Ongoing Projects

Gene regulatory dynamics driving mammalian heart development and disease

Second heart field (SHF) cells are an essential source of cardiac progenitors that migrate into the arterial and venous poles of the growing heart tube during early cardiac development, eventually representing the majority of cells present in the right ventricle (RV) and outflow tract (OFT). Importantly, more than a third of congenital heart disease (CHD) cases in humans is linked to OFT defects. It is hypothesized that defects in the transcriptional regulation of developmental genes, such as transcription factors (TFs) orchestrating differentiation and behavior of cardiac progenitor cells, is a major cause of CHD. In research projects funded by the Swiss National Science Foundation, the Swiss Heart Foundation and the Novartis Foundation for Medical-Biological Research we combine genome engineering, fluorescent reporter tagging and single cell methods to identify and functionally characterize genomic enhancers associated to transcriptional regulation of TFs with key roles in the development of SHF-derived cardiac compartments (OFT/RV). Hereby, we leverage CRISPR/Cas9 genome editing for efficient generation of (fluorescent) reporter transgenes and/or tailored enhancer knockout (KO) alleles in mouse embryonic stem cells (mESCs) or embryos. We use these genetic models in combination with transcriptome and 3D chromatin profiling to investigate tissue or cell type-specific enhancer activities and to explore the impact of cardiac enhancer loss and/or dysfunction on mammalian heart morphogenesis. We recently also used multiome (open chromatin and gene expression) profiling in single cells from mouse embryonic hearts to determine gene-enhancer interactions, providing a rich resource for cardiac enhancer predictions at the cell type level. We expect these projects to shed light on the cis-regulatory complexity, chromatin architecture and transcriptional robustness underlying mammalian heart development, with the ultimate goal to pinpoint the functional implications of noncoding genetic variants in patients suffering from heart defects.

Decoding cardiac regulatory landscapes in an all-human model for cardiogenesis

With HeartX, a project granted in the framework of the SNSF National Research Program 79 (NRP 79) to advance the 3Rs, we aim to introduce a novel type of human cardiac organoids (cardioids) developed in the lab of our project partner Sasha Mendjan (Institute of Molecular Biotechnology, Vienna). Cardioids are entirely derived from human induced pluripotent stem cells (hiPSCs) and reproducibly form in nonadherent 3D cultures following mesodermal differentiation and administration/inhibition of growth and differentiation factors involving FGF, BMP, ACTIVIN and WNT signaling. They exhibit a cavity and display synchronized rhythmic contractions initiated at day 5 (d5) of differentiation. Initially, we will make use of a ventricular cardioid model consisting of a myocardial layer with an endocardial lining to study cardiomyocyte function and electrophysiology. In a second step, using a combination of epigenomic profiling, fluorescent reporter assays, CRISPR genome editing and computational analysis we will then attempt to delineate the enhancer landscapes underlying human cardioid formation and expansion, and compare it with signatures from mouse embryonic in vivo studies. Cardioids thus represent a promising model to study molecular mechanisms and regulatory networks underlying cardiogenesis and CHD directly with a human focus, in a high-throughput and exclusively in vitro setting. HeartX also involves co-applicants Iros Barozzi (Medical University of Vienna) and Christian Zuppinger (Bern Univesity Hospital), as well as additional project partners Nadia Mercader (University of Bern) and Rory Johnson (University College Dublin).

Rewiring developmental gene networks for cardiac reprogramming

The abundant pool of non-myocytes in the adult mammalian heart, of which about 50% are cardiac fibroblasts, has significant potential for conversion into induced cardiomyocyte-like cells (iCMs). Recent studies have demonstrated that reactivation of a cocktail of developmental TFs in resident fibroblasts led to the emergence of iCMs coupled with improved cardiac function in a mouse model of myocardial infarction.

In an additional project we aim to establish a system based on CRISPR epigenome editing (CRISPRa) to enable efficient and more flexible control of cardiac reprogramming factors in target cell types, such as cardiac fibroblasts. Re-activation of developmental enhancers, in association with locus-specific epigenomic remodeling, is expected to play a major role in cardiac reprogramming. Understanding these mechanisms will be important to improve future therapeutic applications with the goal to promote cardiac muscle regeneration, e.g. following ischemic heart disease.