TY - JOUR
T1 - Single-cell mapping of lineage and identity in direct reprogramming
AU - Biddy, Brent A.
AU - Kong, Wenjun
AU - Kamimoto, Kenji
AU - Guo, Chuner
AU - Waye, Sarah E.
AU - Sun, Tao
AU - Morris, Samantha A.
N1 - Funding Information:
Acknowledgements 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.
Publisher Copyright:
© 2018, Springer Nature Limited.
PY - 2018/12/13
Y1 - 2018/12/13
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85058522901&partnerID=8YFLogxK
U2 - 10.1038/s41586-018-0744-4
DO - 10.1038/s41586-018-0744-4
M3 - Article
C2 - 30518857
AN - SCOPUS:85058522901
SN - 0028-0836
VL - 564
SP - 219
EP - 224
JO - Nature
JF - Nature
IS - 7735
ER -