Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding

• Published in: Cell stem cell 2020-09, Vol.27 (3), p.383-395.e8
• Main Authors: Pei, Weike, Shang, Fuwei, Wang, Xi, Fanti, Ann-Kathrin, Greco, Alessandro, Busch, Katrin, Klapproth, Kay, Zhang, Qin, Quedenau, Claudia, Sauer, Sascha, Feyerabend, Thorsten B., Höfer, Thomas, Rodewald, Hans-Reimer
• Format: Article
• Language: English
• Subjects: Cell Differentiation - genetics; Cell Lineage - genetics; clonal fate coherence; Clone Cells; Hematopoiesis - genetics; hematopoietic stem cell fates; hematopoietic stem cell quiescence; Hematopoietic Stem Cells; high-resolution RNA barcoding; lineage tracing; single-cell transcriptomics; transcriptional landscape; Transcriptome - genetics
• ISSN: 1934-5909; 1875-9777
• DOI: 10.1016/j.stem.2020.07.018

Lineage tracing reveals hematopoietic stem cell (HSC) fates, while single-cell RNA sequencing identifies snapshots of HSC transcriptomes. To obtain information on fate plus transcriptome in the same cell, we developed the PolyloxExpress allele, enabling Cre-recombinase-dependent RNA barcoding in situ. Linking fates to single HSC transcriptomes provided the information required to identify transcriptional signatures of HSC fates, which were not apparent in single-HSC transcriptomes alone. We find that differentiation-inactive, multilineage, and lineage-restricted HSC clones reside in distinct regions of the transcriptional landscape of hematopoiesis. Differentiation-inactive HSC clones are closer to the origin of the transcriptional trajectory, yet they are not characterized by a quiescent gene signature. Fate-specific gene signatures imply coherence of clonal HSC fates, and HSC output toward short-lived lineage progenitors indicates stability of HSC fates over time. These combined analyses of fate and transcriptome under physiological conditions may pave the way toward identifying molecular determinants of HSC fates. [Display omitted] •PolyloxExpress barcoding jointly uncovers stem cell fate and single-cell transcriptome•Multilineage and myelo-erythroid-restricted HSC clones dominate•A subset of HSCs does not differentiate; differentiation-inactive HSCs are not quiescent•PolyloxExpress reveals transcriptome signatures associated with distinct HSC fates Snapshot transcriptome data lack precursor-product (fate) information, while lineage tracing reveals stem cell fate but lacks transcriptome information. Pei and colleagues developed a mouse RNA barcoding system (PolyloxExpress) that reports fate and transcriptome in single cells, providing transcriptional signatures associated with distinct hematopoietic stem cell fates and output.