Cardiovascular diseases including congenital heart disease (CHD), ischemic heart disease and stroke remain the leading cause of death worldwide. Nearly 1% of newborn children exhibit some form of congenital heart defect and there are estimates that cardiac malformations account for at least 10% of embryos/fetuses lost before birth. However, most of the genetic alterations that affect cardiac development and lead to congenital heart defects remain insufficiently understood.
The formation of the heart involves a series of complex morphogenetic and cellular processes that require tight control of gene expression. This process is orchestrated through genetic networks of evolutionarily conserved transcription factors (TFs) including the Nkx, Gata, Mef, Tbx and Hand TF families. These essential genes integrate cell signaling pathways and control the expression of downstream structural and functional cardiac genes, such as those involved in cardiac cell fate specification or myocyte differentiation. Accurate cell type-specific and/or temporally restricted expression of these TFs is therefore critical for heart development and controlled by cis-regulatory modules, predominantly transcriptional enhancers (typically 0.5-4kb), which can be located up to 1 Megabase away from target gene promoters .
Epigenomic profiling has uncovered tens of thousands of predicted heart enhancer signatures in mouse and human genomes and large-scale enhancer discovery studies based on transgenic reporter assays have uncovered hundreds of enhancers with cardiac activities in the mouse embryo (see VISTA Enhancer Browser). Despite all these efforts, the cell type specificities, transcriptional contributions and biological functions of the vast majority of cardiac enhancers remain unknown. In addition, recent genomic analyses of human cardiac disease-associated nucleotide variants point to a substantial role of transcriptional enhancers underlying the genetic etiology of heart disease.
Cardiac enhancers and their roles in heart development and disease
The morphogenetic processes underlying the formation of cardiac compartments are orchestrated by genetic networks of evolutionarily conserved TFs. These cardiac TFs control cardiac progenitor cell fate specification and differentiation, and integrate with cell signaling pathways to regulate proliferation and expression of structural or functional cardiac genes. Despite the critical functions of cardiac TFs the cis-regulatory landscapes controlling the expression of these genes has been insufficiently characterized and the functionally relevant cardiac enhancers remain largely elusive. This hampers our mechanistic understanding of how cardiac gene networks are wired in mammalian genomes and how cardiac cell types are controlled at the single cell level.
We use the mouse embryo as a highly relevant model system in combination with CRISPR genome editing, transcriptome sequencing and fluorescent imaging to functionally dissect cardiac enhancer landscapes and to study the cell specificities of cardiac enhancers in direct relation to heart development and disease.
Functional characterization of mammalian heart enhancer landscapes
Genome-wide association studies (GWAS) and whole-genome sequencing (WGS) approaches are currently identifying an increasing number of human heart disease-associated variants that potentially cause heart defects. However, many of the critical cardiac enhancer landscapes have been only partially characterized and the cell type-specificities and 3D chromatin interactions of individual cis-regulatory modules remain to be determined. This limits our ability to relate disease-associated genomic variants to biological function.
In research projects funded by the SNSF Eccellenza, Swiss Heart Foundation and Novartis Foundation for Medical-Biological Research we are using single-cell multiomic profiling, mouse genome editing and chromatin conformation capture to study the functional contributions and biological relevance of transcriptional enhancer landscapes associated to key regulators of heart development, such as cardiac TFs. We have also implemented a novel CRISPR/Cas9-mediated transgenic approach termed enSERT to for more precise and efficient in vivo validation of cell type-specific or subregional enhancer activities in mouse embryos.
Decoding cardiac regulatory landscapes in human cardiac organoid models
(NRP79 and BCPM Lighthouse projects)
We have recently introduced cardioid models developed in the lab of our NRP79 project partner Sasha Mendjan (Institute of Molecular Biotechnology, Vienna). Cardioids are derived from human induced pluripotent stem cells (hiPSCs) and form by self-regulation after mesodermal induction and nonadherent 3D cultures. Cardioids exhibit a cavity and display synchronized rhythmic contractions initiated at day 5 of differentiation. We are making use of a ventricular cardioid model consisting of a myocardial layer with an endocardial lining to study cardiac cell-cell interactions and electrophysiology in context of heart disease mutations. Using functional genomics methods, it is further our goal to delineate the enhancer landscapes underlying cardioid morphogenesis. We will particularly define the regulatory modules active also during mouse heart development and those that are seemingly unique to human cardiogenesis.
Epigenomic mechanisms underlying cardiac reprogramming
Heart disease continues to be a leading cause of adult and childhood mortality, and heart failure affects yearly 23 million people worldwide. A main cause of heart failure is myocardial infarction (MI), in which a portion of the functional myocardium is lost and replaced with a fibrotic scar that prevents rupture of the ventricular wall.
The in-situ conversion of resident cardiac fibroblasts into cardiomyocyte-like cells, e.g. through reactivation of a specific combination of TF genes, is a phenomenon of considerable therapeutic potential that remains incompletely understood at the mechanistic regulatory level.
We will use epigenome editing for transdifferentiation of cardiac fibroblasts into cardiomyocyte-like cells to study the enhancer landscapes and cis-regulatory changes underlying this fascinating process.