Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes

  • Biology
  • Cancer
  • Chemistry
  • Genomics
  • R&D
  • Technology
  • Alex Genshaft
  • Carly Ziegler
  • Constantine Tzouanas
  • Ben Mead
  • Andrew Navia
  • Alex K. Shalek
  • Genshaft et al.▾
    Genshaft, A.S., Ziegler, C.G.K., Tzouanas, C.N., Mead, B.E., Jaeger, A.M., Navia, A.W., King, R.P., Jacks, T., Van Humbeck, J.F., Shalek, A.K.
  • bioRxiv
  • March, 2020
Biology
Cancer
Chemistry
Genomics
R&D
Technology
Alex Genshaft
Carly Ziegler
Constantine Tzouanas
Ben Mead
Andrew Navia
Alex K. Shalek

Abstract

Whether cultured in vitro or part of a complex tissue in vivo, a cell’s phenotype and function are significantly influenced by dynamic interactions with its microenvironment. To explicitly examine how a cell’s spatiotemporal activity impacts its behavior, we developed and validated a strategy termed SPACECAT – Spatially PhotoActivatable Color Encoded Cell Address Tags – to annotate, track, and isolate specific cells in a non-destructive, viability-preserving manner. In SPACECAT, a biological sample is immersed in a photocaged fluorescent molecule, and cells within a location of interest are labeled for further study by uncaging that molecule with user-patterned near-UV light. SPACECAT offers high spatial precision and temporal stability across diverse cell and tissue types, and is compatible with common downstream assays, including flow cytometry and single-cell RNA-Seq. Illustratively, we leveraged this approach in patient-derived intestinal organoids, a spatially complex system less amenable to genetic manipulations, to select for crypt-like regions enriched in stem-like and actively mitotic cells. Moreover, we demonstrate its applicability and utility on ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model, uncovering spatially-biased gene expression patterns among immune cell subsets and identifying rare myeloid phenotypes enriched around tumor/healthy border regions. In sum, our method provides a minimally invasive and broadly applicable approach to link cellular spatiotemporal features and/or behavioral phenotypes with diverse downstream assays, enabling fundamental insights into the connections between tissue microenvironments and biological (dys)function.

Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes