Mosaic Organoids to Study the Brains of Multiple Patients Simultaneously

An international team of scientists from Human Technopole and the University of Milan has developed and validated an innovative approach to studying human brain development across multiple individuals simultaneously using single organoids—laboratory models that replicate key cellular processes of human neurodevelopment. The research paves the way for in vitro population studies. Additionally, the scientists have developed a novel computational method to more accurately quantify the genetic identity of individual cells profiled from multiple individuals concurrently. The findings have been published in Nature Methods.

Reproducing the neurodevelopment of multiple individuals simultaneously within individual mosaic organoids, in vitro models replicating the development of human cortical brain cells: this is the groundbreaking achievement of a study coordinated by researchers from Human Technopole (HT) and the University of Milan. The study developed and validated the effectiveness of two analytical methods for leveraging single-cell data collected from these innovative models. The researchers also devised a new algorithm that enhances the reconstruction of the genetic identity of profiled cells, thereby improving the analysis of the mosaic organoids.

The project, conducted in collaboration with the European Institute of Oncology and the Helmholtz Center in Munich, has been published in the prestigious scientific journal Nature Methods.

Organoids have recently enabled significant advances in understanding human brain development,  in physiological and pathological processes, such as neurodevelopmental disorders like autism, epilepsy, and intellectual disabilities. However, a critical challenge in recent years has been the need to study neurobiology not only at the level of individual patients but also across multiple individuals simultaneously and under diverse conditions. To address this, the scientists combined reprogrammed stem cells from different individuals to form so-called “mosaic organoids,” which simulate human brain evolution and its responses to specific stimuli or environmental conditions, such as drug exposure or pollutants. The accuracy of this experimental model was also compared with a second approach in which cells from the same individuals were differentiated and profiled in independent organoids.

To better analyse these organoids, the authors developed a computational method named “SCanSNP,” which accurately identifies the origin of each individual cell, enabling the tracking of its evolution over time.

By integrating these findings, the researchers demonstrated that mosaic organoids provide an exceptionally effective model for studying the impact of genetic variants on human neurodevelopment. This represents a transformative approach, enabling in vitro population studies.

Giuseppe Testa, Head of the Neurogenomics Research Programme at Human Technopole in partnership with the University of Milan, Professor of Molecular Biology at the Department of Oncology and Haematology-Oncology of the University of Milan, and corresponding author of the study, stated: “Thanks to our research, we have further expanded the remarkable versatility of brain organoids, reaffirming their role as an indispensable tool for studying and understanding neurodevelopment. The two methods developed during our experiments, alongside the computational system we established, open the door to modelling and analysing not just the brain development of a single patient but entire populations in vitro—a key goal of our research programme and the broader mission of Human Technopole.”

Caporale, N., Castaldi, D., Rigoli, M.T. et al. Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution. Nat Methods (2024).

DOI: https://doi.org/10.1038/s41592-024-02555-5