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Neoantigen-directed immune escape in lung cancer evolution

Author

Listed:
  • Rachel Rosenthal

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London
    The Francis Crick Institute)

  • Elizabeth Larose Cadieux

    (The Francis Crick Institute)

  • Roberto Salgado

    (GZA-ZNA
    University of Melbourne)

  • Maise Al Bakir

    (The Francis Crick Institute)

  • David A. Moore

    (University College London Cancer Institute, University College London)

  • Crispin T. Hiley

    (University College London Cancer Institute, University College London
    The Francis Crick Institute)

  • Tom Lund

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London)

  • Miljana Tanić

    (University College London Cancer Institute, University College London)

  • James L. Reading

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London)

  • Kroopa Joshi

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London)

  • Jake Y. Henry

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London)

  • Ehsan Ghorani

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London)

  • Gareth A. Wilson

    (University College London Cancer Institute, University College London
    The Francis Crick Institute)

  • Nicolai J. Birkbak

    (University College London Cancer Institute, University College London
    The Francis Crick Institute)

  • Mariam Jamal-Hanjani

    (University College London Cancer Institute, University College London)

  • Selvaraju Veeriah

    (University College London Cancer Institute, University College London)

  • Zoltan Szallasi

    (Boston Children’s Hospital, Harvard Medical School
    Danish Cancer Society Research Center)

  • Sherene Loi

    (University of Melbourne)

  • Matthew D. Hellmann

    (Memorial Sloan Kettering Cancer Center
    Cornell University)

  • Andrew Feber

    (University College London)

  • Benny Chain

    (University College London
    University College London)

  • Javier Herrero

    (University College London Cancer Institute, University College London)

  • Sergio A. Quezada

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London)

  • Jonas Demeulemeester

    (The Francis Crick Institute
    University of Leuven)

  • Peter Loo

    (The Francis Crick Institute
    University of Leuven)

  • Stephan Beck

    (University College London Cancer Institute, University College London)

  • Nicholas McGranahan

    (University College London Cancer Institute, University College London
    University College London Cancer Institute, University College London)

  • Charles Swanton

    (University College London Cancer Institute, University College London
    The Francis Crick Institute)

Abstract

The interplay between an evolving cancer and a dynamic immune microenvironment remains unclear. Here we analyse 258 regions from 88 early-stage, untreated non-small-cell lung cancers using RNA sequencing and histopathology-assessed tumour-infiltrating lymphocyte estimates. Immune infiltration varied both between and within tumours, with different mechanisms of neoantigen presentation dysfunction enriched in distinct immune microenvironments. Sparsely infiltrated tumours exhibited a waning of neoantigen editing during tumour evolution, indicative of historical immune editing, or copy-number loss of previously clonal neoantigens. Immune-infiltrated tumour regions exhibited ongoing immunoediting, with either loss of heterozygosity in human leukocyte antigens or depletion of expressed neoantigens. We identified promoter hypermethylation of genes that contain neoantigenic mutations as an epigenetic mechanism of immunoediting. Our results suggest that the immune microenvironment exerts a strong selection pressure in early-stage, untreated non-small-cell lung cancers that produces multiple routes to immune evasion, which are clinically relevant and forecast poor disease-free survival.

Suggested Citation

  • Rachel Rosenthal & Elizabeth Larose Cadieux & Roberto Salgado & Maise Al Bakir & David A. Moore & Crispin T. Hiley & Tom Lund & Miljana Tanić & James L. Reading & Kroopa Joshi & Jake Y. Henry & Ehsan , 2019. "Neoantigen-directed immune escape in lung cancer evolution," Nature, Nature, vol. 567(7749), pages 479-485, March.
    • Handle: RePEc:nat:nature:v:567:y:2019:i:7749:d:10.1038_s41586-019-1032-7
    DOI: 10.1038/s41586-019-1032-7
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    Cited by:

    1. Guozhong Jiang & Zhizhong Wang & Zhenguo Cheng & Weiwei Wang & Shuangshuang Lu & Zifang Zhang & Chinedu A. Anene & Faraz Khan & Yue Chen & Emma Bailey & Huisha Xu & Yunshu Dong & Peinan Chen & Zhongxi, 2024. "The integrated molecular and histological analysis defines subtypes of esophageal squamous cell carcinoma," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Sijia Cui & Nicholas McGranahan & Jing Gao & Peng Chen & Wei Jiang & Lingrong Yang & Li Ma & Junfang Liao & Tian Xie & Congying Xie & Tariq Enver & Shixiu Wu, 2023. "Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Juan Blanco-Heredia & Carla Anjos Souza & Juan L. Trincado & Maria Gonzalez-Cao & Samuel Gonçalves-Ribeiro & Sara Ruiz Gil & Dmytro Pravdyvets & Samandhy Cedeño & Maurizio Callari & Antonio Marra & An, 2024. "Converging and evolving immuno-genomic routes toward immune escape in breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    4. Phuong H. D. Nguyen & Martin Wasser & Chong Teik Tan & Chun Jye Lim & Hannah L. H. Lai & Justine Jia Wen Seow & Ramanuj DasGupta & Cheryl Z. J. Phua & Siming Ma & Jicheng Yang & Sheena D/O Suthen & Wa, 2022. "Trajectory of immune evasion and cancer progression in hepatocellular carcinoma," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Tian-Yu Song & Min Long & Hai-Xin Zhao & Miao-Wen Zou & Hong-Jie Fan & Yang Liu & Chen-Lu Geng & Min-Fang Song & Yu-Feng Liu & Jun-Yi Chen & Yu-Lin Yang & Wen-Rong Zhou & Da-Wei Huang & Bo Peng & Zhen, 2021. "Tumor evolution selectively inactivates the core microRNA machinery for immune evasion," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    6. Philip East & Gavin P. Kelly & Dhruva Biswas & Michela Marani & David C. Hancock & Todd Creasy & Kris Sachsenmeier & Charles Swanton & Julian Downward & Sophie de Carné Trécesson, 2022. "RAS oncogenic activity predicts response to chemotherapy and outcome in lung adenocarcinoma," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    7. Huapan Fang & Zhaopei Guo & Jie Chen & Lin Lin & Yingying Hu & Yanhui Li & Huayu Tian & Xuesi Chen, 2021. "Combination of epigenetic regulation with gene therapy-mediated immune checkpoint blockade induces anti-tumour effects and immune response in vivo," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
    8. Ming Chen & Runzhe Chen & Ying Jin & Jun Li & Xin Hu & Jiexin Zhang & Junya Fujimoto & Shawna M. Hubert & Carl M. Gay & Bo Zhu & Yanhua Tian & Nicholas McGranahan & Won-Chul Lee & Julie George & Xiao , 2021. "Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    9. Chandler D. Gatenbee & Ann-Marie Baker & Ryan O. Schenck & Maximilian Strobl & Jeffrey West & Margarida P. Neves & Sara Yakub Hasan & Eszter Lakatos & Pierre Martinez & William C. H. Cross & Marnix Ja, 2022. "Immunosuppressive niche engineering at the onset of human colorectal cancer," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    10. Haodong Xu & Ruifeng Hu & Xianjun Dong & Lan Kuang & Wenchao Zhang & Chao Tu & Zhihong Li & Zhongming Zhao, 2024. "ImmuneApp for HLA-I epitope prediction and immunopeptidome analysis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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