Decoding enhancer usage and gene expression of human heart development in 3-D cardioids

Project Information

3-D Cardioid

Grant agreement ID: 101063575

DOI

10.3030/101063575

Project closed

EC signature date 15 June 2022

Start date 1 September 2022

End date 31 August 2024

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 189 687,36

Coordinated by

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Germany

Periodic Reporting for period 1 - 3-D Cardioid (Decoding enhancer usage and gene expression of human heart development in 3-D cardioids)

Reporting period: 2022-09-01 to 2024-08-31

Summary of the context and overall objectives of the project

The heart is the first organ to form and function during embryo development, and understanding how it develops is crucial for addressing birth defects. While animal models have provided valuable insights, they don't fully represent human heart development. Recent advances in stem cell technology and 3D organoid models offer a technological leap to study human heart development in the lab. However, current organoid models have limitations, such as producing immature cells or favoring certain cell types over others. To overcome these challenges, advanced techniques measuring single-cell gene expression and chromatin accessibility sequencing can help identify the genes and regulatory elements involved in heart development with great detail, potentially leading to a better understanding of how heart defects occurs during early heart development. The primary objectives of the project were 1) to catalog dynamic changes in gene activity and regulation throughout the development of heart organoids, 2) to assess the extent to which these laboratory-grown organoids mirror the development of real human heart development 3) to investigate how genetic mutations associated with heart defects influence the developmental trajectories of these organoids. Together, the results of this research will significantly advance our understanding of heart development and may lead to novel approaches for preventing or treating congenital heart disorders.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

I successfully implemented cardioid generation from human induced pluripotent stem cells (hiPSCs) followed by comprehensive morphological and gene expression validation of the generated cardioids. After successfully differentiating hiPSCs into 3-D cardioids and collecting samples across five developmental timepoints, single-cell ATAC sequencing (measuring chromatin accessibility) and single-cell RNA sequencing (measuring gene expression) were performed to identify genetic and epigenetic changes crucial for cardiac development. Moreover, single-cell chromatin modification profiling technique have been employed to measure the activity of cis-regulatory regions during organoid differentiation. To validate whether the organoid model is similar to real human heart, the single cell transcriptome and genome profiling of human embryonic heart tissue has been performed. This will help us to understand cell fate decisions during cardiac organoid development and how well it resembles real heart.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project has made significant advances in understanding heart development by producing critical single-cell data on chromatin accessibility and gene expression from rare human embryonic heart tissue, overcoming historical challenges due to limited sample availability. This dataset is a valuable resource for uncovering genetic mechanisms of heart development and serves as a foundation for creating more accurate lab-based models of heart disease. Additionally, we employed single-cell profiling of chromatin modifications in heart organoids—a novel approach that has not been performed before—allowing for us to assess the activity of cis-regulatory elements during heart development. These insights have strong potential for future applications in disease modeling and therapeutic research.

project summary