Subcellular proteomics of dopamine neurons in the mouse brain

  1. Benjamin D Hobson
  2. Se Joon Choi
  3. Eugene V Mosharov
  4. Rajesh K Soni
  5. David Sulzer  Is a corresponding author
  6. Peter Sims  Is a corresponding author
  1. 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.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Benjamin D Hobson

    Depart of Systems Biology, Columbia University Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2745-5318
  2. Se Joon Choi

    New York State Psychiatric Institute, Columbia University Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Eugene V Mosharov

    New York State Psychiatric Institute, Columbia University Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Rajesh K Soni

    Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4556-4358
  5. David Sulzer

    Department of Psychiatry, Columbia University Medical Center, New York, United States
    For correspondence
    ds43@cumc.columbia.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7632-0439
  6. Peter Sims

    Department of Systems Biology, Columbia University Medical Center, New York, United States
    For correspondence
    pas2182@columbia.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3921-4837

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.

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).

Reviewing Editor

  1. Andrew B West, Duke University, United States

Version history

  1. Preprint posted: June 1, 2021 (view preprint)
  2. Received: June 2, 2021
  3. Accepted: January 30, 2022
  4. Accepted Manuscript published: January 31, 2022 (version 1)
  5. 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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  1. Benjamin D Hobson
  2. Se Joon Choi
  3. Eugene V Mosharov
  4. Rajesh K Soni
  5. David Sulzer
  6. Peter Sims
(2022)
Subcellular proteomics of dopamine neurons in the mouse brain
eLife 11:e70921.
https://doi.org/10.7554/eLife.70921

Share this article

https://doi.org/10.7554/eLife.70921

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