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Nat Commun DOI:10.1038/s41467-021-25279-y

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

Publication TypeJournal Article
Year of Publication2021
AuthorsGenshaft, AS, Ziegler, CGK, Tzouanas, CN, Mead, BE, Jaeger, AM, Navia, AW, King, RP, Mana, MD, Huang, S, Mitsialis, V, Snapper, SB, Yilmaz, ÖH, Jacks, T, Van Humbeck, JF, Shalek, AK
JournalNat Commun
Date Published2021 08 17

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.


Alternate JournalNat Commun
PubMed ID34404785
Grant ListT32 GM007753 / GM / NIGMS NIH HHS / United States
K99 CA241072 / CA / NCI NIH HHS / United States
DP2 GM119419 / GM / NIGMS NIH HHS / United States
RM1 HG006193 / HG / NHGRI NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States