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Saliba-Gustafsson P, Justesen JM, Ranta A, Sharma D, Bielczyk-Maczynska E, Li J, Najmi LA, Apodaka M, Aspichueta P, Björck HM, Eriksson P, Franco-Cereceda A, Gloudemans M, Mujica E, den Hoed M, Assimes TL, Quertermous T, Carcamo-Orive I, Park CY, Knowles JW. A functional genomic framework to elucidate novel causal non-alcoholic fatty liver disease genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.03.24302258. [PMID: 38352379 PMCID: PMC10863038 DOI: 10.1101/2024.02.03.24302258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Background & Aims Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver pathology in western countries, with serious public health consequences. Efforts to identify causal genes for NAFLD have been hampered by the relative paucity of human data from gold-standard magnetic resonance quantification of hepatic fat. To overcome insufficient sample size, genome-wide association studies using NAFLD surrogate phenotypes have been used, but only a small number of loci have been identified to date. In this study, we combined GWAS of NAFLD composite surrogate phenotypes with genetic colocalization studies followed by functional in vitro screens to identify bona fide causal genes for NAFLD. Approach & Results We used the UK Biobank to explore the associations of our novel NAFLD score, and genetic colocalization to prioritize putative causal genes for in vitro validation. We created a functional genomic framework to study NAFLD genes in vitro using CRISPRi. Our data identify VKORC1, TNKS, LYPLAL1 and GPAM as regulators of lipid accumulation in hepatocytes and suggest the involvement of VKORC1 in the lipid storage related to the development of NAFLD. Conclusions Complementary genetic and genomic approaches are useful for the identification of NAFLD genes. Our data supports VKORC1 as a bona fide NAFLD gene. We have established a functional genomic framework to study at scale putative novel NAFLD genes from human genetic association studies.
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Affiliation(s)
- Peter Saliba-Gustafsson
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- CardioMetabolic Unit at the Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
- Stanford Diabetes Research Center, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
| | - Johanne M. Justesen
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Amanda Ranta
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
| | - Disha Sharma
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
| | - Ewa Bielczyk-Maczynska
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
- The Hormel Institute, University of Minnesota, MN, USA
| | - Jiehan Li
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
| | - Laeya A. Najmi
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
| | - Maider Apodaka
- University of the Basque Country (UPV/EHU), Faculty of Medicine and Nursing, Department of Physiology, Leioa, Spain
| | - Patricia Aspichueta
- University of the Basque Country (UPV/EHU), Faculty of Medicine and Nursing, Department of Physiology, Leioa, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III)
| | - Hanna M. Björck
- Division of Cardiovascular Medicine, Centre for Molecular Medicine, Department of Medicine, Solna, Karolinska Inistitutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Per Eriksson
- Division of Cardiovascular Medicine, Centre for Molecular Medicine, Department of Medicine, Solna, Karolinska Inistitutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | | | - Mike Gloudemans
- Department of Pathology, Stanford University School of Medicine, CA, USA
| | - Endrina Mujica
- Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Marcel den Hoed
- Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Themistocles L. Assimes
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto CA, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Ivan Carcamo-Orive
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Chong Y. Park
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Joshua W. Knowles
- Department of Medicine, Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
- Stanford Prevention Research Center, Stanford, CA, USA
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