Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma

Jenette Creaney, Ann Marie Patch, Venkateswar Addala, Sophie A. Sneddon, Katia Nones, Ian M. Dick, Y. C.Gary Lee, Felicity Newell, Ebony J. Rouse, Marjan M. Naeini, Olga Kondrashova, Vanessa Lakis, Apostolos Nakas, David Waller, Annabel Sharkey, Pamela Mukhopadhyay, Stephen H. Kazakoff, Lambros T. Koufariotis, Aimee L. Davidson, Priya Ramarao-MilneOliver Holmes, Qinying Xu, Conrad Leonard, Scott Wood, Sean M. Grimmond, Raphael Bueno, Dean A. Fennell, John V. Pearson, Bruce W. Robinson, Nicola Waddell

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

Background: Malignant pleural mesothelioma (MPM) has a poor overall survival with few treatment options. Whole genome sequencing (WGS) combined with the immune features of MPM offers the prospect of identifying changes that could inform future clinical trials. Methods: We analysed somatic mutations from 229 MPM samples, including previously published data and 58 samples that had undergone WGS within this study. This was combined with RNA-seq analysis to characterize the tumour immune environment. Results: The comprehensive genome analysis identified 12 driver genes, including new candidate genes. Whole genome doubling was a frequent event that correlated with shorter survival. Mutational signature analysis revealed SBS5/40 were dominant in 93% of samples, and defects in homologous recombination repair were infrequent in our cohort. The tumour immune environment contained high M2 macrophage infiltrate linked with MMP2, MMP14, TGFB1 and CCL2 expression, representing an immune suppressive environment. The expression of TGFB1 was associated with overall survival. A small subset of samples (less than 10%) had a higher proportion of CD8 T cells and a high cytolytic score, suggesting a ‘hot’ immune environment independent of the somatic mutations. Conclusions: We propose accounting for genomic and immune microenvironment status may influence therapeutic planning in the future.

Original languageEnglish
Article number58
JournalGenome Medicine
Volume14
Issue number1
DOIs
Publication statusPublished - Dec 2022

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