Single-cell protein profiling in microchambers with barcoded beads

• Published in: Microsystems & nanoengineering 2019-11, Vol.5 (1), p.1-11, Article 55
• Main Authors: Armbrecht, Lucas, Müller, Rafael Sebastian, Nikoloff, Jonas, Dittrich, Petra Stephanie
• Format: Article
• Language: English
• Subjects: 639/166; 639/638; Beads; Biotechnology; Breast cancer; Cancer; Data acquisition; Engineering; Galectin-3; Genomic analysis; Glyceraldehyde-3-phosphate dehydrogenase; Levels; Lipids; Mammalian cells; Mammals; Metabolites; Metastases; Microfluidics; Multiplexing; Proteins; Single-cell protein; Tumor cell lines; Tumors; Yeast
• ISSN: 2055-7434; 2096-1030; 2055-7434
• DOI: 10.1038/s41378-019-0099-5

Single-cell profiling provides insights into cellular behaviour that macroscale cell cultures and bulk measurements cannot reveal. In the context of personalized cancer treatment, the profiling of individual tumour cells may lead to higher success rates for therapies by rapidly selecting the most efficacious drugs. Currently, genomic analysis at the single-cell level is available through highly sensitive sequencing approaches. However, the identification and quantification of intracellular or secreted proteins or metabolites remains challenging. Here, we introduce a microfluidic method that facilitates capture, automated data acquisition and the multiplexed quantification of proteins from individual cells. The microfluidic platform comprises 1026 chambers with a volume of 152 pL each, in which single cells and barcoded beads are co-immobilized. We demonstrated multiplexed single-cell protein quantification with three different mammalian cell lines, including two model breast cancer cell lines. We established on-chip immunoassays for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), galectin-3 (Gal-3) and galectin-3 binding protein (Gal-3bp) with detection limits as low as 7.0 × 10 4 , 2.3 × 10 5 and 1.8 × 10 3 molecules per cell, respectively. The three investigated cell types had high cytosolic levels of GAPDH and could be clearly differentiated by their expression levels of Gal-3 and Gal-3bp, which are important factors that contribute to cancer metastasis. Because it employed commercially available barcoded beads for this study, our platform could be easily used for the single-cell protein profiling of several hundred different targets. Moreover, this versatile method is applicable to the analysis of bacteria, yeast and mammalian cells and nanometre-sized lipid vesicles. Microfluidics: Identifying and quantifying a single cell’s proteins An assay that traps cells in micrometre-sized chambers is able to identify and quantify a single cell’s proteins. This technique could prove beneficial in situations such as cancer, in which elucidating the variation between tumour cells could improve pharmacological strategies. Identifying and quantifying the proteins of a single cell has been a challenge for researchers, leading Petra Dittrich and her team from Switzerland’s ETH Zurich to develop their system which traps antibody-based assays bound to tiny barcoded beads in microfluidic chambers with single cells. The team identified and quantified three different pro