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Choi J, Xu Z, Sun R. Variance-components tests for genetic association with multiple interval-censored outcomes. Stat Med 2024; 43:2560-2574. [PMID: 38636557 PMCID: PMC11116038 DOI: 10.1002/sim.10081] [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: 10/19/2022] [Revised: 02/18/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
Massive genetic compendiums such as the UK Biobank have become an invaluable resource for identifying genetic variants that are associated with complex diseases. Due to the difficulties of massive data collection, a common practice of these compendiums is to collect interval-censored data. One challenge in analyzing such data is the lack of methodology available for genetic association studies with interval-censored data. Genetic effects are difficult to detect because of their rare and weak nature, and often the time-to-event outcomes are transformed to binary phenotypes for access to more powerful signal detection approaches. However transforming the data to binary outcomes can result in loss of valuable information. To alleviate such challenges, this work develops methodology to associate genetic variant sets with multiple interval-censored outcomes. Testing sets of variants such as genes or pathways is a common approach in genetic association settings to lower the multiple testing burden, aggregate small effects, and improve interpretations of results. Instead of performing inference with only a single outcome, utilizing multiple outcomes can increase statistical power by aggregating information across multiple correlated phenotypes. Simulations show that the proposed strategy can offer significant power gains over a single outcome approach. We apply the proposed test to the investigation that motivated this study, a search for the genes that perturb risks of bone fractures and falls in the UK Biobank.
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Affiliation(s)
- Jaihee Choi
- Department of Statistics, Rice University, Texas, USA
| | - Zhichao Xu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Texas, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Texas, USA
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2
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Yang Q, Liu H, Xi Y, Lu Y, Han X, He X, Qi J, Zhu Y, He H, Wang J, Hu J, Li L. Genome-wide association study for bone quality of ducks during the laying period. Poult Sci 2024; 103:103575. [PMID: 38447311 PMCID: PMC11067773 DOI: 10.1016/j.psj.2024.103575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
The cage-rearing model of the modern poultry industry makes the bones of birds, especially egg-laying birds, more vulnerable to fracture, which poses serious damage to the health of birds. Research confirms that genetic material plays an important role in regulating bone growth, development, and remodeling. However, the genetic architecture underlying bone traits is not well understood. The objectives of this study are to identify valuable genes and genetic markers through a genome-wide association study (GWAS) for breeding to improve the duck bone quality. First, we quantified the tibia and femur quality traits of 260 laying ducks. Based on GWAS, a total of 75 SNP loci significantly associated with bone quality traits were identified, and 67 potential candidate genes were annotated. According to gene function analysis, genes P4HA2, WNT3A, and BST1 et al may influence bone quality by regulating bone cell activity, calcium and phosphate metabolism, or bone collagen maturation and cross-linking. Meanwhile, combined with the transcriptome results, we found that HOXB cluster genes are also important in bone growth and development. Therefore, our findings were helpful in further understanding the genetic architecture of the duck bone quality and provided a worthy theoretical basis and technological support to improve duck bone quality by breeding.
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Affiliation(s)
- Qinglan Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Hehe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Yang Xi
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Yinjuan Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Xu Han
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Xinxin He
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Jingjing Qi
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Yuanchun Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Hua He
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Jiwen Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Jiwei Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 613000, China.
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Jia Y, Qi X, Ma M, Cheng S, Cheng B, Liang C, Guo X, Zhang F. Integrating genome-wide association study with regulatory SNP annotations identified novel candidate genes for osteoporosis. Bone Joint Res 2023; 12:147-154. [PMID: 37051837 PMCID: PMC10003063 DOI: 10.1302/2046-3758.122.bjr-2022-0206.r1] [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] [Indexed: 04/14/2023] Open
Abstract
Osteoporosis (OP) is a metabolic bone disease, characterized by a decrease in bone mineral density (BMD). However, the research of regulatory variants has been limited for BMD. In this study, we aimed to explore novel regulatory genetic variants associated with BMD. We conducted an integrative analysis of BMD genome-wide association study (GWAS) and regulatory single nucleotide polymorphism (rSNP) annotation information. Firstly, the discovery GWAS dataset and replication GWAS dataset were integrated with rSNP annotation database to obtain BMD associated SNP regulatory elements and SNP regulatory element-target gene (E-G) pairs, respectively. Then, the common genes were further subjected to HumanNet v2 to explore the biological effects. Through discovery and replication integrative analysis for BMD GWAS and rSNP annotation database, we identified 36 common BMD-associated genes for BMD irrespective of regulatory elements, such as FAM3C (pdiscovery GWAS = 1.21 × 10-25, preplication GWAS = 1.80 × 10-12), CCDC170 (pdiscovery GWAS = 1.23 × 10-11, preplication GWAS = 3.22 × 10-9), and SOX6 (pdiscovery GWAS = 4.41 × 10-15, preplication GWAS = 6.57 × 10-14). Then, for the 36 common target genes, multiple gene ontology (GO) terms were detected for BMD such as positive regulation of cartilage development (p = 9.27 × 10-3) and positive regulation of chondrocyte differentiation (p = 9.27 × 10-3). We explored the potential roles of rSNP in the genetic mechanisms of BMD and identified multiple candidate genes. Our study results support the implication of regulatory genetic variants in the development of OP.
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Affiliation(s)
- Yumeng Jia
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mei Ma
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chujun Liang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiong Guo
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
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microRNAs in newborns with low birth weight: relation to birth size and body composition. Pediatr Res 2022; 92:829-837. [PMID: 34799665 DOI: 10.1038/s41390-021-01845-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Children with low birth weight (LBW) have a higher risk of developing endocrine-metabolic disorders later in life. Deregulation of specific microRNAs (miRNAs) could underscore the programming of adult pathologies. We analyzed the miRNA expression pattern in both umbilical cord serum samples from LBW and appropriate-for-gestational-age (AGA) newborns and maternal serum samples in the 3rd trimester of gestation, and delineated the relationships with fetal growth, body composition, and markers of metabolic risk. METHODS Serum samples of 12 selected mother-newborn pairs, including 6 LBW and 6 AGA newborns, were used for assessing miRNA profile by RNA-sequencing. The miRNAs with differential expression were validated in a larger cohort [49 maternal samples and 49 umbilical cord samples (24 LBW, 25 AGA)] by RT-qPCR. Anthropometric, endocrine-metabolic markers and body composition (by DXA) in infants were determined longitudinally over 12 months. RESULTS LBW newborns presented reduced circulating concentrations of miR-191-3p (P = 0.015). miR-191-3p levels reliably differentiated LBW from AGA individuals (ROC AUC = 0.76) and were positively associated with anthropometric and body composition measures at birth and weight Z-score at 12 months (P < 0.05). CONCLUSIONS miR-191-3p was reliably different in LBW individuals, and could be a new player in the epigenetic mechanisms linking LBW and future endocrine-metabolic adverse outcomes. IMPACT Children with low birth weight (LBW) have a higher risk of developing endocrine-metabolic disorders. Deregulation of specific microRNAs (miRNAs) could underscore the programming of those pathologies. miR-191-3p is downregulated in serum of LBW newborns, and its concentrations associate positively with neonatal anthropometric measures, with lean mass and bone accretion at age 15 days and with weight Z-score at age 12 months. miR-191-3p was reliably different in individuals with LBW, and could be a new player in the epigenetic mechanisms connecting LBW and future endocrine-metabolic adverse outcomes.
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5
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Kang X, Chen L, Yang S, Gong Z, Hu H, Zhang X, Liang C, Xu Y. Zuogui Wan slowed senescence of bone marrow mesenchymal stem cells by suppressing Wnt/β-catenin signaling. JOURNAL OF ETHNOPHARMACOLOGY 2022; 294:115323. [PMID: 35483559 DOI: 10.1016/j.jep.2022.115323] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In traditional Chinese medicine (TCM), Zuogui Wan (ZGW) is a classical prescription for senile disorders and delay aging. Modern studies show that ZGW promotes central nerve cell regeneration, prevents and cures osteoporosis, enhances the body's antioxidant capacity, regulates the body's immune function, and promotes mesenchymal stem cells (MSCs) proliferation. AIM OF THE STUDY It has been shown that MSCs aging is closely associated with organism's aging and age-related disorders. The study aimed to define the effects of ZGW on the aging bone marrow mesenchymal stem cells (BMSCs) and to identify the mechanisms of ZGW delaying BMSCs senescence. MATERIALS AND METHODS Network pharmacology analysis combined with GEO data mining, molecular docking and experimental validation were used to evaluate the mechanisms by which ZGW delays MSCs senescence (MSCS). LC-MS was used for quality control analysis of ZGW. RESULTS PPI network analysis revealed that EGF, TNF, JUN, MMPs, IL-6, MAPK8, and MYC are components of the core PPI network. GO and KEGG analyses revealed that oxidative stress, regulation of response to DNA damage stimuli, and Wnt signaling were significantly enriched. GEO database validation also indicated that Wnt signaling closely correlated with MSCs aging. Molecular docking analysis of the top-13 active components in the "ZGW-Targets-MSCS" network indicated that most components have strong affinity for key proteins in Wnt signaling, suggesting that modulation of Wnt signaling is an important mechanism of ZGW activity against MSCS. Further experimental validation found that ZGW indeed regulates Wnt signaling and suppresses the expression of age-related factors to enhance cell proliferation, ameliorate DNA damage, and reduce senescence-related secretory phenotype (SASP) secretion, thereby maintaining multidirectional differentiation of rat BMSCs. Similar results were obtained using the Wnt inhibitor, XAV-939. CONCLUSIONS Together, our data show that ZGW slows BMSCs aging by suppressing Wnt signaling.
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Affiliation(s)
- Xiangping Kang
- College of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Long Chen
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Shuchen Yang
- College of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Zhangbin Gong
- College of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Haiyan Hu
- College of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Xueli Zhang
- College of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Chao Liang
- College of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Yanwu Xu
- College of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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6
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Chatzopoulos GS, Koidou VP, Wolff LF. Expression of Wnt signaling agonists and antagonists in periodontitis and healthy subjects, before and after non-surgical periodontal treatment: A systematic review. J Periodontal Res 2022; 57:698-710. [PMID: 35719081 DOI: 10.1111/jre.13029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
Periodontitis is a preventable and treatable multifactorial chronic inflammatory disease that can lead to irreversible periodontal destruction and tooth loss. Wnt signaling and its regulators play an important role in periodontal inflammation, destruction, regeneration, and reconstruction. This systematic review aimed at investigating the involvement of Wnt signaling agonists and antagonists in periodontitis and healthy subjects, before and after periodontal treatment. Electronic searches were carried out using MEDLINE/PubMed, EMBASE, and Cochrane Library databases in addition to hand searches. Studies having different designs assessing the levels of Wnt signaling antagonist and agonist levels in gingival crevicular fluid, serum, and tissue in patients diagnosed with periodontitis or gingivitis, compared with healthy individuals were included. In addition, studies compared these levels in periodontitis patients before and after non-surgical periodontal therapy were also eligible. Sixteen studies met the eligibility criteria. Sclerostin (SOST) has been mainly investigated in the literature (8 publications). Sclerostin (5 studies), Wnt-5a (2 studies), secreted frizzled-related protein 1 (SFRP1) (3 studies), and β-catenin (3 studies) show increased levels in periodontitis compared with periodontal health. Strong correlations between marker levels and periodontal clinical parameters were identified for SOST (5 studies), SFRP1 (2 studies), and β-catenin (2 studies). SOST (3 studies) and SFRP1 (1 study) levels significantly decrease following non-surgical periodontal treatment. The present systematic review demonstrated an association between Wnt signaling agonist and antagonist levels and periodontitis. Wnt agonists and antagonists may serve as valuable diagnostic and prognostic markers for periodontitis onset and progression. Further case-control and longitudinal studies should be conducted for different Wnt signaling agonists and antagonists.
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Affiliation(s)
- Georgios S Chatzopoulos
- Division of Periodontology, Department of Developmental and Surgical Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Preventive Dentistry, Periodontology and Implant Biology, School of Dentistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vasiliki P Koidou
- Division of Periodontology, Department of Developmental and Surgical Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA.,Centre for Oral Immunobiology and Regenerative Medicine and Centre for Oral Clinical Research, Institute of Dentistry, Queen Mary University London (QMUL), London, UK
| | - Larry F Wolff
- Division of Periodontology, Department of Developmental and Surgical Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
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Skripnikova IA, Kolchina MA, Meshkov AN, Kiseleva AV, Drapkina OM. Arterial calcification, atherosclerosis and osteoporosis: only clinical associations or a genetic platform? КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2021. [DOI: 10.15829/1728-8800-2021-3034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The review is devoted to the comorbidity of two multifactorial diseases — atherosclerosis and osteoporosis. Numerous epidemiological, experimental and clinical studies have confirmed the relationship between these diseases based on common risk factors and pathogenetic mechanisms. At the same time, to assess the associations between osteoporosis and atherosclerosis-related cardiovascular diseases, the following surrogate markers are used: vascular calcification, vascular stiffness, bone mineral density. It is known that atherosclerosis and osteoporosis depend on the human genotype, and they are caused by the interaction between the environment and genes. The modifiable risk factors for these diseases are largely similar, and the common features of atherosclerosis and osteoporosis pathogenesis make it possible to formulate the concept of a unified genetic basis of their development. Advances in molecular technology have made it possible to conduct a genome-wide association study (GWAS) and successfully identify genetic markers associated with both atherosclerosis and osteoporosis. The review aim was to describe the genes associated with developing atherosclerosis, arterial calcification and osteoporosis, as well as to provide information on the current understanding of the general genetic basis for plaque formation, vascular calcium deposition, and a decrease in bone mass. The analysis of publications from the PubMed, Medline, Web of Science and Cochrane Library databases since 2000 have been carried out. The article describes the genetic markers associated with atherosclerosis and osteoporosis, as well as considers the achievements in studying genetics of osteoporosis and atherosclerosis-related cardiovascular diseases. In addition, modern approaches and directions for further research of these diseases was established. The review can be useful for medical practitioners to clarify various genetic associations and mechanisms that lead to this comorbidity.
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Affiliation(s)
- I. A. Skripnikova
- National Medical Research Center for Therapy and Preventive Medicine
| | - M. A. Kolchina
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. V. Kiseleva
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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Chen M, Lin W, Yi J, Zhao Z. Exploring the Epigenetic Regulatory Role of m6A-Associated SNPs in Type 2 Diabetes Pathogenesis. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:1369-1378. [PMID: 34737607 PMCID: PMC8558037 DOI: 10.2147/pgpm.s334346] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/13/2021] [Indexed: 02/05/2023]
Abstract
Purpose Genetic factors in type 2 diabetes (T2D) pathogenesis have been widely explored by the genome-wide association studies (GWAS), identifying a great amount of susceptibility loci. With the development of high-resolution sequencing, the N(6)-methyladenosine (m6A) RNA modification has been proved to be affected by genetic variation. In this study, we identified the T2D-associated m6A-SNPs from T2D GWAS data and explored the underlying mechanism of the pathogenesis of T2D. Methods We examined the association of m6A-SNPs with T2D among large-scale T2D GWAS summary statistics and further performed multi-omics integrated analysis to explore the potential role of the identified m6A-SNPs in T2D pathogenesis. Results Among the 15,124 T2D-associated m6A-SNPs, 71 of them reach the genome-wide significant threshold (5.0e-05). The leading SNP rs4993986 (C>G), which is located near the m6A modification site at the 3' end of the HLA-DQB1 transcript, is expected to participate in the pathogenesis of T2D by influencing m6A modification to regulate the HLA-DQB1 expression. Conclusion The current study has suggested a potential correlation between m6A-SNPs and T2D pathogenesis and also provided new insights into the pathogenic mechanism of the T2D susceptibility loci identified by GWAS.
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Affiliation(s)
- Miao Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Jianru Yi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China
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9
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Ding X, Cai M, Wang S, Yang Q, Zheng X, Zuo X, Liu S. Gene-based association analysis identified a novel gene associated with systemic lupus erythematosus. Ann Hum Genet 2021; 85:213-220. [PMID: 34145571 DOI: 10.1111/ahg.12439] [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: 12/05/2020] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a complex autoimmune disease with strong genetic predisposition. Genome-wide association studies (GWAS) of SLE have identified more than 50 robust susceptibility loci. However, traditional individual SNP-based GWAS have made it difficult to identify variants with small effects. Moreover, variants revealed by GWAS only explain a limited disease heritability, suggesting that many susceptibility genes remain uncovered. METHODS We first curated the published SLE GWAS data from 1047 SLE patients and 1205 healthy controls of Chinese ancestry and performed a gene-based association study. Then quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was conducted to verify novel genes identified above. RESULTS Gene-based association study identified 10 SLE-associated genes, nine of which were reported by previous GWAS, the other one, ILRUN, is a newly identified gene and was further validated by qRT-PCR. Gene expression analysis of Gene Expression Omnibus (GEO) datasets also showed that the expression of ILRUN in patients with SLE was lower than that in normal subjects. CONCLUSION In this study, gene-based association study and qRT-PCR identified that ILRUN is a novel susceptibility gene of SLE. ILRUN may regulate inflammation and antiviral response through its effect on the transcription of type I interferons )I-IFN, and participate in the pathogenesis of SLE.
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Affiliation(s)
- Xian Ding
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Minglong Cai
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Sun Wang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qingqing Yang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xianbo Zuo
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Shengxiu Liu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
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10
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Huang M, Lyu C, Li X, Qureshi AA, Han J, Li M. Identifying Susceptibility Loci for Cutaneous Squamous Cell Carcinoma Using a Fast Sequence Kernel Association Test. Front Genet 2021; 12:657499. [PMID: 34040636 PMCID: PMC8141858 DOI: 10.3389/fgene.2021.657499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) accounts for about 20% of all skin cancers, the most common type of malignancy in the United States. Genome-wide association studies (GWAS) have successfully identified multiple genetic variants associated with the risk of cSCC. Most of these studies were single-locus-based, testing genetic variants one-at-a-time. In this article, we performed gene-based association tests to evaluate the joint effect of multiple variants, especially rare variants, on the risk of cSCC by using a fast sequence kernel association test (fastSKAT). The study included 1,710 cSCC cases and 24,304 cancer-free controls from the Nurses' Health Study, the Nurses' Health Study II and the Health Professionals Follow-up Study. We used UCSC Genome Browser to define gene units as candidate loci, and further evaluated the association between all variants within each gene unit and disease outcome. Four genes HP1BP3, DAG1, SEPT7P2, and SLFN12 were identified using Bonferroni adjusted significance level. Our study is complementary to the existing GWASs, and our findings may provide additional insights into the etiology of cSCC. Further studies are needed to validate these findings.
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Affiliation(s)
- Manyan Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University at Bloomington, Bloomington, IN, United States
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University at Bloomington, Bloomington, IN, United States
| | - Xin Li
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States
| | - Abrar A Qureshi
- Department of Dermatology, Alpert Medical School, Brown University, Providence, RI, United States
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States.,Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States
| | - Ming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University at Bloomington, Bloomington, IN, United States
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11
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Liu X, Li YG, Tan F, Liu J, Yi R, Zhao X. Three functional polymorphisms in CCDC170 were associated with osteoporosis phenotype. Biol Open 2021; 10:bio.050930. [PMID: 33785515 PMCID: PMC8061906 DOI: 10.1242/bio.050930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) play essential roles in regulating bone formation and homeostasis. Genomic variations within miRNA target sites may therefore be important sources of genetic differences in osteoporosis risk. The function of CCDC170 in bone biology is still unclear. To verify the function of CCDC170, we knocked down CCDC170 in cells and mice and searched for miRNA recognition sites within CCDC170 using the TargetScan, miRNASNP, and miRBase databases. In this study, our results demonstrated that CCDC170 plays an important role in the positive regulation of bone formation. MiR-153-3p, miR-374b-3p, miR-4274, miR-572 and miR-2964a-5p inhibited CCDC170 expression in an allele-specific manner by binding GWAS lead SNPs rs6932603, rs3757322 and rs3734806. These findings may improve our understanding of the association between CCDC170, miRNAs, GWAS lead SNPs, and osteoporosis pathogenesis and may provide a potential therapeutic target for osteoporosis therapy. Summary: CCDC170 may provide a potential therapeutic target for osteoporosis therapy.
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Affiliation(s)
- Xinhong Liu
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China.,College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, China
| | - Yu-Gang Li
- Department of Orthopedics, the First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China
| | - Fang Tan
- Department of Public Health, Our Lady of Fatima University, Valenzuela 838, Philippines
| | - Jia Liu
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
| | - Ruokun Yi
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
| | - Xin Zhao
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
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12
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Yu F, Xu C, Deng HW, Shen H. A novel computational strategy for DNA methylation imputation using mixture regression model (MRM). BMC Bioinformatics 2020; 21:552. [PMID: 33261550 PMCID: PMC7708217 DOI: 10.1186/s12859-020-03865-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND DNA methylation is an important heritable epigenetic mark that plays a crucial role in transcriptional regulation and the pathogenesis of various human disorders. The commonly used DNA methylation measurement approaches, e.g., Illumina Infinium HumanMethylation-27 and -450 BeadChip arrays (27 K and 450 K arrays) and reduced representation bisulfite sequencing (RRBS), only cover a small proportion of the total CpG sites in the human genome, which considerably limited the scope of the DNA methylation analysis in those studies. RESULTS We proposed a new computational strategy to impute the methylation value at the unmeasured CpG sites using the mixture of regression model (MRM) of radial basis functions, integrating information of neighboring CpGs and the similarities in local methylation patterns across subjects and across multiple genomic regions. Our method achieved a better imputation accuracy over a set of competing methods on both simulated and empirical data, particularly when the missing rate is high. By applying MRM to an RRBS dataset from subjects with low versus high bone mineral density (BMD), we recovered methylation values of ~ 300 K CpGs in the promoter regions of chromosome 17 and identified some novel differentially methylated CpGs that are significantly associated with BMD. CONCLUSIONS Our method is well applicable to the numerous methylation studies. By expanding the coverage of the methylation dataset to unmeasured sites, it can significantly enhance the discovery of novel differential methylation signals and thus reveal the mechanisms underlying various human disorders/traits.
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Affiliation(s)
- Fangtang Yu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Chao Xu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hui Shen
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
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13
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Kim BH, Choi YH, Yang JJ, Kim S, Nho K, Lee JM. Identification of Novel Genes Associated with Cortical Thickness in Alzheimer’s Disease: Systems Biology Approach to Neuroimaging Endophenotype. J Alzheimers Dis 2020; 75:531-545. [DOI: 10.3233/jad-191175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bo-Hyun Kim
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - Yong-Ho Choi
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - Jin-Ju Yang
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine and Clinical Neuroscience Center of Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jong-Min Lee
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
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14
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Hu W, He J, Qi L, Wang C, Yue H, Gu J, Zhang H, Wang Y, Zhang Z. Association of HIVEP3 Gene and Lnc RNA with Femoral Neck Bone Mineral Content and Hip Geometry by Genome-Wide Association Analysis in Chinese People. Int J Endocrinol 2020; 2020:6929073. [PMID: 33110425 PMCID: PMC7579678 DOI: 10.1155/2020/6929073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/27/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE GWAS has successfully located and analyzed the pathogenic genes of osteoporosis. Genetic studies have found that heritability of BMD is 50%-85% while the other half is caused by hip geometric parameters and tissue horizontal characteristics. This study was designed to study the GWAS of osteoporosis in Shanghai Han population. METHODS We collected 1224 unrelated healthy young men (20-40 years old), young women (20-40 years old), and postmenopausal women (over 50 years old) who lived in Shanghai. BMD and hip geometric parameters were measured by dual-energy X-ray absorptiometry. The genomic DNA of peripheral blood was extracted and analyzed by using Illumina Human Asian Screening Array-24 + v1.0 (ASA) gene chip. Statistical analysis was carried out to evaluate the relationship between these SNPs and BMD and hip geometric parameters. RESULTS A total of 1155 subjects were included. We found that one SNP rs35282355 located in the human immunodeficiency virus type 1 enhancer-binding protein 3 gene (HIVEP3) and another 25 SNPs located in LINC RNA were significantly correlated with bone mineral content (BMC) in the femoral neck (P= 2.30 × 10-9, P < 5 × 10-8). We also found that the correlation between SNP rs35282355 and cross-sectional area (CSA) of hip geometry was a significant marginal statistical difference (P = 5.95 × 10-8). CONCLUSIONS Through this study, we found that HIVEP3 gene and LINC RNA are potentially correlated with femoral neck BMC. These results provide important information for us to further understand the etiology and genetic pathogenesis of osteoporosis. In the future, we will expand the sample size to verify these loci and carry out molecular research.
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Affiliation(s)
- Weiwei Hu
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Jinwei He
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Luyue Qi
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Chun Wang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Hua Yue
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Jiemei Gu
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Hao Zhang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Yishan Road 600, Shanghai 200233, China
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15
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de Souza LC, Cavalla F, Maili L, Garlet GP, Vieira AR, Silva RM, Letra A. WNT gene polymorphisms and predisposition to apical periodontitis. Sci Rep 2019; 9:18980. [PMID: 31831777 PMCID: PMC6908593 DOI: 10.1038/s41598-019-55293-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) in WNT genes may impact gene/protein function and contribute to individual predisposition to apical periodontitis (AP). Here, we investigated the association of SNPs in/nearby WNT3, WNT3A, WNT5A, WNT8A, WNT9B and WNT11 genes with AP using a case-control dataset. Cases were defined as individuals with deep caries and AP (n = 188); controls had deep caries and no AP (n = 230). Genotyping was performed using Taqman chemistry in real time PCR. Data analyses was performed using Fisher Exact tests assuming a Bonferroni correction threshold value of 0.005. Single-SNP association analysis revealed a trend for association with WNT3 rs9890413 genotypes (P = 0.009) under a dominant model and allelic association for WNT3A rs1745420 (P = 0.009). Haplotypes involving WNT3-WNT9B-WNT3A alleles were also significantly associated with AP (P ≤ 0.003). Luciferase reporter assays showed higher transcriptional activity (1.4-fold) with the alternate G allele in rs1745420. Expression of WNT3, WNT3A and WNT5A in AP tissues was significantly higher than in control tissues, and inversely correlated with the expression of SERPINB1, COL1A1 and TIMP1 (P < 0.05). Our results suggest that WNT genes have a role in modulating AP and polymorphisms in these genes may increase susceptibility to AP.
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Affiliation(s)
- Letícia Chaves de Souza
- Department of Endodontics, University of Texas Health Science Center School of Dentistry, Houston, 77054, USA
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry, Houston, 77054, USA
| | - Franco Cavalla
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry, Houston, 77054, USA
- Department of Conservative Dentistry, School of Dentistry, University of Chile, Santiago, 7520355, Chile
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, 17012, Brazil
| | - Lorena Maili
- Department of Pediatrics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, 77030, USA
- Pediatric Research Center, University of Texas Health Science Center at Houston McGovern Medical School, Houston, 77030, USA
| | - Gustavo P Garlet
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, 17012, Brazil
| | - Alexandre R Vieira
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, 15229, USA
| | - Renato M Silva
- Department of Endodontics, University of Texas Health Science Center School of Dentistry, Houston, 77054, USA
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry, Houston, 77054, USA
| | - Ariadne Letra
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry, Houston, 77054, USA.
- Pediatric Research Center, University of Texas Health Science Center at Houston McGovern Medical School, Houston, 77030, USA.
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center School of Dentistry, Houston, 77054, USA.
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16
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Lin W, Xu H, Wu Y, Wang J, Yuan Q. In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis. J Cell Physiol 2019; 235:900-908. [PMID: 31245852 DOI: 10.1002/jcp.29005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/04/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Weimin Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Hao Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Yunshu Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Jun Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
- Department of Periodontics, West China Hospital of Stomatology Sichuan University Chengdu China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology Sichuan University Chengdu China
- Department of Oral Implantology, West China Hospital of Stomatology Sichuan University Chengdu China
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17
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Zeng Q, Wu KH, Liu K, Hu Y, Chen XD, Zhang L, Shen H, Tian Q, Zhao LJ, Deng HW, Tan LJ. Genome-wide association study of lncRNA polymorphisms with bone mineral density. Ann Hum Genet 2018; 82:244-253. [PMID: 29663307 PMCID: PMC6298226 DOI: 10.1111/ahg.12247] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/30/2017] [Accepted: 01/25/2018] [Indexed: 01/10/2023]
Abstract
Recent studies suggested that long noncoding RNAs (lncRNAs) were widely transcribed in the genome, but their potential roles in the genetic complexity of human disorders required further exploration. The purpose of the present study was to explore genetic polymorphisms of lncRNAs associated with bone mineral density (BMD) and its potential value. Based on the lncRNASNP database, 55,906 lncSNPs were selected to conduct a genome-wide association study meta-analysis among 11,140 individuals of seven independent studies for BMDs at femoral neck (FN), lumbar spine, and total hip (HIP). Promising results were replicated in Genetic Factors for Osteoporosis Consortium (GEFOS Sequencing, n = 32,965). We found two lncRNA loci that were significantly associated with BMD. MEF2C antisense RNA 1 (MEF2C-AS1) located at 5q14.3 was significantly associated with FN-BMD after Bonferroni correction, and the strongest association signal was detected at rs6894139 (P = 3.03 × 10-9 ). LOC100506136 rs6465531 located at 7q21.3 showed significant association with HIP-BMD (P = 7.43 × 10-7 ). MEF2C-AS1 rs6894139 was replicated in GEFOS Sequencing with P-value of 1.43 × 10-23 . Our results illustrated the important role of polymorphisms in lncRNAs in determining variations of BMD and provided justification and evidence for subsequent functional studies.
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Affiliation(s)
- Qin Zeng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Ke-Hao Wu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Kun Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yuan Hu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiang-Ding Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Lei Zhang
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, PR, China
| | - Hui Shen
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Qin Tian
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Lan-Juan Zhao
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Li-Jun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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18
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Mo XB, Zhang YH, Lei SF. Genome-wide identification of m 6A-associated SNPs as potential functional variants for bone mineral density. Osteoporos Int 2018; 29:2029-2039. [PMID: 29980810 DOI: 10.1007/s00198-018-4573-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/13/2018] [Indexed: 01/12/2023]
Abstract
UNLABELLED This study investigated the effect of the N6-methyladenosine (m6A)-associated SNPs on bone mineral density (BMD) and found plenty of m6A-SNPs that were associated with BMD. This study increases our understanding on the regulation patterns of SNP and may provide new clues for further detection of functional mechanism underlying the associations between SNPs and osteoporosis. INTRODUCTION m6A plays critical roles in many fundamental biological processes and a variety of diseases. The m6A-associated SNPs may be potential functional variants for BMD. The aim of this study was to investigate the effect of the genome-wide m6A-SNPs on BMD. METHODS We examined the association of m6A-SNPs with femoral neck (FN) and lumbar spine (LS) BMD in 32,961 individuals and quantitative heel ultrasounds (eBMD) in 142,487 individuals. Furthermore, we performed expression quantitative trait locus (eQTL) analyses for the m6A-SNPs using whole genome data of about 10.5 million SNPs and 21,323 mRNAs from 43 Chinese individuals, as well as public available data. Differential expression analyses were also performed to support the identified genes. RESULTS We found 138, 125, and 993 m6A-SNPs which were associated with FN-BMD, LS-BMD, and eBMD (P < 0.05), respectively. The associations of rs11614913 (P = 8.92 × 10-10) in MIR196A2 and rs1110720 (P = 2.05 × 10-10) in ESPL1 with LS-BMD reached the genome-wide significance level. In addition, a total of 24 m6A-SNPs were significantly associated with eBMD (P < 5.0 × 10-8). Further eQTL analyses showed that 47 of these BMD-associated m6A-SNPs were associated with expressions of the 46 corresponding local genes. Moreover, the expressions of 26 of these genes were associated with BMD. CONCLUSION The present study represents the first effort of investigating the associations and the mechanisms underlying the link between m6A-SNPs and BMD. The results suggested that m6A-SNP may play important roles in the pathology of osteoporosis.
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Affiliation(s)
- X B Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Y H Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China
| | - S F Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China.
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, 199 Renai Road, Suzhou, 215123, Jiangsu, People's Republic of China.
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19
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McDonald MM, Morse A, Schindeler A, Mikulec K, Peacock L, Cheng T, Bobyn J, Lee L, Baldock PA, Croucher PI, Tam PPL, Little DG. Homozygous Dkk1 Knockout Mice Exhibit High Bone Mass Phenotype Due to Increased Bone Formation. Calcif Tissue Int 2018; 102:105-116. [PMID: 29105022 DOI: 10.1007/s00223-017-0338-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/03/2017] [Indexed: 12/17/2022]
Abstract
Wnt antagonist Dkk1 is a negative regulator of bone formation and Dkk1 +/- heterozygous mice display a high bone mass phenotype. Complete loss of Dkk1 function disrupts embryonic head development. Homozygous Dkk1 -/- mice that were heterozygous for Wnt3 loss of function mutation (termed Dkk1 KO) are viable and allowed studying the effects of homozygous inactivation of Dkk1 on bone formation. Dkk1 KO mice showed a high bone mass phenotype exceeding that of heterozygous mice as well as a high incidence of polydactyly and kinky tails. Whole body bone density was increased in the Dkk1 KO mice as shown by longitudinal dual-energy X-ray absorptiometry. MicroCT analysis of the distal femur revealed up to 3-fold increases in trabecular bone volume and up to 2-fold increases in the vertebrae, compared to wild type controls. Cortical bone was increased in both the tibiae and vertebrae, which correlated with increased strength in tibial 4-point bending and vertebral compression tests. Dynamic histomorphometry identified increased bone formation as the mechanism underlying the high bone mass phenotype in Dkk1 KO mice, with no changes in bone resorption. Mice featuring only Wnt3 heterozygosity showed no evident bone phenotype. Our findings highlight a critical role for Dkk1 in the regulation of bone formation and a gene dose-dependent response to loss of DKK1 function. Targeting Dkk1 to enhance bone formation offers therapeutic potential for osteoporosis.
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Affiliation(s)
- Michelle M McDonald
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
- Bone Biology Division, The Garvan Institute for Medical Research, Sydney, Australia
| | - Alyson Morse
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
- Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Aaron Schindeler
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
- Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Kathy Mikulec
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
| | - Lauren Peacock
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
| | - Tegan Cheng
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
- Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Justin Bobyn
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
- Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Lucinda Lee
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia
- Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Paul A Baldock
- Bone Biology Division, The Garvan Institute for Medical Research, Sydney, Australia
| | - Peter I Croucher
- Bone Biology Division, The Garvan Institute for Medical Research, Sydney, Australia
| | - Patrick P L Tam
- Embryology Unit, The Children's Medical Research Institute, Westmead, Australia
- Discipline of Anatomy and Histology, School of Medical Sciences, Sydney Medical School, University of Sydney, Sydney, Australia
| | - David G Little
- Orthopaedic Research & Biotechnology Unit, The Children's Hospital at Westmead, Research Building, Locked Bag 4001, Westmead, NSW, 2145, Australia.
- Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Sydney, Australia.
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20
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Functional relevance for associations between osteoporosis and genetic variants. PLoS One 2017; 12:e0174808. [PMID: 28369098 PMCID: PMC5378394 DOI: 10.1371/journal.pone.0174808] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/15/2017] [Indexed: 11/19/2022] Open
Abstract
Osteoporosis is characterized by increased bone loss and deterioration of bone microarchitecture, which will lead to reduced bone strength and increased risk of fragility fractures. Previous studies have identified many genetic loci associated with osteoporosis, but functional mechanisms underlying the associations have rarely been explored. In order to explore the potential molecular functional mechanisms underlying the associations for osteoporosis, we performed integrative analyses by using the publically available datasets and resources. We searched 128 identified osteoporosis associated SNPs (P<10-6), and 8 SNPs exert cis-regulation effects on 11 eQTL target genes. Among the 8 SNPs, 2 SNPs (RPL31 rs2278729 and LRP5 rs3736228) were confirmed to impact the expression of 3 genes (RPL31, CPT1A and MTL5) that were differentially expressed between human subjects of high BMD group and low BMD group. All of the functional evidence suggested the important functional mechanisms underlying the associations of the 2 SNPs (rs2278729 and rs3736228) and 3 genes (RPL31, CPT1A and MTL5) with osteoporosis. This study may provide novel insights into the functional mechanisms underlying the osteoporosis associated genetic variants, which will help us to comprehend the potential mechanisms underlying the genetic association for osteoporosis.
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Zhu H, Xia W, Mo XB, Lin X, Qiu YH, Yi NJ, Zhang YH, Deng FY, Lei SF. Gene-Based Genome-Wide Association Analysis in European and Asian Populations Identified Novel Genes for Rheumatoid Arthritis. PLoS One 2016; 11:e0167212. [PMID: 27898717 PMCID: PMC5127563 DOI: 10.1371/journal.pone.0167212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/10/2016] [Indexed: 12/27/2022] Open
Abstract
Objective Rheumatoid arthritis (RA) is a complex autoimmune disease. Using a gene-based association research strategy, the present study aims to detect unknown susceptibility to RA and to address the ethnic differences in genetic susceptibility to RA between European and Asian populations. Methods Gene-based association analyses were performed with KGG 2.5 by using publicly available large RA datasets (14,361 RA cases and 43,923 controls of European subjects, 4,873 RA cases and 17,642 controls of Asian Subjects). For the newly identified RA-associated genes, gene set enrichment analyses and protein-protein interactions analyses were carried out with DAVID and STRING version 10.0, respectively. Differential expression verification was conducted using 4 GEO datasets. The expression levels of three selected ‘highly verified’ genes were measured by ELISA among our in-house RA cases and controls. Results A total of 221 RA-associated genes were newly identified by gene-based association study, including 71‘overlapped’, 76 ‘European-specific’ and 74 ‘Asian-specific’ genes. Among them, 105 genes had significant differential expressions between RA patients and health controls at least in one dataset, especially for 20 genes including 11 ‘overlapped’ (ABCF1, FLOT1, HLA-F, IER3, TUBB, ZKSCAN4, BTN3A3, HSP90AB1, CUTA, BRD2, HLA-DMA), 5 ‘European-specific’ (PHTF1, RPS18, BAK1, TNFRSF14, SUOX) and 4 ‘Asian-specific’ (RNASET2, HFE, BTN2A2, MAPK13) genes whose differential expressions were significant at least in three datasets. The protein expressions of two selected genes FLOT1 (P value = 1.70E-02) and HLA-DMA (P value = 4.70E-02) in plasma were significantly different in our in-house samples. Conclusion Our study identified 221 novel RA-associated genes and especially highlighted the importance of 20 candidate genes on RA. The results addressed ethnic genetic background differences for RA susceptibility between European and Asian populations and detected a long list of overlapped or ethnic specific RA genes. The study not only greatly increases our understanding of genetic susceptibility to RA, but also provides important insights into the ethno-genetic homogeneity and heterogeneity of RA in both ethnicities.
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Affiliation(s)
- Hong Zhu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, China
- Department of Child and Adolescent Health, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Wei Xia
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Xing-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Xiang Lin
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, China
| | - Ying-Hua Qiu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, China
| | - Neng-Jun Yi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, China
- * E-mail:
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Boudin E, Fijalkowski I, Hendrickx G, Van Hul W. Genetic control of bone mass. Mol Cell Endocrinol 2016; 432:3-13. [PMID: 26747728 DOI: 10.1016/j.mce.2015.12.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 11/16/2015] [Accepted: 12/28/2015] [Indexed: 01/01/2023]
Abstract
Bone mineral density (BMD) is a quantitative traits used as a surrogate phenotype for the diagnosis of osteoporosis, a common metabolic disorder characterized by increased fracture risk as a result of a decreased bone mass and deterioration of the microarchitecture of the bone. Normal variation in BMD is determined by both environmental and genetic factors. According to heritability studies, 50-85% of the variance in BMD is controlled by genetic factors which are mostly polygenic. In contrast to the complex etiology of osteoporosis, there are disorders with deviating BMD values caused by one mutation with a large impact. These mutations can result in monogenic bone disorders with either an extreme high (sclerosteosis, Van Buchem disease, osteopetrosis, high bone mass phenotype) or low BMD (osteogenesis imperfecta, juvenile osteoporosis, primary osteoporosis). Identification of the disease causing genes, increased the knowledge on the regulation of BMD and highlighted important signaling pathways and novel therapeutic targets such as sclerostin, RANKL and cathepsin K. Genetic variation in genes involved in these pathways are often also involved in the regulation of normal variation in BMD and osteoporosis susceptibility. In the last decades, identification of genetic factors regulating BMD has proven to be a challenge. Several approaches have been tested such as linkage studies and candidate and genome wide association studies. Although, throughout the years, technological developments made it possible to study increasing numbers of genetic variants in populations with increasing sample sizes at the same time, only a small fraction of the genetic impact can yet be explained. In order to elucidate the missing heritability, the focus shifted to studying the role of rare variants, copy number variations and epigenetic influences. This review summarizes the genetic cause of different monogenic bone disorders with deviating BMD and the knowledge on genetic factors explaining normal variation in BMD and osteoporosis risk.
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Affiliation(s)
- Eveline Boudin
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Igor Fijalkowski
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Gretl Hendrickx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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Bae YS, Im SW, Kang MS, Kim JH, Lee SH, Cho BL, Park JH, Nam YS, Son HY, Yang SD, Sung J, Oh KH, Yun JM, Kim JI. Genome-Wide Association Study of Bone Mineral Density in Korean Men. Genomics Inform 2016; 14:62-8. [PMID: 27445649 PMCID: PMC4951402 DOI: 10.5808/gi.2016.14.2.62] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/06/2016] [Accepted: 05/08/2016] [Indexed: 01/19/2023] Open
Abstract
Osteoporosis is a medical condition of global concern, with increasing incidence in both sexes. Bone mineral density (BMD), a highly heritable trait, has been proven a useful diagnostic factor in predicting fracture. Because medical information is lacking about male osteoporotic genetics, we conducted a genome-wide association study of BMD in Korean men. With 1,176 participants, we analyzed 4,414,664 single nucleotide polymorphisms (SNPs) after genomic imputation, and identified five SNPs and three loci correlated with bone density and strength. Multivariate linear regression models were applied to adjust for age and body mass index interference. Rs17124500 (p = 6.42 × 10-7), rs34594869 (p = 6.53 × 10-7) and rs17124504 (p = 6.53 × 10-7) in 14q31.3 and rs140155614 (p = 8.64 × 10-7) in 15q25.1 were significantly associated with lumbar spine BMD (LS-BMD), while rs111822233 (p = 6.35 × 10-7) was linked with the femur total BMD (FT-BMD). Additionally, we analyzed the relationship between BMD and five genes previously identified in Korean men. Rs61382873 (p = 0.0009) in LRP5, rs9567003 (p = 0.0033) in TNFSF11 and rs9935828 (p = 0.0248) in FOXL1 were observed for LS-BMD. Furthermore, rs33997547 (p = 0.0057) in ZBTB and rs1664496 (p = 0.0012) in MEF2C were found to influence FT-BMD and rs61769193 (p = 0.0114) in ZBTB to influence femur neck BMD. We identified five SNPs and three genomic regions, associated with BMD. The significance of our results lies in the discovery of new loci, while also affirming a previously significant locus, as potential osteoporotic factors in the Korean male population.
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Affiliation(s)
- Ye Seul Bae
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sun-Wha Im
- Neuro-Immune Information Storage Network Research Center, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Mi So Kang
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jin Hee Kim
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Soon Hang Lee
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Be Long Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jin Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - You-Seon Nam
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Ho-Young Son
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - San Deok Yang
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Joohon Sung
- Department of Epidemiology, Seoul National University School of Public Health/Institute of Health and Environment, Seoul National University, Seoul 08826, Korea
| | - Kwang Ho Oh
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jong Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
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Crespi BJ, Go MC. Diametrical diseases reflect evolutionary-genetic tradeoffs: Evidence from psychiatry, neurology, rheumatology, oncology and immunology. Evol Med Public Health 2015; 2015:216-53. [PMID: 26354001 PMCID: PMC4600345 DOI: 10.1093/emph/eov021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022] Open
Abstract
Tradeoffs centrally mediate the expression of human adaptations. We propose that tradeoffs also influence the prevalence and forms of human maladaptation manifest in disease. By this logic, increased risk for one set of diseases commonly engenders decreased risk for another, diametric, set of diseases. We describe evidence for such diametric sets of diseases from epidemiological, genetic and molecular studies in four clinical domains: (i) psychiatry (autism vs psychotic-affective conditions), (ii) rheumatology (osteoarthritis vs osteoporosis), (iii) oncology and neurology (cancer vs neurodegenerative disorders) and (iv) immunology (autoimmunity vs infectious disease). Diametric disorders are important to recognize because genotypes or environmental factors that increase risk for one set of disorders protect from opposite disorders, thereby providing novel and direct insights into disease causes, prevention and therapy. Ascertaining the mechanisms that underlie disease-related tradeoffs should also indicate means of circumventing or alleviating them, and thus reducing the incidence and impacts of human disease in a more general way.
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Affiliation(s)
| | - Matthew C Go
- Department of Biological Sciences; Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6 Present address: Department of Anthropology, University of Illinois at Urbana-Champaign, 109 Davenport Hall, 607 S Mathews Avenue, Urbana, IL 61801, USA
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