Abstract
Purpose :
Trigeminal ganglion (TG) neurons in the ophthalmic branch (V1) play a crucial role in the perception of pain at the ocular surface. While single-cell transcriptomics has defined 15 different cell types in the mouse TG, the spatial organization of cells is lost due to the dissociation of tissue that is required prior to profiling. This study seeks to establish the first single-cell spatial atlas of the mouse trigeminal ganglion using spatial transcriptome technology.
Methods :
We conducted single-cell spatial transcriptomics analysis on wild type C57Bl/6J mouse trigeminal ganglion utilizing multiplexed error-robust fluorescence in situ hybridization (MERFISH) to generate the spatial atlas of the mouse TG. A probe panel consisting of 491 marker genes was curated by consolidating data from four publicly available single-cell RNA-seq (scRNA-seq) datasets specific to the TG. To achieve accurate cell segmentation in the TG, a set of oligo-conjugated antibodies specific to a cell membrane protein was co-stained with MERFISH probes. Deep-learning segmentation algorithms were then utilized for identifying cell boundaries and assigning transcripts to individual cells. Using single-cell analysis tools like scVI, tangram, and Giotto, we conducted cell type annotation alongside subsequent spatial analysis.
Results :
MERFISH experiments on mouse trigeminal ganglion, each comprising 4-8 tissue sections, were performed to generate spatial transcriptomic profiles of more than 25,000 cells in total. By leveraging scRNA-seq data through data co-embedding, all major neuronal and non-neuronal cell types in the TG have been identified. Spatial proximity analysis revealed the distribution pattern of cell classes, revealing interesting cell-cell interactions involved in eye pain pathways. Furthermore, unique distribution patterns of neurons expressing genetic markers of ion channels critical for pain processing (e.g. SCN9A, SCN11A, TRPV1) were observed.
Conclusions :
As the first spatial single-cell atlas of the mouse trigeminal ganglion, this study brings further insight into the cell types, genes, and epigenomic features correlated with ocular nociception, inflammation, and pain mediated by trigeminal ganglion neurons.
This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.