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Phenotype molding of stromal cells in the lung tumor microenvironment

Nature Medicine volume 24, pages 1277–1289 (2018)Cite this article

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Abstract

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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Fig. 1: Overview of the 52,698 single cells from lung tumors and distal non-malignant lung samples.
Fig. 2: Endothelial cell clusters.
Fig. 3: Fibroblast clusters in lungs and lung tumors.
Fig. 4: B-cell and myeloid-like cell clusters in lungs and lung tumors.
Fig. 5: T-cell clusters in lungs and lung tumors.
Fig. 6: Distribution of stromal cells in tumor samples and their role as markers of patient survival.

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Acknowledgements

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).

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Authors and Affiliations

  1. VIB Center for Cancer Biology, Leuven, Belgium

    Diether Lambrechts, Bram Boeckx, Ayse Bassez, Andreas Pircher, Peter Carmeliet & Bernard Thienpont

  2. Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium

    Diether Lambrechts, Bram Boeckx & Ayse Bassez

  3. Respiratory Oncology Unit (Pneumology) and Leuven Lung Cancer Group, University Hospitals KU Leuven, Leuven, Belgium

    Els Wauters & Johan Vansteenkiste

  4. Laboratory of Pneumology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium

    Els Wauters & Johan Vansteenkiste

  5. Laboratory for Computational Biology, Department of Human Genetics, KU Leuven, Leuven, Belgium

    Sara Aibar & Stein Aerts

  6. VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium

    Sara Aibar, Oliver Burton, Adrian Liston & Stein Aerts

  7. Histopathology Expertise Center, VIB Leuven Center for Cancer Biology, VIB, Leuven, Belgium

    David Nittner

  8. Department of Oncology, KU Leuven, Leuven, Belgium

    David Nittner

  9. Laboratory of Genetics of Autoimmunity, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium

    Oliver Burton & Adrian Liston

  10. Department of Thoracic Surgery, University Hospitals KU Leuven, Leuven, Belgium

    Herbert Decaluwé

  11. Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium

    Herbert Decaluwé & Paul De Leyn

  12. Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven, Belgium

    Andreas Pircher & Peter Carmeliet

  13. Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium

    Kathleen Van den Eynde, Birgit Weynand & Erik Verbeken

  14. State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, SunYat-Sen University, Guangzhou, China

    Peter Carmeliet

  15. Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium

    Bernard Thienpont

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  1. Diether Lambrechts
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  2. Els Wauters
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Contributions

D.L. and B.T. designed and supervised the study and wrote the manuscript. E.W. supervised sample collection and clinical annotation, with important help from H.D., A.P., K.V.d.E., B.W., E.V., P.D.L. and J.V. B.T. performed data analysis, with significant contributions from B.B., S.Ai., S.Ae. and A.B. D.N. and B.T. performed immunohistofluorescence analyses. O.B., A.L., P.C. and S.Ae. contributed critical data interpretation. All of the authors have read or provided comments on the manuscript.

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Correspondence to Diether Lambrechts or Bernard Thienpont.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–20 and Supplementary Tables 1–3

Reporting Summary

Supplementary Table 4

Gene expression data for all 52 clusters

Supplementary Table 5

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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Lambrechts, D., Wauters, E., Boeckx, B. et al. Phenotype molding of stromal cells in the lung tumor microenvironment. Nat Med 24, 1277–1289 (2018). https://doi.org/10.1038/s41591-018-0096-5

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