1
|
Jiang J, Hiron TK, Agbaedeng TA, Malhotra Y, Drydale E, Bancroft J, Ng E, Reschen ME, Davison LJ, O’Callaghan CA. A Novel Macrophage Subpopulation Conveys Increased Genetic Risk of Coronary Artery Disease. Circ Res 2024; 135:6-25. [PMID: 38747151 PMCID: PMC11191562 DOI: 10.1161/circresaha.123.324172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Coronary artery disease (CAD), the leading cause of death worldwide, is influenced by both environmental and genetic factors. Although over 250 genetic risk loci have been identified through genome-wide association studies, the specific causal variants and their regulatory mechanisms are still largely unknown, particularly in disease-relevant cell types such as macrophages. METHODS We utilized single-cell RNA-seq and single-cell multiomics approaches in primary human monocyte-derived macrophages to explore the transcriptional regulatory network involved in a critical pathogenic event of coronary atherosclerosis-the formation of lipid-laden foam cells. The relative genetic contribution to CAD was assessed by partitioning disease heritability across different macrophage subpopulations. Meta-analysis of single-cell RNA-seq data sets from 38 human atherosclerotic samples was conducted to provide high-resolution cross-referencing to macrophage subpopulations in vivo. RESULTS We identified 18 782 cis-regulatory elements by jointly profiling the gene expression and chromatin accessibility of >5000 macrophages. Integration with CAD genome-wide association study data prioritized 121 CAD-related genetic variants and 56 candidate causal genes. We showed that CAD heritability was not uniformly distributed and was particularly enriched in the gene programs of a novel CD52-hi lipid-handling macrophage subpopulation. These CD52-hi macrophages displayed significantly less lipoprotein accumulation and were also found in human atherosclerotic plaques. We investigated the cis-regulatory effect of a risk variant rs10488763 on FDX1, implicating the recruitment of AP-1 and C/EBP-β in the causal mechanisms at this locus. CONCLUSIONS Our results provide genetic evidence of the divergent roles of macrophage subsets in atherogenesis and highlight lipid-handling macrophages as a key subpopulation through which genetic variants operate to influence disease. These findings provide an unbiased framework for functional fine-mapping of genome-wide association study results using single-cell multiomics and offer new insights into the genotype-environment interactions underlying atherosclerotic disease.
Collapse
Affiliation(s)
- Jiahao Jiang
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Thomas K. Hiron
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Thomas A. Agbaedeng
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Yashaswat Malhotra
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Edward Drydale
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - James Bancroft
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Esther Ng
- Nuffield Department of Orthopaedics, Kennedy Institute of Rheumatology, Rheumatology and Musculoskeletal Sciences (E.N.), University of Oxford, United Kingdom
| | - Michael E. Reschen
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, United Kingdom (M.E.R.)
| | - Lucy J. Davison
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
- Department of Clinical Science and Services, Royal Veterinary College, Hatfield, United Kingdom (L.J.D.)
| | - Chris A. O’Callaghan
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| |
Collapse
|
2
|
Zuela-Sopilniak N, Morival J, Lammerding J. Multi-level transcriptomic analysis of LMNA -related dilated cardiomyopathy identifies disease-driving processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598511. [PMID: 38915720 PMCID: PMC11195185 DOI: 10.1101/2024.06.11.598511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
LMNA- related dilated cardiomyopathy ( LMNA -DCM) is one of the most severe forms of DCM. The incomplete understanding of the molecular disease mechanisms results in lacking treatment options, leading to high mortality amongst patients. Here, using an inducible, cardiomyocyte-specific lamin A/C depletion mouse model, we conducted a comprehensive transcriptomic study, combining both bulk and single nucleus RNA sequencing, and spanning LMNA -DCM disease progression, to identify potential disease drivers. Our refined analysis pipeline identified 496 genes already misregulated early in disease. The expression of these genes was largely driven by disease specific cardiomyocyte sub-populations and involved biological processes mediating cellular response to DNA damage, cytosolic pattern recognition, and innate immunity. Indeed, DNA damage in LMNA -DCM hearts was significantly increased early in disease and correlated with reduced cardiomyocyte lamin A levels. Activation of cytosolic pattern recognition in cardiomyocytes was independent of cGAS, which is rarely expressed in cardiomyocytes, but likely occurred downstream of other pattern recognition sensors such as IFI16. Altered gene expression in cardiac fibroblasts and immune cell infiltration further contributed to tissue-wide changes in gene expression. Our transcriptomic analysis further predicted significant alterations in cell-cell communication between cardiomyocytes, fibroblasts, and immune cells, mediated through early changes in the extracellular matrix (ECM) in the LMNA -DCM hearts. Taken together, our work suggests a model in which nuclear damage in cardiomyocytes leads to activation of DNA damage responses, cytosolic pattern recognition pathway, and other signaling pathways that activate inflammation, immune cell recruitment, and transcriptional changes in cardiac fibroblasts, which collectively drive LMNA -DCM pathogenesis.
Collapse
|
3
|
Liu X, Zeng Q, Yang H, Li W, Chen Q, Yin K, Pan Z, Wang K, Luo M, Shu C, Zhou Z. Single-Nucleus Multiomic Analyses Identifies Gene Regulatory Dynamics of Phenotypic Modulation in Human Aneurysmal Aortic Root. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400444. [PMID: 38552156 PMCID: PMC11165511 DOI: 10.1002/advs.202400444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Indexed: 06/12/2024]
Abstract
Aortic root aneurysm is a potentially life-threatening condition that may lead to aortic rupture and is often associated with genetic syndromes, such as Marfan syndrome (MFS). Although studies with MFS animal models have provided valuable insights into the pathogenesis of aortic root aneurysms, this understanding of the transcriptomic and epigenomic landscape in human aortic root tissue remains incomplete. This knowledge gap has impeded the development of effective targeted therapies. Here, this study performs the first integrative analysis of single-nucleus multiomic (gene expression and chromatin accessibility) and spatial transcriptomic sequencing data of human aortic root tissue under healthy and MFS conditions. Cell-type-specific transcriptomic and cis-regulatory profiles in the human aortic root are identified. Regulatory and spatial dynamics during phenotypic modulation of vascular smooth muscle cells (VSMCs), the cardinal cell type, are delineated. Moreover, candidate key regulators driving the phenotypic modulation of VSMC, such as FOXN3, TEAD1, BACH2, and BACH1, are identified. In vitro experiments demonstrate that FOXN3 functions as a novel key regulator for maintaining the contractile phenotype of human aortic VSMCs through targeting ACTA2. These findings provide novel insights into the regulatory and spatial dynamics during phenotypic modulation in the aneurysmal aortic root of humans.
Collapse
Affiliation(s)
- Xuanyu Liu
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| | - Qingyi Zeng
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| | - Hang Yang
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| | - Wenke Li
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| | - Qianlong Chen
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| | - Kunlun Yin
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| | - Zihang Pan
- Department of Physiology and PathophysiologySchool of Basic Medical SciencesState Key Laboratory of Vascular Homeostasis and RemodelingPeking UniversityBeijing100191China
| | - Kai Wang
- Department of Physiology and PathophysiologySchool of Basic Medical SciencesState Key Laboratory of Vascular Homeostasis and RemodelingPeking UniversityBeijing100191China
| | - Mingyao Luo
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
- Center of Vascular SurgeryFuwai HospitalChinese Academy of Medical SciencesBeijing100037China
- Department of Vascular SurgeryFuwai Yunnan Cardiovascular HospitalAffiliated Cardiovascular Hospital of Kunming Medical UniversityKunmingYunnan650102China
- Department of Vascular SurgeryCentral‐China Subcenter of National Center for Cardiovascular DiseasesHenan Cardiovascular Disease CenterFuwai Central‐China Cardiovascular HospitalCentral China Fuwai Hospital of Zhengzhou UniversityZhengzhou450046China
| | - Chang Shu
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
- Center of Vascular SurgeryFuwai HospitalChinese Academy of Medical SciencesBeijing100037China
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100037China
| |
Collapse
|
4
|
Choudhury S, Sivankutty I, Jung Y, Huang A, Araten S, Kenny C, An Z, Doan R, Foijer F, Matsu E, Rosen I, Marciano J, Jain A, Sun L, Hilal N, Lee E, Walsh C, Chen M. Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart. RESEARCH SQUARE 2024:rs.3.rs-4414468. [PMID: 38853931 PMCID: PMC11160865 DOI: 10.21203/rs.3.rs-4414468/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has long been considered the primary source of polyploid human cardiomyocytes, recent animal work suggests the potential for cardiomyocyte fusion. Moreover, the effects of polyploidization on the genomic-transcriptomic repertoire of human cardiomyocytes have not been studied previously. We applied single-nuclei whole genome sequencing, single nuclei RNA sequencing, and multiome ATAC + gene expression (from the same nuclei) techniques to nuclei isolated from 11 healthy hearts. Utilizing post-zygotic non-inherited somatic mutations occurring during development as "endogenous barcodes," to reconstruct lineage relationships of polyploid cardiomyocytes. Of 482 cardiomyocytes from multiple healthy donor hearts 75.7% can be sorted into several developmental clades marked by one or more somatic single-nucleotide variants (SNVs). At least ~10% of tetraploid cardiomyocytes contain cells from distinct clades, indicating fusion of lineally distinct cells, whereas 60% of higher-ploidy cardiomyocytes contain fused cells from distinct clades. Combined snRNA-seq and snATAC-seq revealed transcriptome and chromatin landscapes of polyploid cardiomyocytes distinct from diploid cardiomyocytes, and show some higher-ploidy cardiomyocytes with transcriptional signatures suggesting fusion between cardiomyocytes and endothelial and fibroblast cells. These observations provide the first evidence for cell and nuclear fusion of human cardiomyocytes, raising the possibility that cell fusion may contribute to developing or maintaining polyploid cardiomyocytes in the human heart.
Collapse
|
5
|
Linna-Kuosmanen S, Schmauch E, Galani K, Ojanen J, Boix CA, Örd T, Toropainen A, Singha PK, Moreau PR, Harju K, Blazeski A, Segerstolpe Å, Lahtinen V, Hou L, Kang K, Meibalan E, Agudelo LZ, Kokki H, Halonen J, Jalkanen J, Gunn J, MacRae CA, Hollmén M, Hartikainen JEK, Kaikkonen MU, García-Cardeña G, Tavi P, Kiviniemi T, Kellis M. Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease. Cell Rep Med 2024; 5:101556. [PMID: 38776872 PMCID: PMC11148807 DOI: 10.1016/j.xcrm.2024.101556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 11/27/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Cardiovascular disease plays a central role in the electrical and structural remodeling of the right atrium, predisposing to arrhythmias, heart failure, and sudden death. Here, we dissect with single-nuclei RNA sequencing (snRNA-seq) and spatial transcriptomics the gene expression changes in the human ex vivo right atrial tissue and pericardial fluid in ischemic heart disease, myocardial infarction, and ischemic and non-ischemic heart failure using asymptomatic patients with valvular disease who undergo preventive surgery as the control group. We reveal substantial differences in disease-associated gene expression in all cell types, collectively suggesting inflammatory microvascular dysfunction and changes in the right atrial tissue composition as the valvular and vascular diseases progress into heart failure. The data collectively suggest that investigation of human cardiovascular disease should expand to all functionally important parts of the heart, which may help us to identify mechanisms promoting more severe types of the disease.
Collapse
Affiliation(s)
- Suvi Linna-Kuosmanen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Eloi Schmauch
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kyriakitsa Galani
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Johannes Ojanen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Anu Toropainen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Prosanta K Singha
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Pierre R Moreau
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kristiina Harju
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Adriana Blazeski
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Åsa Segerstolpe
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Veikko Lahtinen
- Heart Center, Turku University Hospital, 20521 Turku, Finland; MediCity Research Laboratories and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - Lei Hou
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kai Kang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elamaran Meibalan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Leandro Z Agudelo
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hannu Kokki
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jari Halonen
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland; Heart Center, Kuopio University Hospital, 70200 Kuopio, Finland
| | - Juho Jalkanen
- MediCity Research Laboratories and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - Jarmo Gunn
- Heart Center, Turku University Hospital, 20521 Turku, Finland; Department of Medicine, University of Turku, 20500 Turku, Finland
| | - Calum A MacRae
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Cardiovascular Medicine and Network Medicine Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Maija Hollmén
- MediCity Research Laboratories and InFLAMES Flagship, University of Turku, 20500 Turku, Finland
| | - Juha E K Hartikainen
- School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland; Heart Center, Kuopio University Hospital, 70200 Kuopio, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Guillermo García-Cardeña
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Pasi Tavi
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Tuomas Kiviniemi
- Heart Center, Turku University Hospital, 20521 Turku, Finland; Department of Medicine, University of Turku, 20500 Turku, Finland; Cardiovascular Medicine and Network Medicine Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
6
|
Tikhomirov R, Oakley RH, Anderson C, Xiang Y, Al-Othman S, Smith M, Yaar S, Torre E, Li J, Wilson LR, Goulding DR, Donaldson I, Harno E, Soattin L, Shiels HA, Morris GM, Zhang H, Boyett MR, Cidlowski JA, Mesirca P, Mangoni ME, D'Souza A. Cardiac GR Mediates the Diurnal Rhythm in Ventricular Arrhythmia Susceptibility. Circ Res 2024; 134:1306-1326. [PMID: 38533639 PMCID: PMC11081863 DOI: 10.1161/circresaha.123.323464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/15/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Ventricular arrhythmias (VAs) demonstrate a prominent day-night rhythm, commonly presenting in the morning. Transcriptional rhythms in cardiac ion channels accompany this phenomenon, but their role in the morning vulnerability to VAs and the underlying mechanisms are not understood. We investigated the recruitment of transcription factors that underpins transcriptional rhythms in ion channels and assessed whether this mechanism was pertinent to the heart's intrinsic diurnal susceptibility to VA. METHODS AND RESULTS Assay for transposase-accessible chromatin with sequencing performed in mouse ventricular myocyte nuclei at the beginning of the animals' inactive (ZT0) and active (ZT12) periods revealed differentially accessible chromatin sites annotating to rhythmically transcribed ion channels and distinct transcription factor binding motifs in these regions. Notably, motif enrichment for the glucocorticoid receptor (GR; transcriptional effector of corticosteroid signaling) in open chromatin profiles at ZT12 was observed, in line with the well-recognized ZT12 peak in circulating corticosteroids. Molecular, electrophysiological, and in silico biophysically-detailed modeling approaches demonstrated GR-mediated transcriptional control of ion channels (including Scn5a underlying the cardiac Na+ current, Kcnh2 underlying the rapid delayed rectifier K+ current, and Gja1 responsible for electrical coupling) and their contribution to the day-night rhythm in the vulnerability to VA. Strikingly, both pharmacological block of GR and cardiomyocyte-specific genetic knockout of GR blunted or abolished ion channel expression rhythms and abolished the ZT12 susceptibility to pacing-induced VA in isolated hearts. CONCLUSIONS Our study registers a day-night rhythm in chromatin accessibility that accompanies diurnal cycles in ventricular myocytes. Our approaches directly implicate the cardiac GR in the myocyte excitability rhythm and mechanistically link the ZT12 surge in glucocorticoids to intrinsic VA propensity at this time.
Collapse
Affiliation(s)
- Roman Tikhomirov
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, United Kingdom (R.T., M.S., A.D.)
| | - Robert H Oakley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Cali Anderson
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Yirong Xiang
- Department of Physics and Astronomy (Y.X., H.Z.), The University of Manchester, United Kingdom
| | - Sami Al-Othman
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Matthew Smith
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, United Kingdom (R.T., M.S., A.D.)
| | - Sana Yaar
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Eleonora Torre
- Institut de Génomique Fonctionnelle, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), F-34094 Montpellier France (E.T., P.M., M.E.M.)
| | - Jianying Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Leslie R Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - David R Goulding
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Ian Donaldson
- Bioinformatics Core Facility (I.D.), The University of Manchester, United Kingdom
| | - Erika Harno
- Division of Diabetes, Endocrinology and Gastroenterology (E.H.), The University of Manchester, United Kingdom
| | - Luca Soattin
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Holly A Shiels
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
| | - Gwilym M Morris
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Department of Cardiology, John Hunter Hospital, Newcastle, NSW, Australia (G.M.M.)
| | - Henggui Zhang
- Department of Physics and Astronomy (Y.X., H.Z.), The University of Manchester, United Kingdom
| | - Mark R Boyett
- Faculty of Life Sciences, University of Bradford, United Kingdom (M.R.B.)
| | - John A Cidlowski
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health (R.H.O., J.L., L.R.W., D.R.G., J.A.C.)
| | - Pietro Mesirca
- Institut de Génomique Fonctionnelle, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), F-34094 Montpellier France (E.T., P.M., M.E.M.)
| | - Matteo E Mangoni
- Institut de Génomique Fonctionnelle, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), F-34094 Montpellier France (E.T., P.M., M.E.M.)
| | - Alicia D'Souza
- Division of Cardiovascular Sciences (R.T., C.A., S.A.O., M.S., S.Y., L.S., H.A.S., G.M.M., A.D.), The University of Manchester, United Kingdom
- Myocardial Function Section, National Heart and Lung Institute, Imperial College London, United Kingdom (R.T., M.S., A.D.)
| |
Collapse
|
7
|
Baudic M, Murata H, Bosada FM, Melo US, Aizawa T, Lindenbaum P, van der Maarel LE, Guedon A, Baron E, Fremy E, Foucal A, Ishikawa T, Ushinohama H, Jurgens SJ, Choi SH, Kyndt F, Le Scouarnec S, Wakker V, Thollet A, Rajalu A, Takaki T, Ohno S, Shimizu W, Horie M, Kimura T, Ellinor PT, Petit F, Dulac Y, Bru P, Boland A, Deleuze JF, Redon R, Le Marec H, Le Tourneau T, Gourraud JB, Yoshida Y, Makita N, Vieyres C, Makiyama T, Mundlos S, Christoffels VM, Probst V, Schott JJ, Barc J. TAD boundary deletion causes PITX2-related cardiac electrical and structural defects. Nat Commun 2024; 15:3380. [PMID: 38643172 PMCID: PMC11032321 DOI: 10.1038/s41467-024-47739-x] [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: 02/17/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.
Collapse
Affiliation(s)
- Manon Baudic
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Hiroshige Murata
- The Department of Cardiovascular Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Fernanda M Bosada
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353, Berlin, Germany
| | - Takanori Aizawa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Pierre Lindenbaum
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Lieve E van der Maarel
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Amaury Guedon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Estelle Baron
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Enora Fremy
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Adrien Foucal
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Taisuke Ishikawa
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Hiroya Ushinohama
- Department of Cardiology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Experimental Cardiology, Heart Center, Amsterdam Cardiovascular Sciences, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Florence Kyndt
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Solena Le Scouarnec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Aurélie Thollet
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Annabelle Rajalu
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Tadashi Takaki
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Takeda-CiRA Joint Program for iPS Cell Applications, Fujisawa, Japan
- Department of Pancreatic Islet Cell Transplantation, National Center for Global Health and Medicine, Tokyo, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Wataru Shimizu
- The Department of Cardiovascular Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Ohtsu, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, Hôpital Jeanne de Flandre, F-59000, Lille, France
- University of Lille, EA 7364-RADEME, F-59000, Lille, France
| | - Yves Dulac
- Unité de Cardiologie Pédiatrique, Hôpital des Enfants, F-31000, Toulouse, France
| | - Paul Bru
- Service de Cardiologie, GH La Rochelle, F-17019, La Rochelle, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Richard Redon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Hervé Le Marec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Thierry Le Tourneau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
| | - Jean-Baptiste Gourraud
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands
| | - Yoshinori Yoshida
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Naomasa Makita
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
- Department of Cardiology, Sapporo Teishinkai Hospital, Sapporo, Japan
| | - Claude Vieyres
- Cabinet Cardiologique, Clinique St. Joseph, F-16000, Angoulême, France
| | - Takeru Makiyama
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Community Medicine Supporting System, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Stephan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353, Berlin, Germany
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Vincent Probst
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands
| | - Jean-Jacques Schott
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France.
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands.
| | - Julien Barc
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du Thorax, F-44000, Nantes, France.
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart: ERN GUARD-Heart, Amsterdam, The Netherlands.
| |
Collapse
|
8
|
Li Z, Brittan M, Mills NL. A Multimodal Omics Framework to Empower Target Discovery for Cardiovascular Regeneration. Cardiovasc Drugs Ther 2024; 38:223-236. [PMID: 37421484 PMCID: PMC10959818 DOI: 10.1007/s10557-023-07484-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2023] [Indexed: 07/10/2023]
Abstract
Ischaemic heart disease is a global healthcare challenge with high morbidity and mortality. Early revascularisation in acute myocardial infarction has improved survival; however, limited regenerative capacity and microvascular dysfunction often lead to impaired function and the development of heart failure. New mechanistic insights are required to identify robust targets for the development of novel strategies to promote regeneration. Single-cell RNA sequencing (scRNA-seq) has enabled profiling and analysis of the transcriptomes of individual cells at high resolution. Applications of scRNA-seq have generated single-cell atlases for multiple species, revealed distinct cellular compositions for different regions of the heart, and defined multiple mechanisms involved in myocardial injury-induced regeneration. In this review, we summarise findings from studies of healthy and injured hearts in multiple species and spanning different developmental stages. Based on this transformative technology, we propose a multi-species, multi-omics, meta-analysis framework to drive the discovery of new targets to promote cardiovascular regeneration.
Collapse
Affiliation(s)
- Ziwen Li
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
| | - Mairi Brittan
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Nicholas L Mills
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
9
|
Bridges J, Ramirez-Guerrero JA, Rosa-Garrido M. Gender-specific genetic and epigenetic signatures in cardiovascular disease. Front Cardiovasc Med 2024; 11:1355980. [PMID: 38529333 PMCID: PMC10962446 DOI: 10.3389/fcvm.2024.1355980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Cardiac sex differences represent a pertinent focus in pursuit of the long-awaited goal of personalized medicine. Despite evident disparities in the onset and progression of cardiac pathology between sexes, historical oversight has led to the neglect of gender-specific considerations in the treatment of patients. This oversight is attributed to a predominant focus on male samples and a lack of sex-based segregation in patient studies. Recognizing these sex differences is not only relevant to the treatment of cisgender individuals; it also holds paramount importance in addressing the healthcare needs of transgender patients, a demographic that is increasingly prominent in contemporary society. In response to these challenges, various agencies, including the National Institutes of Health, have actively directed their efforts toward advancing our comprehension of this phenomenon. Epigenetics has proven to play a crucial role in understanding sex differences in both healthy and disease states within the heart. This review presents a comprehensive overview of the physiological distinctions between males and females during the development of various cardiac pathologies, specifically focusing on unraveling the genetic and epigenetic mechanisms at play. Current findings related to distinct sex-chromosome compositions, the emergence of gender-biased genetic variations, and variations in hormonal profiles between sexes are highlighted. Additionally, the roles of DNA methylation, histone marks, and chromatin structure in mediating pathological sex differences are explored. To inspire further investigation into this crucial subject, we have conducted global analyses of various epigenetic features, leveraging data previously generated by the ENCODE project.
Collapse
Affiliation(s)
| | | | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine, School of Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
10
|
Deng L, Pollmeier L, Bednarz R, Cao C, Laurette P, Wirth L, Mamazhakypov A, Bode C, Hein L, Gilsbach R, Lother A. Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression. SCIENCE ADVANCES 2024; 10:eadj5101. [PMID: 38446896 PMCID: PMC10917356 DOI: 10.1126/sciadv.adj5101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Endothelial cells play crucial roles in physiology and are increasingly recognized as therapeutic targets in cardiovascular disease. Here, we analyzed the regulatory landscape of cardiac endothelial cells by assessing chromatin accessibility, histone modifications, and 3D chromatin organization and confirmed the functional relevance of enhancer-promoter interactions by CRISPRi-mediated enhancer silencing. We used this dataset to explore mechanisms of transcriptional regulation in cardiovascular disease and compared six different experimental models of heart failure, hypertension, or diabetes. Enhancers that regulate gene expression in diseased endothelial cells were enriched with binding sites for a distinct set of transcription factors, including the mineralocorticoid receptor (MR), a known drug target in heart failure and hypertension. For proof of concept, we applied endothelial cell-specific MR deletion in mice to confirm MR-dependent gene expression and predicted direct MR target genes. Overall, we have compiled here a comprehensive atlas of cardiac endothelial cell enhancer elements that provides insight into the role of transcription factors in cardiovascular disease.
Collapse
Affiliation(s)
- Lisa Deng
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Cardiovascular Research Track, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Luisa Pollmeier
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rebecca Bednarz
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Can Cao
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Patrick Laurette
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Luisa Wirth
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Argen Mamazhakypov
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christine Bode
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Ralf Gilsbach
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Interdisciplinary Medical Intensive Care, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
11
|
Broberg M, Ampuja M, Jones S, Ojala T, Rahkonen O, Kivelä R, Priest J, Palotie A, Ollila HM, Helle E. Genome-wide association studies highlight novel risk loci for septal defects and left-sided congenital heart defects. BMC Genomics 2024; 25:256. [PMID: 38454350 PMCID: PMC10918883 DOI: 10.1186/s12864-024-10172-x] [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: 08/04/2023] [Accepted: 02/28/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Congenital heart defects (CHD) are structural defects of the heart affecting approximately 1% of newborns. They exhibit low penetrance and non-Mendelian patterns of inheritance as varied and complex traits. While genetic factors are known to play an important role in the development of CHD, the specific genetics remain unknown for the majority of patients. To elucidate the underlying genetic risk, we performed a genome wide association study (GWAS) of CHDs in general and specific CHD subgroups using the FinnGen Release 10 (R10) (N > 393,000), followed by functional fine-mapping through eQTL and co-localization analyses using the GTEx database. RESULTS We discovered three genome-wide significant loci associated with general CHD. Two of them were located in chromosome 17: 17q21.32 (rs2316327, intronic: LRRC37A2, Odds ratio (OR) [95% Confidence Interval (CI)] = 1.17[1.12-1.23], p = 1.5 × 10-9) and 17q25.3 (rs1293973611, nearest: BAHCC1, OR[95%CI] = 4.48[2.80-7.17], p = 7.0 × 10-10), respectively, and in addition to general CHD, the rs1293973611 locus was associated with the septal defect subtype. The third locus was in band 1p21.2 (rs35046143, nearest: PALMD, OR[95%CI] = 1.15[1.09-1.21], p = 7.1 × 10-9), and it was associated with general CHD and left-sided lesions. In the subgroup analysis, two additional loci were associated with septal defects (rs75230966 and rs6824295), and one with left-sided lesions (rs1305393195). In the eQTL analysis the variants rs2316327 (general CHD), and rs75230966 (septal defects) both located in 17q21.32 (with a LD r2 of 0.41) were both predicted to significantly associate with the expression of WNT9B in the atrial appendage tissue category. This effect was further confirmed by co-localization analysis, which also implicated WNT3 expression in the atrial appendage. A meta-analysis of general CHD together with the UK Biobank (combined N = 881,678) provided a different genome-wide significant locus in LRRC37A2; rs16941382 (OR[95%CI] = 1.15[1.11-1.20], p = 1.5 × 10-9) which is in significant LD with rs2316327. CONCLUSIONS Our results of general CHD and different CHD subcategories identified a complex risk locus on chromosome 17 near BAHCC1 and LRRC37A2, interacting with the genes WNT9B, WNT3 and MYL4, may constitute potential novel CHD risk associated loci, warranting future experimental tests to determine their role.
Collapse
Affiliation(s)
- Martin Broberg
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Minna Ampuja
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Samuel Jones
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Tiina Ojala
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Otto Rahkonen
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Riikka Kivelä
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Wihuri Research Institute, 00290, Helsinki, Finland
- Faculty of Sport and Health Sciences, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - James Priest
- School of Medicine, Stanford University, Stanford University, Stanford, CA, 94305, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Emmi Helle
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland.
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland.
- , Haartmaninkatu 8, Helsinki, 00014, Finland.
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, 00271, Finland.
| |
Collapse
|
12
|
Farah EN, Hu RK, Kern C, Zhang Q, Lu TY, Ma Q, Tran S, Zhang B, Carlin D, Monell A, Blair AP, Wang Z, Eschbach J, Li B, Destici E, Ren B, Evans SM, Chen S, Zhu Q, Chi NC. Spatially organized cellular communities form the developing human heart. Nature 2024; 627:854-864. [PMID: 38480880 PMCID: PMC10972757 DOI: 10.1038/s41586-024-07171-z] [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: 11/21/2022] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
The heart, which is the first organ to develop, is highly dependent on its form to function1,2. However, how diverse cardiac cell types spatially coordinate to create the complex morphological structures that are crucial for heart function remains unclear. Here we integrated single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization to resolve the identity of the cardiac cell types that develop the human heart. This approach also provided a spatial mapping of individual cells that enables illumination of their organization into cellular communities that form distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, which support their specialization according to the cellular ecosystem and anatomical region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and formed, with other cell subpopulations, several cellular communities. Interrogating cell-cell interactions within these communities using in vivo conditional genetic mouse models and in vitro human pluripotent stem cell systems revealed multicellular signalling pathways that orchestrate the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis. These detailed findings into the cellular social interactions and specialization of cardiac cell types constructing and remodelling the human heart offer new insights into structural heart diseases and the engineering of complex multicellular tissues for human heart repair.
Collapse
Affiliation(s)
- Elie N Farah
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Robert K Hu
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qingquan Zhang
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Ting-Yu Lu
- Materials Science and Engineering Program, University of California San Diego, La Jolla, CA, USA
| | - Qixuan Ma
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Shaina Tran
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Bo Zhang
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel Carlin
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Alexander Monell
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew P Blair
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Zilu Wang
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Jacqueline Eschbach
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eugin Destici
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sylvia M Evans
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shaochen Chen
- Materials Science and Engineering Program, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Quan Zhu
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Neil C Chi
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Sassu E, Tumlinson G, Stefanovska D, Fernández MC, Iaconianni P, Madl J, Brennan TA, Koch M, Cameron BA, Preissl S, Ravens U, Schneider-Warme F, Kohl P, Zgierski-Johnston CM, Hortells L. Age-related structural and functional changes of the intracardiac nervous system. J Mol Cell Cardiol 2024; 187:1-14. [PMID: 38103633 DOI: 10.1016/j.yjmcc.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Although aging is known to be associated with an increased incidence of both atrial and ventricular arrhythmias, there is limited knowledge about how Schwann cells (SC) and the intracardiac nervous system (iCNS) remodel with age. Here we investigate the differences in cardiac SC, parasympathetic nerve fibers, and muscarinic acetylcholine receptor M2 (M2R) expression in young and old mice. Additionally, we examine age-related changes in cardiac responses to sympathomimetic and parasympathomimetic drugs. METHODS AND RESULTS Lower SC density, lower SC proliferation and fewer parasympathetic nerve fibers were observed in cardiac and, as a control sciatic nerves from old (20-24 months) compared to young mice (2-3 months). In old mice, chondroitin sulfate proteoglycan 4 (CSPG4) was increased in sciatic but not cardiac nerves. Expression of M2R was lower in ventricular myocardium and ventricular conduction system from old mice compared to young mice, while no significant difference was seen in M2R expression in sino-atrial or atrio-ventricular node pacemaker tissue. Heart rate was slower and PQ intervals were longer in Langendorff-perfused hearts from old mice. Ventricular tachycardia and fibrillation were more frequently observed in response to carbachol administration in hearts from old mice versus those from young mice. CONCLUSIONS On the background of reduced presence of SC and parasympathetic nerve fibers, and of lower M2R expression in ventricular cardiomyocytes and conduction system of aged hearts, the propensity of ventricular arrhythmogenesis upon parasympathomimetic drug application is increased. Whether this is caused by an increase in heterogeneity of iCNS structure and function remains to be elucidated.
Collapse
Affiliation(s)
- Eliza Sassu
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany
| | - Gavin Tumlinson
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Dragana Stefanovska
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany
| | - Marbely C Fernández
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Pia Iaconianni
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Josef Madl
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Tomás A Brennan
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Manuel Koch
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Breanne A Cameron
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Sebastian Preissl
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany
| | - Ursula Ravens
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Franziska Schneider-Warme
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Callum M Zgierski-Johnston
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany.
| | - Luis Hortells
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79110 Freiburg, Germany.
| |
Collapse
|
15
|
Jain R, Epstein JA. Epigenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:341-364. [PMID: 38884720 DOI: 10.1007/978-3-031-44087-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Epigenetics is the study of heritable changes to the genome and gene expression patterns that are not caused by direct changes to the DNA sequence. Examples of these changes include posttranslational modifications to DNA-bound histone proteins, DNA methylation, and remodeling of nuclear architecture. Collectively, epigenetic changes provide a layer of regulation that affects transcriptional activity of genes while leaving DNA sequences unaltered. Sequence variants or mutations affecting enzymes responsible for modifying or sensing epigenetic marks have been identified in patients with congenital heart disease (CHD), and small-molecule inhibitors of epigenetic complexes have shown promise as therapies for adult heart diseases. Additionally, transgenic mice harboring mutations or deletions of genes encoding epigenetic enzymes recapitulate aspects of human cardiac disease. Taken together, these findings suggest that the evolving field of epigenetics will inform our understanding of congenital and adult cardiac disease and offer new therapeutic opportunities.
Collapse
Affiliation(s)
- Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, Epigenetics Institute and the Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Jonathan A Epstein
- Departments of Medicine and Cell and Developmental Biology, Institute for Regenerative Medicine, Epigenetics Institute and the Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
16
|
Shafi O, Siddiqui G, Jaffry HA. The benign nature and rare occurrence of cardiac myxoma as a possible consequence of the limited cardiac proliferative/ regenerative potential: a systematic review. BMC Cancer 2023; 23:1245. [PMID: 38110859 PMCID: PMC10726542 DOI: 10.1186/s12885-023-11723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Cardiac Myxoma is a primary tumor of heart. Its origins, rarity of the occurrence of primary cardiac tumors and how it may be related to limited cardiac regenerative potential, are not yet entirely known. This study investigates the key cardiac genes/ transcription factors (TFs) and signaling pathways to understand these important questions. METHODS Databases including PubMed, MEDLINE, and Google Scholar were searched for published articles without any date restrictions, involving cardiac myxoma, cardiac genes/TFs/signaling pathways and their roles in cardiogenesis, proliferation, differentiation, key interactions and tumorigenesis, with focus on cardiomyocytes. RESULTS The cardiac genetic landscape is governed by a very tight control between proliferation and differentiation-related genes/TFs/pathways. Cardiac myxoma originates possibly as a consequence of dysregulations in the gene expression of differentiation regulators including Tbx5, GATA4, HAND1/2, MYOCD, HOPX, BMPs. Such dysregulations switch the expression of cardiomyocytes into progenitor-like state in cardiac myxoma development by dysregulating Isl1, Baf60 complex, Wnt, FGF, Notch, Mef2c and others. The Nkx2-5 and MSX2 contribute predominantly to both proliferation and differentiation of Cardiac Progenitor Cells (CPCs), may possibly serve roles based on the microenvironment and the direction of cell circuitry in cardiac tumorigenesis. The Nkx2-5 in cardiac myxoma may serve to limit progression of tumorigenesis as it has massive control over the proliferation of CPCs. The cardiac cell type-specific genetic programming plays governing role in controlling the tumorigenesis and regenerative potential. CONCLUSION The cardiomyocytes have very limited proliferative and regenerative potential. They survive for long periods of time and tightly maintain the gene expression of differentiation genes such as Tbx5, GATA4 that interact with tumor suppressors (TS) and exert TS like effect. The total effect such gene expression exerts is responsible for the rare occurrence and benign nature of primary cardiac tumors. This prevents the progression of tumorigenesis. But this also limits the regenerative and proliferative potential of cardiomyocytes. Cardiac Myxoma develops as a consequence of dysregulations in these key genes which revert the cells towards progenitor-like state, hallmark of CM. The CM development in carney complex also signifies the role of TS in cardiac cells.
Collapse
Affiliation(s)
- Ovais Shafi
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan.
| | - Ghazia Siddiqui
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
| | - Hassam A Jaffry
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
| |
Collapse
|
17
|
Xie L, Wu S, Guo X. An important resource and analytic platform for human and mouse cardiovascular-related cis-regulatory elements. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102033. [PMID: 37808923 PMCID: PMC10556829 DOI: 10.1016/j.omtn.2023.102033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Affiliation(s)
- Longxiang Xie
- Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, Academy for Advanced Interdisciplinary Studies, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Shengnan Wu
- Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, Academy for Advanced Interdisciplinary Studies, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Xiangqian Guo
- Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, Academy for Advanced Interdisciplinary Studies, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| |
Collapse
|
18
|
Dann E, Cujba AM, Oliver AJ, Meyer KB, Teichmann SA, Marioni JC. Precise identification of cell states altered in disease using healthy single-cell references. Nat Genet 2023; 55:1998-2008. [PMID: 37828140 PMCID: PMC10632138 DOI: 10.1038/s41588-023-01523-7] [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: 11/09/2022] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Abstract
Joint analysis of single-cell genomics data from diseased tissues and a healthy reference can reveal altered cell states. We investigate whether integrated collections of data from healthy individuals (cell atlases) are suitable references for disease-state identification and whether matched control samples are needed to minimize false discoveries. We demonstrate that using a reference atlas for latent space learning followed by differential analysis against matched controls leads to improved identification of disease-associated cells, especially with multiple perturbed cell types. Additionally, when an atlas is available, reducing control sample numbers does not increase false discovery rates. Jointly analyzing data from a COVID-19 cohort and a blood cell atlas, we improve detection of infection-related cell states linked to distinct clinical severities. Similarly, we studied disease states in pulmonary fibrosis using a healthy lung atlas, characterizing two distinct aberrant basal states. Our analysis provides guidelines for designing disease cohort studies and optimizing cell atlas use.
Collapse
Affiliation(s)
- Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ana-Maria Cujba
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter Group, The Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Genentech, San Francisco, CA, USA.
| |
Collapse
|
19
|
Song C, Zhang Y, Huang H, Wang Y, Zhao X, Zhang G, Yin M, Feng C, Wang Q, Qian F, Shang D, Zhang J, Liu J, Li C, Tang H. Cis-Cardio: A comprehensive analysis platform for cardiovascular-relavant cis-regulation in human and mouse. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:655-667. [PMID: 37637211 PMCID: PMC10458290 DOI: 10.1016/j.omtn.2023.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Cis-regulatory elements are important molecular switches in controlling gene expression and are regarded as determinant hubs in the transcriptional regulatory network. Collection and processing of large-scale cis-regulatory data are urgent to decipher the potential mechanisms of cardiovascular diseases from a cis-regulatory element aspect. Here, we developed a novel web server, Cis-Cardio, which aims to document a large number of available cardiovascular-related cis-regulatory data and to provide analysis for unveiling the comprehensive mechanisms at a cis-regulation level. The current version of Cis-Cardio catalogs a total of 45,382,361 genomic regions from 1,013 human and mouse epigenetic datasets, including ATAC-seq, DNase-seq, Histone ChIP-seq, TF/TcoF ChIP-seq, RNA polymerase ChIP-seq, and Cohesin ChIP-seq. Importantly, Cis-Cardio provides six analysis tools, including region overlap analysis, element upstream/downstream analysis, transcription regulator enrichment analysis, variant interpretation, and protein-protein interaction-based co-regulatory analysis. Additionally, Cis-Cardio provides detailed and abundant (epi-) genetic annotations in cis-regulatory regions, such as super-enhancers, enhancers, transcription factor binding sites (TFBSs), methylation sites, common SNPs, risk SNPs, expression quantitative trait loci (eQTLs), motifs, DNase I hypersensitive sites (DHSs), and 3D chromatin interactions. In summary, Cis-Cardio is a valuable resource for elucidating and analyzing regulatory cues of cardiovascular-specific cis-regulatory elements. The platform is freely available at http://www.licpathway.net/Cis-Cardio/index.html.
Collapse
Affiliation(s)
- Chao Song
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Yuexin Zhang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Hong Huang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan 421001, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xilong Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Guorui Zhang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
| | - Mingxue Yin
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Fengcui Qian
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Desi Shang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jiaqi Liu
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Chunquan Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Key Laboratory of Rare Pediatric Diseases, Ministry of Education, University of South China, Hengyang, Hunan 421001, China
| | - Huifang Tang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
- Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan 421001, China
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Jameson HS, Hanley A, Hill MC, Xiao L, Ye J, Bapat A, Ronzier E, Hall AW, Hucker WJ, Clauss S, Barazza M, Silber E, Mina J, Tucker NR, Mills RW, Dong JT, Milan DJ, Ellinor PT. Loss of the Atrial Fibrillation-Related Gene, Zfhx3, Results in Atrial Dilation and Arrhythmias. Circ Res 2023; 133:313-329. [PMID: 37449401 PMCID: PMC10527554 DOI: 10.1161/circresaha.123.323029] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND ZFHX3 (zinc finger homeobox 3), a gene that encodes a large transcription factor, is at the second-most significantly associated locus with atrial fibrillation (AF), but its function in the heart is unknown. This study aims to identify causative genetic variation related to AF at the ZFHX3 locus and examine the impact of Zfhx3 loss on cardiac function in mice. METHODS CRISPR-Cas9 genome editing, chromatin immunoprecipitation, and luciferase assays in pluripotent stem cell-derived cardiomyocytes were used to identify causative genetic variation related to AF at the ZFHX3 locus. Cardiac function was assessed by echocardiography, magnetic resonance imaging, electrophysiology studies, calcium imaging, and RNA sequencing in mice with heterozygous and homozygous cardiomyocyte-restricted Zfhx3 loss (Zfhx3 Het and knockout, respectively). Human cardiac single-nucleus ATAC (assay for transposase-accessible chromatin)-sequencing data was analyzed to determine which genes in atrial cardiomyocytes are directly regulated by ZFHX3. RESULTS We found single-nucleotide polymorphism (SNP) rs12931021 modulates an enhancer regulating ZFHX3 expression, and the AF risk allele is associated with decreased ZFHX3 transcription. We observed a gene-dose response in AF susceptibility with Zfhx3 knockout mice having higher incidence, frequency, and burden of AF than Zfhx3 Het and wild-type mice, with alterations in conduction velocity, atrial action potential duration, calcium handling and the development of atrial enlargement and thrombus, and dilated cardiomyopathy. Zfhx3 loss results in atrial-specific differential effects on genes and signaling pathways involved in cardiac pathophysiology and AF. CONCLUSIONS Our findings implicate ZFHX3 as the causative gene at the 16q22 locus for AF, and cardiac abnormalities caused by loss of cardiac Zfhx3 are due to atrial-specific dysregulation of pathways involved in AF susceptibility. Together, these data reveal a novel and important role for Zfhx3 in the control of cardiac genes and signaling pathways essential for normal atrial function.
Collapse
Affiliation(s)
- Heather S. Jameson
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Alan Hanley
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew C. Hill
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ling Xiao
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jiangchuan Ye
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Aneesh Bapat
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Elsa Ronzier
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Amelia Weber Hall
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA
| | - William J. Hucker
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Sebastian Clauss
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine I, University Hospital Munich, Campus Grosshadern, Ludwig-Maximilians University Munich (LMU), 81377 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
- Walter Brendel Centre of Experimental Medicine, University Hospital, LMU Munich, Germany
| | - Miranda Barazza
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Silber
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Julie Mina
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Robert W. Mills
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Patrick T. Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA
| |
Collapse
|
22
|
Hasman M, Mayr M, Theofilatos K. Uncovering Protein Networks in Cardiovascular Proteomics. Mol Cell Proteomics 2023; 22:100607. [PMID: 37356494 PMCID: PMC10460687 DOI: 10.1016/j.mcpro.2023.100607] [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: 11/14/2022] [Revised: 05/01/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023] Open
Abstract
Biological networks have been widely used in many different diseases to identify potential biomarkers and design drug targets. In the present review, we describe the main computational techniques for reconstructing and analyzing different types of protein networks and summarize the previous applications of such techniques in cardiovascular diseases. Existing tools are critically compared, discussing when each method is preferred such as the use of co-expression networks for functional annotation of protein clusters and the use of directed networks for inferring regulatory associations. Finally, we are presenting examples of reconstructing protein networks of different types (regulatory, co-expression, and protein-protein interaction networks). We demonstrate the necessity to reconstruct networks separately for each cardiovascular tissue type and disease entity and provide illustrative examples of the importance of taking into consideration relevant post-translational modifications. Finally, we demonstrate and discuss how the findings of protein networks could be interpreted using single-cell RNA-sequencing data.
Collapse
Affiliation(s)
- Maria Hasman
- King's British Heart Foundation Centre, Kings College London, London, United Kingdom
| | - Manuel Mayr
- King's British Heart Foundation Centre, Kings College London, London, United Kingdom
| | | |
Collapse
|
23
|
Gaulton KJ, Preissl S, Ren B. Interpreting non-coding disease-associated human variants using single-cell epigenomics. Nat Rev Genet 2023; 24:516-534. [PMID: 37161089 PMCID: PMC10629587 DOI: 10.1038/s41576-023-00598-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
Genome-wide association studies (GWAS) have linked hundreds of thousands of sequence variants in the human genome to common traits and diseases. However, translating this knowledge into a mechanistic understanding of disease-relevant biology remains challenging, largely because such variants are predominantly in non-protein-coding sequences that still lack functional annotation at cell-type resolution. Recent advances in single-cell epigenomics assays have enabled the generation of cell type-, subtype- and state-resolved maps of the epigenome in heterogeneous human tissues. These maps have facilitated cell type-specific annotation of candidate cis-regulatory elements and their gene targets in the human genome, enhancing our ability to interpret the genetic basis of common traits and diseases.
Collapse
Affiliation(s)
- Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego School of Medicine, La Jolla, CA, USA.
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
| |
Collapse
|
24
|
Lother A, Kohl P. The heterocellular heart: identities, interactions, and implications for cardiology. Basic Res Cardiol 2023; 118:30. [PMID: 37495826 PMCID: PMC10371928 DOI: 10.1007/s00395-023-01000-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
The heterocellular nature of the heart has been receiving increasing attention in recent years. In addition to cardiomyocytes as the prototypical cell type of the heart, non-myocytes such as endothelial cells, fibroblasts, or immune cells are coming more into focus. The rise of single-cell sequencing technologies enables identification of ever more subtle differences and has reignited the question of what defines a cell's identity. Here we provide an overview of the major cardiac cell types, describe their roles in homeostasis, and outline recent findings on non-canonical functions that may be of relevance for cardiology. We highlight modes of biochemical and biophysical interactions between different cardiac cell types and discuss the potential implications of the heterocellular nature of the heart for basic research and therapeutic interventions.
Collapse
Affiliation(s)
- Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany.
- Interdisciplinary Medical Intensive Care, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany.
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, Faculty of Medicine, University Heart Center, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| |
Collapse
|
25
|
López Rodríguez M, Arasu UT, Kaikkonen MU. Exploring the genetic basis of coronary artery disease using functional genomics. Atherosclerosis 2023; 374:87-98. [PMID: 36801133 DOI: 10.1016/j.atherosclerosis.2023.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Genome-wide Association Studies (GWAS) have identified more than 300 loci associated with coronary artery disease (CAD), defining the genetic risk map of the disease. However, the translation of the association signals into biological-pathophysiological mechanisms constitute a major challenge. Through a group of examples of studies focused on CAD, we discuss the rationale, basic principles and outcomes of the main methodologies implemented to prioritize and characterize causal variants and their target genes. Additionally, we highlight the strategies as well as the current methods that integrate association and functional genomics data to dissect the cellular specificity underlying the complexity of disease mechanisms. Despite the limitations of existing approaches, the increasing knowledge generated through functional studies helps interpret GWAS maps and opens novel avenues for the clinical usability of association data.
Collapse
Affiliation(s)
- Maykel López Rodríguez
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland; Department of Pathology and Laboratory Medicine, University of California, UCLA, Los Angeles, USA.
| | - Uma Thanigai Arasu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland.
| |
Collapse
|
26
|
Poirion OB, Zuo W, Spruce C, Daigle SL, Olson A, Skelly DA, Chesler EJ, Baker CL, White BS. Enhlink infers distal and context-specific enhancer-promoter linkages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540453. [PMID: 37214950 PMCID: PMC10197707 DOI: 10.1101/2023.05.11.540453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Enhancers play a crucial role in regulating gene expression and their functional status can be queried with cell type precision using using single-cell (sc)ATAC-seq. To facilitate analysis of such data, we developed Enhlink, a novel computational approach that leverages single-cell signals to infer linkages between regulatory DNA sequences, such as enhancers and promoters. Enhlink uses an ensemble strategy that integrates cell-level technical covariates to control for batch effects and biological covariates to infer robust condition-specific links and their associated p-values. It can integrate simultaneous gene expression and chromatin accessibility measurements of individual cells profiled by multi-omic experiments for increased specificity. We evaluated Enhlink using simulated and real scATAC-seq data, including those paired with physical enhancer-promoter links enumerated by promoter capture Hi-C and with multi-omic scATAC-/RNA-seq data we generated from the mouse striatum. These examples demonstrated that our method outperforms popular alternative strategies. In conjunction with eQTL analysis, Enhlink revealed a putative super-enhancer regulating key cell type-specific markers of striatal neurons. Taken together, our analyses demonstrate that Enhlink is accurate, powerful, and provides features that can lead to novel biological insights.
Collapse
Affiliation(s)
| | - Wulin Zuo
- The Jackson Laboratory, Bar Harbor, ME, USA
| | | | | | - Ashley Olson
- The Jackson Laboratory, Bar Harbor, ME, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
| | | | - Elissa J Chesler
- The Jackson Laboratory, Bar Harbor, ME, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
| | - Christopher L Baker
- The Jackson Laboratory, Bar Harbor, ME, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
| | | |
Collapse
|
27
|
Dong S, Zhao N, Spragins E, Kagda MS, Li M, Assis P, Jolanki O, Luo Y, Cherry JM, Boyle AP, Hitz BC. Annotating and prioritizing human non-coding variants with RegulomeDB v.2. Nat Genet 2023; 55:724-726. [PMID: 37173523 PMCID: PMC10989417 DOI: 10.1038/s41588-023-01365-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Shengcheng Dong
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Nanxiang Zhao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Emma Spragins
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Mingjie Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Pedro Assis
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford, CA, USA.
| |
Collapse
|
28
|
Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science 2023; 380:eabm1696. [PMID: 37104607 PMCID: PMC10999243 DOI: 10.1126/science.abm1696] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2023] [Indexed: 04/29/2023]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.
Collapse
Affiliation(s)
- Kathleen C Keough
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Tyler Fair
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Hane Ryu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Alex Pollen
- Eli and Edythe Broad Center for 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
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
29
|
Wang RS, Maron BA, Loscalzo J. Multiomics Network Medicine Approaches to Precision Medicine and Therapeutics in Cardiovascular Diseases. Arterioscler Thromb Vasc Biol 2023; 43:493-503. [PMID: 36794589 PMCID: PMC10038904 DOI: 10.1161/atvbaha.122.318731] [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: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Cardiovascular diseases (CVD) are the leading cause of death worldwide and display complex phenotypic heterogeneity caused by many convergent processes, including interactions between genetic variation and environmental factors. Despite the identification of a large number of associated genes and genetic loci, the precise mechanisms by which these genes systematically influence the phenotypic heterogeneity of CVD are not well understood. In addition to DNA sequence, understanding the molecular mechanisms of CVD requires data from other omics levels, including the epigenome, the transcriptome, the proteome, as well as the metabolome. Recent advances in multiomics technologies have opened new precision medicine opportunities beyond genomics that can guide precise diagnosis and personalized treatment. At the same time, network medicine has emerged as an interdisciplinary field that integrates systems biology and network science to focus on the interactions among biological components in health and disease, providing an unbiased framework through which to integrate systematically these multiomics data. In this review, we briefly present such multiomics technologies, including bulk omics and single-cell omics technologies, and discuss how they can contribute to precision medicine. We then highlight network medicine-based integration of multiomics data for precision medicine and therapeutics in CVD. We also include a discussion of current challenges, potential limitations, and future directions in the study of CVD using multiomics network medicine approaches.
Collapse
Affiliation(s)
- Rui-Sheng Wang
- Division of Cardiovascular Medicine
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Joseph Loscalzo
- Division of Cardiovascular Medicine
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
30
|
Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts. Cardiovasc Res 2023; 119:64-78. [PMID: 35325060 DOI: 10.1093/cvr/cvac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The response of an organ to stimuli emerges from the actions of individual cells. Recent cardiac single-cell RNA-sequencing studies of development, injury, and reprogramming have uncovered heterogeneous populations even among previously well-defined cell types, raising questions about what level of experimental resolution corresponds to disease-relevant, tissue-level phenotypes. In this review, we explore the biological meaning behind this cellular heterogeneity by undertaking an exhaustive analysis of single-cell transcriptomics in the heart (including a comprehensive, annotated compendium of studies published to date) and evaluating new models for the cardiac function that have emerged from these studies (including discussion and schematics that depict new hypotheses in the field). We evaluate the evidence to support the biological actions of newly identified cell populations and debate questions related to the role of cell-to-cell variability in development and disease. Finally, we present emerging epigenomic approaches that, when combined with single-cell RNA-sequencing, can resolve basic mechanisms of gene regulation and variability in cell phenotype.
Collapse
Affiliation(s)
- Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natalie D Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| |
Collapse
|
31
|
Cao Y, Zhang X, Akerberg BN, Yuan H, Sakamoto T, Xiao F, VanDusen NJ, Zhou P, Sweat ME, Wang Y, Prondzynski M, Chen J, Zhang Y, Wang P, Kelly DP, Pu WT. In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen-Related Receptor as a Regulator of Ventricular Cardiomyocyte Identity. Circulation 2023; 147:881-896. [PMID: 36705030 PMCID: PMC10010668 DOI: 10.1161/circulationaha.122.061955] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Cardiac chamber-selective transcriptional programs underpin the structural and functional differences between atrial and ventricular cardiomyocytes (aCMs and vCMs). The mechanisms responsible for these chamber-selective transcriptional programs remain largely undefined. METHODS We nominated candidate chamber-selective enhancers (CSEs) by determining the genome-wide occupancy of 7 key cardiac transcription factors (GATA4, MEF2A, MEF2C, NKX2-5, SRF, TBX5, TEAD1) and transcriptional coactivator P300 in atria and ventricles. Candidate enhancers were tested using an adeno-associated virus-mediated massively parallel reporter assay. Chromatin features of CSEs were evaluated by performing assay of transposase accessible chromatin sequencing and acetylation of histone H3 at lysine 27-HiChIP on aCMs and vCMs. CSE sequence requirements were determined by systematic tiling mutagenesis of 29 CSEs at 5 bp resolution. Estrogen-related receptor (ERR) function in cardiomyocytes was evaluated by Cre-loxP-mediated inactivation of ERRα and ERRγ in cardiomyocytes. RESULTS We identified 134 066 and 97 506 regions reproducibly occupied by at least 1 transcription factor or P300, in atria or ventricles, respectively. Enhancer activities of 2639 regions bound by transcription factors or P300 were tested in aCMs and vCMs by adeno-associated virus-mediated massively parallel reporter assay. This identified 1092 active enhancers in aCMs or vCMs. Several overlapped loci associated with cardiovascular disease through genome-wide association studies, and 229 exhibited chamber-selective activity in aCMs or vCMs. Many CSEs exhibited differential chromatin accessibility between aCMs and vCMs, and CSEs were enriched for aCM- or vCM-selective acetylation of histone H3 at lysine 27-anchored loops. Tiling mutagenesis of 29 CSEs identified the binding motif of ERRα/γ as important for ventricular enhancer activity. The requirement of ERRα/γ to activate ventricular CSEs and promote vCM identity was confirmed by loss of the vCM gene profile in ERRα/γ knockout vCMs. CONCLUSIONS We identified 229 CSEs that could be useful research tools or direct therapeutic gene expression. We showed that chamber-selective multi-transcription factor, P300 occupancy, open chromatin, and chromatin looping are predictive features of CSEs. We found that ERRα/γ are essential for maintenance of ventricular identity. Finally, our gene expression, epigenetic, 3-dimensional genome, and enhancer activity atlas provide key resources for future studies of chamber-selective gene regulation.
Collapse
Affiliation(s)
- Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Haiyun Yuan
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangzhou, China (H.Y.)
| | - Tomoya Sakamoto
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (T.S., D.P.K.)
| | - Feng Xiao
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Nathan J VanDusen
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis (N.J.V.)
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Yi Wang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Maksymilian Prondzynski
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Yan Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Peizhe Wang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Daniel P Kelly
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (T.S., D.P.K.)
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.).,Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
| |
Collapse
|
32
|
Young WJ, Haessler J, Benjamins JW, Repetto L, Yao J, Isaacs A, Harper AR, Ramirez J, Garnier S, van Duijvenboden S, Baldassari AR, Concas MP, Duong T, Foco L, Isaksen JL, Mei H, Noordam R, Nursyifa C, Richmond A, Santolalla ML, Sitlani CM, Soroush N, Thériault S, Trompet S, Aeschbacher S, Ahmadizar F, Alonso A, Brody JA, Campbell A, Correa A, Darbar D, De Luca A, Deleuze JF, Ellervik C, Fuchsberger C, Goel A, Grace C, Guo X, Hansen T, Heckbert SR, Jackson RD, Kors JA, Lima-Costa MF, Linneberg A, Macfarlane PW, Morrison AC, Navarro P, Porteous DJ, Pramstaller PP, Reiner AP, Risch L, Schotten U, Shen X, Sinagra G, Soliman EZ, Stoll M, Tarazona-Santos E, Tinker A, Trajanoska K, Villard E, Warren HR, Whitsel EA, Wiggins KL, Arking DE, Avery CL, Conen D, Girotto G, Grarup N, Hayward C, Jukema JW, Mook-Kanamori DO, Olesen MS, Padmanabhan S, Psaty BM, Pattaro C, Ribeiro ALP, Rotter JI, Stricker BH, van der Harst P, van Duijn CM, Verweij N, Wilson JG, Orini M, Charron P, Watkins H, Kooperberg C, Lin HJ, Wilson JF, Kanters JK, Sotoodehnia N, Mifsud B, Lambiase PD, Tereshchenko LG, Munroe PB. Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease. Nat Commun 2023; 14:1411. [PMID: 36918541 PMCID: PMC10015012 DOI: 10.1038/s41467-023-36997-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: 05/27/2022] [Accepted: 02/26/2023] [Indexed: 03/15/2023] Open
Abstract
The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.
Collapse
Affiliation(s)
- William J Young
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS trust, London, UK
| | - Jeffrey Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jan-Walter Benjamins
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, the Netherlands
| | - Linda Repetto
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Aaron Isaacs
- Dept. of Physiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
- Maastricht Center for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Andrew R Harper
- Radcliffe Department of Medicine, University of Oxford, Division of Cardiovascular Medicine, John Radcliffe Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Julia Ramirez
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
- Aragon Institute of Engineering Research, University of Zaragoza, Zaragoza, Spain and Center of Biomedical Research Network, Bioengineering, Biomaterials and Nanomedicine, Zaragoza, Spain
| | - Sophie Garnier
- Sorbonne Universite, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Disease, Paris, 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, 75013, France
| | - Stefan van Duijvenboden
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
| | - Antoine R Baldassari
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - ThuyVy Duong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Luisa Foco
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Jonas L Isaksen
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Raymond Noordam
- Department of Internal Medicine, section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Casia Nursyifa
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Meddly L Santolalla
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, 15152, Peru
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Negin Soroush
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sébastien Thériault
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, QC, Canada
| | - 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
| | - Stefanie Aeschbacher
- Cardiovascular Research Institute Basel, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Julius Global Health, University Utrecht Medical Center, Utrecht, the Netherlands
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Archie Campbell
- Usher Institute, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, UK
- Health Data Research UK, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Adolfo Correa
- Departments of Medicine, Pediatrics and Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Dawood Darbar
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Antonio De Luca
- Cardiothoracovascular Department, Division of Cardiology, Azienda Sanitaria Universitaria Giuliano Isontina and University of Trieste, Trieste, Italy
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
- Laboratory of Excellence GENMED (Medical Genomics), Paris, France
- Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Christina Ellervik
- Department of Data and Data Support, Region Zealand, 4180, Sorø, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Anuj Goel
- Radcliffe Department of Medicine, University of Oxford, Division of Cardiovascular Medicine, John Radcliffe Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Christopher Grace
- Radcliffe Department of Medicine, University of Oxford, Division of Cardiovascular Medicine, John Radcliffe Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Rebecca D Jackson
- Center for Clinical and Translational Science, Ohio State Medical Center, Columbus, OH, USA
| | - Jan A Kors
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, København, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter W Macfarlane
- Institute of Health and Wellbeing, School of Health and Wellbeing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - 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, USA
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA, USA
| | - Lorenz Risch
- Labormedizinisches zentrum Dr. Risch, Vaduz, Liechtenstein
- Faculty of Medical Sciences, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
- Center of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, Inselspital, Bern, Switzerland
| | - Ulrich Schotten
- Dept. of Physiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Xia Shen
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou, China
| | - Gianfranco Sinagra
- Cardiothoracovascular Department, Division of Cardiology, Azienda Sanitaria Universitaria Giuliano Isontina and University of Trieste, Trieste, Italy
| | - Elsayed Z Soliman
- Epidemiological Cardiology Research Center (EPICARE), Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Monika Stoll
- Maastricht Center for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
- Dept. of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
- Institute of Human Genetics, Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Eduardo Tarazona-Santos
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andrew Tinker
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Eric Villard
- Sorbonne Universite, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Disease, Paris, 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, 75013, France
| | - Helen R Warren
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christy L Avery
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Conen
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
- Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
- Durrer Center for Cardiovascular Research, Amsterdam, the Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands, Leiden, the Netherlands
| | | | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattte, WA, USA
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Antonio Luiz P Ribeiro
- Department of Internal Medicine, Faculdade de Medicina, Universidade Federal de Minas Gerais, Brazil, Belo Horizonte, Minas Gerais, Brazil
- Cardiology Service and Telehealth Center, Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil, Belo Horizonte, Minas Gerais, Brazil
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
- Departments of Pediatrics and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pim van der Harst
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, the Netherlands
- Department of Cardiology, Heart and Lung Division, University Medical Center Utrecht, Utrecht, the Netherlands
| | - 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
| | - Niek Verweij
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, the Netherlands
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michele Orini
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS trust, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
| | - Philippe Charron
- Sorbonne Universite, INSERM, UMR-S1166, Research Unit on Cardiovascular Disorders, Metabolism and Nutrition, Team Genomics & Pathophysiology of Cardiovascular Disease, Paris, 75013, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, 75013, France
- APHP, Cardiology Department, Pitié-Salpêtrière Hospital, Paris, 75013, France
- APHP, Département de Génétique, Centre de Référence Maladies Cardiaques Héréditaires, Pitié-Salpêtrière Hospital, Paris, 75013, France
| | - Hugh Watkins
- Radcliffe Department of Medicine, University of Oxford, Division of Cardiovascular Medicine, John Radcliffe Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Henry J Lin
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Jørgen K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Borbala Mifsud
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Pier D Lambiase
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS trust, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
| | - Larisa G Tereshchenko
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Medicine, Cardiovascular Division, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
| | - Patricia B Munroe
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK.
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| |
Collapse
|
33
|
Hemerich D, Smit RAJ, Preuss M, Stalbow L, van der Laan SW, Asselbergs FW, van Setten J, Tragante V. Effect of tissue-grouped regulatory variants associated to type 2 diabetes in related secondary outcomes. Sci Rep 2023; 13:3579. [PMID: 36864090 PMCID: PMC9981672 DOI: 10.1038/s41598-023-30369-6] [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: 06/29/2022] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
Genome-wide association studies have identified over five hundred loci that contribute to variation in type 2 diabetes (T2D), an established risk factor for many diseases. However, the mechanisms and extent through which these loci contribute to subsequent outcomes remain elusive. We hypothesized that combinations of T2D-associated variants acting on tissue-specific regulatory elements might account for greater risk for tissue-specific outcomes, leading to diversity in T2D disease progression. We searched for T2D-associated variants acting on regulatory elements and expression quantitative trait loci (eQTLs) in nine tissues. We used T2D tissue-grouped variant sets as genetic instruments to conduct 2-Sample Mendelian Randomization (MR) in ten related outcomes whose risk is increased by T2D using the FinnGen cohort. We performed PheWAS analysis to investigate whether the T2D tissue-grouped variant sets had specific predicted disease signatures. We identified an average of 176 variants acting in nine tissues implicated in T2D, and an average of 30 variants acting on regulatory elements that are unique to the nine tissues of interest. In 2-Sample MR analyses, all subsets of regulatory variants acting in different tissues were associated with increased risk of the ten secondary outcomes studied on similar levels. No tissue-grouped variant set was associated with an outcome significantly more than other tissue-grouped variant sets. We did not identify different disease progression profiles based on tissue-specific regulatory and transcriptome information. Bigger sample sizes and other layers of regulatory information in critical tissues may help identify subsets of T2D variants that are implicated in certain secondary outcomes, uncovering system-specific disease progression.
Collapse
Affiliation(s)
- Daiane Hemerich
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roelof A J Smit
- 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
| | - Lauren Stalbow
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Jessica van Setten
- Department of Cardiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Vinicius Tragante
- Department of Cardiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
Hecker D, Behjati Ardakani F, Karollus A, Gagneur J, Schulz MH. The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. Bioinformatics 2023; 39:7008325. [PMID: 36708003 PMCID: PMC9931646 DOI: 10.1093/bioinformatics/btad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/05/2022] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION Identifying regulatory regions in the genome is of great interest for understanding the epigenomic landscape in cells. One fundamental challenge in this context is to find the target genes whose expression is affected by the regulatory regions. A recent successful method is the Activity-By-Contact (ABC) model which scores enhancer-gene interactions based on enhancer activity and the contact frequency of an enhancer to its target gene. However, it describes regulatory interactions entirely from a gene's perspective, and does not account for all the candidate target genes of an enhancer. In addition, the ABC model requires two types of assays to measure enhancer activity, which limits the applicability. Moreover, there is neither implementation available that could allow for an integration with transcription factor (TF) binding information nor an efficient analysis of single-cell data. RESULTS We demonstrate that the ABC score can yield a higher accuracy by adapting the enhancer activity according to the number of contacts the enhancer has to its candidate target genes and also by considering all annotated transcription start sites of a gene. Further, we show that the model is comparably accurate with only one assay to measure enhancer activity. We combined our generalized ABC model with TF binding information and illustrated an analysis of a single-cell ATAC-seq dataset of the human heart, where we were able to characterize cell type-specific regulatory interactions and predict gene expression based on TF affinities. All executed processing steps are incorporated into our new computational pipeline STARE. AVAILABILITY AND IMPLEMENTATION The software is available at https://github.com/schulzlab/STARE. CONTACT marcel.schulz@em.uni-frankfurt.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Dennis Hecker
- Institute of Cardiovascular Regeneration, Goethe University Hospital.,Cardio-Pulmonary Institute, Goethe University.,German Centre for Cardiovascular Research, Partner site Rhine-Main, Frankfurt am Main 60590
| | - Fatemeh Behjati Ardakani
- Institute of Cardiovascular Regeneration, Goethe University Hospital.,Cardio-Pulmonary Institute, Goethe University.,German Centre for Cardiovascular Research, Partner site Rhine-Main, Frankfurt am Main 60590
| | - Alexander Karollus
- School of Computation, Information and Technology, Technical University of Munich, Garching 85748
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching 85748.,Institute of Human Genetics, Technical University of Munich, Munich 81675.,Computational Health Center, Helmholtz Center Munich, Neuherberg 85764.,Munich Data Science Institute, Technical University of Munich, Garching 85748, Germany
| | - Marcel H Schulz
- Institute of Cardiovascular Regeneration, Goethe University Hospital.,Cardio-Pulmonary Institute, Goethe University.,German Centre for Cardiovascular Research, Partner site Rhine-Main, Frankfurt am Main 60590
| |
Collapse
|
36
|
Lineage-specific regulatory changes in hypertrophic cardiomyopathy unraveled by single-nucleus RNA-seq and spatial transcriptomics. Cell Discov 2023; 9:6. [PMID: 36646705 PMCID: PMC9842679 DOI: 10.1038/s41421-022-00490-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 10/29/2022] [Indexed: 01/18/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common cardiac genetic disorder characterized by cardiomyocyte hypertrophy and cardiac fibrosis. Pathological cardiac remodeling in the myocardium of HCM patients may progress to heart failure. An in-depth elucidation of the lineage-specific changes in pathological cardiac remodeling of HCM is pivotal for the development of therapies to mitigate the progression. Here, we performed single-nucleus RNA-seq of the cardiac tissues from HCM patients or healthy donors and conducted spatial transcriptomic assays on tissue sections from patients. Unbiased clustering of 55,122 nuclei from HCM and healthy conditions revealed 9 cell lineages and 28 clusters. Lineage-specific changes in gene expression, subpopulation composition, and intercellular communication in HCM were discovered through comparative analyses. According to the results of pseudotime ordering, differential expression analysis, and differential regulatory network analysis, potential key genes during the transition towards a failing state of cardiomyocytes such as FGF12, IL31RA, and CREB5 were identified. Transcriptomic dynamics underlying cardiac fibroblast activation were also uncovered, and potential key genes involved in cardiac fibrosis were obtained such as AEBP1, RUNX1, MEOX1, LEF1, and NRXN3. Using the spatial transcriptomic data, spatial activity patterns of the candidate genes, pathways, and subpopulations were confirmed on patient tissue sections. Moreover, we showed experimental evidence that in vitro knockdown of AEBP1 could promote the activation of human cardiac fibroblasts, and overexpression of AEBP1 could attenuate the TGFβ-induced activation. Our study provided a comprehensive analysis of the lineage-specific regulatory changes in HCM, which laid the foundation for targeted drug development in HCM.
Collapse
|
37
|
Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023; 24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin. Tremendous progress has been made in cataloguing CREs in the human genome using bulk transcriptomic and epigenomic methods. However, single-cell epigenomic and multi-omic technologies have the potential to provide deeper insight into cell type-specific gene regulatory programmes as well as into how they change during development, in response to environmental cues and through disease pathogenesis. Here, we highlight recent advances in single-cell epigenomic methods and analytical tools and discuss their readiness for human tissue profiling.
Collapse
Affiliation(s)
- Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
| |
Collapse
|
38
|
Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B. Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. Cell Res 2022; 32:1008-1021. [PMID: 36207411 PMCID: PMC9652396 DOI: 10.1038/s41422-022-00719-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/21/2022] [Indexed: 01/31/2023] Open
Abstract
Loss of heterochromatin has been implicated as a cause of pre-mature aging and age-associated decline in organ functions in mammals; however, the specific cell types and gene loci affected by this type of epigenetic change have remained unclear. To address this knowledge gap, we probed chromatin accessibility at single-cell resolution in the brains, hearts, skeletal muscles, and bone marrows from young, middle-aged, and old mice, and assessed age-associated changes at 353,126 candidate cis-regulatory elements (cCREs) across 32 major cell types. Unexpectedly, we detected increased chromatin accessibility within specific heterochromatin domains in old mouse excitatory neurons. The gain of chromatin accessibility at these genomic loci was accompanied by the cell-type-specific loss of heterochromatin and activation of LINE1 elements. Immunostaining further confirmed the loss of the heterochromatin mark H3K9me3 in the excitatory neurons but not in inhibitory neurons or glial cells. Our results reveal the cell-type-specific changes in chromatin landscapes in old mice and shed light on the scope of heterochromatin loss in mammalian aging.
Collapse
Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- School of Life Sciences, Westlake University, Hangzhou, China.
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Steven Francis Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Liqi Tong
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
39
|
Destici E, Zhu F, Tran S, Preissl S, Farah EN, Zhang Y, Hou X, Poirion OB, Lee AY, Grinstein JD, Bloomekatz J, Kim HS, Hu R, Evans SM, Ren B, Benner C, Chi NC. Human-gained heart enhancers are associated with species-specific cardiac attributes. NATURE CARDIOVASCULAR RESEARCH 2022; 1:830-843. [PMID: 36817700 PMCID: PMC9937543 DOI: 10.1038/s44161-022-00124-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
The heart, a vital organ which is first to develop, has adapted its size, structure and function in order to accommodate the circulatory demands for a broad range of animals. Although heart development is controlled by a relatively conserved network of transcriptional/chromatin regulators, how the human heart has evolved species-specific features to maintain adequate cardiac output and function remains to be defined. Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain cardiac developmental roles through the evolutionary acquisition of enhancers.
Collapse
Affiliation(s)
- Eugin Destici
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Fugui Zhu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaina Tran
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elie N. Farah
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Xiameng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olivier B. Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Jonathan D. Grinstein
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Hong Sook Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Hu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Neil C. Chi
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
40
|
Young WJ, Lahrouchi N, Isaacs A, Duong T, Foco L, Ahmed F, Brody JA, Salman R, Noordam R, Benjamins JW, Haessler J, Lyytikäinen LP, Repetto L, Concas MP, van den Berg ME, Weiss S, Baldassari AR, Bartz TM, Cook JP, Evans DS, Freudling R, Hines O, Isaksen JL, Lin H, Mei H, Moscati A, Müller-Nurasyid M, Nursyifa C, Qian Y, Richmond A, Roselli C, Ryan KA, Tarazona-Santos E, Thériault S, van Duijvenboden S, Warren HR, Yao J, Raza D, Aeschbacher S, Ahlberg G, Alonso A, Andreasen L, Bis JC, Boerwinkle E, Campbell A, Catamo E, Cocca M, Cutler MJ, Darbar D, De Grandi A, De Luca A, Ding J, Ellervik C, Ellinor PT, Felix SB, Froguel P, Fuchsberger C, Gögele M, Graff C, Graff M, Guo X, Hansen T, Heckbert SR, Huang PL, Huikuri HV, Hutri-Kähönen N, Ikram MA, Jackson RD, Junttila J, Kavousi M, Kors JA, Leal TP, Lemaitre RN, Lin HJ, Lind L, Linneberg A, Liu S, MacFarlane PW, Mangino M, Meitinger T, Mezzavilla M, Mishra PP, Mitchell RN, Mononen N, Montasser ME, Morrison AC, Nauck M, Nauffal V, Navarro P, Nikus K, Pare G, Patton KK, Pelliccione G, Pittman A, Porteous DJ, Pramstaller PP, Preuss MH, Raitakari OT, Reiner AP, Ribeiro ALP, Rice KM, Risch L, Schlessinger D, Schotten U, Schurmann C, Shen X, Shoemaker MB, Sinagra G, Sinner MF, Soliman EZ, Stoll M, Strauch K, Tarasov K, Taylor KD, Tinker A, Trompet S, Uitterlinden A, Völker U, Völzke H, Waldenberger M, Weng LC, Whitsel EA, Wilson JG, Avery CL, Conen D, Correa A, Cucca F, Dörr M, Gharib SA, Girotto G, Grarup N, Hayward C, Jamshidi Y, Järvelin MR, Jukema JW, Kääb S, Kähönen M, Kanters JK, Kooperberg C, Lehtimäki T, Lima-Costa MF, Liu Y, Loos RJF, Lubitz SA, Mook-Kanamori DO, Morris AP, O'Connell JR, Olesen MS, Orini M, Padmanabhan S, Pattaro C, Peters A, Psaty BM, Rotter JI, Stricker B, van der Harst P, van Duijn CM, Verweij N, Wilson JF, Arking DE, Ramirez J, Lambiase PD, Sotoodehnia N, Mifsud B, Newton-Cheh C, Munroe PB. Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways. Nat Commun 2022; 13:5144. [PMID: 36050321 PMCID: PMC9436946 DOI: 10.1038/s41467-022-32821-z] [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: 11/19/2021] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.
Collapse
Affiliation(s)
- William J Young
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS trust, London, UK
| | - Najim Lahrouchi
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron Isaacs
- Deptartment of Physiology, Cardiovascular Research Institute Maastricht CARIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Center for Systems Biology MaCSBio, Maastricht University, Maastricht, The Netherlands
| | - ThuyVy Duong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Luisa Foco
- Eurac Research, Institute for Biomedicine affiliated with the University of Lübeck, Bolzano, Italy
| | - Farah Ahmed
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Reem Salman
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
| | - Raymond Noordam
- Department of Internal Medicine, section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan-Walter Benjamins
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, The Netherlands
| | - Jeffrey Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Linda Repetto
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Marten E van den Berg
- Department of Epidemiology, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Stefan Weiss
- DZHK German Centre for Cardiovascular Research; partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics; Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Antoine R Baldassari
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, Seattle, WA, USA
| | - James P Cook
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Daniel S Evans
- California Pacific Medical Center, Research Institute, San Francisco, CA, USA
| | - Rebecca Freudling
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Oliver Hines
- Genetics Research Centre, St George's University of London, London, UK
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Jonas L Isaksen
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Honghuang Lin
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics IMBEI, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Casia Nursyifa
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yong Qian
- Translational Gerontology Branch, National Institute on Aging, National Institute of Health, Baltimore, US
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Carolina Roselli
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, The Netherlands
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eduardo Tarazona-Santos
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte/Minas Gerais, Brazil
| | - Sébastien Thériault
- Population Health Research Institute, McMaster University, Hamilton, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, Canada
| | - Stefan van Duijvenboden
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
| | - Helen R Warren
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Dania Raza
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Brighton and Sussex Medical School, Brighton, UK
| | - Stefanie Aeschbacher
- Cardiovascular Research Institute Basel, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Gustav Ahlberg
- Laboratory for Molecular Cardiology, The Heart Centre, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Laura Andreasen
- Laboratory for Molecular Cardiology, The Heart Centre, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- 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, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Archie Campbell
- Usher Institute, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, UK
- Health Data Research UK, University of Edinburgh, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Eulalia Catamo
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Massimiliano Cocca
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Murray, UT, USA
| | - Dawood Darbar
- Department of Medicine, University of Illinois at Chicago, Chicago, USA
| | - Alessandro De Grandi
- Eurac Research, Institute for Biomedicine affiliated with the University of Lübeck, Bolzano, Italy
| | - Antonio De Luca
- Cardiothoracovascular Department, ASUGI, University of Trieste, Trieste, Italy
| | - Jun Ding
- Translational Gerontology Branch, National Institute on Aging, National Institute of Health, Baltimore, US
| | - Christina Ellervik
- Department of Data and Data Support, Region Zealand, 4180, Sorø, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Demoulas Center for Cardiac Arrhythmias and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Stephan B Felix
- DZHK German Centre for Cardiovascular Research; partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B - Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine; University Medicine Greifswald, Greifswald, Germany
| | - Philippe Froguel
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine affiliated with the University of Lübeck, Bolzano, Italy
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, USA
| | - Martin Gögele
- Eurac Research, Institute for Biomedicine affiliated with the University of Lübeck, Bolzano, Italy
| | - Claus Graff
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics/Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics/David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology/University of Washington, Seattle, WA, USA
| | - Paul L Huang
- Cardiology Division and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Heikki V Huikuri
- Research Unit of Internal Medicine, Medical Research Center Oulu, University of Oulu and University Hospital of Oulu, Oulu, Finland
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
- Department of Pediatrics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Centre for Skills Training and Simulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Rebecca D Jackson
- Center for Clinical and Translational Science, Ohio State Medical Center, Columbus, OH, USA
| | - Juhani Junttila
- Research Unit of Internal Medicine, Medical Research Center Oulu, University of Oulu and University Hospital of Oulu, Oulu, Finland
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Jan A Kors
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, NL, The Netherlands
| | - Thiago P Leal
- Department of Genetics, Ecology and Evolution, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte/Minas Gerais, Brazil
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Henry J Lin
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics/Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics/David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Lars Lind
- Deptartment of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simin Liu
- Center for Global Cardiometabolic Health, Departments of Epidemiology, Medicine and Surgery, Brown University, Providence, USA
| | - Peter W MacFarlane
- Institute of Health and Wellbeing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Thomas Meitinger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research, partner site: Munich Heart Alliance, Munich, Germany
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Rebecca N Mitchell
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 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, USA
| | - Matthias Nauck
- DZHK German Centre for Cardiovascular Research; partner site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Victor Nauffal
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Guillaume Pare
- Population Health Research Institute, McMaster University, Hamilton, Canada
| | - Kristen K Patton
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Giulia Pelliccione
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Alan Pittman
- Genetics Research Centre, St George's University of London, London, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine affiliated with the University of Lübeck, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Alexander P Reiner
- Department of Epidemiology/University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA, USA
| | - Antonio Luiz P Ribeiro
- Department of Internal Medicine, Faculdade de Medicina, Universidade Federal de Minas Gerais, Brazil, Belo Horizonte, Minas Gerais, Brazil
- Cardiology Service and Telehealth Center, Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil, Belo Horizonte, Minas Gerais, Brazil
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lorenz Risch
- Labormedizinisches zentrum Dr. Risch, Vaduz, Liechtenstein
- Faculty of Medical Sciences, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
- Center of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, Inselspital, Bern, Switzerland
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institute of Health, Baltimore, US
| | - Ulrich Schotten
- Deptartment of Physiology, Cardiovascular Research Institute Maastricht CARIM, Maastricht University, Maastricht, The Netherlands
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xia Shen
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Greater Bay Area Institute of Precision Medicine Guangzhou, Fudan University, Nansha District, Guangzhou, China
| | - M Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine, Arrhythmia Section, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gianfranco Sinagra
- Cardiothoracovascular Department, ASUGI, University of Trieste, Trieste, Italy
| | - Moritz F Sinner
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research, partner site: Munich Heart Alliance, Munich, Germany
| | - Elsayed Z Soliman
- Epidemiological Cardiology Research Center EPICARE, Wake Forest School of Medicine, Winston Salem, USA
| | - Monika Stoll
- Maastricht Center for Systems Biology MaCSBio, Maastricht University, Maastricht, The Netherlands
- Dept. of Biochemistry, Cardiovascular Research Institute Maastricht CARIM, Maastricht University, Maastricht, NL, The Netherlands
- Institute of Human Genetics, Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- IBE, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics IMBEI, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Kirill Tarasov
- Laboratory of Cardiovascular Sciences, National Institute on Aging, National Institute of Health, Baltimore, US
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics/Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics/David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Andrew Tinker
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 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
| | | | - Uwe Völker
- DZHK German Centre for Cardiovascular Research; partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics; Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- DZHK German Centre for Cardiovascular Research; partner site Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- DZHK (German Centre for Cardiovascular Research, partner site: Munich Heart Alliance, Munich, Germany
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Lu-Chen Weng
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, USA
- Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, USA
| | - Christy L Avery
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - David Conen
- Population Health Research Institute, McMaster University, Hamilton, Canada
| | - Adolfo Correa
- Departments of Medicine, Pediatrics and Population Health Science, University of Mississippi Medical Center, Jackson, USA
| | - Francesco Cucca
- Institute of Genetic and Biomedical Rsearch, Italian National Research Council, Monserrato, Italy
| | - Marcus Dörr
- DZHK German Centre for Cardiovascular Research; partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B - Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine; University Medicine Greifswald, Greifswald, Germany
| | - Sina A Gharib
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Yalda Jamshidi
- Genetics Research Centre, St George's University of London, London, UK
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Stefan Kääb
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research, partner site: Munich Heart Alliance, Munich, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jørgen K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Yongmei Liu
- Department of Medicine, Duke University, Durham, NC, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A Lubitz
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Demoulas Center for Cardiac Arrhythmias and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - 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
| | - Andrew P Morris
- Department of Health Data Science, University of Liverpool, Liverpool, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Michele Orini
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS trust, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine affiliated with the University of Lübeck, Bolzano, Italy
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research, partner site: Munich Heart Alliance, Munich, Germany
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology/University of Washington, Seattle, WA, USA
- Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences/The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics/Harbor-UCLA Medical Center, Torrance, CA, USA
- Departments of Pediatrics and Human Genetics/David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Bruno Stricker
- Department of Epidemiology, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Pim van der Harst
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, The Netherlands
- Department of Cardiology, Heart and Lung Division, University Medical Center Utrecht, Utrecht, The Netherlands
| | - 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
| | - Niek Verweij
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, The Netherlands
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julia Ramirez
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
| | - Pier D Lambiase
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS trust, London, UK
- Institute of Cardiovascular Sciences, University of College London, London, UK
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Borbala Mifsud
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK
- Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Christopher Newton-Cheh
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Cardiovascular Research Center, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Patricia B Munroe
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, UK.
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| |
Collapse
|
41
|
Zhang X, Qiu H, Zhang F, Ding S. Advances in Single-Cell Multi-Omics and Application in Cardiovascular Research. Front Cell Dev Biol 2022; 10:883861. [PMID: 35733851 PMCID: PMC9207481 DOI: 10.3389/fcell.2022.883861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022] Open
Abstract
With the development of ever more powerful and versatile high-throughput sequencing techniques and innovative ways to capture single cells, mapping the multicellular tissues at the single-cell level is becoming routine practice. However, it is still challenging to depict the epigenetic landscape of a single cell, especially the genome-wide chromatin accessibility, histone modifications, and DNA methylation. We summarize the most recent methodologies to profile these epigenetic marks at the single-cell level. We also discuss the development and advancement of several multi-omics sequencing technologies from individual cells. Advantages and limitations of various methods to compare and integrate datasets obtained from different sources are also included with specific practical notes. Understanding the heart tissue at single-cell resolution and multi-modal levels will help to elucidate the cell types and states involved in physiological and pathological events during heart development and disease. The rich information produced from single-cell multi-omics studies will also promote the research of heart regeneration and precision medicine on heart diseases.
Collapse
Affiliation(s)
- Xingwu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
- *Correspondence: Xingwu Zhang,
| | - Hui Qiu
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Fengzhi Zhang
- First Hospital of Tsinghua University, Beijing, China
| | - Shuangyuan Ding
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
42
|
Turner AW, Hu SS, Mosquera JV, Ma WF, Hodonsky CJ, Wong D, Auguste G, Song Y, Sol-Church K, Farber E, Kundu S, Kundaje A, Lopez NG, Ma L, Ghosh SKB, Onengut-Gumuscu S, Ashley EA, Quertermous T, Finn AV, Leeper NJ, Kovacic JC, Björkgren JLM, Zang C, Miller CL. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. Nat Genet 2022; 54:804-816. [PMID: 35590109 PMCID: PMC9203933 DOI: 10.1038/s41588-022-01069-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/31/2022] [Indexed: 12/24/2022]
Abstract
Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies (GWAS) have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements (CREs). Here, we applied single-nucleus ATAC-seq to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants. . We identified elements in smooth muscle cell (SMC) transition states (e.g. fibromyocytes) and functional variants predicted to alter SMC and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.
Collapse
Affiliation(s)
- Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Wei Feng Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Katia Sol-Church
- Department of Pathology, University of Virginia, Charlottesville, VA, USA.,Genome Analysis & Technology Core, University of Virginia, Charlottesville, VA, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Genome Sciences Laboratory, University of Virginia, Charlottesville, VA, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Nicolas G Lopez
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Genome Sciences Laboratory, University of Virginia, Charlottesville, VA, USA.,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Euan A Ashley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Johan L M Björkgren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
43
|
Abstract
The Human Genome Project marked a major milestone in the scientific community as it unravelled the ~3 billion bases that are central to crucial aspects of human life. Despite this achievement, it only scratched the surface of understanding how each nucleotide matters, both individually and as part of a larger unit. Beyond the coding genome, which comprises only ~2% of the whole genome, scientists have realized that large portions of the genome, not known to code for any protein, were crucial for regulating the coding genes. These large portions of the genome comprise the 'non-coding genome'. The history of gene regulation mediated by proteins that bind to the regulatory non-coding genome dates back many decades to the 1960s. However, the original definition of 'enhancers' was first used in the early 1980s. In this Review, we summarize benchmark studies that have mapped the role of cardiac enhancers in disease and development. We highlight instances in which enhancer-localized genetic variants explain the missing link to cardiac pathogenesis. Finally, we inspire readers to consider the next phase of exploring enhancer-based gene therapy for cardiovascular disease.
Collapse
|
44
|
Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A, Preissl S, Ren B. A single-cell atlas of chromatin accessibility in the human genome. Cell 2021; 184:5985-6001.e19. [PMID: 34774128 PMCID: PMC8664161 DOI: 10.1016/j.cell.2021.10.024] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/30/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]
Abstract
Current catalogs of regulatory sequences in the human genome are still incomplete and lack cell type resolution. To profile the activity of gene regulatory elements in diverse cell types and tissues in the human body, we applied single-cell chromatin accessibility assays to 30 adult human tissue types from multiple donors. We integrated these datasets with previous single-cell chromatin accessibility data from 15 fetal tissue types to reveal the status of open chromatin for ∼1.2 million candidate cis-regulatory elements (cCREs) in 222 distinct cell types comprised of >1.3 million nuclei. We used these chromatin accessibility maps to delineate cell-type-specificity of fetal and adult human cCREs and to systematically interpret the noncoding variants associated with complex human traits and diseases. This rich resource provides a foundation for the analysis of gene regulatory programs in human cell types across tissues, life stages, and organ systems.
Collapse
Affiliation(s)
- Kai Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - James D Hocker
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Olivier B Poirion
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yang E Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Center for Epigenomics, University of California San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
45
|
Whitehead AJ, Hocker JD, Ren B, Engler AJ. Improved epicardial cardiac fibroblast generation from iPSCs. J Mol Cell Cardiol 2021; 164:58-68. [PMID: 34826415 DOI: 10.1016/j.yjmcc.2021.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Since the initial isolation of human embryonic stem cells and subsequent discovery of reprogramming methods for somatic cells, thousands of protocols have been developed to create each of the hundreds of cell types found in-vivo with significant focus on disease-prone systems, e.g., cardiovascular. Robust protocols exist for many of these cell types, except for cardiac fibroblasts (CF). Very recently, several competing methods have been developed to generate these cells through a developmentally conserved epicardial pathway. Such methods generate epicardial cells, but here we report that prolonged exposure to growth factors such as bFGF induces fibroblast spindle-like morphology and similar chromatin architecture to primary CFs. Media conditions for growth and assays are provided, as well as suggestions for seeding densities and timepoints for protein harvest of extracellular matrix. We demonstrate marker expression and matrix competency of resultant cells as shown next to primary human cardiac fibroblasts. These methods provide additional guidance to the original protocol and result in an increasingly stable phenotype.
Collapse
Affiliation(s)
- Alexander J Whitehead
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - James D Hocker
- Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093, USA; Laboratory of Gene Regulation, Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Bing Ren
- Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093, USA; Laboratory of Gene Regulation, Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
| |
Collapse
|
46
|
Li G, Luan C, Dong Y, Xie Y, Zentz SC, Zelt R, Roach J, Liu J, Qian L, Li Y, Yang Y. ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells. Int J Mol Sci 2021; 22:8943. [PMID: 34445647 PMCID: PMC8396223 DOI: 10.3390/ijms22168943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 12/03/2022] Open
Abstract
Unveiling the molecular features in the heart is essential for the study of heart diseases. Non-cardiomyocytes (nonCMs) play critical roles in providing structural and mechanical support to the working myocardium. There is an increasing amount of single-cell RNA-sequencing (scRNA-seq) data characterizing the transcriptomic profiles of nonCM cells. However, no tool allows researchers to easily access the information. Thus, in this study, we develop an open-access web portal, ExpressHeart, to visualize scRNA-seq data of nonCMs from five laboratories encompassing three species. ExpressHeart enables comprehensive visualization of major cell types and subtypes in each study; visualizes gene expression in each cell type/subtype in various ways; and facilitates identifying cell-type-specific and species-specific marker genes. ExpressHeart also provides an interface to directly combine information across datasets, for example, generating lists of high confidence DEGs by taking the intersection across different datasets. Moreover, ExpressHeart performs comparisons across datasets. We show that some homolog genes (e.g., Mmp14 in mice and mmp14b in zebrafish) are expressed in different cell types between mice and zebrafish, suggesting different functions across species. We expect ExpressHeart to serve as a valuable portal for investigators, shedding light on the roles of genes on heart development in nonCM cells.
Collapse
Affiliation(s)
- Gang Li
- Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Changfei Luan
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA; (C.L.); (S.C.Z.)
| | - Yanhan Dong
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.D.); (Y.X.); (J.L.); (L.Q.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yifang Xie
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.D.); (Y.X.); (J.L.); (L.Q.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott C. Zentz
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA; (C.L.); (S.C.Z.)
| | - Rob Zelt
- Research Computing, University of North Carolina, Chapel Hill, NC 27599, USA; (R.Z.); (J.R.)
| | - Jeff Roach
- Research Computing, University of North Carolina, Chapel Hill, NC 27599, USA; (R.Z.); (J.R.)
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.D.); (Y.X.); (J.L.); (L.Q.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.D.); (Y.X.); (J.L.); (L.Q.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA; (C.L.); (S.C.Z.)
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.D.); (Y.X.); (J.L.); (L.Q.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
47
|
Jiang X, Li T, Liu S, Fu Q, Li F, Chen S, Sun K, Xu R, Xu Y. Variants in a cis-regulatory element of TBX1 in conotruncal heart defect patients impair GATA6-mediated transactivation. Orphanet J Rare Dis 2021; 16:334. [PMID: 34332615 PMCID: PMC8325851 DOI: 10.1186/s13023-021-01981-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/25/2021] [Indexed: 12/14/2022] Open
Abstract
Background TBX1 (T-box transcription factor 1) is a major candidate gene that likely contributes to the etiology of velo-cardio-facial syndrome/DiGeorge syndrome (VCFS/DGS). Although the haploinsufficiency of TBX1 in both mice and humans results in congenital cardiac malformations, little has been elucidated about its upstream regulation. We aimed to explore the transcriptional regulation and dysregulation of TBX1. Methods Different TBX1 promoter reporters were constructed. Luciferase assays and electrophoretic mobility shift assays (EMSAs) were used to identify a cis-regulatory element within the TBX1 promoter region and its trans-acting factor. The expression of proteins was identified by immunohistochemistry and immunofluorescence. Variants in the cis-regulatory element were screened in conotruncal defect (CTD) patients. In vitro functional assays were performed to show the effects of the variants found in CTD patients on the transactivation of TBX1. Results We identified a cis-regulatory element within intron 1 of TBX1 that was found to be responsive to GATA6 (GATA binding protein 6), a transcription factor crucial for cardiogenesis. The expression patterns of GATA6 and TBX1 overlapped in the pharyngeal arches of human embryos. Transfection experiments and EMSA indicated that GATA6 could activate the transcription of TBX1 by directly binding with its GATA cis-regulatory element in vitro. Furthermore, sequencing analyses of 195 sporadic CTD patients without the 22q11.2 deletion or duplication identified 3 variants (NC_000022.11:g.19756832C > G, NC_000022.11:g.19756845C > T, and NC_000022.11:g. 19756902G > T) in the non-coding cis-regulatory element of TBX1. Luciferase assays showed that all 3 variants led to reduced transcription of TBX1 when incubated with GATA6. Conclusions Our findings showed that TBX1 might be a direct transcriptional target of GATA6, and variants in the non-coding cis-regulatory element of TBX1 disrupted GATA6-mediated transactivation. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01981-4.
Collapse
Affiliation(s)
- Xuechao Jiang
- Scientific Research Center, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Tingting Li
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Sijie Liu
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Qihua Fu
- Medical Laboratory, Shanghai Children's Medical Center, Affiliated to Shanghai Jiao Tong University School of Medicine , Shanghai, 200127, China
| | - Fen Li
- Department of Pediatric Cardiology, Shanghai Children's Medical Center, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Kun Sun
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Rang Xu
- Scientific Research Center, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Yuejuan Xu
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| |
Collapse
|