High-coverage single-cell RNA-sequencing identifies somatosensory neuron types

Sensory neurons are distinguished by distinct signaling networks and receptive characteristics. Thus, sensory neuron types can be defined by linking transcriptome-based neuron typing with the sensory phenotypes. Here researchers from the Shanghai Institutes for Biological Sciences classify somatosensory neurons of the mouse dorsal root ganglion (DRG) by high-coverage single-cell RNA-sequencing (10 950 ± 1 218 genes per neuron) and neuron size-based hierarchical clustering. Moreover, single DRG neurons responding to cutaneous stimuli are recorded using an in vivo whole-cell patch clamp technique and classified by neuron-type genetic markers. Small diameter DRG neurons are classified into one type of low-threshold mechanoreceptor and five types of mechanoheat nociceptors (MHNs). Each of the MHN types is further categorized into two subtypes. Large DRG neurons are categorized into four types, including neurexophilin 1-expressing MHNs and mechanical nociceptors (MNs) expressing BAI1-associated protein 2-like 1 (Baiap2l1). Mechanoreceptors expressing trafficking protein particle complex 3-like and Baiap2l1-marked MNs are subdivided into two subtypes each. These results provide a new system for cataloging somatosensory neurons and their transcriptome databases.


DRG neuron subclusters and the “hybrid states” of subclusters. (A) An enlargement of C4 on the heatmap of the correlation matrix and WGCNA eigengenes (Figure 2A and 2B) reveal two distinct subclusters, C4-1 and C4-2, outlined by black frames. (B) Single-cell real-time PCR confirming the differential expression of Mrgpra3, Mrgprb4 and Mrgprd in C4-1 and C4-2 neurons (n = 3). (C) Double fluorescent ISH showing the co-expression of Mrgprb4 in a subpopulation of Mrgpra3-positive small DRG neurons (arrows). Scale bars, 100 μm (left) and 20 μm (right). (D) Differential distribution of Mrgpra3, Mrgprb4 and Mrgprd in C4 and C5. (E) Gene co-expression network identified by WGCNA shows that the Mrgpra3-containing network is separate from the Mrgprb4 network in the pink module. (F) An enlargement of C2-1 and C2-2 in the heatmap of the correlation matrix and WGCNA (Figure 2A and 2B). (G) Single-cell PCR confirming the differential expression of representative genes in C2-1 and C2-2 neurons (n = 3). (H) Single-cell PCR showing expression of Pvalb in an Nppb-positive, IB4-negative neuron. (I) Double fluorescent ISH showing co-expression of Il31ra with S100b or Cpne6 in a small DRG neuron (arrow). Scale bar, 20 μm. (J) The correlation among Nppb, Il31ra, S100b and Cpne6 expression in clusters of small and large neurons and their predicted relationships with different types of afferent fibers.

Li CL, Li KC, Wu D, Chen Y, Luo H, Zhao JR, Wang SS, Sun MM, Lu YJ, Zhong YQ, Hu XY, Hou R, Zhou BB, Bao L, Xiao HS, Zhang X. (2015) Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity. Cell Res [Epub ahead of print]. [abstract]

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