Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research

Abstract

Molecular neurobiological insight into human nervous tissues is needed to generate next-generation therapeutics for neurological disorders such as chronic pain. We obtained human dorsal root ganglia (hDRG) samples from organ donors and performed RNA-sequencing (RNA-seq) to study the hDRG transcriptional landscape, systematically comparing it with publicly available data from a variety of human and orthologous mouse tissues, including mouse DRG (mDRG). We characterized the hDRG transcriptional profile in terms of tissue-restricted gene coexpression patterns and putative transcriptional regulators, and formulated an information-theoretic framework to quantify DRG enrichment. Relevant gene families and pathways were also analyzed, including transcription factors, G-protein-coupled receptors, and ion channels. Our analyses reveal an hDRG-enriched protein-coding gene set (∼140), some of which have not been described in the context of DRG or pain signaling. Most of these show conserved enrichment in mDRG and were mined for known drug-gene product interactions. Conserved enrichment of the vast majority of transcription factors suggests that the mDRG is a faithful model system for studying hDRG, because of evolutionarily conserved regulatory programs. Comparison of hDRG and tibial nerve transcriptomes suggests trafficking of neuronal mRNA to axons in adult hDRG, and are consistent with studies of axonal transport in rodent sensory neurons. We present our work as an online, searchable repository (https://www.utdallas.edu/bbs/painneurosciencelab/sensoryomics/drgtxome), creating a valuable resource for the community. Our analyses provide insight into DRG biology for guiding development of novel therapeutics and a blueprint for cross-species transcriptomic analyses.

Figure 1. Cell-type specific and cell compartment specific gene expression in the hDRG

(A) Microarray analysis of human DRG, TG, cultured Schwann cells (NHSC) and fibroblasts (FIBRO) reveal that over 3500 probes are expressed in vivo in DRG and TG but not detected in Schwann cells or fibroblasts, suggesting regulatory programs driving gene expression specifically in sensory neurons and SGCs. (B) Clustering of human and mouse tissue transcriptomes based on a Pearson’s correlation coefficient (PCC)-based distance measure (1 – PCC) and average linkage for tissue-restricted genes.

Figure 2. Identification of common tissue-restricted human gene co-expression patterns in our analyzed tissue panel

Heatmaps with hallmark genes and potential transcriptional regulators which are differentially expressed in (A) neural versus non-neural tissue (B) brain tissues versus remaining tissue (C) CNS versus non-CNS tissue (D) DRG versus remaining tissues.

Figure 3. Identification of hDRG enriched genes

(A) Flowchart for identifying DRG-enriched genes with conserved expression patterns in human and mouse. (B) Estimated density function in DRG-enriched genes for Pearson’s correlation across vectors of relative abundance in orthologous tissues. (C) The set of hDRG and mDRG enriched genes (based on the DRG enrichment score) with one-to-one orthology and correlated gene expression abundances (based on Pearson correlation) across our panel of analyzed tissues. Many of the 81 genes belong to gene families known to play important functional roles in nociceptors, including GPCRs, ion channels, TFs, and transmembrane proteins. (D) Assessment of expression of hDRG genes in mDRG scRNA-seq data [114] for prediction of potential sensory neuronal subtype expression.

Figure 4. hDRG-enriched genes that potentially regulate the transcriptomic landscape

Orthologous human and mouse gene expression in the corresponding tissues is depicted as heatmaps. Differentially expressed genes that are hDRG-enriched or neural enriched are shown. Gene families characterized are TFs (A), splicing factors, mRNA transport molecules, and RNA binding proteins are shown (B).

Figure 5. hDRG-enriched genes for pharmacological targets: ion channels, neuropeptides and cell adhesion molecules

Orthologous human and mouse gene expression in the corresponding tissues is depicted as heatmaps. Differentially expressed ion channels (A), neuropeptide signaling (B) and cell adhesion molecules (C) show several candidate genes for pharmacological targeting, including several neuropeptides.

Figure 6. hDRG-enriched genes for pharmacological targets: GPCRs, phosphatases and kinases

Orthologous human and mouse gene expression in the corresponding tissues is depicted as heatmaps. Differentially expressed GPCRs (A), phosphatases (B) and kinases (C) show several candidate genes, including several receptor tyrosine kinases and phosphatases, and olfactory receptors for pharmacological targeting.

Figure 7. Enrichment of NGF/trkA signaling components in hDRG

(A) The NGF neurotrophin signaling pathway, based on the KEGG database, showing hDRG and human tibial nerve (hTN) expression and hDRG-enrichment for members of the pathway. Several signaling molecules in this pathway are expressed or enriched in the hDRG compared to other tissues analyzed in this study (figure based on KEGG visualization with permission from Kanehisa Laboratories who retain copyright). KEGG protein group IDs are in italicized boldface, with associated genes written below the ID. If the associated gene name is lexically identical to the protein group ID, then it is not shown.

Figure 8. Identification of axonally transported mRNA in the human tibial nerve transcriptome

(A) Several key genes that have been shown in the literature to be locally translated in the axon and retrograde transported show gene expression in hDRG and hTN samples, and also show expression in an mDRG neuronal subpopulation. (B) A large majority of genes with mRNAs that were detected to be to be axonally transported in rat DRG neurons have human orthologs that are expressed ( > 1.0 TPM ) in both the hDRG and hTN, as shown based on the estimated probability density of the relative abundances ( in TPM) in the respective tissues. (C) We identified several strongly and weakly enriched hDRG genes that are also expressed in hTN, and in mDRG neuronal subpopulations. Their potential for expression in non-neuronal cells is shown as the h neural proportion score.