Network based subcellular proteomics in monocyte membrane revealed novel candidate genes involved in osteoporosis

In this study, label-free-based quantitative subcellular proteomics integrated with network analysis highlighted several candidate genes including P4HB, ITGB1, CD36, and ACTN1 that may be involved in osteoporosis. All of them are predicted as significant membrane proteins with high confidence and enriched in bone-related biological process. The results were further verified in transcriptomic and genomic levels.

INTRODUCTION

Osteoporosis is a metabolic bone disease mainly characterized by low bone mineral density (BMD). As the precursors of osteoclasts, peripheral blood monocytes (PBMs) are supported to be important candidates for identifying genes related to osteoporosis. We performed subcellular proteomics study to identify significant membrane proteins that involved in osteoporosis.

METHODS

To investigate the association between monocytes, membrane proteins, and osteoporosis, we performed label-free quantitative subcellular proteomics in 59 male subjects with discordant BMD levels, with 30 high vs. 29 low BMD subjects. Subsequently, we performed integrated gene enrichment analysis, functional annotation, and pathway and network analysis based on multiple bioinformatics tools.

RESULTS

A total of 1070 membrane proteins were identified and quantified. By comparing the proteins' expression level, we found 36 proteins that were differentially expressed between high and low BMD groups. Protein localization prediction supported the notion that the differentially expressed proteins, P4HB (p = 0.0021), CD36 (p = 0.0104), ACTN1 (p = 0.0381), and ITGB1 (p = 0.0385), are significant membrane proteins. Functional annotation and pathway and network analysis highlighted that P4HB, ITGB1, CD36, and ACTN1 are enriched in osteoporosis-related pathways and terms including "ECM-receptor interaction," "calcium ion binding," "leukocyte transendothelial migration," and "reduction of cytosolic calcium levels." Results from transcriptomic and genomic levels provided additional supporting evidences.

CONCLUSION

Our study strongly supports the significance of the genes P4HB, ITGB1, CD36, and ACTN1 to the etiology of osteoporosis risk.

Cytosolic proteome profiling of monocytes for male osteoporosis

In male Caucasians with discordant hip bone mineral density (BMD), we applied the subcellular separation and proteome profiling to investigate the monocytic cytosol. Three BMD-associated proteins (ALDOA, MYH14, and Rap1B) were identified based on multiple omics evidence, and they may influence the pathogenic mechanisms of osteoporosis by regulating the activities of monocytes.

INTRODUCTION

Osteoporosis is a serious public health problem, leading to significant mortality not only in aging females but also in males. Peripheral blood monocytes (PBMs) play important roles in bone metabolism by acting as precursors of osteoclasts and producing cytokines important for osteoclast development. The first cytosolic sub-proteome profiling analysis was performed in male PBMs to identify differentially expressed proteins (DEPs) that are associated with BMDs and risk of osteoporosis.

METHODS

Here, we conducted a comparative proteomics analysis in PBMs from Caucasian male subjects with discordant hip BMD (29 low BMD vs. 30 high BMD). To decrease the proteome complexity and expand the coverage range of the cellular proteome, we separated the PBM proteome into several subcellular compartments and focused on the cytosolic fractions, which are involved in a wide range of fundamental biochemical processes.

RESULTS

Of the total of 3796 detected cytosolic proteins, we identified 16 significant (P < 0.05) and an additional 22 suggestive (P < 0.1) DEPs between samples with low vs. high hip BMDs. Some of the genes for DEPs, including ALDOA, MYH14, and Rap1B, showed an association with BMD in multiple omics studies (proteomic, transcriptomic, and genomic). Further bioinformatics analysis revealed the enrichment of DEPs in functional terms for monocyte proliferation, differentiation, and migration.

CONCLUSIONS

The combination strategy of subcellular separation and proteome profiling allows an in-depth and refined investigation into the composition and functions of cytosolic proteome, which may shed light on the monocyte-mediated pathogenic mechanisms of osteoporosis.

Genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians

Osteoporotic fracture (OF) is a serious outcome of osteoporosis. Important risk factors for OF include reduced bone mineral density and unstable bone structure. This genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians.

INTRODUCTION

Bone mineral density (BMD) and femoral neck cross-sectional geometric parameters (FNCSGPs) are under strong genetic control. DNA copy number variation (CNV) is an important source of genetic diversity for human diseases. This study aims to identify CNVs associated with BMD and FNCSGPs.

METHODS

Genome-wide CNV association analyses were conducted in 1,000 unrelated Caucasian subjects for BMD at the spine, hip, femoral neck, and for three FNCSGPs -cortical thickness (CT), cross-section area (CSA), and buckling ratio (BR). BMD was measured by dual energy X-ray absorptiometry (DEXA). CT, CSA, and BR were estimated using DEXA measurements. Affymetrix 500K arrays and copy number analysis tool was used to identify CNVs.

RESULTS

A CNV in VPS13B gene was significantly associated with spine, hip and FN BMDs, and CT, CSA, and BR (p < 0.05). Compared to subjects with two copies of the CNV, carriers of one copy had an average of 14.6%, 12.4%, and 13.6% higher spine, hip, and FN BMD, 20.0% thicker CT, 10.6% larger CSA, and 12.4% lower BR. Thus, a decrease of the CNV consistently produced stronger bone, thereby reducing osteoporotic fracture risk.

CONCLUSIONS

VPS13B gene, via affecting BMD and FNCSGPs, is a novel osteoporosis risk gene.

Searching for genes underlying susceptibility to osteoporotic fracture: current progress and future prospect

INTRODUCTION

Osteoporotic fracture (OF) is a public health problem. It is a common practice in the genetics of osteoporosis that bone mineral density (BMD) was studied as a major surrogate phenotype in gene search for risk of OF (ROF) because of their high phenotypic correlation. However, some studies indicate that the genetic correlation between BMD and ROF is very low. This implies that most genes found important for BMD may not be relevant to ROF. Ideally, employing OF per se as a direct study phenotype can directly find the relevant genes underlying ROF.

EVIDENCE

Here, we summarized some evidence supporting ROF under moderate genetic control, and the current progress of molecular genetic studies employing OF as the direct study phenotype, then give our consideration on the future prospects in the genetics of ROF.

Relationship of total body fatness and five anthropometric indices in Chinese aged 20–40 years: different effects of age and gender

OBJECTIVES

We aim to evaluate the ethnic-specific relationship of total fat mass and anthropometric indices in Chinese.

DESIGN

Cross-section study.

SETTING

This study was performed at the College of Life Sciences, Hunan Normal University, P.R. China.

SUBJECTS AND METHOD

To increase our understanding of the relationship of total fat mass and anthropometric indices in Chinese, 793 females and 1091 males aged 20-40 years were randomly recruited from Changsha city of P. R. China. Hip circumference (HC) and waist circumference (WC) were measured using standardized equipments, and other three anthropometric indices of body mass index (BMI), waist-to-hip ratio (WHR), and conicity index (CI) were calculated using weight, height, HC and WC. Total body fatness (TBF) in kg was measured using a Hologic QDR 4500 W dual-energy X-ray absorptiometry (DEXA) scanner.

RESULTS

There was an increasing trend of TBF, %TBF (percent total body fatness) and the five anthropometric indices in successively older age groups. Compared with females, males generally had high average BMI, WC, HC, WHR and CI, but had low average TBF and %TBF. Except for some correlations in 25-29 years age groups, TBF and %TBF were significantly correlated with five anthropometric indices with the Pearson's correlation coefficients ranging from 0.07 to 0.87. Principal component analysis (PCA) was performed to form four principal components (PCs) that interpreted over 99% of the total variation of the five related anthropometric indices in all age groups, with over 53% of the total variation accounted for by the PC1. Multiple regression analyses showed that four PCs combined explained a greater variance (R (2)=55.2-80.8%) in TBF than did BMI alone (R (2)=40-74.9%).

CONCLUSION

Our results suggest that there is an increasing trend of total fat mass and five anthropometric indices with aging; that age and sex have the important effects on influencing the correlations of TBF and the studied anthropometric indices; and that the accuracy of predicting the TBF using five anthropometric indices is higher than using BMI alone.

Clinical and genetic study on a new Chinese family with benign familial infantile seizures

Three loci for benign familial infantile seizures (BFIS, traditionally named benign familial infantile convulsions) have been mapped to the chromosome regions of 19q12-13.1, 2q24, and 16p12-q12. We characterized the clinical features of a newly discovered Chinese family with BFIS and investigated whether it is linked to these loci. A four-generation Chinese family was investigated and nineteen family members were examined. Fourteen microsatellite markers covering the three BFIS loci on the chromosome regions of 19q12-13.1, 2q24, and 16p12-q12 were genotyped. Linkage analysis was performed. The main clinical features of our patients include onset of afebrile seizures between 3 and 10 months, normal psychomotor development, normal interictal electroencephalogram (EEG), and autosomal dominant inheritance. Magnetic resonance imaging (MRI) changes were found in the proband. Two-point LOD scores are < -2.0 at the recombination rate of 0.0 for all the markers on the 2q24 region. Multipoint LOD scores are < -3.0 for the regions of 19q12-13.1 and 16p12-q12. Linkage analysis showed no evidence that the disease gene of this BFIS family is linked to the chromosome regions previously identified as the critical regions of the disease. Another chromosome region harboring the disease gene may exist in the new Chinese family.

Tests of linkage and association of the COL1A2 gene with bone phenotypes' variation in Chinese nuclear families

In the present study, we simultaneously test linkage and/or association of the collagen type I alpha 2 (COL1A2) gene with bone mineral density (BMD) and bone area. A total of 1280 subjects from 407 Chinese nuclear families (including both parents and their daughters) were genotyped for an intragenic marker MspI in the COL1A2 gene. BMD and bone area at the lumbar spine and hip were measured by dual-energy X-ray absorptiometry. Applying the QTDT (quantitative transmission disequilibrium test) program, we performed tests for population stratification, within-family association (via transmission disequilibrium test), total association, linkage, and linkage while modeling association. Significant or marginal within-family associations were found with BMD at the lumbar spine (P = 0.013), trochanter (P = 0.004), and total hip (P = 0.053) and with bone area at the intertrochanteric region (P = 0.024) and total hip (P = 0.048). The positive associations were confirmed in permutations except for bone area at total hip (P > 0.10). A small proportion (<1%) of the population variance of bone phenotypes can be explained by the MspI polymorphism; however, it may be underestimated given the significant population stratification detected in our sample. Due to the limited number of sib pairs in this sample, we did not find evidence of linkage. In summary, the MspI polymorphism is likely to be in linkage disequilibrium with a nearby functional mutation affecting BMD and bone area.