Abstract
Linking single-cell genomic or transcriptomic profiles to functional cellular characteristics, in particular time-varying phenotypic changes, could help unravel molecular mechanisms driving the growth of tumour-cell subpopulations. Here we show that a custom-built optical microscope with an ultrawide field of view, fast automated image analysis and a dye activatable by visible light enables the screening and selective photolabelling of cells of interest in large heterogeneous cell populations on the basis of specific functional cellular dynamics, such as fast migration, morphological variation, small-molecule uptake or cell division. Combining such functional single-cell selection with single-cell RNA sequencing allowed us to (1) functionally annotate the transcriptomic profiles of fast-migrating and spindle-shaped MCF10A cells, of fast-migrating MDA-MB-231 cells and of patient-derived head-and-neck squamous carcinoma cells, and (2) identify critical genes and pathways driving aggressive migration and mesenchymal-like morphology in these cells. Functional single-cell selection upstream of single-cell sequencing does not depend on molecular biomarkers, allows for the enrichment of sparse subpopulations of cells, and can facilitate the identification and understanding of the molecular mechanisms underlying functional phenotypes.
Original language | English |
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Pages (from-to) | 667-675 |
Number of pages | 9 |
Journal | Nature Biomedical Engineering |
Volume | 6 |
Issue number | 5 |
DOIs | |
Publication status | Published - May 2022 |
Bibliographical note
Funding Information:M.-P.C. acknowledges support from the Oncode Institute, Cancer GenomiCs.nl (CGC), NWO (the Netherlands Organization for Scientific Research) Veni Grant, and Erasmus MC grant. M.-P.C. appreciates Josephine Nefkens Stichting’s support on the UFO microscope. D.B. acknowledges support by an NWO Start-up Grant (740.018.018) and ERC Starting Grant (850818 - MULTIVIsion). P.-R.S. acknowledges support from Ministry of Science and Technology (MOST) in Taiwan (Dragon Gate program: 107-2911-I-002-577 and Columbus Program: 108-2636-M-002-008- &109-2636-M-002-005-). We thank R. Agami and M. Paul for the kind gift of MCF10A-H2B-GFP and U2OS-H2B-mMaple3 cell lines, respectively; A. Theil and T. W. Kan for technical assistance with FACS sorting; J. Kraan and J. Martens for the use of their cell separation machine; the Erasmus MC Center for Biomics for the bulk-cell transcriptomic sequencing; K. T. Chen for the phototagging purification; and P. Keller for discussions about TGMM.
Funding Information:
M.-P.C. acknowledges support from the Oncode Institute, Cancer GenomiCs.nl (CGC), NWO (the Netherlands Organization for Scientific Research) Veni Grant, and Erasmus MC grant. M.-P.C. appreciates Josephine Nefkens Stichting’s support on the UFO microscope. D.B. acknowledges support by an NWO Start-up Grant (740.018.018) and ERC Starting Grant (850818 - MULTIVIsion). P.-R.S. acknowledges support from Ministry of Science and Technology (MOST) in Taiwan (Dragon Gate program: 107-2911-I-002-577 and Columbus Program: 108-2636-M-002-008- &109-2636-M-002-005-). We thank R. Agami and M. Paul for the kind gift of MCF10A-H2B-GFP and U2OS-H2B-mMaple3 cell lines, respectively; A. Theil and T. W. Kan for technical assistance with FACS sorting; J. Kraan and J. Martens for the use of their cell separation machine; the Erasmus MC Center for Biomics for the bulk-cell transcriptomic sequencing; K. T. Chen for the phototagging purification; and P. Keller for discussions about TGMM.
Publisher Copyright:
© 2022, The Author(s), under exclusive licence to Springer Nature Limited.