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

Pin-Rui Su; Li You; Cecile Beerens; Karel Bezstarosti; Jeroen Demmers; Martin Pabst; Roland Kanaar; Cheng-Chih Hsu; Miao-Ping Chien

doi:10.1016/j.crmeth.2022.100237

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

Cell Rep Methods. 2022 Jun 13;2(6):100237. doi: 10.1016/j.crmeth.2022.100237. eCollection 2022 Jun 20.

Authors

Pin-Rui Su^{1

2

3}, Li You^{1

2}, Cecile Beerens^{1

2}, Karel Bezstarosti⁴, Jeroen Demmers⁴, Martin Pabst⁵, Roland Kanaar^{1

2

6}, Cheng-Chih Hsu³, Miao-Ping Chien^{1

2

6}

Affiliations

¹ Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.
² Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
³ Department of Chemistry, National Taiwan University, Taipei, Taiwan.
⁴ Proteomics Core Facility, Erasmus University Medical Center, Rotterdam, the Netherlands.
⁵ Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
⁶ Oncode Institute, Utrecht, the Netherlands.

Abstract

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.

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

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Cycle Proteins
DNA Damage*
Microscopy*
Proteomics / methods
Radiation, Ionizing

Substances

Cell Cycle Proteins