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Li JJ, Wang BQ, Fei Q, Yang Y, Li D. Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res 2016; 5:594-601. [PMID: 27908864 PMCID: PMC5227060 DOI: 10.1302/2046-3758.512.bjr-2016-0073.r1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/05/2016] [Indexed: 11/06/2022] Open
Abstract
Objectives In order to screen the altered gene expression profile in peripheral blood mononuclear cells of patients with osteoporosis, we performed an integrated analysis of the online microarray studies of osteoporosis. Methods We searched the Gene Expression Omnibus (GEO) database for microarray studies of peripheral blood mononuclear cells in patients with osteoporosis. Subsequently, we integrated gene expression data sets from multiple microarray studies to obtain differentially expressed genes (DEGs) between patients with osteoporosis and normal controls. Gene function analysis was performed to uncover the functions of identified DEGs. Results A total of three microarray studies were selected for integrated analysis. In all, 1125 genes were found to be significantly differentially expressed between osteoporosis patients and normal controls, with 373 upregulated and 752 downregulated genes. Positive regulation of the cellular amino metabolic process (gene ontology (GO): 0033240, false discovery rate (FDR) = 1.00E + 00) was significantly enriched under the GO category for biological processes, while for molecular functions, flavin adenine dinucleotide binding (GO: 0050660, FDR = 3.66E-01) and androgen receptor binding (GO: 0050681, FDR = 6.35E-01) were significantly enriched. DEGs were enriched in many osteoporosis-related signalling pathways, including those of mitogen-activated protein kinase (MAPK) and calcium. Protein-protein interaction (PPI) network analysis showed that the significant hub proteins contained ubiquitin specific peptidase 9, X-linked (Degree = 99), ubiquitin specific peptidase 19 (Degree = 57) and ubiquitin conjugating enzyme E2 B (Degree = 57). Conclusion Analysis of gene function of identified differentially expressed genes may expand our understanding of fundamental mechanisms leading to osteoporosis. Moreover, significantly enriched pathways, such as MAPK and calcium, may involve in osteoporosis through osteoblastic differentiation and bone formation. Cite this article: J. J. Li, B. Q. Wang, Q. Fei, Y. Yang, D. Li. Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res 2016;5:594–601. DOI: 10.1302/2046-3758.512.BJR-2016-0073.R1.
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Affiliation(s)
- J J Li
- Department of Orthopaedics, Beijing Friendship Hospital, Capital Medical University, Yongan Road 95, Xicheng District, Beijing 100050, China
| | - B Q Wang
- Department of Orthopaedics, Beijing Friendship Hospital, Capital Medical University, Yongan Road 95, Xicheng District, Beijing 100050, China
| | - Q Fei
- Department of Orthopaedics, Beijing Friendship Hospital, Capital Medical University, Yongan Road 95, Xicheng District, Beijing 100050, China
| | - Y Yang
- Department of Orthopaedics, Beijing Friendship Hospital, Capital Medical University, Yongan Road 95, Xicheng District, Beijing 100050, China
| | - D Li
- Department of Orthopaedics, Beijing Friendship Hospital, Capital Medical University, Yongan Road 95, Xicheng District, Beijing 100050, China
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Athanasiadis G, Arranz L, Ziyatdinov A, Brunel H, Camacho M, Malouf J, Sosa NHD, Vila L, Casademont J, Soria JM. Exploring correlation between bone metabolism markers and densitometric traits in extended families from Spain. Bone 2016; 90:1-6. [PMID: 27241279 DOI: 10.1016/j.bone.2016.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
Osteoporosis is a common multifactorial disorder characterized by low bone mass and reduced bone strength that may cause fragility fractures. In recent years, there have been substantial advancements in the biochemical monitoring of bone metabolism through the measurement of bone turnover markers. Currently, good knowledge of the genetics of such markers has become an indispensable part of osteoporosis research. In this study, we used the Genetic Analysis of Osteoporosis Project to study the genetics of the plasma levels of 12 markers related to bone metabolism and osteoporosis. Plasma phenotypes were determined through biochemical assays and log-transformed values were used together with a set of covariates to model genetic and environmental contributions to phenotypic variation, thus estimating the heritability of each trait. In addition, we studied correlations between the 12 markers and a wide variety of previously described densitometric traits. All of the 12 bone metabolism markers showed significant heritability, ranging from 0.194 for osteocalcin to 0.516 for sclerostin after correcting for covariate effects. Strong genetic correlations were observed between osteocalcin and several bone mineral densitometric traits, a finding with potentially useful diagnostic applications. In addition, suggestive genetic correlations with densitometric traits were observed for leptin and sclerostin. Overall, the few strong and several suggestive genetic correlations point out the existence of a complex underlying genetic architecture for bone metabolism plasma phenotypes and provide a strong motivation for pursuing novel whole-genome gene-mapping strategies.
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Affiliation(s)
- Georgios Athanasiadis
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
| | - Laura Arranz
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Andrey Ziyatdinov
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Helena Brunel
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Mercedes Camacho
- Laboratory of Angiology, Vascular Biology and Inflammation, Institute of Biomedical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jorge Malouf
- Departament of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | - Luis Vila
- Laboratory of Angiology, Vascular Biology and Inflammation, Institute of Biomedical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Casademont
- Departament of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jose Manuel Soria
- Unit of Genomics of Complex Diseases, Institute of Biomedical Research, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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Athanasiadis G, Jørgensen FG, Cheng JY, Kjærgaard PC, Schierup MH, Mailund T. Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study. PLoS One 2016; 11:e0161822. [PMID: 27571202 PMCID: PMC5003382 DOI: 10.1371/journal.pone.0161822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 08/14/2016] [Indexed: 11/18/2022] Open
Abstract
Scientific outreach delivers science to the people. But it can also deliver people to the science. In this work, we report our experience from a large-scale public engagement project promoting genomic literacy among Danish high school students with the additional benefit of collecting data for studying the genetic makeup of the Danish population. Not only did we confirm that students have a great interest in their genetic past, but we were also gratified to see that, with the right motivation, adolescents can provide high-quality data for genetic studies.
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Affiliation(s)
- Georgios Athanasiadis
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
- * E-mail:
| | | | - Jade Y. Cheng
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
| | - Peter C. Kjærgaard
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
- Department of Culture and Society, Aarhus University, 8000, Aarhus, Denmark
- The Natural History Museum of Denmark, University of Copenhagen, 1471, Copenhagen, Denmark
| | - Mikkel H. Schierup
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
- Department of Bioscience, Aarhus University, 8000, Aarhus, Denmark
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
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Hernandez-de Sosa N, Athanasiadis G, Malouf J, Laiz A, Marin A, Herrera S, Farrerons J, Soria JM, Casademont J. Genetic Contribution of Femoral Neck Bone Geometry to the Risk of Developing Osteoporosis: A Family-Based Study. PLoS One 2016; 11:e0154833. [PMID: 27163365 PMCID: PMC4862643 DOI: 10.1371/journal.pone.0154833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/20/2016] [Indexed: 11/19/2022] Open
Abstract
Femoral neck geometry parameters are believed to be as good as bone mineral density as independent factors in predicting hip fracture risk. This study was conducted to analyze the roles of genetic and environmental factors in femoral properties measured in a sample of Spanish families with osteoporotic fractures and extended genealogy. The "Genetic Analysis of Osteoporosis (GAO) Project" involved 11 extended families with a total number of 376 individuals. We studied three categorical phenotypes of particular clinical interest and we used a Hip structural analysis based on DXA to analyze 17 strength and geometrical phenotypes of the hip. All the femoral properties had highly significant heritability, ranging from 0.252 to 0.586. The most significant correlations were observed at the genetic level (ρG). Osteoporotic fracture status (Affected 2) and, particularly, low bone mass and osteoporotic condition (Affected 3) had the highest number of significant genetic correlations with diverse femoral properties. In conclusion, our findings suggest that a relatively simple and easy to use method based on DXA studies can provide useful data on properties of the Hip in clinical practice. Furthermore, our results provide a strong motivation for further studies in order to improve the understanding of the pathophysiological mechanism underlying bone architecture and the genetics of osteoporosis.
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Affiliation(s)
- Nerea Hernandez-de Sosa
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail:
| | - Georgios Athanasiadis
- Department of Genomics of Complex Diseases, Research Institute, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Jorge Malouf
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ana Laiz
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ana Marin
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Silvia Herrera
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Farrerons
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jose Manuel Soria
- Department of Genomics of Complex Diseases, Research Institute, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jordi Casademont
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
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5
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Sánchez-Duffhues G, Hiepen C, Knaus P, Ten Dijke P. Bone morphogenetic protein signaling in bone homeostasis. Bone 2015; 80:43-59. [PMID: 26051467 DOI: 10.1016/j.bone.2015.05.025] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/11/2015] [Accepted: 05/20/2015] [Indexed: 01/06/2023]
Abstract
Bone morphogenetic proteins (BMPs) are cytokines belonging to the transforming growth factor-β (TGF-β) superfamily. They play multiple functions during development and tissue homeostasis, including regulation of the bone homeostasis. The BMP signaling pathway consists in a well-orchestrated manner of ligands, membrane receptors, co-receptors and intracellular mediators, that regulate the expression of genes controlling the normal functioning of the bone tissues. Interestingly, BMP signaling perturbation is associated to a variety of low and high bone mass diseases, including osteoporosis, bone fracture disorders and heterotopic ossification. Consistent with these findings, in vitro and in vivo studies have shown that BMPs have potent effects on the activity of cells regulating bone function, suggesting that manipulation of the BMP signaling pathway may be employed as a therapeutic approach to treat bone diseases. Here we review the recent advances on BMP signaling and bone homeostasis, and how this knowledge may be used towards improved diagnosis and development of novel treatment modalities. This article is part of a Special Issue entitled "Muscle Bone Interactions".
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Affiliation(s)
- Gonzalo Sánchez-Duffhues
- Department of Molecular Cell Biology and Cancer Genomics Centre Netherlands, Leiden University Medical Center, The Netherlands
| | - Christian Hiepen
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Berlin Brandenburg School of Regenerative Therapies (BSRT), Charité Universitätsmedizin, Berlin, Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Berlin Brandenburg School of Regenerative Therapies (BSRT), Charité Universitätsmedizin, Berlin, Germany.
| | - Peter Ten Dijke
- Department of Molecular Cell Biology and Cancer Genomics Centre Netherlands, Leiden University Medical Center, The Netherlands.
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Hernandez-de Sosa N, Athanasiadis G, Malouf J, Laiz A, Marin A, Herrera S, Farrerons J, Soria JM, Casademont J. Heritability of bone mineral density in a multivariate family-based study. Calcif Tissue Int 2014; 94:590-6. [PMID: 24687525 DOI: 10.1007/s00223-014-9852-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 03/14/2014] [Indexed: 01/01/2023]
Abstract
There is evidence for a genetic contribution to bone mineral density (BMD×). Different loci affecting BMD have been identified by diverse linkage and genome-wide association studies. We studied the heritability of and the correlations among six densitometric phenotypes and four bone mass/fracture phenotypes. For this purpose, we used a family-based study of the genetics of osteoporosis, the Genetic Analysis of Osteoporosis Project. The primary aim of our study was to examine the roles of genetic and environmental factors in determining osteoporosis-related phenotypes. The project consisted of 11 extended families from Spain. All of them were selected through a proband with osteoporosis. BMD was measured using dual-energy X-ray absorptiometry. The proportion of variance of BMD attributable to significant covariates ranged from 25% (for femoral neck BMD) to 48% (for whole-body total BMD). The vast majority of the densitometric phenotypes had highly significant heritability, ranging from 0.252 (whole-body total BMD) to 0.537 (trochanteric BMD) after correcting for covariate effects. All of the densitometric phenotypes showed high and significant genetic correlations (from -0.772 to -1.000) with a low bone mass/osteopenia condition (Affected 3). Our findings provide additional evidence on the heritability of BMD and a strong genetic correlation between BMD and bone mass/fracture phenotypes in a Spanish population. Our results emphasize the importance of detecting genetic risk factors and the benefit of early diagnosis and especially therapeutic and preventive strategies.
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Affiliation(s)
- Nerea Hernandez-de Sosa
- Department of Internal Medicine, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain,
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