High-throughput measurement of neuronal projections and synapses using Synapse-seq

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SUMMARY The brain is composed of thousands of highly specialized cell types that form very specific synaptic connections with each other. Together, these connections form neural circuits that are the structural basis of brain function. Despite their importance, synaptic connections amongst cell types are largely unascertained, because of the dearth of existing tools to do so. In this project, we will develop a suite of genomics-based tools--collectively termed Synapse-seq--that allow us to quantify neuronal projections, postsynaptic densities, and synaptic connections in individual cells in vivo. First, we will use AAV to introduce a molecular tool that trafficks a barcoded mRNA reporter to the presynaptic compartments of infected cells, combined with single-cell sequencing and spatial transcriptomics (Slide-seq) to jointly match cell body positions to projection targets. Next, we will use a postsynaptic targeting system, also delivered by AAV, combined with synaptosome preparations and in situ sequencing to quantify spine densities across thousands of single cells. Finally, we will combine our pre- and postsynaptic labeling systems with novel in situ sequencing readouts to measure synaptic connectivity in vivo. Together, the successful development of these technologies will provide neuroscientists with a suite of powerful tools to routinely measure fundamental aspects of neural connectivity in vivo.