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Zhu K, Jin Y, Zhao Y, He A, Wang R, Cao C. Proteomic scrutiny of nasal microbiomes: implications for the clinic. Expert Rev Proteomics 2024; 21:169-179. [PMID: 38420723 DOI: 10.1080/14789450.2024.2323983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
INTRODUCTION The nasal cavity is the initial site of the human respiratory tract and is one of the habitats where microorganisms colonize. The findings from a growing number of studies have shown that the nasal microbiome is an important factor for human disease and health. 16S rRNA sequencing and metagenomic next-generation sequencing (mNGS) are the most commonly used means of microbiome evaluation. Among them, 16S rRNA sequencing is the primary method used in previous studies of nasal microbiomes. However, neither 16S rRNA sequencing nor mNGS can be used to analyze the genes specifically expressed by nasal microorganisms and their functions. This problem can be addressed by proteomic analysis of the nasal microbiome. AREAS COVERED In this review, we summarize current advances in research on the nasal microbiome, introduce the methods for proteomic evaluation of the nasal microbiome, and focus on the important roles of proteomic evaluation of the nasal microbiome in the diagnosis and treatment of related diseases. EXPERT OPINION The detection method for microbiome-expressed proteins is known as metaproteomics. Metaproteomic analysis can help us dig deeper into the nasal microbiomes and provide new targets and ideas for clinical diagnosis and treatment of many nasal dysbiosis-related diseases.
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Affiliation(s)
- Ke Zhu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yan Jin
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Municipal Hospital Affiliated to Taizhou University, Taizhou, China
| | - Yun Zhao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Andong He
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Ran Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chao Cao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
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Yu F, Qiu C, Xu C, Tian Q, Zhao LJ, Wu L, Deng HW, Shen H. Mendelian Randomization Identifies CpG Methylation Sites With Mediation Effects for Genetic Influences on BMD in Peripheral Blood Monocytes. Front Genet 2020; 11:60. [PMID: 32180791 PMCID: PMC7059767 DOI: 10.3389/fgene.2020.00060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
Osteoporosis is mainly characterized by low bone mineral density (BMD) and is an increasingly serious public health concern. DNA methylation is a major epigenetic mechanism that may contribute to the variation in BMD and may mediate the effects of genetic and environmental factors of osteoporosis. In this study, we performed an epigenome-wide DNA methylation analysis in peripheral blood monocytes of 118 Caucasian women with extreme BMD values. Further, we developed and implemented a novel analytical framework that integrates Mendelian randomization with genetic fine mapping and colocalization to evaluate the causal relationships between DNA methylation and BMD phenotype. We identified 2,188 differentially methylated CpGs (DMCs) between the low and high BMD groups and distinguished 30 DMCs that may mediate the genetic effects on BMD. The causal relationship was further confirmed by eliminating the possibility of horizontal pleiotropy, linkage effect and reverse causality. The fine-mapping analysis determined 25 causal variants that are most likely to affect the methylation levels at these mediator DMCs. The majority of the causal methylation quantitative loci and DMCs reside within cell type-specific histone mark peaks, enhancers, promoters, promoter flanking regions and CTCF binding sites, supporting the regulatory potentials of these loci. The established causal pathways from genetic variant to BMD phenotype mediated by DNA methylation provide a gene list to aid in designing future functional studies and lead to a better understanding of the genetic and epigenetic mechanisms underlying the variation of BMD.
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Affiliation(s)
- Fangtang Yu
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Chuan Qiu
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Chao Xu
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Qing Tian
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Lan-Juan Zhao
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Li Wu
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,School of Basic Medical Science, Central South University, Changsha, China
| | - Hui Shen
- Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
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Yang TL, Shen H, Liu A, Dong SS, Zhang L, Deng FY, Zhao Q, Deng HW. A road map for understanding molecular and genetic determinants of osteoporosis. Nat Rev Endocrinol 2020; 16:91-103. [PMID: 31792439 PMCID: PMC6980376 DOI: 10.1038/s41574-019-0282-7] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/18/2019] [Indexed: 12/16/2022]
Abstract
Osteoporosis is a highly prevalent disorder characterized by low bone mineral density and an increased risk of fracture, termed osteoporotic fracture. Notably, bone mineral density, osteoporosis and osteoporotic fracture are highly heritable; however, determining the genetic architecture, and especially the underlying genomic and molecular mechanisms, of osteoporosis in vivo in humans is still challenging. In addition to susceptibility loci identified in genome-wide association studies, advances in various omics technologies, including genomics, transcriptomics, epigenomics, proteomics and metabolomics, have all been applied to dissect the pathogenesis of osteoporosis. However, each technology individually cannot capture the entire view of the disease pathology and thus fails to comprehensively identify the underlying pathological molecular mechanisms, especially the regulatory and signalling mechanisms. A change to the status quo calls for integrative multi-omics and inter-omics analyses with approaches in 'systems genetics and genomics'. In this Review, we highlight findings from genome-wide association studies and studies using various omics technologies individually to identify mechanisms of osteoporosis. Furthermore, we summarize current studies of data integration to understand, diagnose and inform the treatment of osteoporosis. The integration of multiple technologies will provide a road map to illuminate the complex pathogenesis of osteoporosis, especially from molecular functional aspects, in vivo in humans.
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Affiliation(s)
- Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Hui Shen
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Anqi Liu
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Qi Zhao
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA.
- School of Basic Medical Science, Central South University, Changsha, China.
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Serum Proteomic Analysis Reveals Vitamin D-Binding Protein (VDBP) as a Potential Biomarker for Low Bone Mineral Density in Mexican Postmenopausal Women. Nutrients 2019; 11:nu11122853. [PMID: 31766436 PMCID: PMC6950314 DOI: 10.3390/nu11122853] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 12/16/2022] Open
Abstract
Osteoporosis is a skeletal disease mainly affecting women over 50 years old and it represents a serious public health problem because of the high socioeconomic burden. This disease is characterized by deterioration of bone microarchitecture, low bone mineral density (BMD), and increased risk of fragility fractures. This study aimed to identify serum useful proteins as biomarkers for the diagnosis and/or prognosis of osteoporosis and fracture risk. We collected 446 serum samples from postmenopausal women aged ≥45 years old. Based on the BMD measurement, we classified the participants into three groups: osteoporotic, osteopenic, and normal. In an initial discovery stage, we conducted a proteomic approach using two-dimensional differential gel electrophoresis (2D-DIGE). The peptides into the spots of interest were identified through matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF/TOF). Enzyme-linked immunosorbent assay (ELISA) was performed to validate the proteins of interest. We identified 27 spots of interest when comparing low BMD versus normal BMD postmenopausal women. Based on their relevance in bone metabolism, we analyzed three proteins: ceruloplasmin (CP), gelsolin (GSN), and vitamin D-binding protein (VDBP). Our results demonstrated that low serum VDBP levels correlate with low BMD (osteopenic and osteoporotic). Therefore, VDBP could be considered as a novel, potential, and non-invasive biomarker for the early detection of osteoporosis.
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Plasma gelsolin is associated with hip BMD in Chinese postmenopausal women. PLoS One 2018; 13:e0197732. [PMID: 29787615 PMCID: PMC5963809 DOI: 10.1371/journal.pone.0197732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 05/08/2018] [Indexed: 12/18/2022] Open
Abstract
Gelsolin (GSN) protein, expressed in circulating monocytes, was previously reported to be associated with osteoporosis in both Chinese and Caucasian women. This study aims to test if plasma GSN protein level is associated with hip bone mineral density (BMD) in Chinese population. Based on two study Groups containing 6,308 old Chinese, we adopted extreme sampling scheme and selected 3 independent samples (Subgroups 1-3) for discovery, replication, and validation purposes. We tested plasma GSN concentration, and analyzed whether plasma GSN level differs between subjects with extremely low vs. high hip BMD. In Group 1 (N = 1,860), the plasma GSN level increased in the female with low BMD, which was discovered in the Subgroup 1 (N = 42, p = 0.093) and replicated in the Subgroup 2 (N = 39, p = 0.095). With more extreme sampling for the Subgroup 3 from the Group 2 (N = 4,448), the difference of plasma GSN level in the female with low BMD vs. high BMD is more significant (N = 45, p = 0.037). After the subjects were pooled from Subgroups 2 and 3, the difference in plasma GSN between low and high BMD subjects became even more significant (p = 0.016). The plasma GSN level was negatively correlated with total hip BMD (r = -0.26, p = 0.033). We concluded that plasma GSN was associated with hip BMD in Chinese postmenopausal women and plasma GSN might be a potential risk biomarker for osteoporosis.
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"Omics" Signatures in Peripheral Monocytes from Women with Low BMD Condition. J Osteoporos 2018; 2018:8726456. [PMID: 29744028 PMCID: PMC5878888 DOI: 10.1155/2018/8726456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 02/12/2018] [Indexed: 01/20/2023] Open
Abstract
Postmenopausal osteoporosis (PMO) is a result of increased bone resorption compared to formation. Osteoclasts are responsible for bone resorption, which are derived from circulating monocytes that undertake a journey from the blood to the bone for the process of osteoclastogenesis. In recent times, the use of high throughput technologies to explore monocytes from women with low versus high bone density has led to the identification of candidate molecules that may be deregulated in PMO. This review provides a list of molecules in monocytes relevant to bone density which have been identified by "omics" studies in the last decade or so. The molecules in monocytes that are deregulated in low BMD condition may contribute to processes such as monocyte survival, migration/chemotaxis, adhesion, transendothelial migration, and differentiation into the osteoclast lineage. Each of these processes may be crucial to the overall route of osteoclastogenesis and an increase in any/all of these processes can lead to increased bone resorption and subsequently low bone density. Whether these molecules are indeed the cause or effect is an arena currently unexplored.
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Zhu W, Shen H, Zhang JG, Zhang L, Zeng Y, Huang HL, Zhao YC, He H, Zhou Y, Wu KH, Tian Q, Zhao LJ, Deng FY, Deng HW. Cytosolic proteome profiling of monocytes for male osteoporosis. Osteoporos Int 2017; 28:1035-1046. [PMID: 27844135 PMCID: PMC5779619 DOI: 10.1007/s00198-016-3825-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
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.
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Affiliation(s)
- W Zhu
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - H Shen
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - J-G Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - L Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Y Zeng
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - H-L Huang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Y-C Zhao
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - H He
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Y Zhou
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - K-H Wu
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Q Tian
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - L-J Zhao
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - F-Y Deng
- Center for Genetic Epidemiology and Genomics, Soochow University School of Public Health, Suzhou, Jiangsu, 215123, China
| | - H-W Deng
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China.
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
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8
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Zeng Y, Deng FY, Zhu W, Zhang L, He H, Xu C, Tian Q, Zhang JG, Zhang LS, Hu HG, Deng HW. Mass spectrometry based proteomics profiling of human monocytes. Protein Cell 2016; 8:123-133. [PMID: 27878450 PMCID: PMC5291777 DOI: 10.1007/s13238-016-0342-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022] Open
Abstract
Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged. Biological functions of these monocyte-expressed genes were annotated and classified via Gene Ontology (GO) analysis. Furthermore, by extracting the overlapped genes from in vivo and in vitro datasets, a core gene list including 541 unique genes was generated. Based on the core gene list, further gene-disease associations, pathway and network analyses were performed. Data analyses based on multiple bioinformatics tools produced a large body of biologically meaningful information, and revealed a number of genes such as SAMHD1, G6PD, GPD2 and ENO1, which have been reported to be related to immune response, blood biology, bone remodeling, and cancer respectively. As a unique resource, this study can serve as a reference map for future in-depth research on monocytes biology and monocyte-involved human diseases.
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Affiliation(s)
- Yong Zeng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.,Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Fei-Yan Deng
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.,Laboratory of Proteins and Proteomics, Department of Epidemiology, Soochow University School of Public Health, Suzhou, 205123, China
| | - Wei Zhu
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.,College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lan Zhang
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Hao He
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Chao Xu
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Qing Tian
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Ji-Gang Zhang
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Li-Shu Zhang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Hong-Gang Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Hong-Wen Deng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China. .,Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
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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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Chen YC, Guo YF, He H, Lin X, Wang XF, Zhou R, Li WT, Pan DY, Shen J, Deng HW. Integrative Analysis of Genomics and Transcriptome Data to Identify Potential Functional Genes of BMDs in Females. J Bone Miner Res 2016; 31:1041-9. [PMID: 26748680 DOI: 10.1002/jbmr.2781] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/27/2015] [Accepted: 12/30/2015] [Indexed: 02/01/2023]
Abstract
Osteoporosis is known to be highly heritable. However, to date, the findings from more than 20 genome-wide association studies (GWASs) have explained less than 6% of genetic risks. Studies suggest that the missing heritability data may be because of joint effects among genes. To identify novel heritability for osteoporosis, we performed a system-level study on bone mineral density (BMD) by weighted gene coexpression network analysis (WGCNA), using the largest GWAS data set for BMD in the field, Genetic Factors for Osteoporosis Consortium (GEFOS-2), and a transcriptomic gene expression data set generated from transiliac bone biopsies in women. A weighted gene coexpression network was generated for 1574 genes with GWAS nominal evidence of association (p ≤ 0.05) based on dissimilarity measurement on the expression data. Twelve distinct gene modules were identified, and four modules showed nominally significant associations with BMD (p ≤ 0.05), but only one module, the yellow module, demonstrated a good correlation between module membership (MM) and gene significance (GS), suggesting that the yellow module serves an important biological role in bone regulation. Interestingly, through characterization of module content and topology, the yellow module was found to be significantly enriched with contractile fiber part (GO:044449), which is widely recognized as having a close relationship between muscle and bone. Furthermore, detailed submodule analyses of important candidate genes (HOMER1, SPTBN1) by all edges within the yellow module implied significant enrichment of functional connections between bone and cytoskeletal protein binding. Our study yielded novel information from system genetics analyses of GWAS data jointly with transcriptomic data. The findings highlighted a module and several genes in the model as playing important roles in the regulation of bone mass in females, which may yield novel insights into the genetic basis of osteoporosis. © 2016 American Society for Bone and Mineral Research.
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Affiliation(s)
- Yuan-Cheng Chen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China
| | - Yan-Fang Guo
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China.,Institute of Bioinformatics, School of Basic Medical Science, Southern Medical University, Guangzhou, PR China
| | - Hao He
- Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA.,Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, USA
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China
| | - Xia-Fang Wang
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China
| | - Rou Zhou
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China
| | - Wen-Ting Li
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China
| | - Dao-Yan Pan
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China
| | - Jie Shen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China
| | - Hong-Wen Deng
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, PR China.,Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
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11
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Zhang L, Liu YZ, Zeng Y, Zhu W, Zhao YC, Zhang JG, Zhu JQ, He H, Shen H, Tian Q, Deng FY, Papasian CJ, Deng HW. Network-based proteomic analysis for postmenopausal osteoporosis in Caucasian females. Proteomics 2015; 16:12-28. [DOI: 10.1002/pmic.201500005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 09/06/2015] [Accepted: 10/28/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Lan Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Yao-Zhong Liu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Yong Zeng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; Beijing P. R. China
| | - Wei Zhu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Ying-Chun Zhao
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Ji-Gang Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Jia-Qiang Zhu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Hao He
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Hui Shen
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Qing Tian
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
| | - Fei-Yan Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
- Laboratory of Proteins and Proteomics, Department of Epidemiology; Soochow University School of Public Health; Suzhou P. R. China
| | - Christopher J. Papasian
- Department of Basic Medical Sciences, School of Medicine; University of Missouri - Kansas City; MO USA
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine; Tulane University; New Orleans LA USA
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; Beijing P. R. China
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12
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Alam I, Koller DL, Cañete T, Blázquez G, Mont-Cardona C, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T. Fine mapping of bone structure and strength QTLs in heterogeneous stock rat. Bone 2015; 81:417-426. [PMID: 26297441 PMCID: PMC4641024 DOI: 10.1016/j.bone.2015.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 11/26/2022]
Abstract
We previously demonstrated that skeletal structure and strength phenotypes vary considerably in heterogeneous stock (HS) rats. These phenotypes were found to be strongly heritable, suggesting that the HS rat model represents a unique genetic resource for dissecting the complex genetic etiology underlying bone fragility. The purpose of this study was to identify and localize genes associated with bone structure and strength phenotypes using 1524 adult male and female HS rats between 17 to 20 weeks of age. Structure measures included femur length, neck width, head width; femur and lumbar spine (L3-5) areas obtained by DXA; and cross-sectional areas (CSA) at the midshaft, distal femur and femoral neck, and the 5th lumbar vertebra measured by CT. In addition, measures of strength of the whole femur and femoral neck were obtained. Approximately 70,000 polymorphic SNPs distributed throughout the rat genome were selected for genotyping, with a mean linkage disequilibrium coefficient between neighboring SNPs of 0.95. Haplotypes were estimated across the entire genome for each rat using a multipoint haplotype reconstruction method, which calculates the probability of descent at each locus from each of the 8 HS founder strains. The haplotypes were then tested for association with each structure and strength phenotype via a mixed model with covariate adjustment. We identified quantitative trait loci (QTLs) for structure phenotypes on chromosomes 3, 8, 10, 12, 17 and 20, and QTLs for strength phenotypes on chromosomes 5, 10 and 11 that met a conservative genome-wide empiric significance threshold (FDR=5%; P<3×10(-6)). Importantly, most QTLs were localized to very narrow genomic regions (as small as 0.3 Mb and up to 3 Mb), each harboring a small set of candidate genes, both novel and previously shown to have roles in skeletal development and homeostasis.
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Affiliation(s)
- Imranul Alam
- Medicine, Indiana University School of Medicine, IN, USA.
| | - Daniel L Koller
- Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - Toni Cañete
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Gloria Blázquez
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Carme Mont-Cardona
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | | | - Esther Martínez-Membrives
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Sira Díaz-Morán
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Adolf Tobeña
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Alberto Fernández-Teruel
- Department of Psychiatry and Forensic Medicine, Institute of Neurosciences, School of Medicine, Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Pernilla Stridh
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Margarita Diez
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Tomas Olsson
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Martina Johannesson
- Clinical Neuroscience, Center for Molecular Medicine, Neuroimmunolgy Unit, Karolinska Institutet, S171 76 Stockholm, Sweden
| | - Amelie Baud
- Wellcome Trust Center for Human Genetics, Oxford OX3 7BN, United Kingdom
| | - Michael J Econs
- Medicine, Indiana University School of Medicine, IN, USA; Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - Tatiana Foroud
- Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
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13
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Zhou Y, Deng HW, Shen H. Circulating monocytes: an appropriate model for bone-related study. Osteoporos Int 2015; 26:2561-72. [PMID: 26194495 DOI: 10.1007/s00198-015-3250-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/10/2015] [Indexed: 10/23/2022]
Abstract
Peripheral blood monocytes (PBMs) are an important source of precursors of osteoclasts, the bone-resorbing cells and the cytokines produced by PBMs that have profound effects on osteoclast differentiation, activation, and apoptosis. So PBMs represent a highly valuable and unique working cell model for bone-related study. Finding an appropriate working cell model for clinical and (epi-)genomic studies of human skeletal disorders is a challenge. Peripheral blood monocytes (PBMs) can give rise to osteoclasts, the bone-resorbing cells. Particularly, PBMs provide the sole source of osteoclast precursors for adult peripheral skeleton where the bone marrow is normally hematopoietically inactive. PBMs can secrete potent pro- and anti-inflammatory cytokines, which are important for osteoclast differentiation, activation, and apoptosis. Reduced production of PBM cytokines represents a major mechanism for the inhibitory effects of sex hormones on osteoclastogenesis and bone resorption. Abnormalities in PBMs have been linked to various skeletal disorders/traits, strongly supporting for the biological relevance of PBMs with bone metabolism and disorders. Here, we briefly review the origin and further differentiation of PBMs. In particular, we discuss the close relationship between PBMs and osteoclasts, and highlight the utility of PBMs in study the pathophysiological mechanisms underlying various skeletal disorders.
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Affiliation(s)
- Y Zhou
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Cell and Molecular Biology Department, Tulane University, New Orleans, LA, 70118, USA
| | - H-W Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Cell and Molecular Biology Department, Tulane University, New Orleans, LA, 70118, USA
| | - H Shen
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA.
- Cell and Molecular Biology Department, Tulane University, New Orleans, LA, 70118, USA.
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St., Suite 2001, New Orleans, LA, 70112, USA.
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Monocyte Proteomics Reveals Involvement of Phosphorylated HSP27 in the Pathogenesis of Osteoporosis. DISEASE MARKERS 2015; 2015:196589. [PMID: 26063949 PMCID: PMC4439496 DOI: 10.1155/2015/196589] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/30/2015] [Accepted: 04/07/2015] [Indexed: 01/23/2023]
Abstract
Peripheral monocytes, precursors of osteoclasts, have emerged as important candidates for identifying proteins relevant to osteoporosis, a condition characterized by low Bone Mineral Density (BMD) and increased susceptibility for fractures. We employed 4-plex iTRAQ (isobaric tags for relative and absolute quantification) coupled with LC-MS/MS (liquid chromatography coupled with tandem mass spectrometry) to identify differentially expressed monocyte proteins from premenopausal and postmenopausal women with low versus high BMD. Of 1801 proteins identified, 45 were differentially abundant in low versus high BMD, with heat shock protein 27 (HSP27) distinctly upregulated in low BMD condition in both premenopausal and postmenopausal categories. Validation in individual samples (n = 80) using intracellular ELISA confirmed that total HSP27 (tHSP27) as well as phosphorylated HSP27 (pHSP27) was elevated in low BMD condition in both categories (P < 0.05). Further, using transwell assays, pHSP27, when placed in the upper chamber, could increase monocyte migration (P < 0.0001) and this was additive in combination with RANKL (receptor activator of NFkB ligand) placed in the lower chamber (P = 0.05). Effect of pHSP27 in monocyte migration towards bone milieu can result in increased osteoclast formation and thus contribute to pathogenesis of osteoporosis. Overall, this study reveals for the first time a novel link between monocyte HSP27 and BMD.
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