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Lv W, Babu A, Morley MP, Musunuru K, Guerraty MA. Resource of Gene Expression Data From a Multiethnic Population Cohort of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004218. [PMID: 38372139 PMCID: PMC11021142 DOI: 10.1161/circgen.123.004218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Affiliation(s)
- Wenjian Lv
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Apoorva Babu
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Michael P Morley
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Kiran Musunuru
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Marie A Guerraty
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
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2
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Pinheiro EA, DeKeyser JM, Lenny B, Sapkota Y, Burridge PW. Nilotinib-induced alterations in endothelial cell function recapitulate clinical vascular phenotypes independent of ABL1. Sci Rep 2024; 14:7123. [PMID: 38532120 DOI: 10.1038/s41598-024-57686-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
Nilotinib is a highly effective treatment for chronic myeloid leukemia but has been consistently associated with the development of nilotinib-induced arterial disease (NAD) in a subset of patients. To date, which cell types mediate this effect and whether NAD results from on-target mechanisms is unknown. We utilized human induced pluripotent stem cells (hiPSCs) to generate endothelial cells and vascular smooth muscle cells for in vitro study of NAD. We found that nilotinib adversely affects endothelial proliferation and migration, in addition to increasing intracellular nitric oxide. Nilotinib did not alter endothelial barrier function or lipid uptake. No effect of nilotinib was observed in vascular smooth muscle cells, suggesting that NAD is primarily mediated through endothelial cells. To evaluate whether NAD results from enhanced inhibition of ABL1, we generated multiple ABL1 knockout lines. The effects of nilotinib remained unchanged in the absence of ABL1, suggesting that NAD results from off- rather than on-target signaling. The model established in the present study can be applied to future mechanistic and patient-specific pharmacogenomic studies.
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Affiliation(s)
- Emily A Pinheiro
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, 320 E Superior St, Searle 8-525, Chicago, IL, 60611, USA
| | - Jean-Marc DeKeyser
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, 320 E Superior St, Searle 8-525, Chicago, IL, 60611, USA
| | - Brian Lenny
- Department of Epidemiology and Cancer Control, St. Jude Children's Hospital, Memphis, TN, 38105, USA
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Hospital, Memphis, TN, 38105, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, 320 E Superior St, Searle 8-525, Chicago, IL, 60611, USA.
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3
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Das S, Hilman MC, Yang F, Mourkioti F, Yang W, Cullen DK. Motor neurons and endothelial cells additively promote development and fusion of human iPSC-derived skeletal myocytes. Skelet Muscle 2024; 14:5. [PMID: 38454511 PMCID: PMC10921694 DOI: 10.1186/s13395-024-00336-4] [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: 08/08/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Neurovascular cells have wide-ranging implications on skeletal muscle biology regulating myogenesis, maturation, and regeneration. Although several in vitro studies have investigated how motor neurons and endothelial cells interact with skeletal myocytes independently, there is limited knowledge about the combined effect of neural and vascular cells on muscle maturation and development. METHODS Here, we report a triculture system comprising human-induced pluripotent stem cell (iPSC)-derived skeletal myocytes, human iPSC-derived motor neurons, and primary human endothelial cells maintained under controlled media conditions. Briefly, iPSCs were differentiated to generate skeletal muscle progenitor cells (SMPCs). These SMPCs were seeded at a density of 5 × 104 cells/well in 12-well plates and allowed to differentiate for 7 days before adding iPSC-derived motor neurons at a concentration of 0.5 × 104 cells/well. The neuromuscular coculture was maintained for another 7 days in coculture media before addition of primary human umbilical vein endothelial cells (HUVEC) also at 0.5 × 104 cells/well. The triculture was maintained for another 7 days in triculture media comprising equal portions of muscle differentiation media, coculture media, and vascular media. Extensive morphological, genetic, and molecular characterization was performed to understand the combined and individual effects of neural and vascular cells on skeletal muscle maturation. RESULTS We observed that motor neurons independently promoted myofiber fusion, upregulated neuromuscular junction genes, and maintained a molecular niche supportive of muscle maturation. Endothelial cells independently did not support myofiber fusion and downregulated expression of LRP4 but did promote expression of type II specific myosin isoforms. However, neurovascular cells in combination exhibited additive increases in myofiber fusion and length, enhanced production of Agrin, along with upregulation of several key genes like MUSK, RAPSYN, DOK-7, and SLC2A4. Interestingly, more divergent effects were observed in expression of genes like MYH8, MYH1, MYH2, MYH4, and LRP4 and secretion of key molecular factors like amphiregulin and IGFBP-4. CONCLUSIONS Neurovascular cells when cultured in combination with skeletal myocytes promoted myocyte fusion with concomitant increase in expression of various neuromuscular genes. This triculture system may be used to gain a deeper understanding of the effects of the neurovascular niche on skeletal muscle biology and pathophysiology.
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Affiliation(s)
- Suradip Das
- Department of Neurosurgery, Center for Brain Injury & Repair, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA, 19104, USA.
| | - Melanie C Hilman
- Department of Neurosurgery, Center for Brain Injury & Repair, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA, 19104, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Feikun Yang
- Department of Medicine, Penn Institute for Regenerative Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Foteini Mourkioti
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Musculoskeletal Program, Penn Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wenli Yang
- Department of Medicine, Penn Institute for Regenerative Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - D Kacy Cullen
- Department of Neurosurgery, Center for Brain Injury & Repair, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center for Neurotrauma, Neurodegeneration & Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA, 19104, USA.
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Musculoskeletal Program, Penn Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Connor L, Carpenter AE, Singh S, Nehme R, Raychaudhuri S. High-dimensional phenotyping to define the genetic basis of cellular morphology. Nat Commun 2024; 15:347. [PMID: 38184653 PMCID: PMC10771466 DOI: 10.1038/s41467-023-44045-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/28/2023] [Indexed: 01/08/2024] Open
Abstract
The morphology of cells is dynamic and mediated by genetic and environmental factors. Characterizing how genetic variation impacts cell morphology can provide an important link between disease association and cellular function. Here, we combine genomic sequencing and high-content imaging approaches on iPSCs from 297 unique donors to investigate the relationship between genetic variants and cellular morphology to map what we term cell morphological quantitative trait loci (cmQTLs). We identify novel associations between rare protein altering variants in WASF2, TSPAN15, and PRLR with several morphological traits related to cell shape, nucleic granularity, and mitochondrial distribution. Knockdown of these genes by CRISPRi confirms their role in cell morphology. Analysis of common variants yields one significant association and nominate over 300 variants with suggestive evidence (P < 10-6) of association with one or more morphology traits. We then use these data to make predictions about sample size requirements for increasing discovery in cellular genetic studies. We conclude that, similar to molecular phenotypes, morphological profiling can yield insight about the function of genes and variants.
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Affiliation(s)
- Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Centre for Gene Therapy and Regenerative Medicine, King's College, London, UK
| | - Jatin Arora
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samira Asgari
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ajay Nadig
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Peirent
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dhara Liyanage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory P Way
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tiffany Amariuta
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Halıcıoğlu Data Science Institute, University of California, La Jolla, CA, USA
- Department of Medicine, University of California, La Jolla, CA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Marzieh Haghighi
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke O'Connor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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5
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Du Z, Iyyanki T, Lessard S, Chao M, Asbrand C, Nassar D, Klinger K, de Rinaldis E, Khader S, Chatelain C. Genome-wide association study analysis of disease severity in Acne reveals novel biological insights. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.13.23298473. [PMID: 38014089 PMCID: PMC10680891 DOI: 10.1101/2023.11.13.23298473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Acne vulgaris is a common skin disease that affects >85% of teenage young adults among which >8% develop severe lesions that leaves permanent scars. Genetic heritability studies of acne in twin cohorts have estimated that the heritability for acne is 80%. Previous genome-wide association studies (GWAS) have identified 50 genetic loci associated with increased risk of developing acne when compared to healthy individuals. However only a few studies have investigated genetic association with disease severity. GWAS of disease progression may provide a more effective approach to unveil potential disease modifying therapeutic targets. Here, we performed a multi-ethnic GWAS analysis to capture disease severity in acne patients by using individuals with normal acne as a control. Our cohort consists of a total of 2,956 participants, including 290 severe acne cases and 930 normal acne controls from FinnGen, and 522 cases and 1,214 controls from BioVU. We also performed mendelian randomization (MR), colocalization analyses and transcriptome-wide association study (TWAS) to identify putative causal genes. Lastly, we performed gene-set enrichment analysis using MAGMA to implicate biological pathways that drive disease severity in Acne. We identified two new loci associated with acne severity at the genome-wide significance level, six novel associated genes by MR, colocalization and TWAS analyses, including genes CDC7, SLC7A1, ADAM23, TTLL10, CDK20 and DNAJA4 , and 5 novel pathways by MAGMA analyses. Our study suggests that the etiologies of acne susceptibility and severity have limited overlap, with only 26% of known acne risk loci presenting nominal association with acne severity and none of the novel severity associated genes reported as associated with acne risk in previous GWAS.
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Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nat Rev Genet 2023; 24:687-711. [PMID: 36737647 PMCID: PMC9897628 DOI: 10.1038/s41576-022-00568-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/05/2023]
Abstract
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.
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Affiliation(s)
- Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Umut Kilik
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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7
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs. PLoS Genet 2023; 19:e1010932. [PMID: 37721944 PMCID: PMC10538656 DOI: 10.1371/journal.pgen.1010932] [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: 04/17/2023] [Revised: 09/28/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023] Open
Abstract
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex traits. Over the past two years, we have increased the number of uniformly processed studies from 21 to 31 and added X chromosome QTLs for 19 compatible studies. We have also implemented Leafcutter to directly identify splice-junction usage QTLs in all RNA sequencing datasets. Finally, to improve the interpretability of transcript-level QTLs, we have developed static QTL coverage plots that visualise the association between the genotype and average RNA sequencing read coverage in the region for all 1.7 million fine mapped associations. To illustrate the utility of these updates to the eQTL Catalogue, we performed colocalisation analysis between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. Although most GWAS loci colocalised both with eQTLs and transcript-level QTLs, we found that visual inspection could sometimes be used to distinguish primary splicing QTLs from those that appear to be secondary consequences of large-effect gene expression QTLs. While these visually confirmed primary splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - James D. Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Hans J. Teras
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - William Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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8
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Shevade K, Peddada S, Mader K, Przybyla L. Functional genomics in stem cell models: considerations and applications. Front Cell Dev Biol 2023; 11:1236553. [PMID: 37554308 PMCID: PMC10404852 DOI: 10.3389/fcell.2023.1236553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Protocols to differentiate human pluripotent stem cells have advanced in terms of cell type specificity and tissue-level complexity over the past 2 decades, which has facilitated human disease modeling in the most relevant cell types. The ability to generate induced PSCs (iPSCs) from patients further enables the study of disease mutations in an appropriate cellular context to reveal the mechanisms that underlie disease etiology and progression. As iPSC-derived disease models have improved in robustness and scale, they have also been adopted more widely for use in drug screens to discover new therapies and therapeutic targets. Advancement in genome editing technologies, in particular the discovery of CRISPR-Cas9, has further allowed for rapid development of iPSCs containing disease-causing mutations. CRISPR-Cas9 technologies have now evolved beyond creating single gene edits, aided by the fusion of inhibitory (CRISPRi) or activation (CRISPRa) domains to a catalytically dead Cas9 protein, enabling inhibition or activation of endogenous gene loci. These tools have been used in CRISPR knockout, CRISPRi, or CRISPRa screens to identify genetic modifiers that synergize or antagonize with disease mutations in a systematic and unbiased manner, resulting in identification of disease mechanisms and discovery of new therapeutic targets to accelerate drug discovery research. However, many technical challenges remain when applying large-scale functional genomics approaches to differentiated PSC populations. Here we review current technologies in the field of iPSC disease modeling and CRISPR-based functional genomics screens and practical considerations for implementation across a range of modalities, applications, and disease areas, as well as explore CRISPR screens that have been performed in iPSC models to-date and the insights and therapies these screens have produced.
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Affiliation(s)
- Kaivalya Shevade
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Sailaja Peddada
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Karl Mader
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Laralynne Przybyla
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
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Luo Q, Wang N, Que H, Mai E, Hu Y, Tan R, Gu J, Gong P. Pluripotent Stem Cell-Derived Hepatocyte-like Cells: Induction Methods and Applications. Int J Mol Sci 2023; 24:11592. [PMID: 37511351 PMCID: PMC10380504 DOI: 10.3390/ijms241411592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The development of regenerative medicine provides new options for the treatment of end-stage liver diseases. Stem cells, such as bone marrow mesenchymal stem cells, embryonic stem cells, and induced pluripotent stem cells (iPSCs), are effective tools for tissue repair in regenerative medicine. iPSCs are an appropriate source of hepatocytes for the treatment of liver disease due to their unlimited multiplication capacity, their coverage of the entire range of genetics required to simulate human disease, and their evasion of ethical implications. iPSCs have the ability to gradually produce hepatocyte-like cells (HLCs) with homologous phenotypes and physiological functions. However, how to induce iPSCs to differentiate into HLCs efficiently and accurately is still a hot topic. This review describes the existing approaches for inducing the differentiation of iPSCs into HLCs, as well as some challenges faced, and summarizes various parameters for determining the quality and functionality of HLCs. Furthermore, the application of iPSCs for in vitro hepatoprotective drug screening and modeling of liver disease is discussed. In conclusion, iPSCs will be a dependable source of cells for stem-cell therapy to treat end-stage liver disease and are anticipated to facilitate individualized treatment for liver disease in the future.
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Affiliation(s)
- Qiulin Luo
- College of Pharmacy, Southwest Minzu University, Chengdu 610225, China
| | - Nan Wang
- College of Pharmacy, Southwest Minzu University, Chengdu 610225, China
| | - Hanyun Que
- College of Pharmacy, Southwest Minzu University, Chengdu 610225, China
| | - Erziya Mai
- College of Pharmacy, Southwest Minzu University, Chengdu 610225, China
| | - Yanting Hu
- College of Pharmacy, Southwest Minzu University, Chengdu 610225, China
| | - Rui Tan
- College of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610032, China
| | - Jian Gu
- College of Pharmacy, Southwest Minzu University, Chengdu 610225, China
| | - Puyang Gong
- College of Pharmacy, Southwest Minzu University, Chengdu 610225, China
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10
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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: 36] [Impact Index Per Article: 36.0] [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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11
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535816. [PMID: 37066341 PMCID: PMC10104061 DOI: 10.1101/2023.04.06.535816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data normalisation which often renders the direction of the genetic effect as well as its magnitude difficult to interpret. This is further complicated by the fact that strong expression QTLs often manifest as weak splicing QTLs and vice versa, making it difficult to uniquely identify the underlying molecular mechanism at each locus. We find that these ambiguities can be mitigated by visualising the association between the genotype and average RNA sequencing read coverage in the region. Here, we generate these QTL coverage plots for 1.7 million molecular QTL associations in the eQTL Catalogue identified with five quantification methods. We illustrate the utility of these QTL coverage plots by performing colocalisation between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. We find that while visually confirmed splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases. All our association summary statistics and QTL coverage plots are freely available at https://www.ebi.ac.uk/eqtl/.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - James D Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Hans J Teras
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Will Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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12
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Sakata Y, Cheng K, Mayama M, Seita Y, Detlefsen AJ, Mesaros CA, Penning TM, Shishikura K, Yang W, Auchus RJ, Strauss JF, Sasaki K. Reconstitution of human adrenocortical specification and steroidogenesis using induced pluripotent stem cells. Dev Cell 2022; 57:2566-2583.e8. [PMID: 36413950 PMCID: PMC9927873 DOI: 10.1016/j.devcel.2022.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/18/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022]
Abstract
The mechanisms leading to adrenal cortex development and steroid synthesis in humans remain poorly understood due to the paucity of model systems. Herein, we recapitulate human fetal adrenal cortex specification processes through stepwise induction of human-induced pluripotent stem cells through posterior intermediate mesoderm-like and adrenocortical progenitor-like states to ultimately generate fetal zone adrenal-cortex-like cells (FZLCs), as evidenced by histomorphological, ultrastructural, and transcriptome features and adrenocorticotropic hormone (ACTH)-independent Δ5 steroid biosynthesis. Furthermore, FZLC generation is promoted by SHH and inhibited by NOTCH, ACTIVIN, and WNT signaling, and steroid synthesis is amplified by ACTH/PKA signaling and blocked by inhibitors of Δ5 steroid synthesis enzymes. Finally, NR5A1 promotes FZLC survival and steroidogenesis. Together, these findings provide a framework for understanding and reconstituting human adrenocortical development in vitro, paving the way for cell-based therapies of adrenal insufficiency.
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Affiliation(s)
- Yuka Sakata
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,These authors contributed equally to this work
| | - Keren Cheng
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,These authors contributed equally to this work
| | - Michinori Mayama
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,These authors contributed equally to this work
| | - Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Bell Research Center for Reproductive Health and Cancer, Nagoya 460-0003, Japan
| | - Andrea J. Detlefsen
- Department of Biochemistry and Biophysics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clementina A. Mesaros
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Trevor M. Penning
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyosuke Shishikura
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenli Yang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Richard J. Auchus
- Division of Metabolism, Endocrinology, and Diabetes, Departments of Internal Medicine and Pharmacology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Jerome F. Strauss
- Department of Obstetrics and Gynecology, University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
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13
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Transplanted human induced pluripotent stem cells- derived retinal ganglion cells embed within mouse retinas and are electrophysiologically functional. iScience 2022; 25:105308. [DOI: 10.1016/j.isci.2022.105308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/22/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
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14
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Patoori S, Barnada SM, Large C, Murray JI, Trizzino M. Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors. Development 2022; 149:276504. [PMID: 36052683 PMCID: PMC9641669 DOI: 10.1242/dev.200413] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 08/21/2022] [Indexed: 01/19/2023]
Abstract
The hippocampus is associated with essential brain functions, such as learning and memory. Human hippocampal volume is significantly greater than expected compared with that of non-human apes, suggesting a recent expansion. Intermediate progenitors, which are able to undergo multiple rounds of proliferative division before a final neurogenic division, may have played a role in evolutionary hippocampal expansion. To investigate the evolution of gene regulatory networks underpinning hippocampal neurogenesis in apes, we leveraged the differentiation of human and chimpanzee induced pluripotent stem cells into TBR2 (or EOMES)-positive hippocampal intermediate progenitor cells (hpIPCs). We found that the gene networks active in hpIPCs are significantly different between humans and chimpanzees, with ∼2500 genes being differentially expressed. We demonstrate that species-specific transposon-derived enhancers contribute to these transcriptomic differences. Young transposons, predominantly endogenous retroviruses and SINE-Vntr-Alus (SVAs), were co-opted as enhancers in a species-specific manner. Human-specific SVAs provided substrates for thousands of novel TBR2-binding sites, and CRISPR-mediated repression of these SVAs attenuated the expression of ∼25% of the genes that are upregulated in human intermediate progenitors relative to the same cell population in the chimpanzee.
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Affiliation(s)
- Sruti Patoori
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Samantha M. Barnada
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Christopher Large
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John I. Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA,Author for correspondence ()
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15
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Ramdas S, Judd J, Graham SE, Kanoni S, Wang Y, Surakka I, Wenz B, Clarke SL, Chesi A, Wells A, Bhatti KF, Vedantam S, Winkler TW, Locke AE, Marouli E, Zajac GJM, Wu KHH, Ntalla I, Hui Q, Klarin D, Hilliard AT, Wang Z, Xue C, Thorleifsson G, Helgadottir A, Gudbjartsson DF, Holm H, Olafsson I, Hwang MY, Han S, Akiyama M, Sakaue S, Terao C, Kanai M, Zhou W, Brumpton BM, Rasheed H, Havulinna AS, Veturi Y, Pacheco JA, Rosenthal EA, Lingren T, Feng Q, Kullo IJ, Narita A, Takayama J, Martin HC, Hunt KA, Trivedi B, Haessler J, Giulianini F, Bradford Y, Miller JE, Campbell A, Lin K, Millwood IY, Rasheed A, Hindy G, Faul JD, Zhao W, Weir DR, Turman C, Huang H, Graff M, Choudhury A, Sengupta D, Mahajan A, Brown MR, Zhang W, Yu K, Schmidt EM, Pandit A, Gustafsson S, Yin X, Luan J, Zhao JH, Matsuda F, Jang HM, Yoon K, Medina-Gomez C, Pitsillides A, Hottenga JJ, Wood AR, Ji Y, Gao Z, Haworth S, Mitchell RE, Chai JF, Aadahl M, Bjerregaard AA, Yao J, Manichaikul A, Lee WJ, Hsiung CA, Warren HR, Ramirez J, Bork-Jensen J, Kårhus LL, Goel A, Sabater-Lleal M, Noordam R, Mauro P, Matteo F, McDaid AF, Marques-Vidal P, Wielscher M, Trompet S, Sattar N, Møllehave LT, Munz M, Zeng L, Huang J, Yang B, Poveda A, Kurbasic A, Schönherr S, Forer L, Scholz M, Galesloot TE, Bradfield JP, Ruotsalainen SE, Daw EW, Zmuda JM, Mitchell JS, Fuchsberger C, Christensen H, Brody JA, Le P, Feitosa MF, Wojczynski MK, Hemerich D, Preuss M, Mangino M, Christofidou P, Verweij N, Benjamins JW, Engmann J, Noah TL, Verma A, Slieker RC, Lo KS, Zilhao NR, Kleber ME, Delgado GE, Huo S, Ikeda DD, Iha H, Yang J, Liu J, Demirkan A, Leonard HL, Marten J, Emmel C, Schmidt B, Smyth LJ, Cañadas-Garre M, Wang C, Nakatochi M, Wong A, Hutri-Kähönen N, Sim X, Xia R, Huerta-Chagoya A, Fernandez-Lopez JC, Lyssenko V, Nongmaithem SS, Sankareswaran A, Irvin MR, Oldmeadow C, Kim HN, Ryu S, Timmers PRHJ, Arbeeva L, Dorajoo R, Lange LA, Prasad G, Lorés-Motta L, Pauper M, Long J, Li X, Theusch E, Takeuchi F, Spracklen CN, Loukola A, Bollepalli S, Warner SC, Wang YX, Wei WB, Nutile T, Ruggiero D, Sung YJ, Chen S, Liu F, Yang J, Kentistou KA, Banas B, Morgan A, Meidtner K, Bielak LF, Smith JA, Hebbar P, Farmaki AE, Hofer E, Lin M, Concas MP, Vaccargiu S, van der Most PJ, Pitkänen N, Cade BE, van der Laan SW, Chitrala KN, Weiss S, Bentley AR, Doumatey AP, Adeyemo AA, Lee JY, Petersen ERB, Nielsen AA, Choi HS, Nethander M, Freitag-Wolf S, Southam L, Rayner NW, Wang CA, Lin SY, Wang JS, Couture C, Lyytikäinen LP, Nikus K, Cuellar-Partida G, Vestergaard H, Hidalgo B, Giannakopoulou O, Cai Q, Obura MO, van Setten J, He KY, Tang H, Terzikhan N, Shin JH, Jackson RD, Reiner AP, Martin LW, Chen Z, Li L, Kawaguchi T, Thiery J, Bis JC, Launer LJ, Li H, Nalls MA, Raitakari OT, Ichihara S, Wild SH, Nelson CP, Campbell H, Jäger S, Nabika T, Al-Mulla F, Niinikoski H, Braund PS, Kolcic I, Kovacs P, Giardoglou T, Katsuya T, de Kleijn D, de Borst GJ, Kim EK, Adams HHH, Ikram MA, Zhu X, Asselbergs FW, Kraaijeveld AO, Beulens JWJ, Shu XO, Rallidis LS, Pedersen O, Hansen T, Mitchell P, Hewitt AW, Kähönen M, Pérusse L, Bouchard C, Tönjes A, Ida Chen YD, Pennell CE, Mori TA, Lieb W, Franke A, Ohlsson C, Mellström D, Cho YS, Lee H, Yuan JM, Koh WP, Rhee SY, Woo JT, Heid IM, Stark KJ, Zimmermann ME, Völzke H, Homuth G, Evans MK, Zonderman AB, Polasek O, Pasterkamp G, Hoefer IE, Redline S, Pahkala K, Oldehinkel AJ, Snieder H, Biino G, Schmidt R, Schmidt H, Bandinelli S, Dedoussis G, Thanaraj TA, Peyser PA, Kato N, Schulze MB, Girotto G, Böger CA, Jung B, Joshi PK, Bennett DA, De Jager PL, Lu X, Mamakou V, Brown M, Caulfield MJ, Munroe PB, Guo X, Ciullo M, Jonas JB, Samani NJ, Kaprio J, Pajukanta P, Tusié-Luna T, Aguilar-Salinas CA, Adair LS, Bechayda SA, de Silva HJ, Wickremasinghe AR, Krauss RM, Wu JY, Zheng W, den Hollander AI, Bharadwaj D, Correa A, Wilson JG, Lind L, Heng CK, Nelson AE, Golightly YM, Wilson JF, Penninx B, Kim HL, Attia J, Scott RJ, Rao DC, Arnett DK, Walker M, Scott LJ, Koistinen HA, Chandak GR, Mercader JM, Villalpando CG, Orozco L, Fornage M, Tai ES, van Dam RM, Lehtimäki T, Chaturvedi N, Yokota M, Liu J, Reilly DF, McKnight AJ, Kee F, Jöckel KH, McCarthy MI, Palmer CNA, Vitart V, Hayward C, Simonsick E, van Duijn CM, Jin ZB, Lu F, Hishigaki H, Lin X, März W, Gudnason V, Tardif JC, Lettre G, T Hart LM, Elders PJM, Rader DJ, Damrauer SM, Kumari M, Kivimaki M, van der Harst P, Spector TD, Loos RJF, Province MA, Parra EJ, Cruz M, Psaty BM, Brandslund I, Pramstaller PP, Rotimi CN, Christensen K, Ripatti S, Widén E, Hakonarson H, Grant SFA, Kiemeney L, de Graaf J, Loeffler M, Kronenberg F, Gu D, Erdmann J, Schunkert H, Franks PW, Linneberg A, Jukema JW, Khera AV, Männikkö M, Jarvelin MR, Kutalik Z, Francesco C, Mook-Kanamori DO, Willems van Dijk K, Watkins H, Strachan DP, Grarup N, Sever P, Poulter N, Huey-Herng Sheu W, Rotter JI, Dantoft TM, Karpe F, Neville MJ, Timpson NJ, Cheng CY, Wong TY, Khor CC, Li H, Sabanayagam C, Peters A, Gieger C, Hattersley AT, Pedersen NL, Magnusson PKE, Boomsma DI, de Geus EJC, Cupples LA, van Meurs JBJ, Ikram A, Ghanbari M, Gordon-Larsen P, Huang W, Kim YJ, Tabara Y, Wareham NJ, Langenberg C, Zeggini E, Tuomilehto J, Kuusisto J, Laakso M, Ingelsson E, Abecasis G, Chambers JC, Kooner JS, de Vries PS, Morrison AC, Hazelhurst S, Ramsay M, North KE, Daviglus M, Kraft P, Martin NG, Whitfield JB, Abbas S, Saleheen D, Walters RG, Holmes MV, Black C, Smith BH, Baras A, Justice AE, Buring JE, Ridker PM, Chasman DI, Kooperberg C, Tamiya G, Yamamoto M, van Heel DA, Trembath RC, Wei WQ, Jarvik GP, Namjou B, Hayes MG, Ritchie MD, Jousilahti P, Salomaa V, Hveem K, Åsvold BO, Kubo M, Kamatani Y, Okada Y, Murakami Y, Kim BJ, Thorsteinsdottir U, Stefansson K, Zhang J, Chen YE, Ho YL, Lynch JA, Tsao PS, Chang KM, Cho K, O'Donnell CJ, Gaziano JM, Wilson P, Mohlke KL, Frayling TM, Hirschhorn JN, Kathiresan S, Boehnke M, Struan Grant, Natarajan P, Sun YV, Morris AP, Deloukas P, Peloso G, Assimes TL, Willer CJ, Zhu X, Brown CD. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids. Am J Hum Genet 2022; 109:1366-1387. [PMID: 35931049 PMCID: PMC9388392 DOI: 10.1016/j.ajhg.2022.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
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Affiliation(s)
- Shweta Ramdas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Judd
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brandon Wenz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shoa L Clarke
- VA Palo Alto Health Care Systems, Palo Alto, CA, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alessandra Chesi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Wells
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Konain Fatima Bhatti
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Sailaja Vedantam
- Endocrinology, Boston Childrens Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Adam E Locke
- McDonnell Genome Institute and Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Eirini Marouli
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Greg J M Zajac
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kuan-Han H Wu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ioanna Ntalla
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA; Atlanta VA Health Care System, Decatur, GA, USA
| | - Derek Klarin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Malcolm Randall VA Medical Center, Gainesville, FL, USA; Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville, FL, USA
| | | | - Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA; Atlanta VA Health Care System, Decatur, GA, USA
| | - Chao Xue
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anna Helgadottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 102, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 102, Iceland; School of Engineering and Natural Sciences, University of Iceland, Sæmundargötu 2, Reykjavik 102, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 102, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali - National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Chungbuk, South Korea
| | - Sohee Han
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Chungbuk, South Korea
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, The University of Tokyo, Tokyo, Japan; Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ben M Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, BS8 2BN Bristol, UK; Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Humaira Rasheed
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, BS8 2BN Bristol, UK; Division of Medicine and Laboratory Sciences, University of Oslo, Oslo, Norway
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, 00014 Helsinki, Finland; Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Yogasudha Veturi
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer Allen Pacheco
- Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA, USA
| | - Todd Lingren
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN, USA
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Jun Takayama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | | | - Karen A Hunt
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Bhavi Trivedi
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jeffrey Haessler
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Yuki Bradford
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jason E Miller
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, EH4 2XU Edinburgh, UK; Usher Institute, The University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, EH16 4UX Edinburgh, UK
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK
| | - Iona Y Millwood
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, SD, Pakistan & Faisalabad Institute of Cardiology, Faislabad, Pakistan
| | - George Hindy
- Department of Population Medicine, Qatar University College of Medicine, QU Health, Doha, Qatar
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Hongyan Huang
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Michael R Brown
- Human Genetics Center, 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
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG London, UK; Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, UB1 3HW Middlesex, UK; Imperial College Healthcare NHS Trust, Imperial College London, W12 0HS London, UK
| | - Ketian Yu
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Ellen M Schmidt
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Anita Pandit
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Xianyong Yin
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, CB2 0QQ Cambridge, UK
| | - Jing-Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, CB1 8RN Cambridge, UK
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hye-Mi Jang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Chungbuk, South Korea
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Chungbuk, South Korea
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Achilleas Pitsillides
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, the Netherlands
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Yingji Ji
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Zishan Gao
- Department of Clinical Acupuncture and Moxibustion, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210029, China; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Simon Haworth
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, BS8 2BN Bristol, UK; Bristol Dental School, University of Bristol, Lower Maudlin Street, BS1 2LY Bristol, UK
| | - Ruth E Mitchell
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, BS8 2BN Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield Grove, BS8 2BN Bristol, UK
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Mette Aadahl
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne A Bjerregaard
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan; No. 1650, Sec. 4, Taiwan Boulevard, Taichung City 40705, Taiwan
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Helen R Warren
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK; NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Julia Ramirez
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line L Kårhus
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Anuj Goel
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU Oxford, UK
| | - Maria Sabater-Lleal
- Unit of Genomics of Complex Diseases. Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain; Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Pala Mauro
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Floris Matteo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Rome, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sardinia, Italy
| | - Aaron F McDaid
- University Center for Primary Care and Public Health, University of Lausanne, Rte de Berne 113, 1010 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG London, UK
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands; Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, Glasgow, UK
| | - Line T Møllehave
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Matthias Munz
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Heart Center Lübeck, Lübeck and Charité - University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Dental and Craniofacial Sciences, Department of Periodontology and Synoptic Dentistry, Berlin, Germany
| | - Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany; Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK) e.V., partner site Munich Heart Alliance, Munich, Germany
| | - Jianfeng Huang
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Bin Yang
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Alaitz Poveda
- Lund University Diabetes Centre, Lunds University, Malmö, Sweden
| | - Azra Kurbasic
- Lund University Diabetes Centre, Lunds University, Malmö, Sweden
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria and German Chronic Kidney Disease Study, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria and German Chronic Kidney Disease Study, Austria
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany; LIFE Research Centre for Civilization Diseases, University of Leipzig, Philipp-Rosenthal-Straße 27, 04103 Leipzig, Germany
| | - Tessel E Galesloot
- Radboud university medical center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | | | - Sanni E Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, 00014 Helsinki, Finland
| | - E Warwick Daw
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph M Zmuda
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Jonathan S Mitchell
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Christian Fuchsberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Henry Christensen
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Phuong Le
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daiane Hemerich
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, SE1 7EH London, UK; NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, SE1 9RT London, UK
| | - Paraskevi Christofidou
- Department of Twin Research and Genetic Epidemiology, King's College London, SE1 7EH London, UK
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, the Netherlands
| | - Jan W Benjamins
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, the Netherlands
| | - Jorgen Engmann
- Institute of Cardiovascular Sciences, University College London, Gower Street, WC1E 6BT London, UK; Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, WC1E 6BT London, UK
| | - Tsao L Noah
- Department of Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roderick C Slieker
- Amsterdam UMC, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam 1081HV, the Netherlands; Leiden University Medical Center, Department of Cell and Chemical Biology, Leiden 2333ZA, the Netherlands
| | - Ken Sin Lo
- Montreal Heart Institute, Université de Montréal, 5000 Belanger street, Montreal, QC H1T1C8, Canada
| | | | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; SYNLAB MVZ Humangenetik Mannheim GmbH, 68163 Mannheim, Germany
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Shaofeng Huo
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Daisuke D Ikeda
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Hiroyuki Iha
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK; Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Ayşe Demirkan
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Section of Statistical Multi-omics, Department of Clinical and Experimental research, University of Surrey, Guildford, Surrey, UK
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA; Data Tecnica International, Glen Echo, MD, USA
| | - Jonathan Marten
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Carina Emmel
- Institute for Medical Informatics, Biometrie and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Börge Schmidt
- Institute for Medical Informatics, Biometrie and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Laura J Smyth
- Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - Marisa Cañadas-Garre
- Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland; Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain; Hematology Department, Hospital Universitario Virgen de las Nieves, Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya 461-8673, Japan
| | - Andrew Wong
- University of Alabama at Birmingham, Epidemiology, School of Public Health, Birmingham, AL, USA
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Rui Xia
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX 77030, USA
| | - Alicia Huerta-Chagoya
- CONACYT, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | | | - Valeriya Lyssenko
- Lund University Diabetes Centre, Lunds University, Malmö, Sweden; Center for diabetes research, University of Bergen, Bergen, Norway
| | - Suraj S Nongmaithem
- Genomic Research on Complex diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Alagu Sankareswaran
- Genomic Research on Complex diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, New Delhi, India
| | - Marguerite R Irvin
- University of Alabama at Birmingham, Epidemiology, School of Public Health, Birmingham, AL, USA
| | | | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; Department of Clinical Research Design & Evaluation, SAIHST, Sungkyunkwan University, Seoul 06355, Korea
| | - Seungho Ryu
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 04514, Korea; Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea
| | - Paul R H J Timmers
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Liubov Arbeeva
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore; Health Services and Systems Research, Duke-NUS Medical School, 169857, Singapore
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, Anschutz Medical Campus, University of Colorado, Denver, Aurora, CO 80045, USA
| | - Gauri Prasad
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, New Delhi, India; Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110020, India
| | - Laura Lorés-Motta
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Philips van Leydenlaan 15, Nijmegen 6525 EX, the Netherlands
| | - Marc Pauper
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Philips van Leydenlaan 15, Nijmegen 6525 EX, the Netherlands
| | - Jirong Long
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA 94609, USA
| | - Fumihiko Takeuchi
- National Center for Global Health and Medicine, Tokyo 1628655, Japan
| | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, MA 01003, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, 00014 Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, 00014 Helsinki, Finland
| | - Sophie C Warner
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, 17 Hougou Lane, Chong Wen Men, Beijing 100005, China
| | - Wen B Wei
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Dong Cheng District, Beijing 100730, China
| | - Teresa Nutile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso" - CNR, Naples, Italy
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso" - CNR, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shufeng Chen
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Fangchao Liu
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Bernhard Banas
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Anna Morgan
- Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34127 Trieste, Italy
| | - Karina Meidtner
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA; Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Prashantha Hebbar
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Eleftheriou Venizelou, Athens, Greece; Department of Population Science and Experimental Medicine, University College London, London, UK
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria; Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Maoxuan Lin
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34127 Trieste, Italy
| | - Simona Vaccargiu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Sassari, Italy
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Brian E Cade
- Sleep Medicine and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Science National Institute on Aging Intramural Research Program, NIH 251 Bayview Blvd, NIH Biomedical Research Center, Baltimore, MD 21224, USA; Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University of Greifswald and University Medicine Greifswald, Greifswald, Germany
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Room 4047, Bethesda, MD 20892, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Room 4047, Bethesda, MD 20892, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Room 4047, Bethesda, MD 20892, USA
| | - Jong Young Lee
- Oneomics. co. ltd. 2F, Soonchunhyang Mirai Medical Center 173, Buheuyng-ro, Bucheon-si Gyeonggi-do 14585, Korea
| | - Eva R B Petersen
- Department of Clinical Biochemistry and Immunology, Hospital of Southern Jutland, Kresten Philipsens Vej 15, 6200 Aabenraa, Denmark
| | - Aneta A Nielsen
- Department of Clinical Biochemistry, Lillebaelt Hospital, Kolding, Denmark
| | - Hyeok Sun Choi
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon 24252, Korea
| | - Maria Nethander
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Lorraine Southam
- Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK; Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nigel W Rayner
- Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, UK
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Shih-Yi Lin
- Center for Geriatrics and Gerontology, Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan; School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Jun-Sing Wang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Department of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Christian Couture
- Department of Kinesiology, Université Laval, Quebec City, QC, Canada
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, 33520 Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, 33521 Tampere, Finland; Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Gabriel Cuellar-Partida
- University of Queensland Diamantina Institute, Translational Research Institute, Kent St, Woolloongabba, Brisbane, QLD 4102, Australia
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Bertha Hidalgo
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olga Giannakopoulou
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Qiuyin Cai
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Morgan O Obura
- Amsterdam UMC, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam 1081HV, the Netherlands
| | - Jessica van Setten
- Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Karen Y He
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Jae Hun Shin
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon 24252, Korea
| | - Rebecca D Jackson
- Ohio State University, Division of Endricinology, Columbus, OH 43210, USA
| | - Alexander P Reiner
- University of Washington, Department of Epidemiology, Seattle, WA 98195, USA
| | - Lisa Warsinger Martin
- George Washington University, School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK
| | - Liming Li
- Department of Epidemiology, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Joachim Thiery
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Philipp-Rosenthal-Straße 27, 04103 Leipzig, Germany; Institute for Laboratory Medicine, University Hospital Leipzig, Paul-List-Strasse 13/15, 04103 Leipzig, Germany
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD 20892-9205, USA
| | - Huaixing Li
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD, USA; Data Tecnica International, Glen Echo, MD, USA
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke 329-0498, Japan
| | - Sarah H Wild
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Susanne Jäger
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Harri Niinikoski
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland; Department of Physiology, University of Turku, Turku, Finland
| | - Peter S Braund
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Šoltanska 2, 21000 Split, Croatia
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Liebigstr. 21, 04103 Leipzig, Germany
| | - Tota Giardoglou
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Eleftheriou Venizelou, Athens, Greece
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita 5650871, Japan; Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita 5650871, Japan
| | - Dominique de Kleijn
- Department of Vascular Surgery, Division of Surgical Specialties, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gert J de Borst
- Department of Vascular Surgery, Division of Surgical Specialties, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Eung Kweon Kim
- Corneal Dystrophy Research Institute, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hieab H H Adams
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Folkert W Asselbergs
- Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Adriaan O Kraaijeveld
- Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Joline W J Beulens
- Amsterdam UMC, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam 1081HV, the Netherlands; Julius Centre for Health Sciences and Primary Care, University Medical Ceslrntre Utrecht, Utrecht 3584CG, the Netherlands
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Loukianos S Rallidis
- Second Department of Cardiology, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paul Mitchell
- Center for Vision Research, Department of Ophthalmology and The Westmead Institute, University of Sydney, Hawkesbury Rd, Sydney, NSW 2145, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Liverpool St, Hobart, TAS 7000, Australia; Centre for Eye Research Australia, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, 33521 Tampere, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Louis Pérusse
- Department of Kinesiology, Université Laval, Quebec City, QC, Canada; Centre Nutrition, santé et société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Quebec, QC, Canada
| | - Claude Bouchard
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Liebigstr. 21, 04103 Leipzig, Germany
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Trevor A Mori
- Discipline of Internal Medicine, Medical School, The University of Western Australia, Perth, WA, Australia
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Drug Treatment, Gothenburg, Sweden
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Geriatric Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon 24252, Korea
| | - Hyejin Lee
- Department of Internal Medicine, EwhaWomans University School of Medicine, Seoul, Korea
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15232, USA; Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A∗STAR), Singapore 117609, Singapore
| | - Sang Youl Rhee
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul 02447, Korea
| | - Jeong-Taek Woo
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine, Seoul 02447, Korea
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Martina E Zimmermann
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University of Greifswald and University Medicine Greifswald, Greifswald, Germany
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD 20892-9205, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD 20892-9205, USA
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Šoltanska 2, 21000 Split, Croatia; Algebra University College, Ilica 242, Zagreb, Croatia
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Imo E Hoefer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Susan Redline
- Sleep Medicine and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Paavo Nurmi Centre, Sports and Exercise Medicine Unit, Department of Physical Activity and Health, University of Turku, Turku, Finland
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation (ICPE), University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Helena Schmidt
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Eleftheriou Venizelou, Athens, Greece
| | | | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo 1628655, Japan
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany; Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Giorgia Girotto
- Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34127 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany; Department of Nephrology, Diabetology, Rheumatology, Traunstein Hospital, Traunstein, Germany; KfH Kidney Center Traunstein, Traunstein, Germany
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany; Department of Nephrology, Diabetology, Rheumatology, Traunstein Hospital, Traunstein, Germany; KfH Kidney Center Traunstein, Traunstein, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Center for Translational and Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Xiangfeng Lu
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Vasiliki Mamakou
- Medical School, National and Kapodistrian University Athens, 75 M. Assias Street, 115 27 Athens, Greece; Dromokaiteio Psychiatric Hospital, 124 61 Athens, Greece
| | - Morris Brown
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK; NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK; NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK; NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Marina Ciullo
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso" - CNR, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Jost B Jonas
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, 17 Hougou Lane, Chong Wen Men, Beijing 100005, China; Department of Ophthalmology, Medical Faculty Mannheim, Heidelberg University, Kutzerufer 1, Mannheim 68167, Germany; Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland; Privatpraxis Prof Jonas und Dr Panda-Jonas, Heidelberg, Germany
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, 00014 Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; Dirección de Nutrición and Unidad de Estudios de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Population Center, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Sonny Augustin Bechayda
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City 6000, Philippines; Department of Anthropology, Sociology, and History, University of San Carlos, Cebu City 6000, Philippines
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama 11010, Sri Lanka
| | - Ananda R Wickremasinghe
- Department of Public Health, Faculty of Medicine, University of Kelaniya, Ragama 11010, Sri Lanka
| | - Ronald M Krauss
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei Zheng
- Vanderbilt Epidemiology Center, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anneke I den Hollander
- Departments of Ophthalmology and Human Genetics, Radboud University Nijmegen Medical Center, Philips van Leydenlaan 15, Nijmegen 6525 EX, the Netherlands
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, New Delhi, India; Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore; and Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Amanda E Nelson
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Yvonne M Golightly
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA; Injury Prevention Research Center, University of North Carolina, Chapel Hill, NC, USA; Division of Physical Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Brenda Penninx
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, VU Medical Center Amsterdam, Amsterdam, the Netherlands
| | - Hyung-Lae Kim
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - John Attia
- Hunter Medical Research Institute, Newcastle, NSW, Australia; School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Rodney J Scott
- Hunter Medical Research Institute, Newcastle, NSW, Australia; School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna K Arnett
- University of Kentucky, College of Public Health, Lexington, KY, USA
| | - Mark Walker
- Institute of Cellular Medicine (Diabetes), The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Laura J Scott
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Heikki A Koistinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; University of Helsinki and Department of Medicine, Helsinki University Hospital, P.O.Box 340, Haartmaninkatu 4, 00029 Helsinki, Finland; Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, 00290 Helsinki, Finland
| | - Giriraj R Chandak
- Genomic Research on Complex diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, New Delhi, India; JSS Academy of Higher Education and Research, Mysuru, India
| | - Josep M Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston TX 77030, USA; Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore 119228, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore 119228, Singapore
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, 33520 Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Nish Chaturvedi
- MRC Unit for Lifelong Health and Ageing at UCL, 1-19 Torrington Place, WC1E 7HB London, UK
| | | | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Dermot F Reilly
- Genetics, Merck Sharp & Dohme Corp, Kenilworth, NJ 07033, USA
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - Frank Kee
- Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometrie and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, UK
| | - Colin N A Palmer
- Division of Population Health and Genomics, University of Dundee, Ninwells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Eleanor Simonsick
- Intramural Research Program, National Institute on Aging, 3001 S. Hanover St., Baltimore, MD 21225, USA
| | - Cornelia M van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK; Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, 1 Dong Jiao Min Xiang, Dong Cheng District, Beijing 100730, China; The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Fan Lu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Haretsugu Hishigaki
- Biomedical Technology Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Xu Lin
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim and Augsburg, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Jean-Claude Tardif
- Montreal Heart Institute, Université de Montréal, 5000 Belanger street, Montreal, QC H1T1C8, Canada
| | - Guillaume Lettre
- Montreal Heart Institute, Université de Montréal, 5000 Belanger street, Montreal, QC H1T1C8, Canada
| | - Leen M T Hart
- Amsterdam UMC, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam 1081HV, the Netherlands; Leiden University Medical Center, Department of Cell and Chemical Biology, Leiden 2333ZA, the Netherlands; Leiden University Medical Center, Department of Biomedical Data Sciences, Section Molecular Epidemiology, 2333ZA Leiden, the Netherlands
| | - Petra J M Elders
- Amsterdam UMC, Department of General Practice and Elderly Care, Amsterdam Public Health Research Institute, 1081HV Amsterdam, the Netherlands
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott M Damrauer
- Department of Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Meena Kumari
- Institute of Social and Economic Research, University of Essex, Wivenhoe Park CO4 3SQ, UK
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, 1-19 Torrington Place, WC1E 6BT London, UK
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, the Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, SE1 7EH London, UK
| | - Ruth J F Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; University of Washington, Department of Epidemiology, Seattle, WA 98195, USA; Department of Health Services, University of Washington, Seattle, WA, USA
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark; Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Charles N Rotimi
- 16Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Room 4047, Bethesda, MD 20892, USA
| | - Kaare Christensen
- Danish Aging Research Center, University of Southern Denmark, Odense C, Denmark
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, 00014 Helsinki, Finland; Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, 00014 Helsinki, Finland
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lambertus Kiemeney
- Radboud university medical center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Jacqueline de Graaf
- Radboud university medical center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany; LIFE Research Centre for Civilization Diseases, University of Leipzig, Philipp-Rosenthal-Straße 27, 04103 Leipzig, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria and German Chronic Kidney Disease Study, Austria
| | - Dongfeng Gu
- Key Laboratory of Cardiovascular Epidemiology & Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Heart Center Lübeck, Lübeck and Charité - University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Dental and Craniofacial Sciences, Department of Periodontology and Synoptic Dentistry, Berlin, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany; Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK) e.V., partner site Munich Heart Alliance, Munich, Germany
| | - Paul W Franks
- Lund University Diabetes Centre, Lunds University, Malmö, Sweden
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands; Netherlands Heart Institute, Utrecht, the Netherlands
| | - Amit V Khera
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Northern Finland Birth Cohorts, Infrastructure for population studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Minna Männikkö
- Northern Finland Birth Cohorts, Infrastructure for population studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG London, UK; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Biocenter of Oulu, University of Oulu, Oulu, Finland
| | - Zoltan Kutalik
- University Center for Primary Care and Public Health, University of Lausanne, Rte de Berne 113, 1010 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Cucca Francesco
- Institute for Genetic and Biomedical Research, Italian National Council of Research (IRGB CNR), Cagliari, Italy; University of Sassari, Sassari, Italy
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands; Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Ko Willems van Dijk
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU Oxford, UK; Unit of Genomics of Complex Diseases. Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, SW17 0RE London, UK
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, W2 1PG London, UK
| | - Neil Poulter
- School of Public Health, Imperial College London, W12 7RH London, UK
| | - Wayne Huey-Herng Sheu
- Taichung Veterans General Hospital, Taichung, Taiwan; No. 1650, Sec. 4, Taiwan Boulevard, Xitun District Taichung City 40705, Taiwan; Division of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; No. 201, Sec. 2, Shipai Road, Beitou District, Taipei City 112201, Taiwan
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovations (Formerly LABioMed) at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Thomas M Dantoft
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Fredrik Karpe
- OCDEM, University of Oxford, Churchill Hospital, OX3 7LE Oxford, UK; NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Matt J Neville
- OCDEM, University of Oxford, Churchill Hospital, OX3 7LE Oxford, UK; NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, BS8 2BN Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield Grove, BS8 2BN Bristol, UK
| | - Ching-Yu Cheng
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tien-Yin Wong
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore 169857, Singapore
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Hengtong Li
- Data Science, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Charumathi Sabanayagam
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore 169857, Singapore
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK) e.V., partner site Munich Heart Alliance, Munich, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Andrew T Hattersley
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, VU Medical Center Amsterdam, Amsterdam, the Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, VU Medical Center Amsterdam, Amsterdam, the Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA; Framingham Heart Study, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Population Center, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Chungbuk, South Korea
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, CB2 0QQ Cambridge, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, CB2 0QQ Cambridge, UK
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK; Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Jaakko Tuomilehto
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA
| | - Goncalo Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA; Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG London, UK; Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, UB1 3HW Middlesex, UK; Imperial College Healthcare NHS Trust, Imperial College London, W12 0HS London, UK; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, UB1 3HW Middlesex, UK; Imperial College Healthcare NHS Trust, Imperial College London, W12 0HS London, UK; National Heart and Lung Institute, Imperial College London, W2 1PG London, UK; MRC-PHE Centre for Environment and Health, Imperial College London, London W2 1PG, UK
| | - Paul S de Vries
- Human Genetics Center, 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
| | - Alanna C Morrison
- Human Genetics Center, 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
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; School of Electrical & Information Engineering, University of the Witwatersrand, Witwatersrand, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois College of Medicine, Chicago, IL, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, QLD 4006, Australia
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, QLD 4006, Australia
| | - Shahid Abbas
- Center for Non-Communicable Diseases, Karachi, SD, Pakistan & Faisalabad Institute of Cardiology, Faislabad, Pakistan
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, SD, Pakistan & Faisalabad Institute of Cardiology, Faislabad, Pakistan; Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA; Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK; Big Data Instutute, University of Oxford, OX3 7LF Oxford, UK
| | - Michael V Holmes
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, OX3 7LF Oxford, UK; NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Corri Black
- Aberdeen Centre for Health Data Science,1:042 Polwarth Building School of Medicine, Medical Science and Nutrition University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Blair H Smith
- Division of Population Health and Genomics, University of Dundee, Ninwells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Aris Baras
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Anne E Justice
- Biomedical and Translational Informatics, Geisinger Health, Danville, PA 17822, USA
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard C Trembath
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - M Geoffrey Hayes
- Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA; Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Marylyn D Ritchie
- Department of Genetics, Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger 7600, Norway; Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger 7600, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger 7600, Norway; Department of Endocrinology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, South Korea
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 102, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 102, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Jifeng Zhang
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Y Eugene Chen
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | - Julie A Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA; University of Massachusetts, Boston, MA, USA
| | - Philip S Tsao
- VA Palo Alto Health Care Systems, Palo Alto, CA, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyong-Mi Chang
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - John M Gaziano
- VA Boston Healthcare System, Boston, MA, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Peter Wilson
- Atlanta VA Health Care System, Decatur, GA, USA; Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Joel N Hirschhorn
- Endocrinology, Boston Childrens Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Struan Grant
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 75 Ames street, Cambridge, MA 02142, USA; Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA; Atlanta VA Health Care System, Decatur, GA, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
| | - Panos Deloukas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK; Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Gina Peloso
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Themistocles L Assimes
- VA Palo Alto Health Care Systems, Palo Alto, CA, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiang Zhu
- VA Palo Alto Health Care Systems, Palo Alto, CA, USA; Department of Statistics, The Pennsylvania State University, University Park, PA, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; Department of Statistics, Stanford University, Stanford, CA, USA.
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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16
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Garcia-Llorens G, Lopez-Navarro S, Jaijo T, Castell JV, Bort R. Modeling a Novel Variant of Glycogenosis IXa Using a Clonal Inducible Reprogramming System to Generate "Diseased" Hepatocytes for Accurate Diagnosis. J Pers Med 2022; 12:jpm12071111. [PMID: 35887608 PMCID: PMC9322025 DOI: 10.3390/jpm12071111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
The diagnosis of inherited metabolic disorders is a long and tedious process. The matching of clinical data with a genomic variant in a specific metabolic pathway is an essential step, but the link between a genome and the clinical data is normally difficult, primarily for new missense variants or alterations in intron sequences. Notwithstanding, elucidation of the pathogenicity of a specific variant might be critical for an accurate diagnosis. In this study, we described a novel intronic variant c.2597 + 5G > T in the donor splice sequence of the PHKA2 gene. To investigate PHKA2 mRNA splicing, as well as the functional consequences on glycogen metabolism, we generated hepatocyte-like cells from a proband’s fibroblasts by direct reprogramming. We demonstrated an aberrant splicing of PHKA2, resulting in the incorporation of a 27 bp upstream of intron 23 into exon 23, which leads to an immediate premature STOP codon. The truncated protein was unable to phosphorylate the PYGL protein, causing a 4-fold increase in the accumulation of glycogen in hepatocyte-like cells. Collectively, the generation of personalized hepatocyte-like cells enabled an unequivocal molecular diagnosis and qualified the sister’s proband, a carrier of the same mutation, as a candidate for a preimplantation genetic diagnosis. Additionally, our direct reprogramming strategy allows for an unlimited source of “diseased” hepatocyte-like cells compatible with high-throughput platforms.
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Affiliation(s)
- Guillem Garcia-Llorens
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, 46026 Valencia, Spain; (G.G.-L.); (S.L.-N.); (J.V.C.)
- Biochemistry and Molecular Biology Department, Universidad de Valencia, 46026 Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sergi Lopez-Navarro
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, 46026 Valencia, Spain; (G.G.-L.); (S.L.-N.); (J.V.C.)
| | - Teresa Jaijo
- Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, 46026 Valencia, Spain;
| | - Jose V. Castell
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, 46026 Valencia, Spain; (G.G.-L.); (S.L.-N.); (J.V.C.)
- Biochemistry and Molecular Biology Department, Universidad de Valencia, 46026 Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Roque Bort
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, 46026 Valencia, Spain; (G.G.-L.); (S.L.-N.); (J.V.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-961-246-621
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17
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Vujkovic M, Ramdas S, Lorenz KM, Guo X, Darlay R, Cordell HJ, He J, Gindin Y, Chung C, Myers RP, Schneider CV, Park J, Lee KM, Serper M, Carr RM, Kaplan DE, Haas ME, MacLean MT, Witschey WR, Zhu X, Tcheandjieu C, Kember RL, Kranzler HR, Verma A, Giri A, Klarin DM, Sun YV, Huang J, Huffman JE, Creasy KT, Hand NJ, Liu CT, Long MT, Yao J, Budoff M, Tan J, Li X, Lin HJ, Chen YDI, Taylor KD, Chang RK, Krauss RM, Vilarinho S, Brancale J, Nielsen JB, Locke AE, Jones MB, Verweij N, Baras A, Reddy KR, Neuschwander-Tetri BA, Schwimmer JB, Sanyal AJ, Chalasani N, Ryan KA, Mitchell BD, Gill D, Wells AD, Manduchi E, Saiman Y, Mahmud N, Miller DR, Reaven PD, Phillips LS, Muralidhar S, DuVall SL, Lee JS, Assimes TL, Pyarajan S, Cho K, Edwards TL, Damrauer SM, Wilson PW, Gaziano JM, O'Donnell CJ, Khera AV, Grant SFA, Brown CD, Tsao PS, Saleheen D, Lotta LA, Bastarache L, Anstee QM, Daly AK, Meigs JB, Rotter JI, Lynch JA, Rader DJ, Voight BF, Chang KM. A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation. Nat Genet 2022; 54:761-771. [PMID: 35654975 PMCID: PMC10024253 DOI: 10.1038/s41588-022-01078-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/18/2022] [Indexed: 02/05/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a growing cause of chronic liver disease. Using a proxy NAFLD definition of chronic elevation of alanine aminotransferase (cALT) levels without other liver diseases, we performed a multiancestry genome-wide association study (GWAS) in the Million Veteran Program (MVP) including 90,408 cALT cases and 128,187 controls. Seventy-seven loci exceeded genome-wide significance, including 25 without prior NAFLD or alanine aminotransferase associations, with one additional locus identified in European American-only and two in African American-only analyses (P < 5 × 10-8). External replication in histology-defined NAFLD cohorts (7,397 cases and 56,785 controls) or radiologic imaging cohorts (n = 44,289) replicated 17 single-nucleotide polymorphisms (SNPs) (P < 6.5 × 10-4), of which 9 were new (TRIB1, PPARG, MTTP, SERPINA1, FTO, IL1RN, COBLL1, APOH and IFI30). Pleiotropy analysis showed that 61 of 77 multiancestry and all 17 replicated SNPs were jointly associated with metabolic and/or inflammatory traits, revealing a complex model of genetic architecture. Our approach integrating cALT, histology and imaging reveals new insights into genetic liability to NAFLD.
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Affiliation(s)
- Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shweta Ramdas
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kim M Lorenz
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Rebecca Darlay
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Heather J Cordell
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jing He
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Robert P Myers
- Gilead Sciences, Inc., Foster City, CA, USA
- The Liver Company, Palo Alto, CA, USA
| | - Carolin V Schneider
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Joseph Park
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kyung Min Lee
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Marina Serper
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rotonya M Carr
- Division of Gastroenterology, University of Washington, Seattle, WA, USA
| | - David E Kaplan
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mary E Haas
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew T MacLean
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Walter R Witschey
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Xiang Zhu
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Catherine Tcheandjieu
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel L Kember
- Mental Illness Research Education and Clinical Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Henry R Kranzler
- Mental Illness Research Education and Clinical Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Anurag Verma
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayush Giri
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Derek M Klarin
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yan V Sun
- Atlanta VA Medical Center, Decatur, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Jie Huang
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | | | - Kate Townsend Creasy
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicholas J Hand
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Michelle T Long
- Department of Medicine, Section of Gastroenterology, Boston University School of Medicine, Boston, MA, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Matthew Budoff
- Department of Cardiology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Henry J Lin
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ruey-Kang Chang
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ronald M Krauss
- Departments of Pediatrics and Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Silvia Vilarinho
- Section of Digestive Diseases, Department of Internal Medicine, and Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Joseph Brancale
- Section of Digestive Diseases, Department of Internal Medicine, and Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - K Rajender Reddy
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Jeffrey B Schwimmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Arun J Sanyal
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Naga Chalasani
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathleen A Ryan
- Program for Personalized and Genomic Medicine, Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elisabetta Manduchi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yedidya Saiman
- Department of Medicine, Section of Hepatology, Lewis Katz School of Medicine at Temple University, Temple University Hospital, Philadelphia, PA, USA
| | - Nadim Mahmud
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Donald R Miller
- Center for Healthcare Organization and Implementation Research, Bedford VA Healthcare System, Bedford, MA, USA
- Center for Population Health, Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
| | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, USA
- College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - Lawrence S Phillips
- Atlanta VA Medical Center, Decatur, GA, USA
- Division of Endocrinology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sumitra Muralidhar
- Office of Research and Development, Veterans Health Administration, Washington, DC, USA
| | - Scott L DuVall
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jennifer S Lee
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Todd L Edwards
- Nashville VA Medical Center, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter W Wilson
- Atlanta VA Medical Center, Decatur, GA, USA
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Amit V Khera
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Struan F A Grant
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Danish Saleheen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Non-Communicable Diseases, Karachi, Sindh, Pakistan
| | | | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quentin M Anstee
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ann K Daly
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, 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, USA
| | - Julie A Lynch
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- College of Nursing and Health Sciences, University of Massachusetts, Lowell, MA, USA
| | - Daniel J Rader
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F Voight
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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18
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Brooks IR, Garrone CM, Kerins C, Kiar CS, Syntaka S, Xu JZ, Spagnoli FM, Watt FM. Functional genomics and the future of iPSCs in disease modeling. Stem Cell Reports 2022; 17:1033-1047. [PMID: 35487213 PMCID: PMC9133703 DOI: 10.1016/j.stemcr.2022.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 10/28/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are valuable in disease modeling because of their potential to expand and differentiate into virtually any cell type and recapitulate key aspects of human biology. Functional genomics are genome-wide studies that aim to discover genotype-phenotype relationships, thereby revealing the impact of human genetic diversity on normal and pathophysiology. In this review, we make the case that human iPSCs (hiPSCs) are a powerful tool for functional genomics, since they provide an in vitro platform for the study of population genetics. We describe cutting-edge tools and strategies now available to researchers, including multi-omics technologies, advances in hiPSC culture techniques, and innovations in drug development. Functional genomics approaches based on hiPSCs hold great promise for advancing drug discovery, disease etiology, and the impact of genetic variation on human biology.
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Affiliation(s)
- Imogen R Brooks
- St John's Institute of Dermatology, King's College London, London, SE1 9RT, UK
| | - Cristina M Garrone
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Caoimhe Kerins
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Cher Shen Kiar
- Peter Gorer Department of Immunobiology, King's College London, London, SE1 9RT, UK
| | - Sofia Syntaka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Jessie Z Xu
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Francesca M Spagnoli
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK.
| | - Fiona M Watt
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK; Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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19
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Zhao Y, Wu J, Li D, Liu J, Chen W, Hou Z, Liu K, Jiang L, Chen X, Wang L, Hu B, Zong F, Wang Y, Wang Y. Human ESC-derived immunity- and matrix- regulatory cells ameliorated white matter damage and vascular cognitive impairment in rats subjected to chronic cerebral hypoperfusion. Cell Prolif 2022; 55:e13223. [PMID: 35437845 PMCID: PMC9136497 DOI: 10.1111/cpr.13223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/24/2022] [Accepted: 03/03/2022] [Indexed: 11/29/2022] Open
Abstract
Objectives This study investigated the ability of immunity‐ and matrix‐ regulatory cells (IMRCs) to improve cognitive function in a rat model of vascular cognitive impairment. Materials and Methods A chronic cerebral hypoperfusion (CCH) model was established in rats via permanent bilateral occlusion of the common carotid arteries (two‐vessel occlusion, 2VO). The rats then received intravenous injections of IMRCs or saline. A single injection of different doses of IMRCs (1 × 106 cells/rat, 2 × 106 cells/rat, or 4 × 106 cells/rat) was administered via tail vein 72 h after establishment of the model. To evaluate functional recovery, the rats were subjected to behavioural tests after 30 days of CCH. Imaging, western blotting, immunofluorescence staining, and quantitative real‐time PCR were used to analyse neuroinflammation and white matter injury after 14 and 40 days of CCH. RNA sequencing (RNA‐seq) was used to profile gene expression changes in copine 1 (CPNE1) in response to IMRCs treatment. Results Intravenous injection of 4 × 106 IMRCs alleviated white matter damage and ameliorated cognitive deficits in rats subjected to CCH. Immunofluorescence staining suggested that activation of microglia and astrocytes was reduced, and RNA sequencing showed that CPNE1 expression was significantly elevated following treatment with IMRCs. Conclusions Intravenous injection of IMRCs protected against CCH‐induced white matter injury and cognitive impairment inhibition of microglial activation and regulation of microglia polarization.
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Affiliation(s)
- Yilong Zhao
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
| | - Jun Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,National Stem Cell Resource Center, Chinese Academy of Sciences, Beijing, China
| | - Da Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jing Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Weiqi Chen
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
| | - Zongren Hou
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Kailun Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Lingling Jiang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
| | - Xiaowei Chen
- University of Chinese Academy of Sciences, Beijing, China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Liu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,National Stem Cell Resource Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,National Stem Cell Resource Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fangrong Zong
- China National Clinical Research Center for Neurological Diseases, Beijing, China.,School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Yukai Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,National Stem Cell Resource Center, Chinese Academy of Sciences, Beijing, China
| | - Yilong Wang
- China National Clinical Research Center for Neurological Diseases, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China.,Chinese Institute for Brain Research, Beijing, China
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20
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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21
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Blaszkiewicz J, Duncan SA. Advancements in Disease Modeling and Drug Discovery Using iPSC-Derived Hepatocyte-like Cells. Genes (Basel) 2022; 13:573. [PMID: 35456379 PMCID: PMC9030659 DOI: 10.3390/genes13040573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/05/2023] Open
Abstract
Serving as the metabolic hub of the human body, the liver is a vital organ that performs a variety of important physiological functions. Although known for its regenerative potential, it remains vulnerable to a variety of diseases. Despite decades of research, liver disease remains a leading cause of mortality in the United States with a multibillion-dollar-per-year economic burden. Prior research with model systems, such as primary hepatocytes and murine models, has provided many important discoveries. However, progress has been impaired by numerous obstacles associated with these models. In recent years, induced pluripotent stem cell (iPSC)-based systems have emerged as advantageous platforms for studying liver disease. Benefits, including preserved differentiation and physiological function, amenability to genetic manipulation via tools such as CRISPR/Cas9, and availability for high-throughput screening, make these systems increasingly attractive for both mechanistic studies of disease and the identification of novel therapeutics. Although limitations exist, recent studies have made progress in ameliorating these issues. In this review, we discuss recent advancements in iPSC-based models of liver disease, including improvements in model system construction as well as the use of high-throughput screens for genetic studies and drug discovery.
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Affiliation(s)
| | - Stephen A. Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA;
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22
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Fakunle ES, Pratola VG, Peterson SE, Loring JF, Madanat H. The Promoting Equity in Stem Cell Genomics Survey. Regen Med 2022; 17:203-218. [PMID: 35255713 DOI: 10.2217/rme-2021-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study aimed to determine knowledge and attitudes toward induced pluripotent stem cell technology and biobanking. Methods: A survey instrument was developed to determine individuals' knowledge of and attitudes toward these technologies. Results: Results from 276 ethnically diverse participants who took the online survey demonstrated significant associations (p ≤ 0. 05) in knowledge by ethnicity and race regarding properties of stem cells, different types of stem cells and previous sample donation behavior. Significantly more Whites 39% (n = 53) compared with Blacks or African-Americans 19.2% (n = 14) had previous knowledge of induced pluripotent stem cells (χ2 = 8.544; p = 0.003) Conclusion: Overall, White race was associated with greater knowledge about stem cells and biobanks and greater willingness to donate samples for future research.
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Affiliation(s)
- Eyitayo S Fakunle
- Founder at IFASEMB & Ilera "I am Pluripotent", Chandler, AZ 85286, USA.,Currently employed at Covis Pharmaceuticals, Grafenauweg 12, 6300 Zug, Switzerland.,J. Orin Edson Entrepreneurship + Innovation Institute, Venture Devils Program for startups, Arizona State University, Tempe, AZ 85281, USA
| | - Victoria Glenn Pratola
- The Scripps Research Institute, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Suzanne E Peterson
- The Scripps Research Institute, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Jeanne F Loring
- The Scripps Research Institute, Center for Regenerative Medicine, La Jolla, CA 92037 USA.,Graduate School of Public Health, Division of Health Promotion and Behavioral Science San Diego State University, San Diego, CA 92182, USA
| | - Hala Madanat
- Interim Vice President for Research and Innovation, Distinguished Professor, School of Public Health, Core Investigator, Institute for Behavioral and Community Health San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4162
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23
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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24
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Bellomo TR, Bone WP, Chen BY, Gawronski KAB, Zhang D, Park J, Levin M, Tsao N, Klarin D, Lynch J, Assimes TL, Gaziano JM, Wilson PW, Cho K, Vujkovic M, O'Donnell CJ, Chang KM, Tsao PS, Rader DJ, Ritchie MD, Damrauer SM, Voight BF. Multi-Trait Genome-Wide Association Study of Atherosclerosis Detects Novel Pleiotropic Loci. Front Genet 2022; 12:787545. [PMID: 35186008 PMCID: PMC8847690 DOI: 10.3389/fgene.2021.787545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Although affecting different arterial territories, the related atherosclerotic vascular diseases coronary artery disease (CAD) and peripheral artery disease (PAD) share similar risk factors and have shared pathobiology. To identify novel pleiotropic loci associated with atherosclerosis, we performed a joint analysis of their shared genetic architecture, along with that of common risk factors. Using summary statistics from genome-wide association studies of nine known atherosclerotic (CAD, PAD) and atherosclerosis risk factors (body mass index, smoking initiation, type 2 diabetes, low density lipoprotein, high density lipoprotein, total cholesterol, and triglycerides), we perform 15 separate multi-trait genetic association scans which resulted in 25 novel pleiotropic loci not yet reported as genome-wide significant for their respective traits. Colocalization with single-tissue eQTLs identified candidate causal genes at 14 of the detected signals. Notably, the signal between PAD and LDL-C at the PCSK6 locus affects PCSK6 splicing in human liver tissue and induced pluripotent derived hepatocyte-like cells. These results show that joint analysis of related atherosclerotic disease traits and their risk factors allowed identification of unified biology that may offer the opportunity for therapeutic manipulation. The signal at PCSK6 represent possible shared causal biology where existing inhibitors may be able to be leveraged for novel therapies.
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Affiliation(s)
- Tiffany R Bellomo
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - William P Bone
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Brian Y Chen
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States
| | | | - David Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States
| | - Joseph Park
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael Levin
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.,Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
| | - Noah Tsao
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
| | - Derek Klarin
- VA Boston Healthcare System, Boston, MA, United States.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Division of Vascular Surgery and Endovascular Therapy, University of Florida School of Medicine, Gainesville, FL, United States.,Department of Surgery, Massachusetts General Hospital, Boston, MA, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, United States.,University of Massachusetts College of Nursing and Health Sciences, Boston, MA, United States
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, United States.,Department of Medicine, Stanford University, Stanford, CA, United States
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA, United States.,Massachusetts Veterans Epidemiology Research and Information Center, Veterans Affairs Boston Healthcare System, Boston, MA, United States.,Department of Medicine, Brigham Women's Hospital, Boston, MA, United States
| | - Peter W Wilson
- Atlanta VA Medical Center, Decatur, GA, United States.,Division of Cardiology, Emory University School of Medicine, Atlanta, GA, United States
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, United States.,Department of Medicine, Brigham Women's Hospital, Boston, MA, United States
| | - Marijana Vujkovic
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, United States.,Department of Medicine, Brigham Women's Hospital, Boston, MA, United States
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, United States.,Department of Medicine, Stanford University, Stanford, CA, United States
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, United States
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Center for Precision Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States.,Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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25
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Messina A, Luce E, Benzoubir N, Pasqua M, Pereira U, Humbert L, Eguether T, Rainteau D, Duclos-Vallée JC, Legallais C, Dubart-Kupperschmitt A. Evidence of Adult Features and Functions of Hepatocytes Differentiated from Human Induced Pluripotent Stem Cells and Self-Organized as Organoids. Cells 2022; 11:cells11030537. [PMID: 35159346 PMCID: PMC8834365 DOI: 10.3390/cells11030537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Human-induced pluripotent stem cell-derived hepatocytes (iHeps) have been shown to have considerable potential in liver diseases, toxicity, and pharmacological studies. However, there is a growing need to obtain iHeps that are truly similar to primary adult hepatocytes in terms of morphological features and functions. We generated such human iHeps, self-assembled as organoids (iHep-Orgs). Methods: iPSC-derived hepatoblasts were self-assembled into spheroids and differentiated into mature hepatocytes modulating final step of differentiation. Results: In about four weeks of culture, the albumin secretion levels and the complete disappearance of α-fetoprotein from iHep-Orgs suggested the acquisition of a greater degree of maturation than those previously reported. The expression of apical transporters and bile acid secretion evidenced the acquisition of complex hepatocyte polarity as well as the development of a functional and well-defined bile canalicular network confirmed by computational analysis. Activities recorded for CYP450, UGT1A1, and alcohol dehydrogenase, response to hormonal stimulation, and glucose metabolism were also remarkable. Finally, iHep-Orgs displayed a considerable ability to detoxify pathological concentrations of lactate and ammonia. Conclusions: With features similar to those of primary adult hepatocytes, the iHep-Orgs thus produced could be considered as a valuable tool for the development and optimization of preclinical and clinical applications.
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Affiliation(s)
- Antonietta Messina
- UMR_S 1193, INSERM/Université Paris-Saclay, F-94800 Villejuif, France; (E.L.); (N.B.); (J.-C.D.-V.)
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
- Correspondence: (A.M.); (A.D.-K.)
| | - Eléanor Luce
- UMR_S 1193, INSERM/Université Paris-Saclay, F-94800 Villejuif, France; (E.L.); (N.B.); (J.-C.D.-V.)
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
| | - Nassima Benzoubir
- UMR_S 1193, INSERM/Université Paris-Saclay, F-94800 Villejuif, France; (E.L.); (N.B.); (J.-C.D.-V.)
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
| | - Mattia Pasqua
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
- UMR CNRS 7338 Biomechanics & Bioengineering, Université de Technologie de Compiègne, Sorbonne Universités, 60203 Compiegne, France
| | - Ulysse Pereira
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
- UMR CNRS 7338 Biomechanics & Bioengineering, Université de Technologie de Compiègne, Sorbonne Universités, 60203 Compiegne, France
| | - Lydie Humbert
- Centre de Recherche Saint-Antoine, Sorbonne Université, INSERM, CRSA, AP-HP, Hôpital Saint Antoine, Metomics, 75012 Paris, France; (L.H.); (T.E.); (D.R.)
| | - Thibaut Eguether
- Centre de Recherche Saint-Antoine, Sorbonne Université, INSERM, CRSA, AP-HP, Hôpital Saint Antoine, Metomics, 75012 Paris, France; (L.H.); (T.E.); (D.R.)
| | - Dominique Rainteau
- Centre de Recherche Saint-Antoine, Sorbonne Université, INSERM, CRSA, AP-HP, Hôpital Saint Antoine, Metomics, 75012 Paris, France; (L.H.); (T.E.); (D.R.)
| | - Jean-Charles Duclos-Vallée
- UMR_S 1193, INSERM/Université Paris-Saclay, F-94800 Villejuif, France; (E.L.); (N.B.); (J.-C.D.-V.)
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
| | - Cécile Legallais
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
- UMR CNRS 7338 Biomechanics & Bioengineering, Université de Technologie de Compiègne, Sorbonne Universités, 60203 Compiegne, France
| | - Anne Dubart-Kupperschmitt
- UMR_S 1193, INSERM/Université Paris-Saclay, F-94800 Villejuif, France; (E.L.); (N.B.); (J.-C.D.-V.)
- Centre Hépatobiliaire, Fédération Hospitalo-Universitaire (FHU) Hépatinov, AP-HP, Hôpital Paul Brousse, F-94800 Villejuif, France; (M.P.); (U.P.); (C.L.)
- Correspondence: (A.M.); (A.D.-K.)
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26
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Ernzen K, Trask AJ, Peeples ME, Garg V, Zhao MT. Human Stem Cell Models of SARS-CoV-2 Infection in the Cardiovascular System. Stem Cell Rev Rep 2021; 17:2107-2119. [PMID: 34365591 PMCID: PMC8349465 DOI: 10.1007/s12015-021-10229-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 11/28/2022]
Abstract
The virus responsible for coronavirus disease 2019 (COVID-19), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected over 190 million people to date, causing a global pandemic. SARS-CoV-2 relies on binding of its spike glycoprotein to angiotensin-converting enzyme 2 (ACE2) for infection. In addition to fever, cough, and shortness of breath, severe cases of SARS-CoV-2 infection may result in the rapid overproduction of pro-inflammatory cytokines. This overactive immune response is known as a cytokine storm, which leads to several serious clinical manifestations such as acute respiratory distress syndrome and myocardial injury. Cardiovascular disorders such as acute coronary syndrome (ACS) and heart failure not only enhance disease progression at the onset of infection, but also arise in hospitalized patients with COVID-19. Tissue-specific differentiated cells and organoids derived from human pluripotent stem cells (hPSCs) serve as an excellent model to address how SARS-CoV-2 damages the lungs and the heart. In this review, we summarize the molecular basis of SARS-CoV-2 infection and the current clinical perspectives of the bidirectional relationship between the cardiovascular system and viral progression. Furthermore, we also address the utility of hPSCs as a dynamic model for SARS-CoV-2 research and clinical translation.
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Affiliation(s)
- Kyle Ernzen
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
- MCDB Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Aaron J Trask
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Mark E Peeples
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Center for Vaccine and Immunity, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Vidu Garg
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
- MCDB Graduate Program, The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ming-Tao Zhao
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA.
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA.
- MCDB Graduate Program, The Ohio State University, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, OH, USA.
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27
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Application of the Pluripotent Stem Cells and Genomics in Cardiovascular Research-What We Have Learnt and Not Learnt until Now. Cells 2021; 10:cells10113112. [PMID: 34831333 PMCID: PMC8623147 DOI: 10.3390/cells10113112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/06/2021] [Accepted: 11/07/2021] [Indexed: 12/16/2022] Open
Abstract
Personalized regenerative medicine and biomedical research have been galvanized and revolutionized by human pluripotent stem cells in combination with recent advances in genomics, artificial intelligence, and genome engineering. More recently, we have witnessed the unprecedented breakthrough life-saving translation of mRNA-based vaccines for COVID-19 to contain the global pandemic and the investment in billions of US dollars in space exploration projects and the blooming space-tourism industry fueled by the latest reusable space vessels. Now, it is time to examine where the translation of pluripotent stem cell research stands currently, which has been touted for more than the last two decades to cure and treat millions of patients with severe debilitating degenerative diseases and tissue injuries. This review attempts to highlight the accomplishments of pluripotent stem cell research together with cutting-edge genomics and genome editing tools and, also, the promises that have still not been transformed into clinical applications, with cardiovascular research as a case example. This review also brings to our attention the scientific and socioeconomic challenges that need to be effectively addressed to see the full potential of pluripotent stem cells at the clinical bedside.
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Yi SA, Zhang Y, Rathnam C, Pongkulapa T, Lee KB. Bioengineering Approaches for the Advanced Organoid Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007949. [PMID: 34561899 PMCID: PMC8682947 DOI: 10.1002/adma.202007949] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/09/2021] [Indexed: 05/09/2023]
Abstract
Recent advances in 3D cell culture technology have enabled scientists to generate stem cell derived organoids that recapitulate the structural and functional characteristics of native organs. Current organoid technologies have been striding toward identifying the essential factors for controlling the processes involved in organoid development, including physical cues and biochemical signaling. There is a growing demand for engineering dynamic niches characterized by conditions that resemble in vivo organogenesis to generate reproducible and reliable organoids for various applications. Innovative biomaterial-based and advanced engineering-based approaches have been incorporated into conventional organoid culture methods to facilitate the development of organoid research. The recent advances in organoid engineering, including extracellular matrices and genetic modulation, are comprehensively summarized to pinpoint the parameters critical for organ-specific patterning. Moreover, perspective trends in developing tunable organoids in response to exogenous and endogenous cues are discussed for next-generation developmental studies, disease modeling, and therapeutics.
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Affiliation(s)
- Sang Ah Yi
- Epigenome Dynamics Control Research Center, School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Yixiao Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Christopher Rathnam
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Thanapat Pongkulapa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
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Guo H, Liu L, Nishiga M, Cong L, Wu JC. Deciphering pathogenicity of variants of uncertain significance with CRISPR-edited iPSCs. Trends Genet 2021; 37:1109-1123. [PMID: 34509299 DOI: 10.1016/j.tig.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
Genetic variants play an important role in conferring risk for cardiovascular diseases (CVDs). With the rapid development of next-generation sequencing (NGS), thousands of genetic variants associated with CVDs have been identified by genome-wide association studies (GWAS), but the function of more than 40% of genetic variants is still unknown. This gap of knowledge is a barrier to the clinical application of the genetic information. However, determining the pathogenicity of a variant of uncertain significance (VUS) is challenging due to the lack of suitable model systems and accessible technologies. By combining clustered regularly interspaced short palindromic repeats (CRISPR) and human induced pluripotent stem cells (iPSCs), unprecedented advances are now possible in determining the pathogenicity of VUS in CVDs. Here, we summarize recent progress and new strategies in deciphering pathogenic variants for CVDs using CRISPR-edited human iPSCs.
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Affiliation(s)
- Hongchao Guo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lichao Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Le Cong
- Department of Pathology and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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30
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Yoo T, Joo SK, Kim HJ, Kim HY, Sim H, Lee J, Kim HH, Jung S, Lee Y, Jamialahmadi O, Romeo S, Jeong WI, Hwang GS, Kang KW, Kim JW, Kim W, Choi M. Disease-specific eQTL screening reveals an anti-fibrotic effect of AGXT2 in non-alcoholic fatty liver disease. J Hepatol 2021; 75:514-523. [PMID: 33892010 DOI: 10.1016/j.jhep.2021.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Non-alcoholic fatty liver disease (NAFLD) poses an increasing clinical burden. Genome-wide association studies have revealed a limited contribution of genomic variants to the disease, requiring alternative but robust approaches to identify disease-associated variants and genes. We carried out a disease-specific expression quantitative trait loci (eQTL) screen to identify novel genetic factors that specifically act on NAFLD progression on the basis of genotype. METHODS We recruited 125 Korean patients (83 with biopsy-proven NAFLD and 42 without NAFLD) and performed eQTL analyses using 21,272 transcripts and 3,234,941 genotyped and imputed single nucleotide polymorphisms. We then selected eQTLs that were detected only in the NAFLD group, but not in the control group (i.e., NAFLD-eQTLs). An additional cohort of 162 Korean individuals with NAFLD was used for replication. The function of the selected eQTL toward NAFLD development was validated using HepG2, primary hepatocytes and NAFLD mouse models. RESULTS The NAFLD-specific eQTL screening yielded 242 loci. Among them, AGXT2, encoding alanine-glyoxylate aminotransferase 2, displayed decreased expression in patients with NAFLD homozygous for the non-reference allele of rs2291702, compared to no-NAFLD individuals with the same genotype (p = 4.79 × 10-6). This change was replicated in an additional 162 individuals, yielding a combined p value of 8.05 × 10-8 from a total of 245 patients with NAFLD and 42 controls. Knockdown of AGXT2 induced palmitate-overloaded hepatocyte death by increasing endoplasmic reticulum stress, and exacerbated NAFLD diet-induced liver fibrosis in mice, while overexpression of AGXT2 attenuated liver fibrosis and steatosis. CONCLUSIONS We identified a new molecular role for AGXT2 in NAFLD. Our overall approach will serve as an efficient tool for uncovering novel genetic factors that contribute to liver steatosis and fibrosis in patients with NAFLD. LAY SUMMARY Elucidating causal genes for non-alcoholic fatty liver disease (NAFLD) has been challenging due to limited tissue availability and the polygenic nature of the disease. Using liver and blood samples from 125 Korean individuals (83 with NAFLD and 42 without NAFLD), we devised a new analytic method to identify causal genes. Among the candidates, we found that AGXT2-rs2291702 protects against liver fibrosis in a genotype-dependent manner with the potential for therapeutic interventions. Our approach enables the discovery of causal genes that act on the basis of genotype.
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Affiliation(s)
- Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sae Kyung Joo
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Republic of Korea
| | - Hyo Jung Kim
- Department of Biochemistry and Molecular Biology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Young Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jieun Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Republic of Korea
| | - Hee-Hoon Kim
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Sunhee Jung
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Oveis Jamialahmadi
- Salhgrenska Academy, Institute of Medicine, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden
| | - Stefano Romeo
- Salhgrenska Academy, Institute of Medicine, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden; Sahlgrenska University Hospital, Cardiology Department, Sweden; Department of Medical and Clinical Science, Clinical Nutrition Unit, University Magna Graecia, Catanzaro, Italy
| | - Won-Il Jeong
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea; Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Keon Wook Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jae Woo Kim
- Department of Biochemistry and Molecular Biology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Republic of Korea.
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
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31
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Hu W, Jiang C, Kim M, Yang W, Zhu K, Guan D, Lv W, Xiao Y, Wilson JR, Rader DJ, Pui CH, Relling MV, Lazar MA. Individual-specific functional epigenomics reveals genetic determinants of adverse metabolic effects of glucocorticoids. Cell Metab 2021; 33:1592-1609.e7. [PMID: 34233159 PMCID: PMC8340270 DOI: 10.1016/j.cmet.2021.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/26/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023]
Abstract
Glucocorticoids (GCs) are widely used as anti-inflammatory drugs, but their long-term use has severe metabolic side effects. Here, by treating multiple individual adipose stem cell-derived adipocytes and induced pluripotent stem cell-derived hepatocytes with the potent GC dexamethasone (Dex), we uncovered cell-type-specific and individual-specific GC-dependent transcriptomes and glucocorticoid receptor (GR) cistromes. Individual-specific GR binding could be traced to single-nucleotide polymorphisms (SNPs) that altered the binding motifs of GR or its cooperating factors. We also discovered another set of genetic variants that modulated Dex response through affecting chromatin accessibility or chromatin architecture. Several SNPs that altered Dex-regulated GR binding and gene expression controlled Dex-driven metabolic perturbations. Remarkably, these genetic variations were highly associated with increases in serum glucose, lipids, and body mass in subjects on GC therapy. Knowledge of the genetic variants that predispose individuals to metabolic side effects allows for a precision medicine approach to the use of clinically relevant GCs.
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Affiliation(s)
- Wenxiang Hu
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; The Max-Planck Center for Tissue Stem Cell Research and Regenerative Medicine, Bioland Laboratory, Guangzhou, China.
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mindy Kim
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kun Zhu
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wenjian Lv
- Division of Cardiology and Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jessica R Wilson
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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32
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Abbey D, Conlon D, Rainville C, Elwyn S, Quiroz-Figueroa K, Billheimer J, Schultz DC, Hand NJ, Cherry S, Rader DJ. Lipid droplet screen in human hepatocytes identifies TRRAP as a regulator of cellular triglyceride metabolism. Clin Transl Sci 2021; 14:1369-1379. [PMID: 34156146 PMCID: PMC8301584 DOI: 10.1111/cts.12988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Hepatocytes store triglycerides (TGs) in the form of lipid droplets (LDs), which are increased in hepatosteatosis. The regulation of hepatic LDs is poorly understood and new therapies to reduce hepatosteatosis are needed. We performed a siRNA kinase and phosphatase screen in HuH‐7 cells using high‐content automated imaging of LDs. Changes in accumulated lipids were quantified with developed pipeline that measures intensity, area, and number of LDs. Selected “hits,” which reduced lipid accumulation, were further validated with other lipid and expression assays. Among several siRNAs that resulted in significantly reduced LDs, one was targeted to the nuclear adapter protein, transformation/transcription domain‐associated protein (TRRAP). Knockdown of TRRAP reduced triglyceride accumulation in HuH‐7 hepatocytes, in part by reducing C/EBPα‐mediated de novo synthesis of TGs. These findings implicate TRRAP as a novel regulator of hepatic TG metabolism and nominate it as a potential drug target for hepatosteatosis.
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Affiliation(s)
- Deepti Abbey
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Donna Conlon
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher Rainville
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susannah Elwyn
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine Quiroz-Figueroa
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jeffrey Billheimer
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas J Hand
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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33
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Dannemann M, Gallego Romero I. Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J 2021; 289:2992-3010. [PMID: 33876573 DOI: 10.1111/febs.15885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
The study of human evolution, long constrained by a lack of experimental model systems, has been transformed by the emergence of the induced pluripotent stem cell (iPSC) field. iPSCs can be readily established from noninvasive tissue sources, from both humans and other primates; they can be maintained in the laboratory indefinitely, and they can be differentiated into other tissue types. These qualities mean that iPSCs are rapidly becoming established as viable and powerful model systems with which it is possible to address questions in human evolution that were until now logistically and ethically intractable, especially in the quest to understand humans' place among the great apes, and the genetic basis of human uniqueness. In this review, we discuss the key lessons and takeaways of this nascent field; from the types of research, iPSCs make possible to lingering challenges and likely future directions. We provide a comprehensive overview of how the seemingly unlikely combination of iPSCs and explicit evolutionary frameworks is transforming what is possible in our understanding of humanity's past and present.
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Affiliation(s)
| | - Irene Gallego Romero
- Institute of Genomics, University of Tartu, Estonia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Australia.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Centre for Stem Cell Systems, The University of Melbourne, Parkville, Australia
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34
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Akerman I, Maestro MA, De Franco E, Grau V, Flanagan S, García-Hurtado J, Mittler G, Ravassard P, Piemonti L, Ellard S, Hattersley AT, Ferrer J. Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene. Cell Rep 2021; 35:108981. [PMID: 33852861 PMCID: PMC8052186 DOI: 10.1016/j.celrep.2021.108981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/04/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their genomic location. This limits our understanding of disease-causing regulatory variants. INS promoter mutations cause recessive neonatal diabetes. We show that all INS promoter point mutations in 60 patients disrupt a CC dinucleotide, whereas none affect other elements important for episomal promoter function. To model CC mutations, we humanized an ∼3.1-kb region of the mouse Ins2 gene. This recapitulated developmental chromatin states and cell-specific transcription. A CC mutant allele, however, abrogated active chromatin formation during pancreas development. A search for transcription factors acting through this element revealed that another neonatal diabetes gene product, GLIS3, has a pioneer-like ability to derepress INS chromatin, which is hampered by the CC mutation. Our in vivo analysis, therefore, connects two human genetic defects in an essential mechanism for developmental activation of the INS gene.
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Affiliation(s)
- Ildem Akerman
- Institute of Metabolism and Systems Research (IMSR), Medical School, University of Birmingham, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), University of Birmingham, Birmingham, UK.
| | - Miguel Angel Maestro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Vanessa Grau
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Sarah Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Javier García-Hurtado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Gerhard Mittler
- Max-Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Philippe Ravassard
- INSERM, CNRS, Paris Brain Institute - Hôpital Pitié-Salpêtrière, Paris, France
| | - Lorenzo Piemonti
- Diabetes Research Institute, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK; Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain; Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
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35
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Neavin D, Nguyen Q, Daniszewski MS, Liang HH, Chiu HS, Wee YK, Senabouth A, Lukowski SW, Crombie DE, Lidgerwood GE, Hernández D, Vickers JC, Cook AL, Palpant NJ, Pébay A, Hewitt AW, Powell JE. Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biol 2021; 22:76. [PMID: 33673841 PMCID: PMC7934233 DOI: 10.1186/s13059-021-02293-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) has provided a foundation for in vitro human disease modelling, drug development and population genetics studies. Gene expression plays a critical role in complex disease risk and therapeutic response. However, while the genetic background of reprogrammed cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells which would provide significant resolution. By integrating single cell RNA-sequencing (scRNA-seq) and population genetics, we apply a framework in which to evaluate cell type-specific effects of genetic variation on gene expression. RESULTS Here, we perform scRNA-seq on 64,018 fibroblasts from 79 donors and map expression quantitative trait loci (eQTLs) at the level of individual cell types. We demonstrate that the majority of eQTLs detected in fibroblasts are specific to an individual cell subtype. To address if the allelic effects on gene expression are maintained following cell reprogramming, we generate scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type-specific eQTLs in iPSCs and show that the eQTLs in fibroblasts almost entirely disappear during reprogramming. CONCLUSIONS This work provides an atlas of how genetic variation influences gene expression across cell subtypes and provides evidence for patterns of genetic architecture that lead to cell type-specific eQTL effects.
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Affiliation(s)
- Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Maciej S Daniszewski
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Yong Kiat Wee
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Duncan E Crombie
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
| | - Grace E Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Damián Hernández
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia.
- UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, Australia.
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36
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Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D'Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet 2021; 53:313-321. [PMID: 33664507 PMCID: PMC7944648 DOI: 10.1038/s41588-021-00800-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/25/2021] [Indexed: 12/18/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of novel colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.
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Affiliation(s)
- Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Craig Smail
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA. .,Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA.
| | - Michael J Gloudemans
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Laure Frésard
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - David Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Matteo D'Antonio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, USA
| | - Xin Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nicole M Ferraro
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Ivan Carcamo-Orive
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Bogdan Mirauta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Daniel D Seaton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Na Cai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dara Vakili
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Faculty of Medicine, Imperial College London, London, UK
| | - Danilo Horta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Chunli Zhao
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Diane B Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Devon E Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Matthew T Wheeler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Helena Kilpinen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.,UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Joshua W Knowles
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Erin N Smith
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
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37
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Barbeira AN, Bonazzola R, Gamazon ER, Liang Y, Park Y, Kim-Hellmuth S, Wang G, Jiang Z, Zhou D, Hormozdiari F, Liu B, Rao A, Hamel AR, Pividori MD, Aguet F, Bastarache L, Jordan DM, Verbanck M, Do R, Stephens M, Ardlie K, McCarthy M, Montgomery SB, Segrè AV, Brown CD, Lappalainen T, Wen X, Im HK. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol 2021; 22:49. [PMID: 33499903 PMCID: PMC7836161 DOI: 10.1186/s13059-020-02252-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
The resources generated by the GTEx consortium offer unprecedented opportunities to advance our understanding of the biology of human diseases. Here, we present an in-depth examination of the phenotypic consequences of transcriptome regulation and a blueprint for the functional interpretation of genome-wide association study-discovered loci. Across a broad set of complex traits and diseases, we demonstrate widespread dose-dependent effects of RNA expression and splicing. We develop a data-driven framework to benchmark methods that prioritize causal genes and find no single approach outperforms the combination of multiple approaches. Using colocalization and association approaches that take into account the observed allelic heterogeneity of gene expression, we propose potential target genes for 47% (2519 out of 5385) of the GWAS loci examined.
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Affiliation(s)
- Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Rodrigo Bonazzola
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Data Science Institute, Vanderbilt University, Nashville, TN, USA
- Clare Hall, University of Cambridge, Cambridge, UK
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Yanyu Liang
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - YoSon Park
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah Kim-Hellmuth
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Gao Wang
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Zhuoxun Jiang
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Dan Zhou
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Farhad Hormozdiari
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Boxiang Liu
- Department of Biology, Stanford University, Stanford, 94305, CA, USA
| | - Abhiram Rao
- Department of Biology, Stanford University, Stanford, 94305, CA, USA
| | - Andrew R Hamel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Milton D Pividori
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Department of Medicine, Vanderbilt University, Nashville, TN, USA
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel M Jordan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marie Verbanck
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Université de Paris - EA 7537 BIOSTM, Paris, France
| | - Ron Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ayellet V Segrè
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
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38
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Chang S, Hur SK, Naveh NSS, Thorvaldsen JL, French DL, Gagne AL, Jobaliya CD, Anguera MC, Bartolomei MS, Kalish JM. Derivation and investigation of the first human cell-based model of Beckwith-Wiedemann syndrome. Epigenetics 2020; 16:1295-1305. [PMID: 33300436 DOI: 10.1080/15592294.2020.1861172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Genomic imprinting is a rare form of gene expression in mammals in which a small number of genes are expressed in a parent-of-origin-specific manner. The aetiology of human imprinting disorders is diverse and includes chromosomal abnormalities, mutations, and epigenetic dysregulation of imprinted genes. The most common human imprinting disorder is Beckwith-Wiedemann syndrome (BWS), frequently caused by uniparental isodisomy and DNA methylation alterations. Because these lesions cannot be easily engineered, induced pluripotent stem cells (iPSC) are a compelling alternative. Here, we describe the first iPSC model derived from patients with BWS. Due to the mosaic nature of BWS patients, both BWS and non-BWS iPSC lines were derived from the same patient's fibroblasts. Importantly, we determine that DNA methylation and gene expression patterns of the imprinted region in the iPSC lines reflect the parental cells and are stable over time. Additionally, we demonstrate that differential expression in insulin signalling, cell proliferation, and cell cycle pathways was seen in hepatocyte lineages derived from BWS lines compared to controls. Thus, this cell based-model can be used to investigate the role of imprinting in the pathogenesis of BWS in disease-relevant cell types.
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Affiliation(s)
- Suhee Chang
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stella K Hur
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natali S Sobel Naveh
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deborah L French
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alyssa L Gagne
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chintan D Jobaliya
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Montserrat C Anguera
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Departments of Genetics and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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39
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Shao X, Guha S, Lu W, Campagno KE, Beckel JM, Mills JA, Yang W, Mitchell CH. Polarized Cytokine Release Triggered by P2X7 Receptor from Retinal Pigmented Epithelial Cells Dependent on Calcium Influx. Cells 2020; 9:cells9122537. [PMID: 33255431 PMCID: PMC7760537 DOI: 10.3390/cells9122537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Cytokine release from non-inflammatory cells is a key step in innate immunity, and agonists triggering cytokine release are central in coordinating responses. P2X7 receptor (P2X7R) stimulation by extracellular ATP is best known to active the NLRP3 inflammasome and release IL-1β, but stimulation also leads to release of other cytokines. As cytokine signaling by retinal pigmented epithelial (RPE) cells is implicated in retinal neurodegeneration, the role of P2X7R in release of cytokine IL-6 from RPE cells was investigated. P2X7R stimulation triggered IL-6 release from primary mouse RPE, human iPS-RPE and human ARPE-19 cells. IL-6 release was polarized, with predominant rise across apical membranes. IL-6 release was inhibited by P2X7R antagonists A438079, A839977, and AZ10606120, but not the NRTI lamivudine (3TC), P2X1R antagonist NF279, or P2Y1R antagonist MRS2179. P2X7R-mediated IL-6 release required extracellular Ca2+ and was blocked by Ca2+ chelator BAPTA. IL-6 release and Ca2+ elevation occurred rapidly, consistent with vesicular IL-6 staining in unstimulated cells. P2X7R stimulation did not trigger IL-1β release in these unprimed cells. P2X7R-mediated IL-6 release was enhanced in RPE cells from the ABCA4−/− mouse model of retinal degeneration. In summary, P2X7R stimulation triggers rapid Ca2+-dependent IL-6 release across the apical membrane of RPE cells.
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Affiliation(s)
- Xiaolei Shao
- Shenzhen Eye Hospital, School of Optometry, Shenzhen University, Shenzhen 518060, China;
- Department of Anatomy and Cell Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.G.); (J.M.B.)
| | - Sonia Guha
- Department of Anatomy and Cell Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.G.); (J.M.B.)
- Jules Stein Eye Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Wennan Lu
- Department of Basic and Translational Science, University of Pennsylvania, Philadelphia, PA 19104, USA; (W.L.); (K.E.C.)
| | - Keith E. Campagno
- Department of Basic and Translational Science, University of Pennsylvania, Philadelphia, PA 19104, USA; (W.L.); (K.E.C.)
| | - Jonathan M. Beckel
- Department of Anatomy and Cell Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.G.); (J.M.B.)
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jason A. Mills
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Kirby Center for Molecular Ophthalmology and Center for Advanced Retinal and Ocular Therapeutics (CAROT), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenli Yang
- Department of Medicine and Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Claire H. Mitchell
- Department of Anatomy and Cell Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.G.); (J.M.B.)
- Department of Basic and Translational Science, University of Pennsylvania, Philadelphia, PA 19104, USA; (W.L.); (K.E.C.)
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: ; Tel.: +1-215-573-2176
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40
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Renganaath K, Chong R, Day L, Kosuri S, Kruglyak L, Albert FW. Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross. eLife 2020; 9:e62669. [PMID: 33179598 PMCID: PMC7685706 DOI: 10.7554/elife.62669] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5832 natural DNA variants in the promoters of 2503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, which is consistent with the action of negative selection. Causal variants were also enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis-acting regulatory variation.
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Affiliation(s)
- Kaushik Renganaath
- Department of Genetics, Cell Biology, & Development, University of MinnesotaMinneapolisUnited States
| | - Rockie Chong
- Department of Chemistry & Biochemistry, University of California, Los AngelesLos AngelesUnited States
| | - Laura Day
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - Sriram Kosuri
- Department of Chemistry & Biochemistry, University of California, Los AngelesLos AngelesUnited States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - Frank W Albert
- Department of Genetics, Cell Biology, & Development, University of MinnesotaMinneapolisUnited States
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41
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Li Y, Renner DM, Comar CE, Whelan JN, Reyes HM, Cardenas-Diaz FL, Truitt R, Tan LH, Dong B, Alysandratos KD, Huang J, Palmer JN, Adappa ND, Kohanski MA, Kotton DN, Silverman RH, Yang W, Morrisey E, Cohen NA, Weiss SR. SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32995797 DOI: 10.1101/2020.09.24.312553] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronaviruses are adept at evading host antiviral pathways induced by viral double-stranded RNA, including interferon (IFN) signaling, oligoadenylate synthetase-ribonuclease L (OAS-RNase L), and protein kinase R (PKR). While dysregulated or inadequate IFN responses have been associated with severe coronavirus infection, the extent to which the recently emerged SARS-CoV-2 activates or antagonizes these pathways is relatively unknown. We found that SARS-CoV-2 infects patient-derived nasal epithelial cells, present at the initial site of infection, induced pluripotent stem cell-derived alveolar type 2 cells (iAT2), the major cell type infected in the lung, and cardiomyocytes (iCM), consistent with cardiovascular consequences of COVID-19 disease. Robust activation of IFN or OAS-RNase L is not observed in these cell types, while PKR activation is evident in iAT2 and iCM. In SARS-CoV-2 infected Calu-3 and A549 ACE2 lung-derived cell lines, IFN induction remains relatively weak; however activation of OAS-RNase L and PKR is observed. This is in contrast to MERS-CoV, which effectively inhibits IFN signaling as well as OAS-RNase L and PKR pathways, but similar to mutant MERS-CoV lacking innate immune antagonists. Remarkably, both OAS-RNase L and PKR are activated in MAVS knockout A549 ACE2 cells, demonstrating that SARS-CoV-2 can induce these host antiviral pathways despite minimal IFN production. Moreover, increased replication and cytopathic effect in RNASEL knockout A549 ACE2 cells implicates OAS-RNase L in restricting SARS-CoV-2. Finally, while SARS-CoV-2 fails to antagonize these host defense pathways, which contrasts with other coronaviruses, the IFN signaling response is generally weak. These host-virus interactions may contribute to the unique pathogenesis of SARS-CoV-2. Significance SARS-CoV-2 emergence in late 2019 led to the COVID-19 pandemic that has had devastating effects on human health and the economy. Early innate immune responses are essential for protection against virus invasion. While inadequate innate immune responses are associated with severe COVID-19 diseases, understanding of the interaction of SARS-CoV-2 with host antiviral pathways is minimal. We have characterized the innate immune response to SARS-CoV-2 infections in relevant respiratory tract derived cells and cardiomyocytes and found that SARS-CoV-2 activates two antiviral pathways, oligoadenylate synthetase-ribonuclease L (OAS-RNase L), and protein kinase R (PKR), while inducing minimal levels of interferon. This in contrast to MERS-CoV which inhibits all three pathways. Activation of these pathways may contribute to the distinctive pathogenesis of SARS-CoV-2.
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42
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Huang D, Gibeley SB, Xu C, Xiao Y, Celik O, Ginsberg HN, Leong KW. Engineering liver microtissues for disease modeling and regenerative medicine. ADVANCED FUNCTIONAL MATERIALS 2020; 30:1909553. [PMID: 33390875 PMCID: PMC7774671 DOI: 10.1002/adfm.201909553] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 05/08/2023]
Abstract
The burden of liver diseases is increasing worldwide, accounting for two million deaths annually. In the past decade, tremendous progress has been made in the basic and translational research of liver tissue engineering. Liver microtissues are small, three-dimensional hepatocyte cultures that recapitulate liver physiology and have been used in biomedical research and regenerative medicine. This review summarizes recent advances, challenges, and future directions in liver microtissue research. Cellular engineering approaches are used to sustain primary hepatocytes or produce hepatocytes derived from pluripotent stem cells and other adult tissues. Three-dimensional microtissues are generated by scaffold-free assembly or scaffold-assisted methods such as macroencapsulation, droplet microfluidics, and bioprinting. Optimization of the hepatic microenvironment entails incorporating the appropriate cell composition for enhanced cell-cell interactions and niche-specific signals, and creating scaffolds with desired chemical, mechanical and physical properties. Perfusion-based culture systems such as bioreactors and microfluidic systems are used to achieve efficient exchange of nutrients and soluble factors. Taken together, systematic optimization of liver microtissues is a multidisciplinary effort focused on creating liver cultures and on-chip models with greater structural complexity and physiological relevance for use in liver disease research, therapeutic development, and regenerative medicine.
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Affiliation(s)
- Dantong Huang
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Sarah B. Gibeley
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Cong Xu
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Ozgenur Celik
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Henry N. Ginsberg
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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43
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An induced pluripotent stem cell model of Fanconi anemia reveals mechanisms of p53-driven progenitor cell differentiation. Blood Adv 2020; 4:4679-4692. [PMID: 33002135 DOI: 10.1182/bloodadvances.2020001593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
Fanconi anemia (FA) is a disorder of DNA repair that manifests as bone marrow (BM) failure. The lack of accurate murine models of FA has refocused efforts toward differentiation of patient-derived induced pluripotent stem cells (IPSCs) to hematopoietic progenitor cells (HPCs). However, an intact FA DNA repair pathway is required for efficient IPSC derivation, hindering these efforts. To overcome this barrier, we used inducible complementation of FANCA-deficient IPSCs, which permitted robust maintenance of IPSCs. Modulation of FANCA during directed differentiation to HPCs enabled the production of FANCA-deficient human HPCs that recapitulated FA genotoxicity and hematopoietic phenotypes relative to isogenic FANCA-expressing HPCs. FANCA-deficient human HPCs underwent accelerated terminal differentiation driven by activation of p53/p21. We identified growth arrest specific 6 (GAS6) as a novel target of activated p53 in FANCA-deficient HPCs and modulate GAS6 signaling to rescue hematopoiesis in FANCA-deficient cells. This study validates our strategy to derive a sustainable, highly faithful human model of FA, uncovers a mechanism of HPC exhaustion in FA, and advances toward future cell therapy in FA.
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44
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Riemens RJM, Kenis G, van den Beucken T. Human-induced pluripotent stem cells as a model for studying sporadic Alzheimer's disease. Neurobiol Learn Mem 2020; 175:107318. [PMID: 32977028 DOI: 10.1016/j.nlm.2020.107318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/24/2022]
Abstract
The discovery of induced pluripotent stem cell (iPSC) technology has the potential to accelerate scientific research for Alzheimer's disease (AD). iPSCs are therefore increasingly considered for AD modeling and drug development. Nevertheless, most of the work conducted so far has mainly focused on iPSC models from patients with familial AD (fAD), while actually sporadic AD (sAD) is more prevalent and represents over 90% of the AD cases in the population. The development of more sAD models is therefore key for studying this multifactorial disorder. In fact, probing the unique genomes of sAD patients and their interaction with AD-associated environmental factors could contribute to a better understanding of this disease. However, initial iPSC-based models for sAD have shown a high degree of variability and inconsistencies in terms of AD hallmarks. In this review, we provide an overview of the studies that have been conducted for sAD so far. In addition, we critically assess important sources of variability related to the model in addition to those that might be explained by the heterogeneous nature of sAD. These considerations might aid in developing more consistent iPSC models of sAD, which could help in developing a better understanding of the molecular mechanisms underlying the disease.
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Affiliation(s)
- R J M Riemens
- Institute of Human Genetics, Julius Maximilian University, Wuerzburg, Germany; Department of Psychiatry & Neuropsychology, Graduate School MHeNS (School for Mental Health and Neuroscience), allocated with the Faculty Health Medicine and Life Sciences of Maastricht University, Maastricht, the Netherlands
| | - G Kenis
- Department of Psychiatry & Neuropsychology, Graduate School MHeNS (School for Mental Health and Neuroscience), allocated with the Faculty Health Medicine and Life Sciences of Maastricht University, Maastricht, the Netherlands
| | - T van den Beucken
- Department of Toxicogenomics, Graduate School GROW (Research School for Oncology and Developmental Biology), allocated with the Faculty Health Medicine and Life Sciences of Maastricht University, Maastricht, the Netherlands.
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45
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Kaserman JE, Hurley K, Dodge M, Villacorta-Martin C, Vedaie M, Jean JC, Liberti DC, James MF, Higgins MI, Lee NJ, Washko GR, San Jose Estepar R, Teckman J, Kotton DN, Wilson AA. A Highly Phenotyped Open Access Repository of Alpha-1 Antitrypsin Deficiency Pluripotent Stem Cells. Stem Cell Reports 2020; 15:242-255. [PMID: 32619491 PMCID: PMC7363960 DOI: 10.1016/j.stemcr.2020.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Individuals with the genetic disorder alpha-1 antitrypsin deficiency (AATD) are at risk of developing lung and liver disease. Patient induced pluripotent stem cells (iPSCs) have been found to model features of AATD pathogenesis but only a handful of AATD patient iPSC lines have been published. To capture the significant phenotypic diversity of the patient population, we describe here the establishment and characterization of a curated repository of AATD iPSCs with associated disease-relevant clinical data. To highlight the utility of the repository, we selected a subset of iPSC lines for functional characterization. Selected lines were differentiated to generate both hepatic and lung cell lineages and analyzed by RNA sequencing. In addition, two iPSC lines were targeted using CRISPR/Cas9 editing to accomplish scarless repair. Repository iPSCs are available to investigators for studies of disease pathogenesis and therapeutic discovery.
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Affiliation(s)
- Joseph E Kaserman
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Killian Hurley
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark Dodge
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Marall Vedaie
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Jyh-Chang Jean
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Derek C Liberti
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Marianne F James
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Michelle I Higgins
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Nora J Lee
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | | | | | | | - Darrell N Kotton
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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46
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Abbey D, Elwyn S, Hand NJ, Musunuru K, Rader DJ. Self-Organizing Human Induced Pluripotent Stem Cell Hepatocyte 3D Organoids Inform the Biology of the Pleiotropic TRIB1 Gene. Hepatol Commun 2020; 4:1316-1331. [PMID: 32923835 PMCID: PMC7471428 DOI: 10.1002/hep4.1538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
Establishment of a physiologically relevant human hepatocyte‐like cell system for in vitro translational research has been hampered by the limited availability of cell models that accurately reflect human biology and the pathophysiology of human disease. Here we report a robust, reproducible, and scalable protocol for the generation of hepatic organoids from human induced pluripotent stem cells (hiPSCs) using short exposure to nonengineered matrices. These hepatic organoids follow defined stages of hepatic development and express higher levels of early (hepatocyte nuclear factor 4A [HNF4A], prospero‐related homeobox 1 [PROX1]) and mature hepatic and metabolic markers (albumin, asialoglycoprotein receptor 1 [ASGR1], CCAAT/enhancer binding protein α [C/EBPα]) than two‐dimensional (2D) hepatocyte‐like cells (HLCs) at day 20 of differentiation. We used this model to explore the biology of the pleiotropic TRIB1 (Tribbles‐1) gene associated with a number of metabolic traits, including nonalcoholic fatty liver disease and plasma lipids. We used genome editing to delete the TRIB1 gene in hiPSCs and compared TRIB1‐deleted iPSC‐HLCs to isogenic iPSC‐HLCs under both 2D culture and three‐dimensional (3D) organoid conditions. Under conventional 2D culture conditions, TRIB1‐deficient HLCs showed maturation defects, with decreased expression of late‐stage hepatic and lipogenesis markers. In contrast, when cultured as 3D hepatic organoids, the differentiation defects were rescued, and a clear lipid‐related phenotype was noted in the TRIB1‐deficient induced pluripotent stem cell HLCs. Conclusion: This work supports the potential of genome‐edited hiPSC‐derived hepatic 3D organoids in exploring human hepatocyte biology, including the functional interrogation of genes identified through human genetic investigation.
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Affiliation(s)
- Deepti Abbey
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia PA.,Department of Translational Medicine and Human Genetics Perelman School of Medicine University of Pennsylvania Philadelphia PA.,Department of Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA
| | - Susannah Elwyn
- Department of Translational Medicine and Human Genetics Perelman School of Medicine University of Pennsylvania Philadelphia PA.,Department of Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA
| | - Nicholas J Hand
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia PA
| | - Kiran Musunuru
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine University of Pennsylvania Philadelphia PA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia PA.,Department of Translational Medicine and Human Genetics Perelman School of Medicine University of Pennsylvania Philadelphia PA.,Department of Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA.,Division of Cardiology and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine University of Pennsylvania Philadelphia PA
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47
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Jakubosky D, D'Antonio M, Bonder MJ, Smail C, Donovan MKR, Young Greenwald WW, Matsui H, D'Antonio-Chronowska A, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA. Properties of structural variants and short tandem repeats associated with gene expression and complex traits. Nat Commun 2020; 11:2927. [PMID: 32522982 PMCID: PMC7286898 DOI: 10.1038/s41467-020-16482-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Structural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.
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Affiliation(s)
- David Jakubosky
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093-0419, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093-0419, USA
| | - Matteo D'Antonio
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Craig Smail
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
| | - Margaret K R Donovan
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093-0419, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - William W Young Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Erin N Smith
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
- Department of Genetics, Stanford University, Stanford, California, 94305, USA
| | - Christopher DeBoever
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
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48
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Pinheiro EA, Magdy T, Burridge PW. Human In Vitro Models for Assessing the Genomic Basis of Chemotherapy-Induced Cardiovascular Toxicity. J Cardiovasc Transl Res 2020; 13:377-389. [PMID: 32078739 PMCID: PMC7365753 DOI: 10.1007/s12265-020-09962-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
Chemotherapy-induced cardiovascular toxicity (CICT) is a well-established risk for cancer survivors and causes diseases such as heart failure, arrhythmia, vascular dysfunction, and atherosclerosis. As our knowledge of the precise cardiovascular risks of each chemotherapy agent has improved, it has become clear that genomics is one of the most influential predictors of which patients will experience cardiovascular toxicity. Most recently, GWAS-led, top-down approaches have identified novel genetic variants and their related genes that are statistically related to CICT. Importantly, the advent of human-induced pluripotent stem cell (hiPSC) models provides a system to experimentally test the effect of these genomic findings in vitro, query the underlying mechanisms, and develop novel strategies to mitigate the cardiovascular toxicity liabilities due to these mechanisms. Here we review the cardiovascular toxicities of chemotherapy drugs, discuss how these can be modeled in vitro, and suggest how these models can be used to validate genetic variants that predispose patients to these effects.
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Affiliation(s)
- Emily A Pinheiro
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tarek Magdy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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49
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Kishore S, De Franco E, Cardenas-Diaz FL, Letourneau-Freiberg LR, Sanyoura M, Osorio-Quintero C, French DL, Greeley SAW, Hattersley AT, Gadue P. A Non-Coding Disease Modifier of Pancreatic Agenesis Identified by Genetic Correction in a Patient-Derived iPSC Line. Cell Stem Cell 2020; 27:137-146.e6. [PMID: 32442395 DOI: 10.1016/j.stem.2020.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 12/17/2019] [Accepted: 04/30/2020] [Indexed: 12/27/2022]
Abstract
GATA6 is a critical regulator of pancreatic development, with heterozygous mutations in this transcription factor being the most common cause of pancreatic agenesis. To study the variability in disease phenotype among individuals harboring these mutations, a patient-induced pluripotent stem cell model was used. Interestingly, GATA6 protein expression remained depressed in pancreatic progenitor cells even after correction of the coding mutation. Screening the regulatory regions of the GATA6 gene in these patient cells and 32 additional agenesis patients revealed a higher minor allele frequency of a SNP 3' of the GATA6 coding sequence. Introduction of this minor allele SNP by genome editing confirmed its functionality in depressing GATA6 expression and the efficiency of pancreas differentiation. This work highlights a possible genetic modifier contributing to pancreatic agenesis and demonstrates the usefulness of using patient-induced pluripotent stem cells for targeted discovery and validation of non-coding gene variants affecting gene expression and disease penetrance.
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Affiliation(s)
- Siddharth Kishore
- Department of Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Fabian L Cardenas-Diaz
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Lisa R Letourneau-Freiberg
- Kovler Diabetes Center and the Section of Adult and Pediatric Endocrinology, Diabetes, and Metabolism, University of Chicago Medicine, Chicago, IL, USA
| | - May Sanyoura
- Kovler Diabetes Center and the Section of Adult and Pediatric Endocrinology, Diabetes, and Metabolism, University of Chicago Medicine, Chicago, IL, USA
| | - Catherine Osorio-Quintero
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Siri Atma W Greeley
- Kovler Diabetes Center and the Section of Adult and Pediatric Endocrinology, Diabetes, and Metabolism, University of Chicago Medicine, Chicago, IL, USA
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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50
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Pinheiro EA, Fetterman KA, Burridge PW. hiPSCs in cardio-oncology: deciphering the genomics. Cardiovasc Res 2020; 115:935-948. [PMID: 30689737 DOI: 10.1093/cvr/cvz018] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/11/2018] [Accepted: 01/21/2019] [Indexed: 12/18/2022] Open
Abstract
The genomic predisposition to oncology-drug-induced cardiovascular toxicity has been postulated for many decades. Only recently has it become possible to experimentally validate this hypothesis via the use of patient-specific human-induced pluripotent stem cells (hiPSCs) and suitably powered genome-wide association studies (GWAS). Identifying the individual single nucleotide polymorphisms (SNPs) responsible for the susceptibility to toxicity from a specific drug is a daunting task as this precludes the use of one of the most powerful tools in genomics: comparing phenotypes to close relatives, as these are highly unlikely to have been treated with the same drug. Great strides have been made through the use of candidate gene association studies (CGAS) and increasingly large GWAS studies, as well as in vivo whole-organism studies to further our mechanistic understanding of this toxicity. The hiPSC model is a powerful technology to build on this work and identify and validate causal variants in mechanistic pathways through directed genomic editing such as CRISPR. The causative variants identified through these studies can then be implemented clinically to identify those likely to experience cardiovascular toxicity and guide treatment options. Additionally, targets identified through hiPSC studies can inform future drug development. Through careful phenotypic characterization, identification of genomic variants that contribute to gene function and expression, and genomic editing to verify mechanistic pathways, hiPSC technology is a critical tool for drug discovery and the realization of precision medicine in cardio-oncology.
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Affiliation(s)
- Emily A Pinheiro
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Searle 8-525, 320 East Superior Street, Chicago, IL, USA
| | - K Ashley Fetterman
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Searle 8-525, 320 East Superior Street, Chicago, IL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Searle 8-525, 320 East Superior Street, Chicago, IL, USA
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