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Teng Z, Zhu Y, Lin D, Hao Q, Yue Q, Yu X, Sun S, Jiang L, Lu S. Deciphering the chromatin spatial organization landscapes during BMMSC differentiation. J Genet Genomics 2023; 50:264-275. [PMID: 36720443 DOI: 10.1016/j.jgg.2023.01.009] [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: 11/03/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
The differentiation imbalance in bone marrow mesenchymal stem cells (BMMSCs) is critical for the development of bone density diseases as the population ages. BMMSCs are precursor cells for osteoblasts and adipocytes; however, the chromatin organization landscapes during BMMSC differentiation remain elusive. In this study, we systematically delineate the four-dimensional (4D) genome and dynamic epigenetic atlas of BMMSCs by RNA sequencing (RNA-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq), and high-throughput chromosome conformation capture (Hi-C). The structure analyses reveal 17.5% common and 28.5%-30% specific loops among BMMSCs, osteoblasts, and adipocytes. The subsequent correlation of genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL) data with multi-omics analysis reveal 274 genes and 3634 single nucleotide polymorphisms (SNPs) associated with bone degeneration and osteoporosis (OP). We hypothesize that SNP mutations affect transcription factor (TF) binding sites, thereby affecting changes in gene expression. Furthermore, 26 motifs, 260 TFs, and 291 SNPs are identified to affect the eQTL. Among these genes, DAAM2, TIMP2, and TMEM241 were found to be essential for diseases such as bone degeneration and OP and may serve as potential drug targets.
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Affiliation(s)
- Zhaowei Teng
- Department of Orthopedics, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, China; Key Laboratory of Yunnan Provincial Innovative Application of Traditional Chinese Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, China; Clinical Medical Research Center, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, China.
| | - Yun Zhu
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653100, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qinggang Hao
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan 650504, China
| | - Qiaoning Yue
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653100, China
| | - Xiaochao Yu
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653100, China
| | - Shuo Sun
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653100, China
| | - Lihong Jiang
- Key Laboratory of Yunnan Provincial Innovative Application of Traditional Chinese Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, China.
| | - Sheng Lu
- Department of Orthopedics, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, China.
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Zeng H, Ge J, Xu W, Ma H, Chen L, Xia M, Pan B, Lin H, Wang S, Gao X. Twelve Loci Associated With Bone Density in Middle-aged and Elderly Chinese: The Shanghai Changfeng Study. J Clin Endocrinol Metab 2023; 108:295-305. [PMID: 36228083 DOI: 10.1210/clinem/dgac597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/08/2022] [Indexed: 01/20/2023]
Abstract
CONTEXT Previous genome-wide association studies (GWASs) of bone mineral density (BMD) were mainly conducted in Europeans. OBJECTIVE To explore genetic variants that affect BMD and sex differences in a Chinese population. METHODS A total of 5428 middle-aged and elderly Chinese were included. Dual-energy X-ray absorptiometry was used to measure BMD at the lumbar spine, and total and specific sites of the hip. A mixed linear model was used to analyze the associations between BMD and autosomal genetic variants, adjusting for age, age squared, sex, and menopausal women (model 1); model 2 was further adjusted for height and weight. A GWAS of osteoporosis in the Biobank Japan (BBJ) project was used for replication. GWAMA software was used to detect the statistical significance of sex differences of estimated effects. Gene annotation and pathway enrichment analysis were performed. RESULTS Women lost BMD at earlier ages and faster than men. The 2 models identified a total of 12 loci that were associated with BMD at any site. Single nucleotide polymorphisms rs72354346, rs2024219, rs1463093, rs10037512, and rs5880932 were successfully replicated in the BBJ. Variations of rs79262027 G>A (VKORC1L1) and rs4795209 A>G (DDX52) were associated with BMD only in men, and rs1239055408 G>GA (KCNJ2) was associated with BMD only in women. Gene enrichment analysis showed that BMD in a Chinese elderly population was mainly related to ossification, bone resorption, sex hormones, and kidney physiology. CONCLUSION The present GWAS identified 12 loci that were significantly associated with BMD at any site in a Chinese population, and 3 of them showed sex differences in their effects.
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Affiliation(s)
- Hailuan Zeng
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
- Fudan Institute for Metabolic Diseases, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Jieyu Ge
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjie Xu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Ma
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingyan Chen
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mingfeng Xia
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
- Fudan Institute for Metabolic Diseases, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Huandong Lin
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
- Fudan Institute for Metabolic Diseases, Shanghai, China
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Xin Gao
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
- Fudan Institute for Metabolic Diseases, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
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Twelve years of GWAS discoveries for osteoporosis and related traits: advances, challenges and applications. Bone Res 2021; 9:23. [PMID: 33927194 PMCID: PMC8085014 DOI: 10.1038/s41413-021-00143-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/21/2020] [Indexed: 02/03/2023] Open
Abstract
Osteoporosis is a common skeletal disease, affecting ~200 million people around the world. As a complex disease, osteoporosis is influenced by many factors, including diet (e.g. calcium and protein intake), physical activity, endocrine status, coexisting diseases and genetic factors. In this review, we first summarize the discovery from genome-wide association studies (GWASs) in the bone field in the last 12 years. To date, GWASs and meta-analyses have discovered hundreds of loci that are associated with bone mineral density (BMD), osteoporosis, and osteoporotic fractures. However, the GWAS approach has sometimes been criticized because of the small effect size of the discovered variants and the mystery of missing heritability, these two questions could be partially explained by the newly raised conceptual models, such as omnigenic model and natural selection. Finally, we introduce the clinical use of GWAS findings in the bone field, such as the identification of causal clinical risk factors, the development of drug targets and disease prediction. Despite the fruitful GWAS discoveries in the bone field, most of these GWAS participants were of European descent, and more genetic studies should be carried out in other ethnic populations to benefit disease prediction in the corresponding population.
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Hamashita Y, Shibata T, Takeuchi A, Okuno T, Kise N, Sakurai T. Inchworm-type PNA-PEG conjugate regulates gene expression based on single nucleotide recognition. Int J Biol Macromol 2021; 181:471-477. [PMID: 33798568 DOI: 10.1016/j.ijbiomac.2021.03.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
In order to detect single nucleotide mutations and suppress gene expression, we synthesized an artificial nucleic acid, an inchworm-type PNA-PEG conjugate (i-PPc), that possessed a chemical structure in which 8 residues of peptide nucleic acid (PNA) were linked to both ends of a polyethylene glycol molecule. I-PPc_T7FM, which forms a complementary strand with the T7 promoter region of luciferase-expressing mRNA, failed to suppress the amount of luciferase produced via gene expression. However, 10 μM of i-PPc_ATGFM, targeting the start codon of luciferase (Luc+), suppressed approximately 85% of Luc+ production compared to that of the control in the cell-free protein synthesis system. Moreover, i-PPc_ATGMM (i-PPc_ATGFM with a single base mutation) only suppressed the amount of luciferase produced by approximately 15%, and such suppression of luciferase expression has not been achieved with block-type PPc or PNA oligos. The thermodynamic parameters suggested that the difference in stability of each PNA segment of the i-PPc contributed to single nucleotide recognition. These results indicate that the i-PPc could be used in antisense therapy to target single nucleotide polymorphisms (SNP).
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Affiliation(s)
- Yusuke Hamashita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8552, Japan
| | - Takahiro Shibata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8552, Japan
| | - Akiko Takeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8552, Japan
| | - Takashi Okuno
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa, Yamagata, 990-8560, Japan
| | - Naoki Kise
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8552, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8552, Japan
| | - Toshihiko Sakurai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8552, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8552, Japan.
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Pharmacogenomics Study for Raloxifene in Postmenopausal Female with Osteoporosis. DISEASE MARKERS 2020; 2020:8855423. [PMID: 32934756 PMCID: PMC7479487 DOI: 10.1155/2020/8855423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/25/2020] [Accepted: 08/07/2020] [Indexed: 01/16/2023]
Abstract
Osteoporosis is characterized by decreased bone mineral density and increased risk of fracture. Raloxifene is one of the treatments of osteoporosis. However, the responses were variable among patients. Previous studies revealed that the genetic variants are involved in the regulation of treatment outcomes. To date, studies that evaluate the influence of genes across all genome on the raloxifene treatment response are still limited. In this study, a total of 41 postmenopausal osteoporosis patients under regular raloxifene treatment were included. Gene-based analysis using MAGMA was applied to investigate the genetic association with the bone mineral density response to raloxifene at the lumbar spine or femoral neck site. Results from gene-based analysis indicated several genes (GHRHR, ABHD8, and TMPRSS6) related to the responses of raloxifene. Besides, the pathways of iron ion homeostasis, osteoblast differentiation, and platelet morphogenesis were enriched which implies that these pathways might be relatively susceptible to raloxifene treatment outcome. Our study provided a novel insight into the response to raloxifene.
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Liu X, Zhang Y, Tian J, Gao F. Analyzing Genome-Wide Association Study Dataset Highlights Immune Pathways in Lip Bone Mineral Density. Front Genet 2020; 11:4. [PMID: 32211016 PMCID: PMC7077504 DOI: 10.3389/fgene.2020.00004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/06/2020] [Indexed: 12/27/2022] Open
Abstract
Osteoporosis is a common complex human disease. Until now, large-scale genome-wide association studies (GWAS) using single genetic variant have reported some novel osteoporosis susceptibility variants. However, these risk variants only explain a small proportion of osteoporosis genetic risk, and most genetic risk is largely unknown. Interestingly, the pathway analysis method has been used in investigation of osteoporosis mechanisms and reported some novel pathways. Until now, it remains unclear whether there are other risk pathways involved in BMD. Here, we selected a lip BMD GWAS with 301,019 SNPs in 5,858 Europeans, and conducted a gene-based analysis (SET SCREEN TEST) and a pathway-based analysis (WebGestalt). On the gene level, BMD susceptibility genes reported by previous GWAS were identified to be the top 10 significant signals. On the pathway level, we identified 27 significant KEGG pathways. Three immune pathways including T cell receptor signaling pathway (hsa04660), complement and coagulation cascades (hsa04610), and intestinal immune network for IgA production (hsa04672) are ranked the top three significant signals. Evidence from the PubMed and Google Scholar databases further supports our findings. In summary, our findings provide complementary information to these nine risk pathways.
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Affiliation(s)
- Xiaodong Liu
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yiwei Zhang
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jun Tian
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Feng Gao
- Department of Trauma and Emergency Surgeon, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
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Xu X, Zheng L, Yuan Q, Zhen G, Crane JL, Zhou X, Cao X. Transforming growth factor-β in stem cells and tissue homeostasis. Bone Res 2018; 6:2. [PMID: 29423331 PMCID: PMC5802812 DOI: 10.1038/s41413-017-0005-4] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/12/2017] [Accepted: 11/15/2017] [Indexed: 02/05/2023] Open
Abstract
TGF-β 1-3 are unique multi-functional growth factors that are only expressed in mammals, and mainly secreted and stored as a latent complex in the extracellular matrix (ECM). The biological functions of TGF-β in adults can only be delivered after ligand activation, mostly in response to environmental perturbations. Although involved in multiple biological and pathological processes of the human body, the exact roles of TGF-β in maintaining stem cells and tissue homeostasis have not been well-documented until recent advances, which delineate their functions in a given context. Our recent findings, along with data reported by others, have clearly shown that temporal and spatial activation of TGF-β is involved in the recruitment of stem/progenitor cell participation in tissue regeneration/remodeling process, whereas sustained abnormalities in TGF-β ligand activation, regardless of genetic or environmental origin, will inevitably disrupt the normal physiology and lead to pathobiology of major diseases. Modulation of TGF-β signaling with different approaches has proven effective pre-clinically in the treatment of multiple pathologies such as sclerosis/fibrosis, tumor metastasis, osteoarthritis, and immune disorders. Thus, further elucidation of the mechanisms by which TGF-β is activated in different tissues/organs and how targeted cells respond in a context-dependent way can likely be translated with clinical benefits in the management of a broad range of diseases with the involvement of TGF-β.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Gehua Zhen
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Janet L. Crane
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD USA
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xu Cao
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
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Taylor KC, Evans DS, Edwards DRV, Edwards TL, Sofer T, Li G, Liu Y, Franceschini N, Jackson RD, Giri A, Donneyong M, Psaty B, Rotter JI, LaCroix AZ, Jordan JM, Robbins JA, Lewis B, Stefanick ML, Liu Y, Garcia M, Harris T, Cauley JA, North KE. A genome-wide association study meta-analysis of clinical fracture in 10,012 African American women. Bone Rep 2016; 5:233-242. [PMID: 28580392 PMCID: PMC5440953 DOI: 10.1016/j.bonr.2016.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/25/2016] [Indexed: 01/01/2023] Open
Abstract
Background Osteoporosis is a major public health problem associated with excess disability and mortality. It is estimated that 50–70% of the variation in osteoporotic fracture risk is attributable to genetic factors. The purpose of this hypothesis-generating study was to identify possible genetic determinants of fracture among African American (AA) women in a GWAS meta-analysis. Methods Data on clinical fractures (all fractures except fingers, toes, face, skull or sternum) were analyzed among AA female participants in the Women's Health Initiative (WHI) (N = 8155), Cardiovascular Health Study (CHS) (N = 504), BioVU (N = 704), Health ABC (N = 651), and the Johnston County Osteoarthritis Project (JoCoOA) (N = 291). Affymetrix (WHI) and Illumina (Health ABC, JoCoOA, BioVU, CHS) GWAS panels were used for genotyping, and a 1:1 ratio of YRI:CEU HapMap haplotypes was used as an imputation reference panel. We used Cox proportional hazard models or logistic regression to evaluate the association of ~ 2.5 million SNPs with fracture risk, adjusting for ancestry, age, and geographic region where applicable. We conducted a fixed-effects, inverse variance-weighted meta-analysis. Genome-wide significance was set at P < 5 × 10− 8. Results One SNP, rs12775980 in an intron of SVIL on chromosome 10p11.2, reached genome-wide significance (P = 4.0 × 10− 8). Although this SNP has a low minor allele frequency (0.03), there was no evidence for heterogeneity of effects across the studies (I2 = 0). This locus was not reported in any previous osteoporosis-related GWA studies. We also interrogated previously reported GWA-significant loci associated with fracture or bone mineral density in our data. One locus (SMOC1) generalized, but overall there was not substantial evidence of generalization. Possible reasons for the lack of generalization are discussed. Conclusion This GWAS meta-analysis of fractures in African American women identified a potentially novel locus in the supervillin gene, which encodes a platelet-associated factor and was previously associated with platelet thrombus formation in African Americans. If validated in other populations of African descent, these findings suggest potential new mechanisms involved in fracture that may be particularly important among African Americans. This was a hypothesis-generating GWAS for fracture in African Americans. One potentially novel locus (SVIL) was identified at GWA-significant levels. SVIL has been associated with platelet thrombus formation in African-Americans.
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Key Words
- AA, African American
- ASW, African ancestry individuals from Southwest USA
- African American
- BMD, bone mineral density
- BMI, body mass index
- BMP, bone morphogenetic protein
- CES-D, Center for Epidemiological Studies-Depression scale
- CEU, CEPH-Utah (Utah residents with ancestors from central and western Europe)
- CHS, Cardiovascular Health Study
- DNA, deoxyribonucleic acid
- EAF, effect allele frequency
- Fracture
- GEFOS, Genetic Factors of Osteoporosis
- GPGE, genetically predicted gene expression
- GTEx Project, Genotype-Tissue Expression project
- GWAS, genome-wide association study
- Genetic association study
- Genome-wide association study (GWAS)
- JoCoOA, Johnston County Osteoarthritis Project
- MAC, minor allele count
- MAF, minor allele frequency
- Meta-analysis
- OF, osteoporotic fracture
- Osteoporosis
- RNA, ribonucleic acid
- SD, standard deviation
- SHARe, SNP Health Association Resource
- SNP, single nucleotide polymorphism
- WHI, Women's Health Initiative
- YRI, Yoruban (Nigeria)
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Affiliation(s)
- Kira C Taylor
- School of Public Health and Information Sciences, University of Louisville, 485 E Gray St., Louisville, KY 40202, USA.,Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 137 E. Franklin St., Chapel Hill, NC 27514, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, 550 16th Street, Box 0560, San Francisco, CA 94158-2549, USA
| | - Digna R Velez Edwards
- Vanderbilt Epidemiology Center, Department of Obstetrics and Gynecology, Vanderbilt Genetics Institute, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203, USA
| | - Todd L Edwards
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, UW Tower 15th floor, 4333 Brooklyn Ave NE, Seattle 98105, USA
| | - Guo Li
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Metropolitan Park East Tower, 1730 Minor Ave, Suite 1360, Seattle, WA 98101, USA
| | - Youfang Liu
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, 3300 Thurston Bldg., CB# 7280, Chapel Hill NC 27599-7280, NC, USA
| | - Nora Franceschini
- University of North Carolina at Chapel Hill, 137 E. Franklin St., Chapel Hill, NC 27514, USA
| | - Rebecca D Jackson
- The Ohio State University, 376 W 10th Avenue, Suite 260, Columbus, OH 43210, USA
| | - Ayush Giri
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203, USA
| | - Macarius Donneyong
- School of Public Health and Information Sciences, University of Louisville, 485 E Gray St., Louisville, KY 40202, USA.,Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital, 1620 Tremont St, St 3030, Boston, MA 02120, USA
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington; Group Health Research Institute, Group Health Cooperative, Metropolitan Park East Tower, 1730 Minor Ave, Suite 1360, Seattle, WA 98101, USA
| | - Jerome I Rotter
- Institute of Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, 1124 W. Carson Street, Bldg., E-5, Torrance, CA 90502, USA
| | - Andrea Z LaCroix
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Joanne M Jordan
- Department of Medicine, University of California at Davis Medical Center, PSSB Building, 4150 V St., Sacramento, CA 95817, USA
| | - John A Robbins
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, 3300 Thurston Bldg., CB# 7280, Chapel Hill NC 27599-7280, NC, USA
| | - Beth Lewis
- University of Alabama, Medical Towers 614, 1717 11th Avenue South, Birmingham, AL 35205, USA
| | - Marcia L Stefanick
- Stanford Prevention Research Center, Stanford University School of Medicine, Medical School Office Building, 1265 Welch Road, Mail Code 5411, Stanford, CA 94305, USA
| | - Yongmei Liu
- Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Melissa Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, 7201 Wisconsin Ave, Suite 3C309, Bethesda, MD 20892, USA
| | - Tamara Harris
- Laboratory of Epidemiology and Population Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Jane A Cauley
- University of Pittsburgh Graduate School of Public Health, Department of Epidemiology, A510 Crabtree Hall, Pittsburgh, PA 15261, USA
| | - Kari E North
- Carolina Center for Genome Sciences, 250 Bell Tower Dr., Chapel Hill, NC 27514, USA.,Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 137 E. Franklin St., Chapel Hill, NC 27514, USA
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Dehghan M, Pourahmad-Jaktaji R. The Effect of Some Polymorphisms in Vitamin D Receptor Gene in Menopausal Women with Osteoporosis. J Clin Diagn Res 2016; 10:RC06-10. [PMID: 27504361 DOI: 10.7860/jcdr/2016/17147.8006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 12/02/2015] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Vitamin D receptor gene is one of candidate genes related to osteoporosis expansion. The association of ApaI, TaqI, BsmI polymorphisms in vitamin D receptor gene with bone metabolism and density has been area of interest in many studies. AIM This study was conducted to further investigate the association between the ApaI, TaqI, BsmI polymorphisms and bone density. This study was analytical study. Centers for bone density measurement in southwestern Iran. MATERIALS AND METHODS In this analytical study, 200 participants aged 45- and above 45-year-old women referring the centers of bone density measurement participated. The bone density of femoral neck and lumbar vertebrae was measured using dual-energy X-ray absorptiometry method. Based on t-score, the participants were assigned into patients (n=130) and healthy individuals (n=70). Different genotypes of ApaI (AA/Aa/aa), TaqI (TT/Tt/tt), and BsmI (BB/Bb/bb) were determined by PCR-RFLP. The data on bone density and PCR-RFLP were analysed by chi-square and ANOVA. Also, triad combination of the genotypes was statistically analysed. For each genotype combination, chi-square was run between the patients and control group and p-value was calculated. RESULTS No significant association was seen between ApaI polymorphism and bone density (p>0.05). TaqI and BsmI polymorphisms had a significant association with femoral neck's bone density (p<0.05), but these polymorphisms were not significantly associated with lumbar vertebrae's (p>0.05). Patients with homozygous dominant TT genotype had the least bone density in femoral neck compared to other genotypes. Lumbar vertebrae's bone density was similar in three TaqI genotypes. The patients with homozygous recessive bb genotype had the least bone density in femoral neck and lumbar vertebrae compared to other genotypes. CONCLUSION TaqI and BsmI polymorphisms could be desirable markers in diagnosis of women at risk of osteoporosis in the studied region in Iran. Therefore, these women will receive suitable medical treatment at proper time.
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Affiliation(s)
- Morteza Dehghan
- Associate Professor, Department of Orthopedics, Shahrekord University of Medical Sciences , Shahrekord, Iran
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Abstract
Osteoporosis is characterized by low bone mass and an increased risk of fracture. Genetic factors, environmental factors and gene-environment interactions all contribute to a person's lifetime risk of developing an osteoporotic fracture. This Review summarizes key advances in understanding of the genetics of bone traits and their role in osteoporosis. Candidate-gene approaches dominated this field 20 years ago, but clinical and preclinical genetic studies published in the past 5 years generally utilize more-sophisticated and better-powered genome-wide association studies (GWAS). High-throughput DNA sequencing, large genomic databases and improved methods of data analysis have greatly accelerated the gene-discovery process. Linkage analyses of single-gene traits that segregate in families with extreme phenotypes have led to the elucidation of critical pathways controlling bone mass. For example, components of the Wnt-β-catenin signalling pathway have been validated (in both GWAS and functional studies) as contributing to various bone phenotypes. These notable advances in gene discovery suggest that the next decade will witness cataloguing of the hundreds of genes that influence bone mass and osteoporosis, which in turn will provide a roadmap for the development of new drugs that target diseases of low bone mass, including osteoporosis.
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Mori S, Zhou H. Implementation of personalized medicine for fracture risk assessment in osteoporosis. Geriatr Gerontol Int 2016; 16 Suppl 1:57-65. [DOI: 10.1111/ggi.12721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Seijiro Mori
- Center for the Promotion of Clinical Investigation; Tokyo Metropolitan Geriatric Hospital; Tokyo Japan
| | - Heying Zhou
- Center for the Promotion of Clinical Investigation; Tokyo Metropolitan Geriatric Hospital; Tokyo Japan
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Association Study between the FTCDNL1 (FONG) and Susceptibility to Osteoporosis. PLoS One 2015; 10:e0140549. [PMID: 26492493 PMCID: PMC4619591 DOI: 10.1371/journal.pone.0140549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/26/2015] [Indexed: 11/19/2022] Open
Abstract
Osteoporosis is a systemic skeletal disease characterized by a decreased bone mineral density that results in an increased risk of fragility fractures. Previous studies indicated that genetic factors are involved in the pathogenesis of osteoporosis. Polymorphisms of the FONG (FTCDNL1) gene (rs7605378) were reported to be associated with the risk of osteoporosis in a Japanese population. To assess whether polymorphisms of the FTCDNL1 gene contribute to the susceptibility and severity of osteoporosis in a Taiwanese population, 326 osteoporosis patients and 595 controls of a Taiwanese population were included in this study. Our results indicated that rs10203122 was significantly associated with osteoporosis susceptibility among female. Our findings provide evidence that rs10203122 in FTCDNL1 is associated with a susceptibility to osteoporosis.
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Abstract
Osteoporosis is a skeletal disorder characterized by low bone mineral density (BMD) and an increased susceptibility to fractures. Evidence from genetic studies indicates that BMD, a complex quantitative trait with a normal distribution, is genetically controlled. Genome-wide association studies (GWAS) as well as studies using candidate gene approaches have identified single-nucleotide polymorphisms (SNPs) that are associated with BMD, osteoporosis and osteoporotic fractures. These SNPs have been mapped close to or within genes including those encoding WNT/β-catenin signaling proteins. Understanding the genetics of osteoporosis will help to identify novel candidates for diagnostic and therapeutic targets. Genetic factors are also important for the development of sarcopenia, which is characterized by a loss of lean body mass, and obesity, which is characterized by high fat mass. Hence, in this review, we discuss the genetic factors, identified by genetic studies, which regulate the body components related to osteoporosis, sarcopenia, and obesity.
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Affiliation(s)
- Tomohiko Urano
- Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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15
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Urano T, Inoue S. Genetics of osteoporosis. Biochem Biophys Res Commun 2014; 452:287-93. [DOI: 10.1016/j.bbrc.2014.07.141] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 07/18/2014] [Indexed: 01/22/2023]
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Mizuno S, Dinh TTH, Kato K, Mizuno-Iijima S, Tanimoto Y, Daitoku Y, Hoshino Y, Ikawa M, Takahashi S, Sugiyama F, Yagami KI. Simple generation of albino C57BL/6J mice with G291T mutation in the tyrosinase gene by the CRISPR/Cas9 system. Mamm Genome 2014; 25:327-34. [DOI: 10.1007/s00335-014-9524-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/25/2014] [Indexed: 01/28/2023]
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Ikegawa S. Genetics of ossification of the posterior longitudinal ligament of the spine: a mini review. J Bone Metab 2014; 21:127-32. [PMID: 25006569 PMCID: PMC4075266 DOI: 10.11005/jbm.2014.21.2.127] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 04/23/2014] [Accepted: 04/23/2014] [Indexed: 11/11/2022] Open
Abstract
Ossification of the posterior longitudinal ligament of the spine (OPLL) is a common disease in aging populations and sometimes results in serious neurological problems due to compression of the spinal cord and nerve roots. OPLL is a multi-factorial (polygenic) disease controlled by genetic and environmental factors. Studies searching for the genetic component of OPLL, using linkage and association analyses, are in progress and several susceptibility genes have been reported. This paper reviews the recent progress in the genetic study of OPLL and comments on its future task.
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Affiliation(s)
- Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Genomic Medicine, RIKEN, Tokyo, Japan
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Further delineation of the SATB2 phenotype. Eur J Hum Genet 2013; 22:1034-9. [PMID: 24301056 DOI: 10.1038/ejhg.2013.280] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/18/2013] [Accepted: 10/30/2013] [Indexed: 12/16/2022] Open
Abstract
SATB2 is an evolutionarily highly conserved chromatin remodeling gene located on chromosome 2q33.1. Vertebrate animal models have shown that Satb2 has a crucial role in craniofacial patterning and osteoblast differentiation, as well as in determining the fates of neuronal projections in the developing neocortex. In humans, chromosomal translocations and deletions of 2q33.1 leading to SATB2 haploinsufficiency are associated with cleft palate (CP), facial dysmorphism and intellectual disability (ID). A single patient carrying a nonsense mutation in SATB2 has been described to date. In this study, we performed trio-exome sequencing in a 3-year-old girl with CP and severely delayed speech development, and her unaffected parents. Previously, the girl had undergone conventional and molecular karyotyping (microarray analysis), as well as targeted analysis for different diseases associated with developmental delay, including Angelman syndrome, Rett syndrome and Fragile X syndrome. No diagnosis could be established. Exome sequencing revealed a de novo nonsense mutation in the SATB2 gene (c.715C>T; p.R239*). The identification of a second patient carrying a de novo nonsense mutation in SATB2 confirms that this gene is essential for normal craniofacial patterning and cognitive development. Based on our data and the literature published so far, we propose a new clinically recognizable syndrome - the SATB2-associated syndrome (SAS). SAS is likely to be underdiagnosed and should be considered in children with ID, severe speech delay, cleft or high-arched palate and abnormal dentition with crowded and irregularly shaped teeth.
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Wu S, Liu Y, Zhang L, Han Y, Lin Y, Deng HW. Genome-wide approaches for identifying genetic risk factors for osteoporosis. Genome Med 2013; 5:44. [PMID: 23731620 PMCID: PMC3706967 DOI: 10.1186/gm448] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Osteoporosis, the most common type of bone disease worldwide, is clinically characterized by low bone mineral density (BMD) and increased susceptibility to fracture. Multiple genetic and environmental factors and gene-environment interactions have been implicated in its pathogenesis. Osteoporosis has strong genetic determination, with the heritability of BMD estimated to be as high as 60%. More than 80 genes or genetic variants have been implicated in risk of osteoporosis by hypothesis-free genome-wide studies. However, these genes or genetic variants can only explain a small portion of BMD variation, suggesting that many other genes or genetic variants underlying osteoporosis risk await discovery. Here, we review recent progress in genome-wide studies of osteoporosis and discuss their implications for medicine and the major challenges in the field.
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Affiliation(s)
- Shuyan Wu
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Yongjun Liu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
| | - Lei Zhang
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China ; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
| | - Yingying Han
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Yong Lin
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Hong-Wen Deng
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China ; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
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Association of the formiminotransferase N-terminal sub-domain containing gene and thrombospondin, type 1, domain-containing 7A gene with the prevalence of vertebral fracture in 2427 consecutive autopsy cases. J Hum Genet 2013; 58:109-12. [PMID: 23303384 DOI: 10.1038/jhg.2012.145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We previously reported 2 osteoporosis-susceptibility genes--formiminotransferase N-terminal sub-domain containing gene (FONG) and thrombospondin, type 1, domain-containing 7A (THSD7A)--in which we identified two common single-nucleotide polymorphisms, rs7605378 (FONG) and rs12673692 (THSD7A). The former was associated with a predisposition to osteoporosis and the latter with bone mineral density. To further elucidate the importance of these polymorphisms in the pathogenesis of osteoporosis, we examined their association with the incidence of vertebral fracture. DNA extracted from the renal cortex of 2427 consecutive Japanese autopsies (1331 men, mean age: 79 years; 1096 women, mean age: 82 years) were examined in this study. The presence or absence of vertebral fracture during each subject's lifetime was determined by a thorough examination of the clinical records, as well as autopsy reports. After adjustments for sex and age at autopsy, logistic regression analysis revealed that homozygotes for the risk alleles of rs7605378 (A-allele) or rs12673629 (A-allele) possess an increased risk of vertebral fracture. The subjects simultaneously homozygous for both the risk alleles of rs7605378 (AA genotype) and rs12673629 (AA genotype) showed significantly higher risk of vertebral fracture (odds ratio 2.401, 95% confidence interval 1.305-4.416, P = 0.0048) than those who had at least one non-risk allele of either rs7605378 (AC/CC genotypes) or rs12673629 (AG/GG genotypes). The results suggest that Japanese subjects homozygous for the risk alleles of rs7605378 and rs12673629 have a higher risk of vertebral fracture.
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Ikegawa S. A short history of the genome-wide association study: where we were and where we are going. Genomics Inform 2012; 10:220-5. [PMID: 23346033 PMCID: PMC3543921 DOI: 10.5808/gi.2012.10.4.220] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 10/31/2012] [Accepted: 11/01/2012] [Indexed: 01/03/2023] Open
Abstract
Recent rapid advances in genetic research are ushering us into the genome sequence era, where an individual's genome information is utilized for clinical practice. The most spectacular results of the human genome study have been provided by genome-wide association studies (GWASs). This is a review of the history of GWASs as related to my work. Further efforts are necessary to make full use of its potential power to medicine.
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Affiliation(s)
- Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Genomic Medicine, RIKEN, Tokyo 108-8639, Japan
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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: 1.1] [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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Qin G, Dong Z, Zeng P, Liu M, Liao X. Association of vitamin D receptor BsmI gene polymorphism with risk of osteoporosis: a meta-analysis of 41 studies. Mol Biol Rep 2012; 40:497-506. [PMID: 23054016 DOI: 10.1007/s11033-012-2086-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 10/03/2012] [Indexed: 12/01/2022]
Abstract
Vitamin D receptor (VDR) BsmI gene polymorphism has been reported to be strongly associated with osteoporosis risk in some studies. However, the results from those studies are still conflicting. We performed a meta-analysis of studies relating the VDR BsmI gene polymorphism to the risk of osteoporosis. The search was performed in the databases of PubMed, Embase, Cochrane Library and CBM-disc (China Biological Medicine Database) as of October 1, 2011, and the eligible investigations were recruited for this meta-analysis. Forty-one investigations were identified for the meta-analysis of association between VDR BsmI gene polymorphism and osteoporosis risk. There lacked an association between VDR BsmI gene polymorphism and osteoporosis risk for overall populations, Caucasians and Asians (overall populations: B vs b: p = 0.65, BB vs (Bb + bb): p = 0.14, bb vs (BB + Bb): p = 0.86; Caucasians: B vs b: p = 0.65, BB vs (Bb + bb): p = 0.38, bb vs (BB + Bb): p = 0.83; Asians: B vs b: p = 0.87, BB vs (Bb + bb): p = 0.62, bb vs (BB + Bb): p = 0.66). In conclusion, VDR BsmI B/b gene polymorphism is not associated with the susceptibility of osteoporosis in overall populations, Caucasians, and Asians.
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Affiliation(s)
- Gang Qin
- Department of Osteoarthrosis, The First Affiliated Hospital Guangxi Traditional Chinese Medical University, No. 89-9, Dongge Road, Nanning 530023, Guangxi, People's Republic of China.
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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: 80] [Impact Index Per Article: 6.7] [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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Osteoporosis genetics: year 2011 in review. BONEKEY REPORTS 2012; 1:114. [PMID: 23951496 DOI: 10.1038/bonekey.2012.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/09/2012] [Indexed: 02/08/2023]
Abstract
Increased rates of osteoporotic fractures represent a worldwide phenomenon, which result from a progressing aging in the population around the world and creating socioeconomic problems. This review will focus mostly on human genetic studies identifying genomic regions, genes and mutations associated with osteoporosis (bone mineral density (BMD) and bone loss) and related fractures, which were published during 2011. Although multiple genome-wide association studies (GWAS) were performed to date, the genetic cause of osteoporosis and fractures has not yet been found, and only a small fraction of high heritability of bone mass was successfully explained. GWAS is a successful tool to initially define and prioritize specific chromosomal regions showing associations with the desired traits or diseases. Following the initial discovery and replication, targeted sequencing is needed in order to detect those rare variants which GWAS does not reveal by design. Recent GWAS findings for BMD included WNT16 and MEF2C. The role of bone morphogenetic proteins in fracture healing has been explored by several groups, and new single-nucleotide polymorphisms present in genes such as NOGGIN and SMAD6 were found to be associated with a greater risk of fracture non-union. Finding new candidate genes, and mutations associated with BMD and fractures, also provided new biological connections. Thus, candidates for molecular link between bone metabolism and lactation (for example, RAP1A gene), as well as possible pleiotropic effects for bone and muscle (ACTN3 gene) were suggested. The focus of contemporary studies seems to move toward whole-genome sequencing, epigenetic and functional genomics strategies to find causal variants for osteoporosis.
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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: 1.9] [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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Hwang JY, Lee SH, Go MJ, Kim BJ, Kim YJ, Kim DJ, Oh JH, Koo HJ, Cha MJ, Lee MH, Yun JY, Yoo HS, Kang YA, Oh KW, Kang MI, Son HY, Kim SY, Kim GS, Han BG, Cho YS, Koh JM, Lee JY. Genome-wide Association Study Identification of a New Genetic Locus with Susceptibility to Osteoporotic Fracture in the Korean Population. Genomics Inform 2011. [DOI: 10.5808/gi.2011.9.2.52] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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