Comparative Gene Signature of Nociceptors innervating Mouse Molar Teeth, Cranial Meninges and Cornea

Background: The trigeminal ganglion (TG) collects afferent sensory information from various tissues. Recent large-scale RNA sequencing of neurons of the TG and dorsal root ganglion has revealed a variety of functionally distinct neuronal subpopulations, but organ-specific information is lacking. Methods: To link transcriptomic and tissue-specific information, we labelled small-diameter neurons of three specific subpopulations of the TG by local application of lipophilic carbocyanine dyes to their innervation site in the dental pulp, cornea and meninges (dura mater). We then collected mRNA sequencing data from fluorescent neurons. Differentially expressed genes (DEGs) were analyzed and subjected to downstream gene set enrichment analysis (GSEA), and ion channel profiling was performed. Results: A total of 10903 genes were mapped to the mouse genome (> 500 reads). DEG analysis revealed 18 and 81 genes with differential expression (Log2 fold change > 2, padj < 0.05) in primary afferent neurons innervating the dental pulp (DPANs) compared to those innervating the meninges (MPANs) and the cornea (CPANs). We found 250 and 292 genes differentially expressed in MPANs as compared to DPANs and to CPANs, and 21 and 12 in CPANs as compared to DPANs and MPANs. Scn2b had the highest Log2 fold change when comparing DPANs vs. MPANs and Mmp12 was the most prominent DEG when comparing DPANs vs. CPANs and, MPAN vs CPAN. GSEA revealed genes of the immune and mitochondrial oxidative phosphorylation system for the DPAN vs. MPAN comparison, cilium- and ribosome-related genes for the CPAN vs. DPAN comparison and respirasome, immune cell- and ribosome related gene sets for the CPAN vs. MPAN comparison. DEG analysis for ion channels revealed no significant differences between the neurons set except for the sodium voltage-gated channel beta subunit 2, Scn2b. However, in each tissue a few ion channels turned up with robust number of reads. In DPANs these were Cacna1b, Trpv2, Cnga4, Hcn1 and Hcn3, in CPANs Trpa1, Trpv1, Cacna1a and Kcnk13 and, in MPANS Trpv2 and Scn11a. Conclusions: Our study uncovers previously unknown differences in gene expression between sensory neuron subpopulations from the dental pulp, cornea and dura mater and provides the basis for functional studies, including the investigation of ion channel function and their suitability as targets for tissue-specific analgesia.