Institute for Medical Engineering & Science, MIT, Cambridge, MA, USA.
Department of Chemistry, MIT, Cambridge, MA, USA.
Nat Commun. 2021 Aug 17;12(1):4995. doi: 10.1038/s41467-021-25279-y.
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.
细胞的表型和功能受到与其微环境动态相互作用的影响。为了研究细胞的时空活性，我们开发了 SPACECAT（Spatially PhotoActivatable Color Encoded Cell Address Tags），这是一种可对细胞进行标记、追踪和分离，同时保持细胞活力的方法。在 SPACECAT 中，样品用光笼闭荧光分子染色，然后用用户设计的近紫外光将这些分子光解，从而对细胞进行标记。SPACECAT 可提供单细胞精度和跨多种细胞和组织类型的时间稳定性。有实例表明，我们针对源自患者的肠道类器官中的隐窝样区域进行靶向，以富集具有干细胞样和活跃有丝分裂特征的细胞，这与文献预期相符。此外，我们还将 SPACECAT 应用于来自四个健康器官和一个自发肺肿瘤模型的离体组织切片。最后，我们提供了一个计算框架，用于识别空间偏向的转录组模式和富集的表型。这种最小干扰且广泛适用的方法将细胞的时空和/或行为表型与各种下游检测方法联系起来，使我们能够深入了解组织微环境与（功能障碍）之间的联系。
