Cited by 1,342Single-cell and spatial transcriptomicsNeonatal Respiratory Health ResearchDevelopmental Biology and Gene Regulation

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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

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Treutlein, Barbara, Brownfield, Doug G., Wu, Angela R., Neff, Norma F., Mantalas, Gary L., Espinoza, F. Hernan, Desai, Tushar J., Krasnow, Mark A., Quake, Stephen R.·2014·Nature

DOI 10.1038/nature13173PMC PMC4145853

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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.

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Authors: Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A., & Quake, S. R.
Affiliations: Howard Hughes Medical Institute (US)
Stanford Medicine (US)
Corresponding author: Desai, Tushar J.
Krasnow, Mark A.
Quake, Stephen R.
ORCID: Treutlein, Barbara
Wu, Angela R.
Neff, Norma F.
Mantalas, Gary L.
Desai, Tushar J.
Krasnow, Mark A.
Quake, Stephen R.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2014-04-13
Volume: 509
Issue: 7500
Pages: 371-375
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature13173
PMC: PMC4145853
OpenAlex: W2068881679
Cited by: 1,342
References: 41
Citations by year: 2026: 25 · 2025: 52 · 2024: 65 · 2023: 97 · 2022: 113 · 2021: 120 · 2020: 134 · 2019: 146 · 2018: 161 · 2017: 155 · 2016: 137 · 2015: 106 · 2014: 25
FWCI: 57.77
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Howard Hughes Medical Institute
National Heart, Lung, and Blood Institute (K08HL084095, U01HL099995, U01HL099999)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (T32HD007249)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Neonatal Respiratory Health Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords: distal lung epithelium, lung development, alveolar progenitor cells, alveolar type II cells, alveolar type I cells, cell type markers, lineage hierarchy, alveolar differentiation, transcription factors, mouse lung
MeSH terms: Animals, Bronchi, Cell Differentiation, Epithelial Cells, Female, Genetic Markers, Lung, Mice, Inbred C57BL, Pulmonary Alveoli, Pulmonary Gas Exchange, Stem Cells, Genome, Sequence Analysis, RNA, Cell Lineage, Genomics, Mice, Single-Cell Analysis, Transcriptome

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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

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