M-TRACK: a platform for live cell multiplex imaging reveals cell phenotypic transition dynamics inherently missing in snapshot data

Recent advances in single cell techniques catalyze an emerging field of studying how cells convert from one phenotype to another, in a step-by-step process. Two grand technical challenges, however, impede further development of the field. Fixed cell-based approaches can provide genome-wide snapshots of cell status but have fundamental limits on revealing temporal information, and fluorescence-based live cell imaging approaches provide temporal information but are technically challenging for multiplex long- term imaging. We present a live-cell imaging platform, Multiplex Trajectory Recording and Analysis of Cellular Kinetics, or M-TRACK, that tracks cellular status change through combining endogenous fluorescent labeling that minimizes perturbation to cell physiology and live cell imaging of high-dimensional cell morphological and texture features. To test the functionality of our platform, we used the A549 VIM-RFP EMT reporter line (ATCC(R) CCL-185EMT) to explore cell phenotypic transition in live cells. Live cell trajectories reveal parallel paths of epithelial-to-mesenchymal transition despite presence of heterogeneous single cell dynamics, emphasizing the importance of live cell studies. This framework, together with an accompanying computational package, is generally applicable to cell phenotypic transition processes.