Pseudo-time trajectory of single-cell lipidomics: Suggestion for experimental setup and computational analysis

Cellular heterogeneity is a fundamental facet of cell biology, influencing cellular signaling, metabolism, and gene regulation. Its accurate quantification requires measurements at the single-cell level. Most high-throughput single-cell technologies provide only a snapshot of cellular heterogeneity at a specific time point because the measurement is destructive. This limits our current ability to understand the dynamics of cellular behavior and quantify cell-specific parameters. We propose an experimental setup combined with a model-based analysis framework, enabling the extraction of longitudinal data from a single destructive measurement. Although broadly applicable, we focus on lipid metabolism, a domain where obtaining longitudinal single-cell data has remained elusive due to technical constraints. Our method leverages multiple labels whose measurements are linked to a shared dynamic. This allows the estimation of cell-specific parameters and the quantification of heterogeneity. This framework establishes a foundation for future investigations, providing a roadmap toward a deeper understanding of dynamic cellular processes.