The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease.

Advanced Technologies Cores Baylor College of Medicine One Baylor Plaza Houston Texas United States of America

Chair of Developmental Genetics TUM School of Life Sciences Technische Universität München Freising Germany

Chair of Experimental Genetics TUM School of Life Sciences Technische Universität München Freising Germany

Czech Center for Phenogenomics Institute of Molecular Genetics of the Czech Academy of Sciences Vestec Czech Republic

Dan L Duncan Comprehensive Cancer Center Baylor College of Medicine One Baylor Plaza Houston Texas United States of America

Department of Statistics University of Manitoba Winnipeg Manitoba Canada

Department of Surgery School of Medicine and Mouse Biology Program University of California Davis

Department of Surgical and Radiological Sciences University of California Davis California United States of America

Departments of Molecular Physiology and Biophysics Baylor College of Medicine One Baylor Plaza Houston Texas United States of America

Deutsches Institut für Neurodegenerative Erkrankungen Site Munich Munich Germany

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton United Kingdom

Garvan Institute of Medical Research Sydney New South Wales Australia

German Center for Diabetes Research Neuherberg Germany

German Mouse Clinic Institute of Experimental Genetics Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany

Institute of Developmental Genetics Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany

Institute of Experimental Genetics Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany

Internal Medicine Nephrology and Center for Computational Medicine and Bioinformatics University of Michigan Ann Arbor Michigan United States of America

Lunenfeld Tanenbaum Research Institute Sinai Health System Toronto Ontario Canada

Molecular and Human Genetics Baylor College of Medicine Houston Texas United States of America

Molecular Endocrinology Laboratory Department of Metabolism Digestion and Reproduction Imperial College London Hammersmith Campus London United Kingdom

Mouse Informatics Group Wellcome Sanger Institute Hinxton United Kingdom

Mouse Pipelines Wellcome Sanger Institute Hinxton United Kingdom

MRC Harwell Institute Mammalian Genetics Unit Harwell Campus Oxfordshire United Kingdom

MRC Harwell Institute Mary Lyon Centre Harwell Campus Oxfordshire United Kingdom

Munich Cluster for Systems Neurology Adolf Butenandt Institut Ludwig Maximilians Universität München Munich Germany

Research Unit of Molecular Epidemiology Institute of Epidemiology Helmholtz Zentrum München Neuherberg Germany

School of Biotechnology and Biomolecular Sciences UNSW Australia Sydney New South Wales Australia

St Vincent's Clinical School Faculty of Medicine Sydney New South Wales Australia

The Center for Phenogenomics Toronto Ontario Canada

The Hospital for Sick Children University of Toronto Toronto Ontario Canada

The Jackson Laboratory 600 Main Street Bar Harbor Maine United States of America

Université de Strasbourg CNRS INSERM IGBMC Illkirch France

Université de Strasbourg CNRS INSERM IGBMC PHENOMIN ICS Illkirch France

University of California Davis School of Medicine Sacramento California United States of America

Zobrazit více v PubMed

Harvey N, Dennison E, Cooper C. Osteoporosis: impact on health and economics. Nature reviews Rheumatology. 2010;6(2):99–105. 10.1038/nrrheum.2009.260 PubMed DOI

Flicker L, Hopper JL, Rodgers L, Kaymakci B, Green RM, Wark JD. Bone density determinants in elderly women: a twin study. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 1995;10(11):1607–13. 10.1002/jbmr.5650101102 PubMed DOI

Ralston SH, de Crombrugghe B. Genetic regulation of bone mass and susceptibility to osteoporosis. Genes & development. 2006;20(18):2492–506. 10.1101/gad.1449506 PubMed DOI

Duncan EL, Danoy P, Kemp JP, Leo PJ, McCloskey E, Nicholson GC, et al. Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk. PLoS genetics. 2011;7(4):e1001372 10.1371/journal.pgen.1001372 PubMed DOI PMC

Medina-Gomez C, Kemp JP, Trajanoska K, Luan J, Chesi A, Ahluwalia TS, et al. Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects. American journal of human genetics. 2018;102(1):88–102. 10.1016/j.ajhg.2017.12.005 PubMed DOI PMC

Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A, Leo PJ, et al. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. Nature. 2015;526(7571):112–7. 10.1038/nature14878 PubMed DOI PMC

Kemp JP, Medina-Gomez C, Estrada K, St Pourcain B, Heppe DH, Warrington NM, et al. Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. PLoS genetics. 2014;10(6):e1004423 10.1371/journal.pgen.1004423 PubMed DOI PMC

Rivadeneira F, Styrkarsdottir U, Estrada K, Halldorsson BV, Hsu YH, Richards JB, et al. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. Nature genetics. 2009;41(11):1199–206. 10.1038/ng.446 PubMed DOI PMC

Kemp JP, Morris JA, Medina-Gomez C, Forgetta V, Warrington NM, Youlten SE, et al. Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis. Nature genetics. 2017;49(10):1468–75. 10.1038/ng.3949 PubMed DOI PMC

Morris JA, Kemp JP, Youlten SE, Laurent L, Logan JG, Chai RC, et al. An atlas of genetic influences on osteoporosis in humans and mice. Nature genetics. 2019;51(2):258–66. 10.1038/s41588-018-0302-x PubMed DOI PMC

Tachmazidou I, Hatzikotoulas K, Southam L, Esparza-Gordillo J, Haberland V, Zheng J, et al. Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data. Nature genetics. 2019;51(2):230–6. 10.1038/s41588-018-0327-1 PubMed DOI PMC

Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells S. High-throughput mouse phenomics for characterizing mammalian gene function. Nat Rev Genet. 2018;19(6):357–70. 10.1038/s41576-018-0005-2 PubMed DOI PMC

Hrabe de Angelis M, Nicholson G, Selloum M, White JK, Morgan H, Ramirez-Solis R, et al. Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics. Nature genetics. 2015;47(9):969–78. 10.1038/ng.3360 PubMed DOI PMC

Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, et al. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nature genetics. 2017;49(8):1231–8. 10.1038/ng.3901 PubMed DOI PMC

Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, et al. A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction. Nature communications. 2017;8(1):886 10.1038/s41467-017-00595-4 PubMed DOI PMC

Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, et al. High-throughput discovery of novel developmental phenotypes. Nature. 2016;537(7621):508–14. 10.1038/nature19356 PubMed DOI PMC

Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, et al. Prevalence of sexual dimorphism in mammalian phenotypic traits. Nature communications. 2017;8:15475 10.1038/ncomms15475 PubMed DOI PMC

Rozman J, Rathkolb B, Oestereicher MA, Schutt C, Ravindranath AC, Leuchtenberger S, et al. Identification of genetic elements in metabolism by high-throughput mouse phenotyping. Nature communications. 2018;9(1):288 10.1038/s41467-017-01995-2 PubMed DOI PMC

Reinwald S, Burr D. Review of nonprimate, large animal models for osteoporosis research. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 2008;23(9):1353–68. PubMed PMC

D'Amelio P, Sassi F. Osteoimmunology: from mice to humans. BoneKEy reports. 2016;5:802 10.1038/bonekey.2016.29 PubMed DOI PMC

Black DM, Rosen CJ. Postmenopausal Osteoporosis. The New England journal of medicine. 2016;374(21):2096–7. PubMed

Stewart TL, Ralston SH. Role of genetic factors in the pathogenesis of osteoporosis. J Endocrinol. 2000;166(2):235–45. 10.1677/joe.0.1660235 PubMed DOI

Brommage R, Liu J, Hansen GM, Kirkpatrick LL, Potter DG, Sands AT, et al. High-throughput screening of mouse gene knockouts identifies established and novel skeletal phenotypes. Bone research. 2014;2:14034 10.1038/boneres.2014.34 PubMed DOI PMC

Liu CT, Estrada K, Yerges-Armstrong LM, Amin N, Evangelou E, Li G, et al. Assessment of gene-by-sex interaction effect on bone mineral density. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 2012;27(10):2051–64. 10.1002/jbmr.1679 PubMed DOI PMC

Beamer WG, Shultz KL, Ackert-Bicknell CL, Horton LG, Delahunty KM, Coombs HF, 3rd, et al. Genetic dissection of mouse distal chromosome 1 reveals three linked BMD QTLs with sex-dependent regulation of bone phenotypes. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 2007;22(8):1187–96. 10.1359/jbmr.070419 PubMed DOI

Edderkaoui B, Baylink DJ, Beamer WG, Shultz KL, Wergedal JE, Mohan S. Genetic regulation of femoral bone mineral density: complexity of sex effect in chromosome 1 revealed by congenic sublines of mice. Bone. 2007;41(3):340–5. 10.1016/j.bone.2007.05.013 PubMed DOI

Ioannidis JP, Ng MY, Sham PC, Zintzaras E, Lewis CM, Deng HW, et al. Meta-analysis of genome-wide scans provides evidence for sex- and site-specific regulation of bone mass. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 2007;22(2):173–83. PubMed PMC

Peng YM, Lei SF, Guo Y, Xiong DH, Yan H, Wang L, et al. Sex-specific association of the glucocorticoid receptor gene with extreme BMD. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 2008;23(2):247–52. 10.1359/jbmr.071017 PubMed DOI PMC

Almeida M, Laurent MR, Dubois V, Claessens F, O'Brien CA, Bouillon R, et al. Estrogens and Androgens in Skeletal Physiology and Pathophysiology. Physiol Rev. 2017;97(1):135–87. 10.1152/physrev.00033.2015 PubMed DOI PMC

Ober C, Loisel DA, Gilad Y. Sex-specific genetic architecture of human disease. Nat Rev Genet. 2008;9(12):911–22. 10.1038/nrg2415 PubMed DOI PMC

Watari K, Shibata T, Nabeshima H, Shinoda A, Fukunaga Y, Kawahara A, et al. Impaired differentiation of macrophage lineage cells attenuates bone remodeling and inflammatory angiogenesis in Ndrg1 deficient mice. Sci Rep. 2016;6:19470 10.1038/srep19470 PubMed DOI PMC

Enderli TA, Burtch SR, Templet JN, Carriero A. Animal models of osteogenesis imperfecta: applications in clinical research. Orthop Res Rev. 2016;8:41–55. 10.2147/ORR.S85198 PubMed DOI PMC

Daley E, Streeten EA, Sorkin JD, Kuznetsova N, Shapses SA, Carleton SM, et al. Variable bone fragility associated with an Amish COL1A2 variant and a knock-in mouse model. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 2010;25(2):247–61. 10.1359/jbmr.090720 PubMed DOI PMC

Nicholls AC, Valler D, Wallis S, Pope FM. Homozygosity for a splice site mutation of the COL1A2 gene yields a non-functional pro(alpha)2(I) chain and an EDS/OI clinical phenotype. J Med Genet. 2001;38(2):132–6. 10.1136/jmg.38.2.132 PubMed DOI PMC

Costantini A, Tournis S, Kampe A, Ul Ain N, Taylan F, Doulgeraki A, et al. Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation. Calcif Tissue Int. 2018;103(3):353–8. 10.1007/s00223-018-0414-4 PubMed DOI

Nicholls AC, Osse G, Schloon HG, Lenard HG, Deak S, Myers JC, et al. The clinical features of homozygous alpha 2(I) collagen deficient osteogenesis imperfecta. J Med Genet. 1984;21(4):257–62. 10.1136/jmg.21.4.257 PubMed DOI PMC

Papamerkouriou YM, Doulgeraki A, Gyftodimou Y, Athanasopoulou H, Tsiridis E, Anastasopoulos J. Osteogenesis imperfecta due to a possible new COL1A2 mutation; the importance of phenotyping and diagnostic challenges. J Musculoskelet Neuronal Interact. 2016;16(2):168–71. PubMed PMC

Cundy T, Dray M, Delahunt J, Hald JD, Langdahl B, Li C, et al. Mutations That Alter the Carboxy-Terminal-Propeptide Cleavage Site of the Chains of Type I Procollagen Are Associated With a Unique Osteogenesis Imperfecta Phenotype. Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research. 2018;33(7):1260–71. 10.1002/jbmr.3424 PubMed DOI PMC

Forwood MR, Vashishth D. Translational aspects of bone quality—vertebral fractures, cortical shell, microdamage and glycation: a tribute to Pierre D. Delmas. Osteoporos Int. 2009;20 Suppl 3:S247–53. PubMed

Sankaran VG, Joshi M, Agrawal A, Schmitz-Abe K, Towne MC, Marinakis N, et al. Rare complete loss of function provides insight into a pleiotropic genome-wide association study locus. Blood. 2013;122(23):3845–7. 10.1182/blood-2013-09-528315 PubMed DOI

O'Connell AE, Gerashchenko MV, O'Donohue MF, Rosen SM, Huntzinger E, Gleeson D, et al. Mammalian Hbs1L deficiency causes congenital anomalies and developmental delay associated with Pelota depletion and 80S monosome accumulation. PLoS genetics. 2019;15(2):e1007917 10.1371/journal.pgen.1007917 PubMed DOI PMC

Canalis E. Wnt signalling in osteoporosis: mechanisms and novel therapeutic approaches. Nature reviews Endocrinology. 2013;9(10):575–83. 10.1038/nrendo.2013.154 PubMed DOI

Holmen SL, Zylstra CR, Mukherjee A, Sigler RE, Faugere MC, Bouxsein ML, et al. Essential role of beta-catenin in postnatal bone acquisition. The Journal of biological chemistry. 2005;280(22):21162–8. 10.1074/jbc.M501900200 PubMed DOI

Gonzalez-Mariscal I, Martin-Montalvo A, Vazquez-Fonseca L, Pomares-Viciana T, Sanchez-Cuesta A, Fernandez-Ayala DJ, et al. The mitochondrial phosphatase PPTC7 orchestrates mitochondrial metabolism regulating coenzyme Q10 biosynthesis. Biochim Biophys Acta Bioenerg. 2018;1859(11):1235–48. 10.1016/j.bbabio.2018.09.369 PubMed DOI

Moon HJ, Ko WK, Han SW, Kim DS, Hwang YS, Park HK, et al. Antioxidants, like coenzyme Q10, selenite, and curcumin, inhibited osteoclast differentiation by suppressing reactive oxygen species generation. Biochem Biophys Res Commun. 2012;418(2):247–53. 10.1016/j.bbrc.2012.01.005 PubMed DOI

Hattula K, Furuhjelm J, Arffman A, Peranen J. A Rab8-specific GDP/GTP exchange factor is involved in actin remodeling and polarized membrane transport. Mol Biol Cell. 2002;13(9):3268–80. 10.1091/mbc.e02-03-0143 PubMed DOI PMC

Nakai W, Kondo Y, Saitoh A, Naito T, Nakayama K, Shin HW. ARF1 and ARF4 regulate recycling endosomal morphology and retrograde transport from endosomes to the Golgi apparatus. Mol Biol Cell. 2013;24(16):2570–81. 10.1091/mbc.E13-04-0197 PubMed DOI PMC

Ivings L, Pennington SR, Jenkins R, Weiss JL, Burgoyne RD. Identification of Ca2+-dependent binding partners for the neuronal calcium sensor protein neurocalcin delta: interaction with actin, clathrin and tubulin. Biochem J. 2002;363(Pt 3):599–608. 10.1042/0264-6021:3630599 PubMed DOI PMC

Zhao H. Membrane trafficking in osteoblasts and osteoclasts: new avenues for understanding and treating skeletal diseases. Traffic. 2012;13(10):1307–14. 10.1111/j.1600-0854.2012.01395.x PubMed DOI PMC

Leblond CP. Synthesis and secretion of collagen by cells of connective tissue, bone, and dentin. Anat Rec. 1989;224(2):123–38. PubMed

Ito S, Nagata K. Roles of the endoplasmic reticulum-resident, collagen-specific molecular chaperone Hsp47 in vertebrate cells and human disease. The Journal of biological chemistry. 2019;294(6):2133–41. 10.1074/jbc.TM118.002812 PubMed DOI PMC

Aoe T, Cukierman E, Lee A, Cassel D, Peters PJ, Hsu VW. The KDEL receptor, ERD2, regulates intracellular traffic by recruiting a GTPase-activating protein for ARF1. EMBO J. 1997;16(24):7305–16. 10.1093/emboj/16.24.7305 PubMed DOI PMC

Vitale N, Chasserot-Golaz S, Bailly Y, Morinaga N, Frohman MA, Bader MF. Calcium-regulated exocytosis of dense-core vesicles requires the activation of ADP-ribosylation factor (ARF)6 by ARF nucleotide binding site opener at the plasma membrane. J Cell Biol. 2002;159(1):79–89. 10.1083/jcb.200203027 PubMed DOI PMC

Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA. PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data. PloS one. 2015;10(7):e0131274 10.1371/journal.pone.0131274 PubMed DOI PMC

Kim SK. Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteoporosis and fracture. PloS one. 2018;13(7):e0200785 10.1371/journal.pone.0200785 PubMed DOI PMC

Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, et al. Pervasive sharing of genetic effects in autoimmune disease. PLoS genetics. 2011;7(8):e1002254 10.1371/journal.pgen.1002254 PubMed DOI PMC

Bassett JH, Gogakos A, White JK, Evans H, Jacques RM, van der Spek AH, et al. Rapid-throughput skeletal phenotyping of 100 knockout mice identifies 9 new genes that determine bone strength. PLoS genetics. 2012;8(8):e1002858 10.1371/journal.pgen.1002858 PubMed DOI PMC

Eastell R, Szulc P. Use of bone turnover markers in postmenopausal osteoporosis. Lancet Diabetes Endocrinol. 2017;5(11):908–23. 10.1016/S2213-8587(17)30184-5 PubMed DOI

Kuo TR, Chen CH. Bone biomarker for the clinical assessment of osteoporosis: recent developments and future perspectives. Biomark Res. 2017;5:18 10.1186/s40364-017-0097-4 PubMed DOI PMC

Millan JL. The role of phosphatases in the initiation of skeletal mineralization. Calcif Tissue Int. 2013;93(4):299–306. 10.1007/s00223-012-9672-8 PubMed DOI PMC

Trackman PC. Diverse biological functions of extracellular collagen processing enzymes. J Cell Biochem. 2005;96(5):927–37. 10.1002/jcb.20605 PubMed DOI PMC

Zhu L, Tang Y, Li XY, Keller ET, Yang J, Cho JS, et al. Osteoclast-mediated bone resorption is controlled by a compensatory network of secreted and membrane-tethered metalloproteinases. Sci Transl Med. 2020;12(529). 10.1126/scitranslmed.aaw6143 PubMed DOI PMC

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47 10.1093/nar/gkv007 PubMed DOI PMC

A review of standardized high-throughput cardiovascular phenotyping with a link to metabolism in mice

Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy