Molecular characterization of projection neuron subtypes in the mouse olfactory bulb

Abstract
Data availability
Article and author information
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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

1. Zeppilli S
2. Ackels T
3. Attey R
4. Klimpert N
5. Ritola KD
6. Boeing S
7. Crombach A
8. Schaefer AT
9. Fleischmann A
(2020) single nucleus RNA sequencing data
NCBI Gene Expression Omnibus, GSE162654.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162654
1. Zeppilli S
2. Ackels T
3. Attey R
4. Klimpert N
5. Ritola KD
6. Boeing S
7. Crombach A
8. Schaefer AT
9. Fleischmann A
(2020) RNA deep sequencing data
NCBI Gene Expression Omnibus, GSE162655.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162655
1. Zeppilli S
2. Ackels T
3. Attey R
4. Klimpert N
5. Ritola KD
6. Boeing S
7. Crombach A
8. Schaefer AT
9. Fleischmann A
(2021) single nucleus RNA sequencing data
NCBI Gene Expression Omnibus, GSM5363097.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5363097

Article and author information

Author details

Sara Zeppilli

Neuroscience, Brown University, Providence, United States

Competing interests
No competing interests declared.
Tobias Ackels

Neurophysiology of Behaviour Laboratory, The Francis Crick Institute, London, United Kingdom

Competing interests
No competing interests declared.
Robin Attey

Institute of Neuroscience; Department of Psychology, Brown University, Providence, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-9652-8103
Nell Klimpert

Neuroscience, Brown University, Providence, United States

Competing interests
No competing interests declared.
Dr. Kimberly Ritola

Howard Hughes Medical Institute, Ashburn, United States

Competing interests
No competing interests declared.
Stefan Boeing

Bionformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-0495-5659
Anton Crombach

Antenne Lyon La Doua, Inria, Villeurbanne, France

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-2889-5120
Andreas T Schaefer

Neurophysiology of Behaviour Laboratory, The Francis Crick Institute, London, United Kingdom

Competing interests
Andreas T Schaefer, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-4677-8788
Alexander Fleischmann

Neuroscience, Brown University, Providence, United States

For correspondence
alexander_fleischmann@brown.edu

Competing interests
No competing interests declared.

"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.

Copyright

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.