Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing
Abstract
The primary sensory system requires the integrated function of multiple cell types, although its full complexity remains unclear. We used comprehensive transcriptome analysis of 622 single mouse neurons to classify them in an unbiased manner, independent of any a priori knowledge of sensory subtypes. Our results reveal eleven types: three distinct low-threshold mechanoreceptive neurons, two proprioceptive, and six principal types of thermosensitive, itch sensitive, type C low-threshold mechanosensitive and nociceptive neurons with markedly different molecular and operational properties. Confirming previously anticipated major neuronal types, our results also classify and provide markers for new, functionally distinct subtypes. For example, our results suggest that itching during inflammatory skin diseases such as atopic dermatitis is linked to a distinct itch-generating type. We demonstrate single-cell RNA-seq as an effective strategy for dissecting sensory responsive cells into distinct neuronal types. The resulting catalog illustrates the diversity of sensory types and the cellular complexity underlying somatic sensation.
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The division of peripheral sensory neurons suggests refinements to previous classifications.
“Within the peripheral sensory neurons (of the dorsal root ganglia), cell types were divided into three main branches: peptidergic (eight types), non-peptidergic (six types), and neurofilament (three types), which suggests refinements to previous classifications (Li et al., 2016, Usoskin et al., 2015) (Figure S4 and Table S2).”
From Molecular Architecture of the Mouse Nervous System (2018) · cites this paper as Usoskin et al., 2015
Within the peripheral sensory neurons (of the dorsal root ganglia), cell types were divided into three main branches: peptidergic (eight types), non-peptidergic (six types), and neurofilament (three types).
“Within the peripheral sensory neurons (of the dorsal root ganglia), cell types were divided into three main branches: peptidergic (eight types), non-peptidergic (six types), and neurofilament (three types), which suggests refinements to previous classifications (Li et al., 2016, Usoskin et al., 2015) (Figure S4 and Table S2).”
From Molecular Architecture of the Mouse Nervous System (2018) · cites this paper as Usoskin et al., 2015
t-SNE is a powerful nonlinear dimensionality-reduction alternative, especially when computed with an efficient approximation that scales to large genomic data sets.
“A powerful, nonlinear alternative5,105–107 is t-distributed stochastic neighbor embedding108 (t-SNE; introduced for single-cell analysis as viSNE105), especially when computed with an efficient approximation109 compatible with the scale of large genomic data sets110.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [107]
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- Authors
- Usoskin, D., Furlan, A., Islam, S., Abdo, H., Lönnerberg, P., Lou, D., Hjerling-Leffler, J., Haeggström, J., Kharchenko, O., Kharchenko, P. V., Linnarsson, S., & Ernfors, P.
- Affiliations
- Karolinska Institutet (SE)
- Boston Children's Hospital (US)
- Corresponding author
- Linnarsson, Sten
- Ernfors, Patrik
- ORCID
- Venue
- Nature Neuroscience
- Published
- 2014-11-24
- Volume
- 18
- Issue
- 1
- Pages
- 145-153
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- OpenAlex
- W2033072655
- Cited by
- 2,136
- References
- 2
- Citations by year
- 2026: 181 · 2025: 168 · 2024: 183 · 2023: 212 · 2022: 206 · 2021: 250 · 2020: 247 · 2019: 186 · 2018: 182 · 2017: 145 · 2016: 106 · 2015: 63 · 2014: 3
- FWCI
- 43.08
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Stiftelsen för Strategisk Forskning
- Vetenskapsrådet
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Sensory Systems › Ion Channels and Receptors
- Health Sciences › Medicine › Physiology › Pain Mechanisms and Treatments
- Keywords
- sensory neurons, primary afferent neurons, mechanoreceptors, nociceptors, thermosensitive neurons, proprioception, transcriptome, atopic dermatitis, mice
- MeSH terms
- Animals, Behavior, Animal, Female, Inflammation, Male, Mice, Inbred C57BL, Pruritus, Sensory Receptor Cells, Gene Expression, Sequence Analysis, RNA, Cell Size, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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