Genomic and multi-omics of malignant pleural mesothelioma using long-read sequencing

Abstract

Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer characterised by extensive genomic instability and poor prognosis. It has a latency period of up to 40 years after exposure to asbestos. Although prior genomic studies have investigated MPM using short-read sequencing, the contribution of large-scale structural variations (SVs) to this malignancy is not yet fully understood. This thesis presents a comprehensive analysis of somatic SVs in MPM using Oxford Nanopore Technology (ONT) long-read whole genome sequencing (WGS), integrating epigenetic and transcriptomic data to elucidate the functional impact of these alterations.

Long-read WGS applied to MPM primary cell lines and tumour-matched normal samples revealed a wide spectrum of SVs, including large-scale deletion, and complex rearrangements, many of which were undetectable by short-read methods. Biallelic inactivation of driver tumour suppressor genes such as NF2, BAP1, and LATS2 was identified through compound events involving copy loss and structural disruption. This biallelic inactivation of significant mutant genes in MPM was identified by both short-read and long-read WGS. Additionally, novel SVs affecting known cancer-related genes, such as WEE1, GPC6, and PRKN, and retrotransposon insertions mediating the loss of MPM driver genes such as BAP1 and CDKN2A were characterised.

Integration with transcriptomic and methylome data demonstrated that SVs, promoter hypermethylation, and gene dosage alteration jointly influence gene expression. Notably, WEE1 and GPC6 overexpression were significantly associated with reduced survival in MPM from TCGA data, supporting these genes’ potential as prognostic biomarkers.

Thus, this work presents the utility of long-read sequencing in resolving the complex and novel SV landscape of MPM and provides new insights into tumour evolution, gene regulation, and clinical stratification. The findings establish a foundation for future research into the timing of somatic events, the role of transposable elements, and the development of SV-based biomarkers and therapeutic targets in MPM.