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Zeng Y, Zhang L, Zhu W, Xu C, He H, Zhou Y, Liu YZ, Tian Q, Zhang JG, Deng FY, Hu HG, Zhang LS, Deng HW. Quantitative proteomics and integrative network analysis identified novel genes and pathways related to osteoporosis. J Proteomics 2016; 142:45-52. [PMID: 27153759 PMCID: PMC5362378 DOI: 10.1016/j.jprot.2016.04.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 04/21/2016] [Accepted: 04/28/2016] [Indexed: 01/18/2023]
Abstract
UNLABELLED 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-MS(E) (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 MS(E) 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 SIGNIFICANCE Mass 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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Affiliation(s)
- Yong Zeng
- College of Life Sciences and Bioengineering, Beijing Jiao Tong University, Beijing 100044, China; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Lan Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Wei Zhu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Chao Xu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Hao He
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Yu Zhou
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Yao-Zhong Liu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Qing Tian
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Ji-Gang Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA
| | - Fei-Yan Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA; Laboratory of Proteins and Proteomics, Department of Epidemiology, Soochow University School of Public Health, Suzhou 205123, Jiangsu, China
| | - Hong-Gang Hu
- College of Life Sciences and Bioengineering, Beijing Jiao Tong University, Beijing 100044, China
| | - Li-Shu Zhang
- College of Life Sciences and Bioengineering, Beijing Jiao Tong University, Beijing 100044, China
| | - Hong-Wen Deng
- College of Life Sciences and Bioengineering, Beijing Jiao Tong University, Beijing 100044, China; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans 70112, LA, USA.
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Nurden AT, Pillois X, Wilcox DA. Glanzmann thrombasthenia: state of the art and future directions. Semin Thromb Hemost 2013; 39:642-55. [PMID: 23929305 DOI: 10.1055/s-0033-1353393] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glanzmann thrombasthenia (GT) is the principal inherited disease of platelets and the most commonly encountered disorder of an integrin. GT is characterized by spontaneous mucocutaneous bleeding and an exaggerated response to trauma caused by platelets that fail to aggregate when stimulated by physiologic agonists. GT is caused by quantitative or qualitative deficiencies of αIIbβ3, an integrin coded by the ITGA2B and ITGB3 genes and which by binding fibrinogen and other adhesive proteins joins platelets together in the aggregate. Widespread genotyping has revealed that mutations spread across both genes, yet the reason for the extensive variation in both the severity and intensity of bleeding between affected individuals remains poorly understood. Furthermore, although genetic defects of ITGB3 affect other tissues with β3 present as αvβ3 (the vitronectin receptor), the bleeding phenotype continues to dominate. Here, we look in detail at mutations that affect (i) the β-propeller region of the αIIb head domain and (ii) the membrane proximal disulfide-rich epidermal growth factor (EGF) domains of β3 and which often result in spontaneous integrin activation. We also examine deep vein thrombosis as an unexpected complication of GT and look at curative procedures for the diseases, including allogeneic stem cell transfer and the potential for gene therapy.
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Affiliation(s)
- Alan T Nurden
- Plateforme Technologique et d'Innovation Biomédicale, Hôpital Xavier Arnozan, Pessac, France.
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