Revolutionary high-resolution human 3D brain organoid platform integrating AI-based analytics

Project Information

3D-BrAIn

Grant agreement ID: 101098791

DOI

10.3030/101098791

EC signature date 17 November 2022

Start date 1 April 2023

End date 31 March 2028

Funded under

• The European Innovation Council (EIC)

Total cost

€ 2 003 347,50

EU contribution

€ 1 998 347,00

Coordinated by

ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM
Netherlands

Periodic Reporting for period 2 - 3D-BrAIn (Revolutionary high-resolution human 3D brain organoid platform integrating AI-based analytics)

Reporting period: 2024-04-01 to 2025-07-31

Summary of the context and overall objectives of the project

The long-term vision of the 3D-BrAIn consortium is to revolutionize personalized precision medicine for central nervous system (CNS) disorders, by developing an innovative bio-digital twin model of the human brain that is personalized, precise, and predictive.
In this project we bring together three breakthrough technologies: 1) a novel, highly reproducible human brain modelling technology using robust adherent human induced pluripotent stem cell (hiPSC)-derived 3D cortical organoid cultures, 2) a unique, state-of-the-art 3D multi-electrode array (MEA) technology for non-invasive high-resolution electrophysiological recordings and 3) a novel approach to analyze and interpret the large quantities of functional data using tailored automated machine learning (ML)-based algorithms.
With this approach we overcome significant hurdles that made it thus far impossible to create a truly representative and functional model of the CNS for personalized medicine, drug screening and neurotoxicity testing. The revolutionary 3D-BrAIn platform will allow robust and accurate modelling of the CNS for a broad range of neuropsychiatric diseases.
In this project a prototype of the 3D-BrAIn platform will be developed by growing functional 3D organoids that faithfully resemble the human cortex on 3D MEA micropillar electrodes, enabling continuous functional monitoring and by developing ML-based algorithms that can process and interpret the large spatiotemporal data sets. Once all individual components are optimized and integrated, proof-of-concept will be obtained by validating the platform using disease-relevant hiPSC cell lines.

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

In RP2, progress was continued, and the consortium closely collaborated to reach the project goals according to schedule, executing five deliverables in this period (D1.2 D2.2 D2.3 D2.4 D5.3 D5.4). Progress was made in defining the cell culture protocol for growing hiPSC-derived adherent cortical organoids on micropillar electrodes (D1.2) further detailing coating conditions and confiner restrictions. At 3Brain, important progress was made towards establishing a 24-well 3D HD-MEA (D2.2) with a well dimension suitable for high-throughput assays (D2.3) along with a hardware platform for data acquisition (D2.4). This novel hardware is currently being shipped to Erasmus MC for integrating adherent cortical organoids in the 24-well HD MEA plates. While no deliverables were scheduled for WP3 and WP4 in this period, intense collaboration between the 4 partners continued to advance the goals for these work packages. For WP3 collaboration focused on advanced data analysis, aided by student exchange of UNIGE bachelor and PhD students visiting Erasmus MC for several months and weekly separate data-focused online work meetings. For WP4 collaboration continued to implement the adherent cortical organoid protocol in LMU, along with parallel techniques such as calcium imaging and working on mutant hiPSC lines towards the goal of validating relevant phenotypes in later deliverables. Finally, for communication and dissemination the RP1 meeting documents (D5.4) and updated Data Management Plan (D5.3) were submitted.

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)

The previously established Erasmus MC adherent cortical organoid model has now been published as peer-reviewed pre-print in open access peer reviewed journal eLife. In parallel, the protocol has been filed as an international patent application (‘Methods for producing brain organoids, multi-well plates containing said organoids, and screening methods’, PCT/NL2025/050152), assuring proper IP protection and commercialization potential in the future.
In addition, a working prototype of the HD-MEA 24-well system has been implemented; the system offers the capability to record simultaneously from more than 6K electrodes (up to 24k electrodes in one plate) from 24 wells, a result never achieved so far by other systems.

Adherent cortical organoids stained for neurons (red), astrocytes (green, orange) and nuclei (blue).

The 3D-BrAIn Project logo

Comparison between real data and synthetically generated data obtained with the VAE-GAN approach.

Template matching used for spike sorting

HD Accura MEA chip with novel biocompatible confiner to facilitate organoid formation.