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Cited by 33Single-cell and spatial transcriptomicsCell Image Analysis TechniquesNeuroscience and Neuropharmacology Research

Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis

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Northcutt, Adam J., Kick, Daniel R., Otopalik, Adriane G., Goetz, Benjamin M., Harris, Rayna M., Santin, Joseph M., Hofmann, Hans A., Marder, Eve +1 more·2019·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1911413116PMC PMC6936480
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Abstract

Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.

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  • In wild-type populations of animals with similar performance profiles, 2-7 fold variations in the mRNA expression of most cellular components are seen in identified neurons across individuals.

    “In wild-type populations of animals with similar performance profiles, 2-7 fold variations in the mRNA expression of most cellular components are seen in identified neurons across individuals [25-30]”

    From A feature and not a bug: Replication failures can lead to new biology (2026) · cites this paper as [28]

    The Discussion (General Insights; page unavailable) says expression patterns vary within defined neuron types, supporting the general point that identified neurons need not have identical mRNA profiles. The paper does not establish a 2–7-fold range for most cellular components, or tie that range to wild-type animals with similar performance profiles. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

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Cited by

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Authors
Northcutt, A. J., Kick, D. R., Otopalik, A. G., Goetz, B. M., Harris, R. M., Santin, J. M., Hofmann, H. A., Marder, E., & Schulz, D. J.
Affiliations
  • Marine Biological Laboratory (US)
  • University of Missouri (US)
  • Brandeis University (US)
  • The University of Texas at Austin (US)
Corresponding author
  • Marder, Eve
  • Schulz, David J.
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2019-12-05
Volume
116
Issue
52
Pages
26980-26990
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.1911413116
PMC
PMC6936480
OpenAlex
W2993647317
Cited by
33
References
13
Citations by year
2026: 5 · 2025: 1 · 2024: 2 · 2023: 4 · 2022: 5 · 2021: 7 · 2020: 8 · 2017: 1
FWCI
1.64
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Open Access Server of the Woods Hole Scientific Community (Woods Hole Scientific Community) (submittedVersion, cc-by-nc-nd)
Funders
  • HHS | NIH | National Institute of Mental Health (R01MH046742-29)
  • HHS | NIH | National Institute of General Medical Sciences (T32GM008396)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
Keywords
gene expression profiling, stomatogastric ganglion, cardiac ganglia, Cancer borealis, unsupervised clustering, supervised learning, neuronal identity

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