Open-Access AAV Toolbox for Basal Ganglia Cell Types and Circuits

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Project Summary We propose to leverage new and existing transcriptomic and epigenetic datasets from mouse, marmoset, macaque and human brain to develop refined approaches for brain cell type enhancer selection for creating cell- type specific enhancer adeno-associated viruses (AAVs), and to make inroads toward prediction of brain-wide expression specificity. We will focus on basal ganglia (BG) cell types for several reasons: 1) BG encompass several brain areas with different embryonic origins and cellular complexity, 2) BG are integral for motor output and reward pathways and have thus been highly conserved through evolution, and we predict many BG enhancers can be found that are conserved across species, 3) BG dysfunction is a shared feature of many brain disorders, and AAV vectors that target BG cell types with high specificity will be useful for basic and translational research, and 4) sufficient epigenetic data are now available that cover BG structures in mouse, marmoset, macaque and human, and our preliminary analysis supports the feasibility of utilizing these data sources for discovery of striatum-specific enhancers with a high success rate. To create a suite of viral tools for BG cell types, we propose to create an end-to-end screening and validation pipeline for discovery of brain cell type enhancer AAVs at the Allen Institute. Multiple epignomic and transcriptomic datasets will be consolidated and interrogated to reveal candidate enhancers that are selectively accessible in the BG cell populations. Enhancer AAVs will be constructed and screened for desirable expression either singly or in multiplexed approaches. A sizeable subset of enhancer AAVs will be subjected to molecular characterization by single cell transcriptomics and/or multiplexed FISH to reveal specificity and completeness of labeling for each virus, as well as brain-wide expression mapping in mouse with serial two-photon tomography. We will deliver a collection of novel viral tools for BG cell types that have been validated for high specificity and completeness of labeling in vivo in both mouse and macaque. Furthermore, we will create an open-access online atlas that will display detailed AAV characterization data. Lastly, we will develop a partnership with Addgene and leverage their self-sustaining and scalable model for plasmid DNA and virus distribution to the scientific community. We will track plasmid and vector requests from our collection to measure the impact of our vectors for the wider research community. If successful, this pilot award will establish a roadmap for integrated analysis of diverse epigenetic datasets for cell type enhancer discovery, scalable enhancer AAV screening methods in the mouse and non-human primate brain, and widespread distribution of knowledge and tools to the research community. Although we focus our efforts on BG cells types and circuits in this pilot U01 project, our goal is to build a scalable pipeline that is generalizable to cell type enhancer discovery for the whole mouse brain.