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Morris JA, Caragine C, Daniloski Z, Domingo J, Barry T, Lu L, Davis K, Ziosi M, Glinos DA, Hao S, Mimitou EP, Smibert P, Roeder K, Katsevich E, Lappalainen T, Sanjana NE. Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens. Science 2023; 380:eadh7699. [PMID: 37141313 PMCID: PMC10518238 DOI: 10.1126/science.adh7699] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci. Using precise variant insertion through base editing, we connected specific variants with gene expression changes. We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs. Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits. This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.
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Affiliation(s)
- John A. Morris
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | | | - Zharko Daniloski
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | | | - Timothy Barry
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Lu Lu
- New York Genome Center, New York, NY, 10013, USA
| | - Kyrie Davis
- New York Genome Center, New York, NY, 10013, USA
| | | | | | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Eleni P. Mimitou
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Eugene Katsevich
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65 Solna, Stockholm, Sweden
| | - Neville E. Sanjana
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
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3
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Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun 2022; 13:7592. [PMID: 36481753 PMCID: PMC9732337 DOI: 10.1038/s41467-022-35354-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
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Affiliation(s)
- Marsha M Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Bjarni V Halldórsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavík, Iceland
| | | | - Jia Wen
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna V Mihkaylova
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Min-Zhi Jiang
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Goo Jun
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Joshua B Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paul S de Vries
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yan Gao
- Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS, 39216, USA
| | - Kai Kammers
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 2115, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Laura Almasy
- Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 2115, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, 5446, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, 1702, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Unnur Þorsteinsdóttir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Magnús K Magnússon
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Nathan D Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98105, USA.
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