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Arthur TD, Joshua IN, Nguyen JP, D'Antonio-Chronowska A, Frazer KA, D'Antonio M. IFN-γ activates an immune-like regulatory network in the cardiac vascular endothelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592380. [PMID: 38746472 PMCID: PMC11092750 DOI: 10.1101/2024.05.03.592380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The regulatory mechanisms underlying the response to pro-inflammatory cytokines during myocarditis are poorly understood. Here, we use iPSC-derived cardiovascular progenitor cells (CVPCs) to model the response to interferon gamma (IFN-γ) during myocarditis. We generate RNA-seq and ATAC-seq for four CVPCs that were treated with IFN-γ and compare them with paired untreated controls. Transcriptional differences after treatment show that IFN-γ initiates an innate immune cell-like response in the vascular cardiac endothelium. IFN-γ treatment also shifts the CVPC transcriptome towards the adult coronary artery and aorta profiles and expands the relative endothelial cell population in all four CVPC lines. Analysis of the accessible chromatin shows that IFN-γ is a potent chromatin remodeler and establishes an IRF-STAT immune-cell like regulatory network. Our findings reveal insights into the endothelial-specific protective mechanisms during myocarditis.
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2
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Cao M, Liu Y, Sun Y, Han R, Jiang H. Current advances in human-induced pluripotent stem cell-based models and therapeutic approaches for congenital heart disease. Mol Cell Biochem 2024:10.1007/s11010-024-04997-z. [PMID: 38635080 DOI: 10.1007/s11010-024-04997-z] [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: 12/29/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Congenital heart disease (CHD) represents a significant risk factor with profound implications for neonatal survival rates and the overall well-being of adult patients. The emergence of induced pluripotent stem cells (iPSCs) and their derived cells, combined with CRISPR technology, high-throughput experimental techniques, and organoid technology, which are better suited to contemporary research demands, offer new possibilities for treating CHD. Prior investigations have indicated that the paracrine effect of exosomes may hold potential solutions for therapeutic intervention. This review provides a summary of the advancements in iPSC-based models and clinical trials associated with CHD while elucidating potential therapeutic mechanisms and delineating clinical constraints pertinent to iPSC-based therapy, thereby offering valuable insights for further deliberation.
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Affiliation(s)
- Meiling Cao
- Department of Neonatology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Yanshan Liu
- Department of Pediatrics, The First Hospital of China Medical University, No.155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Ying Sun
- Department of Pediatrics, The First Hospital of China Medical University, No.155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Ruiyi Han
- Department of Pediatrics, The First Hospital of China Medical University, No.155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Hongkun Jiang
- Department of Pediatrics, The First Hospital of China Medical University, No.155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, China.
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3
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Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Jaureguy J, Silva N, Henson B, Panopoulos AD, Belmonte JCI, D'Antonio M, McVicker G, Frazer KA. Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588874. [PMID: 38645112 PMCID: PMC11030419 DOI: 10.1101/2024.04.10.588874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Most GWAS loci are presumed to affect gene regulation, however, only ∼43% colocalize with expression quantitative trait loci (eQTLs). To address this colocalization gap, we identify eQTLs, chromatin accessibility QTLs (caQTLs), and histone acetylation QTLs (haQTLs) using molecular samples from three early developmental (EDev) tissues. Through colocalization, we annotate 586 GWAS loci for 17 traits by QTL complexity, QTL phenotype, and QTL temporal specificity. We show that GWAS loci are highly enriched for colocalization with complex QTL modules that affect multiple elements (genes and/or peaks). We also demonstrate that caQTLs and haQTLs capture regulatory variations not associated with eQTLs and explain ∼49% of the functionally annotated GWAS loci. Additionally, we show that EDev-unique QTLs are strongly depleted for colocalizing with GWAS loci. By conducting one of the largest multi-omic QTL studies to date, we demonstrate that many GWAS loci exhibit phenotypic complexity and therefore, are missed by traditional eQTL analyses.
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4
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Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Greenwald WWY, D'Antonio M, Pera MF, Frazer KA. Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. Nat Commun 2024; 15:1664. [PMID: 38395976 PMCID: PMC10891157 DOI: 10.1038/s41467-024-45506-6] [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: 05/05/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.
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Affiliation(s)
- Timothy D Arthur
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jennifer P Nguyen
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Nayara S Silva
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Isaac N Joshua
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - André D Luchessi
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - William W Young Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Matteo D'Antonio
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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5
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Vinciguerra M, Dobrev D, Nattel S. Atrial fibrillation: pathophysiology, genetic and epigenetic mechanisms. THE LANCET REGIONAL HEALTH. EUROPE 2024; 37:100785. [PMID: 38362554 PMCID: PMC10866930 DOI: 10.1016/j.lanepe.2023.100785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/08/2023] [Accepted: 11/02/2023] [Indexed: 02/17/2024]
Abstract
Atrial fibrillation (AF) is the most common supraventricular arrhythmia affecting up to 1% of the general population. Its prevalence dramatically increases with age and could reach up to ∼10% in the elderly. The management of AF is a complex issue that is object of extensive ongoing basic and clinical research, it depends on its genetic and epigenetic causes, and it varies considerably geographically and also according to the ethnicity. Mechanistically, over the last decade, Genome Wide Association Studies have uncovered over 100 genetic loci associated with AF, and have shown that European ancestry is associated with elevated risk of AF. These AF-associated loci revolve around different types of disturbances, including inflammation, electrical abnormalities, and structural remodeling. Moreover, the discovery of epigenetic regulatory mechanisms, involving non-coding RNAs, DNA methylation and histone modification, has allowed unravelling what modifications reshape the processes leading to arrhythmias. Our review provides a current state of the field regarding the identification and functional characterization of AF-related genetic and epigenetic regulatory networks, including ethnic differences. We discuss clear and emerging connections between genetic regulation and pathophysiological mechanisms of AF.
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Affiliation(s)
- Manlio Vinciguerra
- Department of Translational Stem Cell Biology, Research Institute, Medical University of Varna, Varna, Bulgaria
- Liverpool Centre for Cardiovascular Science, Faculty of Health, Liverpool John Moores University, Liverpool, United Kingdom
| | - Dobromir Dobrev
- Institute of Pharmacology, West German Heart and Vascular Center, University Duisburg-Essen, Duisburg, Germany
- Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montréal, Canada
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Stanley Nattel
- Institute of Pharmacology, West German Heart and Vascular Center, University Duisburg-Essen, Duisburg, Germany
- Department of Medicine and Research Center, Montreal Heart Institute and Université de Montréal, Montréal, Canada
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Faculty of Health, Medicine, and Life Sciences, Maastricht University, Maastricht, Netherlands
- IHU LIRYC and Fondation Bordeaux Université, Bordeaux, France
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
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6
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Peña-Martínez EG, Pomales-Matos DA, Rivera-Madera A, Messon-Bird JL, Medina-Feliciano JG, Sanabria-Alberto L, Barreiro-Rosario AC, Rivera-Del Valle J, Rodríguez-Ríos JM, Rodríguez-Martínez JA. Prioritizing cardiovascular disease-associated variants altering NKX2-5 and TBX5 binding through an integrative computational approach. J Biol Chem 2023; 299:105423. [PMID: 37926287 PMCID: PMC10750078 DOI: 10.1016/j.jbc.2023.105423] [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: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are heavily influenced by genetic factors. Genome-wide association studies have mapped >90% of CVD-associated variants within the noncoding genome, which can alter the function of regulatory proteins, such as transcription factors (TFs). However, due to the overwhelming number of single-nucleotide polymorphisms (SNPs) (>500,000) in genome-wide association studies, prioritizing variants for in vitro analysis remains challenging. In this work, we implemented a computational approach that considers support vector machine (SVM)-based TF binding site classification and cardiac expression quantitative trait loci (eQTL) analysis to identify and prioritize potential CVD-causing SNPs. We identified 1535 CVD-associated SNPs within TF footprints and putative cardiac enhancers plus 14,218 variants in linkage disequilibrium with genotype-dependent gene expression in cardiac tissues. Using ChIP-seq data from two cardiac TFs (NKX2-5 and TBX5) in human-induced pluripotent stem cell-derived cardiomyocytes, we trained a large-scale gapped k-mer SVM model to identify CVD-associated SNPs that altered NKX2-5 and TBX5 binding. The model was tested by scoring human heart TF genomic footprints within putative enhancers and measuring in vitro binding through electrophoretic mobility shift assay. Five variants predicted to alter NKX2-5 (rs59310144, rs6715570, and rs61872084) and TBX5 (rs7612445 and rs7790964) binding were prioritized for in vitro validation based on the magnitude of the predicted change in binding and are in cardiac tissue eQTLs. All five variants altered NKX2-5 and TBX5 DNA binding. We present a bioinformatic approach that considers tissue-specific eQTL analysis and SVM-based TF binding site classification to prioritize CVD-associated variants for in vitro analysis.
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Affiliation(s)
- Edwin G Peña-Martínez
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
| | - Diego A Pomales-Matos
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
| | | | - Jean L Messon-Bird
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
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7
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Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK. Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. Dev Cell 2023; 58:2206-2216.e5. [PMID: 37848026 PMCID: PMC10720985 DOI: 10.1016/j.devcel.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Transcriptional enhancers direct precise gene expression patterns during development and harbor the majority of variants associated with phenotypic diversity, evolutionary adaptations, and disease. Pinpointing which enhancer variants contribute to changes in gene expression and phenotypes is a major challenge. Here, we find that suboptimal or low-affinity binding sites are necessary for precise gene expression during heart development. Single-nucleotide variants (SNVs) can optimize the affinity of ETS binding sites, causing gain-of-function (GOF) gene expression, cell migration defects, and phenotypes as severe as extra beating hearts in the marine chordate Ciona robusta. In human induced pluripotent stem cell (iPSC)-derived cardiomyocytes, a SNV within a human GATA4 enhancer increases ETS binding affinity and causes GOF enhancer activity. The prevalence of suboptimal-affinity sites within enhancers creates a vulnerability whereby affinity-optimizing SNVs can lead to GOF gene expression, changes in cellular identity, and organismal-level phenotypes that could contribute to the evolution of novel traits or diseases.
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Affiliation(s)
- Granton A Jindal
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexis T Bantle
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joe J Solvason
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica L Grudzien
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Fabian Lim
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sophia H Le
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin P Song
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michelle F Ragsac
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adam Klie
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reid O Larsen
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Young Greenwald WW, D'Antonio M, Pera MF, Frazer KA. Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541447. [PMID: 37292794 PMCID: PMC10245835 DOI: 10.1101/2023.05.20.541447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discovered 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which were highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlied the coordinated expression of genes in the GNMs. Epigenetic analyses revealed that regulatory networks underlying self-renewal and pluripotency have a surprising level of complexity. Genetic analyses identified thousands of regulatory variants that overlapped predicted transcription factor binding sites and were associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network were significantly enriched for regulatory variants with large effects, suggesting that they may play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work captures the coordinated activity of tens of thousands of regulatory elements in hiPSCs and bins these elements into discrete functionally characterized regulatory networks, shows that regulatory elements in pluripotency networks harbor variants with large effects, and provides a rich resource for future pluripotent stem cell research.
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9
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Peña-Martínez EG, Pomales-Matos DA, Rivera-Madera A, Messon-Bird JL, Medina-Feliciano JG, Sanabria-Alberto L, Barreiro-Rosario AC, Rodriguez-Rios JM, Rodríguez-Martínez JA. Prioritizing Cardiovascular Disease-Associated Variants Altering NKX2-5 Binding through an Integrative Computational Approach. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.01.23294951. [PMID: 37693486 PMCID: PMC10491373 DOI: 10.1101/2023.09.01.23294951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are heavily influenced by genetic factors. Genome-wide association studies (GWAS) have mapped > 90% of CVD-associated variants within the non-coding genome, which can alter the function of regulatory proteins, like transcription factors (TFs). However, due to the overwhelming number of GWAS single nucleotide polymorphisms (SNPs) (>500,000), prioritizing variants for in vitro analysis remains challenging. In this work, we implemented a computational approach that considers support vector machine (SVM)-based TF binding site classification and cardiac expression quantitative trait loci (eQTL) analysis to identify and prioritize potential CVD-causing SNPs. We identified 1,535 CVD-associated SNPs that occur within human heart footprints/enhancers and 9,309 variants in linkage disequilibrium (LD) with differential gene expression profiles in cardiac tissue. Using hiPSC-CM ChIP-seq data from NKX2-5 and TBX5, two cardiac TFs essential for proper heart development, we trained a large-scale gapped k-mer SVM (LS-GKM-SVM) predictive model that can identify binding sites altered by CVD-associated SNPs. The computational predictive model was tested by scoring human heart footprints and enhancers in vitro through electrophoretic mobility shift assay (EMSA). Three variants (rs59310144, rs6715570, and rs61872084) were prioritized for in vitro validation based on their eQTL in cardiac tissue and LS-GKM-SVM prediction to alter NKX2-5 DNA binding. All three variants altered NKX2-5 DNA binding. In summary, we present a bioinformatic approach that considers tissue-specific eQTL analysis and SVM-based TF binding site classification to prioritize CVD-associated variants for in vitro experimental analysis.
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10
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Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun 2023; 14:4999. [PMID: 37591828 PMCID: PMC10435551 DOI: 10.1038/s41467-023-40505-5] [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: 02/11/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have linked hundreds of loci to cardiac diseases. However, in most loci the causal variants and their target genes remain unknown. We developed a combined experimental and analytical approach that integrates single cell epigenomics with GWAS to prioritize risk variants and genes. We profiled accessible chromatin in single cells obtained from human hearts and leveraged the data to study genetics of Atrial Fibrillation (AF), the most common cardiac arrhythmia. Enrichment analysis of AF risk variants using cell-type-resolved open chromatin regions (OCRs) implicated cardiomyocytes as the main mediator of AF risk. We then performed statistical fine-mapping, leveraging the information in OCRs, and identified putative causal variants in 122 AF-associated loci. Taking advantage of the fine-mapping results, our novel statistical procedure for gene discovery prioritized 46 high-confidence risk genes, highlighting transcription factors and signal transduction pathways important for heart development. In summary, our analysis provides a comprehensive map of AF risk variants and genes, and a general framework to integrate single-cell genomics with genetic studies of complex traits.
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Affiliation(s)
- Alan Selewa
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Kaixuan Luo
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael Wasney
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Linsin Smith
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaotong Sun
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chenwei Tang
- The College, The University of Chicago, Chicago, IL, 60637, USA
| | - Heather Eckart
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ivan P Moskowitz
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA
| | - Anindita Basu
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Sebastian Pott
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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11
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Peña-Martínez EG, Rivera-Madera A, Pomales-Matos DA, Sanabria-Alberto L, Rosario-Cañuelas BM, Rodríguez-Ríos JM, Carrasquillo-Dones EA, Rodríguez-Martínez JA. Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194906. [PMID: 36690178 PMCID: PMC10013089 DOI: 10.1016/j.bbagrm.2023.194906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/22/2023]
Abstract
Genome-wide association studies (GWAS) have mapped over 90 % of disease- or trait-associated variants within the non-coding genome, like cis-regulatory elements (CREs). Non-coding single nucleotide polymorphisms (SNPs) are genomic variants that can change how DNA-binding regulatory proteins, like transcription factors (TFs), interact with the genome and regulate gene expression. NKX2-5 is a TF essential for proper heart development, and mutations affecting its function have been associated with congenital heart diseases (CHDs). However, establishing a causal mechanism between non-coding genomic variants and human disease remains challenging. To address this challenge, we identified 8475 SNPs predicted to alter NKX2-5 DNA-binding using a position weight matrix (PWM)-based predictive model. Five variants were prioritized for in vitro validation; four of them are associated with traits and diseases that impact cardiovascular health. The impact of these variants on NKX2-5 binding was evaluated with electrophoretic mobility shift assay (EMSA) using purified recombinant NKX2-5 homeodomain. Binding curves were constructed to determine changes in binding between variant and reference alleles. Variants rs7350789, rs7719885, rs747334, and rs3892630 increased binding affinity, whereas rs61216514 decreased binding by NKX2-5 when compared to the reference genome. Our findings suggest that differential TF-DNA binding affinity can be key in establishing a causal mechanism of pathogenic variants.
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12
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D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. Nat Commun 2023; 14:1132. [PMID: 36854752 PMCID: PMC9975214 DOI: 10.1038/s41467-023-36638-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
The causal variants and genes underlying thousands of cardiac GWAS signals have yet to be identified. Here, we leverage spatiotemporal information on 966 RNA-seq cardiac samples and perform an expression quantitative trait locus (eQTL) analysis detecting eQTLs considering both eGenes and eIsoforms. We identify 2,578 eQTLs associated with a specific developmental stage-, tissue- and/or cell type. Colocalization between eQTL and GWAS signals of five cardiac traits identified variants with high posterior probabilities for being causal in 210 GWAS loci. Pulse pressure GWAS loci are enriched for colocalization with fetal- and smooth muscle- eQTLs; pulse rate with adult- and cardiac muscle- eQTLs; and atrial fibrillation with cardiac muscle- eQTLs. Fine mapping identifies 79 credible sets with five or fewer SNPs, of which 15 were associated with spatiotemporal eQTLs. Our study shows that many cardiac GWAS variants impact traits and disease in a developmental stage-, tissue- and/or cell type-specific fashion.
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Affiliation(s)
- Matteo D'Antonio
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
| | - Jennifer P Nguyen
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Arthur
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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13
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Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 2023; 14:346. [PMID: 36681680 PMCID: PMC9867739 DOI: 10.1038/s41467-023-35833-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-seq, ATAC-Seq, RNA-seq, and SNP arrays. We integrate 153 individual data sets from 42 patients and nominate 50 histology-specific master transcription factors (MTF) to define RCC histologic subtypes, including EPAS1 and ETS-1 in ccRCC, HNF1B in pRCC, and FOXI1 in chRCC. We confirm histology-specific MTFs via immunohistochemistry including a ccRCC-specific TF, BHLHE41. FOXI1 overexpression with knock-down of EPAS1 in the 786-O ccRCC cell line induces transcriptional upregulation of chRCC-specific genes, TFCP2L1, ATP6V0D2, KIT, and INSRR, implicating FOXI1 as a MTF for chRCC. Integrating RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data reveals that risk-variants are significantly enriched in allelically-imbalanced peaks. This epigenomic atlas in primary human samples provides a resource for future investigation.
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Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan C Baca
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elio Adib
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Talal El Zarif
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - David A Braun
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Heng Du
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michel Alchoueiry
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sayed G Matar
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Andres Acosta
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yue Hou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacob E Berchuck
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elizabeth Henske
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Toni K Choueiri
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
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14
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Baca SC, Singler C, Zacharia S, Seo JH, Morova T, Hach F, Ding Y, Schwarz T, Huang CCF, Anderson J, Fay AP, Kalita C, Groha S, Pomerantz MM, Wang V, Linder S, Sweeney CJ, Zwart W, Lack NA, Pasaniuc B, Takeda DY, Gusev A, Freedman ML. Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation. Nat Genet 2022; 54:1364-1375. [PMID: 36071171 PMCID: PMC9784646 DOI: 10.1038/s41588-022-01168-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/19/2022] [Indexed: 12/25/2022]
Abstract
Many genetic variants affect disease risk by altering context-dependent gene regulation. Such variants are difficult to study mechanistically using current methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs). To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for identifying genotypic and allele-specific effects on chromatin that are also associated with disease. In prostate cancer, CWAS identified regulatory elements and androgen receptor-binding sites that explained the association at 52 of 98 known prostate cancer risk loci and discovered 17 additional risk loci. CWAS implicated key developmental transcription factors in prostate cancer risk that are overlooked by eQTL-based approaches due to context-dependent gene regulation. We experimentally validated associations and demonstrated the extensibility of CWAS to additional epigenomic datasets and phenotypes, including response to prostate cancer treatment. CWAS is a powerful and biologically interpretable paradigm for studying variants that influence traits by affecting transcriptional regulation.
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Affiliation(s)
- Sylvan C. Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Cassandra Singler
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Soumya Zacharia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tunc Morova
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada
| | - Faraz Hach
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada
| | - Yi Ding
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA
| | | | - Jacob Anderson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - André P. Fay
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cynthia Kalita
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA
| | - Stefan Groha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Mark M. Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Victoria Wang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | | | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Nathan A. Lack
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada,School of Medicine, Koç University, Istanbul, Turkey
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA,Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Y. Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA,Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA,These authors jointly supervised this work. Correspondence should be directed to M.L.F or A.G. ()
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA,These authors jointly supervised this work. Correspondence should be directed to M.L.F or A.G. ()
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15
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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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16
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In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. PLoS Comput Biol 2022; 18:e1009918. [PMID: 35226669 PMCID: PMC8912908 DOI: 10.1371/journal.pcbi.1009918] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/10/2022] [Accepted: 02/10/2022] [Indexed: 01/03/2023] Open
Abstract
Reactivation of fetal-specific genes and isoforms occurs during heart failure. However, the underlying molecular mechanisms and the extent to which the fetal program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal, healthy adult and heart failure have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that reactivation of fetal-specific RNA-binding proteins (RBPs), and the accompanied re-expression of 1,523 fetal-specific isoforms, contribute to the transcriptome differences between heart failure and healthy adult heart. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms encode proteins that tend to have more functions, are more likely to harbor RBP binding sites, have canonical sequences at their splice sites, and contain typical upstream polypyrimidine tracts. Our study suggests that compared with healthy adult, fetal cardiac tissue requires stricter transcriptional regulation, and that during heart failure reversion to this stricter transcriptional regulation occurs. Furthermore, we provide a resource of cardiac developmental stage-specific and heart failure-associated genes and isoforms, which are largely unexplored and can be exploited to investigate novel therapeutics for heart failure. Heart failure is a chronic condition in which the heart does not pump enough blood. It has been shown that in heart failure, the adult heart reverts to a fetal-like metabolic state and oxygen consumption. Additionally, genes and isoforms that are expressed in the heart only during fetal development (i.e. not in the healthy adult heart) are turned on in heart failure. However, the underlying molecular mechanisms and the extent to which the switch to a fetal gene program occurs remains unclear. In this study, we initially characterized the differences between the fetal and adult heart transcriptomes (entire set of expressed genes and isoforms). We found that RNA binding proteins (RBPs), a family of genes that regulate multiple aspects of a transcript’s maturation, including transcription, splicing and post-transcriptional modifications, play a central role in the differences between fetal and adult heart tissues. We observed that many RBPs that are only expressed in the heart during fetal development become reactivated in heart failure, resulting in the expression of 1,523 fetal-specific isoforms. These findings suggest that reactivation of fetal-specific RBPs in heart failure drives a transcriptome-wide switch to expression of fetal-specific isoforms; and hence that RBPs could potentially serve as novel therapeutic targets.
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17
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Ruff KLM, Hollstein R, Fazaal J, Thieme F, Gehlen J, Mangold E, Knapp M, Welzenbach J, Ludwig KU. Allele-specific transcription factor binding in a cellular model of orofacial clefting. Sci Rep 2022; 12:1807. [PMID: 35110662 PMCID: PMC8810875 DOI: 10.1038/s41598-022-05876-7] [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: 08/03/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a frequent congenital malformation with multifactorial etiology. While recent genome-wide association studies (GWAS) have identified several nsCL/P risk loci, the functional effects of the associated non-coding variants are largely unknown. Furthermore, additional risk loci remain undetected due to lack of power. As genetic variants might alter binding of transcription factors (TF), we here hypothesized that the integration of data from TF binding sites, expression analyses and nsCL/P GWAS might help to (i) identify functionally relevant variants at GWAS loci, and (ii) highlight novel risk variants that have been previously undetected. Analysing the craniofacial TF TFAP2A in human embryonic palatal mesenchyme (HEPM) cells, we identified 2845 TFAP2A ChIP-seq peaks, several of which were located near nsCL/P candidate genes (e.g. MSX1 and SPRY2). Comparison with independent data suggest that 802 of them might be specific to craniofacial development, and genes near these peaks are enriched in processes relevant to nsCL/P. Integration with nsCL/P GWAS data, however, did not show robust evidence for co-localization of common nsCL/P risk variants with TFAP2A ChIP-seq peaks. This data set represents a new resource for the analyses of craniofacial processes, and similar approaches with additional cell lines and TFs could be applied to generate further insights into nsCL/P etiology.
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Affiliation(s)
- Katharina L M Ruff
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Ronja Hollstein
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julia Fazaal
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Frederic Thieme
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jan Gehlen
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Elisabeth Mangold
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute for Medical Biometry, Informatics and Epidemiology IMBIE, University of Bonn, Bonn, Germany
| | - Julia Welzenbach
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany.
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18
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Assum I, Krause J, Scheinhardt MO, Müller C, Hammer E, Börschel CS, Völker U, Conradi L, Geelhoed B, Zeller T, Schnabel RB, Heinig M. Tissue-specific multi-omics analysis of atrial fibrillation. Nat Commun 2022; 13:441. [PMID: 35064145 PMCID: PMC8782899 DOI: 10.1038/s41467-022-27953-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWAS) for atrial fibrillation (AF) have uncovered numerous disease-associated variants. Their underlying molecular mechanisms, especially consequences for mRNA and protein expression remain largely elusive. Thus, refined multi-omics approaches are needed for deciphering the underlying molecular networks. Here, we integrate genomics, transcriptomics, and proteomics of human atrial tissue in a cross-sectional study to identify widespread effects of genetic variants on both transcript (cis-eQTL) and protein (cis-pQTL) abundance. We further establish a novel targeted trans-QTL approach based on polygenic risk scores to determine candidates for AF core genes. Using this approach, we identify two trans-eQTLs and five trans-pQTLs for AF GWAS hits, and elucidate the role of the transcription factor NKX2-5 as a link between the GWAS SNP rs9481842 and AF. Altogether, we present an integrative multi-omics method to uncover trans-acting networks in small datasets and provide a rich resource of atrial tissue-specific regulatory variants for transcript and protein levels for cardiovascular disease gene prioritization.
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Affiliation(s)
- Ines Assum
- Computational Health Center, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), München, Germany
- Department of Informatics, Technical University Munich, München, Germany
| | - Julia Krause
- University Center of Cardiovascular Science, University Heart and Vascular Center Hamburg, Hamburg, Germany
- Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany
| | - Markus O Scheinhardt
- Institute of Medical Biometry and Statistics, University of Lübeck, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - Christian Müller
- University Center of Cardiovascular Science, University Heart and Vascular Center Hamburg, Hamburg, Germany
- Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany
| | - Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- Partner site Greifswald, DZHK (German Center for Cardiovascular Research), Greifswald, Germany
| | - Christin S Börschel
- Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany
- Department of Cardiology, University Heart and Vascular Center Hamburg, Hamburg, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- Partner site Greifswald, DZHK (German Center for Cardiovascular Research), Greifswald, Germany
| | - Lenard Conradi
- Department of Cardiovascular Surgery, University Heart and Vascular Center Hamburg, Hamburg, Germany
| | - Bastiaan Geelhoed
- Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany
- Department of Cardiology, University Heart and Vascular Center Hamburg, Hamburg, Germany
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tanja Zeller
- University Center of Cardiovascular Science, University Heart and Vascular Center Hamburg, Hamburg, Germany
- Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany
| | - Renate B Schnabel
- Partner site Hamburg/Kiel/Lübeck, DZHK (German Center for Cardiovascular Research), Hamburg, Germany.
- Department of Cardiology, University Heart and Vascular Center Hamburg, Hamburg, Germany.
| | - Matthias Heinig
- Computational Health Center, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), München, Germany.
- Department of Informatics, Technical University Munich, München, Germany.
- Partner site Munich, DZHK (German Center for Cardiovascular Research), Munich, Germany.
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19
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Human iPSC-Cardiomyocytes as an Experimental Model to Study Epigenetic Modifiers of Electrophysiology. Cells 2022; 11:cells11020200. [PMID: 35053315 PMCID: PMC8774228 DOI: 10.3390/cells11020200] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/31/2021] [Accepted: 01/01/2022] [Indexed: 02/04/2023] Open
Abstract
The epigenetic landscape and the responses to pharmacological epigenetic regulators in each human are unique. Classes of epigenetic writers and erasers, such as histone acetyltransferases, HATs, and histone deacetylases, HDACs, control DNA acetylation/deacetylation and chromatin accessibility, thus exerting transcriptional control in a tissue- and person-specific manner. Rapid development of novel pharmacological agents in clinical testing—HDAC inhibitors (HDACi)—targets these master regulators as common means of therapeutic intervention in cancer and immune diseases. The action of these epigenetic modulators is much less explored for cardiac tissue, yet all new drugs need to be tested for cardiotoxicity. To advance our understanding of chromatin regulation in the heart, and specifically how modulation of DNA acetylation state may affect functional electrophysiological responses, human-induced pluripotent stem-cell-derived cardiomyocyte (hiPSC-CM) technology can be leveraged as a scalable, high-throughput platform with ability to provide patient-specific insights. This review covers relevant background on the known roles of HATs and HDACs in the heart, the current state of HDACi development, applications, and any adverse cardiac events; it also summarizes relevant differential gene expression data for the adult human heart vs. hiPSC-CMs along with initial transcriptional and functional results from using this new experimental platform to yield insights on epigenetic control of the heart. We focus on the multitude of methodologies and workflows needed to quantify responses to HDACis in hiPSC-CMs. This overview can help highlight the power and the limitations of hiPSC-CMs as a scalable experimental model in capturing epigenetic responses relevant to the human heart.
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20
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Shetty A, Seo JH, Bell CA, O’Connor EP, Pomerantz MM, Freedman ML, Gusev A. Allele-specific epigenetic activity in prostate cancer and normal prostate tissue implicates prostate cancer risk mechanisms. Am J Hum Genet 2021; 108:2071-2085. [PMID: 34699744 DOI: 10.1016/j.ajhg.2021.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/15/2021] [Indexed: 11/26/2022] Open
Abstract
Genome-wide association studies (GWASs) of prostate cancer have identified >250 significant risk loci, but the causal variants and mechanisms for these loci remain largely unknown. Here, we sought to identify and characterize risk-harboring regulatory elements by integrating epigenomes from primary prostate tumor and normal tissues of 27 individuals across the H3K27ac, H3K4me3, and H3K4me2 histone marks and FOXA1 and HOXB13 transcription factors. We identified 7,371 peaks with significant allele specificity (allele-specific quantitative trait locus [asQTL] peaks). Showcasing their relevance to prostate cancer risk, H3K27ac T-asQTL peaks were the single annotation most enriched for prostate cancer GWAS heritability (40×), significantly higher than corresponding non-asQTL H3K27ac peaks (14×) or coding regions (14×). Surprisingly, fine-mapped GWAS risk variants were most significantly enriched for asQTL peaks observed in tumors, including asQTL peaks that were differentially imbalanced with respect to tumor-normal states. These data pinpointed putative causal regulatory elements at 20 GWAS loci, of which 11 were detected only in the tumor samples. More broadly, tumor-specific asQTLs were enriched for expression QTLs in benign tissues as well as accessible regions found in stem cells, supporting a hypothesis where some germline variants become reactivated during or after transformation and can be captured by epigenomic profiling of the tumor. Our study demonstrates the power of allele specificity in chromatin signals to uncover GWAS mechanisms, highlights the relevance of tumor-specific regulation in the context of cancer risk, and prioritizes multiple loci for experimental follow-up.
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21
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Korbolina EE, Bryzgalov LO, Ustrokhanova DZ, Postovalov SN, Poverin DV, Damarov IS, Merkulova TI. A Panel of rSNPs Demonstrating Allelic Asymmetry in Both ChIP-seq and RNA-seq Data and the Search for Their Phenotypic Outcomes through Analysis of DEGs. Int J Mol Sci 2021; 22:ijms22147240. [PMID: 34298860 PMCID: PMC8303726 DOI: 10.3390/ijms22147240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Currently, the detection of the allele asymmetry of gene expression from RNA-seq data or the transcription factor binding from ChIP-seq data is one of the approaches used to identify the functional genetic variants that can affect gene expression (regulatory SNPs or rSNPs). In this study, we searched for rSNPs using the data for human pulmonary arterial endothelial cells (PAECs) available from the Sequence Read Archive (SRA). Allele-asymmetric binding and expression events are analyzed in paired ChIP-seq data for H3K4me3 mark and RNA-seq data obtained for 19 individuals. Two statistical approaches, weighted z-scores and predicted probabilities, were used to improve the efficiency of finding rSNPs. In total, we identified 14,266 rSNPs associated with both allele-specific binding and expression. Among them, 645 rSNPs were associated with GWAS phenotypes; 4746 rSNPs were reported as eQTLs by GTEx, and 11,536 rSNPs were located in 374 candidate transcription factor binding motifs. Additionally, we searched for the rSNPs associated with gene expression using an SRA RNA-seq dataset for 281 clinically annotated human postmortem brain samples and detected eQTLs for 2505 rSNPs. Based on these results, we conducted Gene Ontology (GO), Disease Ontology (DO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and constructed the protein-protein interaction networks to represent the top-ranked biological processes with a possible contribution to the phenotypic outcome.
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Affiliation(s)
- Elena E. Korbolina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 LavrentyevaProspekt, 630090 Novosibirsk, Russia; (L.O.B.); (I.S.D.); (T.I.M.)
- Correspondence:
| | - Leonid O. Bryzgalov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 LavrentyevaProspekt, 630090 Novosibirsk, Russia; (L.O.B.); (I.S.D.); (T.I.M.)
- VECTOR-BEST, PO BOX 492, 630117 Novosibirsk, Russia
| | - Diana Z. Ustrokhanova
- Department of Information Biology, The Novosibirsk State University, 1 Pirogovast, 630090 Novosibirsk, Russia;
| | - Sergey N. Postovalov
- Department of Theoretical and Applied Informatics, The Novosibirsk State Technical University, 630073 Novosibirsk, Russia; (S.N.P.); (D.V.P.)
| | - Dmitry V. Poverin
- Department of Theoretical and Applied Informatics, The Novosibirsk State Technical University, 630073 Novosibirsk, Russia; (S.N.P.); (D.V.P.)
| | - Igor S. Damarov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 LavrentyevaProspekt, 630090 Novosibirsk, Russia; (L.O.B.); (I.S.D.); (T.I.M.)
| | - Tatiana I. Merkulova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 LavrentyevaProspekt, 630090 Novosibirsk, Russia; (L.O.B.); (I.S.D.); (T.I.M.)
- Department of Information Biology, The Novosibirsk State University, 1 Pirogovast, 630090 Novosibirsk, Russia;
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22
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Degtyareva AO, Antontseva EV, Merkulova TI. Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. Int J Mol Sci 2021; 22:6454. [PMID: 34208629 PMCID: PMC8235176 DOI: 10.3390/ijms22126454] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
The vast majority of the genetic variants (mainly SNPs) associated with various human traits and diseases map to a noncoding part of the genome and are enriched in its regulatory compartment, suggesting that many causal variants may affect gene expression. The leading mechanism of action of these SNPs consists in the alterations in the transcription factor binding via creation or disruption of transcription factor binding sites (TFBSs) or some change in the affinity of these regulatory proteins to their cognate sites. In this review, we first focus on the history of the discovery of regulatory SNPs (rSNPs) and systematized description of the existing methodical approaches to their study. Then, we brief the recent comprehensive examples of rSNPs studied from the discovery of the changes in the TFBS sequence as a result of a nucleotide substitution to identification of its effect on the target gene expression and, eventually, to phenotype. We also describe state-of-the-art genome-wide approaches to identification of regulatory variants, including both making molecular sense of genome-wide association studies (GWAS) and the alternative approaches the primary goal of which is to determine the functionality of genetic variants. Among these approaches, special attention is paid to expression quantitative trait loci (eQTLs) analysis and the search for allele-specific events in RNA-seq (ASE events) as well as in ChIP-seq, DNase-seq, and ATAC-seq (ASB events) data.
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Affiliation(s)
- Arina O. Degtyareva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Elena V. Antontseva
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
| | - Tatiana I. Merkulova
- Department of Molecular Genetic, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (A.O.D.); (E.V.A.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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23
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A genome-wide association and polygenic risk score study on abnormal electrocardiogram in a Chinese population. Sci Rep 2021; 11:4669. [PMID: 33633301 PMCID: PMC7907205 DOI: 10.1038/s41598-021-84135-7] [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: 08/27/2020] [Accepted: 02/12/2021] [Indexed: 11/21/2022] Open
Abstract
Electrocardiography is a common and widely-performed medical examination based on the measurement and evaluation of electrocardiogram (ECG) to assess the up-to-date cardiac rhythms and thus suggest the health conditions of cardiovascular system and on a larger level the individual’s wellness. Abnormal ECG assessment from the detection of abnormal heart rhythms may have clinical implications including blood clots in formation, ongoing heart attack, coronary artery blockage, etc. Past genetic-phenotypic research focused primarily on the physical parameters of ECG but not the medical evaluation. To unbiasedly uncover the underlying links of genetic variants with normal vs. abnormal ECG assessment, a genome-wide association study (GWAS) is carried out in a 1006-participant cohort of Chinese population effectively genotyped for 243487 single nucleotide polymorphisms (SNPs). Both age and sex are influential factors, and six novel SNPs are identified for potential association with abnormal ECG. With the selected SNPs, a polygenic risk score (PRS) differentiates the case–control subgroups, and correlates well with increased risk of abnormal ECG. The findings are reproduced in an independent validation cohort. The derived PRS may function as a potential biomarker for prospectively screening the high-risk subgroup of heart issues in the Chinese population.
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24
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Ward MC, Banovich NE, Sarkar A, Stephens M, Gilad Y. Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. eLife 2021; 10:57345. [PMID: 33554857 PMCID: PMC7906610 DOI: 10.7554/elife.57345] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
One life-threatening outcome of cardiovascular disease is myocardial infarction, where cardiomyocytes are deprived of oxygen. To study inter-individual differences in response to hypoxia, we established an in vitro model of induced pluripotent stem cell-derived cardiomyocytes from 15 individuals. We measured gene expression levels, chromatin accessibility, and methylation levels in four culturing conditions that correspond to normoxia, hypoxia, and short- or long-term re-oxygenation. We characterized thousands of gene regulatory changes as the cells transition between conditions. Using available genotypes, we identified 1,573 genes with a cis expression quantitative locus (eQTL) in at least one condition, as well as 367 dynamic eQTLs, which are classified as eQTLs in at least one, but not in all conditions. A subset of genes with dynamic eQTLs is associated with complex traits and disease. Our data demonstrate how dynamic genetic effects on gene expression, which are likely relevant for disease, can be uncovered under stress.
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Affiliation(s)
- Michelle C Ward
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, United States
| | - Nicholas E Banovich
- Department of Human Genetics, University of Chicago, Chicago, United States.,Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, United States
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Statistics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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25
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D’Antonio-Chronowska A, D’Antonio M, Frazer KA. In vitro Differentiation of Human iPSC-derived Cardiovascular Progenitor Cells (iPSC-CVPCs). Bio Protoc 2020; 10:e3755. [PMID: 33659414 PMCID: PMC7853936 DOI: 10.21769/bioprotoc.3755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Induced pluripotent stem cell derived cardiovascular progenitor cells (iPSC-CVPCs) provide an unprecedented platform for examining the molecular underpinnings of cardiac development and disease etiology, but also have great potential to play pivotal roles in the future of regenerative medicine and pharmacogenomic studies. Biobanks like iPSCORE ( Stacey et al., 2013 ; Panopoulos et al., 2017 ), which contain iPSCs generated from hundreds of genetically and ethnically diverse individuals, are an invaluable resource for conducting these studies. Here, we present an optimized, cost-effective and highly standardized protocol for large-scale derivation of human iPSC-CVPCs using small molecules and purification using metabolic selection. We have successfully applied this protocol to derive iPSC-CVPCs from 154 different iPSCORE iPSC lines obtaining large quantities of highly pure cardiac cells. An important component of our protocol is Cell confluency estimates (ccEstimate), an automated methodology for estimating the time when an iPSC monolayer will reach 80% confluency, which is optimal for initiating iPSC-CVPC derivation, and enables the protocol to be readily used across iPSC lines with different growth rates. Moreover, we showed that cellular heterogeneity across iPSC-CVPCs is due to varying proportions of two distinct cardiac cell types: cardiomyocytes (CMs) and epicardium-derived cells (EPDCs), both of which have been shown to have a critical function in heart regeneration. This protocol eliminates the need of iPSC line-to-line optimization and can be easily adapted and scaled to high-throughput studies or to generate large quantities of cells suitable for regenerative medicine applications.
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Affiliation(s)
| | - Matteo D’Antonio
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
| | - Kelly A. Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
- Institue for Genomic Medicine, University of California, San Diego, La Jolla, USA
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26
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The Role of Noncoding Variants in Heritable Disease. Trends Genet 2020; 36:880-891. [PMID: 32741549 DOI: 10.1016/j.tig.2020.07.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022]
Abstract
The genetic basis of disease has largely focused on coding regions. However, it has become clear that a large proportion of the noncoding genome is functional and harbors genetic variants that contribute to disease etiology. Here, we review recent examples of inherited noncoding alterations that are responsible for Mendelian disorders or act to influence complex traits. We explore both rare and common genetic variants and discuss the wide range of mechanisms by which they affect gene regulation to promote disease. We also debate the challenges and progress associated with identifying and interpreting the functional and clinical significance of genetic variation in the context of the noncoding regulatory landscape.
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27
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Huang X, Li Y, Zhang J, Wang X, Li Z, Li G. The molecular genetic basis of atrial fibrillation. Hum Genet 2020; 139:1485-1498. [PMID: 32617797 DOI: 10.1007/s00439-020-02203-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
As the most common cardiac arrhythmia, atrial fibrillation (AF) is a major risk factor for stroke, heart failure, and premature death with considerable associated costs. However, no available treatment options have optimal benefit-harm profiles currently, reflecting an incomplete understanding of the biological mechanisms underlying this complex arrhythmia. Recently, molecular epidemiological studies, especially genome-wide association studies, have emphasized the substantial genetic component of AF etiology. A comprehensive mapping of the genetic underpinnings for AF can expand our knowledge of AF mechanism and further facilitate the process of locating novel therapeutics for AF. Here we provide a state-of-the-art review of the molecular genetics of AF incorporating evidence from linkage analysis and candidate gene, as well as genome-wide association studies of common variations and rare copy number variations; potential epigenetic modifications (e.g., DNA methylation, histone modification, and non-coding RNAs) are also involved. We also outline the challenges in mechanism investigation and potential future directions in this article.
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Affiliation(s)
- Xin Huang
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, 466 Newport Middle Road, Haizhu District, Guangzhou, 510317, Guangdong, China
| | - Yuhui Li
- Department of Cardiology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Junguo Zhang
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, 466 Newport Middle Road, Haizhu District, Guangzhou, 510317, Guangdong, China
| | - Xiaojie Wang
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, 466 Newport Middle Road, Haizhu District, Guangzhou, 510317, Guangdong, China
| | - Ziyi Li
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, 466 Newport Middle Road, Haizhu District, Guangzhou, 510317, Guangdong, China
| | - Guowei Li
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, 466 Newport Middle Road, Haizhu District, Guangzhou, 510317, Guangdong, China. .,Department of Health Research Methods, Evidence, and Impact (HEI), McMaster University Hamilton, 1280 Main St West, Hamilton, ON, L8S 4L8, Canada.
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28
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Zhou J, Luo J, Lin J, Zeng Y, Qiu X, Zhu W, Liu G. Perinatal risk factors for congenital hypothyroidism: A retrospective cohort study performed at a tertiary hospital in China. Medicine (Baltimore) 2020; 99:e20838. [PMID: 32590776 PMCID: PMC7328952 DOI: 10.1097/md.0000000000020838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Congenital hypothyroidism (CH) is one of the most common neonatal endocrine diseases. This retrospective cohort study aimed to identify the potential perinatal risk factors for CH and to differentiate between transient and permanent CH (TCH and PCH, respectively) as well as determine their prevalence in a southeastern Chinese population.This study was based on an 18-year surveillance of a neonatal CH screening program in a large tertiary hospital. A retrospective review of the maternal and neonatal perinatal exposures was conducted.Of the 205,834 newborns screened between 2000 and 2018, 189 were diagnosed with CH (1/1089). Among the 131 CH patients who again underwent thyroid function testing (TFT) after discontinuation of levothyroxine at the age of 3 years, 61 (46.6%) were diagnosed with PCH and 70 (53.4%) were diagnosed with TCH. In the maternal characteristics model, women aged 35 years or older and those who had thyroid disease and/or diabetes mellitus during pregnancy had increased risk of having an offspring with CH (P = .001, .000, and .001, respectively). Significant associations were found with regard to parity and the risk of CH in the offspring (P = .000). In the neonatal characteristics model, infants with female sex, preterm birth, post-term birth, low birth weight, other birth defects, and those born as part of multiple births (P = .011, .034, .001, .000, .000, and .003, respectively) had increased risk of CH. The rate of newborns with other birth defects was higher in the PCH group than that in the TCH group (P = .008), whereas the rate of maternal thyroid disease, newborns with low birth weight, and newborns with preterm birth was higher in the TCH group than that in the PCH group (P = .041, .020, and .013, respectively). The levothyroxine dose (μg/kg/day) at 1 year, 2 years, and 3 years old was significantly lower in the TCH group than that in the PCH group (P = .000, .000, and .000, respectively).Perinatal factors should be considered during the diagnosis and treatment of CH.
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Affiliation(s)
| | - Jinying Luo
- Department of Gynaecology and Obstetrics, Fujian Provincial Maternity and Child Hospital, Affiliated Hospital of Fujian Medical Universitya
| | - Junyu Lin
- The First Affiliated Hospital of Fujian Medical University
| | | | | | | | - Guanghua Liu
- Department of Pediatrics, Fujian Provincial Maternity and Child Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
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