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Busse E, Lee B, Nagamani SCS. Genetic Evaluation for Monogenic Disorders of Low Bone Mass and Increased Bone Fragility: What Clinicians Need to Know. Curr Osteoporos Rep 2024; 22:308-317. [PMID: 38600318 DOI: 10.1007/s11914-024-00870-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE OF REVIEW The purpose of this review is to outline the principles of clinical genetic testing and to provide practical guidance to clinicians in navigating genetic testing for patients with suspected monogenic forms of osteoporosis. RECENT FINDINGS Heritability assessments and genome-wide association studies have clearly shown the significant contributions of genetic variations to the pathogenesis of osteoporosis. Currently, over 50 monogenic disorders that present primarily with low bone mass and increased risk of fractures have been described. The widespread availability of clinical genetic testing offers a valuable opportunity to correctly diagnose individuals with monogenic forms of osteoporosis, thus instituting appropriate surveillance and treatment. Clinical genetic testing may identify the appropriate diagnosis in a subset of patients with low bone mass, multiple or unusual fractures, and severe or early-onset osteoporosis, and thus clinicians should be aware of how to incorporate such testing into their clinical practices.
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Affiliation(s)
- Emily Busse
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Houston, TX, USA.
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
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Prijatelj V, Grgic O, Uitterlinden AG, Wolvius EB, Rivadeneira F, Medina-Gomez C. Bone health index in the assessment of bone health: The Generation R Study. Bone 2024; 182:117070. [PMID: 38460828 DOI: 10.1016/j.bone.2024.117070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/25/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Bone Health Index (BHI) has been proposed as a useful instrument for assessing bone health in children. However, its relationship with fracture risk remains unknown. We aimed to investigate whether BHI is associated with bone mineral density (BMD) and prevalent fracture odds in children from the Generation R Study. We also implemented genome-wide association study (GWAS) and polygenic score (PGS) approaches to improve our understanding of BHI and its potential. In total, 4150 children (49.4 % boys; aged 9.8 years) with genotyped data and bone assessments were included in this study. BMD was measured across the total body (less head following ISCD guidelines) using a GE-Lunar iDXA densitometer; and BHI was determined from the hand DXA scans using BoneXpert®. Fractures were self-reported collected with home questionnaires. The association of BHI with BMD and fractures was evaluated using linear models corrected for age, sex, ethnicity, height, and weight. We observed a positive correlation between BHI and BMD (ρ = 0.32, p-value<0.0001). Further, every SD decrease in BHI was associated with an 11 % increased risk of prevalent fractures (OR:1.11, 95 % CI 1.00-1.24, p-value = 0.05). Our BHI GWAS identified variants (lead SNP rs1404264-A, p-value = 2.61 × 10-14) mapping to the ING3/CPED1/WNT16 locus. Children in the extreme tails of the BMD PGS presented a difference in BHI values of -0.10 standard deviations (95% CI -0.14 to -0.07; p-value<0.0001). On top of the demonstrated epidemiological association of BHI with both BMD and fracture risk, our results reveal a partially shared biological background between BHI and BMD. These findings highlight the potential value of using BHI to screen children at risk of fracture.
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Affiliation(s)
- Vid Prijatelj
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, the Netherlands
| | - Olja Grgic
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands
| | - Eppo B Wolvius
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands; The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD, the Netherlands.
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Austin TR, Fink HA, Jalal DI, Törnqvist AE, Buzkova P, Barzilay JI, Lu T, Carbone L, Gabrielsen ME, Grahnemo L, Hveem K, Jonasson C, Kizer JR, Langhammer A, Mukamal KJ, Gerszten RE, Nethander M, Psaty BM, Robbins JA, Sun YV, Skogholt AH, Åsvold BO, Valderrabano RJ, Zheng J, Richards JB, Coward E, Ohlsson C. Large-scale circulating proteome association study (CPAS) meta-analysis identifies circulating proteins and pathways predicting incident hip fractures. J Bone Miner Res 2024; 39:139-149. [PMID: 38477735 PMCID: PMC11070286 DOI: 10.1093/jbmr/zjad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 03/14/2024]
Abstract
Hip fractures are associated with significant disability, high cost, and mortality. However, the exact biological mechanisms underlying susceptibility to hip fractures remain incompletely understood. In an exploratory search of the underlying biology as reflected through the circulating proteome, we performed a comprehensive Circulating Proteome Association Study (CPAS) meta-analysis for incident hip fractures. Analyses included 6430 subjects from two prospective cohort studies (Cardiovascular Health Study and Trøndelag Health Study) with circulating proteomics data (aptamer-based 5 K SomaScan version 4.0 assay; 4979 aptamers). Associations between circulating protein levels and incident hip fractures were estimated for each cohort using age and sex-adjusted Cox regression models. Participants experienced 643 incident hip fractures. Compared with the individual studies, inverse-variance weighted meta-analyses yielded more statistically significant associations, identifying 23 aptamers associated with incident hip fractures (conservative Bonferroni correction 0.05/4979, P < 1.0 × 10-5). The aptamers most strongly associated with hip fracture risk corresponded to two proteins of the growth hormone/insulin growth factor system (GHR and IGFBP2), as well as GDF15 and EGFR. High levels of several inflammation-related proteins (CD14, CXCL12, MMP12, ITIH3) were also associated with increased hip fracture risk. Ingenuity pathway analysis identified reduced LXR/RXR activation and increased acute phase response signaling to be overrepresented among those proteins associated with increased hip fracture risk. These analyses identified several circulating proteins and pathways consistently associated with incident hip fractures. These findings underscore the usefulness of the meta-analytic approach for comprehensive CPAS in a similar manner as has previously been observed for large-scale human genetic studies. Future studies should investigate the underlying biology of these potential novel drug targets.
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Affiliation(s)
- Thomas R Austin
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, United States
| | - Howard A Fink
- Geriatric Research Education and Clinical Center, VA Health Care System, Minneapolis, MN, 56401, United States
| | - Diana I Jalal
- Division of Nephrology, Department of Internal Medicine, Carver College of Medicine, Iowa City, IA, 52242, United States
- Iowa City VA Medical Center, Iowa City, IA, 52246, United States
| | - Anna E Törnqvist
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Petra Buzkova
- Department of Biostatistics, University of Washington, Seattle, WA, 98115, United States
| | - Joshua I Barzilay
- Division of Endocrinology, Kaiser Permanente of Georgia, Atlanta, GA, 30339, United States
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, H3G 0B1, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, H3Y 2W4, Canada
| | - Laura Carbone
- Charlie Norwood VAMC, Augusta, GA, 30901, United States
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, United States
| | - Maiken E Gabrielsen
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Louise Grahnemo
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Kristian Hveem
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- HUNT Research Centre, NTNU, 7600, Levanger, Norway
| | - Christian Jonasson
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Jorge R Kizer
- Cardiology Section, San Francisco VA Health Care System, San Francisco, CA, 94121, United States
- Department of Medicine, Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, United States
| | - Arnulf Langhammer
- HUNT Research Centre, NTNU, 7600, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, 7600, Levanger, Norway
| | - Kenneth J Mukamal
- Department of Medicine, Beth Israel Deaconess Medical Center, Brookline, MA, 2446, United States
| | - Robert E Gerszten
- Department of Medicine, Beth Israel Deaconess Medical Center, Brookline, MA, 2446, United States
| | - Maria Nethander
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
- Bioinformatics and Data Center, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, United States
- Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, 98195, United States
| | - John A Robbins
- Department of Medicine, University of California, Davis, CA, 95817, United States
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, United States
| | - Anne Heidi Skogholt
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Bjørn Olav Åsvold
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, 7491, Trondheim, Norway
| | - Rodrigo J Valderrabano
- Research Program in Men’s Health, Aging and Metabolism, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, 2130, United States
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai, 200025, China
- Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai National Clinical Research Center for Metabolic Diseases, Shanghai Digital Medicine Innovation Center, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai, 200025, China
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Bristol, BS8 2BN, United Kingdom
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, H3Y 2W4, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
- Department of Twin Research, King’s College London, London, SE1 7EH, United Kingdom
| | - Eivind Coward
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
- Department of Drug Treatment, Region Västra Götaland, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
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Wang Y, Zhao W, Ross A, You L, Wang H, Zhou X. Revealing chronic disease progression patterns using Gaussian process for stage inference. J Am Med Inform Assoc 2024; 31:396-405. [PMID: 38055638 PMCID: PMC10797260 DOI: 10.1093/jamia/ocad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
OBJECTIVE The early stages of chronic disease typically progress slowly, so symptoms are usually only noticed until the disease is advanced. Slow progression and heterogeneous manifestations make it challenging to model the transition from normal to disease status. As patient conditions are only observed at discrete timestamps with varying intervals, an incomplete understanding of disease progression and heterogeneity affects clinical practice and drug development. MATERIALS AND METHODS We developed the Gaussian Process for Stage Inference (GPSI) approach to uncover chronic disease progression patterns and assess the dynamic contribution of clinical features. We tested the ability of the GPSI to reliably stratify synthetic and real-world data for osteoarthritis (OA) in the Osteoarthritis Initiative (OAI), bipolar disorder (BP) in the Adolescent Brain Cognitive Development Study (ABCD), and hepatocellular carcinoma (HCC) in the UTHealth and The Cancer Genome Atlas (TCGA). RESULTS First, GPSI identified two subgroups of OA based on image features, where these subgroups corresponded to different genotypes, indicating the bone-remodeling and overweight-related pathways. Second, GPSI differentiated BP into two distinct developmental patterns and defined the contribution of specific brain region atrophy from early to advanced disease stages, demonstrating the ability of the GPSI to identify diagnostic subgroups. Third, HCC progression patterns were well reproduced in the two independent UTHealth and TCGA datasets. CONCLUSION Our study demonstrated that an unsupervised approach can disentangle temporal and phenotypic heterogeneity and identify population subgroups with common patterns of disease progression. Based on the differences in these features across stages, physicians can better tailor treatment plans and medications to individual patients.
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Affiliation(s)
- Yanfei Wang
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Weiling Zhao
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Angela Ross
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Lei You
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Hongyu Wang
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
- Cizik School of Nursing, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
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Ben-Zvi I, Karasik D, Ackert-Bicknell CL. Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies. Curr Osteoporos Rep 2023; 21:650-659. [PMID: 37971665 DOI: 10.1007/s11914-023-00831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW GWAS, as a largely correlational analysis, requires in vitro or in vivo validation. Zebrafish (Danio rerio) have many advantages for studying the genetics of human diseases. Since gene editing in zebrafish has been highly valuable for studying embryonic skeletal developmental processes that are prenatally or perinatally lethal in mammalian models, we are reviewing pros and cons of this model. RECENT FINDINGS The true power for the use of zebrafish is the ease by which the genome can be edited, especially using the CRISPR/Cas9 system. Gene editing, followed by phenotyping, for complex traits such as BMD, is beneficial, but the major physiological differences between the fish and mammals must be considered. Like mammals, zebrafish do have main bone cells; thus, both in vivo stem cell analyses and in vivo imaging are doable. Yet, the "long" bones of fish are peculiar, and their bone cavities do not contain bone marrow. Partial duplication of the zebrafish genome should be taken into account. Overall, small fish toolkit can provide unmatched opportunities for genetic modifications and morphological investigation as a follow-up to human-first discovery.
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Affiliation(s)
- Inbar Ben-Zvi
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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He D, Liu H, Wei W, Zhao Y, Cai Q, Shi S, Chu X, Qin X, Zhang N, Xu P, Zhang F. A longitudinal genome-wide association study of bone mineral density mean and variability in the UK Biobank. Osteoporos Int 2023; 34:1907-1916. [PMID: 37500982 DOI: 10.1007/s00198-023-06852-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023]
Abstract
Bone mineral density (BMD) is an essential predictor of osteoporosis and fracture. We conducted a genome-wide trajectory analysis of BMD and analyzed the BMD change. PURPOSE This study aimed to identify the genetic architecture and potential biomarkers of BMD. METHODS Our analysis included 141,261 white participants from the UK Biobank with heel BMD phenotype data. We used a genome-wide trajectory analysis tool, TrajGWAS, to conduct a genome-wide association study (GWAS) of BMD. Then, we validated our findings in previously reported BMD genetic associations and performed replication analysis in the Asian participants. Finally, gene-set enrichment analysis (GSEA) of the identified candidate genes was conducted using the FUMA platform. RESULTS A total of 52 genes associated with BMD trajectory mean were identified, of which the top three significant genes were WNT16 (P = 1.31 × 10-126), FAM3C (P = 4.18 × 10-108), and CPED1 (P = 8.48 × 10-106). In addition, 114 genes associated with BMD within-subject variability were also identified, such as AC092079.1 (P = 2.72 × 10-13) and RGS7 (P = 4.72 × 10-10). The associations for these candidate genes were confirmed in the previous GWASs and replicated successfully in the Asian participants. GSEA results of BMD change identified multiple GO terms related to skeletal development, such as SKELETAL SYSTEM DEVELOPMENT (Padjusted = 2.45 × 10-3) and REGULATION OF OSSIFICATION (Padjusted = 2.45 × 10-3). KEGG enrichment analysis showed that these genes were mainly enriched in WNT SIGNALING PATHWAY. CONCLUSIONS Our findings indicated that the CPED1-WNT16-FAM3C locus plays a significant role in BMD mean trajectories and identified several novel candidate genes contributing to BMD within-subject variability, facilitating the understanding of the genetic architecture of BMD.
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Affiliation(s)
- Dan He
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Huan Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Wenming Wei
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Yijing Zhao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Qingqing Cai
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Sirong Shi
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Xiaoge Chu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Xiaoyue Qin
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Na Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China.
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Xi'an Jiaotong University, Xi'an, 710061, China.
- Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Xi'an Jiaotong University, Xi'an, China.
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China.
- School of Public Health, Xi'an Jiaotong University Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, China.
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Zheng J, Wheeler E, Pietzner M, Andlauer TFM, Yau MS, Hartley AE, Brumpton BM, Rasheed H, Kemp JP, Frysz M, Robinson J, Reppe S, Prijatelj V, Gautvik KM, Falk L, Maerz W, Gergei I, Peyser PA, Kavousi M, de Vries PS, Miller CL, Bos M, van der Laan SW, Malhotra R, Herrmann M, Scharnagl H, Kleber M, Dedoussis G, Zeggini E, Nethander M, Ohlsson C, Lorentzon M, Wareham N, Langenberg C, Holmes MV, Davey Smith G, Tobias JH. Lowering of Circulating Sclerostin May Increase Risk of Atherosclerosis and Its Risk Factors: Evidence From a Genome-Wide Association Meta-Analysis Followed by Mendelian Randomization. Arthritis Rheumatol 2023; 75:1781-1792. [PMID: 37096546 PMCID: PMC10586470 DOI: 10.1002/art.42538] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/22/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
OBJECTIVE In this study, we aimed to establish the causal effects of lowering sclerostin, target of the antiosteoporosis drug romosozumab, on atherosclerosis and its risk factors. METHODS A genome-wide association study meta-analysis was performed of circulating sclerostin levels in 33,961 European individuals. Mendelian randomization (MR) was used to predict the causal effects of sclerostin lowering on 15 atherosclerosis-related diseases and risk factors. RESULTS We found that 18 conditionally independent variants were associated with circulating sclerostin. Of these, 1 cis signal in SOST and 3 trans signals in B4GALNT3, RIN3, and SERPINA1 regions showed directionally opposite signals for sclerostin levels and estimated bone mineral density. Variants with these 4 regions were selected as genetic instruments. MR using 5 correlated cis-SNPs suggested that lower sclerostin increased the risk of type 2 diabetes mellitus (DM) (odds ratio [OR] 1.32 [95% confidence interval (95% CI) 1.03-1.69]) and myocardial infarction (MI) (OR 1.35 [95% CI 1.01-1.79]); sclerostin lowering was also suggested to increase the extent of coronary artery calcification (CAC) (β = 0.24 [95% CI 0.02-0.45]). MR using both cis and trans instruments suggested that lower sclerostin increased hypertension risk (OR 1.09 [95% CI 1.04-1.15]), but otherwise had attenuated effects. CONCLUSION This study provides genetic evidence to suggest that lower levels of sclerostin may increase the risk of hypertension, type 2 DM, MI, and the extent of CAC. Taken together, these findings underscore the requirement for strategies to mitigate potential adverse effects of romosozumab treatment on atherosclerosis and its related risk factors.
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Affiliation(s)
- Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, and Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the People's Republic of China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, and MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of BristolBristolUK
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic ScienceUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Maik Pietzner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Till F. M. Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of MedicineTechnical University of MunichMunichGermany
| | - Michelle S. Yau
- Marcus Institute for Aging Research, Hebrew SeniorLifeHarvard Medical SchoolBostonMassachusetts
| | | | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, and HUNT Research Centre, Department of Public Health and Nursing, NTNUNorwegian University of Science and TechnologyLevangerNorway
| | - Humaira Rasheed
- MRC IEU, Bristol Medical School, University of Bristol, Bristol, UK, and HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway, and Division of Medicine and Laboratory Sciences, Faculty of MedicineUniversity of OsloOsloNorway
| | - John P. Kemp
- MRC IEU, Bristol Medical School, University of Bristol, Bristol, UK, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia, and The University of Queensland Diamantina InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Monika Frysz
- MRC IEU, Bristol Medical School, University of Bristol, and Musculoskeletal Research UnitUniversity of BristolBristolUK
| | - Jamie Robinson
- MRC IEU, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Sjur Reppe
- Unger‐Vetlesen Institute, Lovisenberg Diaconal Hospital and Department of Plastic and Reconstructive Surgery, Oslo University Hospital and Department of Medical BiochemistryOslo University HospitalOsloNorway
| | - Vid Prijatelj
- Department of Internal MedicineErasmus MC University Medical CenterRotterdamThe Netherlands
| | | | - Louise Falk
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Winfried Maerz
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Austria, and SYNLAB Academy, SYNLAB Holding Deutschland GmbH and Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty MannheimUniversity of HeidelbergMannheimGermany
| | - Ingrid Gergei
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, and Therapeutic Area Cardiovascular MedicineBoehringer Ingelheim International GmbHIngelheimGermany
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn Arbor
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public HealthThe University of Texas Health Science Center at Houston
| | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health SciencesUniversity of VirginiaCharlottesville
| | - Maxime Bos
- Department of Epidemiology, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division of Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center UtrechtUtrecht UniversityUtrechtthe Netherlands
| | - Rajeev Malhotra
- Cardiology Division, Department of MedicineMassachusetts General HospitalBoston
| | - Markus Herrmann
- Clinical Institute of Medical and Chemical Laboratory DiagnosticsMedical University of GrazGrazAustria
| | - Hubert Scharnagl
- Clinical Institute of Medical and Chemical Laboratory DiagnosticsMedical University of GrazGrazAustria
| | - Marcus Kleber
- SYNLAB Academy, SYNLAB Holding Deutschland GmbHMannheimGermany
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and EducationHarokopio UniversityAthensGreece
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, and Technical University of Munich (TUM) and Klinikum Rechts der IsarTUM School of MedicineMunichGermany
| | - Maria Nethander
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg and Bioinformatics and Data Centre, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of MedicineUniversity of GothenburgGothenburgSweden
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden, and Region Västra Götaland, Geriatric Medicine, Sahlgrenska University Hospital, Mölndal, Sweden, and Mary McKillop Institute for Health ResearchAustralian Catholic UniversityMelbourneVictoriaAustralia
| | - Nick Wareham
- MRC Epidemiology Unit, Institute of Metabolic ScienceUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK, and Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin BerlinBerlinGermany
| | - Michael V. Holmes
- MRC IEU, Bristol Medical School, University of Bristol, and Medical Research Council Population Health Research Unit, University of Oxford, and Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population HealthUniversity of Oxford, and National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University HospitalOxfordUK
| | | | - Jonathan H. Tobias
- MRC IEU, Bristol Medical School, University of Bristol, and Musculoskeletal Research UnitUniversity of BristolBristolUK
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8
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Yan M, Tsukasaki M, Muro R, Ando Y, Nakamura K, Komatsu N, Nitta T, Okamura T, Okamoto K, Takayanagi H. Identification of an intronic enhancer regulating RANKL expression in osteocytic cells. Bone Res 2023; 11:43. [PMID: 37563119 PMCID: PMC10415388 DOI: 10.1038/s41413-023-00277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
The bony skeleton is continuously renewed throughout adult life by the bone remodeling process, in which old or damaged bone is removed by osteoclasts via largely unknown mechanisms. Osteocytes regulate bone remodeling by producing the osteoclast differentiation factor RANKL (encoded by the TNFSF11 gene). However, the precise mechanisms underlying RANKL expression in osteocytes are still elusive. Here, we explored the epigenomic landscape of osteocytic cells and identified a hitherto-undescribed osteocytic cell-specific intronic enhancer in the TNFSF11 gene locus. Bioinformatics analyses showed that transcription factors involved in cell death and senescence act on this intronic enhancer region. Single-cell transcriptomic data analysis demonstrated that cell death signaling increased RANKL expression in osteocytic cells. Genetic deletion of the intronic enhancer led to a high-bone-mass phenotype with decreased levels of RANKL in osteocytic cells and osteoclastogenesis in the adult stage, while RANKL expression was not affected in osteoblasts or lymphocytes. These data suggest that osteocytes may utilize a specialized regulatory element to facilitate osteoclast formation at the bone surface to be resorbed by linking signals from cellular senescence/death and RANKL expression.
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Affiliation(s)
- Minglu Yan
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masayuki Tsukasaki
- Department of Osteoimmunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Ryunosuke Muro
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaro Ando
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Microbiology, Tokyo Dental College, Tokyo, Japan
| | - Kazutaka Nakamura
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Oral and Maxillofacial Surgery, Department of Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noriko Komatsu
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Nitta
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuo Okamoto
- Department of Osteoimmunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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9
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Kaspersky U, Levy R, Nashef A, Iraqi FA, Gabet Y. A study of the influence of genetic variance and sex on the density and thickness of the calvarial bone in collaborative cross mice. Animal Model Exp Med 2023; 6:355-361. [PMID: 37448168 PMCID: PMC10486330 DOI: 10.1002/ame2.12319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/13/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Bone microarchitecture is affected by multiple genes, each having a small effect on the external appearance. It is thus challenging to characterize the genes and their specific effect on bone thickness and porosity. The purpose of this study was to assess the heritability and the genetic variation effect, as well as the sex effect on the calvarial bone thickness (Ca.Th) and calvarial porosity (%PoV) using the Collaborative Cross (CC) mouse population. METHODS In the study we examined the parietal bones of 56 mice from 9 lines of CC mice. Morphometric parameters were evaluated using microcomputed tomography (μCT) and included Ca.Th and %PoV. We then evaluated heritability, genetic versus environmental variance and the sex effect for these parameters. RESULTS Our morphometric analysis showed that Ca.Th and %PoV are both significantly different among the CC lines with a broad sense heritability of 0.78 and 0.90, respectively. The sex effect within the lines was significant in line IL111 and showed higher values of Ca.Th and %PoV in females compared to males. In line IL19 there was a borderline sex effect in Ca.Th in which males showed higher values than females. CONCLUSIONS These results stress the complexity of sex and genotype interactions controlling Ca.Th and %PoV, as the skeletal sexual dimorphism was dependent on the genetic background. This study also shows that the CC population is a powerful tool for establishing the genetic effect on these traits.
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Affiliation(s)
- Uriel Kaspersky
- Department of Anatomy and AnthropologyTel Aviv UniversityTel AvivIsrael
| | - Roei Levy
- Department of Anatomy and AnthropologyTel Aviv UniversityTel AvivIsrael
| | - Aysar Nashef
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv69978Israel
- Department of Oral and Maxillofacial SurgeryBaruch Padeh medical centerPoriyaIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv69978Israel
| | - Yankel Gabet
- Department of Anatomy and AnthropologyTel Aviv UniversityTel AvivIsrael
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10
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Wu EY, Singh NP, Choi K, Zakeri M, Vincent M, Churchill GA, Ackert-Bicknell CL, Patro R, Love MI. SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty. Genome Biol 2023; 24:165. [PMID: 37438847 PMCID: PMC10337143 DOI: 10.1186/s13059-023-03003-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution, including gene, isoform, and aggregating isoforms to groups by transcription start site. The aggregation strategies strengthen the signal for transcripts with high uncertainty. The SEESAW suite of methods is shown to have higher power than other allelic imbalance methods when there is isoform-level allelic imbalance. We also introduce a new test for detecting imbalance that varies across a covariate, such as time.
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Affiliation(s)
- Euphy Y Wu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Noor P Singh
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | | | - Mohsen Zakeri
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | | | | | - Cheryl L Ackert-Bicknell
- Department of Orthopedics, School of Medicine, University of Colorado, Anschutz Campus, Aurora, CO, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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11
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Medina-Gomez C, Mullin BH, Chesi A, Prijatelj V, Kemp JP, Shochat-Carvalho C, Trajanoska K, Wang C, Joro R, Evans TE, Schraut KE, Li-Gao R, Ahluwalia TS, Zillikens MC, Zhu K, Mook-Kanamori DO, Evans DS, Nethander M, Knol MJ, Thorleifsson G, Prokic I, Zemel B, Broer L, McGuigan FE, van Schoor NM, Reppe S, Pawlak MA, Ralston SH, van der Velde N, Lorentzon M, Stefansson K, Adams HHH, Wilson SG, Ikram MA, Walsh JP, Lakka TA, Gautvik KM, Wilson JF, Orwoll ES, van Duijn CM, Bønnelykke K, Uitterlinden AG, Styrkársdóttir U, Akesson KE, Spector TD, Tobias JH, Ohlsson C, Felix JF, Bisgaard H, Grant SFA, Richards JB, Evans DM, van der Eerden B, van de Peppel J, Ackert-Bicknell C, Karasik D, Kague E, Rivadeneira F. Bone mineral density loci specific to the skull portray potential pleiotropic effects on craniosynostosis. Commun Biol 2023; 6:691. [PMID: 37402774 PMCID: PMC10319806 DOI: 10.1038/s42003-023-04869-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/25/2023] [Indexed: 07/06/2023] Open
Abstract
Skull bone mineral density (SK-BMD) provides a suitable trait for the discovery of key genes in bone biology, particularly to intramembranous ossification, not captured at other skeletal sites. We perform a genome-wide association meta-analysis (n ~ 43,800) of SK-BMD, identifying 59 loci, collectively explaining 12.5% of the trait variance. Association signals cluster within gene-sets involved in skeletal development and osteoporosis. Among the four novel loci (ZIC1, PRKAR1A, AZIN1/ATP6V1C1, GLRX3), there are factors implicated in intramembranous ossification and as we show, inherent to craniosynostosis processes. Functional follow-up in zebrafish confirms the importance of ZIC1 on cranial suture patterning. Likewise, we observe abnormal cranial bone initiation that culminates in ectopic sutures and reduced BMD in mosaic atp6v1c1 knockouts. Mosaic prkar1a knockouts present asymmetric bone growth and, conversely, elevated BMD. In light of this evidence linking SK-BMD loci to craniofacial abnormalities, our study provides new insight into the pathophysiology, diagnosis and treatment of skeletal diseases.
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Grants
- UL1 TR000128 NCATS NIH HHS
- U01 AG042124 NIA NIH HHS
- U01 AG042145 NIA NIH HHS
- U01 AG042168 NIA NIH HHS
- U01 AG042140 NIA NIH HHS
- U24 AG051129 NIA NIH HHS
- R01 AR051124 NIAMS NIH HHS
- U01 AG027810 NIA NIH HHS
- U01 AR066160 NIAMS NIH HHS
- MC_UU_00007/10 Medical Research Council
- R01 HD058886 NICHD NIH HHS
- RC2 AR058973 NIAMS NIH HHS
- Wellcome Trust
- M01 RR000240 NCRR NIH HHS
- U01 AG042143 NIA NIH HHS
- UL1 RR026314 NCRR NIH HHS
- U01 AG042139 NIA NIH HHS
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- European Cooperation in Science and Technology (COST)
- Wellcome Trust (Wellcome)
- Department of Health | National Health and Medical Research Council (NHMRC)
- U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
- ZonMw (Netherlands Organisation for Health Research and Development)
- EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Vetenskapsrådet (Swedish Research Council)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
- NCHA (Netherlands Consortium Healthy Ageing) Leiden/ Rotterdam; Dutch Ministry of Economic Affairs, Agriculture and Innovation (project KB-15-004-003); the Research Institute for Diseases in the Elderly [Netherlands] (014-93-015; RIDE2)
- Clinical and Translational Research Center (5-MO1-RR-000240 and UL1 RR-026314); U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) GrantRecipient="Au50"
- European Commission FP6 STRP grant number 018947 (LSHG-CT-2006-01947); Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043); Netherlands Brain Foundation (project number F2013(1)-28) GrantRecipient="Au40"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au28"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au38"
- The Pawsey Supercomputing Centre (with Funding from the Australian Government and the Government of Western Australia; PG 16/0162, PG 17/director2025) GrantRecipient="Au45”
- European Commission (EC)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS);NIH Roadmap for Medical Research [USA]: U01 AG027810, U01 AG042124, U01 AG042139, U01 AG042140, U01 AG042143, U01 AG042145, U01 AG042168, U01 AR066160, and UL1 TR000128 GrantRecipient="Au39”
- Versus Arthritis [USA] 21937 GrantRecipient="Au57”
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Affiliation(s)
- Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Alessandra Chesi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Kemp
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | | | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Carol Wang
- School of Women's and Infants' Health, University of Western Australia, Crawley, WA, 6009, Australia
| | - Raimo Joro
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Tavia E Evans
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
- Steno Diabetes Center Copenhagen, Herlev, 2820, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Maria Nethander
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Ivana Prokic
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Babette Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of GI, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Fiona E McGuigan
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
| | - Natasja M van Schoor
- Department of Epidemiology and Data Science, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands
| | - Sjur Reppe
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, 0372, Oslo, Norway
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - Mikolaj A Pawlak
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Neurology, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Nathalie van der Velde
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Geriatric Medicine, Amsterdam Public Health Research Institute, Amsterdam UMC, 1105 AZ, Amsterdam, The Netherlands
| | - Mattias Lorentzon
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | | | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Latin American Brain Health (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Timo A Lakka
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Kaare M Gautvik
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Eric S Orwoll
- Department of Public Health & Preventive Medicine, Oregon Health & Science University, Portland, OR, OR97239, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Kristina E Akesson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
- Department of Orthopedics Malmö, Skåne University Hospital, S-21428, Malmö, Sweden
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jonathan H Tobias
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Bristol, BS10 5NB, UK
| | - Claes Ohlsson
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, SE-413 45, Gothenburg, Sweden
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - J Brent Richards
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
- Lady Davis Institute, Jewish General Hospital, Montreal, H3T 1E2, QC, Canada
| | - David M Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
- Marcus Institute for Aging Research, Hebrew SeniorLife, Roslindale, MA, 02131, USA
| | - Erika Kague
- The School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Fernando Rivadeneira
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands.
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12
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Xu G, Wang Q, Li Z, Wu T. Computed tomography Osteoabsorptiometry: Review of bone density, mechanical strength of material and clinical application. Front Bioeng Biotechnol 2023; 11:1066709. [PMID: 37051272 PMCID: PMC10083511 DOI: 10.3389/fbioe.2023.1066709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Computed Tomography (CT) imaging is an effective non-invasive examination. It is widely used in the diagnosis of fractures, arthritis, tumor, and some anatomical characteristics of patients. The density value (Hounsfield unit, HU) of a material in computed tomography can be the same for materials with varying elemental compositions. This value depends on the mass density of the material and the degree of X-ray attenuation. Computed Tomography Osteoabsorptiometry (CTOAM) imaging technology is developed on the basis of CT imaging technology. By applying pseudo-color image processing to the articular surface, it is used to analyze the distribution of bone mineralization under the articular cartilage, evaluate the position of prosthesis implantation, track the progression of osteoarthritis, and determine the joint injury prognosis. Furthermore, this technique was combined with indentation testing to discuss the relationship between the high bone density area of the articular surface, the mechanical strength of the bone, and the anchorage stability of the implant, in addition to the study of the relationship between mechanical strength and bone density. This narrative study discusses the pre- and postoperative evaluation of medical device implantation position, orthopedic surgery, and the clinical treatment of bone injury and degeneration. It also discusses the research status of CTOAM technology in image post-processing engineering and the relationship between bone material and mechanical strength.
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Affiliation(s)
- Guanghua Xu
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Medical Biomechanics, National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Institute of Sport and Exercise Medicine, North University of China, Taiyuan, China
| | - Qiuyuan Wang
- Graduate School of Beijing University of Chinese Medicine, Beijing, China
| | - Zhiqiang Li
- School of Physical Education, North University of China, Taiyuan, China
| | - Tingrui Wu
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- *Correspondence: Tingrui Wu,
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13
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Rowbotham SK, Mole CG, Tieppo D, Blaszkowska M, Cordner S, Blau S. Reference measurements for average human neurocranial bone density to inform head trauma interpretations. AUST J FORENSIC SCI 2022. [DOI: 10.1080/00450618.2022.2141320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Samantha K Rowbotham
- Victorian Institute of Forensic Medicine, Melbourne, Australia
- Department of Forensic Medicine, Monash University, Melbourne, Australia
| | - Calvin G Mole
- Department of Pathology, Division of Forensic Medicine and Toxicology, University of Cape Town, Cape Town, South Africa
| | - Diana Tieppo
- Department of Forensic Medicine, Monash University, Melbourne, Australia
| | - Magda Blaszkowska
- Centre for Forensic Anthropology, University of Western Australia, Perth, Australia
| | - Stephen Cordner
- Victorian Institute of Forensic Medicine, Melbourne, Australia
- Department of Forensic Medicine, Monash University, Melbourne, Australia
| | - Soren Blau
- Victorian Institute of Forensic Medicine, Melbourne, Australia
- Department of Forensic Medicine, Monash University, Melbourne, Australia
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14
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Vlashi R, Zhang X, Wu M, Chen G. Wnt signaling: essential roles in osteoblast differentiation, bone metabolism and therapeutic implications for bone and skeletal disorders. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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15
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Genetic variation in WNT16 and its association with bone mineral density, fractures and osteoporosis in children with bone fragility. Bone Rep 2022; 16:101525. [PMID: 35535173 PMCID: PMC9077160 DOI: 10.1016/j.bonr.2022.101525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/20/2022] Open
Abstract
Several genome-wide association studies (GWAS), GWAS meta-analyses, and mouse studies have demonstrated that wingless-related integration site 16 (WNT16) gene is associated with bone mineral density (BMD), cortical bone thickness, bone strength and fracture risk. Practically no data exist regarding the significance of WNT16 in childhood-onset osteoporosis and related fractures. We hypothesized that pathogenic variants and genetic variations in WNT16 could explain skeletal fragility in affected children. We screened the WNT16 gene by Sanger sequencing in three pediatric cohorts: 35 with primary osteoporosis, 59 with multiple fractures, and in 95 healthy controls. Altogether, we identified 12 variants in WNT16. Of them one was a rare 5′UTR variant rs1386898215 in genome aggregate and medical trans-omic databases (GnomAD, TOPMED; minor allele frequency (MAF) 0.00 and 0.000008, respectively). One variant rs1554366753, overrepresented in children with osteoporosis (MAF = 0.06 vs healthy controls MAF = 0.01), was significantly associated with lower BMD. This variant was found associated with increased WNT16 gene expression at mRNA level in fibroblast cultures. None of the other identified variants were rare (MAF < 0.001) or deemed pathogenic by predictor programs. WNT16 may play a role in childhood osteoporosis but genetic WNT16 variation is not a common cause of skeletal fragility in childhood. No pathogenic WNT16 variants were found associated with pediatric osteoporosis or fracture-prone patients Altogether, twelve WNT16 variants were found in pediatric osteoporosis or fracture-prone patients The genetic variation rs1554366753 in the WNT16 gene is associated with bone mineral density and primary osteoporosis
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16
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Shen R, Murphy CJ, Xu X, Hu M, Ding J, Wu C. Ras and Rab Interactor 3: From Cellular Mechanisms to Human Diseases. Front Cell Dev Biol 2022; 10:824961. [PMID: 35359443 PMCID: PMC8963869 DOI: 10.3389/fcell.2022.824961] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Ras and Rab interactor 3 (RIN3) functions as a Guanine nucleotide Exchange Factor (GEF) for some members of the Rab family of small GTPase. By promoting the activation of Rab5, RIN3 plays an important role in regulating endocytosis and endocytic trafficking. In addition, RIN3 activates Ras, another small GTPase, that controls multiple signaling pathways to regulate cellular function. Increasing evidence suggests that dysregulation of RIN3 activity may contribute to the pathogenesis of several disease conditions ranging from Paget’s Disease of the Bone (PDB), Alzheimer’s Disease (AD), Chronic Obstructive Pulmonary Disease (COPD) and to obesity. Recent genome-wide association studies (GWAS) identified variants in the RIN3 gene to be linked with these disease conditions. Interestingly, some variants appear to be missense mutations in the functional domains of the RIN3 protein while most variants are located in the noncoding regions of the RIN3 gene, potentially altering its gene expression. However, neither the protein structure of RIN3 nor its exact function(s) (except for its GEF activity) has been fully defined. Furthermore, how the polymorphisms/variants contribute to disease pathogenesis remain to be understood. Herein, we examine, and review published studies in an attempt to provide a better understanding of the physiological function of RIN3; More importantly, we construct a framework linking the polymorphisms/variants of RIN3 to altered cell signaling and endocytic traffic, and to potential disease mechanism(s).
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Affiliation(s)
- Ruinan Shen
- Institute of Neurology, Ruijing Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, United States
| | - Caitlin J Murphy
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, United States
| | - Xiaowen Xu
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, United States
| | - Mingzheng Hu
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, United States
| | - Jianqing Ding
- Institute of Neurology, Ruijing Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Chengbiao Wu
- Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, United States
- *Correspondence: Chengbiao Wu,
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17
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Spielmann N, Miller G, Oprea TI, Hsu CW, Fobo G, Frishman G, Montrone C, Haseli Mashhadi H, Mason J, Munoz Fuentes V, Leuchtenberger S, Ruepp A, Wagner M, Westphal DS, Wolf C, Görlach A, Sanz-Moreno A, Cho YL, Teperino R, Brandmaier S, Sharma S, Galter IR, Östereicher MA, Zapf L, Mayer-Kuckuk P, Rozman J, Teboul L, Bunton-Stasyshyn RKA, Cater H, Stewart M, Christou S, Westerberg H, Willett AM, Wotton JM, Roper WB, Christiansen AE, Ward CS, Heaney JD, Reynolds CL, Prochazka J, Bower L, Clary D, Selloum M, Bou About G, Wendling O, Jacobs H, Leblanc S, Meziane H, Sorg T, Audain E, Gilly A, Rayner NW, Hitz MP, Zeggini E, Wolf E, Sedlacek R, Murray SA, Svenson KL, Braun RE, White JK, Kelsey L, Gao X, Shiroishi T, Xu Y, Seong JK, Mammano F, Tocchini-Valentini GP, Beaudet AL, Meehan TF, Parkinson H, Smedley D, Mallon AM, Wells SE, Grallert H, Wurst W, Marschall S, Fuchs H, Brown SDM, Flenniken AM, Nutter LMJ, McKerlie C, Herault Y, Lloyd KCK, Dickinson ME, Gailus-Durner V, Hrabe de Angelis M. Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy. NATURE CARDIOVASCULAR RESEARCH 2022; 1:157-173. [PMID: 39195995 PMCID: PMC11358025 DOI: 10.1038/s44161-022-00018-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 01/03/2022] [Indexed: 08/29/2024]
Abstract
Clinical presentation of congenital heart disease is heterogeneous, making identification of the disease-causing genes and their genetic pathways and mechanisms of action challenging. By using in vivo electrocardiography, transthoracic echocardiography and microcomputed tomography imaging to screen 3,894 single-gene-null mouse lines for structural and functional cardiac abnormalities, here we identify 705 lines with cardiac arrhythmia, myocardial hypertrophy and/or ventricular dilation. Among these 705 genes, 486 have not been previously associated with cardiac dysfunction in humans, and some of them represent variants of unknown relevance (VUR). Mice with mutations in Casz1, Dnajc18, Pde4dip, Rnf38 or Tmem161b genes show developmental cardiac structural abnormalities, with their human orthologs being categorized as VUR. Using UK Biobank data, we validate the importance of the DNAJC18 gene for cardiac homeostasis by showing that its loss of function is associated with altered left ventricular systolic function. Our results identify hundreds of previously unappreciated genes with potential function in congenital heart disease and suggest causal function of five VUR in congenital heart disease.
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Affiliation(s)
- Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Gregor Miller
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Tudor I Oprea
- Department of Internal Medicine, Division of Translational Informatics and Center of Biomedical Research Excellence in Autophagy, Inflammation, and Metabolism, UNM Health Sciences Center and UNM Comprehensive Cancer Center, Albuquerque, NM, USA
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Gisela Fobo
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Goar Frishman
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Corinna Montrone
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Violeta Munoz Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Stefanie Leuchtenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Andreas Ruepp
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Matias Wagner
- Institut für Humangenetik, Technische Universität Munich, Munich, Germany
| | - Dominik S Westphal
- Institut für Humangenetik, Technische Universität Munich, Munich, Germany
- Klinik und Poliklinik Innere Medizin I, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Cordula Wolf
- Department of Congenital Heart Defects and Pediatric Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Agnes Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich, Munich, Germany
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Yi-Li Cho
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Raffaele Teperino
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefan Brandmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum Munich, Munich, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Sapna Sharma
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum Munich, Munich, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Isabella Rikarda Galter
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuela A Östereicher
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Lilly Zapf
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Philipp Mayer-Kuckuk
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Jan Rozman
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lydia Teboul
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | | | - Heather Cater
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | - Michelle Stewart
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | - Skevoulla Christou
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | - Henrik Westerberg
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | | | | | | | - Audrey E Christiansen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Christopher S Ward
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Jason D Heaney
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Corey L Reynolds
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lynette Bower
- Mouse Biology Program, University of California, Davis, Davis, CA, USA
| | - David Clary
- Mouse Biology Program, University of California, Davis, Davis, CA, USA
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | - Ghina Bou About
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | - Olivia Wendling
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | - Hugues Jacobs
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | - Sophie Leblanc
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | - Hamid Meziane
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
| | - Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nigel W Rayner
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | | | | | | | | | - Lois Kelsey
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | | | - Ying Xu
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, China
| | - Je Kyung Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Fabio Mammano
- CNR Institute of Biochemistry and Cell Biology, Monterotondo, Rome, Italy
| | | | - Arthur L Beaudet
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London, London, UK
| | - Ann-Marie Mallon
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | - Sara E Wells
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum Munich, Munich, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Department of Developmental Genetics, TUM School of Life Sciences, Technische Universität Munich, Freising, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Susan Marschall
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Steve D M Brown
- Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell, UK
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Colin McKerlie
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, IGBMC, Institut Clinique de la Souris, PHENOMIN-ICS, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich (GmbH), German Research Center for Environmental Health, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
- Department of Experimental Genetics, TUM School of Life Science, Technische Universität Munich, Freising, Germany.
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18
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Martínez-Gil N, Ugartondo N, Grinberg D, Balcells S. Wnt Pathway Extracellular Components and Their Essential Roles in Bone Homeostasis. Genes (Basel) 2022; 13:genes13010138. [PMID: 35052478 PMCID: PMC8775112 DOI: 10.3390/genes13010138] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
The Wnt pathway is involved in several processes essential for bone development and homeostasis. For proper functioning, the Wnt pathway is tightly regulated by numerous extracellular elements that act by both activating and inhibiting the pathway at different moments. This review aims to describe, summarize and update the findings regarding the extracellular modulators of the Wnt pathway, including co-receptors, ligands and inhibitors, in relation to bone homeostasis, with an emphasis on the animal models generated, the diseases associated with each gene and the bone processes in which each member is involved. The precise knowledge of all these elements will help us to identify possible targets that can be used as a therapeutic target for the treatment of bone diseases such as osteoporosis.
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19
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Estrogen receptor alpha and NFATc1 bind to a bone mineral density-associated SNP to repress WNT5B in osteoblasts. Am J Hum Genet 2022; 109:97-115. [PMID: 34906330 DOI: 10.1016/j.ajhg.2021.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/17/2021] [Indexed: 12/27/2022] Open
Abstract
Genetic factors and estrogen deficiency contribute to the development of osteoporosis. The single-nucleotide polymorphism (SNP) rs2887571 is predicted from genome-wide association studies (GWASs) to associate with osteoporosis but has had an unknown mechanism. Analysis of osteoblasts from 110 different individuals who underwent joint replacement revealed that the genotype of rs2887571 correlates with WNT5B expression. Analysis of our ChIP-sequencing data revealed that SNP rs2887571 overlaps with an estrogen receptor alpha (ERα) binding site. Here we show that 17β-estradiol (E2) suppresses WNT5B expression and further demonstrate the mechanism of ERα binding at the enhancer containing rs2887571 to suppress WNT5B expression differentially in each genotype. ERα interacts with NFATc1, which is predicted to bind directly at rs2887571. CRISPR-Cas9 and ChIP-qPCR experiments confirm differential regulation of WNT5B between each allele. Homozygous GG has a higher binding affinity for ERα than homozygous AA and results in greater suppression of WNT5B expression. Functionally, WNT5B represses alkaline phosphatase expression and activity, decreasing osteoblast differentiation and mineralization. Furthermore, WNT5B increases interleukin-6 expression and suppresses E2-induced expression of alkaline phosphatase during osteoblast differentiation. We show that WNT5B suppresses the differentiation of osteoblasts via receptor tyrosine kinase-like orphan receptor 1/2 (ROR1/2), which activates DVL2/3/RAC1/CDC42/JNK/SIN3A signaling and inhibits β-catenin activity. Together, our data provide mechanistic insight into how ERα and NFATc1 regulate the non-coding SNP rs2887571, as well as the function of WNT5B on osteoblasts, which could provide alternative therapeutic targets for osteoporosis.
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20
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Kague E, Medina-Gomez C, Boyadjiev SA, Rivadeneira F. The genetic overlap between osteoporosis and craniosynostosis. Front Endocrinol (Lausanne) 2022; 13:1020821. [PMID: 36225206 PMCID: PMC9548872 DOI: 10.3389/fendo.2022.1020821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Osteoporosis is the most prevalent bone condition in the ageing population. This systemic disease is characterized by microarchitectural deterioration of bone, leading to increased fracture risk. In the past 15 years, genome-wide association studies (GWAS), have pinpointed hundreds of loci associated with bone mineral density (BMD), helping elucidate the underlying molecular mechanisms and genetic architecture of fracture risk. However, the challenge remains in pinpointing causative genes driving GWAS signals as a pivotal step to drawing the translational therapeutic roadmap. Recently, a skull BMD-GWAS uncovered an intriguing intersection with craniosynostosis, a congenital anomaly due to premature suture fusion in the skull. Here, we recapitulate the genetic contribution to both osteoporosis and craniosynostosis, describing the biological underpinnings of this overlap and using zebrafish models to leverage the functional investigation of genes associated with skull development and systemic skeletal homeostasis.
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Affiliation(s)
- Erika Kague
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, United Kingdom
- *Correspondence: Erika Kague,
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus Medical Center (MC), University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Simeon A. Boyadjiev
- Department of Pediatrics, University of California, Davis, Sacramento, CA, United States
| | - Fernando Rivadeneira
- Department of Oral and Maxillofacial Surgery, Erasmus Medical Center (MC), University Medical Center Rotterdam, Rotterdam, Netherlands
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21
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Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight. J Mol Med (Berl) 2022; 100:723-734. [PMID: 35314877 PMCID: PMC9110509 DOI: 10.1007/s00109-021-02165-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/13/2021] [Accepted: 11/04/2021] [Indexed: 02/04/2023]
Abstract
An increasing number of epidemiological studies have suggested that birth weight (BW) may be a determinant of bone health later in life, although the underlying genetic mechanism remains unclear. Here, we applied a pleiotropic conditional false discovery rate (cFDR) approach to the genome-wide association study (GWAS) summary statistics for lumbar spine bone mineral density (LS BMD) and BW, aiming to identify novel susceptibility variants shared between these two traits. We detected 5 novel potential pleiotropic loci which are located at or near 7 different genes (NTAN1, PDXDC1, CACNA1G, JAG1, FAT1P1, CCDC170, ESR1), among which PDXDC1 and FAT1P1 have not previously been linked to these phenotypes. To partially validate the findings, we demonstrated that the expression of PDXDC1 was dramatically reduced in ovariectomized (OVX) mice in comparison with sham-operated (SHAM) mice in both the growth plate and trabecula bone. Furthermore, immunohistochemistry assay with serial sections showed that both osteoclasts and osteoblasts express PDXDC1, supporting its potential role in bone metabolism. In conclusion, our study provides insights into some shared genetic mechanisms for BMD and BW as well as a novel potential therapeutic target for the prevention of OP in the early stages of the disease development. KEY MESSAGES : We investigated pleiotropy-informed enrichment between LS BMD and BW. We identified genetic variants related to both LS BMD and BW by utilizing a cFDR approach. PDXDC1 is a novel pleiotropic gene which may be related to both LS BMD and BW. Elevated expression of PDXDC1 is related to higher BMD and lower ratio n-6/n-3 PUFA indicating a bone protective effect of PDXDC1.
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22
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Gomez GA, Rundle CH, Xing W, Kesavan C, Pourteymoor S, Lewis RE, Powell DR, Mohan S. Contrasting effects of <i>Ksr2</i>, an obesity gene, on trabecular bone volume and bone marrow adiposity. eLife 2022; 11:82810. [PMID: 36342465 PMCID: PMC9640193 DOI: 10.7554/elife.82810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/06/2022] [Indexed: 11/25/2022] Open
Abstract
Pathological obesity and its complications are associated with an increased propensity for bone fractures. Humans with certain genetic polymorphisms at the kinase suppressor of ras2 (KSR2) locus develop severe early-onset obesity and type 2 diabetes. Both conditions are phenocopied in mice with <i>Ksr2</i> deleted, but whether this affects bone health remains unknown. Here we studied the bones of global <i>Ksr2</i> null mice and found that <i>Ksr2</i> negatively regulates femoral, but not vertebral, bone mass in two genetic backgrounds, while the paralogous gene, <i>Ksr1</i>, was dispensable for bone homeostasis. Mechanistically, KSR2 regulates bone formation by influencing adipocyte differentiation at the expense of osteoblasts in the bone marrow. Compared with <i>Ksr2</i>'s known role as a regulator of feeding by its function in the hypothalamus, pair-feeding and osteoblast-specific conditional deletion of <i>Ksr2</i> reveals that <i>Ksr2</i> can regulate bone formation autonomously. Despite the gains in appendicular bone mass observed in the absence of <i>Ksr2</i>, bone strength, as well as fracture healing response, remains compromised in these mice. This study highlights the interrelationship between adiposity and bone health and provides mechanistic insights into how <i>Ksr2</i>, an adiposity and diabetic gene, regulates bone metabolism.
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Affiliation(s)
| | - Charles H Rundle
- VA Loma Linda Healthcare SystemLoma LindaUnited States,Loma Linda University Medical CenterLoma LindaUnited States
| | - Weirong Xing
- VA Loma Linda Healthcare SystemLoma LindaUnited States,Loma Linda University Medical CenterLoma LindaUnited States
| | - Chandrasekhar Kesavan
- VA Loma Linda Healthcare SystemLoma LindaUnited States,Loma Linda University Medical CenterLoma LindaUnited States
| | | | | | | | - Subburaman Mohan
- VA Loma Linda Healthcare SystemLoma LindaUnited States,Loma Linda University Medical CenterLoma LindaUnited States
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23
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Ye X, Liu X. Wnt16 signaling in bone homeostasis and osteoarthristis. Front Endocrinol (Lausanne) 2022; 13:1095711. [PMID: 36619549 PMCID: PMC9815800 DOI: 10.3389/fendo.2022.1095711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Wnts are secreted cysteine-rich glycoproteins involved in joint development and skeletal homeostasis and have been implicated in the occurrence of osteoarthritis. Over the past decade, Wnt16, a member of the Wnt family, has received widespread attention for its strong association with bone mineral density, cortical bone thickness, bone strength, and osteoporotic fracture risk. In recent years, further studies have shed light on the role of Wnt16 a positive regulator of bone mass and protective regulator of osteoarthritis progression. Transduction mechanisms and crosstalk involving Wnt16 signaling have also been illustrated. More importantly, local Wnt16 treatment has been shown to ease osteoarthritis, inhibit bone resorption, and promote new bone formation in bone defect models. Thus, Wnt16 is now a potential therapeutic target for skeletal diseases and osteoarthritis. This paper reviews our current understanding of the mechanisms by which Wnt16 signaling regulates bone homeostasis and osteoarthritis.
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24
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Jo S, Weon S, Nam B, Jang MA, Kang H, Kim TJ, Park YS, Kim TH. WNT16 elevation induced cell senescence of osteoblasts in ankylosing spondylitis. Arthritis Res Ther 2021; 23:301. [PMID: 34879876 PMCID: PMC8653593 DOI: 10.1186/s13075-021-02670-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/06/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND WNT16 is critical for bone homeostasis, but the effect of WNT16 in ankylosing spondylitis (AS) is still unknown. Here, we investigated whether WNT16 influences bone formation and pathophysiological changes of AS in an in vitro model. METHODS The bone tissue from the facet joints was obtained from seven disease control and seven AS patients. Primary osteoprogenitor cells of the facet joints were isolated using an outgrowth method. Isolated osteoprogenitor cells from both control and AS tissues were analyzed by microarray, RT-qPCR, immunoblotting, and immunohistochemistry. The bone-forming activity of osteoprogenitor cells was assessed by various in vitro assays. β-galactosidase staining and senescence-associated secretory phenotype (SASP) using RT-qPCR were used to assess cell senescence. RESULTS In microarray analysis, WNT16 expression was significantly elevated in AS osteoprogenitor cells compared to the control. We also validated that WNT16 expression was elevated in AS-osteoprogenitor cells and human AS-bone tissues. WNT16 treatment inhibited bone formation in AS-osteoprogenitor cells but not in the control. Intriguingly, AS-osteoprogenitor cells were stained markedly with β-galactosidase for cell senescence in WNT16 treatment. Furthermore, in an H2O2 stress-induced premature senescence condition, WNT16 treatment increased cell senescence in AS-osteoprogenitor cells and WNT16 treatment under the H2O2 stress condition showed an increase in p21 protein and SASP mRNA expression. The WNT16-induced SASP expression in AS-osteoprogenitor cells was reduced in WNT16 knockdown cultures. CONCLUSION WNT16 is highly expressed in AS and WNT16 treatment facilitated cell senescence in AS-osteoprogenitor cells during osteoblast differentiation accompanied by suppression of bone formation. The identified role of WNT16 in AS could influence bone loss in AS patients.
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Affiliation(s)
- Sungsin Jo
- Hanyang University Institute for Rheumatology Research, Seoul, 04763, Republic of Korea
| | - Subin Weon
- Hanyang University Institute for Rheumatology Research, Seoul, 04763, Republic of Korea
- Department of Translational Medicine, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Bora Nam
- Hanyang University Institute for Rheumatology Research, Seoul, 04763, Republic of Korea
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Disease, 222-1, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonhchunhyang University College of Medicine, Bucheon, 14584, Korea
| | - Hyundeok Kang
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Tae-Jong Kim
- Deparment of Rheumatology, Chonnam National University Medical School and Hospital, Gwangju, 61469, Republic of Korea
| | - Ye-Soo Park
- Department of Orthopedic Surgery, Guri Hospital, Hanyang University College of Medicine, Guri, 11923, Republic of Korea
| | - Tae-Hwan Kim
- Hanyang University Institute for Rheumatology Research, Seoul, 04763, Republic of Korea.
- Department of Translational Medicine, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Disease, 222-1, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
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25
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Liu A, Liu Y, Su KJ, Greenbaum J, Bai Y, Tian Q, Zhao LJ, Deng HW, Shen H. A transcriptome-wide association study to detect novel genes for volumetric bone mineral density. Bone 2021; 153:116106. [PMID: 34252604 PMCID: PMC8478845 DOI: 10.1016/j.bone.2021.116106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 01/02/2023]
Abstract
Transcriptome-wide association studies (TWAS) systematically investigate the association of genetically predicted gene expression with disease risk, providing an effective approach to identify novel susceptibility genes. Osteoporosis is the most common metabolic bone disease, associated with reduced bone mineral density (BMD) and increased risk of osteoporotic fractures, whereas genetic factors explain approximately 70% of the variance in phenotypes associated with bone. BMD is commonly assessed using dual-energy X-ray absorptiometry (DXA) to obtain measurements (g/cm2) of areal BMD. However, quantitative computed tomography (QCT) measured 3D volumetric BMD (vBMD) (g/cm3) has important advantages compared with DXA since it can evaluate cortical and trabecular microstructural features of bone quality, which can be used to directly predict fracture risk. Here, we performed the first TWAS for volumetric BMD (vBMD) by integrating genome-wide association studies (GWAS) data from two independent cohorts, namely the Framingham Heart Study (FHS, n = 3298) and the Osteoporotic Fractures in Men (MrOS, n = 4641), with tissue-specific gene expression data from the Genotype-Tissue Expression (GTEx) project. We first used stratified linkage disequilibrium (LD) score regression approach to identify 12 vBMD-relevant tissues, for which vBMD heritability is enriched in tissue-specific genes of the given tissue. Focusing on these tissues, we subsequently leveraged GTEx expression reference panels to predict tissue-specific gene expression levels based on the genotype data from FHS and MrOS. The associations between predicted gene expression levels and vBMD variation were then tested by MultiXcan, an innovative TWAS method that integrates information available across multiple tissues. We identified 70 significant genes associated with vBMD, including some previously identified osteoporosis-related genes such as LYRM2 and NME8, as well as some novel loci such as DNAAF2 and SPAG16. Our findings provide novel insights into the pathophysiological mechanisms of osteoporosis and highlight several novel vBMD-associated genes that warrant further investigation.
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Affiliation(s)
- Anqi Liu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Yong Liu
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Yuelu, Changsha, Hunan Province, PR China
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Jonathan Greenbaum
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Yuntong Bai
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA; Department of Biomedical Engineering, Tulane University, New Orleans, LA, USA
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Lan-Juan Zhao
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA; Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Yuelu, Changsha, Hunan Province, PR China
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA.
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26
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Greenbaum J, Su KJ, Zhang X, Liu Y, Liu A, Zhao LJ, Luo Z, Tian Q, Shen H, Deng HW. A multiethnic whole genome sequencing study to identify novel loci for bone mineral density. Hum Mol Genet 2021; 31:1067-1081. [PMID: 34673960 PMCID: PMC8976433 DOI: 10.1093/hmg/ddab305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
At present, there have only been a few DNA sequencing-based studies to explore the genetic determinants of bone mineral density (BMD). We carried out the largest whole genome sequencing analysis to date for femoral neck and spine BMD (n = 4981), with one of the highest average sequencing depths implemented thus far at 22×, in a multiethnic sample (58% Caucasian and 42% African American) from the Louisiana Osteoporosis Study (LOS). The LOS samples were combined with summary statistics from the GEFOS consortium and several independent samples of various ethnicities to perform GWAS meta-analysis (n = 44 506). We identified 31 and 30 genomic risk loci for femoral neck and spine BMD, respectively. The findings substantiate many previously reported susceptibility loci (e.g. WNT16 and ESR1) and reveal several others that are either novel or have not been widely replicated in GWAS for BMD, including two for femoral neck (IGF2 and ZNF423) and one for spine (SIPA1). Although we were not able to uncover ethnicity specific differences in the genetic determinants of BMD, we did identify several loci which demonstrated sex-specific associations, including two for women (PDE4D and PIGN) and three for men (TRAF3IP2, NFIB and LYSMD4). Gene-based rare variant association testing detected MAML2, a regulator of the Notch signaling pathway, which has not previously been suggested, for association with spine BMD. The findings provide novel insights into the pathophysiological mechanisms of osteoporosis.
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Affiliation(s)
- Jonathan Greenbaum
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Kuan-Jui Su
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Xiao Zhang
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Yong Liu
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA,School of Basic Medical Science, Central South University, Changsha 410013, Hunan Province, PR China
| | - Anqi Liu
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Lan-Juan Zhao
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zhe Luo
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Qing Tian
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hui Shen
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hong-Wen Deng
- To whom correspondence should be addressed at: Section of Biomedical Informatics and Genomics, Director, Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, 1440 Canal St., RM 1619F, New Orleans, LA 70112, USA.
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27
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Ghatan S, Costantini A, Li R, De Bruin C, Appelman-Dijkstra NM, Winter EM, Oei L, Medina-Gomez C. The Polygenic and Monogenic Basis of Paediatric Fractures. Curr Osteoporos Rep 2021; 19:481-493. [PMID: 33945105 PMCID: PMC8551106 DOI: 10.1007/s11914-021-00680-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 01/19/2023]
Abstract
PURPOSE OF REVIEW Fractures are frequently encountered in paediatric practice. Although recurrent fractures in children usually unveil a monogenic syndrome, paediatric fracture risk could be shaped by the individual genetic background influencing the acquisition of bone mineral density, and therefore, the skeletal fragility as shown in adults. Here, we examine paediatric fractures from the perspective of monogenic and complex trait genetics. RECENT FINDINGS Large-scale genome-wide studies in children have identified ~44 genetic loci associated with fracture or bone traits whereas ~35 monogenic diseases characterized by paediatric fractures have been described. Genetic variation can predispose to paediatric fractures through monogenic risk variants with a large effect and polygenic risk involving many variants of small effects. Studying genetic factors influencing peak bone attainment might help in identifying individuals at higher risk of developing early-onset osteoporosis and discovering drug targets to be used as bone restorative pharmacotherapies to prevent, or even reverse, bone loss later in life.
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Affiliation(s)
- S Ghatan
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - A Costantini
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - R Li
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - C De Bruin
- Department of Paediatrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - N M Appelman-Dijkstra
- Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - E M Winter
- Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - L Oei
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carolina Medina-Gomez
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands.
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28
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Griesemer D, Xue JR, Reilly SK, Ulirsch JC, Kukreja K, Davis JR, Kanai M, Yang DK, Butts JC, Guney MH, Luban J, Montgomery SB, Finucane HK, Novina CD, Tewhey R, Sabeti PC. Genome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution. Cell 2021; 184:5247-5260.e19. [PMID: 34534445 PMCID: PMC8487971 DOI: 10.1016/j.cell.2021.08.025] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/25/2021] [Accepted: 08/19/2021] [Indexed: 12/11/2022]
Abstract
3' untranslated region (3'UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the massively parallel reporter assay for 3'UTRs (MPRAu) to sensitively assay 12,173 3'UTR variants. We applied MPRAu to six human cell lines, focusing on genetic variants associated with genome-wide association studies (GWAS) and human evolutionary adaptation. MPRAu expands our understanding of 3'UTR function, suggesting that simple sequences predominately explain 3'UTR regulatory activity. We adapt MPRAu to uncover diverse molecular mechanisms at base pair resolution, including an adenylate-uridylate (AU)-rich element of LEPR linked to potential metabolic evolutionary adaptations in East Asians. We nominate hundreds of 3'UTR causal variants with genetically fine-mapped phenotype associations. Using endogenous allelic replacements, we characterize one variant that disrupts a miRNA site regulating the viral defense gene TRIM14 and one that alters PILRB abundance, nominating a causal variant underlying transcriptional changes in age-related macular degeneration.
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Affiliation(s)
- Dustin Griesemer
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, USA; Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James R Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02143, USA.
| | - Steven K Reilly
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02143, USA
| | - Jacob C Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kalki Kukreja
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joe R Davis
- BigHat Biosciences, San Carlos, CA 94070, USA
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David K Yang
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA
| | - John C Butts
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mehmet H Guney
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeremy Luban
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Carl D Novina
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan Tewhey
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA; Tufts University School of Medicine, Boston, MA 02111, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA; Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02143, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Vallet M, Sophocleous A, Törnqvist AE, Azfer A, Hof RV, Albagha OM, Ralston SH. Targeted Inactivation of Rin3 Increases Trabecular Bone Mass by Reducing Bone Resorption and Favouring Bone Formation. Calcif Tissue Int 2021; 109:92-102. [PMID: 33725152 PMCID: PMC8225545 DOI: 10.1007/s00223-021-00827-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/14/2021] [Indexed: 12/21/2022]
Abstract
Common genetic variants at the RIN3 locus on chromosome 14q32 predispose to Paget's disease of bone (PDB) but the mechanisms by which they do so are unknown. Here, we analysed the skeletal phenotype of female mice with targeted inactivation of the mouse Rin3 gene (Rin3-/-) as compared with wild-type littermates. The Rin3-/- mice had higher trabecular bone volume (BV/TV%) compared with wild type. Mean ± standard deviation values at the distal femur at 8 weeks were 9.0 ± 2.5 vs. 7.0 ± 1.5 (p = 0.002) and at 52 weeks were 15.8 ± 9.5 vs. 8.5 ± 4.2 (p = 0.002). No differences were observed in femoral cortical bone parameters with the exception of marrow diameter which was significantly smaller in 52-week-old Rin3-/- mice compared to wild type: (0.43 mm ± 0.1 vs. 0.57 mm ± 0.2 (p = 0.001). Bone histomorphometry showed a lower osteoclast surface / bone surface (Oc.S/BS%) at 8 weeks in Rin3-/- mice compared to wild type (24.1 ± 4.7 vs. 29.7 ± 6.6; p = 0.025) but there were no significant differences in markers of bone formation at this time. At 52 weeks, Oc.S/BS did not differ between genotypes but single labelled perimeter (SL.Pm/B.Pm (%)) was significantly higher in Rin3-/- mice (24.4 ± 6.4 vs. 16.5 ± 3.8, p = 0.003). We conclude that Rin3 negatively regulates trabecular bone mass in mice by inhibiting osteoclastic bone resorption and favouring bone formation. Our observations also suggest that the variants that predispose to PDB in humans probably do so by causing a gain-in-function of RIN3.
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Affiliation(s)
- Mahéva Vallet
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Antonia Sophocleous
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Department of Life Sciences, School of Sciences, European University Cyprus, Engomi, Cyprus
| | - Anna E Törnqvist
- Centre for Bone and Arthritis Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Asim Azfer
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Rob Van't Hof
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, England
| | - Omar Me Albagha
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- College of Health and Life, Hamad Bin Khalifa University, Doha, Qatar
| | - Stuart H Ralston
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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30
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Suthon S, Perkins RS, Bryja V, Miranda-Carboni GA, Krum SA. WNT5B in Physiology and Disease. Front Cell Dev Biol 2021; 9:667581. [PMID: 34017835 PMCID: PMC8129536 DOI: 10.3389/fcell.2021.667581] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
WNT5B, a member of the WNT family of proteins that is closely related to WNT5A, is required for cell migration, cell proliferation, or cell differentiation in many cell types. WNT5B signals through the non-canonical β-catenin-independent signaling pathway and often functions as an antagonist of canonical WNT signaling. Although WNT5B has a high amino acid identity with WNT5A and is often assumed to have similar activities, WNT5B often exhibits unique expression patterns and functions. Here, we describe the distinct effects and mechanisms of WNT5B on development, bone, adipose tissue, cardiac tissue, the nervous system, the mammary gland, the lung and hematopoietic cells, compared to WNT5A. We also highlight aberrances in non-canonical WNT5B signaling contributing to diseases such as osteoarthritis, osteoporosis, obesity, type 2 diabetes mellitus, neuropathology, and chronic diseases associated with aging, as well as various cancers.
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Affiliation(s)
- Sarocha Suthon
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Rachel S Perkins
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Vitezslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- Department of Cytokinetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czechia
| | - Gustavo A Miranda-Carboni
- Division of Hematology and Oncology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Susan A Krum
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, United States
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, United States
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31
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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: 83] [Impact Index Per Article: 27.7] [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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Hou R, Cole SA, Graff M, Wang Y, Haack K, Laston S, Mehta NR, Shypailo RJ, Gourlay ML, Comuzzie AG, North KE, Butte NF, Voruganti VS. Genetic variants and physical activity interact to affect bone density in Hispanic children. BMC Pediatr 2021; 21:79. [PMID: 33588791 PMCID: PMC7883422 DOI: 10.1186/s12887-021-02537-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Background Our aim was to investigate if moderate to vigorous physical activity (MVPA), calcium intake interacts with bone mineral density (BMD)-related single nucleotide polymorphisms (SNPs) to influence BMD in 750 Hispanic children (4-19y) of the cross-sectional Viva La Familia Study. Methods Physical activity and dietary intake were measured by accelerometers and multiple-pass 24 h dietary recalls, respectively. Total body and lumbar spine BMD were measured by dual energy X-ray absorptiometry. A polygenic risk score (PRS) was computed based on SNPs identified in published literature. Regression analysis was conducted with PRSs, MVPA and calcium intake with total body and lumbar spine BMD. Results We found evidence of statistically significant interaction effects between the PRS and MVPA on total body BMD and lumbar spine BMD (p < 0.05). Higher PRS was associated with a lower total body BMD (β = − 0.040 ± 0.009, p = 1.1 × 10− 5) and lumbar spine BMD (β = − 0.042 ± 0.013, p = 0.0016) in low MVPA group, as compared to high MVPA group (β = − 0.015 ± 0.006, p = 0.02; β = 0.008 ± 0.01, p = 0.4, respectively). Discussion The study indicated that calcium intake does not modify the relationship between genetic variants and BMD, while it implied physical activity interacts with genetic variants to affect BMD in Hispanic children. Due to limited sample size of our study, future research on gene by environment interaction on bone health and functional studies to provide biological insights are needed. Conclusions Bone health in Hispanic children with high genetic risk for low BMD is benefitted more by MVPA than children with low genetic risk. Our results may be useful to predict disease risk and tailor dietary and physical activity advice delivery to people, especially children. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-021-02537-y.
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Affiliation(s)
- Ruixue Hou
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC, 28081, USA
| | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yujie Wang
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karin Haack
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sandra Laston
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas of the Rio Grande Valley, Brownsville, TX, USA
| | - Nitesh R Mehta
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Roman J Shypailo
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret L Gourlay
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nancy F Butte
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Venkata Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC, 28081, USA.
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Abstract
Bone mass is a key determinant of osteoporosis and fragility fractures. Epidemiologic studies have shown that a 10% increase in peak bone mass (PBM) at the population level reduces the risk of fracture later in life by 50%. Low PBM is possibly due to the bone loss caused by various conditions or processes that occur during adolescence and young adulthood. Race, gender, and family history (genetics) are responsible for the majority of PBM, but other factors, such as physical activity, calcium and vitamin D intake, weight, smoking and alcohol consumption, socioeconomic status, age at menarche, and other secondary causes (diseases and medications), play important roles in PBM gain during childhood and adolescence. Hence, the optimization of lifestyle factors that affect PBM and bone strength is an important strategy to maximize PBM among adolescents and young people, and thus to reduce the low bone mass or osteoporosis risk in later life. This review aims to summarize the available evidence for the common but important factors that influence bone mass gain during growth and development and discuss the advances of developing high PBM.
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Affiliation(s)
- Xiaowei Zhu
- Disease & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Westlake University, Hangzhou, 310024, China
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Houfeng Zheng
- Disease & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou, 310024, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Westlake University, Hangzhou, 310024, China.
- School of Life Sciences, Fudan University, Shanghai, 200433, China.
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34
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Song Q, Song J, Li C, Wang Y, Qi L, Wang H. Genetic variants in the FAM3C gene are associated with lipid traits in Chinese children. Pediatr Res 2021; 89:673-678. [PMID: 32316026 DOI: 10.1038/s41390-020-0897-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/12/2020] [Accepted: 04/01/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND Previous studies have related FAM3C gene with childhood bone health, and the regulation of lipid metabolism in hepatocytes. The present case-control study aimed to analyze the association of FAM3C genetic variants with overweight/obesity and lipid traits among Chinese children. METHODS Two genetic variants (rs7776725 and rs7793554) within the FAM3C gene were genotyped in 3305 Chinese children aged 6-18 years. RESULTS In the whole study population, the T-allele of rs7776725 and A-allele of rs7793554 within the FAM3C gene were associated with 40.2% (95% CI: 11.6-76.1%; P = 0.004) and 29.1% (6.9-56.0%; P = 0.008) increased risk of dyslipidemia, higher triglyceride (P = 0.014 and P = 0.001) and lower HDL-C (P = 0.015 and P = 0.003). In addition, we found that rs7776725 interacted with sex on dyslipidemia (Pfor interaction = 0.004), and sex-stratified analyses showed that it was significantly associated with dyslipidemia only in girls (P = 8.78 × 10-5). The variant also showed nominally significant interactions with sex on total cholesterol and LDL-C (Pfor interaction = 0.012 and 0.008). CONCLUSION We found that FAM3C genetic variants were associated with dyslipidemia and lipid traits among Chinese children. In addition, we found significant gene-by-sex interactions. Our findings provided evidence supporting the role of FAM3C gene in regulating lipid metabolism in humans. IMPACT FAM3C genetic variants were associated with dyslipidemia and lipid traits among Chinese children. In addition, we found significant gene-by-sex interactions. FAM3C/rs7776725 was associated with dyslipidemia and lipid traits only in girls. Our findings provided evidence supporting the role of FAM3C gene in regulating lipid metabolism in humans.
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Affiliation(s)
- Qiying Song
- Department of Maternal and Child Health, School of Public Health, Peking University, 100191, Beijing, China
| | - Jieyun Song
- Institute of Child and Adolescent Health, School of Public Health, Peking University, 100191, Beijing, China
| | - Chenxiong Li
- Department of Maternal and Child Health, School of Public Health, Peking University, 100191, Beijing, China
| | - Yang Wang
- Department of Maternal and Child Health, School of Public Health, Peking University, 100191, Beijing, China
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Haijun Wang
- Department of Maternal and Child Health, School of Public Health, Peking University, 100191, Beijing, China.
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Cousminer DL, Wagley Y, Pippin JA, Elhakeem A, Way GP, Pahl MC, McCormack SE, Chesi A, Mitchell JA, Kindler JM, Baird D, Hartley A, Howe L, Kalkwarf HJ, Lappe JM, Lu S, Leonard ME, Johnson ME, Hakonarson H, Gilsanz V, Shepherd JA, Oberfield SE, Greene CS, Kelly A, Lawlor DA, Voight BF, Wells AD, Zemel BS, Hankenson KD, Grant SFA. Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual. Genome Biol 2021; 22:1. [PMID: 33397451 PMCID: PMC7780623 DOI: 10.1186/s13059-020-02207-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Bone accrual impacts lifelong skeletal health, but genetic discovery has been primarily limited to cross-sectional study designs and hampered by uncertainty about target effector genes. Here, we capture this dynamic phenotype by modeling longitudinal bone accrual across 11,000 bone scans in a cohort of healthy children and adolescents, followed by genome-wide association studies (GWAS) and variant-to-gene mapping with functional follow-up. RESULTS We identify 40 loci, 35 not previously reported, with various degrees of supportive evidence, half residing in topological associated domains harboring known bone genes. Of several loci potentially associated with later-life fracture risk, a candidate SNP lookup provides the most compelling evidence for rs11195210 (SMC3). Variant-to-gene mapping combining ATAC-seq to assay open chromatin with high-resolution promoter-focused Capture C identifies contacts between GWAS loci and nearby gene promoters. siRNA knockdown of gene expression supports the putative effector gene at three specific loci in two osteoblast cell models. Finally, using CRISPR-Cas9 genome editing, we confirm that the immediate genomic region harboring the putative causal SNP influences PRPF38A expression, a location which is predicted to coincide with a set of binding sites for relevant transcription factors. CONCLUSIONS Using a new longitudinal approach, we expand the number of genetic loci putatively associated with pediatric bone gain. Functional follow-up in appropriate cell models finds novel candidate genes impacting bone accrual. Our data also raise the possibility that the cell fate decision between osteogenic and adipogenic lineages is important in normal bone accrual.
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Affiliation(s)
- Diana L Cousminer
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Yadav Wagley
- Department of Orthopedic Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ahmed Elhakeem
- MRC Integrative Epidemiology Unit, Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gregory P Way
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02140, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shana E McCormack
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan A Mitchell
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph M Kindler
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Denis Baird
- MRC Integrative Epidemiology Unit, Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - April Hartley
- MRC Integrative Epidemiology Unit, Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Laura Howe
- MRC Integrative Epidemiology Unit, Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Heidi J Kalkwarf
- Department of Pediatrics, Cincinnati Children's Hospital, University of Cincinnati, Cincinnati, OH, USA
| | - Joan M Lappe
- Department of Medicine and College of Nursing, Creighton University School of Medicine, Omaha, NB, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michelle E Leonard
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vicente Gilsanz
- Center for Endocrinology, Diabetes & Metabolism, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - John A Shepherd
- Department of Epidemiology and Population Science, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Sharon E Oberfield
- Division of Pediatric Endocrinology, Columbia University Medical Center, New York, NY, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA
| | - Andrea Kelly
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Babette S Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kurt D Hankenson
- Department of Orthopedic Surgery, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Bay CP, Levy SM, Janz KF, Smith BJ, Shaffer JR, Marazita ML, Burns TL. Genome-Wide Association Analysis of Longitudinal Bone Mineral Content Data From the Iowa Bone Development Study. J Clin Densitom 2021; 24:44-54. [PMID: 31668963 PMCID: PMC7098844 DOI: 10.1016/j.jocd.2019.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 11/17/2022]
Abstract
The foundation for osteoporosis risk is, in part, established during childhood, adolescence, and young adulthood, all periods of development when bone mass is acquired rapidly. The relative quantity of bone mass accrued is influenced by both lifestyle and genetic factors, although the genetic component is not yet well understood. The purpose of this study was to use a genome-wide association (GWA) analysis to discover single nucleotide polymorphisms (SNPs) associated with: (1) the sex-specific hip bone mineral content at approximately the age of 19 when the amount of bone accrued is near its peak; and (2) the sex-specific rate of hip bone mineral content accrual during the adolescent growth spurt. The Iowa Bone Development Study, a longitudinal cohort study exploring bone health in children, adolescents, and young adults was the source of data. From this cohort, n = 364 (190 females, 174 males) participants were included in GWA analyses to address (1) and n = 258 participants (125 females and 133 males) were included in GWA analyses to address (2). Twenty SNPS were detected having p < 1.0 × 10-5. Of most biologic relevance were 2 suggestive SNPs (rs2051756 and rs2866908) detected in an intron of the DKK2 gene through the GWA analysis that explored peak bone mass in females.
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Affiliation(s)
- Camden P Bay
- Center for Clinical Investigation, Brigham & Women's Hospital, Boston, MA, USA.
| | - Steven M Levy
- Department of Preventive and Community Dentistry, University of Iowa College of Dentistry, Iowa City, IA, USA; Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
| | - Kathleen F Janz
- Department of Health and Human Physiology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
| | - Brian J Smith
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, USA; Department of Biostatistics, University of Iowa College of Public Health, Iowa City, IA, USA
| | - John R Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA; Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA; Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Trudy L Burns
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
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Swan AL, Schütt C, Rozman J, del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P, Grallert H, Werner T, Teperino R, Becker L, Miller G, Moshiri A, Seavitt JR, Cissell DD, Meehan TF, Acar EF, Lelliott CJ, Flenniken AM, Champy MF, Sorg T, Ayadi A, Braun RE, Cater H, Dickinson ME, Flicek P, Gallegos J, Ghirardello EJ, Heaney JD, Jacquot S, Lally C, Logan JG, Teboul L, Mason J, Spielmann N, McKerlie C, Murray SA, Nutter LMJ, Odfalk KF, Parkinson H, Prochazka J, Reynolds CL, Selloum M, Spoutil F, Svenson KL, Vales TS, Wells SE, White JK, Sedlacek R, Wurst W, Lloyd KCK, Croucher PI, Fuchs H, Williams GR, Bassett JHD, Gailus-Durner V, Herault Y, Mallon AM, Brown SDM, Mayer-Kuckuk P, Hrabe de Angelis M. Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density. PLoS Genet 2020; 16:e1009190. [PMID: 33370286 PMCID: PMC7822523 DOI: 10.1371/journal.pgen.1009190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 01/22/2021] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease. Patients affected by osteoporosis frequently present with decreased BMD and increased fracture risk. Genes are known to control the onset and progression of bone diseases such as osteoporosis. Therefore, we aimed to identify osteoporosis-related genes using BMD measures obtained from a large pool of mutant mice genetically modified for deletion of individual genes (knockout mice). In a collaborative endeavor involving several research sites world-wide, we generated and phenotyped 3,823 knockout mice and identified 200 genes which regulated BMD. Of the 200 BMD genes, 141 genes were previously not known to affect BMD. The discovery and study of novel BMD genes will help to better understand the causes and therapeutic options for patients with low BMD. In the long run, this will improve the clinical management of osteoporosis.
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Affiliation(s)
- Anna L. Swan
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | | | - Stefan Brandmaier
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Robert Brommage
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Piia Keskivali-Bond
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Werner
- Internal Medicine Nephrology and Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Raffaele Teperino
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Gregor Miller
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ala Moshiri
- University of California-Davis School of Medicine, Sacramento, California, United States of America
| | - John R. Seavitt
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Derek D. Cissell
- Department of Surgical & Radiological Sciences, University of California, Davis, California, United States of America
| | - Terrence F. Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elif F. Acar
- The Center for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Statistics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ann M. Flenniken
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marie-France Champy
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Abdel Ayadi
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Robert E. Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Heather Cater
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Mary E. Dickinson
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Paul Flicek
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Juan Gallegos
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Elena J. Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Jason D. Heaney
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Sylvie Jacquot
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Connor Lally
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - John G. Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Lydia Teboul
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Colin McKerlie
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stephen A. Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Lauryl M. J. Nutter
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kristian F. Odfalk
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jan Prochazka
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Corey L. Reynolds
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Frantisek Spoutil
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Karen L. Svenson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Taylor S. Vales
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Sara E. Wells
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - K. C. Kent Lloyd
- Department of Surgery, School of Medicine and Mouse Biology Program, University of California Davis
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - J. H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, IGBMC, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Steve D. M. Brown
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Philipp Mayer-Kuckuk
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- * E-mail:
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38
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Liu Y, Shen H, Greenbaum J, Liu A, Su KJ, Zhang LS, Zhang L, Tian Q, Hu HG, He JS, Deng HW. Gene Expression and RNA Splicing Imputation Identifies Novel Candidate Genes Associated with Osteoporosis. J Clin Endocrinol Metab 2020; 105:5895512. [PMID: 32827035 PMCID: PMC7736639 DOI: 10.1210/clinem/dgaa572] [Citation(s) in RCA: 9] [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: 04/16/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
CONTEXT Though genome-wide association studies (GWASs) have identified hundreds of genetic variants associated with osteoporosis related traits, such as bone mineral density (BMD) and fracture, it remains a challenge to interpret their biological functions and underlying biological mechanisms. OBJECTIVE Integrate diverse expression quantitative trait loci and splicing quantitative trait loci data with several powerful GWAS datasets to identify novel candidate genes associated with osteoporosis. DESIGN, SETTING, AND PARTICIPANTS Here, we conducted a transcriptome-wide association study (TWAS) for total body BMD (TB-BMD) (n = 66 628 for discovery and 7697 for validation) and fracture (53 184 fracture cases and 373 611 controls for discovery and 37 857 cases and 227 116 controls for validation), respectively. We also conducted multi-SNP-based summarized mendelian randomization analysis to further validate our findings. RESULTS In total, we detected 88 genes significantly associated with TB-BMD or fracture through expression or ribonucleic acid splicing. Summarized mendelian randomization analysis revealed that 78 of the significant genes may have potential causal effects on TB-BMD or fracture in at least 1 specific tissue. Among them, 64 genes have been reported in previous GWASs or TWASs for osteoporosis, such as ING3, CPED1, and WNT16, as well as 14 novel genes, such as DBF4B, GRN, TMUB2, and UNC93B1. CONCLUSIONS Overall, our findings provide novel insights into the pathogenesis mechanisms of osteoporosis and highlight the power of a TWAS to identify and prioritize potential causal genes.
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Affiliation(s)
- Yong Liu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Jonathan Greenbaum
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Anqi Liu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Li-Shu Zhang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Hong-Gang Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Hong-Wen Deng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
- Correspondence and Reprint Requests: Hong-Wen Deng, PhD, Professor, Director, Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, 1440 Canal St., Suite 2001, New Orleans, LA 70112.
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39
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Hojo H, Ohba S. Gene regulatory landscape in osteoblast differentiation. Bone 2020; 137:115458. [PMID: 32474244 DOI: 10.1016/j.bone.2020.115458] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/29/2022]
Abstract
The development of osteoblasts, a bone-forming cell population, occurs in conjunction with development of the skeleton, which creates our physical framework and shapes the body. In the past two decades, genetic studies have uncovered the molecular framework of this process-namely, transcriptional regulators and signaling pathways coordinate the cell fate determination and differentiation of osteoblasts in a spatial and temporal manner. Recently emerging genome-wide studies provide additional layers of understanding of the gene regulatory landscape during osteoblast differentiation, allowing us to gain novel insight into the modes of action of the key regulators, functional interaction among the regulator-bound enhancers, epigenetic regulations, and the complex nature of regulatory inputs. In this review, we summarize current understanding of the transcriptional regulation in osteoblasts, in terms of the gene regulatory landscape.
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Affiliation(s)
- Hironori Hojo
- Department of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, The University of Tokyo Graduate School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Shinsuke Ohba
- Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan.
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40
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Winter EM, Ireland A, Butterfield NC, Haffner-Luntzer M, Horcajada MN, Veldhuis-Vlug AG, Oei L, Colaianni G, Bonnet N. Pregnancy and lactation, a challenge for the skeleton. Endocr Connect 2020; 9:R143-R157. [PMID: 32438342 PMCID: PMC7354730 DOI: 10.1530/ec-20-0055] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022]
Abstract
In this review we discuss skeletal adaptations to the demanding situation of pregnancy and lactation. Calcium demands are increased during pregnancy and lactation, and this is effectuated by a complex series of hormonal changes. The changes in bone structure at the tissue and whole bone level observed during pregnancy and lactation appear to largely recover over time. The magnitude of the changes observed during lactation may relate to the volume and duration of breastfeeding and return to regular menses. Studies examining long-term consequences of pregnancy and lactation suggest that there are small, site-specific benefits to bone density and that bone geometry may also be affected. Pregnancy- and lactation-induced osteoporosis (PLO) is a rare disease for which the pathophysiological mechanism is as yet incompletely known; here, we discuss and speculate on the possible roles of genetics, oxytocin, sympathetic tone and bone marrow fat. Finally, we discuss fracture healing during pregnancy and lactation and the effects of estrogen on this process.
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Affiliation(s)
- E M Winter
- Leiden University Medical Center, Department of Internal Medicine, Division of Endocrinology, Center for Bone Quality, Leiden, the Netherlands
- Correspondence should be addressed to E M Winter:
| | - A Ireland
- Musculoskeletal Science and Sports Medicine Research Centre, Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - N C Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Commonwealth Building, DuCane Road, London, United Kingdom
| | - M Haffner-Luntzer
- Institute of Orthopaedic Research and Biomechanics, University Medical Center Ulm, Ulm, Germany
| | - M-N Horcajada
- Nestlé Research, Department of Musculoskeletal Health, Innovation EPFL Park, Lausanne, Switzerland.
| | - A G Veldhuis-Vlug
- Leiden University Medical Center, Department of Internal Medicine, Division of Endocrinology, Center for Bone Quality, Leiden, the Netherlands
- Jan van Goyen Medical Center, Department of Internal Medicine, Amsterdam, the Netherlands
| | - L Oei
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - G Colaianni
- Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - N Bonnet
- Nestlé Research, Department of Musculoskeletal Health, Innovation EPFL Park, Lausanne, Switzerland.
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41
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Xiao W, He J, Fu W, Xu Y, Zhang Z. LOX gene polymorphisms are associated with osteoporotic vertebral compression fracture in postmenopausal Chinese women. Gene 2020; 741:144543. [PMID: 32165300 DOI: 10.1016/j.gene.2020.144543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/09/2020] [Accepted: 03/08/2020] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Collagen cross-linking, which is regulated by lysyl oxidase (LOX), plays critical roles in bone mechanical strength. LOX can influence bone remodeling by modulating osteoblast and osteoclast activity. This study aimed to explore the effect of LOX gene polymorphisms on osteoporotic fractures susceptibility in postmenopausal Chinese women. METHODS This was a prospective study of postmenopausal women who visited the outpatient and community clinics of the local Hospital. Five tagging single nucleotide polymorphisms (SNPs) in the LOX gene were determined. Bone mineral density (BMD) was measured at the lumbar spine, femoral neck, and hip using dual-energy X-ray absorptiometry. Fractures were confirmed by X-ray and divided into: vertebral compression fracture (OVCF) and non-OVCF (all other fractures). RESULTS This study included 602 patients with non-traumatic fractures and 1343 healthy volunteers. The rs1800449 was significantly associated with vertebral compression fracture (OVCF) after adjusting for age and BMI (P = 0.012). Compared with subjects with the GG genotype, the risk of having OVCF was 1.28 and 1.74, respectively for subjects with the GA and AA genotypes (P = 0.043 and P = 0.018). A recessive genetic model showed that carriers of the AA genotype had higher fracture risk compared to G carriers (GA and GG genotypes) (P = 0.015). The rs2288393 SNP exhibited marginally significant association with OVCF (P = 0.051). Haplotype analyses corroborated our single SNP results: both haplotype CGA and CCG contained rs10519694, rs2288393, and rs1800449, and were significant associated with OVCF (P = 0.048 and P = 0.032, respectively). On the other hand, we found no evidence of an association of LOX gene allelic variants with either BMD or non-OVCF (all P > 0.05). CONCLUSION The results suggest that genetic polymorphisms in LOX may contribute to susceptibility to OVCF in Chinese postmenopausal women.
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Affiliation(s)
- Wenjin Xiao
- Department of Endocrinology, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Jinwei He
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Wenzhen Fu
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Youjia Xu
- Department of Orthopaedics, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China; Osteoporosis Institute of Soochow University, Suzhou, Jiangsu 215004, China.
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Disease, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China.
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42
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Hou R, Cole SA, Graff M, Haack K, Laston S, Comuzzie AG, Mehta NR, Ryan K, Cousminer DL, Zemel BS, Grant SFA, Mitchell BD, Shypailo RJ, Gourlay ML, North KE, Butte NF, Voruganti VS. Genetic variants affecting bone mineral density and bone mineral content at multiple skeletal sites in Hispanic children. Bone 2020; 132:115175. [PMID: 31790847 PMCID: PMC7120871 DOI: 10.1016/j.bone.2019.115175] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 12/24/2022]
Abstract
CONTEXT Osteoporosis is a major public health burden with significant economic costs. However, the correlates of bone health in Hispanic children are understudied. OBJECTIVE We aimed to identify genetic variants associated with bone mineral density (BMD) and bone mineral content (BMC) at multiple skeletal sites in Hispanic children. METHODS We conducted a cross-sectional genome-wide linkage analysis, genome-wide and exome-wide association analysis of BMD and BMC. The Viva La Familia Study is a family-based cohort with a total of 1030 Hispanic children (4-19 years old at baseline) conducted in Houston, TX. BMD and BMC were measured by Dual-energy X-ray absorptiometry. RESULTS Significant heritability were observed for BMC and BMD at multiple skeletal sites ranging between 44 and 68% (P < 2.8 × 10-9). Significant evidence for linkage was found for BMD of pelvis and left leg on chromosome 7p14, lumbar spine on 20q13 and left rib on 6p21, and BMC of pelvis on chromosome 20q12 and total body on 14q22-23 (logarithm of odds score > 3). We found genome-wide significant association between BMC of right arm and rs762920 at PVALB (P = 4.6 × 10-8), and between pelvis BMD and rs7000615 at PTK2B (P = 7.4 × 10-8). Exome-wide association analysis revealed novel association of variants at MEGF10 and ABRAXAS2 with left arm and lumber spine BMC, respectively (P < 9 × 10-7). CONCLUSIONS We identified novel loci associated with BMC and BMD in Hispanic children, with strongest evidence for PTK2B. These findings provide better understanding of bone genetics and shed light on biological mechanisms underlying BMD and BMC variation.
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Affiliation(s)
- Ruixue Hou
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sandra Laston
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas the Rio Grande Valley, Brownsville, TX, USA
| | | | - Nitesh R Mehta
- Department of Pediatrics and USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Kathleen Ryan
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Diana L Cousminer
- Division of Human Genetics, Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, USA; Department of Genetics, University of Pennsylvania, USA
| | - Babette S Zemel
- Division of GI, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, USA
| | - Struan F A Grant
- Division of Human Genetics, Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, USA; Department of Genetics, University of Pennsylvania, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Roman J Shypailo
- Department of Pediatrics and USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Margaret L Gourlay
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nancy F Butte
- Department of Pediatrics and USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - V Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA.
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Traylor M, Amin Al Olama A, Lyytikäinen LP, Marini S, Chung J, Malik R, Dichgans M, Kähönen M, Lehtimäki T, Anderson CD, Raitakari OT, Markus HS. Influence of Genetic Variation in PDE3A on Endothelial Function and Stroke. Hypertension 2020; 75:365-371. [PMID: 31865795 PMCID: PMC7055937 DOI: 10.1161/hypertensionaha.119.13513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 06/16/2019] [Accepted: 11/27/2019] [Indexed: 11/16/2022]
Abstract
We aimed to characterize the genetics of endothelial function and how this influences risk for cardiovascular diseases such as ischemic stroke. We integrated genetic data from a study of ultrasound flow-mediated dilatation of brachial artery in adolescents from ALSPAC (Avon Longitudinal Study of Parents and Children; n=5214) with a study of ischemic stroke (MEGASTROKE: n=60 341 cases and 452 969 controls) to identify variants that confer risk of ischemic stroke through altered endothelial function. We identified a variant in PDE3A (Phosphodiesterase 3A), encoding phosphodiesterase 3A, which was associated with flow-mediated dilatation in adolescents (9-12 years of age; β[SE], 0.38 [0.070]; P=3.8×10-8) and confers risk of ischemic stroke (odds ratio, 1.04 [95% CI, 1.02-1.06]; P=5.2×10-6). Bayesian colocalization analyses showed the same underlying variation is likely to lead to both associations (posterior probability, 97%). The same variant was associated with flow-mediated dilatation in a second study in young adults (age, 24-27 years; β[SE], 0.47 [0.23]; P=0.047) but not in older adults (β[SE], -0.012 [0.13]; P=0.89). We conclude that a genetic variant in PDE3A influences endothelial function in early life and leads to increased risk of ischemic stroke. Subtle, measurable changes to the vasculature that are influenced by genetics also influence risk of ischemic stroke.
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Affiliation(s)
- Matthew Traylor
- From the Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, United Kingdom (M.T., A.A.A.O., H.S.M.)
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (M.T.)
| | - Ali Amin Al Olama
- From the Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, United Kingdom (M.T., A.A.A.O., H.S.M.)
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland (L.-P.L., T.L.)
- Department of Clinical Chemistry (L.-P.L., T.L.), Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Sandro Marini
- Center for Genomic Medicine, Massachusetts General Hospital, Boston (S.M., J.C., C.D.A.)
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology (S.M., C.D.A.), Massachusetts General Hospital, Boston
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (S.M., J.C., C.D.A.)
| | - Jaeyoon Chung
- Center for Genomic Medicine, Massachusetts General Hospital, Boston (S.M., J.C., C.D.A.)
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (S.M., J.C., C.D.A.)
| | - Rainer Malik
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität München, Germany (R.M., M.D.)
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität München, Germany (R.M., M.D.)
- Munich Cluster for Systems Neurology, Germany (M.D.)
| | - Mika Kähönen
- Department of Clinical Physiology (M.K.), Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Finland
- Department of Clinical Physiology, Tampere University Hospital, Finland (M.K.)
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland (L.-P.L., T.L.)
- Department of Clinical Chemistry (L.-P.L., T.L.), Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Christopher D. Anderson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston (S.M., J.C., C.D.A.)
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology (S.M., C.D.A.), Massachusetts General Hospital, Boston
- Department of Neurology, McCance Center for Brain Health (C.D.A.), Massachusetts General Hospital, Boston
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (S.M., J.C., C.D.A.)
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Finland (O.T.R.)
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Finland (O.T.R.)
| | - Hugh S. Markus
- From the Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, United Kingdom (M.T., A.A.A.O., H.S.M.)
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Montazeri-Najafabady N, Dabbaghmanesh MH, Mohammadian Amiri R, Mirzai Z. Influence of Estrogen Receptor Alpha Polymorphism on Bone Mineral Density in Iranian Children. Hum Hered 2019; 84:82-89. [PMID: 31655805 DOI: 10.1159/000502230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/18/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Bone mass acquisition in childhood is directly linked to adult bone mineral density (BMD) and fracture risk. BMD is a heritable trait, more than 70% of its variability among a population is affected by genetic factors. OBJECTIVES In the present study, we wanted to investigate the association between estrogen receptor alpha (ESR1) polymorphisms, PvuII (rs2234693) and XbaI (rs9340799), and bone area, bone mineral content (BMC), and BMD of the lumbar spine, femoral neck, and also of the total body less the head in Iranian children. METHODS The ESR1 gene PvuII and XbaI genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism. Bone area, BMC, BMD, and bone mineral apparent density (BMAD) were assessed by dual-energy X-ray absorptiometry (DEXA). Linear regression was carried out to examine the effects of the ESR1 (PvuII and XbaI) polymorphisms on DEXA outputs when adjusted for confounding factors (i.e., age, sex, BMI, and pubertal stage) in 3 models. RESULTS ESR1 (PvuII) gene polymorphisms (CT vs. CC) showed significant effects on the BMC of the total body less the head in all 3 models. For ESR1 (XbaI), individuals with the AG genotype had higher lumbar spine BMD and lumbar spine BMAD compared to other genotypes. CONCLUSIONS It seems that the PvuII and XbaI polymorphisms of ESR1 could be associated with BMC and BMD variation in Iranian children and adolescents.
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Affiliation(s)
- Nima Montazeri-Najafabady
- Shiraz Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Dabbaghmanesh
- Shiraz Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran,
| | - Rajeeh Mohammadian Amiri
- Shiraz Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Mirzai
- Shiraz Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
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Orlova E, Carlson JC, Lee MK, Feingold E, McNeil DW, Crout RJ, Weyant RJ, Marazita ML, Shaffer JR. Pilot GWAS of caries in African-Americans shows genetic heterogeneity. BMC Oral Health 2019; 19:215. [PMID: 31533690 PMCID: PMC6751797 DOI: 10.1186/s12903-019-0904-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/30/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Dental caries is the most common chronic disease in the US and disproportionately affects racial/ethnic minorities. Caries is heritable, and though genetic heterogeneity exists between ancestries for a substantial portion of loci associated with complex disease, a genome-wide association study (GWAS) of caries specifically in African Americans has not been performed previously. METHODS We performed exploratory GWAS of dental caries in 109 African American adults (age > 18) and 96 children (age 3-12) from the Center for Oral Health Research in Appalachia (COHRA1 cohort). Caries phenotypes (DMFS, DMFT, dft, and dfs indices) assessed by dental exams were tested for association with 5 million genotyped or imputed single nucleotide polymorphisms (SNPs), separately in the two age groups. The GWAS was performed using linear regression with adjustment for age, sex, and two principal components of ancestry. A maximum of 1 million adaptive permutations were run to determine empirical significance. RESULTS No loci met the threshold for genome-wide significance, though some of the strongest signals were near genes previously implicated in caries such as antimicrobial peptide DEFB1 (rs2515501; p = 4.54 × 10- 6) and TUFT1 (rs11805632; p = 5.15 × 10- 6). Effect estimates of lead SNPs at suggestive loci were compared between African Americans and Caucasians (adults N = 918; children N = 983). Significant (p < 5 × 10- 8) genetic heterogeneity for caries risk was found between racial groups for 50% of the suggestive loci in children, and 12-18% of the suggestive loci in adults. CONCLUSIONS The genetic heterogeneity results suggest that there may be differences in the contributions of genetic variants to caries across racial groups, and highlight the critical need for the inclusion of minorities in subsequent and larger genetic studies of caries in order to meet the goals of precision medicine and to reduce oral health disparities.
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Affiliation(s)
- E Orlova
- Department of Human Genetics, Pittsburgh, USA
| | - J C Carlson
- Department of Biostatistics, Graduate School of Public Health, Pittsburgh, USA
| | - M K Lee
- Center for Craniofacial and Dental Genetics, Dept. of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - E Feingold
- Department of Human Genetics, Pittsburgh, USA
- Department of Biostatistics, Graduate School of Public Health, Pittsburgh, USA
- Center for Craniofacial and Dental Genetics, Dept. of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - D W McNeil
- Departments of Psychology, & Dental Practice and Rural Health, West Virginia University, Morgantown, USA
| | - R J Crout
- Department of Periodontics, School of Dentistry, West Virginia University, Morgantown, WV, USA
| | - R J Weyant
- Department of Dental Public Health and Information Management, Pittsburgh, USA
| | - M L Marazita
- Department of Human Genetics, Pittsburgh, USA
- Center for Craniofacial and Dental Genetics, Dept. of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Sciences Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - J R Shaffer
- Department of Human Genetics, Pittsburgh, USA.
- Center for Craniofacial and Dental Genetics, Dept. of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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Lu HF, Hung KS, Chu HW, Wong HSC, Kim J, Kim MK, Choi BY, Tai YT, Ikegawa S, Cho EC, Chang WC. Meta-Analysis of Genome-Wide Association Studies Identifies Three Loci Associated With Stiffness Index of the Calcaneus. J Bone Miner Res 2019; 34:1275-1283. [PMID: 30779856 DOI: 10.1002/jbmr.3703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/27/2019] [Accepted: 02/12/2019] [Indexed: 01/11/2023]
Abstract
The stiffness index (SI) from quantitative ultrasound measurements is a good indicator of BMD and may be used to predict the risk of osteoporotic fracture. We conducted a genomewide association study (GWAS) for SI using 7742 individuals from the Taiwan Biobank, followed by a replication study in a Korean population (n = 2955). Approximately 6.1 million SNPs were subjected to association analysis, and SI-associated variants were identified. We further conducted a meta-analysis of Taiwan Biobank significant SNPs with a Korean population-based cohort. Candidate genes were prioritized according to epigenetic annotations, gene ontology, protein-protein interaction, GWAS catalog, and expression quantitative trait loci analyses. Our results revealed seven significant single-nucleotide polymorphisms (SNPs) within three loci: 7q31.31, 17p13.3, and 11q14.2. Conditional analysis showed that three SNPs, rs2536195 (CPED1/WNT16), rs1231207 (SMG6), and rs4944661 (LOC10050636/TMEM135), were the most important signals within these regions. The associations for the three SNPs were confirmed in a UK Biobank estimated BMD GWAS; these three cytobands were replicated successfully after a meta-analysis with a Korean population cohort as well. However, two SNPs were not replicated. After prioritization, we identified two novel genes, RAB15 and FNTB, as strong candidates for association with SI. Our study identified three SI-associated SNPs and two novel SI-related genes. Overall, these results provide further insight into the genetic architecture of osteoporosis. Further studies in larger East Asian populations are needed. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Hsing-Fang Lu
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kuo-Sheng Hung
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Neurosurgery, Taipei Medical University-Wan Fang Hospital, Taipei, Taiwan.,Graduate Institute of Injury, Prevention and Control, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Henry Sung-Ching Wong
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jihye Kim
- Department of Preventive Medicine, College of Medicine, Hanyang University, Seoul, South Korea.,Institute for Health and Society, Hanyang University, Seoul, South Korea
| | - Mi Kyung Kim
- Department of Preventive Medicine, College of Medicine, Hanyang University, Seoul, South Korea.,Institute for Health and Society, Hanyang University, Seoul, South Korea
| | - Bo Youl Choi
- Department of Preventive Medicine, College of Medicine, Hanyang University, Seoul, South Korea.,Institute for Health and Society, Hanyang University, Seoul, South Korea
| | - Yu-Ting Tai
- Department of Anesthesiology, Taipei Medical University, Taipei, Taiwan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Er-Chieh Cho
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chiao Chang
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Pharmacy, Taipei Medical University-Wanfang Hospital, Taipei, Taiwan.,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medicine Research, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
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47
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Hsu YH, Estrada K, Evangelou E, Ackert-Bicknell C, Akesson K, Beck T, Brown SJ, Capellini T, Carbone L, Cauley J, Cheung CL, Cummings SR, Czerwinski S, Demissie S, Econs M, Evans D, Farber C, Gautvik K, Harris T, Kammerer C, Kemp J, Koller DL, Kung A, Lawlor D, Lee M, Lorentzon M, McGuigan F, Medina-Gomez C, Mitchell B, Newman A, Nielson C, Ohlsson C, Peacock M, Reppe S, Richards JB, Robbins J, Sigurdsson G, Spector TD, Stefansson K, Streeten E, Styrkarsdottir U, Tobias J, Trajanoska K, Uitterlinden A, Vandenput L, Wilson SG, Yerges-Armstrong L, Young M, Zillikens C, Rivadeneira F, Kiel DP, Karasik D. Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry. J Bone Miner Res 2019; 34:1284-1296. [PMID: 30888730 PMCID: PMC6650334 DOI: 10.1002/jbmr.3698] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 01/29/2019] [Accepted: 02/07/2019] [Indexed: 12/14/2022]
Abstract
Hip geometry is an important predictor of fracture. We performed a meta-analysis of GWAS studies in adults to identify genetic variants that are associated with proximal femur geometry phenotypes. We analyzed four phenotypes: (i) femoral neck length; (ii) neck-shaft angle; (iii) femoral neck width, and (iv) femoral neck section modulus, estimated from DXA scans using algorithms of hip structure analysis. In the Discovery stage, 10 cohort studies were included in the fixed-effect meta-analysis, with up to 18,719 men and women ages 16 to 93 years. Association analyses were performed with ∼2.5 million polymorphisms under an additive model adjusted for age, body mass index, and height. Replication analyses of meta-GWAS significant loci (at adjusted genomewide significance [GWS], threshold p ≤ 2.6 × 10-8 ) were performed in seven additional cohorts in silico. We looked up SNPs associated in our analysis, for association with height, bone mineral density (BMD), and fracture. In meta-analysis (combined Discovery and Replication stages), GWS associations were found at 5p15 (IRX1 and ADAMTS16); 5q35 near FGFR4; at 12p11 (in CCDC91); 11q13 (near LRP5 and PPP6R3 (rs7102273)). Several hip geometry signals overlapped with BMD, including LRP5 (chr. 11). Chr. 11 SNP rs7102273 was associated with any-type fracture (p = 7.5 × 10-5 ). We used bone transcriptome data and discovered several significant eQTLs, including rs7102273 and PPP6R3 expression (p = 0.0007), and rs6556301 (intergenic, chr.5 near FGFR4) and PDLIM7 expression (p = 0.005). In conclusion, we found associations between several genes and hip geometry measures that explained 12% to 22% of heritability at different sites. The results provide a defined set of genes related to biological pathways relevant to BMD and etiology of bone fragility. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Yi-Hsiang Hsu
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
| | - Karol Estrada
- Broad Institute, Cambridge, MA
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Cheryl Ackert-Bicknell
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester, Rochester, New York, USA
| | - Kristina Akesson
- Department of Clinical Sciences Malmö, Lund University, Sweden
- Department of Orthopedics, Skåne University Hospital, S-205 02 Malmö, Sweden
| | - Thomas Beck
- Beck Radiological Innovations, Baltimore, MD
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Terence Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA
| | - Laura Carbone
- Department of Medicine at the Medical College of Georgia at Augusta University, Augusta, GA
| | - Jane Cauley
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Ching-Lung Cheung
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA
| | | | - Serkalem Demissie
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Michael Econs
- Department of Medicine and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Daniel Evans
- California Pacific Medical Center Research Institute, San Francisco, CA
| | - Charles Farber
- Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Kaare Gautvik
- Lovisenberg Diakonale Hospital, Unger-Vetlesen Institute, and University of Oslo, Institute of Basic Medical Sciences, Oslo, Norway
| | - Tamara Harris
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, NIA, Bethesda, MD
| | - Candace Kammerer
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - John Kemp
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, UK
| | - Daniel L Koller
- Department of Medicine and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Annie Kung
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Debbie Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, UK
| | - Miryoung Lee
- University of Texas, School of Public Health at Bronwsville, TX
| | - Mattias Lorentzon
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Fiona McGuigan
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester, Rochester, New York, USA
- Department of Clinical Sciences Malmö, Lund University, Sweden
| | | | - Braxton Mitchell
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, and Geriatric Research and Education Clinical Center - Veterans Administration Medical Center, Baltimore, MD
| | - Anne Newman
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Munro Peacock
- Department of Medicine and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Sjur Reppe
- Lovisenberg Diakonale Hospital, Unger-Vetlesen Institute, and University of Oslo, Institute of Basic Medical Sciences, Oslo, Norway
- Oslo University Hospital, Department of Medical Biochemistry, Oslo, Norway
| | - J Brent Richards
- Department of Human Genetics, McGill University, and Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - John Robbins
- Department of Medicine, University California at Davis, Sacramento, CA
| | | | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK
| | | | - Elizabeth Streeten
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, and Geriatric Research and Education Clinical Center - Veterans Administration Medical Center, Baltimore, MD
| | | | | | | | - André Uitterlinden
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Liesbeth Vandenput
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, UK
- School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
| | | | - Mariel Young
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA
| | - Carola Zillikens
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, 3000 CA Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Douglas P Kiel
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute, Cambridge, MA
| | - David Karasik
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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De Ridder R, Boudin E, Vandeweyer G, Devogelaer JP, Fransen E, Mortier G, Van Hul W. Genetic Variation in RIN3 in the Belgian Population Supports Its Involvement in the Pathogenesis of Paget's Disease of Bone and Modifies the Age of Onset. Calcif Tissue Int 2019; 104:613-621. [PMID: 30726512 DOI: 10.1007/s00223-019-00530-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/28/2019] [Indexed: 12/24/2022]
Abstract
Paget's disease of bone (PDB) is a common, late-onset bone disorder characterized by focal increase of bone turnover. Mutations in the SQSTM1 gene are found in up to 40% of patients and recent GWAS have led to novel associations with several loci. RIN3, the candidate gene located at the associated 14q32 locus, has recently been studied in a British cohort to elucidate its contribution to the pathogenesis. In this study, we performed a genetic screening of RIN3 in an unrelated cohort to validate these findings and to further explore genetic variation in this gene in the context of PDB. In our screening, we examined the 5' untranslated region (UTR), the exonic regions and the intron-exon boundaries of the gene in a control cohort and a patient cohort. Our findings show clustering of variation similar to the British cohort and support a protective role for common genetic variation (rs117068593, p.R279C) in the proline-rich region and a functionally relevant role for rare genetic variation in the domains that mediate binding and activation of its interaction partner, Rab5. Additive regression models, fitted for the common variants, validated the association of the rs117068593 variant with the disease (OR+/+ 0.315; OR+/- 0.562). In addition, our analyses revealed a potentially modifying effect of this variant on the age of onset of the disease. In conclusion, our findings support the involvement of genetic variation in RIN3 in PDB and suggest a role for RIN3 as a potential modifier of the age of onset of the disease.
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Affiliation(s)
- Raphaël De Ridder
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Eveline Boudin
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Geert Vandeweyer
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Jean-Pierre Devogelaer
- Department of Rheumatology, Saint-Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Wim Van Hul
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium.
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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Chesi A, Wagley Y, Johnson ME, Manduchi E, Su C, Lu S, Leonard ME, Hodge KM, Pippin JA, Hankenson KD, Wells AD, Grant SFA. Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density. Nat Commun 2019; 10:1260. [PMID: 30890710 PMCID: PMC6425012 DOI: 10.1038/s41467-019-09302-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 03/05/2019] [Indexed: 12/21/2022] Open
Abstract
Osteoporosis is a devastating disease with an essential genetic component. GWAS have discovered genetic signals robustly associated with bone mineral density (BMD), but not the precise localization of effector genes. Here, we carry out physical and direct variant to gene mapping in human mesenchymal progenitor cell-derived osteoblasts employing a massively parallel, high resolution Capture C based method in order to simultaneously characterize the genome-wide interactions of all human promoters. By intersecting our Capture C and ATAC-seq data, we observe consistent contacts between candidate causal variants and putative target gene promoters in open chromatin for ~ 17% of the 273 BMD loci investigated. Knockdown of two novel implicated genes, ING3 at ‘CPED1-WNT16’ and EPDR1 at ‘STARD3NL’, inhibits osteoblastogenesis, while promoting adipogenesis. This approach therefore aids target discovery in osteoporosis, here on the example of two relevant genes involved in the fate determination of mesenchymal progenitors, and can be applied to other common genetic diseases. GWAS have identified numerous genetic loci for bone mineral density (BMD) and fracture risk. Here, the authors map these variants to putative target genes using ATAC-seq and Capture C of human osteoblasts and confirm ING3 and EPDR1 as BMD genes in in vitro osteoblast differentiation experiments.
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Affiliation(s)
- Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Yadav Wagley
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Elisabetta Manduchi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA.,Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Michelle E Leonard
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Kurt D Hankenson
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA. .,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA. .,Divisions of Genetics and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA.
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