Abstract

Human cerebral organoids offer an extraordinary in vitro cellular model for studying human brain development and early disturbances in neurologic disease. Microelectrode array (MEA) recordings are commonly used to compare neuronal activity in 2D and 3D cultures. Yet, MEA recordings can also reveal cellular-scale network activity (Schroeter et al., 2017), including patterns or motifs in network function seen across spatial scales from cellular to whole brain networks. We have used MEA recordings from human air-liquid interface cerebral organoids (ALI-COs; Giandomenico et al., 2019) to study network function and maturation. We have also demonstrated intact neuronal network function development with MEA recordings in a human cerebral organoid model of amyotrophic lateral sclerosis with frontotemporal dementia (ALS/FTD; Szenbenyi et al., 2021). To facilitate investigations of network development in ALI0C Os and the impact of disease-causing perturbations, we created a MATLAB network analysis pipeline (MEA-NAP) for batch analysis of MEA experiments to compare network function over time and conditions (e.g., genetic mutation or drug treatment). This user-friendly, open source diagnostic tool can process raw voltage time-series acquired from single- (Multichannel System) or multi-well MEAs (Axion) and automatically infer key network properties from organoids or 2D human (or murine) neuronal cultures. Our pipeline enables users to perform MEA analysis beyond standard measures of activity or correlation alone to identify differences in network topology and roles of individual nodes in network activity. Our analyses of network function in ALI -COs demonstrate that they can serve as a platform for investigating disease mechanisms and screening new therapies.