Dataset Information

Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women.

ABSTRACT: Existing microarray studies of bone mineral density (BMD) have been critical for understanding the pathophysiology of osteoporosis, and have identified a number of candidate genes. However, these studies were limited by their relatively small sample sizes and were usually analyzed individually. Here, we propose a novel network-based meta-analysis approach that combines data across six microarray studies to identify functional modules from human protein-protein interaction (PPI) data, and highlight several differentially expressed genes (DEGs) and a functional module that may play an important role in BMD regulation in women.Expression profiling studies were identified by searching PubMed, Gene Expression Omnibus (GEO) and ArrayExpress. Two meta-analysis methods were applied across different gene expression profiling studies. The first, a nonparametric Fisher's method, combined p-values from individual experiments to identify genes with large effect sizes. The second method combined effect sizes from individual datasets into a meta-effect size to gain a higher precision of effect size estimation across all datasets. Genes with Q test's p-values < 0.05 or I(2) values > 50% were assessed by a random effects model and the remainder by a fixed effects model. Using Fisher's combined p-values, functional modules were identified through an integrated analysis of microarray data in the context of large protein-protein interaction (PPI) networks. Two previously published meta-analysis studies of genome-wide association (GWA) datasets were used to determine whether these module genes were genetically associated with BMD. Pathway enrichment analysis was performed with a hypergeometric test.Six gene expression datasets were identified, which included a total of 249 (129 high BMD and 120 low BMD) female subjects. Using a network-based meta-analysis, a consensus module containing 58 genes (nodes) and 83 edges was detected. Pathway enrichment analysis of the 58 module genes revealed that these genes were enriched in several important KEGG pathways including Osteoclast differentiation, B cell receptor signaling pathway, MAPK signaling pathway, Chemokine signaling pathway and Insulin signaling pathway. The importance of module genes was replicated by demonstrating that most module genes were genetically associated with BMD in the GWAS data sets. Meta-analyses were performed at the individual gene level by combining p-values and effect sizes. Five candidate genes (ESR1, MAP3K3, PYGM, RAC1 and SYK) were identified based on gene expression meta-analysis, and their associations with BMD were also replicated by two BMD meta-analysis studies.In summary, our network-based meta-analysis not only identified important differentially expressed genes but also discovered biologically meaningful functional modules for BMD determination. Our study may provide novel therapeutic targets for osteoporosis in women.

SUBMITTER: He H

PROVIDER: S-EPMC4726665 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women.

He Hao H Cao Shaolong S Niu Tianhua T Zhou Yu Y Zhang Lan L Zeng Yong Y Zhu Wei W Wang Yu-ping YP Deng Hong-wen HW

PloS one 20160125 1

<h4>Background</h4>Existing microarray studies of bone mineral density (BMD) have been critical for understanding the pathophysiology of osteoporosis, and have identified a number of candidate genes. However, these studies were limited by their relatively small sample sizes and were usually analyzed individually. Here, we propose a novel network-based meta-analysis approach that combines data across six microarray studies to identify functional modules from human protein-protein interaction (PPI ...[more]

PMID: 26808152

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Project description:Bone mineral density (BMD) is heavily relied upon to reflect structural changes affecting hip strength and fracture risk. Strong correlations between BMD and strength are needed to provide confidence that structural changes are reflected in BMD and, in turn, strength. This study investigated how variation in bone structure gives rise to variation in BMD and strength and tested whether these associations differ with external bone size. Cadaveric proximal femurs (n = 30, White women, 36-89+ years) were imaged using nanocomputed tomography (nano-CT) and loaded in a sideways fall configuration to assess bone strength and brittleness. Bone voxels within the nano-CT images were projected onto a plane to create pseudo dual-energy X-ray absorptiometry (pseudo-DXA) images consistent with a clinical DXA scan. A validation study using 19 samples confirmed pseudo-DXA measures correlated significantly with those measured from a commercially available DXA system, including bone mineral content (BMC) (R 2 = 0.95), area (R 2 = 0.58), and BMD (R 2 = 0.92). BMD-strength associations were conducted using multivariate linear regression analyses with the samples divided into narrow and wide groups by pseudo-DXA area. Nearly 80% of the variation in strength was explained by age, body weight, and pseudo-DXA BMD for the narrow subgroup. Including additional structural or density distribution information in regression models only modestly improved the correlations. In contrast, age, body weight, and pseudo-DXA BMD explained only half of the variation in strength for the wide subgroup. Including bone density distribution or structural details did not improve the correlations, but including post-yield deflection (PYD), a measure of bone material brittleness, did increase the coefficient of determination to more than 70% for the wide subgroup. This outcome suggested material level effects play an important role in the strength of wide femoral necks. Thus, the associations among structure, BMD, and strength differed with external bone size, providing evidence that structure-function relationships may be improved by judiciously sorting study cohorts into subgroups. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Project description:Background and objective: There is limited information as to the association of several key bone markers with bone mineral density (BMD) in understudied ethnic groups. This study investigated the relationship between circulating levels of osteoprotegerin (OPG) and receptor activator of nuclear factor kappa-Β ligand (RANKL) with BMD in Arab postmenopausal women. Materials and methods: In this cross-sectional study, a total of 617 Saudi postmenopausal women from the Osteoporosis Registry of the Chair for Biomarkers of Chronic Diseases were included. Anthropometric data, BMD, and biochemical data were retrieved from the registry. Participants were stratified into three groups based on T-score; n = 169 with osteoporosis, n = 282 with osteopenia, and n = 166 normal. Analysis of bone markers including RANKL, OPG, osteocalcin, and N-terminal telopeptide (NTx) was completed using commercially available bioassays. Results: The results suggested that OPG was significantly and positively correlated with age in the osteoporosis group (r = 0.29, p < 0.05), while it was inversely correlated with BMD femoral neck left (r = -0.56, p < 0.001) and BMD femoral neck right (r = -0.37, p < 0.05) in the same group. Moreover, RANKL showed a significant inverse correlation with NTx in the osteopenia group (r = -0.37, p < 0.05). Furthermore, the RANKL/OPG ratio had a positive and significant correlation with BMI (r = 0.34, p < 0.05), BMD femoral neck left (r = 0.36, p < 0.05) and BMD femoral neck right (r = 0.35, p < 0.05) in the osteopenia group. By contrast, it showed a significant inverse correlation with waist to hip ratio in the osteoporosis group (r = -0.38, p < 0.05). Multiple regression analysis showed that OPG contributes to BMD variations in the osteopenia group (p = 0.03). Conclusions: In conclusion, changes in circulating levels of RANKL and OPG might be a protective mechanism contrary to the increased bone loss in postmenopausal women.

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Dataset Information

Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women.

Publications

Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women.

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