Quantitative proteomics and integrative network analysis identified novel genes and pathways related to osteoporosis

• A total of 2058 proteins were identified in 33 samples by LC-nano-ESI-MSE.
• A total of 30 unique proteins were identified as differentially expressed proteins (p < 0.05).
• Differentially expressed genes: ITGA2B, GSN and RHOA played crucial roles in osteoporosis risk.
• Pathways: “regulation of actin cytoskeleton” and “leukocyte transendothelial migration” are involved in osteoporosis.
• The results were further verified in protein-RNA integrative analysis and genome wide association study.

Osteoporosis is mainly characterized by low bone mineral density (BMD), and can be attributed to excessive bone resorption by osteoclasts. Migration of circulating monocytes from blood to bone is important for subsequent osteoclast differentiation and bone resorption. Identification of those genes and pathways related to osteoclastogenesis and BMD will contribute to a better understanding of the pathophysiological mechanisms of osteoporosis. In this study, we applied the LC-nano-ESI-MSE (Liquid Chromatograph-nano-Electrospray Ionization-Mass Spectrometry) for quantitative proteomic profiling in 33 female Caucasians with discordant BMD levels, with 16 high vs. 17 low BMD subjects. Protein quantitation was accomplished by label-free measurement of total ion currents collected from MSE data. Comparison of protein expression in high vs. low BMD subjects showed that ITGA2B (p = 0.0063) and GSN (p = 0.019) were up-regulated in the high BMD group. Additionally, our protein-RNA integrative analysis showed that RHOA (p = 0.00062) differentially expressed between high vs. low BMD groups. Network analysis based on multiple tools revealed two pathways: “regulation of actin cytoskeleton” (p = 1.13E−5, FDR = 3.34E−4) and “leukocyte transendothelial migration” (p = 2.76E−4, FDR = 4.71E−3) that are functionally relevant to osteoporosis. Consistently, ITGA2B, GSN and RHOA played crucial roles in these two pathways respectively. All together, our study strongly supported the contribution of the genes ITGA2B, GSN and RHOA and the two pathways to osteoporosis risk.Biological significanceMass spectrometry based quantitative proteomics study integrated with network analysis identified novel genes and pathways related to osteoporosis. The results were further verified in multiple level studies including protein-RNA integrative analysis and genome wide association studies.

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