Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics

Microscopy-based single-cell proteomic profiling reveals heterogeneity in DNA damage response dynamics

Su, Pin Rui (Erasmus MC; National Taiwan University)
You, L. (Erasmus MC)
Beerens, Cecile (Erasmus MC)
Bezstarosti, Karel (Erasmus MC)
Demmers, J.A.A. (Erasmus MC)
Pabst, Martin (TU Delft BT/Environmental Biotechnology)
Kanaar, R. (TU Delft Education and Student Affairs; Erasmus MC; The Oncode Institute)
Hsu, Cheng Chih (National Taiwan University)
Chien, M.P. (TU Delft Education and Student Affairs; Erasmus MC; The Oncode Institute)

2022

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.

53BP1
DDR foci dynamics
DNA damage response
functional single-cell selection
PDS5A
phenotype-to-proteome linking
phototagging
single-cell proteomics
tumor heterogeneity
ultrawide field-of-view optical microscope

http://resolver.tudelft.nl/uuid:d7a9a247-23ce-4e0e-92b5-d08dd6cbd37d

https://doi.org/10.1016/j.crmeth.2022.100237

Cell Reports Methods, 2 (6)

Institutional Repository

journal article

© 2022 Pin Rui Su, L. You, Cecile Beerens, Karel Bezstarosti, J.A.A. Demmers, Martin Pabst, R. Kanaar, Cheng Chih Hsu, M.P. Chien