Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment

  1. Vasin Dumrongprechachan
  2. Ryan B Salisbury
  3. Lindsey Butler
  4. Matthew L MacDonald  Is a corresponding author
  5. Yevgenia Kozorovitskiy  Is a corresponding author
  1. Northwestern University, United States
  2. University of Pittsburgh, United States

Abstract

Mammalian axonal development begins in embryonic stages and continues postnatally. After birth, axonal proteomic landscape changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Comprehensive profiling of axonal proteomes across neurodevelopment is limited, with most studies lacking cell-type and neural circuit specificity, resulting in substantial information loss. We create a Cre-dependent APEX2 reporter mouse line and map cell-type specific proteome of corticostriatal projections across postnatal development. We synthesize analysis frameworks to define temporal patterns of axonal proteome and phosphoproteome, identifying co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders. We discover proline-directed kinases as major developmental regulators. APEX2 transgenic reporter proximity labeling offers flexible strategies for subcellular proteomics with cell type specificity in early neurodevelopment, a critical period for neuropsychiatric disease.

Data availability

Mass spectrometry raw data have been deposited in the PRIDE database (accession number: PXD030864. Code is available at Github (link in Materials and Methods). All analyzed proteomics results are also included as supplementary files. All uncropped gels and blots are included as source data.

The following data sets were generated

Article and author information

Author details

  1. Vasin Dumrongprechachan

    Department of Neurobiology, Northwestern University, Evanston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5890-6778
  2. Ryan B Salisbury

    Department of Psychiatry, University of Pittsburgh, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Lindsey Butler

    Department of Neurobiology, Northwestern University, Evanston, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Matthew L MacDonald

    Department of Psychiatry, University of Pittsburgh, Pittsburgh, United States
    For correspondence
    macdonaldml@upmc.edu
    Competing interests
    The authors declare that no competing interests exist.
  5. Yevgenia Kozorovitskiy

    Department of Neurobiology, Northwestern University, Evanston, United States
    For correspondence
    Yevgenia.Kozorovitskiy@northwestern.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3710-1484

Funding

National Institute of Mental Health (R56MH113923)

  • Yevgenia Kozorovitskiy

American Heart Association (19PRE34380056)

  • Vasin Dumrongprechachan

National Institute of General Medical Sciences (2T32GM15538)

  • Vasin Dumrongprechachan

National Institute of Neurological Disorders and Stroke (R01NS107539)

  • Yevgenia Kozorovitskiy

National Institute of Mental Health (R01MH117111)

  • Yevgenia Kozorovitskiy

National Science Foundation (1846234)

  • Yevgenia Kozorovitskiy

Arnold and Mabel Beckman Foundation (Beckman Young Investigator Award)

  • Yevgenia Kozorovitskiy

Kinship Foundation (Searle Scholar Award)

  • Yevgenia Kozorovitskiy

Rita Allen Foundation (Rita Allen Foundation Scholar Award)

  • Yevgenia Kozorovitskiy

Alfred P. Sloan Foundation (Sloan Research Fellowship)

  • Yevgenia Kozorovitskiy

National Institute of Mental Health (R01MH118497)

  • Matthew L MacDonald

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

Ethics

Animal experimentation: Animals were handled according to protocols approved by the Northwestern University AnimalCare and Use Committee. (protocol number: IS00008060).

Copyright

© 2022, Dumrongprechachan 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.

Metrics

  • 2,228
    views
  • 365
    downloads
  • 10
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Vasin Dumrongprechachan
  2. Ryan B Salisbury
  3. Lindsey Butler
  4. Matthew L MacDonald
  5. Yevgenia Kozorovitskiy
(2022)
Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment
eLife 11:e78847.
https://doi.org/10.7554/eLife.78847

Share this article

https://doi.org/10.7554/eLife.78847

Further reading

    1. Neuroscience
    Juan Carlos Boffi, Brice Bathellier ... Robert Prevedel
    Research Article

    Sound location coding has been extensively studied at the central nucleus of the mammalian inferior colliculus (CNIC), supporting a population code. However, this population code has not been extensively characterized on the single-trial level with simultaneous recordings or at other anatomical regions like the dorsal cortex of inferior colliculus (DCIC), which is relevant for learning-induced experience dependent plasticity. To address these knowledge gaps, here we made in two complementary ways large-scale recordings of DCIC populations from awake mice in response to sounds delivered from 13 different frontal horizontal locations (azimuths): volumetric two-photon calcium imaging with ~700 cells simultaneously recorded at a relatively low temporal resolution, and high-density single-unit extracellular recordings with ~20 cells simultaneously recorded at a high temporal resolution. Independent of the method, the recorded DCIC population responses revealed substantial trial-to-trial variation (neuronal noise) which was significantly correlated across pairs of neurons (noise correlations) in the passively listening condition. Nevertheless, decoding analysis supported that these noisy response patterns encode sound location on the single-trial basis, reaching errors that match the discrimination ability of mice. The detected noise correlations contributed to minimize the error of the DCIC population code of sound azimuth. Altogether these findings point out that DCIC can encode sound location in a similar format to what has been proposed for CNIC, opening exciting questions about how noise correlations could shape this code in the context of cortico-collicular input and experience-dependent plasticity.

    1. Neuroscience
    Selene Seoyun Lee, Livia Civitelli, Laura Parkkinen
    Research Article

    The alpha-synuclein (αSyn) seeding amplification assay (SAA) that allows the generation of disease-specific in vitro seeded fibrils (SAA fibrils) is used as a research tool to study the connection between the structure of αSyn fibrils, cellular seeding/spreading, and the clinicopathological manifestations of different synucleinopathies. However, structural differences between human brain-derived and SAA αSyn fibrils have been recently highlighted. Here, we characterize the biophysical properties of the human brain-derived αSyn fibrils from the brains of patients with Parkinson’s disease with and without dementia (PD, PDD), dementia with Lewy bodies (DLB), multiple system atrophy (MSA), and compare them to the ‘model’ SAA fibrils. We report that the brain-derived αSyn fibrils show distinct biochemical profiles, which were not replicated in the corresponding SAA fibrils. Furthermore, the brain-derived αSyn fibrils from all synucleinopathies displayed a mixture of ‘straight’ and ‘twisted’ microscopic structures. However, the PD, PDD, and DLB SAA fibrils had a ’straight’ structure, whereas MSA SAA fibrils showed a ‘twisted’ structure. Finally, the brain-derived αSyn fibrils from all four synucleinopathies were phosphorylated (S129). Interestingly, phosphorylated αSyn were carried over to the PDD and DLB SAA fibrils. Our findings demonstrate the limitation of the SAA fibrils modeling the brain-derived αSyn fibrils and pay attention to the necessity of deepening the understanding of the SAA fibrillation methodology.