Abstract 5693: Mesotheliomas harbor early clonal fusions involving both tumor suppressor drivers and novel oncogenic alterations
Authors: Jama Maymun , Hollox Edward J , Nakas Apostolos , Brannan Lee , Dawson Alan , dudbridge frank , Fennell Dean 
Published: June 2022

Abstract
MPM is a pleural tumour associated with asbestos exposure. There is a long latency period of more than 40 years between asbestos exposure and disease presentation, highlighting an unknown evolutionary trajectory. Throughout the latent years, different somatic structural alterations are acquired by the growing tumour. To elucidate this evolutionary path, we conducted multiregional whole exome sequencing (WES) of 106 samples (5 or 4 regions per tumour and a matched blood sample) for 20 patients as part of the MEDUSA study (Mesothelioma evolution: Drugging somatic alterations). Gene fusions have been shown to have a clinical, diagnostic, and therapeutic significance i.e., the driver fusion EM4-ALK expressed in a minority of peritoneal mesotheliomas. Previous descriptions of gene fusions in MPM have mostly been limited to isolated case reports, with the only genome-wide assessment study identifying fusion events involving known MPM genes including NF2 and BAP1. Therefore, our aim was to identify potential truncal inter- and intra-chromosomal rearrangements generating gene fusions that occurred early in the evolutionary history of the tumour. We used two software tools - Meerkat (v.0.189) and Delly (v0.8.7), to identify gene fusion events in the regional tumour sites for a given patient. We identified tumour-specific events by filtering against the calls made on exome sequence from the matched blood of each patient. Finally, we identified truncal gene fusion events as ones observed across all regional samples of a particular patient. We validated the gene fusions by PCR and Sanger sequencing of the breakpoint junctions. Further work was carried out to identify truncal fusion transcripts at the transcriptomic level using RNA sequencing data (Arriba v2.1.0) and compare the gene fusion predictions detected at the genomic level made by WES. We found a total of 24 truncal fusion events, 3 of which were novel (FMO9P-OR2W5, GBA3 and SP9). Tumour suppressor genes involved included (BAP1, MTAP, and LRP1B). Oncogenic fusions involved (CACNA1D-ERC2). In addition to this, our analysis revealed truncal copy number neutral events such as in-frame PARD3B-NT5DC2 and out of frame STAB2-NT5DC2. Moreover, with transcriptome sequencing we characterised the fusion transcripts events initially detected by WES (i.e. fusions involving AHRR and B3GAL2 genes). Our findings suggest that gene fusions events occur during early evolution with marked heterogeneity across the cohort (no recurrent truncal fusions event were observed in a subset). Some truncal fusion events are likely to be drivers of cancer progression, as they involve mesothelioma associated genes (e.g. MTAP and BAP1). The role of other gene fusions remains unclear, and larger studies are needed to clarify whether somatic rearrangements of these genes are involved in tumour progression in MPM.
Citation Format: Maymun Jama, Edward J Hollox, Apostolos Nakas, Lee Brannan, Alan Dawson, frank dudbridge, Dean Fennell. Mesotheliomas harbor early clonal fusions involving both tumor suppressor drivers and novel oncogenic alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5693.