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Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

A Publisher Correction to this article was published on 09 August 2018

This article has been updated

Abstract

Cancer immunotherapies have shown sustained clinical responses in treating non-small-cell lung cancer1,2,3, but efficacy varies and depends in part on the amount and properties of tumor infiltrating lymphocytes4,5,6. To depict the baseline landscape of the composition, lineage and functional states of tumor infiltrating lymphocytes, here we performed deep single-cell RNA sequencing for 12,346 T cells from 14 treatment-naïve non-small-cell lung cancer patients. Combined expression and T cell antigen receptor based lineage tracking revealed a significant proportion of inter-tissue effector T cells with a highly migratory nature. As well as tumor-infiltrating CD8+ T cells undergoing exhaustion, we observed two clusters of cells exhibiting states preceding exhaustion, and a high ratio of “pre-exhausted” to exhausted T cells was associated with better prognosis of lung adenocarcinoma. Additionally, we observed further heterogeneity within the tumor regulatory T cells (Tregs), characterized by the bimodal distribution of TNFRSF9, an activation marker for antigen-specific Tregs. The gene signature of those activated tumor Tregs, which included IL1R2, correlated with poor prognosis in lung adenocarcinoma. Our study provides a new approach for patient stratification and will help further understand the functional states and dynamics of T cells in lung cancer.

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Fig. 1: Dissection and clustering of tumor-related T cells in NSCLC.
Fig. 2: Clonal expansion of T cells defined by TCRs.
Fig. 3: Relationship among CD8+ T cell clusters based on both expression and TCR data, and the connection to LUAD overall survival.
Fig. 4: The presence of activated tumor Tregs and the clinical implication of T cell heterogeneity in NSCLC.

Change history

  • 09 August 2018

    In the version of this article originally published, the P statistic described in Fig. 3d was incorrect. It was described as “P < 22 × 10–16”. It should have been “P < 2.2 × 10–16”. Also, the “CD8+ Treg” label in Fig. 4f was incorrect. It should have been “CD4+ Treg”. The errors have been corrected in the HTML and PDF versions of this article.

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Acknowledgements

We thank S. Geng for discussions and members of the BIOPIC high-throughput sequencing facility and the Computing Platform of the Centre for Life Science. We also thank the National Centre for Protein Sciences Beijing (Peking University) and F. Wang, X. Zhang, S. Wang and Z. Fu for assistance with FACS. This project was supported by grants from the Beijing Advanced Innovation Centre for Genomics at Peking University, Key Technologies R&D Program (2016YFC0900100), the National Natural Science Foundation of China (81573022, 31530036, 91742203) and Bayer AG (Germany). C. Zheng and L. Zhang were supported by the Postdoctoral Foundation of Centre for Life Sciences at Peking University–Tsinghua University.

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Authors

Contributions

Z.Z. and X.G. designed the experiments. X.G., C.Z., Q.Z., Z.L., L.Z. and R.G. performed the experiments. X.G., Y.Z., L.Z., X.R., H.G.R., D.K., X.H. and M.D. analyzed the sequencing data. J.S., L.J., T.Y. and R.X. collected clinical samples. B.K. built the website. X.G., Y.Z., L.Z., and Z.Z. wrote the manuscript with all authors contributing to writing and providing feedback.

Corresponding authors

Correspondence to Tiansheng Yan or Zemin Zhang.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10

Reporting Summary

Supplementary Table 1

Patient information and sequencing statistics

Supplementary Table 2

TCR typing of single T cells

Supplementary Table 3

List of signature genes of each T cell cluster

Supplementary Table 4

List of genes specifically expressed in exhausted tumor T cells

Supplementary Table 5

Differentially expressed genes of suppressive tumor Treg cells in CD4C9CTLA4

Supplementary Table 6

Differentially expressed genes of activated tumor Treg cells in CD4C9CTLA4

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Guo, X., Zhang, Y., Zheng, L. et al. Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nat Med 24, 978–985 (2018). https://doi.org/10.1038/s41591-018-0045-3

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