Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity

View ORCID ProfileHarrison Specht, View ORCID ProfileEdward Emmott, David H. Perlman, Antonius Koller, View ORCID ProfileNikolai Slavov
doi: https://doi.org/10.1101/665307
Harrison Specht
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Harrison Specht
Edward Emmott
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Edward Emmott
David H. Perlman
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Antonius Koller
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nikolai Slavov
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
3Department of Biology, Northeastern University, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nikolai Slavov
  • For correspondence: nslavov@alum.mit.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

The fate and physiology of individual cells are controlled by networks of proteins. Yet, our ability to quantitatively analyze protein networks in single cells has remained limited. To overcome this barrier, we developed SCoPE2. It integrates concepts from Single-Cell ProtEomics by Mass Spectrometry (SCoPE-MS) with automated and miniaturized sample preparation, substantially lowering cost and hands-on time. SCoPE2 uses data-driven analytics to optimize instrument parameters for sampling more ion copies per protein, thus supporting quantification with improved count statistics. These advances enabled us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiated into macrophage-like cells in the absence of polarizing cytokines. We used SCoPE2 to quantify over 2,000 proteins in 356 single monocytes and macrophages in about 85 hours of instrument time, and the quantified proteins allowed us to discern single cells by cell type. Furthermore, the data uncovered a continuous gradient of proteome states for the macrophage-like cells, suggesting that macrophage heterogeneity may emerge even in the absence of polarizing cytokines. Our methodology lays the foundation for quantitative analysis of protein networks at single-cell resolution.

Figure
  • Download figure
  • Open in new tab

Footnotes

  • ∈ Data, code & protocols: scope2.slavovlab.net

  • Added supplementary notes

  • http://scope2.slavovlab.net

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted July 09, 2019.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity
Harrison Specht, Edward Emmott, David H. Perlman, Antonius Koller, Nikolai Slavov
bioRxiv 665307; doi: https://doi.org/10.1101/665307
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity
Harrison Specht, Edward Emmott, David H. Perlman, Antonius Koller, Nikolai Slavov
bioRxiv 665307; doi: https://doi.org/10.1101/665307

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Immunology
  • Systems Biology
  • Genomics
  • Bioengineering
Subject Areas
All Articles
  • Animal Behavior and Cognition (4087)
  • Biochemistry (8762)
  • Bioengineering (6479)
  • Bioinformatics (23341)
  • Biophysics (11750)
  • Cancer Biology (9149)
  • Cell Biology (13248)
  • Clinical Trials (138)
  • Developmental Biology (7417)
  • Ecology (11369)
  • Epidemiology (2066)
  • Evolutionary Biology (15087)
  • Genetics (10399)
  • Genomics (14009)
  • Immunology (9121)
  • Microbiology (22040)
  • Molecular Biology (8779)
  • Neuroscience (47368)
  • Paleontology (350)
  • Pathology (1420)
  • Pharmacology and Toxicology (2482)
  • Physiology (3704)
  • Plant Biology (8050)
  • Scientific Communication and Education (1431)
  • Synthetic Biology (2208)
  • Systems Biology (6016)
  • Zoology (1249)