The mammalian lung is a highly branched network in which the distal
regions of the bronchial tree transform during development into a
densely packed honeycomb of alveolar air sacs that mediate gas exchange.
Although this transformation has been studied by marker expression
analysis and fate-mapping, the mechanisms that control the progression
of lung progenitors along distinct lineages into mature alveolar
cell types are still incompletely known, in part because of the limited
number of lineage markers and the effects of ensemble averaging in
conventional transcriptome analysis experiments on cell populations.
Here we show that single-cell transcriptome analysis circumvents
these problems and enables direct measurement of the various cell
types and hierarchies in the developing lung. We used microfluidic
single-cell RNA sequencing (RNA-seq) on 198 individual cells at four
different stages encompassing alveolar differentiation to measure
the transcriptional states which define the developmental and cellular
hierarchy of the distal mouse lung epithelium. We empirically classified
cells into distinct groups by using an unbiased genome-wide approach
that did not require a priori knowledge of the underlying cell types
or the previous purification of cell populations. The results confirmed
the basic outlines of the classical model of epithelial cell-type
diversity in the distal lung and led to the discovery of many previously
unknown cell-type markers, including transcriptional regulators that
discriminate between the different populations. We reconstructed
the molecular steps during maturation of bipotential progenitors
along both alveolar lineages and elucidated the full life cycle of
the alveolar type?2 cell lineage. This single-cell genomics approach
is applicable to any developing or mature tissue to robustly delineate
molecularly distinct cell types, define progenitors and lineage hierarchies,
and identify lineage-specific regulatory factors.
Departments of Bioengineering and Applied Physics, Stanford University School of Medicine and Howard Hughes Medical Institute, Stanford, California 94305, USA.
%0 Journal Article
%1 Treutlein2014Reconstructinglineagehierarchies
%A Treutlein, Barbara
%A Brownfield, Doug G
%A Wu, Angela R
%A Neff, Norma F
%A Mantalas, Gary L
%A Espinoza, F. Hernan
%A Desai, Tushar J
%A Krasnow, Mark A
%A Quake, Stephen R
%D 2014
%J Nature
%K Genomics RNA-seq
%R 10.1038/nature13173
%T Reconstructing lineage hierarchies of the distal lung epithelium
using single-cell RNA-seq.
%U http://dx.doi.org/10.1038/nature13173
%X The mammalian lung is a highly branched network in which the distal
regions of the bronchial tree transform during development into a
densely packed honeycomb of alveolar air sacs that mediate gas exchange.
Although this transformation has been studied by marker expression
analysis and fate-mapping, the mechanisms that control the progression
of lung progenitors along distinct lineages into mature alveolar
cell types are still incompletely known, in part because of the limited
number of lineage markers and the effects of ensemble averaging in
conventional transcriptome analysis experiments on cell populations.
Here we show that single-cell transcriptome analysis circumvents
these problems and enables direct measurement of the various cell
types and hierarchies in the developing lung. We used microfluidic
single-cell RNA sequencing (RNA-seq) on 198 individual cells at four
different stages encompassing alveolar differentiation to measure
the transcriptional states which define the developmental and cellular
hierarchy of the distal mouse lung epithelium. We empirically classified
cells into distinct groups by using an unbiased genome-wide approach
that did not require a priori knowledge of the underlying cell types
or the previous purification of cell populations. The results confirmed
the basic outlines of the classical model of epithelial cell-type
diversity in the distal lung and led to the discovery of many previously
unknown cell-type markers, including transcriptional regulators that
discriminate between the different populations. We reconstructed
the molecular steps during maturation of bipotential progenitors
along both alveolar lineages and elucidated the full life cycle of
the alveolar type?2 cell lineage. This single-cell genomics approach
is applicable to any developing or mature tissue to robustly delineate
molecularly distinct cell types, define progenitors and lineage hierarchies,
and identify lineage-specific regulatory factors.
@article{Treutlein2014Reconstructinglineagehierarchies,
abstract = {The mammalian lung is a highly branched network in which the distal
regions of the bronchial tree transform during development into a
densely packed honeycomb of alveolar air sacs that mediate gas exchange.
Although this transformation has been studied by marker expression
analysis and fate-mapping, the mechanisms that control the progression
of lung progenitors along distinct lineages into mature alveolar
cell types are still incompletely known, in part because of the limited
number of lineage markers and the effects of ensemble averaging in
conventional transcriptome analysis experiments on cell populations.
Here we show that single-cell transcriptome analysis circumvents
these problems and enables direct measurement of the various cell
types and hierarchies in the developing lung. We used microfluidic
single-cell RNA sequencing (RNA-seq) on 198 individual cells at four
different stages encompassing alveolar differentiation to measure
the transcriptional states which define the developmental and cellular
hierarchy of the distal mouse lung epithelium. We empirically classified
cells into distinct groups by using an unbiased genome-wide approach
that did not require a priori knowledge of the underlying cell types
or the previous purification of cell populations. The results confirmed
the basic outlines of the classical model of epithelial cell-type
diversity in the distal lung and led to the discovery of many previously
unknown cell-type markers, including transcriptional regulators that
discriminate between the different populations. We reconstructed
the molecular steps during maturation of bipotential progenitors
along both alveolar lineages and elucidated the full life cycle of
the alveolar type?2 cell lineage. This single-cell genomics approach
is applicable to any developing or mature tissue to robustly delineate
molecularly distinct cell types, define progenitors and lineage hierarchies,
and identify lineage-specific regulatory factors.},
added-at = {2014-05-13T16:10:54.000+0200},
author = {Treutlein, Barbara and Brownfield, Doug G and Wu, Angela R and Neff, Norma F and Mantalas, Gary L and Espinoza, F. Hernan and Desai, Tushar J and Krasnow, Mark A and Quake, Stephen R},
biburl = {https://www.bibsonomy.org/bibtex/212cbb66215961c04db6d1866cc540a87/gwotto},
doi = {10.1038/nature13173},
file = {:Treutlein2014Reconstructinglineagehierarchies.pdf:PDF},
institution = {Departments of Bioengineering and Applied Physics, Stanford University School of Medicine and Howard Hughes Medical Institute, Stanford, California 94305, USA.},
interhash = {f970971559a1d5a3c8f49b764c10cb46},
intrahash = {12cbb66215961c04db6d1866cc540a87},
journal = {Nature},
keywords = {Genomics RNA-seq},
language = {eng},
medline-pst = {aheadofprint},
month = apr,
owner = {gotto},
pii = {nature13173},
pmid = {24739965},
timestamp = {2014-05-13T16:10:54.000+0200},
title = {Reconstructing lineage hierarchies of the distal lung epithelium
using single-cell RNA-seq.},
url = {http://dx.doi.org/10.1038/nature13173},
year = 2014
}