Ultra-sensitive digital quantification of proteins and mRNA in single cells

• Published in: Nature communications 2019-08, Vol.10 (1), p.3544-10, Article 3544
• Main Authors: Lin, Jing, Jordi, Christian, Son, Minjun, Van Phan, Hoang, Drayman, Nir, Abasiyanik, Mustafa Fatih, Vistain, Luke, Tu, Hsiung-Lin, Tay, Savaş
• Format: Article
• Language: English
• Subjects: 13; 13/62; 14; 38; 38/77; 631/1647/2196; 631/1647/277; 82/1; 96; 96/63; Animals; Chlorocebus aethiops; Epithelial cells; Gene Dosage; Gene expression; Herpes simplex; Humanities and Social Sciences; Humans; Intravital Microscopy - instrumentation; Intravital Microscopy - methods; Lab-On-A-Chip Devices; Limit of Detection; Mammalian cells; Microfluidics; Microfluidics - instrumentation; Microfluidics - methods; Molecular modelling; multidisciplinary; Parameter sensitivity; Proteins; Proteins - isolation & purification; RNA, Messenger - isolation & purification; Science; Science (multidisciplinary); Sensitivity; Single-Cell Analysis - instrumentation; Single-Cell Analysis - methods; Time-Lapse Imaging - instrumentation; Time-Lapse Imaging - methods; Vero Cells; Viruses
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-11531-z

Simultaneous measurement of proteins and mRNA in single cells enables quantitative understanding and modeling of cellular functions. Here, we present an automated microfluidic system for multi-parameter and ultra-sensitive protein/mRNA measurements in single cells. Our technology improves the sensitivity of digital proximity ligation assay by up to 55-fold, with a detection limit of 2277 proteins per cell and with detection efficiency of as few as 29 protein molecules. Our measurements using this system reveal higher mRNA/protein correlation in single mammalian cells than previous estimates. Furthermore, time-lapse imaging of herpes simplex virus 1 infected epithelial cells enabled by our device shows that expression of ICP4 -a major transcription factor regulating hundreds of viral genes- is only partially correlated with viral protein counts, suggesting that many cells go through abortive infection. These results highlight the importance of high-sensitivity protein/mRNA quantification for understanding fundamental molecular mechanisms in individual cells. Digital proximity ligation assay (dPLA) can measure proteins and mRNAs in single cells, but is not compatible with cell imaging and cannot quantify rare proteins due to a high dilution factor. Here the authors present an automated microfluidic device that combines live-cell imaging, chemical stimulation, and dPLA in a smaller reaction volume.