{"doi":"10.1101/2020.02.28.966598","title":"Spatially-Resolved Live Cell Tagging and Isolation Using Protected Photoactivatable Cell Dyes","abstract":"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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":129038,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9554,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":53209,"name":"Carly G.K. Ziegler","orcid":"0000-0002-8279-7150","position":1,"is_corresponding":false},{"id":104320,"name":"Constantine N. Tzouanas","orcid":"0000-0002-7536-1156","position":2,"is_corresponding":false},{"id":254308,"name":"Ben Mead","orcid":"0000-0001-5855-0097","position":3,"is_corresponding":false},{"id":70390,"name":"Alex M. Jaeger","orcid":"0000-0002-4319-4330","position":4,"is_corresponding":false},{"id":558593,"name":"Andrew W. Navia","orcid":"0000-0002-5429-8012","position":5,"is_corresponding":false},{"id":580742,"name":"Ryan P. King","orcid":null,"position":6,"is_corresponding":false},{"id":14823,"name":"Tyler Jacks","orcid":"0000-0001-5785-8911","position":7,"is_corresponding":false},{"id":580253,"name":"Jeffrey F. Van Humbeck","orcid":"0000-0002-8910-4820","position":8,"is_corresponding":false},{"id":1413,"name":"Alex K. Shalek","orcid":"0000-0001-5670-8778","position":9,"is_corresponding":false},{"id":53201,"name":"Alex S. Genshaft","orcid":"0000-0003-2714-4154","position":0,"is_corresponding":true}],"reference_count":40,"raw_metadata":null,"created_at":"2026-07-18T23:15:45.920615Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}