Cancer cells are embedded in the tumor microenvironment (TME), a complex ecosystem of stromal cells. Here, we present a 52,698-cell catalog of the TME transcriptome in human lung tumors at single-cell resolution, validated in independent samples where 40,250 additional cells were sequenced. By comparing with matching non-malignant lung samples, we reveal a highly complex TME that profoundly molds stromal cells. We identify 52 stromal cell subtypes, including novel subpopulations in cell types hitherto considered to be homogeneous, as well as transcription factors underlying their heterogeneity. For instance, we discover fibroblasts expressing different collagen sets, endothelial cells downregulating immune cell homing and genes coregulated with established immune checkpoint transcripts and correlating with T-cell activity. By assessing marker genes for these cell subtypes in bulk RNA-sequencing data from 1,572 patients, we illustrate how these correlate with survival, while immunohistochemistry for selected markers validates them as separate cellular entities in an independent series of lung tumors. Hence, in providing a comprehensive catalog of stromal cells types and by characterizing their phenotype and co-optive behavior, this resource provides deeper insights into lung cancer biology that will be helpful in advancing lung cancer diagnosis and therapy.
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We thank M. De Waegeneer, T. Van Brussel, G. Peuteman, E. Vanderheyden and B. Tembuyser for technical assistance. This work was supported by a VIB TechWatch Grant to D.L. and B.T., Foundation Against Cancer grants to S.Aerts (2016-070) and E.W., ERC Consolidator Grants to S.Aerts (724226_cis-CONTROL) and D.L. (CHAMELEON), Funds for Research - Flanders grants to H.D. (1701018N) and D.L. (G065615N), an Austrian Science Fund (FWF) grant to A.P. (J3730-B26) and KU Leuven grants to D.L. and S.Aerts (PFV/10/016 SymBioSys), and to B.T. (BOFZAP).
The authors declare no competing interests.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figures 1–20 and Supplementary Tables 1–3
Gene expression data for all 52 clusters
Gene expression data for tumor-derived and non-malignant lung-tissue-derived cells, per cluster having >100 cells from both sources
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