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

doi:10.1016/j.stem.2013.07.017

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

Research output: Contribution to journal › Article › peer-review

185 Scopus citations

Abstract

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 language	English (US)
Pages (from-to)	492-505
Number of pages	14
Journal	Cell Stem Cell
Volume	13
Issue number	4
DOIs	https://doi.org/10.1016/j.stem.2013.07.017
State	Published - Oct 3 2013

ASJC Scopus subject areas

Molecular Medicine
Genetics
Cell Biology

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title = "Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire",

abstract = "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.",

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

note = "Funding Information: We thank H. Skaletsky from Whitehead Institute for extensive help on the multiplexed primer design; Y. Fujiwara, E. Baena, O. Yilmaz, M. Nguyen, X. Han, V. Bragt, D. Linn, and J. Buchman for help with different parts of the sample preparations; and H. Huang, Z. Li, D. Scadden, H. Xie, and H. Hock for insightful discussions on the project. This work was supported by funding from the National Institutes of Health and the Harvard Stem Cell Institute (S.H.O). S.H.O. is an investigator of the Howard Hughes Medical Institute. ",

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T1 - Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire

AU - Guo, Guoji

AU - Luc, Sidinh

AU - Marco, Eugenio

AU - Lin, Ta Wei

AU - Peng, Cong

AU - Kerenyi, Marc A.

AU - Beyaz, Semir

AU - Kim, Woojin

AU - Xu, Jian

AU - Das, Partha Pratim

AU - Neff, Tobias

AU - Zou, Keyong

AU - Yuan, Guo Cheng

AU - Orkin, Stuart H.

N1 - Funding Information: We thank H. Skaletsky from Whitehead Institute for extensive help on the multiplexed primer design; Y. Fujiwara, E. Baena, O. Yilmaz, M. Nguyen, X. Han, V. Bragt, D. Linn, and J. Buchman for help with different parts of the sample preparations; and H. Huang, Z. Li, D. Scadden, H. Xie, and H. Hock for insightful discussions on the project. This work was supported by funding from the National Institutes of Health and the Harvard Stem Cell Institute (S.H.O). S.H.O. is an investigator of the Howard Hughes Medical Institute.

PY - 2013/10/3

Y1 - 2013/10/3

N2 - 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.

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

Abstract

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