HeartBeat.bio and Cubase Bio partner on 3D spatial transcriptomics for cardiovascular drug discovery
HeartBeat.bio AG, a Vienna-based developer of human cardiac organoid technology, and Cubase Bio™, a Stockholm-based genomics company, have entered a research collaboration aimed at applying three-dimensional spatial transcriptomics to the study of myocardial fibrosis and heart failure.
Funding and project scope
The collaboration has secured approximately €1M in funding under Call 10 of the Eurostars programme, for a joint project titled “Fibrosis Analysis in Cardioids via Transcriptomic Spatial-mapping in 3D” (FACTS-3D). National funding is being provided by Vinnova, Sweden’s innovation agency, and the Austrian Research Promotion Agency (FFG), with co-funding from the European Union through Horizon Europe. The project combines HeartBeat.bio’s proprietary Cardioid technology with Cubase Bio’s 3D spatial transcriptomics platform, with the aim of developing a scalable method for examining the molecular and cellular mechanisms underlying myocardial fibrosis.
Limitations of existing preclinical models
Heart failure affects more than 64 million people worldwide and remains a substantial and growing burden on healthcare systems. According to the collaborators, conventional preclinical tools, including animal models and two-dimensional cell cultures, do not fully replicate the complexity of human cardiac biology, cellular interactions or the spatial organisation associated with cardiac disease. Existing 2D spatial transcriptomics methods are also restricted to thin tissue sections, a constraint the partners describe as poorly suited to high-throughput analysis of intact organoids.
Applying 3D spatial profiling to cardiac organoids
FACTS-3D will apply Cubase Bio’s spatial technology, which is designed to scale to 96- and 384-well plate formats, to HeartBeat.bio’s human Cardioid models within their full three-dimensional tissue context. The project will focus particularly on myocardial fibrosis, a recognised driver of cardiac remodelling associated with many forms of heart failure. By resolving gene expression and cellular states within intact 3D cardiac tissue, the partners intend to characterise disease mechanisms and treatment responses to support target discovery and drug development.
Michael Krebs, chief executive of HeartBeat.bio, said the project “brings together two highly complementary technologies to address one of the major challenges in cardiovascular drug discovery: understanding disease biology in a physiologically relevant human context while retaining the spatial information that is essential for complex cardiac phenotypes.”
Malte Kühnemund, chief executive of Cubase Bio, noted that “cardiac biology is a perfect example of why 3D spatial context matters so much,” adding that the way cells organise in three dimensions is central to how a heart chamber is built, what happens when fibrosis occurs and how the heart remodels itself.
HeartBeat.bio, founded in 2021 and based at the Vienna Biocenter, develops iPSC-derived cardiac organoid systems for drug discovery. Cubase Bio, founded in 2024, has developed a sequencing-based approach to reconstructing tissue architecture in three dimensions without specialised optical imaging hardware.
For more information, visit:
• www.heartbeat.bio
• www.cubasebio.com
