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Published in: Journal of Experimental & Clinical Cancer Research 1/2022

Open Access 01-12-2022 | Metastasis | Research

Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma

Authors: Runzhe Chen, Jun Li, Junya Fujimoto, Lingzhi Hong, Xin Hu, Kelly Quek, Ming Tang, Akash Mitra, Carmen Behrens, Chi-Wan Chow, Peixin Jiang, Latasha D. Little, Curtis Gumbs, Xingzhi Song, Jianhua Zhang, Dongfeng Tan, John V. Heymach, Ignacio Wistuba, P. Andrew Futreal, Don L. Gibbons, Lauren A. Byers, Jianjun Zhang, Alexandre Reuben

Published in: Journal of Experimental & Clinical Cancer Research | Issue 1/2022

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Abstract

Background

Lung cancer is the leading cause of cancer death, partially owing to its extensive heterogeneity. The analysis of intertumor heterogeneity has been limited by an inability to concurrently obtain tissue from synchronous metastases unaltered by multiple prior lines of therapy.

Methods

In order to study the relationship between genomic, epigenomic and T cell repertoire heterogeneity in a rare autopsy case from a 32-year-old female never-smoker with left lung primary late-stage lung adenocarcinoma (LUAD), we did whole-exome sequencing (WES), DNA methylation and T cell receptor (TCR) sequencing to characterize the immunogenomic landscape of one primary and 19 synchronous metastatic tumors.

Results

We observed heterogeneous mutation, methylation, and T cell patterns across distinct metastases. Only TP53 mutation was detected in all tumors suggesting an early event while other cancer gene mutations were later events which may have followed subclonal diversification. A set of prevalent T cell clonotypes were completely excluded from left-side thoracic tumors indicating distinct T cell repertoire profiles between left-side and non left-side thoracic tumors. Though a limited number of predicted neoantigens were shared, these were associated with homology of the T cell repertoire across metastases. Lastly, ratio of methylated neoantigen coding mutations was negatively associated with T-cell density, richness and clonality, suggesting neoantigen methylation may partially drive immunosuppression.

Conclusions

Our study demonstrates heterogeneous genomic and T cell profiles across synchronous metastases and how restriction of unique T cell clonotypes within an individual may differentially shape the genomic and epigenomic landscapes of synchronous lung metastases.
Appendix
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Metadata
Title
Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma
Authors
Runzhe Chen
Jun Li
Junya Fujimoto
Lingzhi Hong
Xin Hu
Kelly Quek
Ming Tang
Akash Mitra
Carmen Behrens
Chi-Wan Chow
Peixin Jiang
Latasha D. Little
Curtis Gumbs
Xingzhi Song
Jianhua Zhang
Dongfeng Tan
John V. Heymach
Ignacio Wistuba
P. Andrew Futreal
Don L. Gibbons
Lauren A. Byers
Jianjun Zhang
Alexandre Reuben
Publication date
01-12-2022
Publisher
BioMed Central
Published in
Journal of Experimental & Clinical Cancer Research / Issue 1/2022
Electronic ISSN: 1756-9966
DOI
https://doi.org/10.1186/s13046-022-02361-x

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