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

Area of Science:

• Biotechnology
• Oncology
• Proteomics

Background:

• Circulating tumor cells (CTCs) are rare but offer real-time liquid biopsy insights.
• Existing methods for CTC analysis lack phenotypic and functional protein information.
• Sensitive, high-throughput single-cell proteomic assays for rare cells are needed.

Purpose of the Study:

• To develop a microchip-assisted single-cell proteomic method for profiling CTC surface proteins.
• To enable simultaneous analysis of multiple proteins on rare CTCs with high sensitivity and throughput.

Main Methods:

• A DNA-encoded antibody barcoding strategy combined with cell indexing was employed.
• A 6400-well microchip and automated puncher were used for single CTC retrieval.
• High-throughput sequencing served as the readout for proteomic profiling.

Main Results:

• The method profiles 15 surface proteins on approximately 100 single rare cells simultaneously.
• Minimal cell loss (around 10%) was achieved during single CTC retrieval.
• Generated surface protein profiles for CTCs using cell indexes and antibody-derived barcodes.

Conclusions:

• The developed platform integrates reliable isolation and proteomic analysis of single CTCs.
• This technology provides phenotypic and functional information previously unavailable from CTCs.
• The platform is extendable to analyze hundreds of rare cells for up to 100 proteins with single-cell precision.