Single-cell transcriptomics of dynamic cell behaviors

Despite advances in spatial transcriptomics, linking dynamic behavior of cells in their native environment to molecular profiling remains a major challenge. We present a method, termed behavioral transcriptomics, that allows us to couple physiological behaviors of single cells in an intact tissue to deep molecular profiling of individual cells. This method enables us to establish a novel molecular signature for a striking migratory cellular behavior following tissue injury. Overall design: In order to visualize the airway epithelium at high resolution over days, we explant a mouse trachea and secure it in a custom imaging platform, which minimizes sample movement during imaging and maintains a constant supply of nutrients from below the explant without disrupting the air-liquid interface. To determine the molecular signatures of cells with directional movement compared to regenerating non-moving cells, we marked epithelial regions by photoconversion at 24 hours after injury, imaged every 6 hours, screened for “movers” with >50 µm displacement (>3 µm/hr) at 18 hours after photoconversion, and then isolated photoconverted epithelial cells for plate-based single cell sequencing (scSeq). Dimensionality reduction revealed that cells from “moving” region (M) and a “non-moving” (NM) region cluster separately.