecting health-related metabolic markers.

Association of antihypertensive drugs with fracture and bone mineral density: A comprehensive drug-target Mendelian randomization study

Background

Observational studies have investigated the associations between antihypertensive drugs and fracture risk as well as bone mineral density (BMD), but yielding controversial results.

Methods

In this study, a comprehensive drug-target Mendelian randomization (MR) analysis was conducted to systematically examine the associations between genetic proxies for eight common antihypertensive drugs and three bone health-related traits (fracture, total body BMD [TB-BMD], and estimated heel BMD [eBMD]). The main analysis used the inverse-variance weighted (IVW) method to estimate the causal effect. Multiple MR methods were also employed to test the robustness of the results.

Results

The genetic proxies for angiotensin receptor blockers (ARBs) were associated with a reduced risk of fracture (odds ratio [OR] = 0.67, 95% confidence interval [CI]: 0.54 to 0.84; P = 4.42 × 10-4; P-adjusted = 0.004), higher TB-BMD (β = 0.36, 95% CI: 0.11 to 0.61; P = 0.005; P-adjusted = 0.022), and higher eBMD (β = 0.30, 95% CI: 0.21 to 0.38; P = 3.59 × 10-12; P-adjusted = 6.55 × 10-11). Meanwhile, genetic proxies for calcium channel blockers (CCBs) were associated with an increased risk of fracture (OR = 1.07, 95% CI: 1.03 to 1.12; P = 0.002; P-adjusted = 0.013). Genetic proxies for potassium sparing diuretics (PSDs) showed negative associations with TB-BMD (β = -0.61, 95% CI: -0.88 to -0.33; P = 1.55 × 10-5; P-adjusted = 1.86 × 10-4). Genetic proxies for thiazide diuretics had positive associations with eBMD (β = 0.11, 95% CI: 0.03 to 0.18; P = 0.006; P-adjusted = 0.022). No significant heterogeneity or pleiotropy was identified. The results were consistent across different MR methods.

Conclusions

These findings suggest that genetic proxies for ARBs and thiazide diuretics may have a protective effect on bone health, while genetic proxies for CCBs and PSDs may have a negative effect.

Metabolome-Wide Mendelian Randomization Assessing the Causal Relationship Between Blood Metabolites and Bone Mineral Density

Mounting evidence has supported osteoporosis (OP) as a metabolic disorder. Recent metabolomics studies have discovered numerous metabolites related to bone mineral density (BMD). However, the causal effects of metabolites on BMD at distinct sites remained underexplored. Leveraging genome-wide association datasets, we conducted two-sample Mendelian randomization (MR) analyses to investigate the causal relationship between 486 blood metabolites and bone mineral density at five skeletal sites including heel (H), total body (TB), lumbar spine (LS), femoral neck (FN), and ultra-distal forearm (FA). Sensitivity analyses were performed to test the presence of the heterogeneity and the pleiotropy. To exclude the influences of reverse causation, genetic correlation, and linkage disequilibrium (LD), we further performed reverse MR, linkage disequilibrium regression score (LDSC), and colocalization analyses. In the primary MR analyses, 22, 10, 3, 7, and 2 metabolite associations were established respectively for H-BMD, TB-BMD, LS-BMD, FN-BMD, and FA-BMD at the nominal significance level (IVW, P < 0.05) and passing sensitivity analyses. Among these, one metabolite, androsterone sulfate showed a strong effect on four out of five BMD phenotypes (Odds ratio [OR] for H-BMD = 1.045 [1.020, 1.071]; Odds ratio [OR] for TB-BMD = 1.061 [1.017, 1.107]; Odds ratio [OR] for LS-BMD = 1.088 [1.023, 1.159]; Odds ratio [OR] for FN-BMD = 1.114 [1.054, 1.177]). Reverse MR analysis provided no evidence for the causal effects of BMD measurements on these metabolites. Colocalization analysis have found that several metabolite associations might be driven by shared genetic variants such as mannose for TB-BMD. This study identified some metabolites causally related to BMD at distinct sites and several key metabolic pathways, which shed light on predictive biomarkers and drug targets for OP.

Influence of glycoprotein MUC1 on trafficking of the Ca2+-selective ion channels, TRPV5 and TRPV6, and on in vivo calcium homeostasis

Polymorphism of the gene encoding mucin 1 (MUC1) is associated with skeletal and dental phenotypes in human genomic studies. Animals lacking MUC1 exhibit mild reduction in bone density. These phenotypes could be a consequence of modulation of bodily Ca homeostasis by MUC1, as suggested by the previous observation that MUC1 enhances cell surface expression of the Ca2+-selective channel, TRPV5, in cultured unpolarized cells. Using biotinylation of cell surface proteins, we asked whether MUC1 influences endocytosis of TRPV5 and another Ca2+-selective TRP channel, TRPV6, in cultured polarized epithelial cells. Our results indicate that MUC1 reduces endocytosis of both channels, enhancing cell surface expression. Further, we found that mice lacking MUC1 lose apical localization of TRPV5 and TRPV6 in the renal tubular and duodenal epithelium. Females, but not males, lacking MUC1 exhibit reduced blood Ca2+. However, mice lacking MUC1 exhibited no differences in basal urinary Ca excretion or Ca retention in response to PTH receptor signaling, suggesting compensation by transport mechanisms independent of TRPV5 and TRPV6. Finally, humans with autosomal dominant tubulointerstitial kidney disease due to frame-shift mutation of MUC1 (ADTKD-MUC1) exhibit reduced plasma Ca concentrations compared to control individuals with mutations in the gene encoding uromodulin (ADTKD-UMOD), consistent with MUC1 haploinsufficiency causing reduced bodily Ca2+. In summary, our results provide further insight into the role of MUC1 in Ca2+-selective TRP channel endocytosis and the overall effects on Ca concentrations.

Efficient identification of trait-associated loss-of-function variants in the UK Biobank cohort by exome-sequencing based genotype imputation

The large-scale open access whole-exome sequencing (WES) data of the UK Biobank ~200,000 participants is accelerating a new wave of genetic association studies aiming to identify rare and functional loss-of-function (LoF) variants associated with complex traits and diseases. We proposed to merge the WES genotypes and the genome-wide genotyping (GWAS) genotypes of 167,000 UKB homogeneous European participants into a combined reference panel, and then to impute 241,911 UKB homogeneous European participants who had the GWAS genotypes only. We then used the imputed data to replicate association identified in the discovery WES sample. The average imputation accuracy measure r² is modest to high for LoF variants at all minor allele frequency intervals: 0.942 at MAF interval (0.01, 0.5), 0.807 at (1.0 × 10^-3 , 0.01), 0.805 at (1.0 × 10^-4 , 1.0 × 10^-3 ), 0.664 at (1.0 × 10^-5 , 1.0 × 10^-4 ) and 0.410 at (0, 1.0 × 10^-5 ). As applications, we studied associations of LoF variants with estimated heel BMD and four lipid traits. In addition to replicating dozens of previously reported genes, we also identified three novel associations, two genes PLIN1 and ANGPTL3 for high-density-lipoprotein cholesterol and one gene PDE3B for triglycerides. Our results highlighted the strength of WES based genotype imputation as well as provided useful imputed data within the UKB cohort.

Proteogenomic links to human metabolic diseases

Studying the plasma proteome as the intermediate layer between the genome and the phenome has the potential to identify new disease processes. Here, we conducted a cis-focused proteogenomic analysis of 2,923 plasma proteins measured in 1,180 individuals using antibody-based assays. We (1) identify 256 unreported protein quantitative trait loci (pQTL); (2) demonstrate shared genetic regulation of 224 cis-pQTLs with 575 specific health outcomes, revealing examples for notable metabolic diseases (such as gastrin-releasing peptide as a potential therapeutic target for type 2 diabetes); (3) improve causal gene assignment at 40% (n = 192) of overlapping risk loci; and (4) observe convergence of phenotypic consequences of cis-pQTLs and rare loss-of-function gene burden for 12 proteins, such as TIMD4 for lipoprotein metabolism. Our findings demonstrate the value of integrating complementary proteomic technologies with genomics even at moderate scale to identify new mediators of metabolic diseases with the potential for therapeutic interventions.

Causal Effects of Plasma Proteome on Osteoporosis and Osteoarthritis

The two-sample Mendelian randomization (MR) study revealed a causal association of plasma proteins with osteoporosis (OP) and osteoarthritis (OA). Bone mineral density (BMD) is the gold standard for the clinical assessment of OP. Recent studies have shown that plasma proteins play an essential role in the regulation of bone development. However, the causal association of plasma proteins with BMD and OA remains unclear. We estimated the effects of 2889 plasma proteins on 2 BMD phenotypes and 6 OA phenotypes using two-sample MR analysis based on the genome-wide association study summary statistics. Then, we performed sensitivity analysis and reverse-direction MR analysis to evaluate the robustness of the MR analysis results, followed by gene ontology (GO) enrichment analysis and KEGG pathway analysis to explore the functional relevance of the identified plasma proteins. Overall, we observed a total of 257 protein-estimated heel BMD associations, 17 protein-total-body BMD associations, 2 protein-all-OA associations, and 2 protein-knee-OA associations at P_FDR < 0.05. Reverse-direction MR analysis demonstrated that there was little evidence of the causal association of BMD and OA with plasma proteins. GO enrichment analysis and KEGG pathway analysis identified multiple pathways, which may be involved in the development of OP and OA. Our findings recognized plasma proteins that could be used to regulate changes in OP and OA, thus, providing new insights into protein-mediated mechanisms of bone development.

Risk of Environmental Chemicals on Bone Fractures Is Independent of Low Bone Mass in US Adults: Insights from 2017 to 2018 NHANES

(1) Objective: To assess the association of environmental chemical factors with osteopenia and/or bone fractures. (2) Methods: All data were extracted from the National Health and Nutrition Survey (NHANES) 2017–2018 of American adults aged 20–59 years old; invalid data were excluded based on dual-energy X-ray absorptiometry. For the ultimate valid data set, multivariate logistic regression models were applied to evaluate the association of environmental chemical factors with osteopenia and bone fractures. (3) Results: The valid dataset was obtained from 2640 individuals, who completed a questionnaire of demographic characteristics. Urinary manganese and monomethylarsonic acid were positively associated with osteopenia in American adults, but not bone fracture. However, several environmental factors (e.g., arsenous acid, arsenocholine, dimethylarsinic acid, and 2-thioxothiazolidine-4-carboxylic acid) did not affect bone mineral density, but were significantly associated with bone fracture. (4) Conclusions: Multiple environmental chemical factors significantly affect bone mass or fracture risk. However, the risk of environmental chemical factors on fractures is independent of osteopenia in US Adults. The influence of environmental chemical factors on bone quality should be considered and monitored.

Twelve Loci Associated With Bone Density in Middle-aged and Elderly Chinese: The Shanghai Changfeng Study

CONTEXT

Previous genome-wide association studies (GWASs) of bone mineral density (BMD) were mainly conducted in Europeans.

OBJECTIVE

To explore genetic variants that affect BMD and sex differences in a Chinese population.

METHODS

A total of 5428 middle-aged and elderly Chinese were included. Dual-energy X-ray absorptiometry was used to measure BMD at the lumbar spine, and total and specific sites of the hip. A mixed linear model was used to analyze the associations between BMD and autosomal genetic variants, adjusting for age, age squared, sex, and menopausal women (model 1); model 2 was further adjusted for height and weight. A GWAS of osteoporosis in the Biobank Japan (BBJ) project was used for replication. GWAMA software was used to detect the statistical significance of sex differences of estimated effects. Gene annotation and pathway enrichment analysis were performed.

RESULTS

Women lost BMD at earlier ages and faster than men. The 2 models identified a total of 12 loci that were associated with BMD at any site. Single nucleotide polymorphisms rs72354346, rs2024219, rs1463093, rs10037512, and rs5880932 were successfully replicated in the BBJ. Variations of rs79262027 G>A (VKORC1L1) and rs4795209 A>G (DDX52) were associated with BMD only in men, and rs1239055408 G>GA (KCNJ2) was associated with BMD only in women. Gene enrichment analysis showed that BMD in a Chinese elderly population was mainly related to ossification, bone resorption, sex hormones, and kidney physiology.

CONCLUSION

The present GWAS identified 12 loci that were significantly associated with BMD at any site in a Chinese population, and 3 of them showed sex differences in their effects.

Mendelian randomization analysis does not reveal a causal influence of mental diseases on osteoporosis

Introduction

Osteoporosis (OP) is primarily diagnosed through bone mineral density (BMD) measurements, and it often leads to fracture. Observational studies suggest that several mental diseases (MDs) may be linked to OP, but the causal direction of these associations remain unclear. This study aims to explore the potential causal association between five MDs (Schizophrenia, Depression, Alzheimer's disease, Parkinson's disease, and Epilepsy) and the risk of OP.

Methods

First, single-nucleotide polymorphisms (SNPs) were filtered from summary-level genome-wide association studies using quality control measures. Subsequently, we employed two-sample Mendelian randomization (MR) analysis to indirectly analyze the causal effect of MDs on the risk of OP through bone mineral density (in total body, femoral neck, lumbar spine, forearm, and heel) and fractures (in leg, arm, heel, spine, and osteoporotic fractures). Lastly, the causal effect of the MDs on the risk of OP was evaluated directly through OP. MR analysis was performed using several methods, including inverse variance weighting (IVW)-random effects, IVW-fixed effects, maximum likelihood, weighted median, MR-Egger regression, and penalized weighted median.

Results

The results did not show any evidence of a causal relationship between MDs and the risk of OP (with almost all P values > 0.05). The robustness of the above results was proved to be good.

Discussion

In conclusion, this study did not find evidence supporting the claim that MDs have a definitive impact on the risk of OP, which contradicts many existing observational reports. Further studies are needed to determine the potential mechanisms of the associations observed in observational studies.

Metabolically favorable adiposity and bone mineral density: a Mendelian randomization analysis

OBJECTIVE

This analysis assessed the putative causal association between genetically predicted percent body fat and areal bone mineral density (aBMD) and, more specifically, the association between genetically predicted metabolically "favorable adiposity" (MFA) and aBMD at clinically relevant bone sites.

METHODS

Mendelian randomization was used to assess the relationship of MFA and percent body fat with whole-body, lumbar spine, femoral neck, and forearm aBMD. Sex-stratified and age-stratified exploratory analyses were conducted.

RESULTS

In all MR analyses, genetically predicted MFA was inversely associated with aBMD for the whole body (β = -0.053, p = 0.0002), lumbar spine (β = -0.075; p = 0.0001), femoral neck (β = -0.045; p = 0.008), and forearm (β = -0.115; p = 0.001). This negative relationship was strongest in older individuals and did not differ by sex. The relationship between genetically predicted percent body fat and aBMD was nonsignificant across all Mendelian randomization analyses. Several loci that were associated at a genome-wide significance level (p < 5 × 10^-8 ) in opposite directions with body fat and aBMD measures were also identified.

CONCLUSIONS

This study did not support the hypothesis that MFA protects against low aBMD. Instead, it showed that MFA may result in lower aBMD. Further research is needed to understand how MFA affects aBMD and other components of bone health such as bone turnover, bone architecture, and osteoporotic fractures.

Potential causal association between leisure sedentary behaviors, physical activity and musculoskeletal health: A Mendelian randomization study

BACKGROUND

Increasing evidence shows that leisure sedentary behaviors (LSB) and physical activity (PA) are associated with various musculoskeletal disorders. However, the causality between LSB/PA and musculoskeletal health remained unknown. In this study, we aimed to evaluate the causal relationships between LSB/PA and lower back pain (LBP), intervertebral disc disorder (IVDD), rheumatoid arthritis (RA), and bone mineral density (BMD) by using a two-sample Mendelian randomization method.

METHODS

The exposure data were obtained from large-scale genome-wide association studies (GWAS), including the PA dataset (self-reported PA, n  =  377,234; accelerometer-assessed PA, n  = 91,084) and LSB dataset (n  =  422,218). The outcome data were derived from the FinnGen LBP dataset (n  =  248,528), FinnGen IVDD dataset (n  =  256,896), BMD GWAS dataset (n  =  56,284), and RA GWAS dataset (n  =  58,284). The causal relationships were estimated with inverse variance weighted (IVW), MR-Egger, and weighted median methods. Sensitivity analyses were performed with Cochran's Q test, MR-Egger intercept test, and leave-one-out analysis to estimate the robustness of our findings.

RESULTS

Genetically predicted leisure television watching increased the risk of LBP (OR = 1.68, 95% CI 1.41 to 2.01; P = 8.23×10-9) and IVDD (OR  =  1.62, 95% CI 1.37 to 1.91; P  =  2.13 × 10-8). In addition, this study revealed a potential causal relationship between computer use and a reduced risk of IVDD (OR  = 0.60, 95% CI 0.42 to 0.86; P  =  0.005) and RA (OR  = 0.28, 95% CI 0.13 to 0.60; P  =  0.001).

CONCLUSIONS

Our results suggest that leisure television watching is a risk factor for LBP and IVDD, whereas leisure computer use may act as a protective factor against IVDD and RA. These findings emphasized the importance of distinguishing between different sedentary behaviors in musculoskeletal disease studies.

Unravelling genetic causality of haematopoiesis on bone metabolism in human

OBJECTIVE

Haematopoiesis was shown to regulate bone metabolism in in vivo studies. However, whether haematopoiesis has causal effects on bone health has never been investigated in humans. We aimed to evaluate the causal relationships of blood traits with bone mineral density (BMD) and fracture.

DESIGN AND METHODS

Using two-sample Mendelian randomization, causal relationship of 29 blood traits with estimated BMD (eBMD), total body BMD (TBBMD), lumbar spine BMD (LSBMD), femoral neck BMD (FNBMD) and fracture were evaluated by inverse-variance weighted (IVW) method and multiple sensitivity analyses. Relevant genetic data were obtained from the largest possible publicly available genome-wide association studies.

RESULTS

Eight genetically determined red blood cell traits showed positive causal effects on eBMD, with beta estimates ranging from 0.009 (mean corpuscular haemoglobin) to 0.057 (haemoglobin concentration), while three white blood cell traits, including lymphocyte count (beta: -0.020; 95% CI: -0.033 to -0.007), neutrophil count (beta: -0.020; 95% CI: -0.035 to -0.006) and white blood cell count (beta: -0.027; 95% CI: -0.039 to -0.014), were inversely associated with eBMD. Causal effects for six of these blood traits were validated on TBBMD, LSBMD, FNBMD and/or fracture. The association of reticulocyte count (beta: 0.040; 95% CI: 0.016 to 0.063), haemoglobin (beta: 0.058; 95% CI: 0.021 to 0.094) and mean corpuscular haemoglobin concentration (beta: 0.030; 95% CI: 0.007 to 0.054) with eBMD remained significant in multivariable IVW analyses adjusted for other blood traits.

CONCLUSION

This study provided evidence that haematopoietic system might regulate the skeletal system in humans and suggested the possible pathophysiology of bone diseases among people with haematological diseases.

SIGNIFICANCE STATEMENT

We conducted a novel Mendelian randomization study investigating the causal relationship of blood cells with bone mineral density. Red and white blood cell traits have positive and inverse causal relationship with bone mineral density, respectively, suggesting a potential link of haematopoietic system with the skeletal system in humans. Current findings suggest individuals with related haematological diseases, such as anaemia and leukocytosis, may have a lifelong increased risk of osteoporosis and/or fracture. Given that complete blood count is commonly performed in clinical setting, whether complete blood count can be used to predict fracture risk warrants further investigation.

Bone health in ageing men

Osteoporosis does not only affect postmenopausal women, but also ageing men. The burden of disease is projected to increase with higher life expectancy both in females and males. Importantly, osteoporotic men remain more often undiagnosed and untreated compared to women. Sex steroid deficiency is associated with bone loss and increased fracture risk, and circulating sex steroid levels have been shown to be associated both with bone mineral density and fracture risk in elderly men. However, in contrast to postmenopausal osteoporosis, the contribution of relatively small decrease of circulating sex steroid concentrations in the ageing male to the development of osteoporosis and related fractures, is probably only minor. In this review we provide several clinical and preclinical arguments in favor of a 'bone threshold' for occurrence of hypogonadal osteoporosis, corresponding to a grade of sex steroid deficiency that in general will not occur in many elderly men. Testosterone replacement therapy has been shown to increase bone mineral density in men, however data in osteoporotic ageing males are scarce, and evidence on fracture risk reduction is lacking. We conclude that testosterone replacement therapy should not be used as a sole bone-specific treatment in osteoporotic elderly men.

Inferring causal effects of homocysteine and B-vitamin concentrations on bone mineral density and fractures: Mendelian randomization analyses

OBJECTIVES

In the progress of bone metabolism, homocysteine (Hcy) and B vitamins play substantial roles. However, the causal associations of homocysteine, B-vitamin concentrations with bone mineral density (BMD), and fractures remain unclear. Therefore, we employed a two-sample Mendelian randomization (MR) design to infer the causal effects of Hcy and B vitamins on BMD and fractures.

METHODS

We selected instrumental variables from large genome-wide association studies (GWASs). Specifically, the exposures mainly included Hcy (sample size: 44,147), vitamin B12 (sample size: 45,576), folate (sample size: 37,465), and vitamin B6 (sample size: 1,864). The outcome variables included total body BMD (sample size: 66,628), heel BMD (sample size: 142,487), femoral neck BMD (sample size: 32,735), lumbar spine BMD (sample size: 28,498), and forearm BMD (sample size: 8143). Additionally, the total body BMD in several age strata was also included. Furthermore, the fractures of the forearm, femoral neck, lumbar spine, heel corresponding with the BMD regions, and femoral neck and lumbar spine BMD in men and women, separately, were added as additional outcomes. Two-sample MR approaches were utilized in this study. Inverse variance weighting (IVW) was adopted as the main analysis. MR-PRESSO, MR-Egger, the weighted median estimate, and multivariable MR were performed as sensitivity methods.

RESULTS

In the main analysis, Hcy concentrations have an inverse association with heel BMD (Beta = 0.046, 95% confidence interval (CI) -0.073 to -0.019, P = 9.59E-04) per SD unit. In addition, for one SD increase of vitamin B12, the total body BMD decreased 0.083 unit (95%CI -0.126 to -0.040, P = 1.65E-04). The trend was more obvious in age over 45 years (Beta = -0.135, 95%CI -0.203-0.067, P = 9.86E-05 for age 45-60; Beta = -0.074, 95%CI -0.141 to -0.007, P = 0.031 for age over 60 years). No association of B vitamins and Hcy levels with the risk of fractures and femoral neck and lumbar spine BMD in men and women was found in this study. Other sensitivity MR methods elucidated consistent results.

CONCLUSIONS

Our findings indicated that there exist the inversely causal effects of Hcy and vitamin B12 on BMD in certain body sites and age strata. These give novel clues for intervening bone-related diseases in public health and nutrition.

Association between total body bone mineral density and periodontitis: A Mendelian randomization study

BACKGROUND

The purpose of the study was to examine the association between total body bone mineral density (BMD) and periodontitis using Mendelian randomization (MR) analysis.

METHODS AND MATERIALS

We used 81 single nucleotide polymorphisms (SNPs) associated with BMD at a p-value of < 5 × 10^-8 from a genome-wide association study (GWAS) of 66,628 individuals of European descent. The GWAS for periodontitis was derived from a meta-analysis of seven cohort studies that included 17,353 cases and 28,210 controls of European ancestry.

RESULTS

MR showed no association between BMD and periodontitis (odds ratio per standard deviation increment in genetically predicted BMD = 1.00; 95% confidence interval: 0.92-1.08). Leave-one-out analyses and pleiotropy-robust methods did not indicate any bias.

CONCLUSIONS

The MR study provided no evidence that BMD might be causally linked to periodontitis. Hence it may be concluded as the key finding that BMD depletion does not increase the risk of periodontitis.

Simultaneous detection of novel genes and SNPs by adaptive p-value combination

Combining SNP p-values from GWAS summary data is a promising strategy for detecting novel genetic factors. Existing statistical methods for the p-value-based SNP-set testing confront two challenges. First, the statistical power of different methods depends on unknown patterns of genetic effects that could drastically vary over different SNP sets. Second, they do not identify which SNPs primarily contribute to the global association of the whole set. We propose a new signal-adaptive analysis pipeline to address these challenges using the omnibus thresholding Fisher’s method (oTFisher). The oTFisher remains robustly powerful over various patterns of genetic effects. Its adaptive thresholding can be applied to estimate important SNPs contributing to the overall significance of the given SNP set. We develop efficient calculation algorithms to control the type I error rate, which accounts for the linkage disequilibrium among SNPs. Extensive simulations show that the oTFisher has robustly high power and provides a higher balanced accuracy in screening SNPs than the traditional Bonferroni and FDR procedures. We applied the oTFisher to study the genetic association of genes and haplotype blocks of the bone density-related traits using the summary data of the Genetic Factors for Osteoporosis Consortium. The oTFisher identified more novel and literature-reported genetic factors than existing p-value combination methods. Relevant computation has been implemented into the R package TFisher to support similar data analysis.

Female bone physiology resilience in a past Polynesian Outlier community

Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440-150 BP Taumako in Solomon Islands, a remote 'Polynesian Outlier' island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples-a testament to past female bone physiology resilience, also now observed in the Pacific region.

Causal association between heart failure and bone mineral density: Insights from a two-sample bidirectional Mendelian randomization study

In recent times, the association between HF and BMD has attracted enormous interest in the scientific community. However, published epidemiological observational studies on the relationship between HF and BMD remain inconclusive. Herein, we evaluated from the analytical perspective a two-sample bidirectional MR study to analyze the causal association between HF and BMD using a summary-level GWAS Catalog. To select instrumental SNPs strongly associated with exposure, we took a series of rigorous quality control steps at the time of analysis. The causal MR assessment of HF on the risk of BMD was performed first and then in the opposite direction. To make the conclusions more reliable and robust, the fixed-effects IVW, weighted median-based method, MR-Egger, simple mode and weighted mode were utilized. A maximum likelihood model was also used if necessary. MR-Egger regression, IVW "leave-one-out" sensitivity analysis, MR-PRESSO, MR-Egger intercept test and Cochran's Q statistic methods were used to assess heterogeneity and pleiotropy. Our MR studies supported a meaningful causal association between HF and TB-BMD (IVW: OR = 0.78, 95% CI: 0.68-0.87, p = 0.00588). At the same time, we did not find a significant causal relationship between HF and FA-BMD, FN-BMD or LS-BMD. No significant causal relationships between BMD and HF were observed. This bidirectional MR analysis suggested a causal association of HF with only low TB-BMD, while the reverse causality hypothesis was not found. Studies of the prevention and treatment of total bone mineral density decline in patients with heart failure need to be performed.

Associations of bone mass and polygenic risk of osteoporosis with indicators of arterial wall condition

Background: The identification of genetic factors that are simultaneously responsible for the predisposition to the development of cardiovascular diseases (CVD) and osteoporosis (OP) is important for the prevention of both conditions.

Aim: The aim of this study is to evaluate three genetic risk scales (GRS) that previously showed an association with bone mineral density (BMD) and fracture risk, as well as to study the associations of these GRS with vascular wall pathology.

Materials and methods: 250 female outpatients (aged 45 to 69) were enrolled into a cross-sectional study. The intima-media thickness (IMT), the presence and number of atherosclerotic plaques (AP) were studied using duplex scanning. Pulse wave velocity (PWV), augmentation index (AI) were measured by applanation tonometry. Coronary vessels calcium deposits were registered by multispiral computed tomography (MSCT) using the Agatston calcium index (CI). The BMD of the spine, hip neck (HN) and proximal hip (PH) was measured using double energy x-ray absorptiometry. Bone resorption marker type-1 collagen C-terminal telopeptide (CTx) was assessed solid-phase enzyme immunoassay. The genetic study included DNA extraction from whole blood samples. Targeted sequencing was performed on the Nextseq550 sequencer (Illumina, USA). Statistical analysis was carried out using the SAS software package for Windows, version 9.0 (SAS Institute Inc., USA).

Results: The chance of detecting low bone mass increased more than 4 times at values of IMT ≥0.9 mm (OR=4.17; 95%CI [1.2–14.4], p<0.02), 2.4 times in the presence of AP in the carotid arteries (OR=2.45; 95%CI [1.12–4.88], p><0.05), by 6.7 times with an Agatstone CI ≥ 100 units (OR=6.68; 95%CI [1.56–28.7], p><0.001), 1.4 times (OR=1.43; 95%CI [0.56–3.68], p><0.438) with a PWV ≥10 m/s, 1.2 times (OR=1.2; 95%CI [0.601–2.43], p><0.60) with increased AI ≥ 27%. According to multivariate linear regression analysis (adjusted for age, duration of postmenopause, marker of bone resorption CTx), a significant association of all GRS with BMD in all parts of the skeleton was revealed. Both univariate and multivariate regression models adjusted for several covariants (age, total cholesterol, systolic blood pressure) showed a reliable association of GRS62 with the presence of plaques and GRS63 — with coronary artery CI. Conclusion: The results of the study demonstrated the association of polygenic genetic risk of GRS-based OP with BMD and vascular wall status indicators in women in the peri and postmenopausal periods.>< 0.02), 2.4 times in the presence of AP in the carotid arteries (OR=2.45; 95%CI [1.12–4.88], p< 0.05), by 6.7 times with an Agatstone CI ≥ 100 units (OR=6.68; 95%CI [1.56–28.7], p< 0.001), 1.4 times (OR=1.43; 95%CI [0.56–3.68], p< 0.438) with a PWV ≥10 m/s, 1.2 times (OR=1.2; 95%CI [0.601–2.43], p<0.60) with increased AI ≥ 27%. According to multivariate linear regression analysis (adjusted for age, duration of postmenopause, marker of bone resorption CTx), a significant association of all GRS with BMD in all parts of the skeleton was revealed. Both univariate and multivariate regression models adjusted for several covariants (age, total cholesterol, systolic blood pressure) showed a reliable association of GRS62 with the presence of plaques and GRS63 — with coronary artery CI.>< 0.60) with increased AI ≥ 27%. According to multivariate linear regression analysis (adjusted for age, duration of postmenopause, marker of bone resorption CTx), a significant association of all GRS with BMD in all parts of the skeleton was revealed. Both univariate and multivariate regression models adjusted for several covariants (age, total cholesterol, systolic blood pressure) showed a reliable association of GRS62 with the presence of plaques and GRS63 — with coronary artery CI.

Conclusion: The results of the study demonstrated the association of polygenic genetic risk of GRS-based OP with BMD and vascular wall status indicators in women in the peri and postmenopausal periods.

The immune factors have complex causal regulation effects on bone mineral density

Recent evidence has gradually recognized that the immune and skeletal systems are two closely correlated systems, but the specific immune factors on bone mineral density (BMD) are largely unknown. Based on the summary-level data of genome-wide association studies (GWASs), we performed a series of analyses including two-sample Mendelian randomization (MR) analysis to test potential causal links between 731 immune traits [including median fluorescence intensities (MFIs), absolute cell (AC) counts, relative cell (RC) counts, and morphological parameters (MP)] and BMD. After false discovery rate (FDR) correction, 9 MFI-BMD, 16 AC-BMD, 22 RC-BMD, and 5 MP-BMD pairs reached the level of significance (FDR-adjusted p< 0.05). For MFI traits, the T- and B-cell panels had the largest number of significant immune trait pairs than other panels. CD40, as a molecule expressed by four subsets of monocytes, was highlighted due to its consistently positive correlation with BMD at four sites. For both AC and RC traits, immune traits from the T-cell panel were also highlighted, with CD39-positive T-cell subsets being the most frequently observed feature. For MP traits, the most significant association immune trait with BMD was SSC-A on CD14+ monocyte. Sensitivity analyses suggested that the identified immune factors were robust to pleiotropy. Multivariable MR analysis confirmed the independent causal effect of several immune traits on BMD. Mediation analyses showed that CD40 on monocytes could mediate multiple immune traits, especially the suggestive associations of CD27 on several memory B cells with BMD mediated by CD40 on CD14+ CD16- monocyte. Our study represents the first comprehensive evaluation of the causal effects of immune traits on the risk of osteoporosis. The findings highlighted the complex and important role of immune-derived factors in the pathogenesis of osteoporosis.

The causal relationship between abdominal obesity and lower bone mineral density: A two-sample mendelian randomization study

Aims: The purpose of this study was to assess the causal effect of abdominal obesity on bone mineral density by two-sample Mendelian randomization (MR).

Methods: Abdominal obesity was chosen as exposure in this study. Single nucleotide polymorphisms, extracted from Genome-wide association analysis (GWAS) data, which are closely associated with waist circumference (WC), hip circumference (HC), and waist-to-hip ratio (WHR) were used as instrumental variables to perform MR studies. Different site bone mineral density, such as total bone mineral density (TBMD) and forearm bone mineral density (FBMD) were chosen as outcomes. Inverse variance weighted (IVW) was used as the primary method to assess this causality.

Results: According to the IVW method (β = −0.177; 95% CI = −0.287, −0.067; p = 1.52 × 10^–3), WC had a negative causal relationship with TBMD, besides, with one standard deviation (SD) higher in HC, there was a 0.195 SD decrease in TBMD (95% CI = −0.279, −0.110; p = 6.32 × 10^–6), and with an increase of one SD in HC was related to a decrease of 0.312 SD in FBMD analyzed by the IVW.

Conclusion: This study showed that abdominal obesity has a negative effect on bone mineral density.

Systematic evaluation for the causal effects of blood metabolites on osteoporosis: Genetic risk score and Mendelian randomization

Purpose

Osteoporosis is associated with metabolic alterations, but the causal roles of serum metabolites on osteoporosis have not been identified.

Methods

Based on the large individual-level datasets from UK Biobank as well as GWAS summary datasets, we first constructed genetic risk scores (GRSs) for 308 of 486 human serum metabolites and evaluated the effect of each GRS on 2 major osteoporosis phenotypes, i.e., estimated bone miner density (eBMD) and fracture, respectively. Then, two-sample Mendelian Randomization (MR) was performed to validate the casual metabolites on osteoporosis. Multivariable MR analysis tested whether the effects of metabolites on osteoporosis are independent of possible confounders. Finally, we conducted metabolic pathway analysis for the metabolites involved in bone metabolism.

Results

We identified causal effects of 18 metabolites on eBMD and 1 metabolite on fracture with the GRS method after adjusting for multiple tests. Then, 9 of them were further validated with MR as replication, where comprehensive sensitive analyses proved robust of the causal associations. Although not identified in GRS, 3 metabolites were associated with at least three osteoporosis traits in MR results. Multivariable MR analysis determined the independent causal effect of several metabolites on osteoporosis. Besides, 23 bone metabolic pathways were detected, such as valine, leucine, isoleucine biosynthesis (p = 0.053), and Aminoacyl-tRNA biosynthesis (p = 0.076), and D-glutamine and D-glutamate metabolism (p = 0.004).

Conclusions

The systematic causal analyses strongly suggested that blood metabolites have causal effects on osteoporosis risk.

CNest: A novel copy number association discovery method uncovers 862 new associations from 200,629 whole-exome sequence datasets in the UK Biobank

Copy number variation (CNV) is known to influence human traits, having a rich history of research into common and rare genetic disease, and although CNV is accepted as an important class of genomic variation, progress on copy-number-based genome-wide association studies (GWASs) from next-generation sequencing (NGS) data has been limited. Here we present a novel method for large-scale copy number analysis from NGS data generating robust copy number estimates and allowing copy number GWASs (CN-GWASs) to be performed genome-wide in discovery mode. We provide a detailed analysis in the UK Biobank resource and a specifically designed software package. We use these methods to perform CN-GWAS analysis across 78 human traits, discovering over 800 genetic associations that are likely to contribute strongly to trait distributions. Finally, we compare CNV and SNP association signals across the same traits and samples, defining specific CNV association classes.

Manganese, iron, copper, and selenium co-exposure and osteoporosis risk in Chinese adults

BACKGROUND & AIMS

Previous experimental studies demonstrated that either deficient or excessive trace elements, such as manganese (Mn), iron (Fe), copper (Cu) and selenium (Se), are detrimental to bone health. Epidemiologic evidence for the effect of the four trace elements on osteoporosis (OP) risk remains inadequate. This cross-sectional study aimed to examine their associations with the OP risk among Chinese adults.

METHODS

Concentrations of Mn, Fe, Cu, and Se were measured in plasma using an inductively coupled plasma mass spectrometer among 627 Chinese adults aged ≥ 50 years. Individual effect of the four elements on OP risk was analyzed by logistic regression and Bayesian Kernel Machine Regression (BKMR) models. The latter model was also adopted to examine the exposure-response relationships and joint effects of the four elements on OP risk.

RESULTS

The median Mn, Fe, Cu, and Se levels were 4.78, 1026.63, 904.55, and 105.39 μg/L, respectively, in all participants. Inverse associations of Fe and Se levels with OP risk were observed in the logistic regression model. BKMR analysis revealed a U-shape pattern for the Fe-OP association, and a reduced OP risk in response to co-exposure of the four elements above the 50th percentiles but an elevated one in response to that below the 50th percentiles. Sex discrepancy existed in the findings. No interactions were found for the four elements affecting OP risk.

CONCLUSIONS

Co-exposure to Mn, Fe, Cu, and Se was associated with improved bone density, where Fe contributed most to the beneficial effect. Further studies are needed to verify these findings and explore the underlying biological mechanism.

Identification of a novel splicing mutation and genotype-phenotype correlations in rare PLS3-related childhood-onset osteoporosis

Background

X-linked early-onset osteoporosis, caused by mutations in plastin3 (PLS3), is an extremely rare disease characterized by low bone mineral density (BMD) and recurrent osteoporotic fractures. There is limited information on genetic and phenotypic spectrum, as well as genotype–phenotype correlations of the disease. Moreover, whether decreased PLS3 levels were also involved in osteoporosis among subjects without PLS3 pathogenic mutations remains unknown.

Methods

Whole-exome sequencing and bidirectional Sanger sequencing were performed for screening and validation of pathogenic mutations. Serum biochemical parameters and clinical information of the subjects were retrospectively collected. ELISA and online datasets were utilized to investigate the association between PLS3 expression and BMD.

Results

We identified a novel splicing mutation (c.892-2A > G) which led to the skipping of exon 9 in a family with X-linked early-onset osteoporosis. Scoliosis represents a potential new phenotype in the patients harboring PLS3 mutations, which may be corrected by brace treatment. Genotype–phenotype analysis reveals that there was no significant difference in BMD z-scores between different types of reported mutations including this study (p = 0.5). There is a marginally significant negative correlation between age and BMD z-score (p = 0.059, r = − 0.30). The conditions of osteoporosis in all patients were improved after bisphosphonates therapy, with mean BMD z-score increased from − 2.9 to − 0.57 (p < 0.0001). Serum PLS3 levels in adolescents and adults without PLS3 pathogenic mutations but representing osteoporosis were also evaluated, while no association was found between bone mineral density and PLS3 levels (p > 0.05).

Conclusions

Our findings expanded the mutation and phenotype spectrum of the rare disease and highlights the importance of early diagnosis and early treatment with bisphosphonates. More reports of cases with PLS3 mutation and function studies of the gene are warranted to understand genotype–phenotype correlations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-022-02380-z.

Absence of causal association between Vitamin D and bone mineral density across the lifespan: a Mendelian randomization study

Vitamin D deficiency is a candidate risk factor for osteoporosis, characterized by decreased bone mineral density (BMD). We performed this two-sample Mendelian randomization (MR) analysis to investigate the causal effect of vitamin D on BMD. We extracted 143 single-nucleotide polymorphisms from a recent GWAS on 417,580 participants of European ancestry as instrumental variables, and used summary statistics for BMD at forearm (n = 10,805), femoral neck (n = 49,988), lumbar spine (n = 44,731) and total-body of different age-stages (< 15, 15-30, 30-45, 45-60, > 60) (n = 67,358). We explored the direct effect of vitamin D on BMD with an adjusted body mass index (BMI) in a multivariable MR analysis. We found no support for causality of 25-hydroxyvitamin D on BMD at forearm, femoral neck, lumbar spine, and total-body BMD across the lifespan. There was no obvious difference between the total and direct effect of vitamin D on BMD after adjusting for BMI. Our MR analysis provided evidence that genetically determined vitamin D was not causally associated with BMD in the general population. Large-scale randomized controlled trials are warranted to investigate the role of vitamin D supplementation in preventing osteoporosis in the high-risk population.

Genetic Diagnostics in Routine Osteological Assessment of Adult Low Bone Mass Disorders

CONTEXT

Many different inherited and acquired conditions can result in premature bone fragility/low bone mass disorders (LBMDs).

OBJECTIVE

We aimed to elucidate the impact of genetic testing on differential diagnosis of adult LBMDs and at defining clinical criteria for predicting monogenic forms.

METHODS

Four clinical centers broadly recruited a cohort of 394 unrelated adult women before menopause and men younger than 55 years with a bone mineral density (BMD) Z-score < -2.0 and/or pathological fractures. After exclusion of secondary causes or unequivocal clinical/biochemical hallmarks of monogenic LBMDs, all participants were genotyped by targeted next-generation sequencing.

RESULTS

In total, 20.8% of the participants carried rare disease-causing variants (DCVs) in genes known to cause osteogenesis imperfecta (COL1A1, COL1A2), hypophosphatasia (ALPL), and early-onset osteoporosis (LRP5, PLS3, and WNT1). In addition, we identified rare DCVs in ENPP1, LMNA, NOTCH2, and ZNF469. Three individuals had autosomal recessive, 75 autosomal dominant, and 4 X-linked disorders. A total of 9.7% of the participants harbored variants of unknown significance. A regression analysis revealed that the likelihood of detecting a DCV correlated with a positive family history of osteoporosis, peripheral fractures (> 2), and a high normal body mass index (BMI). In contrast, mutation frequencies did not correlate with age, prevalent vertebral fractures, BMD, or biochemical parameters. In individuals without monogenic disease-causing rare variants, common variants predisposing for low BMD (eg, in LRP5) were overrepresented.

CONCLUSION

The overlapping spectra of monogenic adult LBMD can be easily disentangled by genetic testing and the proposed clinical criteria can help to maximize the diagnostic yield.

GATA4 and estrogen receptor alpha bind at SNPs rs9921222 and rs10794639 to regulate AXIN1 expression in osteoblasts

Osteoporosis is a serious public health problem that affects 200 million people worldwide. Genome-wide association studies have revealed the association between several single nucleotide polymorphisms (SNPs) near WNT/β-catenin signaling genes and bone mineral density (BMD). The activation of β-catenin by WNT ligands is required for osteoblast differentiation. SNP rs9921222 is an intronic variant of AXIN1 (a scaffold protein in the destruction complex that regulates β-catenin signaling) that correlates with BMD. However, the biological mechanism of SNP rs9921222 has never been reported. Here, we show that the genotype of SNP rs9921222 correlates with the expression of AXIN1 in human osteoblasts. RNA and genomic DNA were analyzed from primary osteoblasts from 111 different individuals. Homozygous TT at rs9921222 correlates with a higher expression of AXIN1 than homozygous CC. Regional association analysis showed that rs9921222 is in high linkage disequilibrium (LD) with SNP rs10794639. In silico transcription factor analysis predicted that rs9921222 is within a GATA4 motif and rs10794639 is adjacent to an estrogen receptor alpha (ERα) motif. Mechanistically, GATA4 and ERα bind at SNPs rs9921222 and rs10794639 as detected by ChIP-qPCR. Luciferase assays demonstrate that rs9921222 is the causal SNP to alter ERα and GATA4 binding. GATA4 promoted the expression, and in contrast, ERα suppressed the expression of AXIN1 via the histone deacetylase complex member SIN3A. Functionally, the level of AXIN1 negatively correlates with the level of transcriptionally active β-catenin. In summary, we have discovered a molecular mechanism of the SNP rs9921222 to regulate AXIN1 through GATA4 and ERα binding in human osteoblasts.

A genetic correlation scan identifies blood proteins associated with bone mineral density

Background

Osteoporosis is a common metabolic bone disease that is characterized by low bone mass. However, limited efforts have been made to explore the functional relevance of the blood proteome to bone mineral density across different life stages.

Methods

Using genome-wide association study summary data of the blood proteome and two independent studies of bone mineral density, we conducted a genetic correlation scan of bone mineral density and the blood proteome. Linkage disequilibrium score regression analysis was conducted to assess genetic correlations between each of the 3283 plasma proteins and bone mineral density.

Results

Linkage disequilibrium score regression identified 18 plasma proteins showing genetic correlation signals with bone mineral density in the TB-BMD cohort, such as MYOM2 (coefficient = 0.3755, P value = 0.0328) among subjects aged 0 ~ 15, POSTN (coefficient = − 0.5694, P value = 0.0192) among subjects aged 30 ~ 45 and PARK7 (coefficient = − 0.3613, P value = 0.0052) among subjects aged over 60.

Conclusions

Our results identified multiple plasma proteins associated with bone mineral density and provided novel clues for revealing the functional relevance of plasma proteins to bone mineral density.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12891-022-05453-z.

Genetic variation in WNT16 and its association with bone mineral density, fractures and osteoporosis in children with bone fragility

Several genome-wide association studies (GWAS), GWAS meta-analyses, and mouse studies have demonstrated that wingless-related integration site 16 (WNT16) gene is associated with bone mineral density (BMD), cortical bone thickness, bone strength and fracture risk. Practically no data exist regarding the significance of WNT16 in childhood-onset osteoporosis and related fractures. We hypothesized that pathogenic variants and genetic variations in WNT16 could explain skeletal fragility in affected children. We screened the WNT16 gene by Sanger sequencing in three pediatric cohorts: 35 with primary osteoporosis, 59 with multiple fractures, and in 95 healthy controls. Altogether, we identified 12 variants in WNT16. Of them one was a rare 5′UTR variant rs1386898215 in genome aggregate and medical trans-omic databases (GnomAD, TOPMED; minor allele frequency (MAF) 0.00 and 0.000008, respectively). One variant rs1554366753, overrepresented in children with osteoporosis (MAF = 0.06 vs healthy controls MAF = 0.01), was significantly associated with lower BMD. This variant was found associated with increased WNT16 gene expression at mRNA level in fibroblast cultures. None of the other identified variants were rare (MAF < 0.001) or deemed pathogenic by predictor programs. WNT16 may play a role in childhood osteoporosis but genetic WNT16 variation is not a common cause of skeletal fragility in childhood.

•

No pathogenic WNT16 variants were found associated with pediatric osteoporosis or fracture-prone patients

•

Altogether, twelve WNT16 variants were found in pediatric osteoporosis or fracture-prone patients

•

The genetic variation rs1554366753 in the WNT16 gene is associated with bone mineral density and primary osteoporosis

Prioritization of Genes Relevant to Bone Fragility Through the Unbiased Integration of Aging Mouse Bone Transcriptomics and Human GWAS Analyses

Identifying new genetic determinants of bone mineral density (BMD) and fracture promises to yield improved diagnostics and therapies for bone fragility. However, prioritizing candidate genes from genome-wide screens can be challenging. To overcome this challenge, we prioritized mouse genes that are differentially expressed in aging mouse bone based on whether their human homolog is associated with human BMD and/or fracture. Unbiased RNA-seq analysis of young and old male C57BL/6 mouse cortical bone identified 1499, 1685, and 5525 differentially expressed genes (DEGs) in 1, 2, and 2.5-year-old bone, relative to 2-month-old bone, respectively. Gene-based scores for heel ultrasound bone mineral density (eBMD) and fracture were estimated using published genome-wide association studies (GWAS) results of these traits in the UK Biobank. Enrichment analysis showed that mouse bone DEG sets for all three age groups, relative to young bone, are significantly enriched for eBMD, but only the oldest two DEG sets are enriched for fracture. Using gene-based scores, this approach prioritizes among thousands of DEGs by a factor of 5- to 100-fold, yielding 10 and 21 genes significantly associated with fracture in the two oldest groups of mouse DEGs. Though these genes were not the most differentially expressed, they included Sost, Lrp5, and others with well-established functions in bone. Several others have, as yet, unknown roles in the skeleton. Therefore, this study accelerates identification of new genetic determinants of bone fragility by prioritizing a clinically relevant and experimentally tractable number of candidate genes for functional analysis. Finally, we provide a website (www.mouse2human.org) to enable other researchers to easily apply our strategy. © 2022 American Society for Bone and Mineral Research (ASBMR).

Shared Genetic Architecture Between Rheumatoid Arthritis and Varying Osteoporotic Phenotypes

Rheumatoid arthritis (RA) and low bone mineral density (BMD), an indicator of osteoporosis (OP), appear epidemiologically associated. Shared genetic factors may explain this association. This study aimed to investigate the presence of pleiotropy to clarify the potential genetic association between RA and OP. We examined BMDs at varying skeletal sites reported in UK Biobank as well as OP fracture acquired from the Genetic Factors for Osteoporosis (GEFOS) Consortium and the TwinsUK study. PRSice-2 was used to assess the potential shared genetic overlap between RA and OP. The presence of pleiotropy was examined using colocalization analysis. PRSice-2 revealed that RA was significantly associated with OP fracture (β = 351.6 ± 83.9, p value = 2.76E-05), total BMD (β = -1763.5 ± 612.8, p = 4.00E-03), spine BMD (β = -919.8 ± 264.6, p value = 5.09E-04), and forearm BMD (β = -66.09 ± 31.40, p value = 3.53E-02). Through colocalization analysis, the same causal genetic variants, associated with both RA and OP, were apparent in 12 genes: PLCL1, BOLL, AC011997.1, TNFAIP3, RP11-158I9.1, CDK6, CHCHD4P2, RP11-505C13.1, PHF19, TRAF1, C5, and C11orf49 with moderate posterior probabilities (>50%). Pleiotropy is involved in the association between RA and OP phenotypes. These findings contribute to the understanding of disease mechanisms and provide insight into possible therapeutic advancements and enhanced screening measures. © 2021 American Society for Bone and Mineral Research (ASBMR).

PGS-server: accuracy, robustness and transferability of polygenic score methods for biobank scale studies

Polygenic scores (PGS) are important tools for carrying out genetic prediction of common diseases and disease related complex traits, facilitating the development of precision medicine. Unfortunately, despite the critical importance of PGS and the vast number of PGS methods recently developed, few comprehensive comparison studies have been performed to evaluate the effectiveness of PGS methods. To fill this critical knowledge gap, we performed a comprehensive comparison study on 12 different PGS methods through internal evaluations on 25 quantitative and 25 binary traits within the UK Biobank with sample sizes ranging from 147 408 to 336 573, and through external evaluations via 25 cross-study and 112 cross-ancestry analyses on summary statistics from multiple genome-wide association studies with sample sizes ranging from 1415 to 329 345. We evaluate the prediction accuracy, computational scalability, as well as robustness and transferability of different PGS methods across datasets and/or genetic ancestries, providing important guidelines for practitioners in choosing PGS methods. Besides method comparison, we present a simple aggregation strategy that combines multiple PGS from different methods to take advantage of their distinct benefits to achieve stable and superior prediction performance. To facilitate future applications of PGS, we also develop a PGS webserver (http://www.pgs-server.com/) that allows users to upload summary statistics and choose different PGS methods to fit the data directly. We hope that our results, method and webserver will facilitate the routine application of PGS across different research areas.

Elevated blood pressure, antihypertensive medications and bone health in the population: revisiting old hypotheses and exploring future research directions

Blood pressure and bone metabolism appear to share commonalities in their physiologic regulation. Specific antihypertensive drug classes may also influence bone mineral density. However, current evidence from existing observational studies and randomised trials is insufficient to establish causal associations for blood pressure and use of blood pressure-lowering drugs with bone health outcomes, particularly with the risks of osteoporosis and fractures. The availability and access to relevant large-scale biomedical data sources as well as developments in study designs and analytical approaches provide opportunities to examine the nature of the association between blood pressure and bone health more reliably and in greater detail than has ever been possible. It is unlikely that a single source of data or study design can provide a definitive answer. However, with appropriate considerations of the strengths and limitations of the different data sources and analytical techniques, we should be able to advance our understanding of the role of raised blood pressure and its drug treatment on the risks of low bone mineral density and fractures. As elevated blood pressure is highly prevalent and blood pressure-lowering drugs are widely prescribed, even small effects of these exposures on bone health outcomes could be important at a population level.

Wnt Pathway Extracellular Components and Their Essential Roles in Bone Homeostasis

The Wnt pathway is involved in several processes essential for bone development and homeostasis. For proper functioning, the Wnt pathway is tightly regulated by numerous extracellular elements that act by both activating and inhibiting the pathway at different moments. This review aims to describe, summarize and update the findings regarding the extracellular modulators of the Wnt pathway, including co-receptors, ligands and inhibitors, in relation to bone homeostasis, with an emphasis on the animal models generated, the diseases associated with each gene and the bone processes in which each member is involved. The precise knowledge of all these elements will help us to identify possible targets that can be used as a therapeutic target for the treatment of bone diseases such as osteoporosis.

OUP accepted manuscript

Rheumatoid arthritis (RA) and osteoporosis (OP) are two comorbid complex inflammatory conditions with evidence of shared genetic background and causal relationships. We aimed to clarify the genetic architecture underlying RA and various OP phenotypes while additionally considering an inflammatory component, C-reactive protein (CRP). Genome-wide association study summary statistics were acquired from the GEnetic Factors for OSteoporosis Consortium, Cohorts for Heart and Aging Research Consortium and UK Biobank. Mendelian randomization (MR) was used to detect the presence of causal relationships. Colocalization analysis was performed to determine shared genetic variants between CRP and OP phenotypes. Analysis of pleiotropy between traits owing to shared causal single nucleotide polymorphisms (SNPs) was performed using PL eiotropic A nalysis under CO mposite null hypothesis (PLACO). MR analysis was suggestive of horizontal pleiotropy between RA and OP traits. RA was a significant causal risk factor for CRP (β = 0.027, 95% confidence interval = 0.016–0.038). There was no evidence of CRP→OP causal relationship, but horizontal pleiotropy was apparent. Colocalization established shared genomic regions between CRP and OP, including GCKR and SERPINA1 genes. Pleiotropy arising from shared causal SNPs revealed through the colocalization analysis was all confirmed by PLACO. These genes were found to be involved in the same molecular function ‘protein binding’ (GO:0005515) associated with RA, OP and CRP. We identified three major components explaining the epidemiological relationship among RA, OP and inflammation: (1) Pleiotropy explains a portion of the shared genetic relationship between RA and OP, albeit polygenically; (2) RA contributes to CRP elevation and (3) CRP, which is influenced by RA, demonstrated pleiotropy with OP.

Polyunsaturated Fatty Acids Level and Bone Mineral Density: A Two-Sample Mendelian Randomization Study

BACKGROUND

This Mendelian randomization (MR) study aimed to explore the causal relationship between polyunsaturated fatty acids (PUFAs) and bone mineral density (BMD).

METHODS

We conducted a two-sample MR analysis to figure out if there is any causal effect of PUFAs on BMD through the summary data from the genome-wide association study (GWAS). Relationships were evaluated through inverse variance weighted (IVW), MR-Egger, weighted median, and maximum likelihood methods. The MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) test was performed to detect the horizontal pleiotropy.

RESULTS

Our findings revealed that omega-6 fatty acids were negatively related to the TB-BMD (beta-estimate: -0.0515; 95% confidence interval [CI]: -0.0911 to -0.0119; standard error [SE]: 0.0201; p-value: 0.0106). The reverse direction MR analysis showed that TB-BMD was linked to the omega-6 FAs (beta-estimate: -0.0699; 95% CI: -0.1304 to -0.0095; SE: 0.0308; p-value: 0.0265). No statistically significant correlations between PUFAs and BMD were observed after adjusting the interactions between metabolites.

CONCLUSION

This two-sample MR analyses produced strong and new genomic evidence that there was a causal relationship between omega-6 FAs and BMD. Further investigations are still required to elucidate the potential mechanism.

The causal association between bone mineral density and risk of osteoarthritis: A Mendelian randomization study

OBJECTIVES

The causal direction and magnitude of the association between total body bone mineral density (TB-BMD) and osteoarthritis (OA) risk is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. The study aimed to explore the relationships between TB-BMD concentration and OA using Mendelian randomization (MR).

METHODS

In this study, we used two-sample MR to obtain unconfounded estimates of the effect of TB-BMD on hip and knee OA. Single nucleotide polymorphisms (SNPs) strongly associated with TB-BMD in a large genome-wide association study (GWAS) were identified and selected as instrumental variables (IVs). In addition to the main analysis using inverse-variance weighted (IVW) method, we applied 2 additional methods to control for pleiotropy(MR-Egger regression, weighted median estimator) and compared the respective MR estimates.

RESULTS

MR analyses suggested that genetically predicted higher TB-BMD is associated with risks of hip OA (For IVW: OR=1.199, 95%CI: 1.02-1.42, P=0.032; for WM: OR=1.257, 95%CI: 1.09-1.45, P=0.002). There was no evidence that the observed causal effect between TB-BMD and the risk of hip OA was affected by genetic pleiotropy(P=0.618). Additionally, our study didn't support causal effects of a genetically increased TB-BMD risk on knee OA risk(OR=1.121, 95%CI: 0.99-1.28, P=0.084 using IVW; OR=1.132, 95%CI: 0.99-1.29, P=0.068 using WM; OR=1.274, 95%CI: 0.88-1.85, P=0.217 using MR-Egger).

CONCLUSIONS

Our findings support a causal effect that a genetic predisposition to systematically higher TB-BMD was associated with the risk of OA. And, TB-BMD likely exerts an effect on the risk of hip OA not knee OA.

Regulatory SNP of RREB1 is Associated With Bone Mineral Density in Chinese Postmenopausal Osteoporosis Patients

Postmenopausal osteoporosis (PMO) is the most common bone disorder in elderly Chinese women. Although genetic factors have been shown to have a pivotal role in PMO, studies on genetic loci associated with PMO in Chinese individuals are still lacking. We aimed to identify SNPs that contribute to PMO in Chinese individuals by conducting a genome-wide association study (GWAS). Bone mineral density (BMD) of postmenopausal Chinese women was assessed. Participants with T-score < -2.5 standard deviations (n = 341) were recruited and divided into a discovery group (n = 150) and a replication group (n = 191). GWAS was performed, with T-score as the quantitative trait, using linear regression. Our results revealed that an SNP cluster upstream of RREB1 showed a trend of association with BMD in Chinese PMO patients. The leading SNP of the cluster was rs475011 (p _combined = 1.15 × 10^-6, beta = 0.51), which is a splicing quantitative trait locus (sQTL) of RREB1. This association was further supported by data from the UK Biobank (UKBB; p = 9.56 × 10^-12). The high BMD-associated allele G of rs475011 is related to a high intron excision ratio. This SNP may increase BMD by upregulating mature RREB1 mRNA, based on data from the Genotype-Tissue Expression (GTEx) database. We identified BMD-associated SNPs that regulate RREB1 in Chinese PMO patients. Future functional experiments are needed to further link rs475011, RREB1, and PMO in Chinese individuals.

The osteoporosis risk variant rs9820407 at 3p22.1 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation

Previous powerful genome-wide association studies (GWASs) and whole-genome sequencing have identified multiple single-nucleotide polymorphisms (SNPs) located over 69 kb upstream of CTNNB1 at 3p22.1 locus associated with osteoporosis. The CTNNB1 gene encodes β-catenin that is an integral part of adherens junctions and the primary mediator of the canonical Wnt signaling pathway. The causal variants and underlying molecular mechanisms of the osteoporosis susceptibility locus 3p22.1 remains unknown. Through comprehensive computational analyses, including expression quantitative trait locus (eQTL), high-throughput chromatin interaction (Hi-C), epigenomic and functional annotation, four enhancer SNPs (rs9820407, rs9878224, rs454690 and rs9832204) were prioritized as potential causal SNPs at 3p22.1 for osteoporosis. Rs9820407 displayed the strongest enhancer activity in dual-luciferase assays. Specifically, the minor rs9820407-A can preferentially bind transcription factor FOXC1, elevate the enhancer activity and increase CTNNB1 expression. The architectural protein CTCF was presumably involved in long-range chromatin interaction between rs9820407 and CTNNB1. Our study provided a mechanistic insight into how noncoding enhancer SNP rs9820407 distally regulates CTNNB1 expression and modulates osteoporosis risk.

Integrating genome-wide association and transcriptome prediction model identifies novel target genes for osteoporosis

In this study, we integrated large-scale GWAS summary data and used the predicted transcriptome-wide association study method to discover novel genes associated with osteoporosis. We identified 204 candidate genes, which provide novel clues for understanding the genetic mechanism of osteoporosis and indicate potential therapeutic targets.

INTRODUCTION

Osteoporosis is a highly polygenetic disease characterized by low bone mass and deterioration of the bone microarchitecture. Our objective was to discover novel candidate genes associated with osteoporosis.

METHODS

To identify potential causal genes of the associated loci, we investigated trait-gene expression associations using the transcriptome-wide association study (TWAS) method. This method directly imputes gene expression effects from genome-wide association study (GWAS) data using a statistical prediction model trained on GTEx reference transcriptome data. We then performed a colocalization analysis to evaluate the posterior probability of biological patterns: associations characterized by a single causal variant or multiple distinct causal variants. Finally, a functional enrichment analysis of gene sets was performed using the VarElect and CluePedia tools, which assess the causal relationships between genes and a disease and search for potential gene's functional pathways. The osteoporosis-associated genes were further confirmed based on the differentially expressed genes profiled from mRNA expression data of bone tissue.

RESULTS

Our analysis identified 204 candidate genes, including 154 genes that have been previously associated with osteoporosis, 50 genes that have not been previously discovered. A biological function analysis found that 20 of the candidate genes were directly associated with osteoporosis. Further analysis of multiple gene expression profiles showed that 15 genes were differentially expressed in patients with osteoporosis. Among these, SLC11A2, MAP2K5, NFATC4, and HSP90B1 were enriched in four pathways, namely, mineral absorption pathway, MAPK signaling pathway, Wnt signaling pathway, and PI3K-Akt signaling pathway, which indicates a causal relationship with the occurrence of osteoporosis.

CONCLUSIONS

We demonstrated that transcriptome fine-mapping identifies more osteoporosis-related genes and provides key insight into the development of novel targeted therapeutics for the treatment of osteoporosis.

Associations of multiple metals with bone mineral density: A population-based study in US adults

Epidemiologic studies focus on combined effects of multiple metals on bone mineral density (BMD) are scarce. Therefore, this study was conducted to examine associations of multiple metals exposure with BMD. Data of adults aged ≥20 years (n = 2545) from the US National Health and Nutrition Examination Survey (NHANES, 2011-2016) were collected and analyzed. Concentrations of metals were measured in blood (cadmium [Cd], lead [Pb], mercury [Hg], and manganese [Mn]) and serum (copper [Cu], selenium [Se], and zinc [Zn]) using inductively coupled plasma mass spectrometry and inductively coupled plasma dynamic reaction cell mass spectrometry, respectively. The weighted quantile sum (WQS) and Bayesian kernel machine regression (BKMR) models were performed to determine the joint effects of multiple metals exposure on lumbar and total BMD. The linear regression analyses showed Pb was negatively associated with BMDs. The WQS regression analyses revealed that the WQS index was inversely related to lumbar (β = -0.022, 95% CI: -0.036, -0.008) and total BMD (β = -0.015, 95% CI: -0.024, -0.006), and Se, Mn, and Pb were the main contributors for the combined effects. Additionally, nonlinear dose-response relationships between Pb, Mn, and Se and BMD, as well as a synergistic interaction of Pb and Mn, were found in the BKMR analyses. Our findings suggested co-exposure to Cd, Pb, Hg, Mn, Cu, Se, and Zn (above their 50th percentiles) was associated with reduced BMD, and Pb, Mn, and Se were the main contributors driving the overall effects.

Novel microbiota-related gene set enrichment analysis identified osteoporosis associated gut microbiota from autoimmune diseases

INTRODUCTION

Gut microbiota is now considered to be a hidden organ that interacts bidirectionally with cellular responses in numerous organs belonged to the immune, bone, and nervous systems. Here, we aimed to investigate the relationships between gut microbiota and complex diseases by utilizing multiple publicly available genome-wide association.

MATERIALS AND METHODS

We applied a novel microbiota-related gene set enrichment analysis approach to detect the associations between gut microbiota and complex diseases by processing genome-wide association studies (GWASs) data sets of six autoimmune diseases (including celiac disease (CeD), inflammatory bowel diseases (IBD), multiple sclerosis (MS), primary biliary cirrhosis (PBC), type 1 diabetes (T1D) and primary sclerosing cholangitis (PSC)) and osteoporosis (OP).

RESULTS

The family Oxalobacteraceae and genus Candidatus_Soleaferrea were found to be correlated with all of the six autoimmune diseases (FDR adjusted P < 0.05). Moreover, we observed that the six autoimmune diseases except PBC shared 3 overlapping features (including family Peptostreptococcaceae, order Gastranaerophilales and genus Romboutsia). For all of the six autoimmune diseases and BMDs (LS-BMD and TB-BMD), an association signal was observed for genus Candidatus_Soleaferrea (FDR adjusted P < 0.05). Notably, FA / FN-BMD shared the maximum number of overlapping microbial features (e.g., genus Ruminococcaceae_UCG009, Erysipelatoclostridium and Ruminococcaceae_UCG013).

CONCLUSION

Our study found that part of the gut microbiota could be novel regulators of BMDs and autoimmune diseases via the effects of its metabolites and may lead to a better understanding of the role played by gut microbiota in the communication of the microbiota-skeletal/immune-gut axis.