Molecular characterization of projection neuron subtypes in the mouse olfactory bulb
- Brown University, United States
- The Francis Crick Institute, United Kingdom
- Howard Hughes Medical Institute, United States
- Inria, France
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.
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single nucleus RNA sequencing dataNCBI Gene Expression Omnibus, GSE162654.
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RNA deep sequencing dataNCBI Gene Expression Omnibus, GSE162655.
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single nucleus RNA sequencing dataNCBI Gene Expression Omnibus, GSM5363097.
Article and author information
Author details
Andreas T Schaefer
Alexander Fleischmann
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
© 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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