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Single-cell analysis of long noncoding RNA-mediated transcriptomic perturbations in cardiac fibroblasts

English title Single-cell analysis of long noncoding RNA-mediated transcriptomic perturbations in cardiac fibroblasts
Applicant Pedrazzini Thierry
Number 182322
Funding scheme Project funding
Research institution Département de Cardiologie CHUV
Institution of higher education University of Lausanne - LA
Main discipline Cardiovascular Research
Start/End 01.10.2018 - 30.06.2023
Approved amount 904'000.00
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All Disciplines (2)

Discipline
Cardiovascular Research
Pathophysiology

Keywords (7)

Heart disease; Regeneration; Cardiac fibroblasts; Cardiomyocytes; Single-cell analysis; Long noncoding RNAs; Transgenic mice

Lay Summary (French)

Lead
En s’appuyant sur une analyse de l’expression des gènes dans des cellules individuelles, on peut étudier l’hétérogénéité de populations de cellules apparemment semblables. Cette approche devrait permettre d’identifier des sous-populations de fibroblastes cardiaques associées à la régénération du cœur. Ces sous-populations représentent des cibles thérapeutiques potentielles pour améliorer la cicatrisation du cœur après un infarctus du myocarde et restaurer la fonction cardiaque.
Lay summary

Les maladies du cœur, notamment l’infarctus du myocarde et l’insuffisance cardiaque, représentent une cause majeure de mortalité et de morbidité. Malgré le développement de nouvelles thérapies, la seule option thérapeutique à l’insuffisance cardiaque terminale est la transplantation cardiaque. La médecine a donc besoin d’innovations rapides dans ce domaine. Une approche qui suscite un intérêt considérable est la possibilité d’induire une régénération dans le cœur endommagé.

La régénération cardiaque suite à un infarctus du myocarde peut être observée dans le cœur de souris nouveau-nées. En effet, pendant une courte période après la naissance, les cardiomyocytes, les cellules musculaires du cœur, gardent une capacité à se diviser. Cette capacité est par contre perdue dans le cœur adulte. Dans ce contexte, le rôle des fibroblastes cardiaques n’a pas été étudié. Les fibroblastes possèdent d’importantes fonctions régulatrices dans le cœur normal et suite à un dommage tissulaire. Le projet s’attache dès lors à l’identification des sous-populations de fibroblastes cardiaques susceptibles de soutenir la régénération. Une fois identifiées, ces sous-populations pourront servir de cibles thérapeutiques pour améliorer la cicatrisation du cœur après la survenue d’un infarctus du myocarde.

L’approche expérimentale s’appuie sur une analyse de l’expression des gènes dans des cellules individuelles. L’expression des longs ARN non codants sera mesurée en priorité. Que sont les ARN non codants? Dans le génome humain, les gènes qui codent pour des protéines ne représentent que 2% du génome. The 98% restant est appelé le génome non codant et produit de l’ARN non codant. Ces ARN non codants ont d’importantes fonctions régulatrices et contrôlent l’identité des cellules et leur comportement.

Direct link to Lay Summary Last update: 16.10.2018

Responsible applicant and co-applicants

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Associated projects

Number Title Start Funding scheme
173738 Regenerative strategies for heart disease via targeting the long noncoding transcriptome 01.10.2017 Sinergia
189877 Lnc-ing Cancer Drugs to Cardiotoxicity: Contribution of lncRNAs to Tyrosine Kinase Inhibitor-Related Cardiac Side Effects 01.06.2020 COST (European Cooperation in Science and Technology)
163476 Regenerative therapy for heart disease via modulation of long noncoding RNAs 01.10.2015 Project funding

Abstract

Background and rationale: In the adult human heart, approximately 1 billion cardiomyocytes die after myocardial infarction, and no approaches exist to compensate for this irreversible depletion. One area that has received a lot of attention is the promise of promoting cardiac regeneration. New cardiomyocytes arise primarily from pre-existing cardiomyocytes. However, the natural renewal capacity of the heart does not permit the production of enough cardiomyocytes to restore heart function following myocardial infarction. Several recent lines of evidence point to an important role of the matrix for heart regeneration. The matrix is produced by cardiac fibroblasts. Qualitatively, the matrix differs in a regenerating heart vs. a non-regenerating heart. A matrix from a regenerating heart sustains cardiomyocyte proliferation, favoring cardiomyocyte renewal. Nevertheless, the cardiac fibroblast population is heterogeneous and needs to be evaluated. Stress- or regeneration-specific subpopulations might determine the outcome of the disease. It is the purpose of this project to identify and characterize cardiac fibroblast subsets relevant for the regenerative process.Single-cell RNA-Sequencing (scRNA-Seq) allows comparing the transcriptomes of thousands of individual cells simultaneously. One reason therefore for using scRNA-Seq is to evaluate heterogeneity in seemingly homogenous cell populations. Another reason is to detect small subpopulations that would otherwise be missed in bulk populations. Moreover, advance in high-throughput sequencing technologies has illuminated our understanding of genome organization and regulation. Only 2% of the genome appears to code for proteins. The remaining 98% represents the noncoding portion of the genome. Most of the noncoding genome is transcribed into long noncoding (lnc)RNAs. Several points argue in favor of assessing lncRNA expression in scRNA-Seq studies. In particular, lncRNAs are generally found to be more cell type-specific than protein coding genes, and consolidate the molecular differences between cell types. Moreover, lncRNAs represent crucial regulators of cell identity and behavior, making those ideal molecules for controlling disease- and regeneration-specific cardiac fibroblast subpopulations. In this project, the consequences of distinct perturbations affecting selected lncRNAs to the cardiac fibroblast phenotype will be evaluated. Importantly, methods have been developed to study the impact of perturbations at the single-cell levels. Ultimately, manipulating cardiac fibroblast behavior via modulating lncRNAs should promote regeneration in the adult mammalian heart.Overall objectives:To identify and functionally characterize cardiac fibroblast subpopulations associated to regeneration in the mammalian heart via single-cell analysesSpecific aims:To explore the cardiac fibroblast-specific lncRNA-mediated response via induced perturbations and single-cell analyses in vitro and in vivo in mouse models of cardiac regeneration and disease, and to functionally characterize the importance of selected cardiac fibroblast-specific lncRNAs for heart regeneration after infarctionExpected results: We expect to characterize the cardiac fibroblast response in the heart after infarction at the single-cell levels, and to identify subpopulations emerging specifically in the regenerating heart, such as in the neonatal mouse heart, and in the non-regenerating heart, such as in the adult mouse heart. Ultimately, we expect to identify regulatory lncRNAs that control the emergence of cardiac fibroblast subsets promoting regeneration, and to target those in the adult heart for favoring regenerative repair after infarction.Impact for the field: The only alternative for end-stage heart failure remains heart transplantation. This option is however limited due to the scarcity of donor hearts. heart failure is therefore evolving into a global epidemic, for which medicine has no viable option. The role of cardiac fibroblasts as promoters of the regenerative process has not been evaluated in details. Single-cell approaches, a recent technology, have only been used for assessing cardiac cells in a couple of studies. Moreover, lncRNAs, crucial regulators of cellular responses, have not been studied in this context. We believe that the single-cell approach as proposed in the present project has the potential to provide a large amount of information on gene function and regulation by lncRNAs that should bring the field of cardiac regeneration significantly forward.
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