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Boukhalfa W, Jmel H, Kheriji N, Gouiza I, Dallali H, Hechmi M, Kefi R. Decoding the genetic relationship between Alzheimer's disease and type 2 diabetes: potential risk variants and future direction for North Africa. Front Aging Neurosci 2023; 15:1114810. [PMID: 37342358 PMCID: PMC10277480 DOI: 10.3389/fnagi.2023.1114810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 06/22/2023] Open
Abstract
Introduction Alzheimer's disease (AD) and Type 2 diabetes (T2D) are both age-associated diseases. Identification of shared genes could help develop early diagnosis and preventive strategies. Although genetic background plays a crucial role in these diseases, we noticed an underrepresentation tendency of North African populations in omics studies. Materials and methods First, we conducted a comprehensive review of genes and pathways shared between T2D and AD through PubMed. Then, the function of the identified genes and variants was investigated using annotation tools including PolyPhen2, RegulomeDB, and miRdSNP. Pathways enrichment analyses were performed with g:Profiler and EnrichmentMap. Next, we analyzed variant distributions in 16 worldwide populations using PLINK2, R, and STRUCTURE software. Finally, we performed an inter-ethnic comparison based on the minor allele frequency of T2D-AD common variants. Results A total of 59 eligible papers were included in our study. We found 231 variants and 363 genes shared between T2D and AD. Variant annotation revealed six single nucleotide polymorphisms (SNP) with a high pathogenic score, three SNPs with regulatory effects on the brain, and six SNPs with potential effects on miRNA-binding sites. The miRNAs affected were implicated in T2D, insulin signaling pathways, and AD. Moreover, replicated genes were significantly enriched in pathways related to plasma protein binding, positive regulation of amyloid fibril deposition, microglia activation, and cholesterol metabolism. Multidimensional screening performed based on the 363 shared genes showed that main North African populations are clustered together and are divergent from other worldwide populations. Interestingly, our results showed that 49 SNP associated with T2D and AD were present in North African populations. Among them, 11 variants located in DNM3, CFH, PPARG, ROHA, AGER, CLU, BDNF1, CST9, and PLCG1 genes display significant differences in risk allele frequencies between North African and other populations. Conclusion Our study highlighted the complexity and the unique molecular architecture of North African populations regarding T2D-AD shared genes. In conclusion, we emphasize the importance of T2D-AD shared genes and ethnicity-specific investigation studies for a better understanding of the link behind these diseases and to develop accurate diagnoses using personalized genetic biomarkers.
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Affiliation(s)
- Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Ismail Gouiza
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Mariem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
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Sani MB, Roudbari Z, Karimi O, Banabazi MH, Esmaeilkhanian S, Asadzadeh N, Zare Harofte J, Shafei Naderi A, Burger PA. Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries. Animals (Basel) 2022; 12:184. [PMID: 35049806 PMCID: PMC8773174 DOI: 10.3390/ani12020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
Growth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) associated with growth in domestic animals, but in dromedaries, the number of studies is very low. This project aimed to find biological themes affecting growth in dromedaries. In the first step, 99 candidate SNPs were chosen from a previously established set of SNPs associated with body weight, gain, and birth weight in Iranian dromedaries. Next, 0.5 kb upstream and downstream of each candidate SNP were selected from NCBI (assembly accession: GCA_000803125.3). The annotation of fragments with candidate SNPs regarding the reference genome was retrieved using the Blast2GO tool. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant biological themes were identified to be related to growth in dromedaries. The main biological functions included calcium ion binding, protein binding, DNA-binding transcription factor activity, protein kinase activity, tropomyosin binding, myosin complex, actin-binding, ATP binding, receptor signaling pathway via JAK-STAT, and cytokine activity. EFCAB5, MTIF2, MYO3A, TBX15, IFNL3, PREX1, and TMOD3 genes are candidates for improving growth in camel breeding programs.
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Affiliation(s)
- Morteza Bitaraf Sani
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, Iran; (J.Z.H.); (A.S.N.)
| | - Zahra Roudbari
- Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft 7867155311, Iran;
| | - Omid Karimi
- Department of Animal Viral Diseases Research, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj 3146618361, Iran;
| | - Mohammad Hossein Banabazi
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, Iran; (M.H.B.); (S.E.); (N.A.)
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007 Uppsala, Sweden
| | - Saeid Esmaeilkhanian
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, Iran; (M.H.B.); (S.E.); (N.A.)
| | - Nader Asadzadeh
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, Iran; (M.H.B.); (S.E.); (N.A.)
| | - Javad Zare Harofte
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, Iran; (J.Z.H.); (A.S.N.)
| | - Ali Shafei Naderi
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, Iran; (J.Z.H.); (A.S.N.)
| | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, 1160 Vienna, Austria;
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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: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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4
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Cheung CL, Tan KCB, Kung AWC. Cohort Profile: The Hong Kong Osteoporosis Study and the follow-up study. Int J Epidemiol 2017; 47:397-398f. [DOI: 10.1093/ije/dyx172] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ching-Lung Cheung
- Department of Pharmacology and Pharmacy
- Department of Medicine
- State Key Laboratory of Pharmaceutical Biotechnology
- Centre for Genomic Sciences, University of Hong Kong, Pokfulam, Hong Kong
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Mullin BH, Walsh JP, Zheng HF, Brown SJ, Surdulescu GL, Curtis C, Breen G, Dudbridge F, Richards JB, Spector TD, Wilson SG. Genome-wide association study using family-based cohorts identifies the WLS and CCDC170/ESR1 loci as associated with bone mineral density. BMC Genomics 2016; 17:136. [PMID: 26911590 PMCID: PMC4766752 DOI: 10.1186/s12864-016-2481-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/17/2016] [Indexed: 12/26/2022] Open
Abstract
Background Osteoporosis is a common and debilitating bone disease that is characterised by a low bone mineral density (BMD), a highly heritable trait. Genome-wide association studies (GWAS) have proven to be very successful in identifying common genetic variants associated with BMD adjusted for age, gender and weight, however a large portion of the genetic variance for this trait remains unexplained. There is evidence to suggest significant genetic correlation between body size traits and BMD. It has also recently been suggested that unintended bias can be introduced as a result of adjusting a phenotype for a correlated trait. We performed a GWAS meta-analysis in two populations (total n = 6,696) using BMD data adjusted for only age and gender, in an attempt to identify genetic variants associated with BMD including those that may have potential pleiotropic effects on BMD and body size traits. Results We observed a single variant, rs2566752, associated with spine BMD at the genome-wide significance level in the meta-analysis (P = 3.36 × 10−09). Logistic regression analysis also revealed an association between rs2566752 and fracture rate in one of our study cohorts (P = 0.017, n = 5,654). This is an intronic variant located in the wntless Wnt ligand secretion mediator (WLS) gene (1p31.3), a known BMD locus which encodes an integral component of the Wnt ligand secretion pathway. Bioinformatics analyses of variants in moderate LD with rs2566752 produced strong evidence for a regulatory role for the variants rs72670452, rs17130567 and rs1430738. Expression quantitative trait locus (eQTL) analysis suggested that the variants rs12568456 and rs17130567 are associated with expression of the WLS gene in whole blood, cerebellum and temporal cortex brain tissue (P = 0.034–1.19 × 10−23). Gene-wide association testing using the VErsatile Gene-based Association Study 2 (VEGAS2) software revealed associations between the coiled-coil domain containing 170 (CCDC170) gene, located adjacent to the oestrogen receptor 1 (ESR1) gene, and BMD at the spine, femoral neck and total hip sites (P = 1.0 × 10−06, 2.0 × 10−06 and 2.0 × 10−06 respectively). Conclusions Genetic variation at the WLS and CCDC170/ESR1 loci were found to be significantly associated with BMD adjusted for only age and gender at the genome-wide level in this meta-analysis.
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Affiliation(s)
- Benjamin H Mullin
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia. .,School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia.
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia. .,School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia.
| | - Hou-Feng Zheng
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, and the Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China.
| | - Suzanne J Brown
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia.
| | - Gabriela L Surdulescu
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.
| | - Charles Curtis
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK. .,NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Gerome Breen
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK. .,NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | - J Brent Richards
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK. .,Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Canada.
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.
| | - Scott G Wilson
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia. .,School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia. .,Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.
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Zhang J, Zhang L, Zhang Y, Yang J, Guo M, Sun L, Pan HF, Hirankarn N, Ying D, Zeng S, Lee TL, Lau CS, Chan TM, Leung AMH, Mok CC, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Tong KL, Tse NKC, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Ying SKY, Fung SKS, Lai WM, Garcia-Barceló MM, Cherny SS, Sham PC, Cui Y, Yang S, Ye DQ, Zhang XJ, Lau YL, Yang W. Gene-Based Meta-Analysis of Genome-Wide Association Study Data Identifies Independent Single-Nucleotide Polymorphisms inANXA6as Being Associated With Systemic Lupus Erythematosus in Asian Populations. Arthritis Rheumatol 2015. [PMID: 26202167 DOI: 10.1002/art.39275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jing Zhang
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and Eye and ENT Hospital of Fudan University; Shanghai China
| | - Lu Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yan Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Jing Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Mengbiao Guo
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | - Dingge Ying
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Shuai Zeng
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tsz Leung Lee
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Chak Sing Lau
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tak Mao Chan
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Chi Chiu Mok
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Sik Nin Wong
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Ka Wing Lee
- Pamela Youde Nethersole Eastern Hospital; Hong Kong China
| | - Marco Hok Kung Ho
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | - Chun Yin Chong
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Mo Yin Mok
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stacey S. Cherny
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Pak Chung Sham
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yong Cui
- Anhui Medical University; China Hefei China
| | - Sen Yang
- Anhui Medical University; China Hefei China
| | | | | | - Yu Lung Lau
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and The University of Hong Kong-Shenzhen Hospital; Shenzhen China
| | - Wanling Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
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Mo XB, Lu X, Zhang YH, Zhang ZL, Deng FY, Lei SF. Gene-based association analysis identified novel genes associated with bone mineral density. PLoS One 2015; 10:e0121811. [PMID: 25811989 PMCID: PMC4374695 DOI: 10.1371/journal.pone.0121811] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/04/2015] [Indexed: 12/31/2022] Open
Abstract
Genetic factors contribute to the variation of bone mineral density (BMD), which is a major risk factor of osteoporosis. The aim of this study was to identify more “novel” genes for BMD. Based on the publicly available SNP-based P values, we performed an initial gene-based analysis in a total of 32,961 individuals. Furthermore, we performed differential expression, pathway and protein-protein interaction analyses to find supplementary evidence to support the significance of the identified genes. About 21,695 genes for femoral neck (FN)-BMD and 21,683 genes for lumbar spine (LS)-BMD were analyzed using gene-based association analysis. A total of 35 FN-BMD associated genes and 53 LS-BMD associated genes were identified (P < 2.3×10-6) after Bonferroni correction. Among them, 64 genes have not been reported in previous SNP-based genome-wide association studies. Differential expression analysis further supported the significant associations of 14 genes with FN-BMD and 19 genes with LS-BMD. Especially, WNT3 and WNT9B in the Wnt signaling pathway for FN-BMD were further supported by pathway analysis and protein-protein interaction analysis. The present study took the advantage of gene-based association method to perform a supplementary analysis of the GWAS dataset and found some BMD-associated genes. The evidence taken together supported the importance of Wnt signaling pathway genes in determining osteoporosis. Our findings provided more insights into the genetic basis of osteoporosis.
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Affiliation(s)
- Xing-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yong-Hong Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Zeng-Li Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
- * E-mail:
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Otowa T, Maher BS, Aggen SH, McClay JL, van den Oord EJ, Hettema JM. Genome-wide and gene-based association studies of anxiety disorders in European and African American samples. PLoS One 2014; 9:e112559. [PMID: 25390645 PMCID: PMC4229211 DOI: 10.1371/journal.pone.0112559] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/07/2014] [Indexed: 01/02/2023] Open
Abstract
Anxiety disorders (ADs) are common mental disorders caused by a combination of genetic and environmental factors. Since ADs are highly comorbid with each other, partially due to shared genetic basis, studying AD phenotypes in a coordinated manner may be a powerful strategy for identifying potential genetic loci for ADs. To detect these loci, we performed genome-wide association studies (GWAS) of ADs. In addition, as a complementary approach to single-locus analysis, we also conducted gene- and pathway-based analyses. GWAS data were derived from the control sample of the Molecular Genetics of Schizophrenia (MGS) project (2,540 European American and 849 African American subjects) genotyped on the Affymetrix GeneChip 6.0 array. We applied two phenotypic approaches: (1) categorical case-control comparisons (CC) based upon psychiatric diagnoses, and (2) quantitative phenotypic factor scores (FS) derived from a multivariate analysis combining information across the clinical phenotypes. Linear and logistic models were used to analyse the association with ADs using FS and CC traits, respectively. At the single locus level, no genome-wide significant association was found. A trans-population gene-based meta-analysis across both ethnic subsamples using FS identified three genes (MFAP3L on 4q32.3, NDUFAB1 and PALB2 on 16p12) with genome-wide significance (false discovery rate (FDR] <5%). At the pathway level, several terms such as transcription regulation, cytokine binding, and developmental process were significantly enriched in ADs (FDR <5%). Our approaches studying ADs as quantitative traits and utilizing the full GWAS data may be useful in identifying susceptibility genes and pathways for ADs.
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Affiliation(s)
- Takeshi Otowa
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Steven H. Aggen
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Joseph L. McClay
- Department of Pharmacy, Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Edwin J. van den Oord
- Department of Pharmacy, Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - John M. Hettema
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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9
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He H, Zhang L, Li J, Wang YP, Zhang JG, Shen J, Guo YF, Deng HW. Integrative analysis of GWASs, human protein interaction, and gene expression identified gene modules associated with BMDs. J Clin Endocrinol Metab 2014; 99:E2392-9. [PMID: 25119315 PMCID: PMC4223444 DOI: 10.1210/jc.2014-2563] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CONTEXT To date, few systems genetics studies in the bone field have been performed. We designed our study from a systems-level perspective by integrating genome-wide association studies (GWASs), human protein-protein interaction (PPI) network, and gene expression to identify gene modules contributing to osteoporosis risk. METHODS First we searched for modules significantly enriched with bone mineral density (BMD)-associated genes in human PPI network by using 2 large meta-analysis GWAS datasets through a dense module search algorithm. One included 7 individual GWAS samples (Meta7). The other was from the Genetic Factors for Osteoporosis Consortium (GEFOS2). One was assigned as a discovery dataset and the other as an evaluation dataset, and vice versa. RESULTS In total, 42 modules and 129 modules were identified significantly in both Meta7 and GEFOS2 datasets for femoral neck and spine BMD, respectively. There were 3340 modules identified for hip BMD only in Meta7. As candidate modules, they were assessed for the biological relevance to BMD by gene set enrichment analysis in 2 expression profiles generated from circulating monocytes in subjects with low versus high BMD values. Interestingly, there were 2 modules significantly enriched in monocytes from the low BMD group in both gene expression datasets (nominal P value <.05). Two modules had 16 nonredundant genes. Functional enrichment analysis revealed that both modules were enriched for genes involved in Wnt receptor signaling and osteoblast differentiation. CONCLUSION We highlighted 2 modules and novel genes playing important roles in the regulation of bone mass, providing important clues for therapeutic approaches for osteoporosis.
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Affiliation(s)
- Hao He
- Center of Genomics and Bioinformatics and Department of Biostatistics and Bioinformatics (H.H., L.Z., J.L., Y.-P.W., J.-G.Z., H.-W.D.), Tulane University, New Orleans, Louisiana 70112; Biomedical Engineering Department (Y.-P.W.), Tulane University, New Orleans, Louisiana 70118; and Third Affiliated Hospital (J.S., Y.-F.G., H.-W.D.), China Southern Medical University, Guang Zhou 510000, People's Republic of China
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Cheung CL, Lau KS, Sham PC, Tan KCB, Kung AWC. Genetic variant in vitamin D binding protein is associated with serum 25-hydroxyvitamin D and vitamin D insufficiency in southern Chinese. J Hum Genet 2013; 58:749-51. [DOI: 10.1038/jhg.2013.84] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/10/2013] [Accepted: 06/12/2013] [Indexed: 12/30/2022]
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11
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Gene clustering analysis in human osteoporosis disease and modifications of the jawbone. Arch Oral Biol 2013; 58:912-29. [DOI: 10.1016/j.archoralbio.2013.02.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 01/11/2013] [Accepted: 02/28/2013] [Indexed: 12/18/2022]
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12
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Wu S, Liu Y, Zhang L, Han Y, Lin Y, Deng HW. Genome-wide approaches for identifying genetic risk factors for osteoporosis. Genome Med 2013; 5:44. [PMID: 23731620 PMCID: PMC3706967 DOI: 10.1186/gm448] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Osteoporosis, the most common type of bone disease worldwide, is clinically characterized by low bone mineral density (BMD) and increased susceptibility to fracture. Multiple genetic and environmental factors and gene-environment interactions have been implicated in its pathogenesis. Osteoporosis has strong genetic determination, with the heritability of BMD estimated to be as high as 60%. More than 80 genes or genetic variants have been implicated in risk of osteoporosis by hypothesis-free genome-wide studies. However, these genes or genetic variants can only explain a small portion of BMD variation, suggesting that many other genes or genetic variants underlying osteoporosis risk await discovery. Here, we review recent progress in genome-wide studies of osteoporosis and discuss their implications for medicine and the major challenges in the field.
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Affiliation(s)
- Shuyan Wu
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Yongjun Liu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
| | - Lei Zhang
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China ; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
| | - Yingying Han
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Yong Lin
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China
| | - Hong-Wen Deng
- The Center for System Biomedical Research, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 Jungong Rd, Yangpu district, Shanghai, 200093, China ; Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St, New Orleans, LA 70112, USA
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13
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Benisch P, Schilling T, Klein-Hitpass L, Frey SP, Seefried L, Raaijmakers N, Krug M, Regensburger M, Zeck S, Schinke T, Amling M, Ebert R, Jakob F. The transcriptional profile of mesenchymal stem cell populations in primary osteoporosis is distinct and shows overexpression of osteogenic inhibitors. PLoS One 2012; 7:e45142. [PMID: 23028809 PMCID: PMC3454401 DOI: 10.1371/journal.pone.0045142] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/13/2012] [Indexed: 12/11/2022] Open
Abstract
Primary osteoporosis is an age-related disease characterized by an imbalance in bone homeostasis. While the resorptive aspect of the disease has been studied intensely, less is known about the anabolic part of the syndrome or presumptive deficiencies in bone regeneration. Multipotent mesenchymal stem cells (MSC) are the primary source of osteogenic regeneration. In the present study we aimed to unravel whether MSC biology is directly involved in the pathophysiology of the disease and therefore performed microarray analyses of hMSC of elderly patients (79–94 years old) suffering from osteoporosis (hMSC-OP). In comparison to age-matched controls we detected profound changes in the transcriptome in hMSC-OP, e.g. enhanced mRNA expression of known osteoporosis-associated genes (LRP5, RUNX2, COL1A1) and of genes involved in osteoclastogenesis (CSF1, PTH1R), but most notably of genes coding for inhibitors of WNT and BMP signaling, such as Sclerostin and MAB21L2. These candidate genes indicate intrinsic deficiencies in self-renewal and differentiation potential in osteoporotic stem cells. We also compared both hMSC-OP and non-osteoporotic hMSC-old of elderly donors to hMSC of ∼30 years younger donors and found that the transcriptional changes acquired between the sixth and the ninth decade of life differed widely between osteoporotic and non-osteoporotic stem cells. In addition, we compared the osteoporotic transcriptome to long term-cultivated, senescent hMSC and detected some signs for pre-senescence in hMSC-OP. Our results suggest that in primary osteoporosis the transcriptomes of hMSC populations show distinct signatures and little overlap with non-osteoporotic aging, although we detected some hints for senescence-associated changes. While there are remarkable inter-individual variations as expected for polygenetic diseases, we could identify many susceptibility genes for osteoporosis known from genetic studies. We also found new candidates, e.g. MAB21L2, a novel repressor of BMP-induced transcription. Such transcriptional changes may reflect epigenetic changes, which are part of a specific osteoporosis-associated aging process.
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Affiliation(s)
- Peggy Benisch
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Tatjana Schilling
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Ludger Klein-Hitpass
- Institute of Cell Biology (Tumor Research), University Hospital Essen, Essen, Germany
| | - Sönke P. Frey
- Department of Trauma, Hand-, Plastic- and Reconstructive Surgery, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Lothar Seefried
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Nadja Raaijmakers
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Melanie Krug
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Martina Regensburger
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Sabine Zeck
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Michael Amling
- Department of Osteology and Biomechanics, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Regina Ebert
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Franz Jakob
- Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
- * E-mail:
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