Clonal architecture in mesothelioma is prognostic and shapes the tumour microenvironment.

Malignant Pleural Mesothelioma (MPM) is typically diagnosed 20-50 years after exposure to asbestos and evolves along an unknown evolutionary trajectory. To elucidate this path, we conducted multi-regional exome sequencing of 90 tumour samples from 22 MPMs acquired at surgery. Here we show that exomic intratumour heterogeneity varies widely across the cohort. Phylogenetic tree topology ranges from linear to highly branched, reflecting a steep gradient of genomic instability. Using transfer learning, we detect repeated evolution, resolving 5 clusters that are prognostic, with temporally ordered clonal drivers. BAP1/-3p21 and FBXW7/-chr4 events are always early clonal. In contrast, NF2/-22q events, leading to Hippo pathway inactivation are predominantly late clonal, positively selected, and when subclonal, exhibit parallel evolution indicating an evolutionary constraint. Very late somatic alteration of NF2/22q occurred in one patient 12 years after surgery. Clonal architecture and evolutionary clusters dictate MPM inflammation and immune evasion. These results reveal potentially drugable evolutionary bottlenecking in MPM, and an impact of clonal architecture on shaping the immune landscape, with potential to dictate the clinical response to immune checkpoint inhibition

Detecting Clonal Structural Alterations from Multi-regional Profiling of Malignant Pleural Mesotheliomas

Malignant Pleural Mesothelioma (MPM) is a pleural tumour associated with asbestos exposure. There is a long latency period of 30-40 years between asbestos exposure and disease presentation, highlighting an unknown evolutionary trajectory. Throughout the latent years, different somatic genomic lesions are acquired by the growing tumour. In contrast to other malignancies, MPMs display modest single nucleotide mutational burden but a high frequency of structural alterations, in particular large-scale chromosomal losses. In this thesis, I explore how multiregional sequencing data can shed light into inter- and intra-tumour heterogeneity of MPM, as well as the various cellular processes shaping the tumour evolution. I investigated the mutational diversity between different resected sites within individual tumours, as well as between MPMs in order to infer genomic alterations that occurred during early tumour evolution and potential clonal drivers of tumour development. The existence of branched tumour evolution and widespread heterogeneity in MPMs was demonstrated: Copy number analysis revealed recurring truncal large-scale (aneuploidy level) and the focal losses of the tumour suppressor genes BAP1, PTPN13, FBXW7, CTCLT1, NF2, MYH9, EP300 and oncogenes NSD2, TEC and MTOR. Targeted sequencing of the recurring truncal losses of 1p36, 3p21 and 9p21 was used to attempt to identify deletion breakpoints. Gene fusion analysis revealed the extent of chromosomal rearrangements in MPM tumours, as well as the formation of potentially important fusions such as the potentially oncogenic CACNA1D-ERC2 fusion, in-frame PARD3BSTAB1 fusion, and intergenic fusions resulting in BAP1 and MTAP truncation. Finally, by analysis of gene fusion breakpoints, non-homologous end joining and alternative endjoining were revealed to be the likely structural mechanisms generating early extensive chromosomal rearrangements, in conjunction with truncal losses in homologous recombination and Hippo pathway genes. These truncal genomic alterations are likely to exist throughout the tumour, and potentially drive cancer progression, as they include mesothelioma associated genes, oncogenes, and tumour suppressor genes. Thus, identifying them highlights potential Achilles’ heels for drug targeting and treatment.</p

Jama et al Data from SCNA and gene pathway analysis

An MS Excel file with 12 tabbed sheets 1. SCNA-BAP1: SCNA data from Zhang 2021 of CN segments harbouring the BAP1 gene  2. KEGG gene list: list of KEGG genes for Hippo pathway, Homologous recombination pathway and Non-Homologous End Joining pathway 3. SCNA -HIPPO: SCNA data from Zhang 2021 of CN segments harbouring Hippo pathway genes 4. SCNA-HR: SCNA data from Zhang 2021 of CN segments harbouring HR pathway genes 5. SCNA-NHEJ: SCNA data from Zhang 2021 of CN segments harbouring NHEJ pathway genes 6. TRUNCAL HIPPO: Truncal SCNA changes in Hippo pathway genes according to sample and fusion status 7. TRUNCAL HR: Truncal SCNA changes in HR pathway genes according to sample and fusion status 8. TRUNCAL NHEJ: Truncal SCNA changes in NHEJ pathway genes according to sample and fusion status 9. TRUNCAL + BRANCH HIPPO: SCNA changes in Hippo pathway genes according to sample and fusion status 10. TRUNCAL + BRANCH HR: SCNA changes in HR pathway genes according to sample and fusion status 11. TRUNCAL + BRANCH NHEJ: SCNA changes in NHEJ pathway genes according to sample and fusion status 12. SUMMARY: Two-by-two contingency tables of gene fusion positive/gene fusion negative tumours </p

Gene fusions during the early evolution of mesothelioma correlate with impaired DNA repair and Hippo pathways

Malignant pleural mesothelioma (MPM), a rare cancer a long latency period (up to 40 years) between asbestos exposure and disease presentation. The mechanisms coupling asbestos to recurrent somatic alterations are poorly defined. Gene fusions arising through genomic instability may create novel drivers during early MPM evolution. We explored the gene fusions that occurred early in the evolutionary history of the tumor. We conducted multiregional whole exome sequencing (WES) of 106 samples from 20 patients undergoing pleurectomy decortication and identified 24 clonal nonrecurrent gene fusions, three of which were novel (FMO9P‐OR2W5, GBA3, and SP9). The number of early gene fusion events detected varied from zero to eight per tumor, and presence of gene fusions was associated with clonal losses involving the Hippo pathway genes and homologous recombination DNA repair genes. Fusions involved known tumor suppressors BAP1, MTAP, and LRP1B, and a clonal oncogenic fusion involving CACNA1D‐ERC2, PARD3B‐NT5DC2, and STAB2‐NT5DC2 fusions were also identified as clonal fusions. Gene fusions events occur early during MPM evolution. Individual fusions are rare as no recurrent truncal fusions event were found. This suggests the importance of early disruption of these pathways in generating genomic rearrangements resulting in potentially oncogenic gene fusions.</p