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Genshaft, Alex S; Ziegler, Carly G K; Tzouanas, Constantine N; Mead, Benjamin E; Jaeger, Alex M; Navia, Andrew W; King, Ryan P; Mana, Miyeko D; Huang, Siyi; Mitsialis, Vanessa; Snapper, Scott B; Yilmaz, Ömer H; Jacks, Tyler; Van Humbeck, Jeffrey F; Shalek, Alex K
Nature communications, 08/2021, Volume: 12, Issue: 1Journal Article
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.
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