hiPSC and Progenitor Heterogeneity as Predictors of Variability in 3D Human Neural Differentiation

About This Grant

Project Summary Region-specific brain organoids derived from human induced pluripotent stem cells (hiPSCs) provide a tractable platform to study disease mechanisms in a human cellular context. Moreover, organoids have the capacity to generate a diversity of cell types that can be maintained in culture long-term and assembled in vitro to form physiologically relevant connections. However, despite this exciting potential, the high variability of organoid differentiation across and within hiPSC lines have halted their broad utility and significantly hindered biological and technical interrogations of human neural development reproducibly and at scale. To address these challenges, this MPI group has established the Brain Organoid Hub at Emory University. A primary goal for the hub, and for this proposal, is to understand the underlying biology of progenitor cells that contribute to variability in 3D neural cultures. Additionally, we hope to develop metrics of hiPSC biology (molecular and/or morphological) that accurately predict the likelihood of successful organoid differentiation, as well as attributes of young organoids that correlate with robust molecular and functional maturation at later stages of culture. Towards this goal, we have designed three specific aims to test the hypothesis that progenitor cell states contain information about future differentiation potential. First, we will use molecular profiling of hiPSCs prior to their 3D formation to ask whether cell state heterogeneity and/or specific gene programs correlate with successful cortical organoid differentiation. Second, we will use machine learning-based approaches to ask whether morphological features of hiPSC growth dynamics are correlated with organoid success. Finally, we will address questions of organoid maturation, and ask whether molecular readouts of young organoids can predict successful functional maturation in late-stage organoid cultures. Altogether, these complimentary aims will not only (1) help reveal fundamental principles that contribute to variation in neurodevelopmental patterning, and (2) provide new assays for improving brain organoid reproducibility while avoiding costly and uninformative differentiations, but also 3) uncover novel biological insights into the genetic programs underlying neural cell specification and maturation. This knowledge could circumvent wasteful studies and instead lead to inclusion of additional biological replicates (hiPSC lines) in experiments. Importantly, our questions are deliberately crafted to align with the core objectives of the Brain Organoid Hub, to ensure reproducibility, efficient resource management, accessibility, and effective dissemination in the field of brain organoid cultures.