Abstract Advances of single-cell technologies allow scrutinizing of heterogeneous cell states, however, analyzing transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique for the underlying stochastic dynamical systems that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transition, and distinguishes meta-stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using the coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. Mathematical analysis reveals consistency of the method with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms and benchmarking with seven existing tools, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.

Dissecting Transition Cells from Single-cell Transcriptome Data through Multiscale Stochastic Dynamics