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Baniasadi M, Talebi S, Mokhtari K, Zabolian AH, Khosroshahi EM, Entezari M, Dehkhoda F, Nabavi N, Hashemi M. Role of non-coding RNAs in osteoporosis. Pathol Res Pract 2024; 253:155036. [PMID: 38134836 DOI: 10.1016/j.prp.2023.155036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Osteoporosis, a prevalent bone disorder influenced by genetic and environmental elements, significantly increases the likelihood of fractures and bone weakness, greatly affecting the lives of those afflicted. Yet, the exact epigenetic processes behind the onset of osteoporosis are still unclear. Growing research indicates that epigenetic changes could act as vital mediators that connect genetic tendencies and environmental influences, thereby increasing the risk of osteoporosis and bone fractures. Within these epigenetic factors, certain types of RNA, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have been recognized as key regulatory elements. These RNA types wield significant influence on gene expression through epigenetic regulation, directing various biological functions essential to bone metabolism. This extensive review compiles current research uncovering the complex ways in which miRNAs, lncRNAs, and circRNAs are involved in the development of osteoporosis, especially in osteoblasts and osteoclasts. Gaining a more profound understanding of the roles these three RNA classes play in osteoporosis could reveal new diagnostic methods and treatment approaches for this incapacitating condition. In conclusion, this review delves into the complex domain of epigenetic regulation via non-coding RNA in osteoporosis. It sheds light on the complex interactions and mechanisms involving miRNAs, lncRNAs, and circRNAs within osteoblasts and osteoclasts, offering an in-depth understanding of the less explored aspects of osteoporosis pathogenesis. These insights not only reveal the complexity of the disease but also offer significant potential for developing new diagnostic methods and targeted treatments. Therefore, this review marks a crucial step in deciphering the elusive complexities of osteoporosis, leading towards improved patient care and enhanced quality of life.
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Affiliation(s)
- Mojtaba Baniasadi
- Department of Orthopedics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sina Talebi
- Department of Orthopedics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Khatere Mokhtari
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran; Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan,Iran
| | - Amir Hossein Zabolian
- Department of Orthopedics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elahe Mohandesi Khosroshahi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Farshid Dehkhoda
- Department of Orthopedics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Noushin Nabavi
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Bai XH, Su J, Mu YY, Zhang XQ, Li HZ, He XF, He XF. Association between the ESR1 and ESR2 polymorphisms and osteoporosis risk: An updated meta-analysis. Medicine (Baltimore) 2023; 102:e35461. [PMID: 37832086 PMCID: PMC10578747 DOI: 10.1097/md.0000000000035461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Gene polymorphisms of estrogen receptor (ESR) 1 PvuII (rs2234693), XbaI (rs9340799), G2014A (rs2228480), ESR2 AluI (rs4986938), and RsaI (rs1256049) had been reported to be associated with the risk of osteoporosis. However, these conclusions were inconsistent, therefore, an updated meta-analysis was conducted to further explore these issues. OBJECTIVE To evaluate the association between gene polymorphisms of ESR1 PvuII (rs2234693), XbaI (rs9340799), G2014A (rs2228480), ESR2 AluI (rs4986938), RsaI (rs1256049), and osteoporosis risk. MATERIALS AND METHODS PubMed, Medline, Ovid, Embase, CNKI, and China Wanfang databases were searched. Association was assessed using odds ratio with 95% confidence interval. Moreover, the false-positive reporting probability, Bayesian false-finding probability, and Venetian criteria were used to assess the credibility of statistically significant associations. RESULTS Overall, ESR1 PvuII (rs2234693) and XbaI (rs9340799) were associated with the risk of osteoporosis in Indians. Moreover, ESR1 G2014A (rs2228480) was associated with the decreased risk of osteoporosis in East Asians. Moreover, ESR2 Alul (rs4986938) was associated with the increased risk of osteoporosis in East Asians and Caucasians. There was a significant association between ESR2 Rsal (rs1256049) and osteoporosis risk in overall population. When only high-quality and Hardy-Weinberg equilibrium studies were included in the sensitivity analysis, all results did not change in the present study. When the credibility was evaluated applying false-positive reporting probability, Bayesian false-finding probability, and Venetian criteria, all significant associations were considered as false positive results. CONCLUSIONS In summary, this study shows that all substantial associations between gene polymorphisms of ESR1 (PvuII, XbaI, and G2014A) and ESR 2 (AluI and RsaI) and osteoporosis risk are possibly false positive results instead of real associations or biological variables.
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Affiliation(s)
- Xiao-Hui Bai
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Jiao Su
- Department of Biochemistry, Changzhi Medical College, Changzhi, China
| | - Yi-Yang Mu
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Xi-Qin Zhang
- Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Hong-Zhuo Li
- Department of Orthopaedics, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Xiao-Feng He
- Institute of Evidence-Based Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Xiao-Feng He
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
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Li Y, Liu Q, Ma Q, Ma Z, Chen J, Yu A, Ma C, Qiu L, Shi H, Liang H, Hu M. Identification of key variants correlated with susceptibility of primary osteoporosis in the Chinese Han group. Ann Hum Genet 2023; 87:63-74. [PMID: 36479902 DOI: 10.1111/ahg.12490] [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: 04/19/2022] [Revised: 11/12/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Primary osteoporosis is a systemic skeletal disease characterized by reduced bone mass and vulnerability to fractures. The genetics of osteoporosis in the Chinese population remain unclear, which hinders the prevention and treatment of osteoporosis in China. This study aimed to explore the susceptibility genes and the roles played by their variants in osteoporosis. METHODS Blood samples were collected from 45 osteoporosis patients and 30 healthy individuals, and genome-wide association study was performed on array data. The expression levels of the candidate gene in different genotypes were further determined by using quantitative real-time PCR. Moreover, the differentiation capacity of bone marrow mesenchymal stem cells under different genotypes from osteoporosis patients was investigated. RESULTS The most significant variant rs1891632 located in the upstream (918 bp) region of CRB2, which could down-regulate the expression levels of CRB2 in genotype-tissue expression database and played an essential role in the regulation of osteoblastic and osteoclastic differentiation during skeletal development. Another significant variant rs1061657 located within the 3'UTR region of TBX3 gene. We found that the mRNA levels of TBX3 decreased in the bMSCs of old osteoporosis patients. Interestingly, osteoblast differentiation capacity and TBX3 mRNA levels were similar between the young healthy individuals carrying derived and ancestral allele of rs1061657, whereas the differentiation capacity and TBX3 mRNA levels dramatically declined in elderly patients with osteoporosis. CONCLUSIONS The variant rs1061657 might affect the osteogenesis of bMSCs in an age-dependent manner and that TBX3 may be a key susceptibility gene for primary osteoporosis. In conclusion, CRB2 and TBX3 may influence the development of osteoporosis; additionally, rs1891632 and rs1061657, as the key variants first reported to be associated with primary osteoporosis, may potentially contribute to predicting the risk of osteoporosis (especially for older individuals) and may serve as therapeutic targets.
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Affiliation(s)
- Yanjiao Li
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Qi Liu
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Qiuye Ma
- Orthopedics, Chongqing Jiulongpo District Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Zhaoxia Ma
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Juan Chen
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - An Yu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Changguo Ma
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Lihua Qiu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Hongsuo Liang
- Joint Surgery Department of the Second People's Hospital of Nanning City, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Min Hu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, China
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Aoki H, Suzuki E, Nakamura T, Onodera S, Saito A, Ohtaka M, Nakanishi M, Nishimura K, Saito A, Azuma T. Induced pluripotent stem cells from homozygous Runx2-deficient mice show poor response to vitamin D during osteoblastic differentiation. Med Mol Morphol 2022; 55:174-186. [DOI: 10.1007/s00795-022-00317-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022]
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Estrogen receptor alpha and NFATc1 bind to a bone mineral density-associated SNP to repress WNT5B in osteoblasts. Am J Hum Genet 2022; 109:97-115. [PMID: 34906330 DOI: 10.1016/j.ajhg.2021.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/17/2021] [Indexed: 12/27/2022] Open
Abstract
Genetic factors and estrogen deficiency contribute to the development of osteoporosis. The single-nucleotide polymorphism (SNP) rs2887571 is predicted from genome-wide association studies (GWASs) to associate with osteoporosis but has had an unknown mechanism. Analysis of osteoblasts from 110 different individuals who underwent joint replacement revealed that the genotype of rs2887571 correlates with WNT5B expression. Analysis of our ChIP-sequencing data revealed that SNP rs2887571 overlaps with an estrogen receptor alpha (ERα) binding site. Here we show that 17β-estradiol (E2) suppresses WNT5B expression and further demonstrate the mechanism of ERα binding at the enhancer containing rs2887571 to suppress WNT5B expression differentially in each genotype. ERα interacts with NFATc1, which is predicted to bind directly at rs2887571. CRISPR-Cas9 and ChIP-qPCR experiments confirm differential regulation of WNT5B between each allele. Homozygous GG has a higher binding affinity for ERα than homozygous AA and results in greater suppression of WNT5B expression. Functionally, WNT5B represses alkaline phosphatase expression and activity, decreasing osteoblast differentiation and mineralization. Furthermore, WNT5B increases interleukin-6 expression and suppresses E2-induced expression of alkaline phosphatase during osteoblast differentiation. We show that WNT5B suppresses the differentiation of osteoblasts via receptor tyrosine kinase-like orphan receptor 1/2 (ROR1/2), which activates DVL2/3/RAC1/CDC42/JNK/SIN3A signaling and inhibits β-catenin activity. Together, our data provide mechanistic insight into how ERα and NFATc1 regulate the non-coding SNP rs2887571, as well as the function of WNT5B on osteoblasts, which could provide alternative therapeutic targets for osteoporosis.
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Wang Y, Lu L, Niu Y, Zhang Q, Cheng C, Huang H, Huang X, Huang Q. The osteoporosis risk variant rs9820407 at 3p22.1 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation. Bone 2021; 153:116165. [PMID: 34461284 DOI: 10.1016/j.bone.2021.116165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 11/26/2022]
Abstract
Previous powerful genome-wide association studies (GWASs) and whole-genome sequencing have identified multiple single-nucleotide polymorphisms (SNPs) located over 69 kb upstream of CTNNB1 at 3p22.1 locus associated with osteoporosis. The CTNNB1 gene encodes β-catenin that is an integral part of adherens junctions and the primary mediator of the canonical Wnt signaling pathway. The causal variants and underlying molecular mechanisms of the osteoporosis susceptibility locus 3p22.1 remains unknown. Through comprehensive computational analyses, including expression quantitative trait locus (eQTL), high-throughput chromatin interaction (Hi-C), epigenomic and functional annotation, four enhancer SNPs (rs9820407, rs9878224, rs454690 and rs9832204) were prioritized as potential causal SNPs at 3p22.1 for osteoporosis. Rs9820407 displayed the strongest enhancer activity in dual-luciferase assays. Specifically, the minor rs9820407-A can preferentially bind transcription factor FOXC1, elevate the enhancer activity and increase CTNNB1 expression. The architectural protein CTCF was presumably involved in long-range chromatin interaction between rs9820407 and CTNNB1. Our study provided a mechanistic insight into how noncoding enhancer SNP rs9820407 distally regulates CTNNB1 expression and modulates osteoporosis risk.
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Affiliation(s)
- Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Li Lu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yajing Niu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qiongdan Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Chen Cheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Han Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xinyao Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China.
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7
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Rauner M, Foessl I, Formosa MM, Kague E, Prijatelj V, Lopez NA, Banerjee B, Bergen D, Busse B, Calado Â, Douni E, Gabet Y, Giralt NG, Grinberg D, Lovsin NM, Solan XN, Ostanek B, Pavlos NJ, Rivadeneira F, Soldatovic I, van de Peppel J, van der Eerden B, van Hul W, Balcells S, Marc J, Reppe S, Søe K, Karasik D. Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. Front Endocrinol (Lausanne) 2021; 12:731217. [PMID: 34938269 PMCID: PMC8686830 DOI: 10.3389/fendo.2021.731217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare diseases in the skeletal field. Yet, interpreting results from human association studies remains a challenge. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary. Multiple unknowns exist for putative causal genes, including cellular localization of the molecular function. Intermediate traits ("endophenotypes"), e.g. molecular quantitative trait loci (molQTLs), are needed to identify mechanisms of underlying associations. Furthermore, index variants often reside in non-coding regions of the genome, therefore challenging for interpretation. Knowledge of non-coding variance (e.g. ncRNAs), repetitive sequences, and regulatory interactions between enhancers and their target genes is central for understanding causal genes in skeletal conditions. Animal models with deep skeletal phenotyping and cell culture models have already facilitated fine mapping of some association signals, elucidated gene mechanisms, and revealed disease-relevant biology. However, to accelerate research towards bridging the current gap between association and causality in skeletal diseases, alternative in vivo platforms need to be used and developed in parallel with the current -omics and traditional in vivo resources. Therefore, we argue that as a field we need to establish resource-sharing standards to collectively address complex research questions. These standards will promote data integration from various -omics technologies and functional dissection of human complex traits. In this mission statement, we review the current available resources and as a group propose a consensus to facilitate resource sharing using existing and future resources. Such coordination efforts will maximize the acquisition of knowledge from different approaches and thus reduce redundancy and duplication of resources. These measures will help to understand the pathogenesis of osteoporosis and other skeletal diseases towards defining new and more efficient therapeutic targets.
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Affiliation(s)
- Martina Rauner
- Department of Medicine III, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ines Foessl
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Endocrine Lab Platform, Medical University of Graz, Graz, Austria
| | - Melissa M. Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Erika Kague
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nerea Alonso Lopez
- Rheumatology and Bone Disease Unit, CGEM, Institute of Genetics and Cancer (IGC), Edinburgh, United Kingdom
| | - Bodhisattwa Banerjee
- Musculoskeletal Genetics Laboratory, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Dylan Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ângelo Calado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Eleni Douni
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Institute for Bioinnovation, B.S.R.C. “Alexander Fleming”, Vari, Greece
| | - Yankel Gabet
- Department of Anatomy & Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Natalia García Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Nika M. Lovsin
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Xavier Nogues Solan
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Barbara Ostanek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Nathan J. Pavlos
- Bone Biology & Disease Laboratory, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | | | - Ivan Soldatovic
- Institute of Medical Statistics and Informatic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wim van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Sjur Reppe
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Kent Søe
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
- Marcus Research Institute, Hebrew SeniorLife, Boston, MA, United States
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Ansari MGA, Mohammed AK, Wani KA, Hussain SD, Alnaami AM, Abdi S, Aljohani NJ, Al-Daghri NM. Vitamin D Receptor Gene Variants Susceptible to Osteoporosis in Arab Post-Menopausal Women. Curr Issues Mol Biol 2021; 43:1325-1334. [PMID: 34698098 PMCID: PMC8929051 DOI: 10.3390/cimb43030094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/26/2021] [Accepted: 09/26/2021] [Indexed: 12/03/2022] Open
Abstract
Post-menopausal osteoporosis (PMO) is a multifactorial bone disorder in elderly women. Various vitamin D receptor (VDR) gene variants have been studied and associated with osteoporosis in other populations, but not in a homogenous Arab ethnic group. Herein, the current study explores the association between VDR polymorphisms and susceptibility to osteoporosis in Saudi postmenopausal women. In total, 600 Saudi postmenopausal women (N = 300 osteoporosis; N = 300 control) were genotyped for VDR gene variants (rs7975232, rs1544410, rs731236) using TaqMan® SNP genotyping assays. Bone mineral density (BMD) for the lumbar spine and femur was assessed using dual-energy X-ray absorptiometry (DEXA). The heterozygous frequency distributions AC of rs7975232, CT of rs1544410, and AG of rs731236 were significantly higher in the osteoporosis group than controls (p < 0.05). Heterozygous AC of rs7975232 (1.6; 95% CI 1.1–2.3; p < 0.023), CT of rs1544410 (1.6; 95% CI 1.1–2.4; p < 0.022), and AG of rs731236 (1.6; 95% CI 1.1–2.4; p < 0.024) were significantly associated with increased risk of osteoporosis, independent of age and BMI. In conclusion, VDR gene variants rs7975232, rs1544410, rs731236 had a significant effect on BMD and were associated with osteoporosis risk in Saudi postmenopausal women.
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Affiliation(s)
- Mohammed. G. A. Ansari
- Chair for Biomarkers of Chronic Diseases, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.G.A.A.); (A.K.M.); (K.A.W.); (S.D.H.); (A.M.A.); (N.J.A.)
| | - Abdul Khader Mohammed
- Chair for Biomarkers of Chronic Diseases, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.G.A.A.); (A.K.M.); (K.A.W.); (S.D.H.); (A.M.A.); (N.J.A.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Kaiser A. Wani
- Chair for Biomarkers of Chronic Diseases, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.G.A.A.); (A.K.M.); (K.A.W.); (S.D.H.); (A.M.A.); (N.J.A.)
| | - Syed D. Hussain
- Chair for Biomarkers of Chronic Diseases, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.G.A.A.); (A.K.M.); (K.A.W.); (S.D.H.); (A.M.A.); (N.J.A.)
| | - Abdullah M. Alnaami
- Chair for Biomarkers of Chronic Diseases, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.G.A.A.); (A.K.M.); (K.A.W.); (S.D.H.); (A.M.A.); (N.J.A.)
| | - Saba Abdi
- Biochemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Naji J. Aljohani
- Chair for Biomarkers of Chronic Diseases, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.G.A.A.); (A.K.M.); (K.A.W.); (S.D.H.); (A.M.A.); (N.J.A.)
- Obesity, Endocrine, and Metabolic Center, King Fahad Medical City, Riyadh 59046, Saudi Arabia
| | - Nasser M. Al-Daghri
- Chair for Biomarkers of Chronic Diseases, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.G.A.A.); (A.K.M.); (K.A.W.); (S.D.H.); (A.M.A.); (N.J.A.)
- Correspondence: ; Tel.: +966-1-4675939
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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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10
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Tsai DJ, Fang WH, Wu LW, Tai MC, Kao CC, Huang SM, Chen WT, Hsiao PJ, Chiu CC, Su W, Wu CC, Su SL. The Polymorphism at PLCB4 Promoter (rs6086746) Changes the Binding Affinity of RUNX2 and Affects Osteoporosis Susceptibility: An Analysis of Bioinformatics-Based Case-Control Study and Functional Validation. Front Endocrinol (Lausanne) 2021; 12:730686. [PMID: 34899595 PMCID: PMC8657146 DOI: 10.3389/fendo.2021.730686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Genome-wide association studies have identified numerous genetic variants that are associated with osteoporosis risk; however, most of them are present in the non-coding regions of the genome and the functional mechanisms are unknown. In this study, we aimed to investigate the potential variation in runt domain transcription factor 2 (RUNX2), which is an osteoblast-specific transcription factor that normally stimulates bone formation and osteoblast differentiation, regarding variants within RUNX2 binding sites and risk of osteoporosis in postmenopausal osteoporosis (PMOP). METHODS We performed bioinformatics-based prediction by combining whole genome sequencing and chromatin immunoprecipitation sequencing to screen functional SNPs in the RUNX2 binding site using data from the database of Taiwan Biobank; Case-control studies with 651 postmenopausal women comprising 107 osteoporosis patients, 290 osteopenia patients, and 254 controls at Tri-Service General Hospital between 2015 and 2019 were included. The subjects were examined for bone mass density and classified into normal and those with osteopenia or osteoporosis by T-scoring with dual-energy X-ray absorptiometry. Furthermore, mRNA expression and luciferase reporter assay were used to provide additional evidence regarding the associations identified in the association analyses. Chi-square tests and logistic regression were mainly used for statistical assessment. RESULTS Through candidate gene approaches, 3 SNPs in the RUNX2 binding site were selected. A novel SNP rs6086746 in the PLCB4 promoter was identified to be associated with osteoporosis in Chinese populations. Patients with AA allele had higher risk of osteoporosis than those with GG+AG (adjusted OR = 6.89; 95% confidence intervals: 2.23-21.31, p = 0.001). Moreover, the AA genotype exhibited lower bone mass density (p < 0.05). Regarding mRNA expression, there were large differences in the correlation between PLCB4 and different RUNX2 alleles (Cohen's q = 0.91). Functionally, the rs6086746 A allele reduces the RUNX2 binding affinity, thus enhancing the suppression of PLCB4 expression (p < 0.05). CONCLUSIONS Our results provide further evidence to support the important role of the SNP rs6086746 in the etiology of osteopenia/osteoporosis, thereby enhancing the current understanding of the susceptibility to osteoporosis. We further studied the mechanism underlying osteoporosis regulation by PLCB4.
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Affiliation(s)
- Dung-Jang Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Hui Fang
- Department of Family and Community Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Li-Wei Wu
- Department of Family and Community Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Cheng Tai
- Department of Ophthalmology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chung-Cheng Kao
- Superintendent’s Office, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Ming Huang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Wei-Teing Chen
- Division of Thoracic Medicine, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan
- Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, ROC, Taiwan
| | - Po-Jen Hsiao
- Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Chien Chiu
- Division of Infectious Diseases, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, National Defense Medical Center, Taoyuan, Taiwan
| | - Wen Su
- Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Chun Wu
- Department of Orthopedics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sui-Lung Su
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
- *Correspondence: Sui-Lung Su,
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11
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Fittipaldi S, Visconti VV, Tarantino U, Novelli G, Botta A. Genetic variability in noncoding RNAs: involvement of miRNAs and long noncoding RNAs in osteoporosis pathogenesis. Epigenomics 2020; 12:2035-2049. [PMID: 33264054 DOI: 10.2217/epi-2020-0233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The pathogenesis of osteoporosis is multifactorial and is the consequence of genetic, hormonal and lifestyle factors. Epigenetics, including noncoding RNA (ncRNA) deregulation, represents a link between susceptibility to develop the disease and environmental influences. The majority of studies investigated the expression of ncRNAs in osteoporosis patients; however, very little information is available on their genetic variability. In this review, we focus on two classes of ncRNAs: miRNAs and long noncoding RNAs (lncRNAs). We summarize recent findings on how polymorphisms in miRNAs and lncRNAs can perturb the lncRNA/miRNA/mRNA axis and may be involved in osteoporosis clinical outcome. We also provide a general overview on databases and bioinformatic tools useful for associating miRNAs and lncRNAs variability with complex genetic diseases.
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Affiliation(s)
- Simona Fittipaldi
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy
| | - Virginia Veronica Visconti
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy.,Department of Orthopedics & Traumatology, PTV Foundation, 00133 Rome, Italy
| | - Umberto Tarantino
- Department of Orthopedics & Traumatology, PTV Foundation, 00133 Rome, Italy.,Department of Clinical Sciences & Translational Medicine, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy.,IRCCS Neuromed, Pozzilli, IS, Italy
| | - Annalisa Botta
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy
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12
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Ye W, Wang Y, Hou S, Mei B, Liu X, Huang H, Zhou Q, Niu Y, Chen Y, Zhang M, Huang Q. USF3 modulates osteoporosis risk by targeting WNT16, RANKL, RUNX2, and two GWAS lead SNPs rs2908007 and rs4531631. Hum Mutat 2020; 42:37-49. [PMID: 33058301 DOI: 10.1002/humu.24126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/09/2020] [Accepted: 10/05/2020] [Indexed: 01/15/2023]
Abstract
Osteoporotic fractures cause major morbidity and mortality in the aging population. Genome-wide association studies (GWAS) have identified USF3 as the novel susceptibility gene of osteoporosis. However, the functional role in bone metabolism and the target gene of the basic helix-loop-helix transcription factor USF3 are unclear. Here, we show that USF3 enhances osteoblast differentiation and suppresses osteoclastogenesis in cultured human osteoblast-like U-2OS cells. Mechanistic studies revealed that transcription factor USF3 antagonistically interacts with anti-osteogenic TWIST1/TCF12 heterodimer in the WNT16 and RUNX2 promoter, and counteracts CREB1 and JUN/FOS in the RANKL promoter. Importantly, the osteoporosis GWAS variant g.1744A>G (rs2908007A>G) located in the WNT16 promoter confers G-allele-specific transcriptional modulation by USF3, TWIST1/TCF12 and TBX5/TBX15, and USF3 transactivates the osteoclastogenesis suppressor WNT16 promoter activity and antagonizes the repression of WNT16 by TWIST1 and TCF12. The risk G allele of osteoporosis GWAS variant g.3260A>G (rs4531631A>G) in the RANKL promoter facilitates the binding of CREB1 and JUN/FOS and enhances transactivation of the osteoclastogenesis contributor RANKL that is inhibited by USF3. Our findings uncovered the functional mechanisms of osteoporosis novel GWAS-associated gene USF3 and lead single nucleotide polymorphisms rs2908007 and rs4531631 in the regulation of bone formation and resorption.
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Affiliation(s)
- Weiyuan Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Sasa Hou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Bing Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xinhong Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Han Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qian Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yajing Niu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yuanyuan Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Manling Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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13
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Bisht I, Ambasta RK, Kumar P. An integrated approach to unravel a putative crosstalk network in Alzheimer's disease and Parkinson's disease. Neuropeptides 2020; 83:102078. [PMID: 32807513 DOI: 10.1016/j.npep.2020.102078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 12/31/2022]
Abstract
Integration of multiple profiling data and construction of functional regulatory networks provide a powerful approach to uncover functional relationships and significant molecular entities from transcriptomic data, highlighting the molecular mechanisms of complex diseases. Despite having an overlap in the neuropathologies of AD and PD, the molecular entities overlapped and mechanisms behind them are less known. Here we used an integrated strategy to analyze miRNA and gene transcriptomic data to understand the role of miRNAs and genes in regulatory activities taking place in cells, and find transcriptomic signatures linking AD and PD. We preprocessed and analyzed publicly available microarray datasets and identified 97 DEGs and 21 DEmiRs that may be involved in the overlapped mechanisms between these two disorders. Among the DEGs, we found HSPA9, PGK1, SDHC, FH, DLD, YWHAZ and ACLY as the major protein-coding genes involved in the crosstalk for AD-PD pathogenesis. Further we integrated these DEGs and DEmiRs with regulatory TFs to construct an overlapped dysregulated network of AD and PD. In the network, miR-27a-3p, miR-148a-3p and miR-15a-5p were found to be the most relevant with maximum interactions, describing their significance in the potential crosstalk. We also looked into the dysregulated biological processes and pathways overlapped in AD and PD. In conclusion, we highlighted the DEGs, DEmiRs, their interactions and related pathways overlapped in AD and PD pathogenesis, also describing a potential crosstalk at molecular level. Besides, our findings can further be used for molecular studies to reveal an assured AD-PD crosstalk.
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Affiliation(s)
- Indu Bisht
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, 110042, India.
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14
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Liu H, Zhao H, Lin H, Li Z, Xue H, Zhang Y, Lu J. Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis. Calcif Tissue Int 2020; 106:248-255. [PMID: 31732751 DOI: 10.1007/s00223-019-00629-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022]
Abstract
As one of the most common types of osteoporosis, postmenopausal osteoporosis (PMOP) is caused by both genetic and environmental factors. Previous studies have indicated that SOX9 activity is tightly regulated to ensure normal bone mineral density (BMD) in the adult skeleton, and the COL9A1 promoter region can be transactivated by SOX9. In this study, we aimed to investigate the potential association between PMOP and the COL9A1 and SOX9 genes. A total of 10,443 postmenopausal women, including 2288 patients and 3557 controls in the discovery stage and 1566 patients and 3032 controls in the validation stage, were recruited. Forty-three tag SNPs (36 in COL9A1 and 7 in SOX9) were selected for genotyping to evaluate the association of the SOX9 gene with PMOP and BMD. Association and bioinformatics analyses were performed for PMOP. BMD and serum level of SOX9 were also utilized as quantitative phenotypes in further analyses. SNP rs73354570 of SOX9 was significantly associated with PMOP in both discovery stages (OR 1.24 [1.10-1.39], P = 3.56 × 10-4, χ2 = 12.75) and combined samples (OR 1.25 [1.15-1.37], P = 5.25 × 10-7, χ2 = 25.17). Further analyses showed that the SNP was also significantly associated with BMD and serum levels of the SOX9 protein. Our results provide further supportive evidence for the association of the SOX9 gene with PMOP and of the SOX9 gene with the variation of BMD in postmenopausal Han Chinese women. This study supports a role for SOX9 in the etiology of PMOP, adding to the current understanding of the susceptibility of osteoporosis.
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Affiliation(s)
- Hongliang Liu
- Department of Orthopedic, The First Affiliated Hospital of Xi'an Jiaotong University, No.277, Yanta West Road, Xi'an, 710061, Shaanxi, China
- Department of Trauma Orthopedics, Honghui Hospital, Xi'an Jiaotong University Health Science Center, No.555, Youyi East Road, Xi'an, 710054, Shaanxi, China
| | - Hongmou Zhao
- Department of Foot and Ankle Surgery, Honghui Hospital, Xi'an Jiaotong University Health Science Center, No.555, Youyi East Road, Xi'an, 710054, Shaanxi, China
| | - Hua Lin
- Department of Trauma Orthopedics, Honghui Hospital, Xi'an Jiaotong University Health Science Center, No.555, Youyi East Road, Xi'an, 710054, Shaanxi, China
| | - Zhong Li
- Department of Trauma Orthopedics, Honghui Hospital, Xi'an Jiaotong University Health Science Center, No.555, Youyi East Road, Xi'an, 710054, Shaanxi, China
| | - Hanzhong Xue
- Department of Trauma Orthopedics, Honghui Hospital, Xi'an Jiaotong University Health Science Center, No.555, Youyi East Road, Xi'an, 710054, Shaanxi, China
| | - Yunzhi Zhang
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No.157, Xiwu Road, Xi'an, 710004, Shaanxi, China
| | - Jun Lu
- Department of Internal Medicine, Honghui Hospital, Xi'an Jiaotong University Health Science Center, No.555, Youyi East Road, Xi'an, 710054, Shaanxi, China.
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15
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Gan D, Xu X, Chen D, Feng P, Xu Z. Network Pharmacology-Based Pharmacological Mechanism of the Chinese Medicine Rhizoma drynariae Against Osteoporosis. Med Sci Monit 2019; 25:5700-5716. [PMID: 31368456 PMCID: PMC6688518 DOI: 10.12659/msm.915170] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rhizoma drynariae is the main traditional Chinese medicine used for the treatment of osteoporosis, but its anti-osteoporotic targeting mechanism has not been fully elucidated due to the complexity of its active ingredients. In this study, the pharmacological mechanism of action of Rhizoma drynariae against osteoporosis was studied by integrating pharmacological concepts. The pharmacokinetic characteristics of selected major active constituents of Rhizoma drynariae and the SMILES structural similarity were used to predict related targets. A literature search was conducted to identify known osteoporosis treatment targets, which were then combined with the predicted targets to construct the direct or indirect target interaction network map of Rhizoma drynariae against osteoporosis. Finally, data on the key targets of the interactions, ranked according to relevant node parameters obtained through pathway enrichment analysis and screening of key targets and active ingredients of Rhizoma drynariae, were used to perform molecular docking simulation. We screened 16 active ingredients of Rhizoma drynariae, and 7 key targets with direct or indirect effects with a high frequency were obtained. These main pathways were found to play important roles in the PI3k-akt signaling pathway, osteoclast differentiation, Wnt signaling pathway, and estrogen signaling pathway. Molecular docking showed that most active ingredients of Rhizoma drynariae had strong binding efficiency with key targets. Based on network pharmacology, we conclude that Rhizoma drynariae plays an anti-osteoporotic role by directly or indirectly targeting multiple major signaling pathways and influencing the proliferation and differentiation of multiple types of cells.
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Affiliation(s)
- Donghao Gan
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
| | - Xiaowei Xu
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
| | - Deqiang Chen
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland).,Department of Orthopedics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
| | - Peng Feng
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
| | - Zhanwang Xu
- First College of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland).,Department of Orthopaedics, Affilited Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
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16
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Al Anouti F, Taha Z, Shamim S, Khalaf K, Al Kaabi L, Alsafar H. An insight into the paradigms of osteoporosis: From genetics to biomechanics. Bone Rep 2019; 11:100216. [PMID: 31372373 PMCID: PMC6661363 DOI: 10.1016/j.bonr.2019.100216] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/03/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Considered as one of the major epidemics of the 21st century, osteoporosis affects approximately 200 million people globally, with significant worldwide impact on rates of morbidity and mortality and massive socioeconomic burdens. Mainly characterized by decreased bone mineral density (BMD) and increased risk of bone fragility/deterioration, this devastating silent epidemic typically has no symptoms until a fracture occurs. The multifactorial disease, osteoporosis is instigated by complex interactions between genetic, metabolic and environmental factors, with severe impact on the biomechanics of the musculoskeletal system. This article provides a review of the epidemiology, genetic and biomechanical aspects of primary osteoporosis. The review begins with a summary of the epidemiology and global prevalence of osteoporosis. Sections 1 and 2 discuss the genetic associations and molecular signaling pathways involved in normal and pathological osteogenesis while Section 3 explores the biomechanics of osteoporosis and its quantitative damaging effects on critical bone mechanical properties, and associated bone remodeling. Overall, this review summarizes the recent findings about osteoporosis and emphasizes the importance of an integrative holistic approach in investigating osteoporosis towards providing better informed, more effective preventive and treatment modalities. Importantly, this work also explores the limited available literature on the various aspects of osteoporosis in the United Arab Emirates (UAE), Gulf Cooperation Council (GCC), and Middle East despite its alarming prevalence in the region, and highlights the need for further research and studies taking into consideration the importance of the vitamin D receptor (VDR) gene influencing the development of osteoporosis.
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Affiliation(s)
- Fatme Al Anouti
- Zayed University, College of Natural and Health Sciences, Abu Dhabi, United Arab Emirates
| | - Zainab Taha
- Zayed University, College of Natural and Health Sciences, Abu Dhabi, United Arab Emirates
| | - Sadia Shamim
- Khalifa University Center for Biotechnology, Abu Dhabi, United Arab emirates
| | - Kinda Khalaf
- Khalifa University of Science & Technology, Biomedical Department, Abu Dhabi, United Arab Emirates
| | - Leena Al Kaabi
- Khalifa University of Science & Technology, Biomedical Department, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Khalifa University Center for Biotechnology, Abu Dhabi, United Arab emirates.,Khalifa University of Science & Technology, Biomedical Department, Abu Dhabi, United Arab Emirates
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17
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Guo L, Han J, Guo H, Lv D, Wang Y. Pathway and network analysis of genes related to osteoporosis. Mol Med Rep 2019; 20:985-994. [PMID: 31173222 PMCID: PMC6625186 DOI: 10.3892/mmr.2019.10353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 03/29/2019] [Indexed: 12/20/2022] Open
Abstract
As a common degenerative disease, osteoporosis (OS) is characterized by reduced bone mass and microarchitectural deterioration of bone tissue. Both genetic and environmental factors are involved in OS development. To date, ~300 genes have been confirmed to be involved in the pathogenesis of OS, a large majority of which have been independently investigated. As OS is a polygenetic disease, a comprehensive analysis focusing on the biological functions and interactions of OS‑related genes would provide valuable information. In this study, OS related research deposited in PubMed was retrieved and genes related to OS were catalogued. Pathways with an enriched biological function for these genes were extracted, and the crosstalk between the enriched pathways was analyzed. A comprehensive network was constructed, and a minimal network was extracted using the Steiner minimal network algorithm. In this study, a total of 294 genes in were retrieved from PubMed. Biological processes found to be enriched included those related to bone metabolism and the immune system. In total, 58 pathways were enriched. Furthermore, the comprehensive network consisting of 3,943 nodes and 7,976 edges was constructed, among which 631 nodes and 2,581 edges contributed to the OS‑specific molecular network. In this network, in excess of 300 potential genes associated with OS and two modules were identified. Thus, this study provides a mechanistic insight into OS and suggests more than 300 potential OS‑related genes for future research.
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Affiliation(s)
- Lin Guo
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, P.R. China
| | - Jia Han
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, P.R. China
| | - Hao Guo
- Shandong Wenning Info‑Technology Corp. Ltd., Jinan, Shandong 250012, P.R. China
| | - Dongmei Lv
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, P.R. China
| | - Yun Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221000, P.R. China
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18
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Roca-Ayats N, Martínez-Gil N, Cozar M, Gerousi M, Garcia-Giralt N, Ovejero D, Mellibovsky L, Nogués X, Díez-Pérez A, Grinberg D, Balcells S. Functional characterization of the C7ORF76 genomic region, a prominent GWAS signal for osteoporosis in 7q21.3. Bone 2019; 123:39-47. [PMID: 30878523 DOI: 10.1016/j.bone.2019.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/21/2022]
Abstract
Genome-wide association studies (GWAS) have repeatedly identified genetic variants associated with bone mineral density (BMD) and osteoporotic fracture in non-coding regions of C7ORF76, a poorly studied gene of unknown function. The aim of the present study was to elucidate the causality and molecular mechanisms underlying the association. We re-sequenced the genomic region in two extreme BMD groups from the BARCOS cohort of postmenopausal women to search for functionally relevant variants. Eight selected variants were tested for association in the complete cohort and 2 of them (rs4342521 and rs10085588) were found significantly associated with lumbar spine BMD and nominally associated with osteoporotic fracture. cis-eQTL analyses of these 2 SNPs, together with SNP rs4727338 (GWAS lead SNP in Estrada et al., Nat Genet. 44:491-501, 2012), performed in human primary osteoblasts, disclosed a statistically significant influence on the expression of the proximal neighbouring gene SLC25A13 and a tendency on the distal SHFM1. We then studied the functionality of a putative upstream regulatory element (UPE), containing rs10085588. Luciferase reporter assays showed transactivation capability with a strong allele-dependent effect. Finally, 4C-seq experiments in osteoblastic cell lines showed that the UPE interacted with different tissue-specific enhancers and a lncRNA (LOC100506136) in the region. In summary, this study is the first one to analyse in depth the functionality of C7ORF76 genomic region. We provide functional regulatory evidence for the rs10085588, which may be a causal SNP within the 7q21.3 GWAS signal for osteoporosis.
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Affiliation(s)
- Neus Roca-Ayats
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Núria Martínez-Gil
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Mónica Cozar
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Marina Gerousi
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Natàlia Garcia-Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Diana Ovejero
- National Research Council, Institute of Clinical Physiology, Lecce, Italy
| | - Leonardo Mellibovsky
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Xavier Nogués
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Adolfo Díez-Pérez
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Catalonia, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Catalonia, Spain.
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LncRNA ZBTB40-IT1 modulated by osteoporosis GWAS risk SNPs suppresses osteogenesis. Hum Genet 2019; 138:151-166. [PMID: 30661131 DOI: 10.1007/s00439-019-01969-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
Previous genome-wide linkage and association studies have identified an osteoporosis-associated locus at 1p36 that harbors SNPs rs34920465 and rs6426749. The 1p36 locus also comprises the WNT4 gene with known role in bone metabolism and functionally unknown ZBTB40/lncRNA ZBTB40-IT1 genes. How these might interact to contribute to osteoporosis susceptibility is not known. In this study, we show that lncRNA ZBTB40-IT1 is able to suppress osteogenesis and promote osteoclastogenesis by regulating the expression of WNT4, RUNX2, OSX, ALP, COL1A1, OPG and RANKL in U-2OS and hFOB1.19 cell lines, whereas ZBTB40 plays an opposite role in bone metabolism. Treatment with parathyroid hormone significantly downregulates the expression of ZBTB40-IT1 in U-2OS cell lines. ZBTB40 can suppress ZBTB40-IT1 expression but has no response to parathyroid hormone treatment. Dual-luciferase assay and biotin pull-down assay demonstrate that osteoporosis GWAS lead SNPs rs34920465-G and rs6426749-C alleles can respectively bind transcription factors JUN::FOS and CREB1, and upregulate ZBTB40 and ZBTB40-IT1 expression. Our study discovers the critical role of ZBTB40 and lncRNA ZBTB40-IT1 in bone metabolism, and provides a mechanistic basis for osteoporosis GWAS lead SNPs rs34920465 and rs6426749.
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Hu Y, Tan LJ, Chen XD, Greenbaum J, Deng HW. Identification of novel variants associated with osteoporosis, type 2 diabetes and potentially pleiotropic loci using pleiotropic cFDR method. Bone 2018; 117:6-14. [PMID: 30172742 PMCID: PMC6364698 DOI: 10.1016/j.bone.2018.08.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/16/2022]
Abstract
AIMS Clinical and epidemiological findings point to an association between type 2 diabetes (T2D) and osteoporosis. Genome-wide association studies (GWASs) have been fruitful in identifying some loci potentially associated with osteoporosis and T2D respectively. However, the total genetic variance for each of these two diseases and the shared genetic determination between them are largely unknown. The aim of this study was to identify novel genetic variants for osteoporosis and/or T2D. METHODS First, using a pleiotropic conditional false discovery rate (cFDR) method, we analyzed two GWAS summary data of femoral neck bone mineral density (FN_BMD, n = 53,236) and T2D (n = 159,208) to identify novel shared genetic loci. FN_BMD is an important risk factor for osteoporosis. Next, to explore the potential functions of the identified potential pleiotropic genes, differential expression analysis was performed for them in monocytes and peripheral blood mononuclear cells (PBMCs) as these cells are relevant to the etiology of osteoporosis and/or T2D. Further, weighted gene co-expression analysis (WGCNA) was conducted to identify functional connections between novel pleiotropic genes and known osteoporosis/T2D susceptibility genes by using transcriptomic expression datasets in bone biopsies (E-MEXP-1618) and pancreatic islets (GSE50397). Finally, multi-trait fine mapping for the detected pleiotropic risk loci were conducted to identify the SNPs that have the highest probability of being causal for both FN_BMD and T2D. RESULTS We identified 27 significant SNPs with cFDR<0.05 for FN_BMD and 61 SNPs for T2D respectively. Four loci, rs7068487 (PLEKHA1), rs10885421 (TCF7L2), rs944082 (GNG12-AS1 (WLS)) and rs2065929 (PIFO||PGCP1), were found to be potentially pleiotropic and shared between FN_BMD and T2D (ccFDR<0.05). PLEKHA1 was found differentially expressed in circulating monocytes between high and low BMD subjects, and PBMCs between diabetic and non-diabetic conditions. WGCNA showed that PLEKHA1 and TCF7L2 were interconnected with multiple osteoporosis and T2D associated genes in bone biopsy and pancreatic islets, such as JAG, EN1 and CPE. Fine mapping showed that rs11200594 was a potentially causal variant in the locus of PLEKHA1. rs11200594 is also an eQTL of PLEKHA1 in multiple tissue (e.g. peripheral blood cells, adipose and ovary) and is in strong LD with a number of functional variants. CONCLUSIONS Four potential pleiotropic loci were identified for shared genetic determination of osteoporosis and T2D. Our study highlights PLEKHA1 as an important potentially pleiotropic gene. The findings may help us gain a better understanding of the shared genetic determination between these two important disorders.
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Affiliation(s)
- Yuan Hu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Li-Jun Tan
- 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
- School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China; Center of Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA.
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Cheng M, Mei B, Zhou Q, Zhang M, Huang H, Han L, Huang Q. Computational analyses of obesity associated loci generated by genome-wide association studies. PLoS One 2018; 13:e0199987. [PMID: 29966015 PMCID: PMC6028139 DOI: 10.1371/journal.pone.0199987] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/17/2018] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Genome-wide association studies (GWASs) have discovered associations of numerous SNPs and genes with obesity. However, the underlying molecular mechanisms through which these SNPs and genes affect the predisposition to obesity remain not fully understood. Aims of our study are to comprehensively characterize obesity GWAS SNPs and genes through computational approaches. METHODS For obesity GWAS identified SNPs, functional annotation, effects on miRNAs binding and impact on protein phosphorylation were performed via RegulomeDB and 3DSNP, miRNASNP, and the PhosSNP 1.0 database, respectively. For obesity associated genes, protein-protein interaction network construction, gene ontology and pathway enrichment analyses were performed by STRING, PANTHER and STRING, respectively. RESULTS A total of 445 SNPs are significantly associated with obesity related phenotypes at threshold P < 5×10-8. A number of SNPs were eQTLs for obesity associated genes, some SNPs located at binding sites of obesity related transcription factors. SNPs that might affect miRNAs binding and protein phosphorylation were identified. Protein-protein interaction network analysis identified the highly-interconnected "hub" genes. Obesity associated genes mainly involved in metabolic process and catalytic activity, and significantly enriched in 15 signal pathways. CONCLUSIONS Our results provided the targets for follow-up experimental testing and further shed new light on obesity pathophysiology.
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Affiliation(s)
- Mengrong Cheng
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Bing Mei
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qian Zhou
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Manling Zhang
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Han Huang
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Lanchun Han
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qingyang Huang
- College of Life Sciences, Central China Normal University, Wuhan, Hubei, China
- * E-mail:
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22
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Role of nutritional vitamin D in osteoporosis treatment. Clin Chim Acta 2018; 484:179-191. [PMID: 29782843 DOI: 10.1016/j.cca.2018.05.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 01/02/2023]
Abstract
Osteoporosis is a systemic skeletal disorder characterized by a decrease in bone mass and microarchitectural deterioration of bone tissue. The World Health Organization has defined osteoporosis as a decrease in bone mass (50%) and bony quality (50%). Vitamin D, a steroid hormone, is crucial for skeletal health and in mineral metabolism. Its direct action on osteoblasts and osteoclasts and interaction with nonskeletal tissues help in maintaining a balance between bone turnover and bone growth. Vitamin D affects the activity of osteoblasts, osteoclasts, and osteocytes, suggesting that it affects bone formation, bone resorption, and bone quality. At physiological concentrations, active vitamin D maintains a normal rate of bone resorption and formation through the RANKL/OPG signal. However, active vitamin D at pharmacological concentration inhibits bone resorption at a higher rate than that of bone formation, which influences the bone quality and quantity. Nutritional vitamin D rather than active vitamin D activates osteoblasts and maintains serum 25(OH)D3 concentration. Despite many unanswered questions, much data support nutritional vitamin D use in osteoporosis patients. This article emphasizes the role of nutritional vitamin D replacement in different turnover status (high or low bone turnover disorders) of osteoporosis together with either anti-resorptive (Bisphosphonate, Denosumab et.) or anabolic (Teriparatide) agents when osteoporosis persists.
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23
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Moradifard S, Hoseinbeyki M, Ganji SM, Minuchehr Z. Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach. Sci Rep 2018; 8:4767. [PMID: 29555910 PMCID: PMC5859169 DOI: 10.1038/s41598-018-20959-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Understanding the molecular mechanisms underlying Alzheimer’s disease (AD) is necessary for the diagnosis and treatment of this neurodegenerative disorder. It is therefore important to detect the most important genes and miRNAs, which are associated with molecular events, and studying their interactions for recognition of AD mechanisms. Here we focus on the genes and miRNAs expression profile, which we have detected the miRNA target genes involved in AD. These are the most quintessential to find the most important miRNA, to target genes and their important pathways. A total of 179 differentially expressed miRNAs (DEmiRs) and 1404 differentially expressed genes (DEGs) were obtained from a comprehensive meta-analysis. Also, regions specific genes with their molecular function in AD have been demonstrated. We then focused on miRNAs which regulated most genes in AD, alongside we analyzed their pathways. The miRNA-30a-5p and miRNA-335 elicited a major function in AD after analyzing the regulatory network, we showed they were the most regulatory miRNAs in the AD. In conclusion, we demonstrated the most important genes, miRNAs, miRNA-mRNA interactions and their related pathways in AD using Bioinformatics methods. Accordingly, our defined genes and miRNAs could be used for future molecular studies in the context of AD.
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Affiliation(s)
- Shirin Moradifard
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Moslem Hoseinbeyki
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Zarrin Minuchehr
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Hu Y, Tan LJ, Chen XD, Liu Z, Min SS, Zeng Q, Shen H, Deng HW. Identification of Novel Potentially Pleiotropic Variants Associated With Osteoporosis and Obesity Using the cFDR Method. J Clin Endocrinol Metab 2018; 103:125-138. [PMID: 29145611 PMCID: PMC6061219 DOI: 10.1210/jc.2017-01531] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/12/2017] [Indexed: 01/10/2023]
Abstract
CONTEXT Genome-wide association studies (GWASs) have been successful in identifying loci associated with osteoporosis and obesity. However, the findings explain only a small fraction of the total genetic variance. OBJECTIVE The aim of this study was to identify novel pleiotropic genes important in osteoporosis and obesity. DESIGN AND SETTING A pleiotropic conditional false discovery rate method was applied to three independent GWAS summary statistics of femoral neck bone mineral density, body mass index, and waist-to-hip ratio. Next, differential expression analysis was performed for the potentially pleiotropic genes, and weighted genes coexpression network analysis (WGCNA) was conducted to identify functional connections between the suggested pleiotropic genes and known osteoporosis/obesity genes using transcriptomic expression data sets in osteoporosis/obesity-related cells. RESULTS We identified seven potentially pleiotropic loci-rs3759579 (MARK3), rs2178950 (TRPS1), rs1473 (PUM1), rs9825174 (XXYLT1), rs2047937 (ZNF423), rs17277372 (DNM3), and rs335170 (PRDM6)-associated with osteoporosis and obesity. Of these loci, the PUM1 gene was differentially expressed in osteoporosis-related cells (B lymphocytes) and obesity-related cells (adipocytes). WGCNA showed that PUM1 positively interacted with several known osteoporosis genes (AKAP11, JAG1, and SPTBN1). ZNF423 was the highly connected intramodular hub gene and interconnected with 21 known osteoporosis-related genes, including JAG1, EN1, and FAM3C. CONCLUSIONS Our study identified seven potentially pleiotropic genes associated with osteoporosis and obesity. The findings may provide new insights into a potential genetic determination and codetermination mechanism of osteoporosis and obesity.
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Affiliation(s)
- Yuan Hu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Li-Jun Tan
- 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
| | - Zhen Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shi-Shi Min
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Qin Zeng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Hui Shen
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
- Correspondence and Reprint Requests: Hong-Wen Deng, PhD, Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1610, New Orleans, Louisiana 70112. E-mail:
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Identification of novel genetic loci for osteoporosis and/or rheumatoid arthritis using cFDR approach. PLoS One 2017; 12:e0183842. [PMID: 28854271 PMCID: PMC5576737 DOI: 10.1371/journal.pone.0183842] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/12/2017] [Indexed: 12/19/2022] Open
Abstract
There are co-morbidity between osteoporosis (OP) and rheumatoid arthritis (RA). Some genetic risk factors have been identified for these two phenotypes respectively in previous research; however, they accounted for only a small portion of the underlying total genetic variances. Here, we sought to identify additional common genetic loci associated with OP and/or RA. The conditional false discovery rate (cFDR) approach allows detection of additional genetic factors (those respective ones as well as common pleiotropic ones) for the two associated phenotypes. We collected and analyzed summary statistics provided by large, multi-center GWAS studies of FNK (femoral neck) BMD (a major risk factor for osteoporosis) (n = 53,236) and RA (n = 80,799). The conditional quantile-quantile (Q-Q) plots can assess the enrichment of SNPs related to FNK BMD and RA, respectively. Furthermore, we identified shared loci between FNK BMD and RA using conjunction cFDR (ccFDR). We found strong enrichment of p-values in FNK BMD when conditional Q-Q was done on RA and vice versa. We identified 30 novel OP-RA associated pleiotropic loci that have not been reported in previous OP or RA GWAS, 18 of which located in the MHC (major histocompatibility complex) region previously reported to play an important role in immune system and bone health. We identified some specific novel polygenic factors for OP and RA respectively, and identified 30 novel OP-RA associated pleiotropic loci. These discovery findings may offer novel pathobiological insights, and suggest new targets and pathways for drug development in OP and RA patients.
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Abstract
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes. Our computational analysis identified 6 lead SNPs (rs10119, rs1048699, rs148763909, rs610932, rs6857 and rs714948) and 2 proxy SNPs (rs12539172 and rs2847655) that potentially impacted the miRNA binding. Lead SNP rs2296160 and proxy SNPs rs679620 and rs2228145 were identified as PhosSNPs potentially influencing protein phosphorylation. AD-associated genes showed enrichment of “regulation of beta-amyloid formation”, “regulation of neurofibrillary tangle assembly”, “leukocyte mediated immunity” and “protein-lipid complex assembly” signaling pathway. Protein-protein interaction network and functional module analyses identified highly-interconnected “hub” genes (APOE, PICALM, BIN1, ABCA7, CD2AP, CLU, CR1, MS4A4E and MS4A6A) and bottleneck genes (APOE, TOMM40, NME8, PICALM, CD2AP, ZCWPW1, FAM180B, GAB2 and PTK2B) that created three tight subnetworks. Our results provided the targets for further experimental assessment and further insight on AD pathophysiology.
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Affiliation(s)
- Zengpeng Han
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Han Huang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yue Gao
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qingyang Huang
- School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail:
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27
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Cheng M, Liu X, Yang M, Han L, Xu A, Huang Q. Computational analyses of type 2 diabetes-associated loci identified by genome-wide association studies. J Diabetes 2017; 9:362-377. [PMID: 27121852 DOI: 10.1111/1753-0407.12421] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/31/2016] [Accepted: 04/23/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) of type 2 diabetes (T2D) have discovered a number of loci that contribute to susceptibility to the disease. Future challenges include elucidation of functional mechanisms through which these GWAS-identified loci modulate T2D disease risk. The aim of the present study was to comprehensively characterize T2D associated single nucleotide polymorphisms (SNPs) and genes through computational approaches. METHODS Computational biology approaches used in the present study included comparative genomic analyses and functional annotation using GWAS3D and RegulomeDB, investigation of the effects of T2D-associated SNPs on miRNA binding and protein phosphorylation, and gene ontology, pathway enrichment, protein-protein interaction (PPI) networks and functional module analysis of T2D-associated genes from previously published GWAS. RESULTS Computational analysis identified a number of T2D GWAS-associated SNPs that were located at protein binding sites, including CCCTC-binding factor (CTCF), E1A binding protein p300 (EP300), hepatocyte nuclear factor 4alpha (HNF4A), transcription factor 7 like 2 (TCF7L2), forkhead box A1 (FOXA1) and A2 (FOXA2), and potentially affected the binding of miRNAs and protein phosphorylation. Pathway enrichment analysis confirmed two well-known maturity onset diabetes of the young and T2D pathways, whereas PPI network analysis identified highly interconnected "hub" genes, such as TCF7L2, melatonin receptor 1B (MTNR1B), and solute carrier family 30 (zinc transporter), member 8 (SLC30A8), that created two tight subnetworks. CONCLUSIONS The results provide objectives and clues for future experimental studies and further insights into the molecular pathogenesis of T2D.
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Affiliation(s)
- Mengrong Cheng
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Xinhong Liu
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Mei Yang
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Lanchun Han
- College of Life Sciences, Central China Normal University, Wuhan, China
- Institute of Public Health and Molecular Medicine Analysis, Central China Normal University, Wuhan, China
| | - Aimin Xu
- Li Cha Chung Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qingyang Huang
- College of Life Sciences, Central China Normal University, Wuhan, China
- Institute of Public Health and Molecular Medicine Analysis, Central China Normal University, Wuhan, China
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