Morphodynamical cell state description via live-cell imaging trajectory embedding

Abstract

Time-lapse imaging is a powerful approach to gain insight into the dynamic responses of cells, but the quantitative analysis of morphological changes over time remains challenging. Here, we exploit the concept of “trajectory embedding” to analyze cellular behavior using morphological feature trajectory histories—that is, multiple time points simultaneously, rather than the more common practice of examining morphological feature time courses in single timepoint (snapshot) morphological features. We apply this approach to analyze live-cell images of MCF10A mammary epithelial cells after treatment with a panel of microenvironmental perturbagens that strongly modulate cell motility, morphology, and cell cycle behavior. Our morphodynamical trajectory embedding analysis constructs a shared cell state landscape revealing ligand-specific regulation of cell state transitions and enables quantitative and descriptive models of single-cell trajectories. Additionally, we show that incorporation of trajectories into single-cell morphological analysis enables (i) systematic characterization of cell state trajectories, (ii) better separation of phenotypes, and (iii) more descriptive models of ligand-induced differences as compared to snapshot-based analysis. This morphodynamical trajectory embedding is broadly applicable to the quantitative analysis of cell responses via live-cell imaging across many biological and biomedical applications.

Mesenchymal cell migration on one-dimensional micropatterns

“…In principle, also the effects of drugs could be studied in a time-resolved manner, if appropriate microfluidic flow chamber devices combined with time-lapse live cell imaging allow the continuous observation of cells migrating on 1D microlanes before and after exposure, see Figure 6E . Likewise ligand induced changes in cell state are detectable in situ ( Copperman et al, 2023 ). The addition of cytoskeleton inhibitors represents the most established biochemical manipulation of cell migration.…”

Integrating single-cell transcriptomics with cellular phenotypes: cell morphology, Ca2+ imaging and electrophysiology

“…Various techniques are employed to track phenotypical changes in cells across different timescales. Morphodynamics, for instance, monitors changes occurring over minutes to days (Copperman et al 2023 ). Ca 2+ imaging measures oscillations from tens of milliseconds to minutes, and electrophysiology records cellular activity down to the millisecond, such as action potential firing (Clapham 2007 ; Kulkarni and Miller 2017 ).…”