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Kaur G, Pippin JA, Chang S, Redmond J, Chesi A, Wells AD, Maerz T, Grant SFA, Coleman RM, Hankenson KD, Wagley Y. Osteoporosis GWAS-implicated DNM3 locus contextually regulates osteoblastic and chondrogenic fate of mesenchymal stem/progenitor cells through oscillating miR-199a-5p levels. JBMR Plus 2024; 8:ziae051. [PMID: 38686038 PMCID: PMC11056323 DOI: 10.1093/jbmrpl/ziae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/15/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Genome wide association study (GWAS)-implicated bone mineral density (BMD) signals have been shown to localize in cis-regulatory regions of distal effector genes using 3D genomic methods. Detailed characterization of such genes can reveal novel causal genes for BMD determination. Here, we elected to characterize the "DNM3" locus on chr1q24, where the long non-coding RNA DNM3OS and the embedded microRNA MIR199A2 (miR-199a-5p) are implicated as effector genes contacted by the region harboring variation in linkage disequilibrium with BMD-associated sentinel single nucleotide polymorphism, rs12041600. During osteoblast differentiation of human mesenchymal stem/progenitor cells (hMSC), miR-199a-5p expression was temporally decreased and correlated with the induction of osteoblastic transcription factors RUNX2 and Osterix. Functional relevance of miR-199a-5p downregulation in osteoblastogenesis was investigated by introducing miR-199a-5p mimic into hMSC. Cells overexpressing miR-199a-5p depicted a cobblestone-like morphological change and failed to produce BMP2-dependent extracellular matrix mineralization. Mechanistically, a miR-199a-5p mimic modified hMSC propagated normal SMAD1/5/9 signaling and expressed osteoblastic transcription factors RUNX2 and Osterix but depicted pronounced upregulation of SOX9 and enhanced expression of essential chondrogenic genes ACAN, COMP, and COL10A1. Mineralization defects, morphological changes, and enhanced chondrogenic gene expression associated with miR-199a-5p mimic over-expression were restored with miR-199a-5p inhibitor suggesting specificity of miR-199a-5p in chondrogenic fate specification. The expression of both the DNM3OS and miR-199a-5p temporally increased and correlated with hMSC chondrogenic differentiation. Although miR-199a-5p overexpression failed to further enhance chondrogenesis, blocking miR-199a-5p activity significantly reduced chondrogenic pellet size, extracellular matrix deposition, and chondrogenic gene expression. Taken together, our results indicate that oscillating miR-199a-5p levels dictate hMSC osteoblast or chondrocyte terminal fate. Our study highlights a functional role of miR-199a-5p as a BMD effector gene at the DNM3 BMD GWAS locus, where patients with cis-regulatory genetic variation which increases miR-199a-5p expression could lead to reduced osteoblast activity.
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Affiliation(s)
- Gurcharan Kaur
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - James A Pippin
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Solomon Chang
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Justin Redmond
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Diabetes and Endocrinology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Rhima M Coleman
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Kurt D Hankenson
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, United States
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Yadav Wagley
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109, United States
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Liu Y, Jin G, Wang X, Dong Y, Ding F. Identification of New Genes and Loci Associated With Bone Mineral Density Based on Mendelian Randomization. Front Genet 2021; 12:728563. [PMID: 34567079 PMCID: PMC8456003 DOI: 10.3389/fgene.2021.728563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 02/05/2023] Open
Abstract
Bone mineral density (BMD) is a complex and highly hereditary trait that can lead to osteoporotic fractures. It is estimated that BMD is mainly affected by genetic factors (about 85%). BMD has been reported to be associated with both common and rare variants, and numerous loci related to BMD have been identified by genome-wide association studies (GWAS). We systematically integrated expression quantitative trait loci (eQTL) data with GWAS summary statistical data. We mainly focused on the loci, which can affect gene expression, so Summary data-based Mendelian randomization (SMR) analysis was implemented to investigate new genes and loci associated with BMD. We identified 12,477 single-nucleotide polymorphisms (SNPs) regulating 564 genes, which are associated with BMD. The genetic mechanism we detected could make a contribution in the density of BMD in individuals and play an important role in understanding the pathophysiology of cataclasis.
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Affiliation(s)
- Yijun Liu
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Guang Jin
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Xue Wang
- Department of Anesthesiology, The First Hospital of Jilin University, Changchun, China
| | - Ying Dong
- The Third Department of Radiotherapy, Jilin Provincial Tumor Hospital, Changchun, China
| | - Fupeng Ding
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
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Ning HT, Du Y, Zhao LJ, Tian Q, Feng H, Deng HW. Racial and gender differences in the relationship between sarcopenia and bone mineral density among older adults. Osteoporos Int 2021; 32:841-851. [PMID: 33231702 PMCID: PMC8044008 DOI: 10.1007/s00198-020-05744-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/13/2020] [Indexed: 12/19/2022]
Abstract
Both sarcopenia and low bone mineral density (BMD) have become public health concerns. We found that presarcopenic and/or sarcopenic individuals were more likely to have lower BMD. And this relationship has race and sex-specific discrepancy. PURPOSE The purpose of the study was to investigate the racial and gender differences in the relationship between sarcopenia and BMD among older adults. METHODS Totally, 5476 subjects (mean age = 65.7 ± 6.4) of non-Hispanic White (n = 3297), non-Hispanic Black (n = 1265), and non-Hispanic Asian (n = 914) were analyzed. Sarcopenia was defined according to the revised European consensus on definition and diagnosis of sarcopenia (EWGSOP2). General linear model and multivariable linear regression model were used to examine the relationship between sarcopenia and regional/whole body BMD stratified by race and sex. Adjustments were conducted for physiological, behavioral, and disease factors. RESULTS Comparing with normal older participants, presarcopenic and sarcopenic elderly were more likely to have lower BMD. Although the difference was not statistically significant in a few sub-groups, among the three racial groups, the strongest association between sarcopenia and BMD was found in non-Hispanic Black people, followed by non-Hispanic White people and non-Hispanic Asian people. In addition, significant differences of BMD across sarcopenia stages were found in more sub-groups in women than in men after adjusting for covariates. CONCLUSIONS In this older cohort, sarcopenia is significantly related to low regional/whole-body BMD, and these associations vary by race and sex. Consideration in race and sex is warranted when developing strategies to maintain or minimize BMD loss.
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Affiliation(s)
- H-T Ning
- Xiangya School of Nursing, Central South University, Changsha, Hunan, China
| | - Y Du
- School of Nursing, University of Texas Health Science Center at San Antonio, TX, San Antonio, USA
| | - L-J Zhao
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, LA, New Orleans, USA
| | - Q Tian
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, LA, New Orleans, USA
| | - H Feng
- Xiangya School of Nursing, Xiangya-Oceanwide Health Management Research Institute, Central South University, Changsha, Hunan, China
| | - H-W Deng
- School of Medicine, Tulane University, New Orleans, LA, USA.
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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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Meng XH, Chen XD, Greenbaum J, Zeng Q, You SL, Xiao HM, Tan LJ, Deng HW. Integration of summary data from GWAS and eQTL studies identified novel causal BMD genes with functional predictions. Bone 2018; 113:41-48. [PMID: 29763751 PMCID: PMC6346739 DOI: 10.1016/j.bone.2018.05.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 01/19/2023]
Abstract
PURPOSE Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance. METHODS After quality control of the largest GWAS meta-analysis data of BMD and the largest expression quantitative trait loci (eQTL) meta-analysis data from peripheral blood samples, 5967 genes were tested using the SMR method. Another eQTL data was used to verify the results. Next we performed a fine-mapping association analysis to investigate the functional SNP in the identified loci. Weighted gene co-expression network analysis (WGCNA) was used to explore functional relationships for the identified novel genes with known putative osteoporosis genes. Further, we assessed functions of the identified genes through in vitro cellular study or previous functional studies. RESULTS We identified two potentially causal genes (ASB16-AS1 and SYN2) associated with BMD. SYN2 was a novel osteoporosis candidate gene and ASB16-AS1 locus was known to be associated with BMD but was not the nearest gene to the top GWAS SNP. Fine-mapping association analysis showed that rs184478 and rs795000 was predicted to be possible causal SNPs in ASB16-AS1 and SYN2, respectively. ASB16-AS1 co-expressed with several known putative osteoporosis risk genes. In vitro cellular study showed that over-expressed ASB16-AS1 increased the expression of osteoblastogenesis related genes (BMP2 and ALPL), indicating its functional significance. CONCLUSION Our findings support that ASB16-AS1 and SYN2 may represent two novel functional genes underlying BMD variation. The findings provide a basis for further functional mechanistic studies.
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Affiliation(s)
- Xiang-He Meng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xiang-Ding Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Jonathan Greenbaum
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Qin Zeng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Sheng-Lan You
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Hong-Mei Xiao
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Li-Jun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China.
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Du Y, Zhao LJ, Xu Q, Wu KH, Deng HW. Socioeconomic status and bone mineral density in adults by race/ethnicity and gender: the Louisiana osteoporosis study. Osteoporos Int 2017; 28:1699-1709. [PMID: 28236128 DOI: 10.1007/s00198-017-3951-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 01/27/2017] [Indexed: 11/26/2022]
Abstract
UNLABELLED Low bone mineral density (BMD) and osteoporosis have become a public health problem. We found that non-Hispanic white, black, and Asian adults with extremely low education and personal income are more likely to have lower BMD. This relationship is gender-specific. These findings are valuable to guide bone health interventions. INTRODUCTION The evidence is limited regarding the relationship between socioeconomic status (SES) and bone mineral density (BMD) for minority populations in the USA, as well as the relationship between SES and BMD for men. This study explored and examined the relationship between SES and BMD by race/ethnicity and gender. METHODS Data (n = 6568) from the Louisiana Osteoporosis Study (LOS) was examined, including data for non-Hispanic whites (n = 4153), non-Hispanic blacks (n = 1907), and non-Hispanic Asians (n = 508). General linear models were used to estimate the relationship of SES and BMD (total hip and lumbar spine) stratified by race/ethnicity and gender. Adjustments were made for physiological and behavioral factors. RESULTS After adjusting for covariates, men with education levels below high school graduate experienced relatively low hip BMD than their counterparts with college or graduate education (p < 0.05). In addition, women reporting a personal annual income under $20,000 had relatively low hip and spine BMD than their counterparts with higher income level(s) (p < 0.05). CONCLUSIONS Establishing a conclusive positive or negative association between BMD and SES proved to be difficult. However, individuals who are at an extreme SES disadvantage are the most vulnerable to have relatively low BMD in the study population. Efforts to promote bone health may benefit from focusing on men with low education levels and women with low individual income.
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Affiliation(s)
- Y Du
- Center for Aging, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - L-J Zhao
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St. Ste. 2001, New Orleans, LA, 70112, USA
| | - Q Xu
- Silver School of Social Work, New York University, New York, NY, 10003, USA
| | - K-H Wu
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St. Ste. 2001, New Orleans, LA, 70112, USA
| | - H-W Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St. Ste. 2001, New Orleans, LA, 70112, USA.
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Jin HS, Kim J, Park S, Park E, Kim BY, Choi VN, Yoo YH, Kim BT, Jeong SY. Association of the I264T variant in the sulfide quinone reductase-like (SQRDL) gene with osteoporosis in Korean postmenopausal women. PLoS One 2015; 10:e0135285. [PMID: 26258864 PMCID: PMC4530967 DOI: 10.1371/journal.pone.0135285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/20/2015] [Indexed: 01/21/2023] Open
Abstract
To identify novel susceptibility variants for osteoporosis in Korean postmenopausal women, we performed a genome-wide association analysis of 1180 nonsynonymous single nucleotide polymorphisms (nsSNPs) in 405 individuals with osteoporosis and 722 normal controls of the Korean Association Resource cohort. A logistic regression analysis revealed 72 nsSNPs that showed a significant association with osteoporosis (p<0.05). The top 10 nsSNPs showing the lowest p-values (p = 5.2×10-4-8.5×10-3) were further studied to investigate their effects at the protein level. Based on the results of an in silico prediction of the protein's functional effect based on amino acid alterations and a sequence conservation evaluation of the amino acid residues at the positions of the nsSNPs among orthologues, we selected one nsSNP in the SQRDL gene (rs1044032, SQRDL I264T) as a meaningful genetic variant associated with postmenopausal osteoporosis. To assess whether the SQRDL I264T variant played a functional role in the pathogenesis of osteoporosis, we examined the in vitro effect of the nsSNP on bone remodeling. Overexpression of the SQRDL I264T variant in the preosteoblast MC3T3-E1 cells significantly increased alkaline phosphatase activity, mineralization, and the mRNA expression of osteoblastogenesis markers, Runx2, Sp7, and Bglap genes, whereas the SQRDL wild type had no effect or a negative effect on osteoblast differentiation. Overexpression of the SQRDL I264T variant did not affect osteoclast differentiation of the primary-cultured monocytes. The known effects of hydrogen sulfide (H2S) on bone remodeling may explain the findings of the current study, which demonstrated the functional role of the H2S-catalyzing enzyme SQRDL I264T variant in osteoblast differentiation. In conclusion, the results of the statistical and experimental analyses indicate that the SQRDL I264T nsSNP may be a significant susceptibility variant for osteoporosis in Korean postmenopausal women that is involved in osteoblast differentiation.
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Affiliation(s)
- Hyun-Seok Jin
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Republic of Korea
| | - Jeonghyun Kim
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Sangwook Park
- Department of Biomedical Laboratory Science, College of Health, Kyungwoon University, Gumi, Republic of Korea
| | - Eunkuk Park
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Bo-Young Kim
- Division of Intractable Disease, Center for Biomedical Sciences, National Institute of Health, Korea Centers for Disease Control & Prevention, Cheongju, Republic of Korea
| | - Vit-Na Choi
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Young-Hyun Yoo
- Department of Anatomy and Cell Biology and Mitochondria Hub Regulation Center, College of Medicine, Dong-A University, Busan, Republic of Korea
| | - Bom-Taeck Kim
- Department of Family Practice and Community Health, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seon-Yong Jeong
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
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He H, Zhang L, Li J, Wang YP, Zhang JG, Shen J, Guo YF, Deng HW. Integrative analysis of GWASs, human protein interaction, and gene expression identified gene modules associated with BMDs. J Clin Endocrinol Metab 2014; 99:E2392-9. [PMID: 25119315 PMCID: PMC4223444 DOI: 10.1210/jc.2014-2563] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CONTEXT To date, few systems genetics studies in the bone field have been performed. We designed our study from a systems-level perspective by integrating genome-wide association studies (GWASs), human protein-protein interaction (PPI) network, and gene expression to identify gene modules contributing to osteoporosis risk. METHODS First we searched for modules significantly enriched with bone mineral density (BMD)-associated genes in human PPI network by using 2 large meta-analysis GWAS datasets through a dense module search algorithm. One included 7 individual GWAS samples (Meta7). The other was from the Genetic Factors for Osteoporosis Consortium (GEFOS2). One was assigned as a discovery dataset and the other as an evaluation dataset, and vice versa. RESULTS In total, 42 modules and 129 modules were identified significantly in both Meta7 and GEFOS2 datasets for femoral neck and spine BMD, respectively. There were 3340 modules identified for hip BMD only in Meta7. As candidate modules, they were assessed for the biological relevance to BMD by gene set enrichment analysis in 2 expression profiles generated from circulating monocytes in subjects with low versus high BMD values. Interestingly, there were 2 modules significantly enriched in monocytes from the low BMD group in both gene expression datasets (nominal P value <.05). Two modules had 16 nonredundant genes. Functional enrichment analysis revealed that both modules were enriched for genes involved in Wnt receptor signaling and osteoblast differentiation. CONCLUSION We highlighted 2 modules and novel genes playing important roles in the regulation of bone mass, providing important clues for therapeutic approaches for osteoporosis.
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Affiliation(s)
- Hao He
- Center of Genomics and Bioinformatics and Department of Biostatistics and Bioinformatics (H.H., L.Z., J.L., Y.-P.W., J.-G.Z., H.-W.D.), Tulane University, New Orleans, Louisiana 70112; Biomedical Engineering Department (Y.-P.W.), Tulane University, New Orleans, Louisiana 70118; and Third Affiliated Hospital (J.S., Y.-F.G., H.-W.D.), China Southern Medical University, Guang Zhou 510000, People's Republic of China
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Feltus FA. Systems genetics: a paradigm to improve discovery of candidate genes and mechanisms underlying complex traits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 223:45-8. [PMID: 24767114 DOI: 10.1016/j.plantsci.2014.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 02/18/2014] [Accepted: 03/02/2014] [Indexed: 05/02/2023]
Abstract
Understanding the control of any trait optimally requires the detection of causal genes, gene interaction, and mechanism of action to discover and model the biochemical pathways underlying the expressed phenotype. Functional genomics techniques, including RNA expression profiling via microarray and high-throughput DNA sequencing, allow for the precise genome localization of biological information. Powerful genetic approaches, including quantitative trait locus (QTL) and genome-wide association study mapping, link phenotype with genome positions, yet genetics is less precise in localizing the relevant mechanistic information encoded in DNA. The coupling of salient functional genomic signals with genetically mapped positions is an appealing approach to discover meaningful gene-phenotype relationships. Techniques used to define this genetic-genomic convergence comprise the field of systems genetics. This short review will address an application of systems genetics where RNA profiles are associated with genetically mapped genome positions of individual genes (eQTL mapping) or as gene sets (co-expression network modules). Both approaches can be applied for knowledge independent selection of candidate genes (and possible control mechanisms) underlying complex traits where multiple, likely unlinked, genomic regions might control specific complex traits.
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Affiliation(s)
- F Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
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Liu YJ, Zhang L, Papasian CJ, Deng HW. Genome-wide Association Studies for Osteoporosis: A 2013 Update. J Bone Metab 2014; 21:99-116. [PMID: 25006567 PMCID: PMC4075273 DOI: 10.11005/jbm.2014.21.2.99] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 12/16/2022] Open
Abstract
In the past few years, the bone field has witnessed great advances in genome-wide association studies (GWASs) of osteoporosis, with a number of promising genes identified. In particular, meta-analysis of GWASs, aimed at increasing the power of studies by combining the results from different study populations, have led to the identification of novel associations that would not otherwise have been identified in individual GWASs. Recently, the first whole genome sequencing study for osteoporosis and fractures was published, reporting a novel rare nonsense mutation. This review summarizes the important and representative findings published by December 2013. Comments are made on the notable findings and representative studies for their potential influence and implications on our present understanding of the genetics of osteoporosis. Potential limitations of GWASs and their meta-analyses are evaluated, with an emphasis on understanding the reasons for inconsistent results between different studies and clarification of misinterpretation of GWAS meta-analysis results. Implications and challenges of GWAS are also discussed, including the need for multi- and inter-disciplinary studies.
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Affiliation(s)
- Yong-Jun Liu
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Lei Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA. ; Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, PR, China
| | | | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA. ; Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai, PR, China
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Wu S, Liu Y, Zhang L, Han Y, Lin Y, Deng HW. Genome-wide approaches for identifying genetic risk factors for osteoporosis. Genome Med 2013; 5:44. [PMID: 23731620 PMCID: PMC3706967 DOI: 10.1186/gm448] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Osteoporosis, the most common type of bone disease worldwide, is clinically characterized by low bone mineral density (BMD) and increased susceptibility to fracture. Multiple genetic and environmental factors and gene-environment interactions have been implicated in its pathogenesis. Osteoporosis has strong genetic determination, with the heritability of BMD estimated to be as high as 60%. More than 80 genes or genetic variants have been implicated in risk of osteoporosis by hypothesis-free genome-wide studies. However, these genes or genetic variants can only explain a small portion of BMD variation, suggesting that many other genes or genetic variants underlying osteoporosis risk await discovery. Here, we review recent progress in genome-wide studies of osteoporosis and discuss their implications for medicine and the major challenges in the field.
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Affiliation(s)
- Shuyan Wu
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Yongjun Liu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
| | - Lei Zhang
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China ; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
| | - Yingying Han
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Yong Lin
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Hong-Wen Deng
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China ; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
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