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Boileau E, Li X, Naarmann-de Vries IS, Becker C, Casper R, Altmüller J, Leuschner F, Dieterich C. Full-Length Spatial Transcriptomics Reveals the Unexplored Isoform Diversity of the Myocardium Post-MI. Front Genet 2022; 13:912572. [PMID: 35937994 PMCID: PMC9354982 DOI: 10.3389/fgene.2022.912572] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
We introduce Single-cell Nanopore Spatial Transcriptomics (scNaST), a software suite to facilitate the analysis of spatial gene expression from second- and third-generation sequencing, allowing to generate a full-length near-single-cell transcriptional landscape of the tissue microenvironment. Taking advantage of the Visium Spatial platform, we adapted a strategy recently developed to assign barcodes to long-read single-cell sequencing data for spatial capture technology. Here, we demonstrate our workflow using four short axis sections of the mouse heart following myocardial infarction. We constructed a de novo transcriptome using long-read data, and successfully assigned 19,794 transcript isoforms in total, including clinically-relevant, but yet uncharacterized modes of transcription, such as intron retention or antisense overlapping transcription. We showed a higher transcriptome complexity in the healthy regions, and identified intron retention as a mode of transcription associated with the infarct area. Our data revealed a clear regional isoform switching among differentially used transcripts for genes involved in cardiac muscle contraction and tissue morphogenesis. Molecular signatures involved in cardiac remodeling integrated with morphological context may support the development of new therapeutics towards the treatment of heart failure and the reduction of cardiac complications.
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Affiliation(s)
- Etienne Boileau
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Xue Li
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Isabel S Naarmann-de Vries
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christian Becker
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ramona Casper
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Florian Leuschner
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- *Correspondence: Christoph Dieterich,
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102
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Mohammadi A, Sorensen GL, Pilecki B. MFAP4-Mediated Effects in Elastic Fiber Homeostasis, Integrin Signaling and Cancer, and Its Role in Teleost Fish. Cells 2022; 11:cells11132115. [PMID: 35805199 PMCID: PMC9265350 DOI: 10.3390/cells11132115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Microfibrillar-associated protein 4 (MFAP4) is an extracellular matrix (ECM) protein belonging to the fibrinogen-related domain superfamily. MFAP4 is highly expressed in elastin-rich tissues such as lung, blood vessels and skin. MFAP4 is involved in organization of the ECM, regulating proper elastic fiber assembly. On the other hand, during pathology MFAP4 actively contributes to disease development and progression due to its interactions with RGD-dependent integrin receptors. Both tissue expression and circulating MFAP4 levels are associated with various disorders, including liver fibrosis and cancer. In other experimental models, such as teleost fish, MFAP4 appears to participate in host defense as a macrophage-specific innate immune molecule. The aim of this review is to summarize the accumulating evidence that indicates the importance of MFAP4 in homeostasis as well as pathological conditions, discuss its known biological functions with special focus on elastic fiber assembly, integrin signaling and cancer, as well as describe the reported functions of non-mammalian MFAP4 in fish. Overall, our work provides a comprehensive overview on the role of MFAP4 in health and disease.
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103
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Sun J, Peterson EA, Wang AZ, Ou J, Smith KE, Poss KD, Wang J. hapln1 Defines an Epicardial Cell Subpopulation Required for Cardiomyocyte Expansion During Heart Morphogenesis and Regeneration. Circulation 2022; 146:48-63. [PMID: 35652354 PMCID: PMC9308751 DOI: 10.1161/circulationaha.121.055468] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Certain nonmammalian species such as zebrafish have an elevated capacity for innate heart regeneration. Understanding how heart regeneration occurs in these contexts can help illuminate cellular and molecular events that can be targets for heart failure prevention or treatment. The epicardium, a mesothelial tissue layer that encompasses the heart, is a dynamic structure that is essential for cardiac regeneration in zebrafish. The extent to which different cell subpopulations or states facilitate heart regeneration requires research attention. METHODS To dissect epicardial cell states and associated proregenerative functions, we performed single-cell RNA sequencing and identified 7 epicardial cell clusters in adult zebrafish, 3 of which displayed enhanced cell numbers during regeneration. We identified paralogs of hapln1 as factors associated with the extracellular matrix and largely expressed in cluster 1. We assessed HAPLN1 expression in published single-cell RNA sequencing data sets from different stages and injury states of murine and human hearts, and we performed molecular genetics to determine the requirements for hapln1-expressing cells and functions of each hapln1 paralog. RESULTS A particular cluster of epicardial cells had the strongest association with regeneration and was marked by expression of hapln1a and hapln1b. The hapln1 paralogs are expressed in epicardial cells that enclose dedifferentiated and proliferating cardiomyocytes during regeneration. Induced genetic depletion of hapln1-expressing cells or genetic inactivation of hapln1b altered deposition of the key extracellular matrix component hyaluronic acid, disrupted cardiomyocyte proliferation, and inhibited heart regeneration. We also found that hapln1-expressing epicardial cells first emerge at the juvenile stage, when they associate with and are required for focused cardiomyocyte expansion events that direct maturation of the ventricular wall. CONCLUSIONS Our findings identify a subset of epicardial cells that emerge in postembryonic zebrafish and sponsor regions of active cardiomyogenesis during cardiac growth and regeneration. We provide evidence that, as the heart achieves its mature structure, these cells facilitate hyaluronic acid deposition to support formation of the compact muscle layer of the ventricle. They are also required, along with the function of hapln1b paralog, in the production and organization of hyaluronic acid-containing matrix in cardiac injury sites, enabling normal cardiomyocyte proliferation and muscle regeneration.
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Affiliation(s)
- Jisheng Sun
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA (J.S., E.A.P., K.E.S., J.W.)
| | - Elizabeth A Peterson
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA (J.S., E.A.P., K.E.S., J.W.)
| | - Annabel Z Wang
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC (A.Z.W., J.O., K.D.P.)
| | - Jianhong Ou
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC (A.Z.W., J.O., K.D.P.)
| | - Kieko E Smith
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA (J.S., E.A.P., K.E.S., J.W.)
| | - Kenneth D Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC (A.Z.W., J.O., K.D.P.)
| | - Jinhu Wang
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA (J.S., E.A.P., K.E.S., J.W.)
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104
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Xi X, Li H, Chen S, Lv T, Ma T, Jiang R, Zhang P, Wong WH, Zhang X. Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling. iScience 2022; 25:104790. [PMID: 35992073 PMCID: PMC9386115 DOI: 10.1016/j.isci.2022.104790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/26/2022] [Accepted: 07/14/2022] [Indexed: 12/01/2022] Open
Abstract
Complex traits such as cardiovascular diseases (CVD) are the results of complicated processes jointly affected by genetic and environmental factors. Genome-wide association studies (GWAS) identified genetic variants associated with diseases but usually did not reveal the underlying mechanisms. There could be many intermediate steps at epigenetic, transcriptomic, and cellular scales inside the black box of genotype-phenotype associations. In this article, we present a machine-learning-based cross-scale framework GRPath to decipher putative causal paths (pcPaths) from genetic variants to disease phenotypes by integrating multiple omics data. Applying GRPath on CVD, we identified 646 and 549 pcPaths linking putative causal regions, variants, and gene expressions in specific cell types for two types of heart failure, respectively. The findings suggest new understandings of coronary heart disease. Our work promoted the modeling of tissue- and cell type-specific cross-scale regulation to uncover mechanisms behind disease-associated variants, and provided new findings on the molecular mechanisms of CVD. We defined one type of cross-scale genotype-to-phenotype regulation path We designed a framework GRPath to uncover putative regulation paths for diseases GRPath helped uncover molecular mechanisms for two major types of heart failure
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Affiliation(s)
- Xi Xi
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Haochen Li
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shengquan Chen
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Tingting Lv
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Tianxing Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Rui Jiang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Ping Zhang
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Wing Hung Wong
- Departments of Statistics and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
- School of Medicine, Tsinghua University, Beijing 100084, China
- Corresponding author
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105
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Assessing Drug-Induced Mitochondrial Toxicity in Cardiomyocytes: Implications for Preclinical Cardiac Safety Evaluation. Pharmaceutics 2022; 14:pharmaceutics14071313. [PMID: 35890211 PMCID: PMC9319223 DOI: 10.3390/pharmaceutics14071313] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 02/07/2023] Open
Abstract
Drug-induced cardiotoxicity not only leads to the attrition of drugs during development, but also contributes to the high morbidity and mortality rates of cardiovascular diseases. Comprehensive testing for proarrhythmic risks of drugs has been applied in preclinical cardiac safety assessment for over 15 years. However, other mechanisms of cardiac toxicity have not received such attention. Of them, mitochondrial impairment is a common form of cardiotoxicity and is known to account for over half of cardiovascular adverse-event-related black box warnings imposed by the U.S. Food and Drug Administration. Although it has been studied in great depth, mitochondrial toxicity assessment has not yet been incorporated into routine safety tests for cardiotoxicity at the preclinical stage. This review discusses the main characteristics of mitochondria in cardiomyocytes, drug-induced mitochondrial toxicities, and high-throughput screening strategies for cardiomyocytes, as well as their proposed integration into preclinical safety pharmacology. We emphasize the advantages of using adult human primary cardiomyocytes for the evaluation of mitochondrial morphology and function, and the need for a novel cardiac safety testing platform integrating mitochondrial toxicity and proarrhythmic risk assessments in cardiac safety evaluation.
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106
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Cardiac fibroblasts regulate the development of heart failure via Htra3-TGF-β-IGFBP7 axis. Nat Commun 2022; 13:3275. [PMID: 35672400 PMCID: PMC9174232 DOI: 10.1038/s41467-022-30630-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/03/2022] [Indexed: 01/07/2023] Open
Abstract
Tissue fibrosis and organ dysfunction are hallmarks of age-related diseases including heart failure, but it remains elusive whether there is a common pathway to induce both events. Through single-cell RNA-seq, spatial transcriptomics, and genetic perturbation, we elucidate that high-temperature requirement A serine peptidase 3 (Htra3) is a critical regulator of cardiac fibrosis and heart failure by maintaining the identity of quiescent cardiac fibroblasts through degrading transforming growth factor-β (TGF-β). Pressure overload downregulates expression of Htra3 in cardiac fibroblasts and activated TGF-β signaling, which induces not only cardiac fibrosis but also heart failure through DNA damage accumulation and secretory phenotype induction in failing cardiomyocytes. Overexpression of Htra3 in the heart inhibits TGF-β signaling and ameliorates cardiac dysfunction after pressure overload. Htra3-regulated induction of spatio-temporal cardiac fibrosis and cardiomyocyte secretory phenotype are observed specifically in infarct regions after myocardial infarction. Integrative analyses of single-cardiomyocyte transcriptome and plasma proteome in human reveal that IGFBP7, which is a cytokine downstream of TGF-β and secreted from failing cardiomyocytes, is the most predictable marker of advanced heart failure. These findings highlight the roles of cardiac fibroblasts in regulating cardiomyocyte homeostasis and cardiac fibrosis through the Htra3-TGF-β-IGFBP7 pathway, which would be a therapeutic target for heart failure. Cardiac fibrosis is a hallmark of heart failure. Here the authors use single-cell RNA-sequencing, spatial transcriptomics, and genetic manipulations, to show that Htra3 regulates cardiac fibrosis by keeping fibroblasts quiescent and by degrading TGF-beta.
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107
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Abstract
The discovery of microRNAs and their role in diseases was a breakthrough that inspired research into microRNAs as drug targets. Cardiovascular diseases are an area in which limitations of conventional pharmacotherapy are highly apparent and where microRNA-based drugs have appreciably progressed into preclinical and clinical testing. In this Review, we summarize the current state of microRNAs as therapeutic targets in the cardiovascular system. We report recent advances in the identification and characterization of microRNAs, their manipulation and clinical translation, and discuss challenges and perspectives toward clinical application.
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Affiliation(s)
- Bernhard Laggerbauer
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
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108
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González A, Richards AM, de Boer RA, Thum T, Arfsten H, Hülsmann M, Falcao-Pires I, Díez J, Foo RSY, Chan MY, Aimo A, Anene-Nzelu CG, Abdelhamid M, Adamopoulos S, Anker SD, Belenkov Y, Ben Gal T, Cohen-Solal A, Böhm M, Chioncel O, Delgado V, Emdin M, Jankowska EA, Gustafsson F, Hill L, Jaarsma T, Januzzi JL, Jhund PS, Lopatin Y, Lund LH, Metra M, Milicic D, Moura B, Mueller C, Mullens W, Núñez J, Piepoli MF, Rakisheva A, Ristić AD, Rossignol P, Savarese G, Tocchetti CG, Van Linthout S, Volterrani M, Seferovic P, Rosano G, Coats AJS, Bayés-Genís A. Cardiac remodelling - Part 1: From cells and tissues to circulating biomarkers. A review from the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology. Eur J Heart Fail 2022; 24:927-943. [PMID: 35334137 DOI: 10.1002/ejhf.2493] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/09/2022] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
Cardiac remodelling refers to changes in left ventricular structure and function over time, with a progressive deterioration that may lead to heart failure (HF) development (adverse remodelling) or vice versa a recovery (reverse remodelling) in response to HF treatment. Adverse remodelling predicts a worse outcome, whilst reverse remodelling predicts a better prognosis. The geometry, systolic and diastolic function and electric activity of the left ventricle are affected, as well as the left atrium and on the long term even right heart chambers. At a cellular and molecular level, remodelling involves all components of cardiac tissue: cardiomyocytes, fibroblasts, endothelial cells and leucocytes. The molecular, cellular and histological signatures of remodelling may differ according to the cause and severity of cardiac damage, and clearly to the global trend toward worsening or recovery. These processes cannot be routinely evaluated through endomyocardial biopsies, but may be reflected by circulating levels of several biomarkers. Different classes of biomarkers (e.g. proteins, non-coding RNAs, metabolites and/or epigenetic modifications) and several biomarkers of each class might inform on some aspects on HF development, progression and long-term outcomes, but most have failed to enter clinical practice. This may be due to the biological complexity of remodelling, so that no single biomarker could provide great insight on remodelling when assessed alone. Another possible reason is a still incomplete understanding of the role of biomarkers in the pathophysiology of cardiac remodelling. Such role will be investigated in the first part of this review paper on biomarkers of cardiac remodelling.
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Affiliation(s)
- Arantxa González
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra, and IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - A Mark Richards
- Department of medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
- Christchurch Heart Institute, University of Otago, Dunedin, New Zealand
| | - Rudolf A de Boer
- University Medical Center Groningen, University of Groningen, Department of Cardiology, Groningen, The Netherlands
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) and Rebirth Center for Translational Regenerative Therapies, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
| | - Henrike Arfsten
- Clinical Division of Cardiology, Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
| | - Martin Hülsmann
- Clinical Division of Cardiology, Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Inês Falcao-Pires
- Department od Surgery and Physiology, Cardiovascular Research and Development Center, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Javier Díez
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra, and IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
- Departments of Cardiology and Cardiac Surgery, and Nephrology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Roger S Y Foo
- Department of medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
| | - Mark Y Chan
- Department of medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
| | - Alberto Aimo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- Cardiology Division, Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | - Chukwuemeka G Anene-Nzelu
- Department of medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
- Montreal Heart Institute, Montreal, Canada
| | | | - Stamatis Adamopoulos
- 2nd Department of Cardiovascular Medicine, Onassis Cardiac Surgery Center, Athens, Greece
| | - Stefan D Anker
- Department of Cardiology (CVK), and Berlin Institute of Health Center for Regenerative Therapies (BCRT), German Centre for Cardiovascular Research (DZHK) partner site Berlin, Charité Universitätsmedizin, Berlin, Germany
- Institute of Heart Diseases, Wroclaw Medical University, Wroclaw, Poland
| | | | - Tuvia Ben Gal
- Cardiology Department, Rabin Medical Center, Beilinson, Israel
| | | | - Michael Böhm
- Universitätsklinikum des Saarlandes, Klinik für Innere Medizin III, Kardiologie, Angiologie und Internistische Intensivmedizin, Saarland University, Homburg/Saar, Germany
| | - Ovidiu Chioncel
- Emergency Institute for Cardiovascular Diseases 'Prof. C.C. Iliescu' Bucharest, University of Medicine Carol Davila, Bucharest, Romania
| | - Victoria Delgado
- Institut del Cor, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Michele Emdin
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- Cardiology Division, Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | - Ewa A Jankowska
- Institute of Heart Diseases, Wroclaw Medical University, Wroclaw, Poland
| | - Finn Gustafsson
- Rigshospitalet-Copenhagen University Hospital, Heart Centre, Department of Cardiology, Copenhagen, Denmark
| | | | | | - James L Januzzi
- Massachusetts General Hospital and Baim Institute for Clinical Research, Boston, MA, USA
| | - Pardeep S Jhund
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, Scotland
| | - Yuri Lopatin
- Volgograd State Medical University, Volgograd, Russia
| | - Lars H Lund
- Department of Medicine, Karolinska Institutet, and Department of Cardiology, Karolinska University Hospital, Stockholm, Sweden
| | - Marco Metra
- Cardiology, ASST Spedali Civili; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Davor Milicic
- University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Brenda Moura
- Faculty of Medicine, University of Porto, Porto, Portugal
- Cardiology Department, Porto Armed Forces Hospital, Portugal
| | | | | | - Julio Núñez
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
- Hospital Clínico Universitario de Valencia, INCLIVA, Universidad de Valencia, Valencia, Spain
| | - Massimo F Piepoli
- Cardiology Division, Castelsangiovanni Hospital, Castelsangiovanni, Italy
| | - Amina Rakisheva
- Scientific Research Institute of Cardiology and Internal Medicine, Almaty, Kazakhstan
| | - Arsen D Ristić
- Department of Cardiology, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Patrick Rossignol
- Université de Lorraine, Centre d'Investigations Cliniques- Plurithématique 1433, and Inserm U1116, CHRU Nancy, F-CRIN INI-CRCT, Nancy, France
| | - Gianluigi Savarese
- Department of Medicine, Karolinska Institutet, and Department of Cardiology, Karolinska University Hospital, Stockholm, Sweden
| | - Carlo G Tocchetti
- Cardio-Oncology Unit, Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI), Interdepartmental Center of Clinical and Translational Sciences (CIRCET), Interdepartmental Hypertension Research Center (CIRIAPA), Federico II University, Naples, Italy
| | - Sophie Van Linthout
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany
| | | | - Petar Seferovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Giuseppe Rosano
- St. George's Hospitals, NHS Trust, University of London, London, UK
| | | | - Antoni Bayés-Genís
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
- Institut del Cor, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
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109
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Song W, Lu F, Ding Z, Huang L, Hu K, Chen J, Wei L. Identification of Heparan Sulfate in Dilated Cardiomyopathy by Integrated Bioinformatics Analysis. Front Cardiovasc Med 2022; 9:900428. [PMID: 35711374 PMCID: PMC9197211 DOI: 10.3389/fcvm.2022.900428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/27/2022] [Indexed: 11/23/2022] Open
Abstract
Objectives Heparan sulfate (HS) forms heparan sulfate proteoglycans (HSPGs), such as syndecans (SDCs) and glypicans (GPCs), to perform biological processes in the mammals. This study aimed to explore the role of HS in dilated cardiomyopathy (DCM). Methods Two high throughput RNA sequencing, two microarrays, and one single-cell RNA sequencing dataset of DCM hearts were downloaded from the Gene Expression Omnibus (GEO) database and integrated for bioinformatics analyses. Differential analysis, pathway enrichment, immunocytes infiltration, subtype identification, and single-cell RNA sequencing analysis were used in this study. Results The expression level of most HSPGs was significantly upregulated in DCM and was closely associated with immune activation, cardiac fibrosis, and heart failure. Syndecan2 (SDC2) was highly associated with collagen I and collagen III in cardiac fibroblasts of DCM hearts. HS biosynthetic pathway was activated, while the only enzyme to hydrolyze HS was downregulated. Based on the expression of HSPGs, patients with DCM were classified into three molecular subtypes, i.e., C1, C2, and C3. Cardiac fibrosis and heart failure were more severe in the C1 subtype. Conclusion Heparan sulfate is closely associated with immune activation, cardiac fibrosis, and heart failure in DCM. A novel molecular classification of patients with DCM is established based on HSPGs.
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Affiliation(s)
- Wenyu Song
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fujian Lu
- Department of Cardiology, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Zequan Ding
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Liqi Huang
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kui Hu
- Department of Cardiovascular Surgery, Guizhou Provincial People's Hospital, Guiyang, China
- Kui Hu
| | - Jinmiao Chen
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Jinmiao Chen
| | - Lai Wei
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Lai Wei
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110
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Chen S, Luo Y, Gao H, Li F, Chen Y, Li J, You R, Hao M, Bian H, Xi X, Li W, Li W, Ye M, Meng Q, Zou Z, Li C, Li H, Zhang Y, Cui Y, Wei L, Chen F, Wang X, Lv H, Hua K, Jiang R, Zhang X. hECA: The cell-centric assembly of a cell atlas. iScience 2022; 25:104318. [PMID: 35602947 PMCID: PMC9114628 DOI: 10.1016/j.isci.2022.104318] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/18/2022] [Accepted: 04/25/2022] [Indexed: 12/04/2022] Open
Abstract
The accumulation of massive single-cell omics data provides growing resources for building biomolecular atlases of all cells of human organs or the whole body. The true assembly of a cell atlas should be cell-centric rather than file-centric. We developed a unified informatics framework for seamless cell-centric data assembly and built the human Ensemble Cell Atlas (hECA) from scattered data. hECA v1.0 assembled 1,093,299 labeled human cells from 116 published datasets, covering 38 organs and 11 systems. We invented three new methods of atlas applications based on the cell-centric assembly: “in data” cell sorting for targeted data retrieval with customizable logic expressions, “quantitative portraiture” for multi-view representations of biological entities, and customizable reference creation for generating references for automatic annotations. Case studies on agile construction of user-defined sub-atlases and “in data” investigation of CAR-T off-targets in multiple organs showed the great potential enabled by the cell-centric ensemble atlas. A unified informatics framework for seamless cell-centric assembly of massive single-cell data Built the general-purpose human Ensemble Cell Atlas (hECA) V1.0 from scattered data Three new methods of applications enabling “in data” cell experiments and portraiture Case studies of agile atlas reconstruction and target therapies side-effect discovery
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Affiliation(s)
- Sijie Chen
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yanting Luo
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Haoxiang Gao
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Fanhong Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yixin Chen
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jiaqi Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Renke You
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
| | - Minsheng Hao
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Haiyang Bian
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xi Xi
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wenrui Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Weiyu Li
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
| | - Mingli Ye
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
| | - Qiuchen Meng
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Ziheng Zou
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Chen Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Haochen Li
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yangyuan Zhang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yanfei Cui
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Fufeng Chen
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
| | - Xiaowo Wang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Hairong Lv
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.,Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
| | - Kui Hua
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Rui Jiang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.,School of Medicine, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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111
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Migratory and anti-fibrotic programmes define the regenerative potential of human cardiac progenitors. Nat Cell Biol 2022; 24:659-671. [PMID: 35550611 PMCID: PMC9106586 DOI: 10.1038/s41556-022-00899-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/11/2022] [Indexed: 12/11/2022]
Abstract
Heart regeneration is an unmet clinical need, hampered by limited renewal of adult cardiomyocytes and fibrotic scarring. Pluripotent stem cell-based strategies are emerging, but unravelling cellular dynamics of host–graft crosstalk remains elusive. Here, by combining lineage tracing and single-cell transcriptomics in injured non-human primate heart biomimics, we uncover the coordinated action modes of human progenitor-mediated muscle repair. Chemoattraction via CXCL12/CXCR4 directs cellular migration to injury sites. Activated fibroblast repulsion targets fibrosis by SLIT2/ROBO1 guidance in organizing cytoskeletal dynamics. Ultimately, differentiation and electromechanical integration lead to functional restoration of damaged heart muscle. In vivo transplantation into acutely and chronically injured porcine hearts illustrated CXCR4-dependent homing, de novo formation of heart muscle, scar-volume reduction and prevention of heart failure progression. Concurrent endothelial differentiation contributed to graft neovascularization. Our study demonstrates that inherent developmental programmes within cardiac progenitors are sequentially activated in disease, enabling the cells to sense and counteract acute and chronic injury. In this study, the authors report that pluripotent stem cell-derived ventricular progenitors target loss of myocardium and fibrotic scarring to promote heart regeneration, thus offering new potential therapeutic strategies for heart injury.
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112
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Wehrens M, de Leeuw AE, Wright-Clark M, Eding JEC, Boogerd CJ, Molenaar B, van der Kraak PH, Kuster DWD, van der Velden J, Michels M, Vink A, van Rooij E. Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy. Cell Rep 2022; 39:110809. [PMID: 35545053 DOI: 10.1016/j.celrep.2022.110809] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic heart disease that is characterized by unexplained segmental hypertrophy that is usually most pronounced in the septum. While sarcomeric gene mutations are often the genetic basis for HCM, the mechanistic origin for the heterogeneous remodeling remains largely unknown. A better understanding of the gene networks driving the cardiomyocyte (CM) hypertrophy is required to improve therapeutic strategies. Patients suffering from HCM often receive a septal myectomy surgery to relieve outflow tract obstruction due to hypertrophy. Using single-cell RNA sequencing (scRNA-seq) on septal myectomy samples from patients with HCM, we identify functional links between genes, transcription factors, and cell size relevant for HCM. The data show the utility of using scRNA-seq on the human hypertrophic heart, highlight CM heterogeneity, and provide a wealth of insights into molecular events involved in HCM that can eventually contribute to the development of enhanced therapies.
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Affiliation(s)
- Martijn Wehrens
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Anne E de Leeuw
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Maya Wright-Clark
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands; Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joep E C Eding
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Cornelis J Boogerd
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Bas Molenaar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Petra H van der Kraak
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Diederik W D Kuster
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Michelle Michels
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands
| | - Aryan Vink
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands; Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands.
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113
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Gou B, Chu X, Xiao Y, Liu P, Zhang H, Gao Z, Song M. Single-Cell Analysis Reveals Transcriptomic Reprogramming in Aging Cardiovascular Endothelial Cells. Front Cardiovasc Med 2022; 9:900978. [PMID: 35615560 PMCID: PMC9124831 DOI: 10.3389/fcvm.2022.900978] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 11/18/2022] Open
Abstract
The senescence of cardiovascular endothelial cells (ECs) is a major risk factor in the development of aging-related cardiovascular diseases. However, the molecular dynamics in cardiovascular EC aging are poorly understood. Here, we characterized the transcriptomic landscape of cardiovascular ECs during aging and observed that ribosome biogenesis, inflammation, apoptosis and angiogenesis-related genes and pathways changed with age. We also highlighted the importance of collagen genes in the crosstalk between ECs and other cell types in cardiovascular aging. Moreover, transcriptional regulatory network analysis revealed Jun as a candidate transcription factor involved in murine cardiovascular senescence and we validated the upregulation of Jun in aged cardiovascular ECs both in vitro and in vivo. Altogether, our study reveals the transcriptomic reprogramming in the aging murine cardiovascular ECs, which deepens the understanding of the molecular mechanisms of cardiovascular aging and provides new insights into potential therapeutic targets against age-related cardiovascular diseases.
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Affiliation(s)
- Bo Gou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojing Chu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yi Xiao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pinxuan Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zeyu Gao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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114
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Kanaan R, Medlej-Hashim M, Jounblat R, Pilecki B, Sorensen GL. Microfibrillar-associated protein 4 in health and disease. Matrix Biol 2022; 111:1-25. [DOI: 10.1016/j.matbio.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/04/2022] [Accepted: 05/24/2022] [Indexed: 10/18/2022]
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115
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Lu F, Ma Q, Xie W, Liou CL, Zhang D, Sweat ME, Jardin BD, Naya FJ, Guo Y, Cheng H, Pu WT. CMYA5 establishes cardiac dyad architecture and positioning. Nat Commun 2022; 13:2185. [PMID: 35449169 PMCID: PMC9023524 DOI: 10.1038/s41467-022-29902-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/05/2022] [Indexed: 11/18/2022] Open
Abstract
Cardiac excitation-contraction coupling requires dyads, the nanoscopic microdomains formed adjacent to Z-lines by apposition of transverse tubules and junctional sarcoplasmic reticulum. Disruption of dyad architecture and function are common features of diseased cardiomyocytes. However, little is known about the mechanisms that modulate dyad organization during cardiac development, homeostasis, and disease. Here, we use proximity proteomics in intact, living hearts to identify proteins enriched near dyads. Among these proteins is CMYA5, an under-studied striated muscle protein that co-localizes with Z-lines, junctional sarcoplasmic reticulum proteins, and transverse tubules in mature cardiomyocytes. During cardiac development, CMYA5 positioning adjacent to Z-lines precedes junctional sarcoplasmic reticulum positioning or transverse tubule formation. CMYA5 ablation disrupts dyad architecture, dyad positioning at Z-lines, and junctional sarcoplasmic reticulum Ca2+ release, leading to cardiac dysfunction and inability to tolerate pressure overload. These data provide mechanistic insights into cardiomyopathy pathogenesis by demonstrating that CMYA5 anchors junctional sarcoplasmic reticulum to Z-lines, establishes dyad architecture, and regulates dyad Ca2+ release.
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Affiliation(s)
- Fujian Lu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Wenjun Xie
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi'an Jiaotong University, 710049, Xi'an, Shanxi, China
| | - Carter L Liou
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Donghui Zhang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, 430062, Wuhan, Hubei, China
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Blake D Jardin
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Francisco J Naya
- Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yuxuan Guo
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, 100191, Beijing, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA, 02138, USA.
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116
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Rurik JG, Epstein JA. Uniting Disciplines to Develop Therapeutics: Targeted mRNA Lipid Nanoparticles Reprogram the Immune System In Vivo to Treat Heart Disease. DNA Cell Biol 2022; 41:539-543. [PMID: 35446147 DOI: 10.1089/dna.2022.0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The burgeoning field of immunomedicine is primed to expand beyond oncology (Aghajanian et al., 2022). Over the past several decades, many cell-based therapies have been proposed, developed, and deployed in the clinic. The recent explosion of targeted cell therapies has primarily been aimed at oncological malignancies. In parallel, cardiology researchers have been investigating the various cell types that contribute to heart diseases, especially those responsible for tissue fibrosis and myocardial dysfunction. Our laboratory proposed in 2019 to unite these two disciplines: could a targeted cell therapy be used to ameliorate cardiac fibrosis (Aghajanian et al., 2019). Although preliminary results were encouraging, the genetic engineering approach used to manufacture immune cells would result in persistent cytolytic T cell if directly translated to humans. This would pose a safety concern since activated fibroblasts are essential cells in the setting of acute injury. Therefore, we developed a novel technology to deliver modified RNA to T cells in vivo, resulting in a transient antiactivated fibroblast therapeutic (Rurik et al., 2022). Although active for only a few days, these cells were sufficient to significantly improve cardiac function in a murine model of cardiac fibrosis. These results pave the way for low-cost and scalable, and dose-able and immune therapy for fibrotic disorders.
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Affiliation(s)
- Joel G Rurik
- Department of Cell and Developmental Biology, Penn Cardiovascular Institute, and Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology, Penn Cardiovascular Institute, and Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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117
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Deciphering Cardiac Biology and Disease by Single-Cell Transcriptomic Profiling. Biomolecules 2022; 12:biom12040566. [PMID: 35454155 PMCID: PMC9032111 DOI: 10.3390/biom12040566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Abstract
By detecting minute molecular changes in hundreds to millions of single cells, single-cell RNA sequencing allows for the comprehensive characterization of the diversity and dynamics of cells in the heart. Our understanding of the heart has been transformed through the recognition of cellular heterogeneity, the construction of regulatory networks, the building of lineage trajectories, and the mapping of intercellular crosstalk. In this review, we introduce cardiac progenitors and their transcriptional regulation during embryonic development, highlight cellular heterogeneity and cell subtype functions in cardiac health and disease, and discuss insights gained from the study of pluripotent stem-cell-derived cardiomyocytes.
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118
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Clinical characteristics, predictors, and outcomes of heart failure with improved ejection fraction. Int J Cardiol 2022; 357:72-80. [PMID: 35339576 DOI: 10.1016/j.ijcard.2022.03.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/23/2022]
Abstract
AIMS Improvement in ejection fraction (EF) was observed in a subset of patients with heart failure (HF) and reduced ejection fraction (HFrEF). We analyzed and compared these patients with other HF phenotypes. METHODS Based on left ventricular ejection fraction(LVEF) at baseline and follow-up, the 561 HF patients were divided into 4 groups: HF preserved EF (HFpEF, LVEF ≥ 50% on both occasions, n = 258), HF mid-range EF (HFmrEF, fluctuating between LVEF 40 and 49% on both occasions, n = 61), HFrEF (LVEF < 40% on both occasions, n = 141), and HF improved EF (HFimpEF, defined as LVEF < 40% at baseline and LVEF ≥ 40% at follow-up with ≥10% absolute improvement, n = 101). The composite of HF readmission and all-cause mortality was considered the primary endpoint, and the secondary endpoint was all-cause mortality. RESULTS The characteristics of HFimpEF differed from other HF phenotypes. β-blockers and aldosterone receptor antagonists were associated with improved LVEF. Kaplan-Meier curves showed the lowest incidence of the composite endpoint (p < 0.001) and all-cause mortality (p < 0.001) in HFimpEF. The risk of cardiovascular death was lowest in HFimpEF after controlling for competing events (p < 0.001), as were competing events (p < 0.001). Valvular heart disease (VHD) (HR 8.555, 95 CI% 2.126-34.420, p = 0.003) increased the risk of all-cause death, and anemia increased the risk of all-cause death (HR 5.533, 95 CI% 1.592-19.530, p = 0.007) and cardiovascular death in HFimpEF patients (HR 5.840, 95 CI% 1.088-31.356, p = 0.040). CONCLUSIONS HFimpEF is an independent HF phenotype with a prognosis similar to HFmrEF and superior to HFpEF and HFrEF. When HFimpEF patients had VHD and anemia, the endpoint event rate was increased.
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119
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Anand P, Lenehan PJ, Niesen M, Yoo U, Patwardhan D, Montorzi M, Venkatakrishnan AJ, Soundararajan V. Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. Cell Death Dis 2022; 8:124. [PMID: 35314694 PMCID: PMC8935120 DOI: 10.1038/s41420-022-00914-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/07/2022] [Accepted: 02/24/2022] [Indexed: 01/28/2023]
Abstract
Acute cardiac injury has been observed in a subset of COVID-19 patients, but the molecular basis for this clinical phenotype is unknown. It has been hypothesized that molecular mimicry may play a role in triggering an autoimmune inflammatory reaction in some individuals after SARS-CoV-2 infection. Here we investigate if linear peptides contained in proteins that are primarily expressed in the heart also occur in the SARS-CoV-2 proteome. Specifically, we compared the library of 136,704 8-mer peptides from 144 human proteins (including splicing variants) to 9926 8-mers from all the viral proteins in the reference SARS-CoV-2 proteome. No 8-mers were exactly identical between the reference human proteome and the reference SARS-CoV-2 proteome. However, there were 45 8-mers that differed by only one amino acid when compared to the reference SARS-CoV-2 proteome. Interestingly, analysis of protein-coding mutations from 141,456 individuals showed that one of these 8-mers from the SARS-CoV-2 Replicase polyprotein 1a/1ab (KIALKGGK) is identical to an MYH6 peptide encoded by the c.5410 C > A (Q1804K) genetic variation, which has been observed at low prevalence in Africans/African Americans (0.08%), East Asians (0.3%), South Asians (0.06%), and Latino/Admixed Americans (0.003%). Furthermore, analysis of 4.85 million SARS-CoV-2 genomes from over 200 countries shows that viral evolution has already resulted in 20 additional 8-mer peptides that are identical to human heart-enriched proteins encoded by reference sequences or genetic variants. Whether such mimicry contributes to cardiac inflammation during or after COVID-19 illness warrants further experimental evaluation. We suggest that SARS-CoV-2 variants harboring peptides identical to human cardiac proteins should be investigated as "viral variants of cardiac interest".
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Affiliation(s)
| | | | | | - Unice Yoo
- grid.510985.0nference, Cambridge, MA 02139 USA
| | | | - Marcelo Montorzi
- grid.510985.0nference, Cambridge, MA 02139 USA ,grid.492905.3Southcoast Health, Fairhaven, MA 02719 USA
| | | | - Venky Soundararajan
- nference Labs, Bengaluru, Karnataka 560017 India ,grid.510985.0nference, Cambridge, MA 02139 USA
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120
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Froese N, Cordero J, Abouissa A, Trogisch FA, Grein S, Szaroszyk M, Wang Y, Gigina A, Korf-Klingebiel M, Bosnjak B, Davenport CF, Wiehlmann L, Geffers R, Riechert E, Jürgensen L, Boileau E, Lin Y, Dieterich C, Förster R, Bauersachs J, Ola R, Dobreva G, Völkers M, Heineke J. Analysis of myocardial cellular gene expression during pressure overload reveals matrix based functional intercellular communication. iScience 2022; 25:103965. [PMID: 35281736 PMCID: PMC8908217 DOI: 10.1016/j.isci.2022.103965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/22/2021] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
To identify cellular mechanisms responsible for pressure overload triggered heart failure, we isolated cardiomyocytes, endothelial cells, and fibroblasts as most abundant cell types from mouse hearts in the subacute and chronic stages after transverse aortic constriction (TAC) and performed RNA-sequencing. We detected highly cell-type specific transcriptional responses with characteristic time courses and active intercellular communication. Cardiomyocytes after TAC exerted an early and sustained upregulation of inflammatory and matrix genes and a concomitant suppression of metabolic and ion channel genes. Fibroblasts, in contrast, showed transient early upregulation of inflammatory and matrix genes and downregulation of angiogenesis genes, but sustained induction of cell cycle and ion channel genes during TAC. Endothelial cells transiently induced cell cycle and extracellular matrix genes early after TAC, but exerted a long-lasting upregulation of inflammatory genes. As we found that matrix production by multiple cell types triggers pathological cellular responses, it might serve as a future therapeutic target. TAC induces matrix and growth, but reduces contraction genes in cardiomyocytes TAC induces genes related to matrix, inflammation, and cell cycle in endothelial cells TAC induces matrix and inflammation, but reduces angiogenesis genes in fibroblasts Matrix proteins trigger growth, proliferation, and migration in cardiac cells
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Affiliation(s)
- Natali Froese
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Julio Cordero
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Aya Abouissa
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Felix A Trogisch
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Steve Grein
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany
| | - Malgorzata Szaroszyk
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Yong Wang
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Anna Gigina
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | | | | | - Colin F Davenport
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Eva Riechert
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Etienne Boileau
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.,Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, 69120 Heidelberg, Germany
| | - Yanzhu Lin
- Department of Experimental Pharmacology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Christoph Dieterich
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.,Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, 69120 Heidelberg, Germany
| | | | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, 30625 Hannover, Germany
| | - Roxana Ola
- Department of Experimental Pharmacology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, 68167 Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Mirko Völkers
- Department of Internal Medicine III, Medical Faculty of Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Joerg Heineke
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Ludolf-Krehl-Str. 7-11, 68167 Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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121
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Robinson EL, Baker AH, Brittan M, McCracken I, Condorelli G, Emanueli C, Srivastava PK, Gaetano C, Thum T, Vanhaverbeke M, Angione C, Heymans S, Devaux Y, Pedrazzini T, Martelli F. Dissecting the transcriptome in cardiovascular disease. Cardiovasc Res 2022; 118:1004-1019. [PMID: 33757121 PMCID: PMC8930073 DOI: 10.1093/cvr/cvab117] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
The human transcriptome comprises a complex network of coding and non-coding RNAs implicated in a myriad of biological functions. Non-coding RNAs exhibit highly organized spatial and temporal expression patterns and are emerging as critical regulators of differentiation, homeostasis, and pathological states, including in the cardiovascular system. This review defines the current knowledge gaps, unmet methodological needs, and describes the challenges in dissecting and understanding the role and regulation of the non-coding transcriptome in cardiovascular disease. These challenges include poor annotation of the non-coding genome, determination of the cellular distribution of transcripts, assessment of the role of RNA processing and identification of cell-type specific changes in cardiovascular physiology and disease. We highlight similarities and differences in the hurdles associated with the analysis of the non-coding and protein-coding transcriptomes. In addition, we discuss how the lack of consensus and absence of standardized methods affect reproducibility of data. These shortcomings should be defeated in order to make significant scientific progress and foster the development of clinically applicable non-coding RNA-based therapeutic strategies to lessen the burden of cardiovascular disease.
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Affiliation(s)
- Emma L Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
- The Division of Cardiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ian McCracken
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - G Condorelli
- Humanitas Research Hospital, Humanitas University, Via Manzoni 113, Rozzano, MI 20089, Italy
| | - C Emanueli
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - P K Srivastava
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - C Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, Pavia 27100, Italy
| | - T Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Carl-Neuberg-Straße 1 30625 Hannover, Germany
| | - M Vanhaverbeke
- UZ Gasthuisberg Campus, KU Leuven, Herestraat 49 3000 Leuven, Belgium
| | - C Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, TS4 3BX, UK
| | - S Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
| | - Y Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - T Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland
| | - F Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Piazza Edmondo Malan, 2, 20097 San Donato, Milan, Italy
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122
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Comprehensive evaluation of deconvolution methods for human brain gene expression. Nat Commun 2022; 13:1358. [PMID: 35292647 PMCID: PMC8924248 DOI: 10.1038/s41467-022-28655-4] [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: 09/05/2019] [Accepted: 01/28/2022] [Indexed: 11/08/2022] Open
Abstract
Transcriptome deconvolution aims to estimate the cellular composition of an RNA sample from its gene expression data, which in turn can be used to correct for composition differences across samples. The human brain is unique in its transcriptomic diversity, and comprises a complex mixture of cell-types, including transcriptionally similar subtypes of neurons. Here, we carry out a comprehensive evaluation of deconvolution methods for human brain transcriptome data, and assess the tissue-specificity of our key observations by comparison with human pancreas and heart. We evaluate eight transcriptome deconvolution approaches and nine cell-type signatures, testing the accuracy of deconvolution using in silico mixtures of single-cell RNA-seq data, RNA mixtures, as well as nearly 2000 human brain samples. Our results identify the main factors that drive deconvolution accuracy for brain data, and highlight the importance of biological factors influencing cell-type signatures, such as brain region and in vitro cell culturing. Transcriptome deconvolution aims to estimate cellular composition based on gene expression data. Here the authors evaluate deconvolution methods for human brain transcriptome and conclude that partial deconvolution algorithms work best, but that appropriate cell-type signatures are also important.
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123
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Zhu T, Liu J, Beck S, Pan S, Capper D, Lechner M, Thirlwell C, Breeze CE, Teschendorff AE. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution. Nat Methods 2022; 19:296-306. [PMID: 35277705 PMCID: PMC8916958 DOI: 10.1038/s41592-022-01412-7] [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: 07/11/2021] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data. This resource presents an in silico generated DNA methylation atlas that can be used for cell-type deconvolution of human tissues.
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124
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Abplanalp WT, Tucker N, Dimmeler S. Single-cell technologies to decipher cardiovascular diseases. Eur Heart J 2022; 43:4536-4547. [PMID: 35265972 PMCID: PMC9659476 DOI: 10.1093/eurheartj/ehac095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/30/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Cardiovascular disease remains the leading cause of death worldwide. A deeper understanding of the multicellular composition and molecular processes may help to identify novel therapeutic strategies. Single-cell technologies such as single-cell or single-nuclei RNA sequencing provide expression profiles of individual cells and allow for dissection of heterogeneity in tissue during health and disease. This review will summarize (i) how these novel technologies have become critical for delineating mechanistic drivers of cardiovascular disease, particularly, in humans and (ii) how they might serve as diagnostic tools for risk stratification or individualized therapy. The review will further discuss technical pitfalls and provide an overview of publicly available human and mouse data sets that can be used as a resource for research.
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Affiliation(s)
- Wesley Tyler Abplanalp
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany,German Center for Cardiovascular Research DZHK, Partner site Frankfurt Rhine-Main, Berlin, Germany,Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Nathan Tucker
- Masonic Medical Research Institute, Utica, NY, USA,Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Stefanie Dimmeler
- Corresponding author. Tel: +49 69 6301 5158, Fax: +49 69 6301 83462,
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125
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Marbán E, Liao K. On the cellular origin of cardiosphere-derived cells (CDCs). Basic Res Cardiol 2022; 117:12. [PMID: 35258685 DOI: 10.1007/s00395-022-00914-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Eduardo Marbán
- Cedars-Sinai Medical Center, Smidt Heart Institute, 127 South San Vicente Boulevard, AHSP A3600, Los Angeles, CA, 90048, USA.
| | - Ke Liao
- Cedars-Sinai Medical Center, Smidt Heart Institute, 127 South San Vicente Boulevard, AHSP A3600, Los Angeles, CA, 90048, USA
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126
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A novel single-cell RNA-sequencing approach and its applicability connecting genotype to phenotype in ageing disease. Sci Rep 2022; 12:4091. [PMID: 35260714 PMCID: PMC8904555 DOI: 10.1038/s41598-022-07874-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/23/2022] [Indexed: 12/22/2022] Open
Abstract
Single cell multi-omics analysis has the potential to yield a comprehensive understanding of the cellular events that underlie the basis of human diseases. The cardinal feature to access this information is the technology used for single-cell isolation, barcoding, and sequencing. Most currently used single-cell RNA-sequencing platforms have limitations in several areas including cell selection, documentation and library chemistry. In this study, we describe a novel high-throughput, full-length, single-cell RNA-sequencing approach that combines the CellenONE isolation and sorting system with the ICELL8 processing instrument. This method offers substantial improvements in single cell selection, documentation and capturing rate. Moreover, it allows the use of flexible chemistry for library preparations and the analysis of living or fixed cells, whole cells independent of sizing and morphology, as well as of nuclei. We applied this method to dermal fibroblasts derived from six patients with different segmental progeria syndromes and defined phenotype associated pathway signatures with variant associated expression modifiers. These results validate the applicability of our method to highlight genotype-expression relationships for molecular phenotyping of individual cells derived from human patients.
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127
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Xu Y, Baumgart SJ, Stegmann CM, Hayat S. MACA: marker-based automatic cell-type annotation for single-cell expression data. Bioinformatics 2022; 38:1756-1760. [PMID: 34935911 DOI: 10.1093/bioinformatics/btab840] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/07/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Accurately identifying cell types is a critical step in single-cell sequencing analyses. Here, we present marker-based automatic cell-type annotation (MACA), a new tool for annotating single-cell transcriptomics datasets. We developed MACA by testing four cell-type scoring methods with two public cell-marker databases as reference in six single-cell studies. MACA compares favorably to four existing marker-based cell-type annotation methods in terms of accuracy and speed. We show that MACA can annotate a large single-nuclei RNA-seq study in minutes on human hearts with ∼290K cells. MACA scales easily to large datasets and can broadly help experts to annotate cell types in single-cell transcriptomics datasets, and we envision MACA provides a new opportunity for integration and standardization of cell-type annotation across multiple datasets. AVAILABILITY AND IMPLEMENTATION MACA is written in python and released under GNU General Public License v3.0. The source code is available at https://github.com/ImXman/MACA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Xu
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
| | - Simon J Baumgart
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
| | - Christian M Stegmann
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
| | - Sikander Hayat
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
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128
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Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure. NATURE CARDIOVASCULAR RESEARCH 2022; 1:263-280. [PMID: 35959412 PMCID: PMC9364913 DOI: 10.1038/s44161-022-00028-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heart failure represents a major cause of morbidity and mortality worldwide. Single-cell transcriptomics have revolutionized our understanding of cell composition and associated gene expression. Through integrated analysis of single-cell and single-nucleus RNA-sequencing data generated from 27 healthy donors and 18 individuals with dilated cardiomyopathy, here we define the cell composition of the healthy and failing human heart. We identify cell-specific transcriptional signatures associated with age and heart failure and reveal the emergence of disease-associated cell states. Notably, cardiomyocytes converge toward common disease-associated cell states, whereas fibroblasts and myeloid cells undergo dramatic diversification. Endothelial cells and pericytes display global transcriptional shifts without changes in cell complexity. Collectively, our findings provide a comprehensive analysis of the cellular and transcriptomic landscape of human heart failure, identify cell type-specific transcriptional programs and disease-associated cell states and establish a valuable resource for the investigation of human heart failure.
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129
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The Application of Autopsy and Explanted Heart Samples in Scientific Research. Cardiovasc Pathol 2022; 59:107424. [DOI: 10.1016/j.carpath.2022.107424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 12/28/2022] Open
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130
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Hegenbarth JC, Lezzoche G, De Windt LJ, Stoll M. Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac Transcriptomics. FRONTIERS IN MOLECULAR MEDICINE 2022; 2:839338. [PMID: 39086967 PMCID: PMC11285642 DOI: 10.3389/fmmed.2022.839338] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/31/2022] [Indexed: 08/02/2024]
Abstract
The heart has been the center of numerous transcriptomic studies in the past decade. Even though our knowledge of the key organ in our cardiovascular system has significantly increased over the last years, it is still not fully understood yet. In recent years, extensive efforts were made to understand the genetic and transcriptomic contribution to cardiac function and failure in more detail. The advent of Next Generation Sequencing (NGS) technologies has brought many discoveries but it is unable to comprehend the finely orchestrated interactions between and within the various cell types of the heart. With the emergence of single-cell sequencing more than 10 years ago, researchers gained a valuable new tool to enable the exploration of new subpopulations of cells, cell-cell interactions, and integration of multi-omic approaches at a single-cell resolution. Despite this innovation, it is essential to make an informed choice regarding the appropriate technique for transcriptomic studies, especially when working with myocardial tissue. Here, we provide a primer for researchers interested in transcriptomics using NGS technologies.
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Affiliation(s)
- Jana-Charlotte Hegenbarth
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Giuliana Lezzoche
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Leon J. De Windt
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Monika Stoll
- Department of Biochemistry, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, Netherlands
- Department of Genetic Epidemiology, Institute of Human Genetics, University Hospital Münster, Münster, Germany
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131
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Wu X, Zhao X, Xiong Y, Zheng M, Zhong C, Zhou Y. Deciphering Cell-Type-Specific Gene Expression Signatures of Cardiac Diseases Through Reconstruction of Bulk Transcriptomes. Front Cell Dev Biol 2022; 10:792774. [PMID: 35252172 PMCID: PMC8894713 DOI: 10.3389/fcell.2022.792774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/12/2022] [Indexed: 12/14/2022] Open
Abstract
Cardiac diseases compose a fatal disease category worldwide. Over the past decade, high-throughput transcriptome sequencing of bulk heart tissues has widened our understanding of the onset and progression of cardiac diseases. The recent rise of single-cell RNA sequencing (scRNA-seq) technology further enables deep explorations of their molecular mechanisms in a cell-type-specific manner. However, due to technical difficulties in performing scRNA-seq on heart tissues, there are still few scRNA-seq studies on cardiac diseases. In this study, we demonstrate that an effective alternative could be cell-type-specific computational reconstruction of bulk transcriptomes. An integrative bulk transcriptome dataset covering 110 samples from 12 studies was first constructed by re-analysis of raw sequencing data derived from the heart tissues of four common cardiac disease mouse models (myocardial infarction, dilated cardiomyopathy, hypertrophic cardiomyopathy, and arrhythmogenic right ventricular cardiomyopathy). Based on the single-cell reference covering four major cardiac component cell types and 22 immune cell subtypes, for each sample, the bulk transcriptome was reconstructed into cellular compositions and cell-type-specific expression profiles by CIBERSORTx. Variations in the estimated cell composition revealed elevated abundances of fibroblast and monocyte during myocardial infarction, which were further verified by our flow cytometry experiment. Moreover, through cell-type-specific differential gene expression and pathway enrichment analysis, we observed a series of signaling pathways that mapped to specific cell type in diseases, like MAPK and EGFR1 signaling pathways in fibroblasts in myocardial infarction. We also found an increased expression of several secretory proteins in monocytes which may serve as regulatory factors in cardiac fibrosis. Finally, a ligand–receptor analysis identified key cell types which may serve as hubs in cellular communication in cardiac diseases. Our results provide novel clues for the cell-type-specific signatures of cardiac diseases that would promote better understanding of their pathophysiological mechanisms.
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Affiliation(s)
- Xiaobin Wu
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
| | - Xingyu Zhao
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University, Beijing, China
| | - Yufei Xiong
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Ming Zheng
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chao Zhong
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University, Beijing, China
- *Correspondence: Chao Zhong, ; Yuan Zhou,
| | - Yuan Zhou
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
- *Correspondence: Chao Zhong, ; Yuan Zhou,
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132
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Li L, Wang M, Ma Q, Li Y, Ye J, Sun X, Sun G. Progress of Single-Cell RNA Sequencing Technology in Myocardial Infarction Research. Front Cardiovasc Med 2022; 9:768834. [PMID: 35252379 PMCID: PMC8893277 DOI: 10.3389/fcvm.2022.768834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/20/2022] [Indexed: 01/08/2023] Open
Abstract
After myocardial infarction, the heart enters a remodeling and repair phase that involves myocardial cell damage, inflammatory response, fibroblast activation, and, ultimately, angiogenesis. In this process, the proportions and functions of cardiomyocytes, immune cells, fibroblasts, endothelial cells, and other cells change. Identification of the potential differences in gene expression among cell types and/or transcriptome heterogeneity among cells of the same type greatly contribute to understanding the cellular changes that occur in heart and disease conditions. Recent advent of the single-cell transcriptome sequencing technology has facilitated the exploration of single cell diversity as well as comprehensive elucidation of the natural history and molecular mechanisms of myocardial infarction. In this manner, novel putative therapeutic targets for myocardial infarction treatment may be detected and clinically applied.
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Affiliation(s)
- Lanfang Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Min Wang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qiuxiao Ma
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yunxiu Li
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Molecular Medicine Research Centre, College of Integration Science, College of Pharmacy, Yanbian University, Yanji, China
| | - Jingxue Ye
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Jingxue Ye
| | - Xiaobo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Xiaobo Sun
| | - Guibo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Guibo Sun
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133
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Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Rep Med 2022; 3:100522. [PMID: 35233546 PMCID: PMC8784611 DOI: 10.1016/j.xcrm.2022.100522] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/22/2021] [Accepted: 01/16/2022] [Indexed: 01/07/2023]
Abstract
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.
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Affiliation(s)
- Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Foox
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - David C. Danko
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | - Youngmi Kim
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Daniel J. Butler
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Evan E. Afshin
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - André F. Rendeiro
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Saravia-Butler
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Logyx, LLC, Mountain View, CA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Jonathan Schisler
- McAllister Heart Institute at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, and Department of Pathology and Lab Medicine at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | | - Steven Salvatore
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Nicholas P. Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison J. Kriegel
- Department of Physiology, Cardiovascular Center, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Olivier Elemento
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alain C. Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert E. Schwartz
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E. Mason
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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134
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Shao X, Zhang X, Zhang R, Zhu R, Hou X, Yi W, Wu F, Hao L, Feng R. The atlas of ACE2 expression in fetal and adult human hearts reveals the potential mechanism of heart injured patients infected with SARS-CoV-2. Am J Physiol Cell Physiol 2022; 322:C723-C738. [PMID: 35138176 PMCID: PMC8977135 DOI: 10.1152/ajpcell.00169.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Numerous studies have shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect host cells through binding to angiotensin I converting enzyme 2 (ACE2) expressing in various tissues and organs. In this study, we deeply analyzed the single-cell expression profiles of ACE2 in fetal and adult human hearts to explore the potential mechanism of SARS-CoV-2 harming the heart. The molecular docking software was used to simulate the binding of SARS-CoV-2 and its variant spike protein with ACE2. The genes closely related to ACE2 in renin-angiotensin system (RAS) were identified by constructing a protein-protein interaction network. Through the analysis of single-cell transcription profiles at different stages of human embryos, we found that the expression level of ACE2 in ventricular myocytes was increased with embryonic development. The results of single-cell sequencing analysis showed that the expression of ACE2 in ventricular myocytes was upregulated in heart failure induced by dilated cardiomyopathy compared with normal hearts. The upregulation of ACE2 increases the risk of infection with SARS-CoV-2 in fetal and adult human hearts. We also further confirmed the expression of ACE2 and ACE2-related genes in normal and SARS-CoV-2-infected human pluripotent stem cell-derived cardiomyocytes. In addition, the pathway analysis revealed that ACE2 may regulate the differently expressed genes in heart failure through calcium signaling pathway and Wnt signaling pathway.
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Affiliation(s)
- Xiuli Shao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Xiaolin Zhang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Ruijia Zhang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Rongli Zhu
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Xiuyang Hou
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Weijue Yi
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Fengmin Wu
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Liying Hao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Rui Feng
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
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135
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Cellular Phenotypic Transformation in Heart Failure Caused by Coronary Heart Disease and Dilated Cardiomyopathy: Delineating at Single-Cell Level. Biomedicines 2022; 10:biomedicines10020402. [PMID: 35203611 PMCID: PMC8962334 DOI: 10.3390/biomedicines10020402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 12/10/2022] Open
Abstract
Heart failure (HF) is known as the final manifestation of cardiovascular diseases. Although cellular heterogeneity of the heart is well understood, the phenotypic transformation of cardiac cells in progress of HF remains obscure. This study aimed to analyze phenotypic transformation of cardiac cells in HF through human single-cell RNA transcriptome profile. Here, phenotypic transformation of cardiomyocytes (CMs), endothelial cells (ECs), and fibroblasts was identified by data analysis and animal experiments. Abnormal myosin subunits including the decrease in Myosin Heavy Chain 6, Myosin Light Chain 7 and the increase in Myosin Heavy Chain 7 were found in CMs. Two disease phenotypes of ECs named inflammatory ECs and muscularized ECs were identified. In addition, myofibroblast was increased in HF and highly associated with abnormal extracellular matrix. Our study proposed an integrated map of phenotypic transformation of cardiac cells and highlighted the intercellular communication in HF. This detailed definition of cellular transformation will facilitate cell-based mapping of novel interventional targets for the treatment of HF.
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136
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Theall B, Alcaide P. The heart under pressure: immune cells in fibrotic remodeling. CURRENT OPINION IN PHYSIOLOGY 2022; 25:100484. [PMID: 35224321 PMCID: PMC8881013 DOI: 10.1016/j.cophys.2022.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The complex syndrome of heart failure (HF) is characterized by increased left ventricular pressures. Cardiomyocytes increase in size, cardiac fibroblasts transform and make extracellular matrix, and leukocytes infiltrate the cardiac tissue and alter cardiomyocyte and cardiac fibroblast function. Here we review recent advances in our understanding of the cellular composition of the heart during homeostasis and in response to cardiac pressure overload, with an emphasis on immune cell communication with cardiac fibroblasts and its consequences in cardiac remodeling.
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Affiliation(s)
- Brandon Theall
- Department of Immunology, Tufts University School of Medicine, Boston, MA,Immunology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA
| | - Pilar Alcaide
- Department of Immunology, Tufts University School of Medicine, Boston, MA,Immunology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA
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137
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Fan Y, Zhou H, Liu X, Li J, Xu K, Fu X, Ye L, Li G. Applications of Single-Cell RNA Sequencing in Cardiovascular Research. Front Cell Dev Biol 2022; 9:810232. [PMID: 35174168 PMCID: PMC8841340 DOI: 10.3389/fcell.2021.810232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022] Open
Abstract
In recent years, cardiovascular disease (CVD) continues to be the leading cause of global disease burden. Extensive efforts have been made across basic, translational, and clinical research domains to curb the CVD epidemic and improve the health of the population. The successful completion of the Human Genome Project catapulted sequencing technology into the mainstream and aroused the interests of clinicians and scientific researchers alike. Advances in single-cell RNA sequencing (scRNA-seq), which is based on the transcriptional phenotypes of individual cells, have enabled the investigation of cellular fate, heterogeneity, and cell–cell interactions, as well as cell lineage determination, at a single-cell resolution. In this review, we summarize recent findings on the embryological development of the cardiovascular system and the pathogenesis and treatment of cardiovascular disease, as revealed by scRNA-seq technology. In particular, we discuss how scRNA-seq can help identify potential targets for the treatment of cardiovascular diseases and conclude with future perspectives for scRNA-seq.
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Affiliation(s)
- Yu Fan
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- Department of Obstetrics, Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Han Zhou
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Xuexue Liu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Jingyan Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Ke Xu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Xiaodong Fu
- Department of Obstetrics, Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lei Ye
- National Heart Research Institute of Singapore, Singapore, Singapore
- *Correspondence: Lei Ye, ; Guang Li,
| | - Guang Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- *Correspondence: Lei Ye, ; Guang Li,
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138
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Shi X, Zhang L, Li Y, Xue J, Liang F, Ni HW, Wang X, Cai Z, Shen LH, Huang T, He B. Integrative Analysis of Bulk and Single-Cell RNA Sequencing Data Reveals Cell Types Involved in Heart Failure. Front Bioeng Biotechnol 2022; 9:779225. [PMID: 35071201 PMCID: PMC8766768 DOI: 10.3389/fbioe.2021.779225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Owing to the high mortality rates of heart failure (HF), a more detailed description of the HF becomes extremely urgent. Since the pathogenesis of HF remain elusive, a thorough identification of the genetic factors will provide novel insights into the molecular basis of this cardiac dysfunction. In our research, we performed publicly available transcriptome profiling datasets, including non-failure (NF), dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) hearts tissues. Through principal component analysis (PCA), gene differential expression analysis, gene set enrichment analysis (GSEA), and gene Set Variation Analysis (GSVA), we figured out the candidate genes noticeably altered in HF, the specific biomarkers of endothelial cell (EC) and cardiac fibrosis, then validated the differences of the inflammation-related cell adhesion molecules (CAMs), extracellular matrix (ECM) genes, and immune responses. Taken together, our results suggested the EC and fibroblast could be activated in response to HF. DCM and ICM had both commonality and specificity in the pathogenesis of HF. Higher inflammation in ICM might related to autocrine CCL3/CCL4-CCR5 interaction induced chemokine signaling activation. Furthermore, the activities of neutrophil and macrophage were higher in ICM than DCM. These findings identified features of the landscape of previously underestimated cellular, transcriptomic heterogeneity between ICM and DCM.
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Affiliation(s)
- Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Li Zhang
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science, East China Normal University, Ministry of Education, Shanghai, China
| | - Yi Li
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jieyuan Xue
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Liang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Han-Wen Ni
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Wang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhaohua Cai
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ling-Hong Shen
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Huang
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Ben He
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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139
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Wu ATH, Lawal B, Tzeng YM, Shih CC, Shih CM. Identification of a Novel Theranostic Signature of Metabolic and Immune-Inflammatory Dysregulation in Myocardial Infarction, and the Potential Therapeutic Properties of Ovatodiolide, a Diterpenoid Derivative. Int J Mol Sci 2022; 23:ijms23031281. [PMID: 35163208 PMCID: PMC8836044 DOI: 10.3390/ijms23031281] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 01/27/2023] Open
Abstract
Myocardial infarction (MI) is a multifactorial global disease, recognized as one of the leading causes of cardiovascular morbidity and mortality. Timely and correct diagnoses and effective treatments could significantly reduce incidence of complications and improve patient prognoses. In this study, seven unconventional differentially expressed genes (DEGs) (MAN2A2, TNFRSF12A, SPP1, CSNK1D, PLAUR, PFKFB3, and CXCL16, collectively termed the MTSCPPC signature) were identified through integrating DEGs from six MI microarray datasets. The pathological and theranostic roles of the MTSCPPC signature in MI were subsequently analyzed. We evaluated interactions of the MTSCPPC signature with ovatodiolide, a bioactive compound isolated from Anisomeles indica (L.) Kuntze, using in silico molecular docking tools and compared it to specific inhibitors of the members of the MTSCPPC signature. Single-cell transcriptomic analysis of the public databases revealed high expression levels of the MTSCPPC signature in immune cells of adult human hearts during an MI event. The MTSCPPC signature was significantly associated with the cytokine–cytokine receptor interactions, chemokine signaling, immune and inflammatory responses, and metabolic dysregulation in MI. Analysis of a micro (mi)RNA regulatory network of the MTSCPPC signature suggested post-transcriptional activation and the roles of miRNAs in the pathology of MI. Our molecular docking analysis suggested a higher potential for ovatodiolide to target MAN2A2, CSNK1D, and TNFRSF12A. Collectively, the results derived from the present study further advance our understanding of the complex regulatory mechanisms of MI and provide a potential MI theranostic signature with ovatodiolide as a therapeutic candidate.
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Affiliation(s)
- Alexander T. H. Wu
- The Ph.D. Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
- Taipei Heart Institute, Taipei Medical University, Taipei 11031, Taiwan;
| | - Bashir Lawal
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan;
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yew-Min Tzeng
- Department of Life Science, National Taitung University, Taitung 95092, Taiwan;
| | - Chun-Che Shih
- Taipei Heart Institute, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Cardiovascular Surgery, Department of Surgery, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chun-Ming Shih
- Taipei Heart Institute, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Correspondence:
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140
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Erbe R, Gore J, Gemmill K, Gaykalova DA, Fertig EJ. The use of machine learning to discover regulatory networks controlling biological systems. Mol Cell 2022; 82:260-273. [PMID: 35016036 PMCID: PMC8905511 DOI: 10.1016/j.molcel.2021.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
Abstract
Biological systems are composed of a vast web of multiscale molecular interactors and interactions. High-throughput technologies, both bulk and single cell, now allow for investigation of the properties and quantities of these interactors. Computational algorithms and machine learning methods then provide the tools to derive meaningful insights from the resulting data sets. One such approach is graphical network modeling, which provides a computational framework to explicitly model the molecular interactions within and between the cells comprising biological systems. These graphical networks aim to describe a putative chain of cause and effect between interacting molecules. This feature allows for determination of key molecules in a biological process, accelerated generation of mechanistic hypotheses, and simulation of experimental outcomes. We review the computational concepts and applications of graphical network models across molecular scales for both intracellular and intercellular regulatory biology, examples of successful applications, and the future directions needed to overcome current limitations.
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Affiliation(s)
- Rossin Erbe
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jessica Gore
- Institute for Genome Sciences, University of Maryland Medical Center, Baltimore, MD, USA
| | - Kelly Gemmill
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Daria A Gaykalova
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Institute for Genome Sciences, University of Maryland Medical Center, Baltimore, MD, USA; Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland Medical Center, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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141
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Grisanti Canozo FJ, Zuo Z, Martin JF, Samee MAH. Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain. Cell Syst 2022; 13:58-70.e5. [PMID: 34626538 PMCID: PMC8776574 DOI: 10.1016/j.cels.2021.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/06/2021] [Accepted: 09/10/2021] [Indexed: 01/21/2023]
Abstract
Single-cell spatial transcriptomics (sc-ST) holds the promise to elucidate architectural aspects of complex tissues. Such analyses require modeling cell types in sc-ST datasets through their integration with single-cell RNA-seq datasets. However, this integration, is nontrivial since the two technologies differ widely in the number of profiled genes, and the datasets often do not share many marker genes for given cell types. We developed a neural network model, spatial transcriptomics cell-types assignment using neural networks (STANN), to overcome these challenges. Analysis of STANN's predicted cell types in mouse olfactory bulb (MOB) sc-ST data delineated MOB architecture beyond its morphological layer-based conventional description. We find that cell-type proportions remain consistent within individual morphological layers but vary significantly between layers. Notably, even within a layer, cellular colocalization patterns and intercellular communication mechanisms show high spatial variations. These observations imply a refinement of major cell types into subtypes characterized by spatially localized gene regulatory networks and receptor-ligand usage.
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Affiliation(s)
| | - Zhen Zuo
- Baylor College of Medicine, Houston, TX 77030, USA
| | - James F Martin
- Baylor College of Medicine, Houston, TX 77030, USA; Texas Heart Institute, Houston, TX 77030, USA
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142
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Schoger E, Lelek S, Panáková D, Zelarayán LC. Tailoring Cardiac Synthetic Transcriptional Modulation Towards Precision Medicine. Front Cardiovasc Med 2022; 8:783072. [PMID: 35097003 PMCID: PMC8795974 DOI: 10.3389/fcvm.2021.783072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular and genetic differences between individual cells within tissues underlie cellular heterogeneities defining organ physiology and function in homeostasis as well as in disease states. Transcriptional control of endogenous gene expression has been intensively studied for decades. Thanks to a fast-developing field of single cell genomics, we are facing an unprecedented leap in information available pertaining organ biology offering a comprehensive overview. The single-cell technologies that arose aided in resolving the precise cellular composition of many organ systems in the past years. Importantly, when applied to diseased tissues, the novel approaches have been immensely improving our understanding of the underlying pathophysiology of common human diseases. With this information, precise prediction of regulatory elements controlling gene expression upon perturbations in a given cell type or a specific context will be realistic. Simultaneously, the technological advances in CRISPR-mediated regulation of gene transcription as well as their application in the context of epigenome modulation, have opened up novel avenues for targeted therapy and personalized medicine. Here, we discuss the fast-paced advancements during the recent years and the applications thereof in the context of cardiac biology and common cardiac disease. The combination of single cell technologies and the deep knowledge of fundamental biology of the diseased heart together with the CRISPR-mediated modulation of gene regulatory networks will be instrumental in tailoring the right strategies for personalized and precision medicine in the near future. In this review, we provide a brief overview of how single cell transcriptomics has advanced our knowledge and paved the way for emerging CRISPR/Cas9-technologies in clinical applications in cardiac biomedicine.
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Affiliation(s)
- Eric Schoger
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Goettingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Goettingen, Goettingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Goettingen, Goettingen, Germany
| | - Sara Lelek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Daniela Panáková
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Daniela Panáková
| | - Laura Cecilia Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, Goettingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Goettingen, Goettingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Goettingen, Goettingen, Germany
- *Correspondence: Laura Cecilia Zelarayán
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143
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Abstract
PURPOSE OF REVIEW The pathological remodeling of cardiac tissue after injury or disease leads to scar formation. Our knowledge of the role of nonmyocytes, especially fibroblasts, in cardiac injury and repair continues to increase with technological advances in both experimental and clinical studies. Here, we aim to elaborate on cardiac fibroblasts by describing their origins, dynamic cellular states after injury, and heterogeneity in order to understand their role in cardiac injury and repair. RECENT FINDINGS With the improvement in genetic lineage tracing technologies and the capability to profile gene expression at the single-cell level, we are beginning to learn that manipulating a specific population of fibroblasts could mitigate severe cardiac fibrosis and promote cardiac repair after injury. Cardiac fibroblasts play an indispensable role in tissue homeostasis and in repair after injury. Activated fibroblasts or myofibroblasts have time-dependent impacts on cardiac fibrosis. Multiple signaling pathways are involved in modulating fibroblast states, resulting in the alteration of fibrosis. Modulating a specific population of cardiac fibroblasts may provide new opportunities for identifying novel treatment options for cardiac fibrosis.
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Affiliation(s)
- Maoying Han
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Bin Zhou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China. .,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
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144
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Interlandi M, Kerl K, Dugas M. InterCellar enables interactive analysis and exploration of cell-cell communication in single-cell transcriptomic data. Commun Biol 2022; 5:21. [PMID: 35017628 PMCID: PMC8752611 DOI: 10.1038/s42003-021-02986-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/16/2021] [Indexed: 12/03/2022] Open
Abstract
Deciphering cell-cell communication is a key step in understanding the physiology and pathology of multicellular systems. Recent advances in single-cell transcriptomics have contributed to unraveling the cellular composition of tissues and enabled the development of computational algorithms to predict cellular communication mediated by ligand-receptor interactions. Despite the existence of various tools capable of inferring cell-cell interactions from single-cell RNA sequencing data, the analysis and interpretation of the biological signals often require deep computational expertize. Here we present InterCellar, an interactive platform empowering lab-scientists to analyze and explore predicted cell-cell communication without requiring programming skills. InterCellar guides the biological interpretation through customized analysis steps, multiple visualization options, and the possibility to link biological pathways to ligand-receptor interactions. Alongside convenient data exploration features, InterCellar implements data-driven analyses including the possibility to compare cell-cell communication from multiple conditions. By analyzing COVID-19 and melanoma cell-cell interactions, we show that InterCellar resolves data-driven patterns of communication and highlights molecular signals through the integration of biological functions and pathways. We believe our user-friendly, interactive platform will help streamline the analysis of cell-cell communication and facilitate hypothesis generation in diverse biological systems.
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Affiliation(s)
- Marta Interlandi
- Institute of Medical Informatics, University of Münster, Münster, Germany.
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany.
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
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145
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Chen Y, Zhang T, Yao F, Gao X, Li D, Fu S, Mao L, Liu F, Zhang X, Xu Y, Deng J, Li W, Fan G, Xiao C, Chen Y, Wang L, Guo W, Zhou B. Dysregulation of interaction between LOX high fibroblast and smooth muscle cells contributes to the pathogenesis of aortic dissection. Theranostics 2022; 12:910-928. [PMID: 34976220 PMCID: PMC8692905 DOI: 10.7150/thno.66059] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/16/2021] [Indexed: 12/27/2022] Open
Abstract
Rationale: While cell-cell interaction plays a critical role in physiology and disease, a comprehensive understanding of its dynamics in vascular homeostasis and diseases is yet absent. Methods: Here, by use of single-cell RNA-sequencing and multi-color staining, we delineate the cellular composition and spatial characterization of human aorta with or without aortic dissection (AD). Results: Scrutinization of cell subtype alterations revealed significantly changed fibroblast (FB)-smooth muscle cell (SMC) interactions in AD. Of these cellular interactions, LOXhigh fibroblast (fibroblast subtype 2, FB2) in diseased state exerted the most pronounced effects on pathological deterioration of SMCs in AD. In addition, pharmacologically targeting the BMP (bone morphogenetic protein) signaling pathway effectively suppressed FB2 state transition and reduced AD incidence in mice. Finally, COL5A1 (collagen type V alpha 1 chain), one of the secreted proteins released from FB2, was significantly higher in the plasma of AD patients than in control patients, suggesting its potential use as a biomarker for AD diagnosis. Conclusions: Our work not only identified a pivotal role of a specific FB subtype in AD progression, but also shed light on cell interaction dynamics in vascular diseases.
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146
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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.
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147
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Zhang Z, Cui F, Cao C, Wang Q, Zou Q. Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections. Comput Biol Med 2022; 140:105092. [PMID: 34864302 PMCID: PMC8628631 DOI: 10.1016/j.compbiomed.2021.105092] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of coronavirus disease 2019 (COVID-19) since December 2019 that has led to more than 160 million confirmed cases, including 3.3 million deaths. To understand the mechanism by which SARS-CoV-2 invades human cells and reveal organ-specific susceptible cell types for COVID-19, we conducted comprehensive bioinformatic analysis using public single-cell RNA sequencing datasets. Utilizing the expression information of six confirmed COVID-19 receptors (ACE2, TMPRSS2, NRP1, AXL, FURIN and CTSL), we demonstrated that macrophages are the most likely cells that may be associated with SARS-CoV-2 pathogenesis in lung. Besides the widely reported 'chemokine storm', we identified ribosome related pathways that may also be potential therapeutic target for COVID-19 lung infection patients. Moreover, cell-cell communication analysis and trajectory analysis revealed that M1-like macrophages showed the highest relation to severe COVID-19 patients. And we also demonstrated that up-regulation of chemokine pathways generally lead to severe symptoms, while down-regulation of ribosome and RNA activity related pathways are more likely to be mild. Other organ-specific susceptible cell type analyses could also provide potential targets for COVID-19 therapy. This work can provide clues for understanding the pathogenesis of COVID-19 and contribute to understanding the mechanism by which SARS-CoV-2 invades human cells.
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Affiliation(s)
- Zilong Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Feifei Cui
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Chen Cao
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Qingsuo Wang
- Beidahuang Industry Group General Hospital, Harbin, 150001, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China.
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148
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Olsen MB, Gregersen I, Sandanger Ø, Yang K, Sokolova M, Halvorsen BE, Gullestad L, Broch K, Aukrust P, Louwe MC. Targeting the Inflammasome in Cardiovascular Disease. JACC Basic Transl Sci 2022; 7:84-98. [PMID: 35128212 PMCID: PMC8807732 DOI: 10.1016/j.jacbts.2021.08.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/24/2021] [Accepted: 08/28/2021] [Indexed: 01/10/2023]
Abstract
The pathogenesis of cardiovascular disease (CVD) is complex and multifactorial, and inflammation plays a central role. Inflammasomes are multimeric protein complexes that are activated in a 2-step manner in response to infection or tissue damage. Upon activation the proinflammatory cytokines, interleukins-1β and -18 are released. In the last decade, the evidence that inflammasome activation plays an important role in CVD development became stronger. We discuss the role of different inflammasomes in the pathogenesis of CVD, focusing on atherosclerosis and heart failure. This review also provides an overview of existing experimental studies and clinical trials on inflammasome inhibition as a therapeutic target in these disorders.
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Key Words
- ACS, acute coronary syndrome
- AIM2, absent in melanoma 2
- ASC, apoptosis associated speck-like protein
- ATP, adenosine triphosphate
- CAD, coronary artery disease
- CRP, C-reactive protein
- CVD, cardiovascular disease
- DAMP, damage associated molecular pattern
- GSDMD, gasdermin-D
- GSDMD-NT, gasdermin-D N-terminal
- HF, heart failure
- HFpEF, HF with preserved ejection fraction
- HFrEF, HF with reduced ejection fraction
- IL, interleukin
- IL-1
- LDL, low-density lipoprotein
- LV, left ventricular
- LVEF, left ventricular ejection fraction
- MI, myocardial infarction
- NF-κB, nuclear factor κB
- NLR, NOD-like receptor
- NLRP3
- NLRP3, NOD-like receptor family pyrin domain containing 3
- NOD, nucleotide-binding oligomerization domain
- PRR, pattern recognition receptor
- STEMI, ST-elevation myocardial infarction
- TLR, toll-like receptor
- atherosclerosis
- cardiovascular disease
- heart failure
- inflammasome
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Affiliation(s)
- Maria Belland Olsen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Øystein Sandanger
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Section of Dermatology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Kuan Yang
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Marina Sokolova
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Bente E. Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Lars Gullestad
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
- Department of Cardiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- K.G. Jebsen Cardiac Research Center, Center for Heart Failure Research, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kaspar Broch
- Department of Cardiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- K.G. Jebsen Cardiac Research Center, Center for Heart Failure Research, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Mieke C. Louwe
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
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149
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Kogan PS, Wirth F, Tomar A, Darr J, Teperino R, Lahm H, Dreßen M, Puluca N, Zhang Z, Neb I, Beck N, Luzius T, de la Osa de la Rosa L, Gärtner K, Hüls C, Zeidler R, Ramanujam D, Engelhardt S, Wenk C, Holdt LM, Mononen M, Sahara M, Cleuziou J, Hörer J, Lange R, Krane M, Doppler SA. Uncovering the molecular identity of cardiosphere-derived cells (CDCs) by single-cell RNA sequencing. Basic Res Cardiol 2022; 117:11. [PMID: 35258704 PMCID: PMC8902493 DOI: 10.1007/s00395-022-00913-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 01/31/2023]
Abstract
Cardiosphere-derived cells (CDCs) generated from human cardiac biopsies have been shown to have disease-modifying bioactivity in clinical trials. Paradoxically, CDCs' cellular origin in the heart remains elusive. We studied the molecular identity of CDCs using single-cell RNA sequencing (sc-RNAseq) in comparison to cardiac non-myocyte and non-hematopoietic cells (cardiac fibroblasts/CFs, smooth muscle cells/SMCs and endothelial cells/ECs). We identified CDCs as a distinct and mitochondria-rich cell type that shared biological similarities with non-myocyte cells but not with cardiac progenitor cells derived from human-induced pluripotent stem cells. CXCL6 emerged as a new specific marker for CDCs. By analysis of sc-RNAseq data from human right atrial biopsies in comparison with CDCs we uncovered transcriptomic similarities between CDCs and CFs. By direct comparison of infant and adult CDC sc-RNAseq data, infant CDCs revealed GO-terms associated with cardiac development. To analyze the beneficial effects of CDCs (pro-angiogenic, anti-fibrotic, anti-apoptotic), we performed functional in vitro assays with CDC-derived extracellular vesicles (EVs). CDC EVs augmented in vitro angiogenesis and did not stimulate scarring. They also reduced the expression of pro-apoptotic Bax in NRCMs. In conclusion, CDCs were disclosed as mitochondria-rich cells with unique properties but also with similarities to right atrial CFs. CDCs displayed highly proliferative, secretory and immunomodulatory properties, characteristics that can also be found in activated or inflammatory cell types. By special culture conditions, CDCs earn some bioactivities, including angiogenic potential, which might modify disease in certain disorders.
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Affiliation(s)
- Palgit-S. Kogan
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Felix Wirth
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Archana Tomar
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Jonatan Darr
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Raffaele Teperino
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Harald Lahm
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Martina Dreßen
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Nazan Puluca
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Zhong Zhang
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Irina Neb
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Nicole Beck
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Tatjana Luzius
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Luis de la Osa de la Rosa
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Kathrin Gärtner
- Research Unit Gene Vectors, Helmholtz Center Munich German Research Center for Environmental Health, Munich, Germany
| | - Corinna Hüls
- Research Unit Gene Vectors, Helmholtz Center Munich German Research Center for Environmental Health, Munich, Germany
| | - Reinhard Zeidler
- Research Unit Gene Vectors, Helmholtz Center Munich German Research Center for Environmental Health, Munich, Germany ,Department of Otorhinolaryngology, Klinikum der Universität (KUM), Munich, Germany
| | - Deepak Ramanujam
- DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany ,Institute of Pharmacology and Toxicology, Technische Universität München, Biedersteiner Str. 29, 80802 Munich, Germany
| | - Stefan Engelhardt
- DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany ,Institute of Pharmacology and Toxicology, Technische Universität München, Biedersteiner Str. 29, 80802 Munich, Germany
| | - Catharina Wenk
- Institute of Laboratory Medicine, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Lesca M. Holdt
- Institute of Laboratory Medicine, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Mimmi Mononen
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden ,Department of Surgery, Yale University School of Medicine, CN06510 New Haven, CT USA
| | - Julie Cleuziou
- School of Medicine and Health, Department of Pediatric and Congenital Heart Surgery, Institute Insure, Technical University of Munich, Lazarettstraße 36, 80636 Munich, Germany
| | - Jürgen Hörer
- School of Medicine and Health, Department of Pediatric and Congenital Heart Surgery, Technical University of Munich, German Heart Center Munich, Lazarettstraße 36, 80636 Munich, Germany ,Division of Congenital and Pediatric Heart Surgery, University Hospital of Munich, Ludwig-Maximilians-Universität, Munich, Germany
| | - Rüdiger Lange
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany ,DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany
| | - Markus Krane
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany ,DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany ,Division of Cardiac Surgery, Department of Surgery, Yale University School of Medicine, New Haven, CT USA
| | - Stefanie A. Doppler
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
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150
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Abstract
Myocardial infarction is a leading cause of death worldwide1. Although advances have been made in acute treatment, an incomplete understanding of remodelling processes has limited the effectiveness of therapies to reduce late-stage mortality2. Here we generate an integrative high-resolution map of human cardiac remodelling after myocardial infarction using single-cell gene expression, chromatin accessibility and spatial transcriptomic profiling of multiple physiological zones at distinct time points in myocardium from patients with myocardial infarction and controls. Multi-modal data integration enabled us to evaluate cardiac cell-type compositions at increased resolution, yielding insights into changes of the cardiac transcriptome and epigenome through the identification of distinct tissue structures of injury, repair and remodelling. We identified and validated disease-specific cardiac cell states of major cell types and analysed them in their spatial context, evaluating their dependency on other cell types. Our data elucidate the molecular principles of human myocardial tissue organization, recapitulating a gradual cardiomyocyte and myeloid continuum following ischaemic injury. In sum, our study provides an integrative molecular map of human myocardial infarction, represents an essential reference for the field and paves the way for advanced mechanistic and therapeutic studies of cardiac disease.
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