Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire

Guoji Guo, Sidinh Luc, Eugenio Marco, Ta-Wei Lin, Cong Peng, Marc A. Kerenyi, Semir Beyaz, Woojin Kim, Jian Xu, Partha Pratim Das, Tobias Neff, Keyong Zou, Guo Cheng Yuan, Stuart H. Orkin

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166 Citations (Scopus)


Stem cell differentiation pathways are most often studied at the population level, whereas critical decisions are executed at the level of single cells. We have established a highly multiplexed, quantitative PCR assay to profile in an unbiased manner a panel of all commonly used cell surface markers (280 genes) from individual cells. With this method, we analyzed over 1,500 single cells throughout the mouse hematopoietic system and illustrate its utility for revealing important biological insights. The comprehensive single cell data set permits mapping of the mouse hematopoietic stem cell differentiation hierarchy by computational lineage progression analysis. Further profiling of 180 intracellular regulators enabled construction of a genetic network to assign the earliest differentiation event during hematopoietic lineage specification. Analysis of acute myeloid leukemia elicited by MLL-AF9 uncovered a distinct cellular hierarchy containing two independent self-renewing lineages with different clonal activities. The strategy has broad applicability in other cellular systems.

Original languageEnglish
Pages (from-to)492-505
Number of pages14
JournalCell Stem Cell
Issue number4
Publication statusPublished - 3 Oct 2013
Externally publishedYes

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