Lineage tracing on transcriptional landscapes links state to fate during differentiation

Abstract

A challenge in stem cell biology is to associate molecular differences among progenitor cells with their capacity to generate mature cell types. Though the development of single cell assays allows for the capture of progenitor cell states in great detail, these assays cannot definitively link those molecular states to their long-term fate. Here, we use expressed DNA barcodes to clonally trace single cell transcriptomes dynamically during differentiation and apply this approach to the study of hematopoiesis. Our analysis identifies functional boundaries of cell potential early in the hematopoietic hierarchy and locates them on a continuous transcriptional landscape. Additionally, we find that the monocyte lineage differentiates through two distinct transcriptional and clonal routes, leaving a persistent imprint on mature cells. Finally, we use our approach to reflect on current methods of dynamics inference from single-cell snapshots. We find that for in vitro hematopoiesis, published fate prediction algorithms do not detect lineage priming in early progenitors, and provide evidence that there are hidden properties that influence cell fate but are not detectable with current single-cell sequencing methods.