Identification of a CD8+ T-cell response to a predicted neoantigen in malignant mesothelioma

ABSTRACT

Neoantigens present unique and specific targets for personalized cancer immunotherapy strategies. Given the low mutational burden yet immunotherapy responsiveness of malignant mesothelioma (MM) when compared to other carcinogen-induced malignancies, identifying candidate neoantigens and T cells that recognize them has been a challenge. We used pleural effusions to gain access to MM tumor cells as well as immune cells in order to characterize the tumor-immune interface in MM. We characterized the landscape of potential neoantigens from SNVs identified in 27 MM patients and performed whole transcriptome sequencing of cell populations from 18 patient-matched pleural effusions. IFNγ ELISpot was performed to detect a CD8+ T cell responses to predicted neoantigens in one patient. We detected a median of 68 (range 7–258) predicted neoantigens across the samples. Wild-type non-binding to mutant binding predicted neoantigens increased risk of death in a model adjusting for age, sex, smoking status, histology and treatment (HR: 33.22, CI: 2.55–433.02, p = .007). Gene expression analysis indicated a dynamic immune environment within the pleural effusions. TCR clonotypes increased with predicted neoantigen burden. A strong activated CD8+ T-cell response was identified for a predicted neoantigen produced by a spontaneous mutation in the ROBO3 gene. Despite the challenges associated with the identification of bonafide neoantigens, there is growing evidence that these molecular changes can provide an actionable target for personalized therapeutics in difficult to treat cancers. Our findings support the existence of candidate neoantigens in MM despite the low mutation burden of the tumor, and may present improved treatment opportunities for patients.

KEYWORDS:

• Malignant mesothelioma
• neoantigen
• pleural effusion
• tumor-immune interface

Abbreviations

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Acknowledgments

The authors would like to acknowledge Frans H. J. Claas and Ilias I. N. Doxiadis for supplying the single antigen-expressing lines used in this study.

Ethics approval and consent to participate

This study was approved by the Human Research Ethics Committee of at Sir Charles Gairdner Hospital and the University of Western Australia (Perth, Western Australia). Written informed consent from all participants was obtained.

Availability of data and materials

The dataset supporting the conclusions of this article is available in the NCBI SRA repository, [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA419420].

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

SS, JC and BWSR conceived the study. RA performed the sequencing. CR and SM performed the ELISpot assay and T cell culture. SS, ID and JC performed the data analysis. SB and RA provided the neoantigen prediction pipeline and assisted with transcriptome analysis. SS and ID performed the statistical analysis. SS and JC drafted the manuscript. All authors read and approved the final manuscript.

Supplementary material

Supplemental data for this article can be accessed on the publisher’s website.

Additional information

Funding

This work was supported in part by the Housing Industry of Australia Charitable Foundation, the Insurance Commission of Western Australia and the Australian National Health and Medical Research Council (NHMRC) (APP1089404 and APP1107043). SS receives a scholarship from the Ross Divett Foundation. BR is supported by a NHMRC Practitioner fellowship (APP1108638). The funding agencies played no part in study design, data analysis, interpretation of data or manuscript preparation.