Cubase Bio, operating from Stockholm, has entered into a partnership with HeartBeat.bio, based in Vienna, to accelerate the development of three-dimensional spatial transcriptomics technology for studying heart disease. The joint initiative, backed by approximately €1 million in Eurostars funding, brings together Cubase Bio's proprietary 3D spatial transcriptomics platform with HeartBeat.bio's human cardiac organoids. The resulting FACTS-3D project will focus on understanding myocardial fibrosis, a critical factor in the progression of heart failure. Through this collaboration, Cubase Bio will be able to deploy its technology on complete 3D cardiac tissue samples and establish a reproducible methodology for large-scale pharmaceutical screening across 96- and 384-well plate configurations. The partnership aims to uncover disease mechanisms, evaluate how tissues respond to treatments and identify novel therapeutic targets.
About Cubase Bio
Established in 2024, Cubase Bio operates as a spatial biology enterprise headquartered in Stockholm. The company has engineered 3D spatial transcriptomics technology that enables researchers to map molecular and cellular information across intact biological samples. The platform employs sequencing alongside computational analysis to reconstruct how cells and molecules are organized in three-dimensional space. Applications under development encompass organoid research and pharmaceutical discovery.
About HeartBeat.bio
HeartBeat.bio, a Vienna-based TechBio firm founded in 2021, specializes in drug discovery platforms centered on human cardiac organoids. The company's Cardioid platform leverages iPSC-derived cardiac organoids paired with automated systems and computational analysis to investigate cardiovascular pathologies. Research areas include cardiomyopathies, myocardial fibrosis and heart failure.
The FACTS-3D project
The initiative, formally titled "Fibrosis Analysis in Cardioids via Transcriptomic Spatial-mapping in 3D," received its funding designation under Call 10 of the Eurostars program. Financial support comes from Vinnova, Sweden's national innovation agency, and the Austrian Research Promotion Agency (FFG), with additional backing from the European Union's Horizon Europe initiative. The project will merge HeartBeat.bio's proprietary Cardioid technology with Cubase Bio's 3D spatial transcriptomics capabilities to create a scalable methodology for examining the molecular and cellular foundations of myocardial fibrosis.
The clinical challenge
Despite progress in cardiovascular science, developing new treatments for heart failure continues to present substantial obstacles. The condition affects over 64 million individuals globally and constitutes an expanding public health concern. Existing preclinical approaches—including animal testing and two-dimensional cell culture systems—frequently prove inadequate for capturing the full spectrum of human biological complexity, cell-to-cell interactions and the three-dimensional architecture of cardiac disease.
Why 3D matters for cardiac research
The FACTS-3D initiative tackles this limitation by integrating physiologically accurate human cardiac organoids with high-throughput 3D spatial transcriptomics. Conventional 2D spatial transcriptomics methods operate on thin slices of tissue, rendering them poorly suited for analyzing organoids at scale. By employing Cubase Bio's true 3D spatial technology, which scales to 96- and 384-well formats, the project will examine HeartBeat.bio's human Cardioids while preserving their complete three-dimensional tissue structure.
Myocardial fibrosis—the excessive accumulation of scar tissue in the heart muscle—serves as a central mechanism in cardiac remodeling and underlies numerous forms of heart failure. By mapping gene expression patterns and identifying cellular states within whole 3D cardiac tissue, the research team intends to clarify how disease develops, evaluate treatment effectiveness and uncover fresh opportunities for identifying drug targets.
Partner perspectives
Cardiac biology is a perfect example of why 3D spatial context matters so much. The way cells organize in three dimensions is central to how a heart chamber is built, what happens when fibrosis occurs and how the heart remodels itself. Our technology was built to capture exactly that kind of complexity in full 3 dimensions. It cannot be assessed by sectioning, and 3D imaging hardware lacks the throughput. This makes our 3D spatial transcriptomics technology a natural fit for high-throughput cardiac drug screening. HeartBeat.bio is the ideal partner to translate our 3D spatial technology into actionable insights for complex cardiovascular disease.
Malte Kühnemund, CEO of Cubase Bio
The FACTS-3D 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. For HeartBeat.bio, this collaboration represents an important step toward using Cardioids not only for phenotypic drug discovery, but also to uncover and validate novel mechanisms and targets for heart failure, particularly in myocardial fibrosis and cardiac remodeling.
Michael Krebs, CEO of HeartBeat.bio
Source: ArcticStartup
