Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum

V. Dumrongprechachan; R. B. Salisbury; G. Soto; M. Kumar; M. L. MacDonald; Y. Kozorovitskiy

doi:10.1038/s41467-021-25144-y

Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum

V. Dumrongprechachan, R. B. Salisbury, G. Soto, M. Kumar, M. L. MacDonald^*, Y. Kozorovitskiy^*

^*Corresponding author for this work

Neurobiology

Research output: Contribution to journal › Article › peer-review

34 Scopus citations

Abstract

The vertebrate brain consists of diverse neuronal types, classified by distinct anatomy and function, along with divergent transcriptomes and proteomes. Defining the cell-type specific neuroproteomes is important for understanding the development and functional organization of neural circuits. This task remains challenging in complex tissue, due to suboptimal protein isolation techniques that often result in loss of cell-type specific information and incomplete capture of subcellular compartments. Here, we develop a genetically targeted proximity labeling approach to identify cell-type specific subcellular proteomes in the mouse brain, confirmed by imaging, electron microscopy, and mass spectrometry. We virally express subcellular-localized APEX2 to map the proteome of direct and indirect pathway spiny projection neurons in the striatum. The workflow provides sufficient depth to uncover changes in the proteome of striatal neurons following chemogenetic activation of Gα_q-coupled signaling cascades. This method enables flexible, cell-type specific quantitative profiling of subcellular proteome snapshots in the mouse brain.

Original language	English (US)
Article number	4855
Journal	Nature communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-25144-y
State	Published - Dec 1 2021

Funding

The authors thank the reviewers for helpful feedback, which improved the manuscript. The authors are grateful to Lindsey Butler for mouse colony management, Northwestern Biological Imaging Facility and Dr. Tiffany Schmidt for confocal microscope access, Northwestern University BioCryo Facility (Charlene Wilke and Dr. Reiner Bleher) for TEM sample preparation and microscope, Northwestern High Throughput Analysis laboratory for the microplate reader, and Northwestern University Center for Molecular Innovation and Drug Discovery (Dr. Atul Dilip Jain and Dr. Gary Schultz) for compound synthesis. Some schematics were created with BioRender.com. This work was supported by the NSF CAREER Award 1846234, NIMH R56MH113923, NINDS R01NS107539, NIMH R01MH117111, the Beckman Young Investigator Award, Searle Scholar Award, Rita Allen Foundation Scholar Award, and Sloan Research Fellowship (all Y.K.), and NIMH R01MH118497 (M.L.M.). V.D. is a predoctoral fellow of the American Heart Association (19PRE34380056) and as an affiliate fellow of the NIH 2T32GM15538.

ASJC Scopus subject areas

General Physics and Astronomy
General Chemistry
General Biochemistry, Genetics and Molecular Biology

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abstract = "The vertebrate brain consists of diverse neuronal types, classified by distinct anatomy and function, along with divergent transcriptomes and proteomes. Defining the cell-type specific neuroproteomes is important for understanding the development and functional organization of neural circuits. This task remains challenging in complex tissue, due to suboptimal protein isolation techniques that often result in loss of cell-type specific information and incomplete capture of subcellular compartments. Here, we develop a genetically targeted proximity labeling approach to identify cell-type specific subcellular proteomes in the mouse brain, confirmed by imaging, electron microscopy, and mass spectrometry. We virally express subcellular-localized APEX2 to map the proteome of direct and indirect pathway spiny projection neurons in the striatum. The workflow provides sufficient depth to uncover changes in the proteome of striatal neurons following chemogenetic activation of Gαq-coupled signaling cascades. This method enables flexible, cell-type specific quantitative profiling of subcellular proteome snapshots in the mouse brain.",

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AU - MacDonald, M. L.

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Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum

Abstract

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