Opto-seq reveals input-specific immediate early gene induction in ventral tegmental area cell types

The ventral tegmental area (VTA) is a critical node in circuits governing motivated behavior and is home to diverse populations of neurons that release dopamine, GABA, glutamate, or combinations of these neurotransmitters. The VTA receives inputs from many brain regions, but a comprehensive understanding of input-specific activation of VTA neuronal subpopulations is lacking. To address this, we combined optogenetic stimulation of select VTA inputs with single-nucleus RNA sequencing (snRNAseq) and highly multiplexed in situ hybridization to identify distinct neuronal clusters and characterize their spatial distribution and activation patterns. Quantification of immediate early gene (IEG) expression revealed that different inputs activated select VTA subpopulations, which demonstrated cell-type specific IEG programs. Within dopaminergic subpopulations IEG induction levels correlated with differential expression of ion channel genes. This new transcriptomics-guided circuit analysis reveals the diversity of VTA activation driven by distinct inputs and provides a resource for future analysis of VTA cell types. To perform transcriptomic analysis of the mouse VTA following optogenetic stimulation of specific inputs, we injected Slc32a1-Cre (Vgat-Cre) mice bilaterally in the LH or NAc, and Slc17a7-Cre (Vglut1-Cre) mice bilaterally in the PFC with a Cre-dependent virus encoding channelrhodopsin (AAV1-FLEX-ChR2-YFP). Control mice were injected with AAV1-FLEX-YFP, and all mice were implanted with bilateral fiber optic cannulas above the VTA. Following recovery from surgery and extensive acclimation to the patchcord, mice received 15 min of 20 Hz blue light stimulation. Immediately after stimulation the VTA was microdissected and snap frozen. VTA tissue from 3-4 mice per group was pooled and nuclei were isolated and sequenced using the 10x Genomics Next GEM platform.