title: Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding.
abstract: Disentangling cellular heterogeneity is a challenge in many fields, particularly in the stem cell and cancer biology fields. Here we demonstrate how to combine viral genetic barcoding with high-throughput sequencing to track single cells in a heterogeneous population. We use this technique to track the in vivo differentiation of unitary hematopoietic stem cells (HSCs). The results are consistent with single-cell transplantation studies but require two orders of magnitude fewer mice. In addition to its high throughput, the high sensitivity of the technique allows for a direct examination of the clonality of sparse cell populations such as HSCs. We show how these capabilities offer a clonal perspective of the HSC differentiation process. In particular, our data suggest that HSCs do not equally contribute to blood cells after irradiation-mediated transplantation, and that two distinct HSC differentiation patterns co-exist in the same recipient mouse after irradiation. This technique can be applied to any virus-accessible cell type for both in vitro and in vivo processes.
authors.affiliation: School of Medicine, Stanford University, Stanford, CA, USA. rlu@stanford.edu
authors.forename: Rong
authors.initials: R
authors.lastname: Lu
authors.forename: Norma F
authors.initials: NF
authors.lastname: Neff
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
authors.forename: Irving L
authors.initials: IL
authors.lastname: Weissman
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics / Q000528:radiation effects; D019070:Cell Lineage / Q000235:genetics / Q000528:radiation effects; D002999:Clone Cells; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D015723:Gene Library; D006412:Hematopoietic Stem Cells / Q000166:cytology* / Q000528:radiation effects / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016086:Lentivirus / Q000235:genetics* / Q000528:radiation effects; D051379:Mice; D008810:Mice, Inbred C57BL; D011827:Radiation; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis / Q000379:methods*