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Highly multiplexed profiling of cell surface proteins on single circulating tumor cells based on antibody and cellular barcoding

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Abstract

Circulating tumor cells (CTCs) are extraordinarily rare in blood samples and represent a real-time “liquid biopsy” of tumors. Although genetic and transcriptional sequencing of single CTCs has been reported, these methods fail to provide phenotypic and functional information of CTCs such as protein levels of surface proteins. Studies of single-cell proteomic assays of CTCs have been rare because of a lack of single-cell proteomic methods to handle and analyze rare cells in a high background of non-target cells with high sensitivity, throughput, and multiplexing capacity. Here, we develop a microchip-assisted single-cell proteomic method for profiling surface proteins of CTCs based on antibody and cellular DNA barcoding strategy. We combine DNA-encoded antibody tags and cell indexes to profile 15 proteins in ~ 100 single rare cells simultaneously, and use high-throughput sequencing as the readout to generate surface protein profiles of CTCs according to their cell indexes and antibody-derived protein barcodes. A 6400-well microchip and the automated puncher are used to rapidly retrieve single CTCs from enriched CTC population with minimal cell loss (~ 10%). This technological platform integrates reliable isolation and proteomic analysis of single CTCs and can be extendable to ~ 100 proteins in hundreds of rare cells with single-cell precision.

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Funding

This study received financial support from the National Key Research and Development Program Grant 2016YFC0900200 (to Q.S.) and National Natural Science Foundation of China Grants 81371712 and 21775103 (to Q.S.) and 81701852 (to L.Y.).

Author information

Author notes

  1. Chunying Wang and Liu Yang contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Minhang District, Shanghai, 200240, China

    Chunying Wang

  2. Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 201620, China

    Liu Yang

  3. Minhang Branch, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 201100, China

    Zhuo Wang & Qihui Shi

  4. Abmart (Shanghai) Inc., Shanghai, 200233, China

    Jianjun He

Authors
  1. Chunying Wang
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  2. Liu Yang
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  3. Zhuo Wang
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  4. Jianjun He
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  5. Qihui Shi
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Corresponding author

Correspondence to Qihui Shi.

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Conflict of interest

The authors declare that they have no conflicts of interest.

Research involving human participants and/or animals

This study measured peripheral blood samples from lung adenocarcinoma patients. The clinical sample collection and experiment were carried out in accordance with guidelines and protocols that were approved by the Ethics and Scientific Committees of Shanghai Chest Hospital.

Informed consent

Peripheral blood samples were obtained from healthy donors and lung adenocarcinoma patients in Shanghai Chest Hospital (Shanghai, China) with written informed consent.

Additional information

Published in the topical collection Ultrasmall Sample Biochemical Analysis with guest editors Ryan Kelly and Ying Zhu.

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Wang, C., Yang, L., Wang, Z. et al. Highly multiplexed profiling of cell surface proteins on single circulating tumor cells based on antibody and cellular barcoding. Anal Bioanal Chem 411, 5373–5382 (2019). https://doi.org/10.1007/s00216-019-01666-9

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  • DOI: https://doi.org/10.1007/s00216-019-01666-9

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