Validating the 3D-brAIn platform
Introducing Silvia Cappello and Rebecca Bonrath from Ludwing Maximilians University
Are the innovative techniques from Erasmus MC (for the organoids), 3Brain (for measuring the organoid’s activity) and the University of Genova (for analysing the data) effectively integrated to create a reliable 3D-BrAIn platform? To validate this integration, the Cappello lab – led by Prof. Dr. Silvia Cappello at The Ludwig Maximilian University of Munich (LMU) – is bringing their expertise into play. With research on cell lines of various neurodevelopment disorders such as epilepsy, her team provides the cell lines necessary to assess the accuracy and reliability of the 3D-BrAIn platform.
The Cappello lab focuses on understanding the mechanisms underlying human brain development, particularly genetic mutations that damage normal brain development and result in so-called neurodevelopmental disorders. One of those disorders that Cappello’s group studies in detail is the Van Maldergem Syndrome. Using advanced techniques, they have analysed cell lines from various neurodevelopmental disorders in great detail, making them the perfect candidates for validating the 3D-BrAIn system.
Rebecca Bonrath is a PhD student in Prof. Dr. Silvia Cappello’s team, studying cell lines from neurodevelopmental disorders and focusing on this validation step of the 3D-BrAIn project. This includes generating data with the 3D-BrAIn platform, and comparing it to existing data from previous work by the Cappello team (Di Matteo et al 2024). Rebecca particularly enjoys working with cell lines in her PhD. “You start with cells that you cannot see by eye, but by the end you have an organoid you can actually see by eye. This is amazing to see,” she shares enthusiastically. “An organoid is basically a 3D tissue that can recapitulate parts of the brain. It contains neurons and most of the other cells that are present in the human brain. This means it is a good simulation of the brain development,” Rebecca explains.
Figure 1: Organoid day 20 (Lancaster et al protocol)
This small cluster of human brain cells recapitulates key features of human brain development and shows electrophysiological activity. Therefore, organoids can be used to study underlying mechanisms of brain diseases and potential treatments. However, they still present some limitations, which the 3D-BrAIn project aims to overcome.
An organoid is basically a 3D tissue that can recapitulate parts of the brain. It contains neurons and most of the other cells that are present in the human brain.
Limitations of classic organoids
Classic organoids face several limitations that hinder their precision. For example, they show variability, which can lead to differences between organoids and differentiation batches. Another significant issue is the development of a dead, non-functioning center as they grow, called the necrotic core. “The organoid models lack the blood vessels that are found in the brain,” Rebecca explains. These blood vessels are responsible for transporting the needed nutrients to all cells to properly function and develop. Therefore, nourishment of the organoid’s brain cells relies on the medium that can only diffuse a short distance within the organoid. As a result, cells in the center do not receive enough nourishment and die, leading to the so-called necrotic core. “Due to this necrotic core, we have a heterogeneity in our organoid, as well as from organoid to organoid, and from batch to batch of organoids,” Rebecca adds. Especially for testing drugs, it would be ideal to have a more robust system.
Novel approach of 3D-BrAIn
To overcome these limitations, the 3D-BrAIn project is using a novel approach involving “adherent organoids”. Unlike traditional organoids where they float freely in a petri dish, adherent organoids are placed in separate wells. “These organoids are smaller and flatter. This way, the medium can diffuse all the way through the organoid, so they don’t get a necrotic core. This makes sure that the results are better reproducible,” Rebecca explains. A key innovation of 3D-brAIn is integrating the adherent organoid system with 3Brain MEA plates, enabling high-density measurement of activity which reflects that the platform will be able to measure brain cell activity in more detail.
These organoids are smaller and flatter. This way, the medium can diffuse all the way through the organoid, so they don’t get a necrotic core. This makes sure that the results are better reproducible.
LMU’s expertise
LMU has extensively researched and characterised various cell lines of different neurodevelopmental diseases using a variety of techniques. Specifically, they have studied in detail cell lines with mutations in the FAT4 and DCHS1 genes (Klaus et al, Di Matteo et al). These cell lines are a good starting point to test the 3D-BrAIn platform. “We can compare the data from the 3D-BrAIn platform with the classical data we already have of these cell lines, to see if the 3D-BrAIn platform is working well,” Rebecca explains.
Fig.2 – Schematic representation of classic organoids and adherend organoids
Rebecca spent January to April in Femke de Vrij’s lab at Erasmus MC to learn their techniques and collaborate with the project’s team in the Netherlands. As the 3D-BrAIn platform develops, Silvia, Rebecca and the Cappello group will apply this knowledge to validate the 3D-BrAIn platform.
Ensuring the effectiveness of the 3D-BrAIn platform is a crucial step towards advancing personalised medicine, drug screening, and neurotoxicity testing across a broad range of neuropsychiatric diseases, which is the ultimate goal of the project.
References
Di Matteo et al, bioRXIv https://www.biorxiv.org/content/10.1101/2024.07.10.602948v1
Klaus et al, nature medicine, https://www.nature.com/articles/s41591-019-0371-0
