Multicellular organisms consist of numerous cell types with specialized biological functions. To understand such complex biological systems, genetic access to each cell type is needed for functional analysis and manipulations. Most current cell-type targeting strategies rely on germline transgenesis, which limits their applications in only a few model animals and excludes their uses as therapeutic tools. Viral vectors represent a promising alternative. Using suitable transcriptional regulatory elements to restrict their expression patterns, viral vectors can deliver various genetic payloads in intended cell types in non-genetically modified animals and thereby overcome many limitations associated with germline transgenesis. However, due to the laborious and highly inefficient process for identifying such transcriptional regulatory elements, only a few cell types have been successfully targeted by viral vectors, limiting their use as general tools for cell-type-specific targeting.
Here I propose a novel high-throughput approach to generate cell-type-specific viral vectors. This approach combines single-cell sequencing with large-scale barcoded virus libraries to systematically identify and test cis-regulatory elements of transcription for driving specific viral expression patterns in vivo. I'll establish this pipeline and develop viral vectors targeting mouse hypothalamic cell types. Then, I'll further extend these tools and generate cell-type-specific viral tools for a non-standard model animal. These viral vectors would represent the next-generation cell-type-specific targeting tools for both basic research and therapeutic applications.