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Verleyen M, He Y, Burssens A, Silva MS, Callewaert B, Audenaert E. A systematic review and cross-database analysis of single nucleotide polymorphisms underlying hip morphology and osteoarthritis reveals shared mechanisms. Osteoarthritis Cartilage 2024; 32:872-885. [PMID: 38852879 DOI: 10.1016/j.joca.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE Understanding the mechanisms of hip disease, such as osteoarthritis (OA), is crucial to advance their treatment. Such hip diseases often involve specific morphological changes. Genetic variations, called single nucleotide polymorphisms (SNPs), influence various hip morphological parameters. This study investigated the biological relevance of SNPs correlated to hip morphology in genome-wide association studies (GWAS). The SNP-associated genes were compared to genes associated with OA in other joints, aiming to see if the same genes play a role in both hip development and the risk of OA in other lower limb joints. METHODOLOGY A systematic literature review was conducted to identify SNPs correlated with hip morphology, based on the Population, Intervention, Comparison, Outcome, and Study (PICOS) framework. Afterwards, Gene Ontology (GO) analysis was performed, using EnrichR, on the SNP-associated genes and compared with non-hip OA-associated genes, across different databases. RESULTS Reviewing 49 GWAS identified 436 SNPs associated with hip joint morphology, encompassing variance in bone size, structure and shape. Among the SNP-associated genes, SOX9 plays a pivotal role in size, GDF5 impacts bone structure, and BMP7 affects shape. Overall, skeletal system development, regulation of cell differentiation, and chondrocyte differentiation emerged as crucial processes influencing hip morphology. Eighteen percent of GWAS-identified genes related to hip morphology were also associated with non-hip OA. CONCLUSION Our findings indicate the existence of multiple shared genetic mechanisms across hip morphology and OA, highlighting the necessity for more extensive research in this area, as in contrast to the hip, the genetic background on knee or foot morphology remains largely understudied.
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Affiliation(s)
- Marlies Verleyen
- Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Yukun He
- Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Department of Orthopedic Surgery and Traumatology, Ghent University Hospital, Ghent, Belgium
| | - Arne Burssens
- Department of Orthopedic Surgery and Traumatology, Ghent University Hospital, Ghent, Belgium
| | | | - Bert Callewaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Emmanuel Audenaert
- Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Department of Orthopedic Surgery and Traumatology, Ghent University Hospital, Ghent, Belgium
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Sarver DC, Garcia-Diaz J, Saqib M, Riddle RC, Wong GW. Tmem263 deletion disrupts the GH/IGF-1 axis and causes dwarfism and impairs skeletal acquisition. eLife 2024; 12:RP90949. [PMID: 38241182 PMCID: PMC10945605 DOI: 10.7554/elife.90949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified a large number of candidate genes believed to affect longitudinal bone growth and bone mass. One of these candidate genes, TMEM263, encodes a poorly characterized plasma membrane protein. Single nucleotide polymorphisms in TMEM263 are associated with bone mineral density in humans and mutations are associated with dwarfism in chicken and severe skeletal dysplasia in at least one human fetus. Whether this genotype-phenotype relationship is causal, however, remains unclear. Here, we determine whether and how TMEM263 is required for postnatal growth. Deletion of the Tmem263 gene in mice causes severe postnatal growth failure, proportional dwarfism, and impaired skeletal acquisition. Mice lacking Tmem263 show no differences in body weight within the first 2 weeks of postnatal life. However, by P21 there is a dramatic growth deficit due to a disrupted growth hormone (GH)/insulin-like growth factor 1 (IGF-1) axis, which is critical for longitudinal bone growth. Tmem263-null mice have low circulating IGF-1 levels and pronounced reductions in bone mass and growth plate length. The low serum IGF-1 in Tmem263-null mice is associated with reduced hepatic GH receptor (GHR) expression and GH-induced JAK2/STAT5 signaling. A deficit in GH signaling dramatically alters GH-regulated genes and feminizes the liver transcriptome of Tmem263-null male mice, with their expression profile resembling wild-type female, hypophysectomized male, and Stat5b-null male mice. Collectively, our data validates the causal role for Tmem263 in regulating postnatal growth and raises the possibility that rare mutations or variants of TMEM263 may potentially cause GH insensitivity and impair linear growth.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Jean Garcia-Diaz
- Department of Orthopaedic Surgery, Johns Hopkins University School of MedicineBaltimoreUnited States
- Department of Orthopaedics, University of Maryland School of MedicineBaltimoreUnited States
- Cell and Molecular Medicine graduate program, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Muzna Saqib
- Department of Physiology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Ryan C Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of MedicineBaltimoreUnited States
- Department of Orthopaedics, University of Maryland School of MedicineBaltimoreUnited States
- Research and Development Service, Baltimore Veterans Administration Medical CenterBaltimoreUnited States
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of MedicineBaltimoreUnited States
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3
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Sarver DC, Garcia-Diaz J, Saqib M, Riddle RC, Wong GW. Tmem263 deletion disrupts the GH/IGF-1 axis and causes dwarfism and impairs skeletal acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551694. [PMID: 37577461 PMCID: PMC10418210 DOI: 10.1101/2023.08.02.551694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Genome-wide association studies (GWAS) have identified a large number of candidate genes believed to affect longitudinal bone growth and bone mass. One of these candidate genes, TMEM263, encodes a poorly characterized plasma membrane protein. Single nucleotide polymorphisms in TMEM263 are associated with bone mineral density in humans and mutations are associated with dwarfism in chicken and severe skeletal dysplasia in at least one human fetus. Whether this genotype-phenotype relationship is causal, however, remains unclear. Here, we determine whether and how TMEM263 is required for postnatal growth. Deletion of the Tmem263 gene in mice causes severe postnatal growth failure, proportional dwarfism, and impaired skeletal acquisition. Mice lacking Tmem263 show no differences in body weight within the first two weeks of postnatal life. However, by P21 there is a dramatic growth deficit due to a disrupted GH/IGF-1 axis, which is critical for longitudinal bone growth. Tmem263-null mice have low circulating IGF-1 levels and pronounced reductions in bone mass and growth plate length. The low serum IGF-1 in Tmem263-null mice is associated with reduced hepatic GH receptor (GHR) expression and GH-induced JAK2/STAT5 signaling. A deficit in GH signaling dramatically alters GH-regulated genes and feminizes the liver transcriptome of Tmem263-null male mice, with their expression profile resembling a wild-type female, hypophysectomized male, and Stat5b-null male mice. Collectively, our data validates the causal role for Tmem263 in regulating postnatal growth and raises the possibility that rare mutations or variants of TMEM263 may potentially cause GH insensitivity and impair linear growth.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jean Garcia-Diaz
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Cell and Molecular Medicine graduate program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Muzna Saqib
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ryan C Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research and Development Service, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Moreno P, Gemez-Mata J, Alvarez-Torres D, Garcia-Rosado E, Bejar J, Alonso MC. Genomic characterization and transcription analysis of European sea bass (Dicentrarchus labrax) rtp3 genes. Mol Immunol 2023; 163:243-248. [PMID: 37879238 DOI: 10.1016/j.molimm.2023.10.009] [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: 07/20/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Fish RTP3, belonging to the receptor-transporting protein family, display several functions, including a putative antiviral role as virus-responsive gene. In this work, we have identified and characterized two different European sea bass rtp3 genes. In addition, an in vivo transcription analysis in response to LPS, poly I:C and betanodavirus infection (RGNNV genotype) has been performed. The sequence analysis showed that European sea bass displays two rtp3 genes, X1 and X2, composed of two exons and a single intron (1007-bp and 888-bp long, respectively), located within the ORF sequence. The full-length cDNA is 1969 bp for rtp3 X1, and 1491 bp for rtp3 X2. Several ATTTA motifs have been found in the intron sequence of both genes, whereas rtp3 X1 also contains this motif in both untranslated regions. The transcription analyses revealed significant level of rtp3 X2 mRNA in brain and head kidney after LPS and poly I:C inoculation; however, the induction elicited by RGNNV infection was much higher, suggesting an essential role for this protein in controlling NNV infections.
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Affiliation(s)
- Patricia Moreno
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Juan Gemez-Mata
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Daniel Alvarez-Torres
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), 29071 Málaga, Spain
| | - Esther Garcia-Rosado
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - Julia Bejar
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, 29071 Málaga, Spain
| | - M Carmen Alonso
- Universidad de Málaga, Instituto de Biotecnología y Desarrollo Azul (IBYDA), Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain.
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Tetrault E, Swenson J, Aaronson B, Marcho C, Albertson RC. The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments. Mol Ecol 2023; 32:3922-3941. [PMID: 37160741 PMCID: PMC10524807 DOI: 10.1111/mec.16975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Adaptive phenotypes are shaped by a combination of genetic and environmental forces, but how they interact remains poorly understood. Here, we utilize the cichlid oral jaw apparatus to better understand these gene-by-environment effects. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. We used two Lake Malawi species adapted to different foraging habitats along the pelagic-benthic ecomorphological axis. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when they were challenged with a pelagic versus benthic foraging mode. Expression data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible. This reduced dataset implicated notable candidate genes including the Hedgehog effector, KIAA0586 and the ETS transcription factor, etv4, which connects environmental stress and craniofacial morphogenesis. Taken together, these data provide novel insights into the epigenetic, genetic and cellular bases of species- and environment-specific bone shapes.
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Affiliation(s)
- Emily Tetrault
- Graduate Program in Molecular and Cell Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - John Swenson
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Ben Aaronson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - R. Craig Albertson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
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Moran MM, Ko FC, Mesner LD, Calabrese GM, Al-Barghouthi BM, Farber CR, Sumner DR. Intramembranous bone regeneration in diversity outbred mice is heritable. Bone 2022; 164:116524. [PMID: 36028119 PMCID: PMC9798271 DOI: 10.1016/j.bone.2022.116524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 12/31/2022]
Abstract
There are over one million cases of failed bone repair in the U.S. annually, resulting in substantial patient morbidity and societal costs. Multiple candidate genes affecting bone traits such as bone mineral density have been identified in human subjects and animal models using genome-wide association studies (GWAS). This approach for understanding the genetic factors affecting bone repair is impractical in human subjects but could be performed in a model organism if there is sufficient variability and heritability in the bone regeneration response. Diversity Outbred (DO) mice, which have significant genetic diversity and have been used to examine multiple intact bone traits, would be an excellent possibility. Thus, we sought to evaluate the phenotypic distribution of bone regeneration, sex effects and heritability of intramembranous bone regeneration on day 7 following femoral marrow ablation in 47 12-week old DO mice (23 males, 24 females). Compared to a previous study using 4 inbred mouse strains, we found similar levels of variability in the amount of regenerated bone (coefficient of variation of 86 % v. 88 %) with approximately the same degree of heritability (0.42 v. 0.49). There was a trend toward more bone regeneration in males than females. The amount of regenerated bone was either weakly or not correlated with bone mass at intact sites, suggesting that the genetic factors responsible for bone regeneration and intact bone phenotypes are at least partially independent. In conclusion, we demonstrate that DO mice exhibit variation and heritability of intramembranous bone regeneration that will be suitable for future GWAS.
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Affiliation(s)
- Meghan M Moran
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL, USA; Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA.
| | - Frank C Ko
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL, USA; Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Larry D Mesner
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Gina M Calabrese
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Basel M Al-Barghouthi
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA; Departments of Public Health Sciences and Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - D Rick Sumner
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL, USA; Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
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Liao S, He H, Zeng Y, Yang L, Liu Z, An Z, Zhang M. A nomogram for predicting metabolic steatohepatitis: The combination of NAMPT, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. Open Med (Wars) 2021; 16:773-785. [PMID: 34041361 PMCID: PMC8130015 DOI: 10.1515/med-2021-0286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/17/2021] [Accepted: 04/17/2021] [Indexed: 02/05/2023] Open
Abstract
Objective To identify differentially expressed and clinically significant mRNAs and construct a potential prediction model for metabolic steatohepatitis (MASH). Method We downloaded four microarray datasets, GSE89632, GSE24807, GSE63067, and GSE48452, from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis were performed to screen significant genes. Finally, we constructed a nomogram of six hub genes in predicting MASH and assessed it through receiver operating characteristic (ROC) curve, calibration plot, and decision curve analysis (DCA). In addition, qRT-PCR was used for relative quantitative detection of RNA in QSG-7011 cells to further verify the expression of the selected mRNA in fatty liver cells. Results Based on common DEGs and brown and yellow modules, seven hub genes were identified, which were NAMPT, PHLDA1, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. After logistic regression analysis, six hub genes were used to establish the nomogram, which were NAMPT, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. The area under the ROC of the nomogram was 0.897. The DCA showed that when the threshold probability of MASH was 0–0.8, the prediction model was valuable to GSE48452. In QSG-7011 fatty liver model cells, the relative expression levels of NAMPT, GADD45B, FOSL2, RTP3, RASD1 and RALGDS were lower than the control group. Conclusion We identified seven hub genes NAMPT, PHLDA1, RALGDS, GADD45B, FOSL2, RTP3, and RASD1. The nomogram showed good performance in the prediction of MASH and it had clinical utility in distinguishing MASH from simple steatosis.
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Affiliation(s)
- Shenling Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - He He
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuping Zeng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Lidan Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhi Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhenmei An
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
| | - Mei Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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Liu L, Wen Y, Ning Y, Li P, Cheng B, Cheng S, Zhang L, Ma M, Qi X, Liang C, Yang T, Chen X, Tan L, Shen H, Tian Q, Deng HW, Ma X, Zhang F, Zhu F. A trans-ethnic two-stage polygenetic scoring analysis detects genetic correlation between osteoporosis and schizophrenia. Clin Transl Med 2020; 9:21. [PMID: 32107650 PMCID: PMC7046891 DOI: 10.1186/s40169-020-00272-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUNDS To explore the genetic correlation between schizophrenia (SCZ) and osteoporosis (OP). DESIGN, SETTING, PARTICIPANTS, MEASUREMENTS We conducted a trans-ethnic two-stage genetic correlation analysis of OP and SCZ, totally invoking 2286 Caucasia subjects in discovery stage and 4124 Chinese subjects in replication stage. The bone mineral density (BMD) and bone area values of ulna & radius, hip and spine were measured using Hologic 4500W dual energy X-ray absorptiometry machine. SCZ was diagnosed according to DSM-IV criteria. For the genome-wide association study (GWAS) of Caucasian OP, Chinese OP and Chinese SCZ, SNP genotyping was performed using Affymetrix SNP 6.0 array. For the GWAS of Caucasian SCZ, SNP genotyping was conducted using the Affymetrix 5.0 array, Affymetrix 6.0 array and Illumina 550 K array. Polygenetic risk scoring (PRS) analysis was conducted by PRSice software. Also, Linkage disequilibrium score regression (LD Score regression) analysis was performed to evaluate the genetic correlation between OP and SCZ. Multi-trait analysis of GWAS (MTAG) was performed to detect novel candidate genes for osteoporosis and SCZ. RESULTS In the Caucasia discovery samples, significant genetic correlations were observed for ulna & radius BMD vs. SCZ (P value = 0.010), ulna & radius area vs. SCZ (P value = 0.031). In the Chinese replication samples, we observed significant correlation for ulna & radius area vs. SCZ (P value = 0.019). In addition, LD Score regression also identified significant genetic correlations between SCZ and bone phenotypes in Caucasian and Chinese sample respectively. MTAG analysis identified several novel candidate genes, such as CTNNA2 (MTAG P value = 2.24 × 10-6) for SCZ and FADS2 (MTAG P value = 2.66 × 10-7) for osteoporosis. CONCLUSIONS Our study results support the overlapped genetic basis for osteoporosis and SCZ, and provide novel clues for elucidating the biological mechanism of increased osteoporosis risk in SCZ patients.
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Affiliation(s)
- Li Liu
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Yan Wen
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Yujie Ning
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Ping Li
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Bolun Cheng
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Shiqiang Cheng
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Lu Zhang
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Mei Ma
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Xin Qi
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Chujun Liang
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China
| | - Tielin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Xiangding Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Lijun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of 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, USA
| | - 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, USA
| | - 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, USA
| | - Xiancang Ma
- Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Feng Zhang
- School of Public Health, Xi'an Jiaotong University Health Science Center, Yanta West Road 76, Xi'an, 710061, People's Republic of China.
| | - Feng Zhu
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, 710061, People's Republic of China.
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Hu W, He J, Qi L, Wang C, Yue H, Gu J, Zhang H, Wang Y, Zhang Z. Association of HIVEP3 Gene and Lnc RNA with Femoral Neck Bone Mineral Content and Hip Geometry by Genome-Wide Association Analysis in Chinese People. Int J Endocrinol 2020; 2020:6929073. [PMID: 33110425 PMCID: PMC7579678 DOI: 10.1155/2020/6929073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/27/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE GWAS has successfully located and analyzed the pathogenic genes of osteoporosis. Genetic studies have found that heritability of BMD is 50%-85% while the other half is caused by hip geometric parameters and tissue horizontal characteristics. This study was designed to study the GWAS of osteoporosis in Shanghai Han population. METHODS We collected 1224 unrelated healthy young men (20-40 years old), young women (20-40 years old), and postmenopausal women (over 50 years old) who lived in Shanghai. BMD and hip geometric parameters were measured by dual-energy X-ray absorptiometry. The genomic DNA of peripheral blood was extracted and analyzed by using Illumina Human Asian Screening Array-24 + v1.0 (ASA) gene chip. Statistical analysis was carried out to evaluate the relationship between these SNPs and BMD and hip geometric parameters. RESULTS A total of 1155 subjects were included. We found that one SNP rs35282355 located in the human immunodeficiency virus type 1 enhancer-binding protein 3 gene (HIVEP3) and another 25 SNPs located in LINC RNA were significantly correlated with bone mineral content (BMC) in the femoral neck (P= 2.30 × 10-9, P < 5 × 10-8). We also found that the correlation between SNP rs35282355 and cross-sectional area (CSA) of hip geometry was a significant marginal statistical difference (P = 5.95 × 10-8). CONCLUSIONS Through this study, we found that HIVEP3 gene and LINC RNA are potentially correlated with femoral neck BMC. These results provide important information for us to further understand the etiology and genetic pathogenesis of osteoporosis. In the future, we will expand the sample size to verify these loci and carry out molecular research.
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Affiliation(s)
- Weiwei Hu
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Jinwei He
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Luyue Qi
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Chun Wang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Hua Yue
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Jiemei Gu
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Hao Zhang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
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10
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Hsu YH, Estrada K, Evangelou E, Ackert-Bicknell C, Akesson K, Beck T, Brown SJ, Capellini T, Carbone L, Cauley J, Cheung CL, Cummings SR, Czerwinski S, Demissie S, Econs M, Evans D, Farber C, Gautvik K, Harris T, Kammerer C, Kemp J, Koller DL, Kung A, Lawlor D, Lee M, Lorentzon M, McGuigan F, Medina-Gomez C, Mitchell B, Newman A, Nielson C, Ohlsson C, Peacock M, Reppe S, Richards JB, Robbins J, Sigurdsson G, Spector TD, Stefansson K, Streeten E, Styrkarsdottir U, Tobias J, Trajanoska K, Uitterlinden A, Vandenput L, Wilson SG, Yerges-Armstrong L, Young M, Zillikens C, Rivadeneira F, Kiel DP, Karasik D. Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry. J Bone Miner Res 2019; 34:1284-1296. [PMID: 30888730 PMCID: PMC6650334 DOI: 10.1002/jbmr.3698] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 01/29/2019] [Accepted: 02/07/2019] [Indexed: 12/14/2022]
Abstract
Hip geometry is an important predictor of fracture. We performed a meta-analysis of GWAS studies in adults to identify genetic variants that are associated with proximal femur geometry phenotypes. We analyzed four phenotypes: (i) femoral neck length; (ii) neck-shaft angle; (iii) femoral neck width, and (iv) femoral neck section modulus, estimated from DXA scans using algorithms of hip structure analysis. In the Discovery stage, 10 cohort studies were included in the fixed-effect meta-analysis, with up to 18,719 men and women ages 16 to 93 years. Association analyses were performed with ∼2.5 million polymorphisms under an additive model adjusted for age, body mass index, and height. Replication analyses of meta-GWAS significant loci (at adjusted genomewide significance [GWS], threshold p ≤ 2.6 × 10-8 ) were performed in seven additional cohorts in silico. We looked up SNPs associated in our analysis, for association with height, bone mineral density (BMD), and fracture. In meta-analysis (combined Discovery and Replication stages), GWS associations were found at 5p15 (IRX1 and ADAMTS16); 5q35 near FGFR4; at 12p11 (in CCDC91); 11q13 (near LRP5 and PPP6R3 (rs7102273)). Several hip geometry signals overlapped with BMD, including LRP5 (chr. 11). Chr. 11 SNP rs7102273 was associated with any-type fracture (p = 7.5 × 10-5 ). We used bone transcriptome data and discovered several significant eQTLs, including rs7102273 and PPP6R3 expression (p = 0.0007), and rs6556301 (intergenic, chr.5 near FGFR4) and PDLIM7 expression (p = 0.005). In conclusion, we found associations between several genes and hip geometry measures that explained 12% to 22% of heritability at different sites. The results provide a defined set of genes related to biological pathways relevant to BMD and etiology of bone fragility. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Yi-Hsiang Hsu
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
| | - Karol Estrada
- Broad Institute, Cambridge, MA
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Cheryl Ackert-Bicknell
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester, Rochester, New York, USA
| | - Kristina Akesson
- Department of Clinical Sciences Malmö, Lund University, Sweden
- Department of Orthopedics, Skåne University Hospital, S-205 02 Malmö, Sweden
| | - Thomas Beck
- Beck Radiological Innovations, Baltimore, MD
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Terence Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA
| | - Laura Carbone
- Department of Medicine at the Medical College of Georgia at Augusta University, Augusta, GA
| | - Jane Cauley
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Ching-Lung Cheung
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA
| | | | - Serkalem Demissie
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Michael Econs
- Department of Medicine and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Daniel Evans
- California Pacific Medical Center Research Institute, San Francisco, CA
| | - Charles Farber
- Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Kaare Gautvik
- Lovisenberg Diakonale Hospital, Unger-Vetlesen Institute, and University of Oslo, Institute of Basic Medical Sciences, Oslo, Norway
| | - Tamara Harris
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, NIA, Bethesda, MD
| | - Candace Kammerer
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - John Kemp
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, UK
| | - Daniel L Koller
- Department of Medicine and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Annie Kung
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Debbie Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, UK
| | - Miryoung Lee
- University of Texas, School of Public Health at Bronwsville, TX
| | - Mattias Lorentzon
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Fiona McGuigan
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester, Rochester, New York, USA
- Department of Clinical Sciences Malmö, Lund University, Sweden
| | | | - Braxton Mitchell
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, and Geriatric Research and Education Clinical Center - Veterans Administration Medical Center, Baltimore, MD
| | - Anne Newman
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Munro Peacock
- Department of Medicine and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Sjur Reppe
- Lovisenberg Diakonale Hospital, Unger-Vetlesen Institute, and University of Oslo, Institute of Basic Medical Sciences, Oslo, Norway
- Oslo University Hospital, Department of Medical Biochemistry, Oslo, Norway
| | - J Brent Richards
- Department of Human Genetics, McGill University, and Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - John Robbins
- Department of Medicine, University California at Davis, Sacramento, CA
| | | | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK
| | | | - Elizabeth Streeten
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, and Geriatric Research and Education Clinical Center - Veterans Administration Medical Center, Baltimore, MD
| | | | | | | | - André Uitterlinden
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Liesbeth Vandenput
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK
- School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
| | | | - Mariel Young
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA
| | - Carola Zillikens
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Douglas P Kiel
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
| | - David Karasik
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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11
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Al-Barghouthi BM, Farber CR. Dissecting the Genetics of Osteoporosis using Systems Approaches. Trends Genet 2018; 35:55-67. [PMID: 30470485 DOI: 10.1016/j.tig.2018.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/01/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
Osteoporosis is a condition characterized by low bone mineral density (BMD) and an increased risk of fracture. Traits contributing to osteoporotic fracture are highly heritable, indicating that a comprehensive understanding of bone requires a thorough understanding of the genetic basis of bone traits. Towards this goal, genome-wide association studies (GWASs) have identified over 500 loci associated with bone traits. However, few of the responsible genes have been identified, and little is known of how these genes work together to influence systems-level bone function. In this review, we describe how systems genetics approaches can be used to fill these knowledge gaps.
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Affiliation(s)
- Basel M Al-Barghouthi
- Center for Public Health Genomics, Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Charles R Farber
- Center for Public Health Genomics, Departments of Public Health Sciences and Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
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12
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Huang Z, Cheng C, Wang J, Liu X, Wei H, Han Y, Yang S, Wang X. Icariin regulates the osteoblast differentiation and cell proliferation of MC3T3-E1 cells through microRNA-153 by targeting Runt-related transcription factor 2. Exp Ther Med 2018; 15:5159-5166. [PMID: 29904399 PMCID: PMC5996701 DOI: 10.3892/etm.2018.6127] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/03/2018] [Indexed: 12/02/2022] Open
Abstract
Osteoporosis has become one of the most serious public health problems. Icariin, miR-153 and Runt-related transcription factor 2 (Runx2) have been demonstrated to regulate cell proliferation and differentiation in multiple cells. The aim of the present experiments was to investigate the potential mechanism underlying osteoblast differentiation and cell proliferation of MC3T3-E1 cells treated with icariin. Cell Counting kit-8, alkaline phosphatase (ALP) activity and alizarin red S assays, as well as reverse transcription-quantitative polymerase chain reaction and western blot analysis, were performed to examine whether icariin promoted osteoblast differentiation and cell proliferation in MC3T3-E1 cells. Subsequently, miR-153 target and pathway prediction, and functional analysis were assessed. The results demonstrated that icariin promoted proliferation, mineral content and ALP activity in MC3T3-E1 cells. In addition, miR-153 and Runx2 expression levels were increased following treatment with icariin. Luciferase assay revealed that miR-153 significantly upregulate the luciferase activity of wild-type (Wt) Runx2 3′-untranslated region. Furthermore, the group treated with a combination of miR-153 mimics and icariin exhibited a significantly higher expression of Runx2 in comparison with the miR-153 mimic-treated alone group. Finally, icariin reversed the potential effect of miR-153 inhibitor in MC3T3-E1 cells. In conclusion, icariin exerted a strong osteoblast differentiation effect in MC3T3-E1 cells through the miR-153/Runx2 pathway. The current study provided evidence suggesting that icariin should be considered as an effective candidate for the management of osteoporosis.
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Affiliation(s)
- Zengfa Huang
- Department of Radiology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
| | - Cheng Cheng
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jing Wang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xianzhe Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Hui Wei
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yu Han
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Shuhua Yang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiang Wang
- Department of Radiology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430014, P.R. China
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13
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Zeng Y, Zhang L, Zhu W, He H, Sheng H, Tian Q, Deng FY, Zhang LS, Hu HG, Deng HW. Network based subcellular proteomics in monocyte membrane revealed novel candidate genes involved in osteoporosis. Osteoporos Int 2017; 28:3033-3042. [PMID: 28741036 PMCID: PMC5812280 DOI: 10.1007/s00198-017-4146-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/04/2017] [Indexed: 01/18/2023]
Abstract
UNLABELLED 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.
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Affiliation(s)
- Y 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
| | - L Zhang
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - W 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, Hunan, 410081, China
| | - H He
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - H Sheng
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Q Tian
- Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - F-Y 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, Jiangsu, 205123, China
| | - L-S Zhang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - H-G Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - H-W 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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Liu P, Wang L, Ye BQ, Huang S, Wong SM, Yue GH. Characterization of a novel disease resistance gene rtp3 and its association with VNN disease resistance in Asian seabass. FISH & SHELLFISH IMMUNOLOGY 2017; 61:61-67. [PMID: 27989862 DOI: 10.1016/j.fsi.2016.12.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 06/06/2023]
Abstract
Asian seabass, an important food fish in Southeast Asia, has suffered from nervous necrosis virus (NNV) infection, resulting in massive mortality of Asian seabass larvae and enormous economic losses. Identification and characterization of disease resistance genes is important. Previous transcriptome analysis of Asians seabass epithelial cells after NNV infection revealed a highly inducible gene, receptor-transporting protein 3 (rtp3), indicating it could play an important role in Asian seabass - NNV interaction. To characterize this gene, we determined its expression pattern and subcellular localization. The rtp3 was highly induced in most examined tissues and organs of Asian seabass after NNV infection, and protein Rtp3 was localized in cytoplasm. Further association study in multiple families revealed that a microsatellite marker, (GT)ntt(GT)n, in the 3' UTR of rtp3 was significantly associated with VNN disease resistance in Asian seabass. Our results imply that rtp3 may be a novel disease resistance gene in Asian seabass. This data could improve our understanding of molecular interaction between Asian seabass and NNV, and has the potential to be applied in marker-assisted selection for disease resistance breeding in Asian seabass.
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Affiliation(s)
- Peng Liu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543 Singapore; Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore
| | - Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore
| | - Bao Qing Ye
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore
| | - Shuqing Huang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543 Singapore; Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore; National University of Singapore Suzhou Research Institute, Suzhou, Jiangsu, 215123 China.
| | - Gen Hua Yue
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543 Singapore; Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604 Singapore; School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, 637551 Singapore.
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15
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Wu C, Wen Y, Guo X, Yang T, Shen H, Chen X, Tian Q, Tan L, Deng HW, Zhang F. Genetic association, mRNA and protein expression analysis identify ATG4C as a susceptibility gene for Kashin-Beck disease. Osteoarthritis Cartilage 2017; 25:281-286. [PMID: 27742532 DOI: 10.1016/j.joca.2016.09.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 08/06/2016] [Accepted: 09/24/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Recent study observed defective autophagy in chondrocytes with Kashin-Beck Disease (KBD). To clarify the potential role of autophagy-related ATG4C gene in the development of KBD, we conducted an integrative analysis of genetic association, messenger ribonucleic acid (mRNA) and protein expression of ATG4C in KBD patients. METHODS 1026 subjects (559 KBD patients and 467 healthy cases) were enrolled in discovery association study. Four single nucleotide polymorphisms (SNPs) of ATG4C gene (rs11208030, rs4409690, rs12097658 and rs6587988) were genotyped by Sequenom MassARRAY platform. Association analysis was conducted by PLINK software. The significant SNPs of ATG4C were replicated using an independent sample of 899 subjects (including 90 KBD patients and 809 healthy controls). Ungenotyped SNPs in ATG4C gene were imputed by IMPUTE 2.0. Knee cartilage specimens were collected from five KBD patients and five healthy subjects. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot were performed to compare the mRNA and protein expression levels of ATG4C between KBD cartilage and control cartilage. RESULTS We observed significant association between KBD and rs11208030 (P value = 0.003), rs4409690 (P value = 0.004), rs12097658 (P value = 0.003) and rs6587988 (P value = 0.003) in both discovery and replication samples. The mRNA expression level of ATG4C (ratio = 0.168, P value = 0.007) in KBD chondrocytes was significantly lower than that in normal chondrocytes. Western blot (P value < 0.001) further confirmed the reduced expression of ATG4C protein in both KBD cartilage and chondrocytes. CONCLUSION Our results strongly suggest that ATG4C was a novel autophagy-related susceptibility gene of KBD.
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Affiliation(s)
- C Wu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Y Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - X Guo
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - T Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - H Shen
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - X Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, PR China
| | - Q Tian
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - L Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, PR China
| | - H-W Deng
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - F Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
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16
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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: 1.8] [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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17
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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: 0.3] [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
| | - 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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18
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Novel candidate genes putatively involved in stress fracture predisposition detected by whole-exome sequencing. Genet Res (Camb) 2015; 96:e004. [PMID: 25023003 DOI: 10.1017/s001667231400007x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
While genetic factors in all likelihood contribute to stress fracture (SF) pathogenesis, a few studies focusing on candidate genes have previously been reported. The objective of this study is to gain better understanding on the genetic basis of SF in a gene-naive manner. Exome sequence capture followed by massive parallel sequencing of two pooled DNA samples from Israeli combat soldiers was employed: cases with high grade SF and ethnically matched healthy controls. The resulting sequence variants were individually verified using the Sequenom™ platform and the contribution of the genetic alterations was validated in a second cohort of cases and controls. In the discovery set that included DNA pool of cases (n = 34) and controls (n = 60), a total of 1174 variants with >600 reads/variant/DNA pool were identified, and 146 (in 127 genes) of these exhibited statistically significant (P < 0·05) different rates between SF cases and controls after multiple comparisons correction. Subsequent validation of these 146 sequence variants individually in a total of 136 SF cases and 127 controls using the Sequenom™ platform validated 20/146 variants. Of these, three missense mutations (rs7426114, rs4073918, rs3752135 in the NEB, SLC6A18 and SIGLEC12 genes, respectively) and three synonymous mutations (rs2071856, rs2515941, rs716745 in the ELFN2, GRK4, LRRC55 genes) displayed significant different rates in SF cases compared with controls. Exome sequencing seemingly unravelled novel candidate genes as involved in SF pathogenesis and predisposition.
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Galea GL, Hannuna S, Meakin LB, Delisser PJ, Lanyon LE, Price JS. Quantification of Alterations in Cortical Bone Geometry Using Site Specificity Software in Mouse models of Aging and the Responses to Ovariectomy and Altered Loading. Front Endocrinol (Lausanne) 2015; 6:52. [PMID: 25954246 PMCID: PMC4407614 DOI: 10.3389/fendo.2015.00052] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/03/2015] [Indexed: 11/13/2022] Open
Abstract
Investigations into the effect of (re)modeling stimuli on cortical bone in rodents normally rely on analysis of changes in bone mass and architecture at a narrow cross-sectional site. However, it is well established that the effects of axial loading produce site-specific changes throughout bones' structure. Non-mechanical influences (e.g., hormones) can be additional to or oppose locally controlled adaptive responses and may have more generalized effects. Tools currently available to study site-specific cortical bone adaptation are limited. Here, we applied novel site specificity software to measure bone mass and architecture at each 1% site along the length of the mouse tibia from standard micro-computed tomography (μCT) images. Resulting measures are directly comparable to those obtained through μCT analysis (R (2) > 0.96). Site Specificity analysis was used to compare a number of parameters in tibiae from young adult (19-week-old) versus aged (19-month-old) mice; ovariectomized and entire mice; limbs subjected to short periods of axial loading or disuse induced by sciatic neurectomy. Age was associated with uniformly reduced cortical thickness and site-specific decreases in cortical area most apparent in the proximal tibia. Mechanical loading site-specifically increased cortical area and thickness in the proximal tibia. Disuse uniformly decreased cortical thickness and decreased cortical area in the proximal tibia. Ovariectomy uniformly reduced cortical area without altering cortical thickness. Differences in polar moment of inertia between experimental groups were only observed in the proximal tibia. Aging and ovariectomy also altered eccentricity in the distal tibia. In summary, site specificity analysis provides a valuable tool for measuring changes in cortical bone mass and architecture along the entire length of a bone. Changes in the (re)modeling response determined at a single site may not reflect the response at different locations within the same bone.
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Affiliation(s)
- Gabriel L. Galea
- School of Veterinary Sciences, University of Bristol, Bristol, UK
- *Correspondence: Gabriel L. Galea, School of Veterinary Sciences, University of Bristol, Southwell Street, Bristol BS2 8EJ, UK
| | - Sion Hannuna
- Faculty of Engineering, University of Bristol, Bristol, UK
| | - Lee B. Meakin
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | | | - Lance E. Lanyon
- School of Veterinary Sciences, University of Bristol, Bristol, UK
| | - Joanna S. Price
- School of Veterinary Sciences, University of Bristol, Bristol, UK
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20
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Paria N, Copley LA, Herring JA, Kim HKW, Richards BS, Sucato DJ, Rios JJ, Wise CA. The impact of large-scale genomic methods in orthopaedic disorders: insights from genome-wide association studies. J Bone Joint Surg Am 2014; 96:e38. [PMID: 24599210 DOI: 10.2106/jbjs.m.00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Nandina Paria
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Lawson A Copley
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - John A Herring
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Harry K W Kim
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - B Stephens Richards
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Daniel J Sucato
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Jonathan J Rios
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., J.J.R., and C.A.W.) and Department of Orthopaedics (L.A.C., J.A.H., B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-
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Garg G, Kumar J, McGuigan FE, Ridderstråle M, Gerdhem P, Luthman H, Åkesson K. Variation in the MC4R gene is associated with bone phenotypes in elderly Swedish women. PLoS One 2014; 9:e88565. [PMID: 24516669 PMCID: PMC3916440 DOI: 10.1371/journal.pone.0088565] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/30/2013] [Indexed: 01/01/2023] Open
Abstract
Osteoporosis is characterized by reduced bone mineral density (BMD) and increased fracture risk. Fat mass is a determinant of bone strength and both phenotypes have a strong genetic component. In this study, we examined the association between obesity associated polymorphisms (SNPs) with body composition, BMD, Ultrasound (QUS), fracture and biomarkers (Homocysteine (Hcy), folate, Vitamin D and Vitamin B12) for obesity and osteoporosis. Five common variants: rs17782313 and rs1770633 (melanocortin 4 receptor (MC4R); rs7566605 (insulin induced gene 2 (INSIG2); rs9939609 and rs1121980 (fat mass and obesity associated (FTO) were genotyped in 2 cohorts of Swedish women: PEAK-25 (age 25, n = 1061) and OPRA (age 75, n = 1044). Body mass index (BMI), total body fat and lean mass were strongly positively correlated with QUS and BMD in both cohorts (r2 = 0.2–0.6). MC4R rs17782313 was associated with QUS in the OPRA cohort and individuals with the minor C-allele had higher values compared to T-allele homozygotes (TT vs. CT vs. CC: BUA: 100 vs. 103 vs. 103; p = 0.002); (SOS: 1521 vs. 1526 vs. 1524; p = 0.008); (Stiffness index: 69 vs. 73 vs. 74; p = 0.0006) after adjustment for confounders. They also had low folate (18 vs. 17 vs. 16; p = 0.03) and vitamin D (93 vs. 91 vs. 90; p = 0.03) and high Hcy levels (13.7 vs 14.4 vs. 14.5; p = 0.06). Fracture incidence was lower among women with the C-allele, (52% vs. 58%; p = 0.067). Variation in MC4R was not associated with BMD or body composition in either OPRA or PEAK-25. SNPs close to FTO and INSIG2 were not associated with any bone phenotypes in either cohort and FTO SNPs were only associated with body composition in PEAK-25 (p≤0.001). Our results suggest that genetic variation close to MC4R is associated with quantitative ultrasound and risk of fracture.
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Affiliation(s)
- Gaurav Garg
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences, Lund University and Department of Orthopaedics, Skåne University Hospital, Malmö, Sweden
| | - Jitender Kumar
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fiona E. McGuigan
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences, Lund University and Department of Orthopaedics, Skåne University Hospital, Malmö, Sweden
| | - Martin Ridderstråle
- Clinical Obesity Research, Department of Endocrinology, Skåne University Hospital, Malmö, Sweden
| | - Paul Gerdhem
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Department of Orthopaedics, Karolinska University Hospital, Stockholm, Sweden
| | - Holger Luthman
- Medical Genetics Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Kristina Åkesson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences, Lund University and Department of Orthopaedics, Skåne University Hospital, Malmö, Sweden
- * E-mail:
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22
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Ran S, Pei YF, Liu YJ, Zhang L, Han YY, Hai R, Tian Q, Lin Y, Yang TL, Guo YF, Shen H, Thethi IS, Zhu XZ, Deng HW. Bivariate genome-wide association analyses identified genes with pleiotropic effects for femoral neck bone geometry and age at menarche. PLoS One 2013; 8:e60362. [PMID: 23593202 PMCID: PMC3617200 DOI: 10.1371/journal.pone.0060362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 02/26/2013] [Indexed: 02/05/2023] Open
Abstract
Femoral neck geometric parameters (FNGPs), which include cortical thickness (CT), periosteal diameter (W), buckling ratio (BR), cross-sectional area (CSA), and section modulus (Z), contribute to bone strength and may predict hip fracture risk. Age at menarche (AAM) is an important risk factor for osteoporosis and bone fractures in women. Some FNGPs are genetically correlated with AAM. In this study, we performed a bivariate genome-wide association study (GWAS) to identify new candidate genes responsible for both FNGPs and AAM. In the discovery stage, we tested 760,794 SNPs in 1,728 unrelated Caucasian subject, followed by replication analyses in independent samples of US Caucasians (with 501 subjects) and Chinese (with 826 subjects). We found six SNPs that were associated with FNGPs and AAM. These SNPs are located in three genes (i.e. NRCAM, IDS and LOC148145), suggesting these three genes may co-regulate FNGPs and AAM. Our findings may help improve the understanding of genetic architecture and pathophysiological mechanisms underlying both osteoporosis and AAM.
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Affiliation(s)
- Shu Ran
- Center of System Biomedical Sciences, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yu-Fang Pei
- Center of System Biomedical Sciences, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yong-Jun Liu
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Lei Zhang
- Center of System Biomedical Sciences, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Ying-Ying Han
- Center of System Biomedical Sciences, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Rong Hai
- Inner Mongolia People’s Hospital, Hohhot, P. R. China
| | - Qing Tian
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Yong Lin
- Center of System Biomedical Sciences, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Tie-Lin Yang
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shanxi, P. R. China
| | - Yan-Fang Guo
- School of Basic Medical Science, Institute of Bioinformatics, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Hui Shen
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Inderpal S. Thethi
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Xue-Zhen Zhu
- Center of System Biomedical Sciences, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Hong-Wen Deng
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
- Center of System Biomedical Sciences, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, P. R. China
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23
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Osborne DL, Weaver CM, McCabe LD, McCabe GP, Novotny R, Van Loan MD, Going S, Matkovic V, Boushey CJ, Savaiano DA. Body size and pubertal development explain ethnic differences in structural geometry at the femur in Asian, Hispanic, and white early adolescent girls living in the U.S. Bone 2012; 51:888-95. [PMID: 22944607 PMCID: PMC3491564 DOI: 10.1016/j.bone.2012.08.125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/16/2012] [Accepted: 08/18/2012] [Indexed: 12/21/2022]
Abstract
UNLABELLED Variation in structural geometry is present in adulthood, but when this variation arises and what influences this variation prior to adulthood remains poorly understood. Ethnicity is commonly the focus of research of skeletal integrity and appears to explain some of the variation in quantification of bone tissue. However, why ethnicity explains variation in skeletal integrity is unclear. METHODS Here we examine predictors of bone cross sectional area (CSA) and section modulus (Z), measured using dual-energy X-ray absorptiometry (DXA) and the Advanced Hip Analysis (AHA) program at the narrow neck of the femur in adolescent (9-14 years) girls (n=479) living in the United States who were classified as Asian, Hispanic, or white if the subject was 75% of a given group based on parental reported ethnicity. Protocols for measuring height and weight follow standardized procedures. Total body lean mass (LM) and total body fat mass (FM) were quantified in kilograms using DXA. Total dietary and total dairy calcium intakes from the previous month were estimated by the use of an electronic semi-quantitative food frequency questionnaire (eFFQ). Physical activity was estimated for the previous year by a validated self-administered modifiable activity questionnaire for adolescents with energy expenditure calculated from the metabolic equivalent (MET) values from the Compendium of Physical Activities. Multiple regression models were developed to predict CSA and Z. RESULTS Age, time from menarche, total body lean mass (LM), total body fat mass (FM), height, total calcium, and total dairy calcium all shared a significant (p<0.05), positive relationship with CSA. Age, time from menarche, LM, FM, and height shared significant (p<0.05), positive relationships with Z. For both CSA and Z, LM was the most important covariate. Physical activity was not a significant predictor of geometry at the femoral neck (p≥0.339), even after removing LM as a covariate. After adjusting for covariates, ethnicity was not a significant predictor in regression models for CSA and Z. CONCLUSION Variability in bone geometry at the narrow neck of the femur is best explained by body size and pubertal maturation. After controlling for these covariates there were no differences in bone geometry between ethnic groups.
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Affiliation(s)
- D L Osborne
- Dept. of Anthropology, University of Nebraska, Lincoln, NE 68588, USA.
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Polymorphisms in the inflammatory genes CIITA, CLEC16A and IFNG influence BMD, bone loss and fracture in elderly women. PLoS One 2012; 7:e47964. [PMID: 23133532 PMCID: PMC3485004 DOI: 10.1371/journal.pone.0047964] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 09/25/2012] [Indexed: 12/26/2022] Open
Abstract
Osteoclast activity and the fine balance between bone formation and resorption is affected by inflammatory factors such as cytokines and T lymphocyte activity, mediated by major histocompatibility complex (MHC) molecules, in turn regulated by the MHC class II transactivator (MHC2TA). We investigated the effect of functional polymorphisms in the MHC2TA gene (CIITA), and two additional genes; C-type lectin domain 16A (CLEC16A), in linkage disequilibrium with CIITA and Interferon-γ (IFNG), an inducer of CIITA; on bone density, bone resorption markers, bone loss and fracture risk in 75 year-old women followed for up to 10 years (OPRA n = 1003) and in young adult women (PEAK-25 n = 999). CIITA was associated with BMD at age 75 (lumbar spine p = 0.011; femoral neck (FN) p = 0.049) and age 80 (total body p = 0.015; total hip p = 0.042; FN p = 0.028). Carriers of the CIITA rs3087456(G) allele had 1.8–3.4% higher BMD and displayed increased rate of bone loss between age 75 and 80 (FN p = 0.013; total hip p = 0.030; total body p = 3.8E−5). Despite increasing bone loss, the rs3087456(G) allele was protective against incident fracture overall (p = 0.002), osteoporotic fracture and hip fracture. Carriers of CLEC16A and IFNG variant alleles had lower BMD (p<0.05) and ultrasound parameters and a lower risk of incident fracture (CLEC16A, p = 0.011). In 25-year old women, none of the genes were associated with BMD. In conclusion, variation in inflammatory genes CIITA, CLEC-16A and INFG appear to contribute to bone phenotypes in elderly women and suggest a role for low-grade inflammation and MHC class II expression for osteoporosis pathogenesis.
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Hsu YH, Kiel DP. Clinical review: Genome-wide association studies of skeletal phenotypes: what we have learned and where we are headed. J Clin Endocrinol Metab 2012; 97:E1958-77. [PMID: 22965941 PMCID: PMC3674343 DOI: 10.1210/jc.2012-1890] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/09/2012] [Indexed: 02/07/2023]
Abstract
CONTEXT The primary goals of genome-wide association studies (GWAS) are to discover new molecular and biological pathways involved in the regulation of bone metabolism that can be leveraged for drug development. In addition, the identified genetic determinants may be used to enhance current risk factor profiles. EVIDENCE ACQUISITION There have been more than 40 published GWAS on skeletal phenotypes, predominantly focused on dual-energy x-ray absorptiometry-derived bone mineral density (BMD) of the hip and spine. EVIDENCE SYNTHESIS Sixty-six BMD loci have been replicated across all the published GWAS, confirming the highly polygenic nature of BMD variation. Only seven of the 66 previously reported genes (LRP5, SOST, ESR1, TNFRSF11B, TNFRSF11A, TNFSF11, PTH) from candidate gene association studies have been confirmed by GWAS. Among 59 novel BMD GWAS loci that have not been reported by previous candidate gene association studies, some have been shown to be involved in key biological pathways involving the skeleton, particularly Wnt signaling (AXIN1, LRP5, CTNNB1, DKK1, FOXC2, HOXC6, LRP4, MEF2C, PTHLH, RSPO3, SFRP4, TGFBR3, WLS, WNT3, WNT4, WNT5B, WNT16), bone development: ossification (CLCN7, CSF1, MEF2C, MEPE, PKDCC, PTHLH, RUNX2, SOX6, SOX9, SPP1, SP7), mesenchymal-stem-cell differentiation (FAM3C, MEF2C, RUNX2, SOX4, SOX9, SP7), osteoclast differentiation (JAG1, RUNX2), and TGF-signaling (FOXL1, SPTBN1, TGFBR3). There are still 30 BMD GWAS loci without prior molecular or biological evidence of their involvement in skeletal phenotypes. Other skeletal phenotypes that either have been or are being studied include hip geometry, bone ultrasound, quantitative computed tomography, high-resolution peripheral quantitative computed tomography, biochemical markers, and fractures such as vertebral, nonvertebral, hip, and forearm. CONCLUSIONS Although several challenges lie ahead as GWAS moves into the next generation, there are prospects of new discoveries in skeletal biology. This review integrates findings from previous GWAS and provides a roadmap for future directions building on current GWAS successes.
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Affiliation(s)
- Yi-Hsiang Hsu
- Hebrew SeniorLife Institute for Aging Research, 1200 Centre Street, Boston, Massachusetts 02131, USA
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Mendoza N, Quereda F, Presa J, Salamanca A, Sánchez-Borrego R, Vázquez F, Astorquiza TM. Estrogen-related genes and postmenopausal osteoporosis risk. Climacteric 2012; 15:587-93. [DOI: 10.3109/13697137.2012.656160] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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27
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Piters E, de Freitas F, Nielsen TL, Andersen M, Brixen K, Van Hul W. Association study of polymorphisms in the SOST gene region and parameters of bone strength and body composition in both young and elderly men: data from the Odense Androgen Study. Calcif Tissue Int 2012; 90:30-9. [PMID: 22076526 DOI: 10.1007/s00223-011-9546-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 09/17/2011] [Indexed: 10/15/2022]
Abstract
By means of different genetic association studies the SOST gene, encoding sclerostin, has repeatedly been suggested to regulate bone mineral density (BMD) and osteoporosis susceptibility. This study aimed at a further understanding of the importance of two previously studied single-nucleotide polymorphisms in the SOST gene, rs10534024 (SRP3) and rs9902563 (SRP9), in the Odense Androgen Study (OAS) cohort. This cohort includes a total of 1,383 Danish men from two different age groups, 20-29 years (n = 783) and 60-74 years (n = 600), and is well characterized. Subjects were phenotyped for BMD at several sites and additionally for body composition and hip geometric parameters. In a combined analysis of the young and the elderly OAS, no associations were found for SRP3 either with BMD or with hip geometry. Instead, we found that this polymorphism had a relatively large effect on weight (-1.149 kg) and body mass index (-0.389 kg/m(2)) (P = 0.021 and 0.006 under a codominant model). For SRP9, a significant association was found for femoral neck BMD (+0.020 g/cm(2), P = 0.020) and a trend toward significance for hip geometry (buckling ratio of the narrow neck) but only when considering a recessive effect of the minor allele (C). No age-specific effects were found for either of the two SNPs. In summary, we are the first to find interesting associations between SRP3 and body composition. For SRP9, we replicated a site-specific association with femoral neck BMD. In addition, we report a novel association for this polymorphism with hip geometry.
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Affiliation(s)
- Elke Piters
- Department of Medical Genetics, University and University Hospital of Antwerp, Prins Boudewijnlaan 43B, 2650 Edegem, Belgium
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Sun L, Tan LJ, Lei SF, Chen XD, Li X, Pan R, Yin F, Liu QW, Yan XF, Papasian CJ, Deng HW. Bivariate genome-wide association analyses of femoral neck bone geometry and appendicular lean mass. PLoS One 2011; 6:e27325. [PMID: 22087292 PMCID: PMC3210160 DOI: 10.1371/journal.pone.0027325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Accepted: 10/13/2011] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Femoral neck geometric parameters (FNGPs), such as periosteal diameter (W), cross-sectional area (CSA), cortical thickness (CT), buckling ratio (BR), and section modulus (Z), are highly genetically correlated with body lean mass. However, the specific SNPs/genes shared by these phenotypes are largely unknown. METHODS To identify the specific SNPs/genes shared between FNGPs and appendicular lean mass (ALM), we performed an initial bivariate genome-wide association study (GWAS) by scanning ∼690,000 SNPs in 1,627 unrelated Han Chinese adults (802 males and 825 females) and a follow-up replicate study in 2,286 unrelated US Caucasians. RESULTS We identified 13 interesting SNPs that may be important for both FNGPs and ALM. Two SNPs, rs681900 located in the HK2 (hexokinase 2) gene and rs11859916 in the UMOD (uromodulin) gene, were bivariately associated with FNGPs and ALM (p = 7.58×10(-6) for ALM-BR and p = 2.93×10(-6) for ALM-W, respectively). The associations were then replicated in Caucasians, with corresponding p values of 0.024 for rs681900 and 0.047 for rs11859916. Meta-analyses yielded combined p values of 3.05×10(-6) and 2.31×10(-6) for rs681900 and rs11859916, respectively. Our findings are consistent with previous biological studies that implicated HK2 and UMOD in both FNGPs and ALM. Our study also identified a group of 11 contiguous SNPs, which spanned a region of ∼130 kb, were bivariately associated with FNGPs and ALM, with p values ranging from 3.06×10(-7) to 4.60×10(-6) for ALM-BR. The region contained two neighboring miRNA coding genes, MIR873 (MicroRNA873) and MIR876 (MicroRNA876). CONCLUSION Our study implicated HK2, UMOD, MIR873 and MIR876, as pleiotropic genes underlying variation of both FNGPs and ALM, thus suggesting their important functional roles in co-regulating both FNGPs and ALM.
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Affiliation(s)
- Lu Sun
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Li-Jun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Shu-Feng Lei
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiang-Ding Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xi Li
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Rong Pan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Fang Yin
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Quan-Wei Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiao-Feng Yan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Christopher J. Papasian
- Departments of Orthopedic Surgery and Basic Medical Sciences, School of Medicine, University of Missouri - Kansas City, Kansas City, Missouri, United States of America
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
- Departments of Orthopedic Surgery and Basic Medical Sciences, School of Medicine, University of Missouri - Kansas City, Kansas City, Missouri, United States of America
- Center of Systematic Biomedical Research, Shanghai University of Science and Technology, Shanghai, China
- College of Life Sciences and Technology, Beijing Jiao Tong University, Beijing, China
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Chen CCM, Schwender H, Keith J, Nunkesser R, Mengersen K, Macrossan P. Methods for identifying SNP interactions: a review on variations of Logic Regression, Random Forest and Bayesian logistic regression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:1580-1591. [PMID: 21383421 DOI: 10.1109/tcbb.2011.46] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Due to advancements in computational ability, enhanced technology and a reduction in the price of genotyping, more data are being generated for understanding genetic associations with diseases and disorders. However, with the availability of large data sets comes the inherent challenges of new methods of statistical analysis and modeling. Considering a complex phenotype may be the effect of a combination of multiple loci, various statistical methods have been developed for identifying genetic epistasis effects. Among these methods, logic regression (LR) is an intriguing approach incorporating tree-like structures. Various methods have built on the original LR to improve different aspects of the model. In this study, we review four variations of LR, namely Logic Feature Selection, Monte Carlo Logic Regression, Genetic Programming for Association Studies, and Modified Logic Regression-Gene Expression Programming, and investigate the performance of each method using simulated and real genotype data. We contrast these with another tree-like approach, namely Random Forests, and a Bayesian logistic regression with stochastic search variable selection.
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Affiliation(s)
- Carla Chia-Ming Chen
- Discipline of Mathematical Sciences, Queensland University of Technology, Gardens Point, Brisbane, Queensland 4001, Australia.
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Insights into the genetics of osteoporosis from recent genome-wide association studies. Expert Rev Mol Med 2011; 13:e28. [PMID: 21867596 DOI: 10.1017/s1462399411001980] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Osteoporosis, which is characterised by reduced bone mineral density (BMD) and an increased risk of fragility fractures, is the result of a complex interaction between environmental factors and genetic variants that confer susceptibility. Heritability studies have shown that BMD and other osteoporosis-related traits such as ultrasound properties of bone, skeletal geometry and bone turnover have significant inheritable components. Although previous linkage and candidate gene studies have provided few replicated loci for osteoporosis, genome-wide association approaches have produced clear and reproducible findings. To date, 20 genome-wide association studies (GWASs) for osteoporosis and related traits have been conducted, identifying dozens of genes. Further meta-analyses of GWAS data and deep resequencing of rare variants will uncover more novel susceptibility loci and ultimately provide possible therapeutic targets for fracture prevention.
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Abstract
Osteoporosis is an important and complex disorder that is highly prevalent worldwide. This disease poses a major challenge to modern medicine and its treatment is associated with high costs. Numerous studies have endeavored to decipher the pathogenesis of this disease. The clinical assessment of patients often incorporates information about a family history of osteoporotic fractures. Indeed, the observation of an increased risk of fracture in an individual with a positive parental history of hip fracture provides strong evidence for the heritability of osteoporosis. The onset and progression of osteoporosis are generally controlled by multiple genetic and environmental factors, as well as interactions between them, with rare cases determined by a single gene. In an attempt to identify the genetic markers of complex diseases such as osteoporosis, there has been a move away from traditional linkage mapping studies and candidate gene association studies to higher-density genome-wide association studies. The advent of high-throughput technology enables genotyping of millions of DNA markers in the human genome, and consequently the identification and characterization of causal variants and loci that underlie osteoporosis. This Review presents an overview of the major findings since 2007 and clinical applications of these genome-wide linkage and association studies.
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Chen Y, Xiong DH, Guo YF, Pan F, Zhou Q, Zhang F, Deng HW. Pathway-based genome-wide association analysis identified the importance of EphrinA-EphR pathway for femoral neck bone geometry. Bone 2010; 46:129-36. [PMID: 19786129 PMCID: PMC2818219 DOI: 10.1016/j.bone.2009.09.025] [Citation(s) in RCA: 16] [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: 04/14/2009] [Revised: 09/09/2009] [Accepted: 09/22/2009] [Indexed: 02/07/2023]
Abstract
Femoral neck (FN) bone geometry is an important predictor of bone strength with high heritability. Previous studies have revealed certain candidate genes for FN bone geometry. However, the majority of the underlying genetic factors remain to be discovered. In this study, pathway-based genome-wide association analysis was performed to explore the joint effects of genes within biological pathways on FN bone geometry variations in a cohort of 1000 unrelated US whites. Nominal significant associations (nominal p value<0.05) were observed between 76 pathways and a key FN bone geometry variable-section modulus (Z), biomechanically indicative of bone strength subject to bending. Among them, EphrinA-EphR pathway was most significantly associated with FN Z even after multiple testing adjustments (p(FWER) value=0.035). The association of EphrinA-EphR pathway with FN Z was also observed in an independent sample from Framingham Osteoporosis Study. Overall, these results suggest the significant genetic contribution of EphrinA-EphR pathway to femoral neck bone geometry.
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Affiliation(s)
- Yuan Chen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Dong-Hai Xiong
- Departments of Orthopedic Surgery and Basic Medical Sciences, University of Missouri - Kansas City, Kansas City, MO 64108, USA
| | - Yan-Fang Guo
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Feng Pan
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Qi Zhou
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Feng Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
| | - Hong-Wen Deng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P. R. China
- Departments of Orthopedic Surgery and Basic Medical Sciences, University of Missouri - Kansas City, Kansas City, MO 64108, USA
- College of Life Sciences and Engineering, Beijing Jiaotong University, Beijing 100044, P. R. China
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Li WF, Hou SX, Yu B, Li MM, Férec C, Chen JM. Genetics of osteoporosis: accelerating pace in gene identification and validation. Hum Genet 2009; 127:249-85. [PMID: 20101412 DOI: 10.1007/s00439-009-0773-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 11/25/2009] [Indexed: 02/06/2023]
Abstract
Osteoporosis is characterized by low bone mineral density and structural deterioration of bone tissue, leading to an increased risk of fractures. It is the most common metabolic bone disorder worldwide, affecting one in three women and one in eight men over the age of 50. In the past 15 years, a large number of genes have been reported as being associated with osteoporosis. However, only in the past 4 years we have witnessed an accelerated pace in identifying and validating osteoporosis susceptibility loci. This increase in pace is mostly due to large-scale association studies, meta-analyses, and genome-wide association studies of both single nucleotide polymorphisms and copy number variations. A comprehensive review of these developments revealed that, to date, at least 15 genes (VDR, ESR1, ESR2, LRP5, LRP4, SOST, GRP177, OPG, RANK, RANKL, COLIA1, SPP1, ITGA1, SP7, and SOX6) can be reasonably assigned as confirmed osteoporosis susceptibility genes, whereas, another >30 genes are promising candidate genes. Notably, confirmed and promising genes are clustered in three biological pathways, the estrogen endocrine pathway, the Wnt/beta-catenin signaling pathway, and the RANKL/RANK/OPG pathway. New biological pathways will certainly emerge when more osteoporosis genes are identified and validated. These genetic findings may provide new routes toward improved therapeutic and preventive interventions of this complex disease.
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Affiliation(s)
- Wen-Feng Li
- Department of Orthopaedics, The First Affiliated Hospital, General Hospital of the People's Liberation Army, 100037 Beijing, China
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