FluoroFate: A generalisable platform for time-resolved single-cell analysis of cell fate enables quantification of cell death dynamics

Abstract

Fundamental cellular decisions of life and death are governed by intricate and tightly regulated intracellular signalling pathways that determine whether cells proliferate, enter quiescence, or undergo programmed cell death (apoptosis). Live-cell fluorescence imaging enables these processes to be observed in real time at single-cell resolution, but two problems limit their study. First, existing biosensors do not allow apoptotic status and cell cycle progression to be resolved in tandem within the same cell. Second, interpreting live-cell imaging data is challenging even where multiplex reporters exist, as the biological meaning of fluorescent signals depends on their temporal ordering, and large-scale imaging experiments generate complex, multidimensional data that are difficult to analyse systematically and at scale. Here we address both problems. We present FluoroFate, a generalisable and user-friendly graphical interface-driven tool for time-resolved single-cell analysis of multiplex live-cell imaging datasets, which integrates existing, robust deep learning-based segmentation, cell tracking, and temporal classification methods to quantify fluorescent reporter dynamics in individual cells across time without the need for specialist computational expertise. Alongside FluoroFate, we develop tricistronic Fluorescent Ubiquitination-based Cell Cycle Indicator (Fucci) and apoptosis biosensors, enabling simultaneous monitoring of cell cycle progression and caspase activation within the same cell. Applying FluoroFate, we resolve apoptotic and non-apoptotic cell death at the single-cell level based on the temporal ordering of Annexin V and propidium iodide signals, identifying distinct kinetic and phenotypic cell death profiles in response to pharmacological perturbation. We highlight divergent temporal dynamics and modes of cell death between birinapant and cycloheximide treatment, reflecting differences in how TNF/TNFR1 signalling is disrupted by these agents. At the single-cell level, we uncover parallel, independently regulated death programmes, demonstrating that loss of RIPK1 selectively impairs apoptotic cell death whilst leaving non-apoptotic death largely unaffected. We then use FluoroFate to analyse timelapse images of our combined Fucci-apoptosis reporters, resolving cell cycle progression and caspase activation within the same cell over time. Together, FluoroFate and our new cell cycle and apoptosis biosensors represent a broadly applicable platform for extracting mechanistic insight from live-cell imaging data.