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Lu L, Huang J, Xu F, Xiao Z, Wang J, Zhang B, David NV, Arends D, Gu W, Ackert-Bicknell C, Sabik OL, Farber CR, Quarles LD, Williams RW. Genetic Dissection of Femoral and Tibial Microarchitecture. JBMR Plus 2019; 3:e10241. [PMID: 31844829 PMCID: PMC6894729 DOI: 10.1002/jbm4.10241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/29/2022] Open
Abstract
Our understanding of the genetic control of bone strength has relied mainly on estimates of bone mineral density. Here we have mapped genetic factors that influence femoral and tibial microarchitecture using high‐resolution x‐ray computed tomography (8‐μm isotropic voxels) across a family of 61 BXD strains of mice, roughly 10 isogenic cases per strain and balanced by sex. We computed heritabilities for 25 cortical and trabecular traits. Males and females have well‐matched heritabilities, ranging from 0.25 to 0.75. We mapped 16 genetic loci most of which were detected only in females. There is also a bias in favor of loci that control cortical rather than trabecular bone. To evaluate candidate genes, we combined well‐established gene ontologies with bone transcriptome data to compute bone‐enrichment scores for all protein‐coding genes. We aligned candidates with those of human genome‐wide association studies. A subset of 50 strong candidates fell into three categories: (1) experimentally validated genes already known to modulate bone function (Adamts4, Ddr2, Darc, Adam12, Fkbp10, E2f6, Adam17, Grem2, Ifi204); (2) candidates without any experimentally validated function in bone (eg, Greb1, Ifi202b), but linked to skeletal phenotypes in human cohorts; and (3) candidates that have high bone‐enrichment scores, but for which there is not yet any functional link to bone biology or skeletal system disease (including Ifi202b, Ly9, Ifi205, Mgmt, F2rl1, Iqgap2). Our results highlight contrasting genetic architecture between sexes and among major bone compartments. The alignment of murine and human data facilitates function analysis and should prove of value for preclinical testing of molecular control of bone structure. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Lu Lu
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA
| | - Jinsong Huang
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA
| | - Zhousheng Xiao
- Department of Medicine University of Tennessee Health Science Center Memphis TN USA
| | - Jing Wang
- Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA
| | - Bing Zhang
- Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA
| | - Nicolae Valentin David
- Department of Medicine Northwestern University Feinberg School of Medicine Chicago IL USA
| | - Danny Arends
- Breeding Biology and Molecular Animal Breeding Humboldt University Berlin Germany
| | - Weikuan Gu
- Department of Orthopaedic Surgery and Biomedical Engineering University of Tennessee Health Science Center Memphis TN USA
| | | | - Olivia L Sabik
- Center for Public Health Genomics University of Virginia Charlottesville VA USA
| | - Charles R Farber
- Center for Public Health Genomics University of Virginia Charlottesville VA USA
| | - Leigh Darryl Quarles
- Department of Medicine University of Tennessee Health Science Center Memphis TN USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA
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Shimoyama M, Smith JR, Bryda E, Kuramoto T, Saba L, Dwinell M. Rat Genome and Model Resources. ILAR J 2017; 58:42-58. [PMID: 28838068 PMCID: PMC6057551 DOI: 10.1093/ilar/ilw041] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Indexed: 11/25/2022] Open
Abstract
Rats remain a major model for studying disease mechanisms and discovery, validation, and testing of new compounds to improve human health. The rat’s value continues to grow as indicated by the more than 1.4 million publications (second to human) at PubMed documenting important discoveries using this model. Advanced sequencing technologies, genome modification techniques, and the development of embryonic stem cell protocols ensure the rat remains an important mammalian model for disease studies. The 2004 release of the reference genome has been followed by the production of complete genomes for more than two dozen individual strains utilizing NextGen sequencing technologies; their analyses have identified over 80 million variants. This explosion in genomic data has been accompanied by the ability to selectively edit the rat genome, leading to hundreds of new strains through multiple technologies. A number of resources have been developed to provide investigators with access to precision rat models, comprehensive datasets, and sophisticated software tools necessary for their research. Those profiled here include the Rat Genome Database, PhenoGen, Gene Editing Rat Resource Center, Rat Resource and Research Center, and the National BioResource Project for the Rat in Japan.
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Affiliation(s)
- Mary Shimoyama
- Department of Biomedical Engineering, Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Rat Genome Database, Department of Biomedical Engineering at Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri. Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jennifer R Smith
- Department of Biomedical Engineering, Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Rat Genome Database, Department of Biomedical Engineering at Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri. Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elizabeth Bryda
- Department of Biomedical Engineering, Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Rat Genome Database, Department of Biomedical Engineering at Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri. Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Takashi Kuramoto
- Department of Biomedical Engineering, Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Rat Genome Database, Department of Biomedical Engineering at Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri. Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Laura Saba
- Department of Biomedical Engineering, Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Rat Genome Database, Department of Biomedical Engineering at Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri. Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Melinda Dwinell
- Department of Biomedical Engineering, Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Rat Genome Database, Department of Biomedical Engineering at Marquette University and the Medical College of Wisconsin, Milwaukee, Wisconsin. Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri. Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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