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He P, Meng XH, Zhang X, Lin X, Zhang Q, Jiang RL, Schiller MR, Deng FY, Deng HW. Identifying Pleiotropic SNPs Associated With Femoral Neck and Heel Bone Mineral Density. Front Genet 2020; 11:772. [PMID: 32774344 PMCID: PMC7388689 DOI: 10.3389/fgene.2020.00772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
Background Genome-wide association studies (GWASs) routinely identify loci associated with risk factors for osteoporosis. However, GWASs with relatively small sample sizes still lack sufficient power to ascertain the majority of genetic variants with small to modest effect size, which may together truly influence the phenotype. The loci identified only account for a small percentage of the heritability of osteoporosis. This study aims to identify novel genetic loci associated with DXA-derived femoral neck (FNK) bone mineral density (BMD) and quantitative ultrasound of the heel calcaneus estimated BMD (eBMD), and to detect shared/causal variants for the two traits, to assess whether the SNPs or putative causal SNPs associated with eBMD were also associated with FNK-BMD. Methods Novel loci associated with eBMD and FNK-BMD were identified by the genetic pleiotropic conditional false discovery rate (cFDR) method. Shared putative causal variants between eBMD and FNK-BMD and putative causal SNPs for each trait were identified by the colocalization method. Mendelian randomization analysis addresses the causal relationship between eBMD/FNK-BMD and fracture. Results We identified 9,500 (cFDR < 9.8E-6), 137 (cFDR < 8.9E-4) and 124 SNPs associated with eBMD, FNK-BMD, and both eBMD and FNK-BMD, respectively, with 37 genomic regions where there was a SNP that influences both eBMD and FNK-BMD. Most genomic regions only contained putative causal SNPs associated with eBMD and 3 regions contained two distinct putative causal SNPs influenced both traits, respectively. We demonstrated a causal effect of FNK-BMD/eBMD on fracture. Conclusion Most of SNPs or putative causal SNPs associated with FNK-BMD were also associated with eBMD. However, most of SNPs or putative causal SNPs associated with eBMD were not associated with FNK-BMD. The novel variants we identified may help to account for the additional proportion of variance of each trait and advance our understanding of the genetic mechanisms underlying osteoporotic fracture.
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Affiliation(s)
- Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiang-He Meng
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,Center of Reproductive Health, System Biology and Data Information, School of Basic Medical Science, Central South University, Changsha, China.,Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiao Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xu Lin
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Qiang Zhang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ri-Li Jiang
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Martin R Schiller
- Nevada Institute of Personalized Medicine, School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States.,Center of Reproductive Health, System Biology and Data Information, School of Basic Medical Science, Central South University, Changsha, China.,Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
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Roca-Ayats N, Martínez-Gil N, Cozar M, Gerousi M, Garcia-Giralt N, Ovejero D, Mellibovsky L, Nogués X, Díez-Pérez A, Grinberg D, Balcells S. Functional characterization of the C7ORF76 genomic region, a prominent GWAS signal for osteoporosis in 7q21.3. Bone 2019; 123:39-47. [PMID: 30878523 DOI: 10.1016/j.bone.2019.03.014] [Citation(s) in RCA: 10] [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: 01/29/2019] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/21/2022]
Abstract
Genome-wide association studies (GWAS) have repeatedly identified genetic variants associated with bone mineral density (BMD) and osteoporotic fracture in non-coding regions of C7ORF76, a poorly studied gene of unknown function. The aim of the present study was to elucidate the causality and molecular mechanisms underlying the association. We re-sequenced the genomic region in two extreme BMD groups from the BARCOS cohort of postmenopausal women to search for functionally relevant variants. Eight selected variants were tested for association in the complete cohort and 2 of them (rs4342521 and rs10085588) were found significantly associated with lumbar spine BMD and nominally associated with osteoporotic fracture. cis-eQTL analyses of these 2 SNPs, together with SNP rs4727338 (GWAS lead SNP in Estrada et al., Nat Genet. 44:491-501, 2012), performed in human primary osteoblasts, disclosed a statistically significant influence on the expression of the proximal neighbouring gene SLC25A13 and a tendency on the distal SHFM1. We then studied the functionality of a putative upstream regulatory element (UPE), containing rs10085588. Luciferase reporter assays showed transactivation capability with a strong allele-dependent effect. Finally, 4C-seq experiments in osteoblastic cell lines showed that the UPE interacted with different tissue-specific enhancers and a lncRNA (LOC100506136) in the region. In summary, this study is the first one to analyse in depth the functionality of C7ORF76 genomic region. We provide functional regulatory evidence for the rs10085588, which may be a causal SNP within the 7q21.3 GWAS signal for osteoporosis.
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Affiliation(s)
- Neus Roca-Ayats
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Núria Martínez-Gil
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Mónica Cozar
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Marina Gerousi
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Natàlia Garcia-Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Diana Ovejero
- National Research Council, Institute of Clinical Physiology, Lecce, Italy
| | - Leonardo Mellibovsky
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Xavier Nogués
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Adolfo Díez-Pérez
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain.
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3
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Techapatiphandee M, Tammachote N, Tammachote R, Wongkularb A, Yanatatsaneejit P. VDR and TNFSF11 polymorphisms are associated with osteoporosis in Thai patients. Biomed Rep 2018; 9:350-356. [PMID: 30233789 DOI: 10.3892/br.2018.1137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
Determining molecular markers for osteoporosis may be valuable for improving the quality of life of affected elderly patients by aiding in early detection and disease management. In the present study, the association between single nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) and tumour necrosis factor superfamily number 11 (TNFSF11) genes and the susceptibility of developing osteoporosis was investigated in a Thai female cohort. The study group consisted of 105 Thai postmenopausal patients diagnosed with osteoporosis and 132 healthy Thai postmenopausal female volunteers. DNA extracted from blood samples was used to genotype the VDR and TNFSF11 genes using polymerase chain reaction-restriction fragment length polymorphism and sequencing analysis. For VDR, the frequencies of the genotypes TT, CT and CC for the TaqI SNP (rs731236) were 87.88, 11.36 and 0.76%, respectively, in the control group, while in the osteoporosis cohort were 92.38, 5.71 and 1.91%, respectively. For the FokI SNP (rs2228570), the frequencies of the genotypes CC, CT and TT were 31.06, 55.30 and 13.64%, respectively, in the control group, and in the osteoporosis group were 29.52, 43.81 and 26.67%, respectively. For BsmI SNP (rs1544410), the frequencies of the genotypes GG, GA and AA were 78.03, 18.94 and 3.03%, respectively, in control group, and in the osteoporosis group were 80.95, 18.10 and 0.95%, respectively. The significant risk of osteoporosis associated with the FokI SNP was determined. The odds ratio (95% confidence interval) was 2.30 (1.14-4.69; P=0.01) among patients with osteoporosis with TT as the susceptibility genotype. For TNFSF11, the frequencies of the genotypes TT, CT and CC for the -290C>T SNP (rs9525641) in the control group were 36.36, 50.76 and 12.88%, respectively, while in the osteoporosis group were 31.43, 56.19 and 12.38%, respectively. For the -643C>T SNP (rs9533156), the frequencies of the genotypes TT, CT and CC in the control group were 35.61, 48.48 and 15.91%, respectively, while in the osteoporosis group were 32.38, 55.24 and 12.38%, respectively. For the -693G>C SNP (rs9533155), the frequencies of the genotypes CC, CG, and GG in the control group were 39.39, 46.97 and 13.64%, respectively, and in the osteoporosis group were 36.19, 53.33 and 10.48%, respectively. No significant associations of the TNFSF11 SNPs with osteoporosis were determined; however, it was notable that the GCT haplotype of TNFSF11 may be a protective haplotype for osteoporosis. Therefore, it was concluded that the SNP FokI of VDR may be a potential molecular biomarker for the development of osteoporosis in Thai females.
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Affiliation(s)
- Mananya Techapatiphandee
- Human Genetics Research Group, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nattapol Tammachote
- Department of Orthopaedics, Faculty of Medicine, Thammasat University Hospital, Khlong Nueng, Pathumthani 12120, Thailand
| | - Rachaneekorn Tammachote
- Human Genetics Research Group, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Anna Wongkularb
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Pattamawadee Yanatatsaneejit
- Human Genetics Research Group, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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4
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Varley I, Hughes DC, Greeves JP, Fraser WD, Sale C. SNPs in the vicinity of P2X7R, RANK/RANKL/OPG and Wnt signalling pathways and their association with bone phenotypes in academy footballers. Bone 2018; 108:179-185. [PMID: 29325759 DOI: 10.1016/j.bone.2018.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 12/30/2022]
Abstract
CONTEXT Genotype plays an important role in influencing bone phenotypes, such as bone mineral density, but the role of genotype in determining responses of bone to exercise has yet to be elucidated. OBJECTIVE To determine whether 10 SNPs associated with genes in the vicinity of P2X7R, RANK/RANKL/OPG and Wnt Signalling Pathways are associated with bone phenotypes in elite academy footballers (Soccer players) and to determine whether these genotypes are associated with training induced changes in bone. Design, participants, and methods: 99 elite academy footballers volunteered to participate. Peripheral computed tomography of the tibia (4%, 14%, 38% and 66% sites) was performed immediately before and 12 weeks after an increase in football training volume. Genotypes were determined using proprietary fluorescence-based competitive allele-specific PCR assays. RESULTS No significant genotype by time interactions were shown for any of the SNPs analysed (P > .05). A main effect of genotype was shown. SOST SNP rs1877632 (trabecular density), P2X7R SNPs rs1718119 (cortical thickness and CSA), rs3751143 (SSI, CSA, cortical CSA and periosteal circumference) RANK/RANKL/OPG SNPs rs9594738 (periosteal circumference), rs1021188 (cortical thickness and CSA) and rs9594759 (cortical density) were associated with bone phenotypes (P < .05). CONCLUSIONS No association was shown between P2X7R, RANK/RANKL/OPG and Wnt Signalling SNPs and a change in bone phenotypes following 12 weeks of increased training volume in elite academy footballers. However, SNPs were associated with bone phenotypes pre training. These data highlight the complexity of the interaction between SNPs in the vicinity of the RANK/RANKL/OPG, P2X7R and Wnt metabolic regulatory pathways and bone phenotypes in elite academy footballers.
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Affiliation(s)
- Ian Varley
- Musculoskeletal Physiology Research Group, Sport, Health and Performance Enhancement Research Centre, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK.
| | - David C Hughes
- Department of Life Sciences, School of Health Sciences, Birmingham City University, City South Campus, Edgbaston B15 3TN, UK.
| | | | - William D Fraser
- Norwich Medical School, University of East Anglia, UK; Norfolk and Norwich University Hospital, Norfolk, UK.
| | - Craig Sale
- Musculoskeletal Physiology Research Group, Sport, Health and Performance Enhancement Research Centre, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK.
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5
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P4 medicine and osteoporosis: a systematic review. Wien Klin Wochenschr 2016; 128:480-491. [PMID: 27873024 DOI: 10.1007/s00508-016-1125-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Osteoporosis is the most frequent bone metabolic disease. In order to improve early detection, prediction, prevention, diagnosis, and treatment of the disease, a new model of P4 medicine (personalized, predictive, preventive, and participatory medicine) could be applied. The aim of this work was to systematically review the publications of four different types of "omics" studies related to osteoporosis, in order to discover novel predictive, preventive, diagnostic, and therapeutic targets for better management of the geriatric population. METHODS To systematically search the PubMed database, we created specific groups of criteria for four different types of "omics" information on osteoporosis: genomic, transcriptomic, proteomic, and metabolomic. We then analyzed the intersections between them in order to find correlations and common pathways or molecules with important roles in osteoporosis, and with a potential application in disease prediction, prevention, diagnosis, or treatment. RESULTS Altogether, 180 publications of "omics" studies in the field of osteoporosis were found and reviewed at first selection. After introducing the inclusion and exclusion criteria (the secondary selection), 46 papers were included in the systematic review. CONCLUSIONS The intersection of reviewed papers identified five genes (ESR1, IBSP, CTNNB1, SOX4, and IDUA) and processes like the Wnt pathway, JAK/STAT signaling, and ERK/MAPK, which should be further validated for their predictive, diagnostic, or other clinical value in osteoporosis. Such molecular insights will enable us to fit osteoporosis into the P4 strategy and could increase the effectiveness of disease prediction and prevention, with a decrease in morbidity in the geriatric population.
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6
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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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7
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Yoskovitz G, Garcia-Giralt N, Rodriguez-Sanz M, Urreizti R, Guerri R, Ariño-Ballester S, Prieto-Alhambra D, Mellibovsky L, Grinberg D, Nogues X, Balcells S, Diez-Perez A. Analyses of RANK and RANKL in the post-GWAS context: functional evidence of vitamin D stimulation through a RANKL distal region. J Bone Miner Res 2013; 28:2550-60. [PMID: 23744843 DOI: 10.1002/jbmr.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/09/2013] [Accepted: 05/28/2013] [Indexed: 01/23/2023]
Abstract
Over the past decade, many genome-wide association studies (GWAs) and meta-analyses have identified genes and regions involved in osteoporotic phenotypes. Nevertheless, the large majority of these results were not tested at any functional level. GWA-associated single-nucleotide polymorphisms (SNPs) near candidate genes such as RANK and RANKL suggest that these SNPs and/or other variants nearby may be involved in bone phenotype determination. This study focuses on SNPs along these two genes, which encode proteins with a well-established role in the bone remodeling equilibrium. Thirty-three SNPs, chosen for their location in evolutionary conserved regions or replicated from previous studies, were genotyped in the BARCOS cohort of 1061 postmenopausal women and tested for association with osteoporotic phenotypes. SNP rs9594738, which lies 184 kb upstream of the RANKL gene, was the only SNP found to be associated with a bone phenotype (dominant model: beta coefficient = -0.034, p = 1.5 × 10(-4) , for lumbar spine bone mineral density). Functional experiments exploring a distal region (DR) of 831 bp that harbors this SNP in a centered position (nt 470) demonstrated its capacity to inhibit the RANKL promoter in reporter gene assays. Remarkably, this DR inhibition was significantly reduced in the presence of vitamin D. In conclusion, the GWA-associated SNP rs9594738 lies in a region involved in transcription regulation through which vitamin D could be regulating RANKL expression and bone mineral density.
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Affiliation(s)
- Guy Yoskovitz
- URFOA, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Red Temática de Investigación Cooperativa en Envejecimiento y Fragilidad (RETICEF), Barcelona, Spain
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8
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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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