Linking the genotypes and phenotypes of cancer cells in heterogenous populations via real-time optical tagging and image analysis

Li You, Pin-Rui Su, Max Betjes, Reza Ghadiri Rad, Ting-Chun Chou, Cecile Beerens, Eva van Oosten, Felix Leufkens, Paulina Gasecka, MJ Muraro, Ruud van Tol, Debby van Steenderen, Shazia Farooq, JAU (José) Hardillo, Robert Jan Baatenburg de Jong, Daan Brinks*, Miao Chien*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)

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 languageEnglish
Pages (from-to)667-675
Number of pages9
JournalNature Biomedical Engineering
Volume6
Issue number5
DOIs
Publication statusPublished - 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.

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