@article{7911558f58434b5d9afa87234a913821,
title = "Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes",
abstract = "A cell{\textquoteright}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.",
author = "Genshaft, {Alex S.} and Ziegler, {Carly G.K.} and Tzouanas, {Constantine N.} and Mead, {Benjamin E.} and Jaeger, {Alex M.} and Navia, {Andrew W.} and King, {Ryan P.} and Mana, {Miyeko D.} and Siyi Huang and Vanessa Mitsialis and Snapper, {Scott B.} and Yilmaz, {{\"O}mer H.} and Tyler Jacks and {Van Humbeck}, {Jeffrey F.} and Shalek, {Alex K.}",
note = "Funding Information: T.J. is a member of the Board of Directors of Amgen and Thermo Fisher Scientific and a co-Founder of Dragonfly Therapeutics and T2 Biosystems. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics. T.J. is also President of Break Through Cancer. His laboratory currently receives funding from Johnson & Johnson and Lustgarten Foundation, but these funds did not support the research described in this manuscript. A.K.S. has received compensation for consulting and scientific advisory board membership from Merck, Honeycomb Biotechnologies, Cellarity, Repertoire Immune Medicines, Hovione, Third Rock Ventures, Ochre Bio, and Dahlia Biosciences unrelated to this work. A.S.G., C.G.K.Z., A.K.S., and J.F.V.H. are coinventors on a provisional patent application filed by the Broad Institute (U.S. Patent Application Nos. 16/494,911 and 62/473,222) relating to the methods and results described in this manuscript. The remaining authors declare no competing interests. Funding Information: We thank Marko Vukovic and Rachael Danielle Brust for organoid cell culture and instrument support. We thank the members of the Shalek laboratory for comments and discussion on the project. We thank Ulrich von Andrian for providing biological samples through the HMS Center for Immune Imaging. A.K.S. was supported by the Searle Scholars Program, the Beckman Young Investigator Program, the Pew-Stewart Scholars Program for Cancer Research, a Sloan Fellowship in Chemistry, the NIH (1DP2GM119419, 2RM1HG006193, and U2CCA23319501), and the Ragon Institute of MGH, MIT and Harvard. C.G.K.Z. was supported by T32GM007753 from the National Institute of General Medical Sciences. C.N.T. is funded by fellowships from the Fannie and John Hertz Foundation and the National Science Foundation (NSF) Graduate Research Fellowship Program (1122374). A.M.J. was supported by the Damon Runyon Cancer Research Foundation and an NCI K99 Pathway to Independence Award (5K99CA241072-02). T.J. was supported by the Howard Hughes Medical Institute. Synthetic development, including reagents and instrument time, was supported by Start-Up Funds from MIT and University of Calgary. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = dec,
day = "1",
doi = "10.1038/s41467-021-25279-y",
language = "English (US)",
volume = "12",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}