Subcellular proteomics of dopamine neurons in the mouse brain
- Columbia University Medical Center, United States
Abstract
Dopaminergic neurons modulate neural circuits and behaviors via dopamine release from expansive, long range axonal projections. The elaborate cytoarchitecture of these neurons is embedded within complex brain tissue, making it difficult to access the neuronal proteome using conventional methods. Here, we demonstrate APEX2 proximity labeling within genetically targeted neurons in the mouse brain, enabling subcellular proteomics with cell type-specificity. By combining APEX2 biotinylation with mass spectrometry, we mapped the somatodendritic and axonal proteomes of midbrain dopaminergic neurons. Our dataset reveals the proteomic architecture underlying proteostasis, axonal metabolism, and neurotransmission in these neurons. We identify numerous proteins encoded by dopamine neuron-enriched genes in striatal dopaminergic axons, including ion channels with previously undescribed axonal localization. These proteomic datasets provide a resource for neuronal cell biology, and this approach can be readily adapted for study of other neural cell types.
Data availability
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD026229. Raw label-free quantification intensity values for proteomics data can be found in Figure 2 - source data 2. The scRNA-seq data analyzed are publicly available as GSE116470 (Saunders et al., 2018). High confidence DA neuron profiles used in this study are reported in Figure 5 - source data 3.
Article and author information
Author details
Funding
National Institutes of Health (F30DA047775)
- Benjamin D Hobson
National Institutes of Health (R01NS095435)
- David Sulzer
National Institutes of Health (R01DA007418)
- David Sulzer
National Institutes of Health (R01MH122470)
- David Sulzer
Michael J. Fox Foundation for Parkinson's Research (ASAP-000375)
- David Sulzer
- Peter Sims
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Andrew B West, Duke University, United States
Ethics
Animal experimentation: All experiments were conducted according to NIH guidelines and approved by the Institutional Animal Care and Use Committees of Columbia University and the New York State Psychiatric Institute. Protocol numbers are NYSPI #1584 (Columbia University AABI2605) and NYSPI #1551 (Columbia University AABD8564).
Version history
- Preprint posted: June 1, 2021 (view preprint)
- Received: June 2, 2021
- Accepted: January 30, 2022
- Accepted Manuscript published: January 31, 2022 (version 1)
- Version of Record published: February 21, 2022 (version 2)
Copyright
© 2022, Hobson 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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Subcellular proteomics of dopamine neurons in the mouse brain
eLife 11:e70921.
https://doi.org/10.7554/eLife.70921
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