Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

Alex S Genshaft, Carly G. K. Ziegler, Constantine N. Tzouanas, Benjamin E. Mead, Alex M. Jaeger, Andrew W. Navia, Ryan P. King, Miyeko D. Mana, Siyi Huang, Vanessa Mitsialis, Scott B. Snapper, Ömer H. Yilmaz, Tyler Jacks, Jeffrey F. Van Humbeck and Alex K. Shalek ()
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Alex S Genshaft: MIT
Carly G. K. Ziegler: MIT
Constantine N. Tzouanas: MIT
Benjamin E. Mead: MIT
Alex M. Jaeger: MIT
Andrew W. Navia: MIT
Ryan P. King: MIT
Miyeko D. Mana: MIT
Siyi Huang: MIT and Harvard
Vanessa Mitsialis: Boston Children’s Hospital
Scott B. Snapper: Boston Children’s Hospital
Ömer H. Yilmaz: MIT
Tyler Jacks: MIT
Jeffrey F. Van Humbeck: University of Calgary
Alex K. Shalek: MIT

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract A cell’s phenotype and function are influenced by dynamic interactions with its microenvironment. To examine cellular spatiotemporal activity, we developed SPACECAT—Spatially PhotoActivatable Color Encoded Cell Address Tags—to annotate, track, and isolate cells while preserving viability. In SPACECAT, samples are stained with photocaged fluorescent molecules, and cells are labeled by uncaging those molecules with user-patterned near-UV light. SPACECAT offers single-cell precision and temporal stability across diverse cell and tissue types. Illustratively, we target crypt-like regions in patient-derived intestinal organoids to enrich for stem-like and actively mitotic cells, matching literature expectations. Moreover, we apply SPACECAT to ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model. Lastly, we provide a computational framework to identify spatially-biased transcriptome patterns and enriched phenotypes. This minimally perturbative and broadly applicable method links cellular spatiotemporal and/or behavioral phenotypes with diverse downstream assays, enabling insights into the connections between tissue microenvironments and (dys)function.

Date: 2021
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DOI: 10.1038/s41467-021-25279-y

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