Direct lineage reprogramming involves the conversion of cellular identity. Single-cell technologies are useful for deconstructing the considerable heterogeneity that emerges during lineage conversion. However, lineage relationships are typically lost during cell processing, complicating trajectory reconstruction. Here we present ‘CellTagging’, a combinatorial cell-indexing methodology that enables parallel capture of clonal history and cell identity, in which sequential rounds of cell labelling enable the construction of multi-level lineage trees. CellTagging and longitudinal tracking of fibroblast to induced endoderm progenitor reprogramming reveals two distinct trajectories: one leading to successfully reprogrammed cells, and one leading to a ‘dead-end’ state, paths determined in the earliest stages of lineage conversion. We find that expression of a putative methyltransferase, Mettl7a1, is associated with the successful reprogramming trajectory; adding Mettl7a1 to the reprogramming cocktail increases the yield of induced endoderm progenitors. Together, these results demonstrate the utility of our lineage-tracing method for revealing the dynamics of direct reprogramming.
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All source data, including sequencing reads and single-cell expression matrices, are available from the Gene Expression Omnibus (GEO) under accession code GSE99915.
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We thank members of the Morris laboratory, and T. Druley and R. Mitra for critical discussions; S. McCarroll, E. Macosko and M. Goldman for advice establishing Drop-seq; B. Treutlein for quadratic programming assistance; J. Dick for the gift of the pSMAL backbone; K. Kniepkamp for help with CellTag Viz; and The Genome Technology Access Center in the Department of Genetics. This work was funded by National Institutes of Health (NIH) grants R01-GM126112, R21-HG009750; P30-DK052574; Silicon Valley Community Foundation, Chan Zuckerberg Initiative Grants HCA-A-1704-01646 and HCA2-A-1708-02799; The Children’s Discovery Institute of Washington University and St. Louis Children’s Hospital MI-II-2016-544. S.A.M. is supported by a Vallee Scholar Award; B.A.B.: NIH-T32HG000045-18; C.G.: NIH-5T32GM007200-42; S.E.W.: NIH-5T32GM007067-44; K.K.: Japan Society for the Promotion of Science Postdoctoral Fellowship.
Nature thanks L. Perié, M. Porteus, L. Vallier and the other anonymous reviewer(s) for their contribution to the peer review of this work.