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Conery M, Pippin JA, Wagley Y, Trang K, Pahl MC, Villani DA, Favazzo LJ, Ackert-Bicknell CL, Zuscik MJ, Katsevich E, Wells AD, Zemel BS, Voight BF, Hankenson KD, Chesi A, Grant SF. GWAS-Informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585778. [PMID: 38562830 PMCID: PMC10983984 DOI: 10.1101/2024.03.19.585778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Over 1,100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effector gene(s) for most remain unknown. Informed by a variant-to-gene mapping strategy implicating 89 non-coding elements predicted to regulate osteoblast gene expression at BMD GWAS loci, we executed a single-cell CRISPRi screen in human fetal osteoblasts (hFOBs). The BMD relevance of hFOBs was supported by heritability enrichment from stratified LD-score regression involving 98 cell types grouped into 15 tissues. 23 genes showed perturbation in the screen, with four (ARID5B, CC2D1B, EIF4G2, and NCOA3) exhibiting consistent effects upon siRNA knockdown on three measures of osteoblast maturation and mineralization. Lastly, additional heritability enrichments, genetic correlations, and multi-trait fine-mapping revealed unexpectedly that many BMD GWAS signals are pleiotropic and likely mediate their effects via non-bone tissues. Extending our CRISPRi screening approach to these tissues could play a key role in fully elucidating the etiology of BMD.
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Affiliation(s)
- Mitchell Conery
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yadav Wagley
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Khanh Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David A. Villani
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Cell Biology, Stems Cells and Development Ph.D. Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lacey J. Favazzo
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Cheryl L. Ackert-Bicknell
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Michael J. Zuscik
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Eugene Katsevich
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Babette S. Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Benjamin F. Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kurt D. Hankenson
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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