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Title: Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets

Abstract

Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution because of the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 µm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-µm-thick rat brain cortex tissue sections having diameters of 50, 100, and 200 µm, respectively. We also analyzed 100-µm-diameter sections corresponding to 10–18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues.

Authors:
ORCiD logo; ; ORCiD logo; ; ORCiD logo; ; ; ; ; ; ; ; ORCiD logo; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1503624
Report Number(s):
PNNL-SA-138815
Journal ID: ISSN 1535-9476
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Molecular and Cellular Proteomics
Additional Journal Information:
Journal Volume: 17; Journal Issue: 9; Journal ID: ISSN 1535-9476
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English

Citation Formats

Zhu, Ying, Dou, Maowei, Piehowski, Paul D., Liang, Yiran, Wang, Fangjun, Chu, Rosalie K., Chrisler, William B., Smith, Jordan N., Schwarz, Kaitlynn C., Shen, Yufeng, Shukla, Anil K., Moore, Ronald J., Smith, Richard D., Qian, Wei-Jun, and Kelly, Ryan T. Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets. United States: N. p., 2018. Web. doi:10.1074/mcp.TIR118.000686.
Zhu, Ying, Dou, Maowei, Piehowski, Paul D., Liang, Yiran, Wang, Fangjun, Chu, Rosalie K., Chrisler, William B., Smith, Jordan N., Schwarz, Kaitlynn C., Shen, Yufeng, Shukla, Anil K., Moore, Ronald J., Smith, Richard D., Qian, Wei-Jun, & Kelly, Ryan T. Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets. United States. doi:10.1074/mcp.TIR118.000686.
Zhu, Ying, Dou, Maowei, Piehowski, Paul D., Liang, Yiran, Wang, Fangjun, Chu, Rosalie K., Chrisler, William B., Smith, Jordan N., Schwarz, Kaitlynn C., Shen, Yufeng, Shukla, Anil K., Moore, Ronald J., Smith, Richard D., Qian, Wei-Jun, and Kelly, Ryan T. Sun . "Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets". United States. doi:10.1074/mcp.TIR118.000686.
@article{osti_1503624,
title = {Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets},
author = {Zhu, Ying and Dou, Maowei and Piehowski, Paul D. and Liang, Yiran and Wang, Fangjun and Chu, Rosalie K. and Chrisler, William B. and Smith, Jordan N. and Schwarz, Kaitlynn C. and Shen, Yufeng and Shukla, Anil K. and Moore, Ronald J. and Smith, Richard D. and Qian, Wei-Jun and Kelly, Ryan T.},
abstractNote = {Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution because of the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 µm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-µm-thick rat brain cortex tissue sections having diameters of 50, 100, and 200 µm, respectively. We also analyzed 100-µm-diameter sections corresponding to 10–18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues.},
doi = {10.1074/mcp.TIR118.000686},
journal = {Molecular and Cellular Proteomics},
issn = {1535-9476},
number = 9,
volume = 17,
place = {United States},
year = {2018},
month = {6}
}

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