TY - JOUR T1 - Mapping lineage-traced cells across time points with moslin JF - bioRxiv DO - 10.1101/2023.04.14.536867 SP - 2023.04.14.536867 AU - Marius Lange AU - Zoe Piran AU - Michal Klein AU - Bastiaan Spanjaard AU - Dominik Klein AU - Jan Philipp Junker AU - Fabian J. Theis AU - Mor Nitzan Y1 - 2023/01/01 UR - http://biorxiv.org/content/early/2023/04/17/2023.04.14.536867.abstract N2 - Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making beyond simpler pseudotime-based approaches. However, it is currently unclear how lineage and gene expression information across experimental time points can be combined in destructive experiments, which is particularly challenging for in-vivo systems. Here we present moslin, a Fused Gromov-Wasserstein-based model to couple matching cellular profiles across time points. In contrast to existing methods, moslin leverages both intra-individual lineage relations and inter-individual gene expression similarity. We demonstrate on simulated and real data that moslin outperforms state-of-the-art approaches that use either one or both data modalities, even when the lineage information is noisy. On C. elegans embryonic development, we show how moslin, combined with trajectory inference methods, predicts fate probabilities and putative decision driver genes. Finally, we use moslin to delineate lineage relationships among transiently activated fibroblast states during zebrafish heart regeneration. We anticipate moslin to play a crucial role in deciphering complex state change trajectories from lineage-traced single-cell data.Competing Interest StatementF.J.T. consults for Immunai Inc., Singularity Bio B.V., CytoReason Ltd, Cellarity, and Omniscope Ltd, and has ownership interest in Dermagnostix GmbH and Cellarity. The remaining authors declare no competing interests. ER -