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Schnitzler GR, Kang H, Fang S, Angom RS, Lee-Kim VS, Ma XR, Zhou R, Zeng T, Guo K, Taylor MS, Vellarikkal SK, Barry AE, Sias-Garcia O, Bloemendal A, Munson G, Guckelberger P, Nguyen TH, Bergman DT, Hinshaw S, Cheng N, Cleary B, Aragam K, Lander ES, Finucane HK, Mukhopadhyay D, Gupta RM, Engreitz JM. Convergence of coronary artery disease genes onto endothelial cell programs. Nature 2024; 626:799-807. [PMID: 38326615 PMCID: PMC10921916 DOI: 10.1038/s41586-024-07022-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Linking variants from genome-wide association studies (GWAS) to underlying mechanisms of disease remains a challenge1-3. For some diseases, a successful strategy has been to look for cases in which multiple GWAS loci contain genes that act in the same biological pathway1-6. However, our knowledge of which genes act in which pathways is incomplete, particularly for cell-type-specific pathways or understudied genes. Here we introduce a method to connect GWAS variants to functions. This method links variants to genes using epigenomics data, links genes to pathways de novo using Perturb-seq and integrates these data to identify convergence of GWAS loci onto pathways. We apply this approach to study the role of endothelial cells in genetic risk for coronary artery disease (CAD), and discover 43 CAD GWAS signals that converge on the cerebral cavernous malformation (CCM) signalling pathway. Two regulators of this pathway, CCM2 and TLNRD1, are each linked to a CAD risk variant, regulate other CAD risk genes and affect atheroprotective processes in endothelial cells. These results suggest a model whereby CAD risk is driven in part by the convergence of causal genes onto a particular transcriptional pathway in endothelial cells. They highlight shared genes between common and rare vascular diseases (CAD and CCM), and identify TLNRD1 as a new, previously uncharacterized member of the CCM signalling pathway. This approach will be widely useful for linking variants to functions for other common polygenic diseases.
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Affiliation(s)
- Gavin R Schnitzler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Helen Kang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Shi Fang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ramcharan S Angom
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL, USA
| | - Vivian S Lee-Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - X Rosa Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Ronghao Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Tony Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Katherine Guo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shamsudheen K Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Aurelie E Barry
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Oscar Sias-Garcia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
| | - Glen Munson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Tung H Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Drew T Bergman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Stephen Hinshaw
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan Cheng
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Faculty of Computing and Data Sciences, Departments of Biology and Biomedical Engineering, Biological Design Center, and Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Krishna Aragam
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL, USA
| | - Rajat M Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA.
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
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