Comprehensive RNA-Seq Expression Analysis of Sensory Ganglia with a Focus on Ion Channels and GPCRs in Trigeminal Ganglia

Abstract

The specific functions of sensory systems depend on the tissue-specific expression of genes that code for molecular sensor proteins that are necessary for stimulus detection and membrane signaling. Using the Next Generation Sequencing technique (RNA-Seq), we analyzed the complete transcriptome of the trigeminal ganglia (TG) and dorsal root ganglia (DRG) of adult mice. Focusing on genes with an expression level higher than 1 FPKM (fragments per kilobase of transcript per million mapped reads), we detected the expression of 12984 genes in the TG and 13195 in the DRG. To analyze the specific gene expression patterns of the peripheral neuronal tissues, we compared their gene expression profiles with that of the liver, brain, olfactory epithelium, and skeletal muscle. The transcriptome data of the TG and DRG were scanned for virtually all known G-protein-coupled receptors (GPCRs) as well as for ion channels. The expression profile was ranked with regard to the level and specificity for the TG. In total, we detected 106 non-olfactory GPCRs and 33 ion channels that had not been previously described as expressed in the TG. To validate the RNA-Seq data, in situ hybridization experiments were performed for several of the newly detected transcripts. To identify differences in expression profiles between the sensory ganglia, the RNA-Seq data of the TG and DRG were compared. Among the differentially expressed genes (> 1 FPKM), 65 and 117 were expressed at least 10-fold higher in the TG and DRG, respectively. Our transcriptome analysis allows a comprehensive overview of all ion channels and G protein-coupled receptors that are expressed in trigeminal ganglia and provides additional approaches for the investigation of trigeminal sensing as well as for the physiological and pathophysiological mechanisms of pain.

Neuronal UCP1 expression suggests a mechanism for local thermogenesis during hibernation

“…To our knowledge, this report is the first demonstration of UCP1 protein in neuronal mitochondria of a mammal. Earlier reports did not identify UCP1 in mouse TG and DRG (23) and detected only trace amounts of UCP1 transcript in mouse cortex (∼0.01% of UCP1 level in BAT) (21,22), suggesting neuronal UCP1 expression could be a specific feature pertaining to animals that have to withstand prolonged periods of extreme hypothermia.…”

“…It was suggested that this temperatureinduced UCP1 expression in carp may support local cranial endothermy necessary to survive winter dormancy. Trace amounts of UCP1 mRNA have been detected in mouse cortex (21,22), but no expression was observed in peripheral nervous tissues (23).…”

Standardized Profiling of The Membrane-Enriched Proteome of Mouse Dorsal Root Ganglia (DRG) Provides Novel Insights Into Chronic Pain

“…Several -omics approaches have been developed to study pain-related changes in gene expression (7,8) or of proteins (9 -14). Deep-sequencing transcriptomics (RNA-Seq) is able to quantify the majority of the transcriptome (7,8), but only half of mRNA changes account for protein variability (15) limiting the ability to relate results to protein function.…”

G Protein–Coupled Receptor (GPCR) Expression in Native Cells: “Novel” endoGPCRs as Physiologic Regulators and Therapeutic Targets

“…Such studies have recently included the profiling of GPCRs expressed in single cells (Manteniotis et al, 2013;Spaethling et al, 2014).…”

“…Even in such studies, however, one analyzes a population of cells. The use of techniques such as high-resolution RNA sequencing (Manteniotis et al, 2013;Spaethling et al, 2014) and perhaps proteomic methods (Davies et al, 2007;Wu et al, 2012;Eisen et al, 2013) to assess GPCRs in individual cells will thus be an important future direction for defining the profile and variability in GPCR expression in particular cell types. 2) Reproducibility and consistency of methods used to prepare mRNA, cDNA, or protein and to assess gene and protein expression: Standards have been developed to facilitate reproducibility in microarray (Brazma et al, 2001;Hansen et al, 2007;Rung and Brazma, 2013) and proteomic studies (Davies et al, 2007;Taylor et al, 2007), but results from different laboratories can differ.…”