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Exploring functional protein covariation across single cells using nPOP

View ORCID ProfileAndrew Leduc, View ORCID ProfileR. Gray Huffman, Joshua Cantlon, View ORCID ProfileSaad Khan, View ORCID ProfileNikolai Slavov
doi: https://doi.org/10.1101/2021.04.24.441211
Andrew Leduc
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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R. Gray Huffman
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Joshua Cantlon
2Scienion AG, Phoenix, AZ 85042, USA
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Saad Khan
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Nikolai Slavov
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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  • ORCID record for Nikolai Slavov
  • For correspondence: nslavov@alum.mit.edu nslavov@northeastern.edu
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Abstract

Many biological processes, such as the cell division cycle, are reflected in protein covariation across single cells. This covariation can be quantified and interpreted by single-cell proteomics with sufficiently high throughput and accuracy. Toward this goal, we developed the nano-ProteOmic sample Preparation (nPOP) method for single-cell proteomics. nPOP uses piezo acoustic dispensing to isolate individual cells in 300 picoliter volumes and performs all subsequent preparation steps in small droplets on a fluorocarbon-coated slide. This design enables simultaneous sample preparation of thousands of single cells, including lysing, digesting, and labeling individual cells in volumes below 20 nl. We used nPOP to prepare 1,888 single cells and 128 negative controls in a single batch. Their analysis enabled quantifying the covariation between thousands of proteins and cell-cycle protein markers. Many protein sets covaried with the cell cycle similarly across all cell types and states, reflecting cell-type independent cell cycle functions. However, the cell cycle covariation of other protein sets differed markedly between cell types, even within subpopulation of melanoma cells expressing markers for drug-resistance priming. The cells expressing these markers accumulated in the G1 phase of the cell cycle and exhibited different covariation of enzymes catabolizing glucose. These results demonstrate that protein covariation across single cells may reveal functionally concerted biological differences between closely related cell states.

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Competing Interest Statement

Joshua Cantlon is an employee of Scienion.

Footnotes

  • ∈ Data, code & protocols: scp.slavovlab.net/nPOP

  • We included a new and larger dataset (https://scp.slavovlab.net/Leduc_et_al_2022) acquired by prioritized analysis (https://scp.slavovlab.net/pSCoPE) and more in depth analysis of protein covariation, including in melanoma cells.

  • https://scp.slavovlab.net/nPOP

  • https://scp.slavovlab.net/Leduc_et_al_2022

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.
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Posted March 30, 2022.
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Exploring functional protein covariation across single cells using nPOP
Andrew Leduc, R. Gray Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov
bioRxiv 2021.04.24.441211; doi: https://doi.org/10.1101/2021.04.24.441211
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Exploring functional protein covariation across single cells using nPOP
Andrew Leduc, R. Gray Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov
bioRxiv 2021.04.24.441211; doi: https://doi.org/10.1101/2021.04.24.441211

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