1. Neuroscience
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Molecular characterization of projection neuron subtypes in the mouse olfactory bulb

  1. Sara Zeppilli
  2. Tobias Ackels
  3. Robin Attey
  4. Nell Klimpert
  5. Dr. Kimberly Ritola
  6. Stefan Boeing
  7. Anton Crombach
  8. Andreas T Schaefer
  9. Alexander Fleischmann  Is a corresponding author
  1. Brown University, United States
  2. The Francis Crick Institute, United Kingdom
  3. Howard Hughes Medical Institute, United States
  4. Inria, France
Research Article
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Cite this article as: eLife 2021;10:e65445 doi: 10.7554/eLife.65445

Abstract

Projection neurons (PNs) in the mammalian olfactory bulb (OB) receive input from the nose and project to diverse cortical and subcortical areas. Morphological and physiological studies have highlighted functional heterogeneity, yet no molecular markers have been described that delineate PN subtypes. Here, we used viral injections into olfactory cortex and fluorescent nucleus sorting to enrich PNs for high-throughput single nucleus and bulk RNA deep sequencing. Transcriptome analysis and RNA in situ hybridization identified distinct mitral and tufted cell populations with characteristic transcription factor network topology, cell adhesion and excitability-related gene expression. Finally, we describe a new computational approach for integrating bulk and snRNA-seq data, and provide evidence that different mitral cell populations preferentially project to different target regions. Together, we have identified potential molecular and gene regulatory mechanisms underlying PN diversity and provide new molecular entry points into studying the diverse functional roles of mitral and tufted cell subtypes.

Data availability

Raw single nucleus RNA sequencing data (large sn-R1/R2/R3 and targeted sn-PCx datasets) have been deposited in Gene Expression Omnibus (GEO) under the accession numbers GSE162654 and GSM5363097 respectively. Bulk RNA deep sequencing data has been deposited in GEO under the accession number GSE162655. The R and Python analysis scripts developed for this paper are available at the GitLab links https://gitlab.com/fleischmann-lab/papers/molecular-characterization-of-projection-neuron-subtypes-in-the-mouse-olfactory-bulb and https://gitlab.inria.fr/acrombac/projection-neurons-mouse-olfactory-bulb. Extensive computational tools for additional in-depth exploration of our data sets are available through our website: https://biologic.crick.ac.uk/OB_projection_neurons.

The following data sets were generated

Article and author information

Author details

  1. Sara Zeppilli

    Neuroscience, Brown University, Providence, United States
    Competing interests
    No competing interests declared.
  2. Tobias Ackels

    Neurophysiology of Behaviour Laboratory, The Francis Crick Institute, London, United Kingdom
    Competing interests
    No competing interests declared.
  3. Robin Attey

    Institute of Neuroscience; Department of Psychology, Brown University, Providence, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9652-8103
  4. Nell Klimpert

    Neuroscience, Brown University, Providence, United States
    Competing interests
    No competing interests declared.
  5. Dr. Kimberly Ritola

    Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
  6. Stefan Boeing

    Bionformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0495-5659
  7. Anton Crombach

    Antenne Lyon La Doua, Inria, Villeurbanne, France
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2889-5120
  8. Andreas T Schaefer

    Neurophysiology of Behaviour Laboratory, The Francis Crick Institute, London, United Kingdom
    Competing interests
    Andreas T Schaefer, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4677-8788
  9. Alexander Fleischmann

    Neuroscience, Brown University, Providence, United States
    For correspondence
    alexander_fleischmann@brown.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7956-9096

Funding

Cancer Research UK (FC001153)

  • Andreas T Schaefer

Wellcome Trust (FC001153)

  • Andreas T Schaefer

Deutsche Forschungsgemeinschaft

  • Tobias Ackels

National Institutes of Health (1R01DC017437-03)

  • Alexander Fleischmann

National Institutes of Health (1U19NS112953-01)

  • Alexander Fleischmann

National Institutes of Health (S10OD025181)

  • Alexander Fleischmann

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All animal protocols were performed in strict accordance with the recommendations approved by the Ethics Committee of the board of the Francis Crick Institute and the United Kingdom Home Office under the Animals (Scientific Procedures) Act 1986 (project license number PA2F6DA12), as well as Brown University's Institutional Animal Care and Use Committee (protocol number: 21-03-0004) followed by the guidelines provided by the National Institutes of Health.

Reviewing Editor

  1. Naoshige Uchida, Harvard University, United States

Publication history

  1. Preprint posted: December 2, 2020 (view preprint)
  2. Received: December 4, 2020
  3. Accepted: July 21, 2021
  4. Accepted Manuscript published: July 22, 2021 (version 1)
  5. Version of Record published: August 9, 2021 (version 2)

Copyright

© 2021, Zeppilli et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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