One of the most important steps in understanding the biology of autism spectrum disorder (ASD) is elucidating the basic neurodevelopmental mechanisms governing cell type specification and how these mechanisms are disrupted due to mutations in ASD-risk genes. This requires addressing three major outstanding questions in autism research: What are the cell identities affected in ASD development? How do autism risk genes affect developmental trajectories of neural specification? And how is the regulatory code, which is responsible for specifying distinct cell types in the vertebrate brain, disrupted in ASD? Antonio Giraldez and his colleague Smita Krishnaswamy propose to use a novel combination of time-resolved single-cell RNA sequencing, combinatorial gene knockout and innovative computational methods to decipher normal vertebrate neurodevelopment and how these processes are disrupted in ASD.

Giraldez and Krisjnaswamy will use two complementary vertebrate models to address these questions. First, the team will use the zebra-fish system, which exhibits rapid developmental specification of roughly 100,000 neurons over a five-day period that are capable of eliciting complex behaviors. This in vivo vertebrate model is ideal for the complex genetic manipulations required to address the gene regulatory networks driving neural specification. Second, Giraldez and Krishnaswamy will use human induced pluripotent stem cells (iPSC)-derived neurospheres and organoids from healthy and affected individuals to serve as an in vitro system to study human brain development and function.

Using these systems, the team will obtain gene expression profiles of neural cells throughout normal development and in cells with loss-of-function mutations in ASD-risk genes. This will allow the group to characterize the genetic pathways that drive neurodevelopment and the disruptions that are caused by specific ASD-risk mutations. This interdisciplinary proposal will identify a vertebrate neurodevelopment regulatory map, providing fundamental insight into key developmental processes and the underlying causes and progression of ASD.