Spatially Resolved Transcriptomic Signatures of Hippocampal Subregions andArc-Expressing Ensembles in Active Place Avoidance Memory

Abstract

The rodent hippocampus is a spatially organized neuronal network that supports the formation of spatial and episodic memories. We conducted bulk RNA sequencing and spatial transcriptomics experiments to measure gene expression changes in the dorsal hippocampus following recall of active place avoidance memory. Our analysis focused on two specific levels of spatial resolution: hippocampal subregions and Immediate Early Gene (IEG) expressing cellular assemblies. Through bulk RNA sequencing, we examined the gene expression changes following memory recall across the functionally distinct subregions of the dorsal hippocampus. We found that training induced differentially expressed genes (DEGs) in the CA1 and CA3 hippocampal subregions were enriched with genes involved in synaptic transmission and synaptic plasticity, while DEGs in the dentate gyrus (DG) were enriched with genes involved in energy balance and ribosomal function. Through spatial transcriptomics, we examined gene expression changes following memory recall in putative memory-associated neuronal ensembles marked by the expression of the IEGs Arc, Egr1, and c-Jun. Within samples from both trained and untrained mice, the subpopulations of spatial transcriptomic spots marked by these IEGs were functionally and spatially distinct from one another. In only the hippocampus of trained mice, DEGs detected between Arc+ and Arc- spots were enriched in several memory-related gene ontology terms, including "regulation of synaptic plasticity" and "memory." Our results suggest that memory recall is supported by region-specific gene expression changes and transcriptionally distinct IEG expressing ensembles of neurons in the hippocampus.