Single-cell proteomics has the potential to decipher tumor heterogeneity, and a method like single-cell proteomics by mass spectrometry (SCoPE-MS) allows profiling several tens of single cells for >1,000 proteins per cell. This method, however, cannot link the proteome of individual cells with phenotypes of interest. Here, we developed a microscopy-based functional single-cell proteomic-profiling technology, called FUNpro, to address this. FUNpro enables screening, identification, and isolation of single cells of interest in a real-time fashion, even if the phenotypes are dynamic or the cells of interest are rare. We applied FUNpro to proteomically profile a newly identified small subpopulation of U2OS osteosarcoma cells displaying an abnormal, prolonged DNA damage response (DDR) after ionizing radiation (IR). With this, we identified the PDS5A protein contributing to the abnormal DDR dynamics and helping the cells survive after IR.
M.-P.C. acknowledges support from the Oncode Institute, Cancer GenomiCs.nl (CGC), NWO (the Netherlands Organization for Scientific Research) Veni Grant, and Stichting Ammodo and Erasmus MC grant. M.-P.C. appreciates Josephine Nefkens Stichting’s support on the UFO microscope. C.-C.H. acknowledges support from the Ministry of Science and Technology (MOST) in Taiwan (Dragon Gate program: 107-2911-I-002-577 and Columbus Program: 108-2636-M-002-008- and 109-2636-M-002-005-). We thank Hanny Odijk for the kind gift of the PB-mScarlet-53BP1 plasmid. We thank Tsung Wai Kan for the assistance on FACS. We thank Daan Brinks for the discussion on the manuscript.
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