Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (timepoints)

Midbrain organoids are advanced in vitro cellular models for disease modelling. They have been used successfully over the past decade for Parkinson’s disease (PD) research and drug development. The three-dimensional structure and multicellular composition allow disease research under more physiological conditions than is possible with conventional 2D cellular models. However, there are concerns in the field regarding the organoid batch-to-batch variability and thus the reproducibility of the results. In this manuscript, we generate multiple independent midbrain organoid batches derived from healthy individuals or GBA-N370S mutation-carrying PD patients to evaluate the reproducibility of the GBA-N370S mutation-associated PD transcriptomic and metabolic signature as well as selected protein abundance. Our analysis shows that GBA-PD-associated phenotypes are reproducible across organoid generation batches and time points. This proves that midbrain organoids are not only suitable for PD in vitro modelling, but also represent robust and highly reproducible cellular models. RNA sequencing data of midbrain organoids from 3 healthy (WT1-3) and PD patients with GBA-N409S mutation (GBA1-3). Data comes from 30 or 60 days old organoids (D30 or D60) and 4 individual organoid generation batches (B1-4).