Genomic landscape of uveal melanoma

Uveal melanoma (UM) is the most common cancer of the adult eye which can manifest as a highly aggressive form approximately half of the time. Here a comprehensive landscape of genetic alterations in UMs is described. It was identified by integrating copy number alterations (CNAs), and transcriptomic and whole exome sequencing data from 207 primary UMs. Focal copy number analysis with the GISTIC algorithm refined the boundaries of chromosomal segments with chromosomal gains or losses and candidate cancer genes within these segments were identified. Chromosome 8q24.3 was the region most frequently amplified in UMs, being detected in 72% of tumours. A comparison of focal copy gains and losses with that described by a pan-cancer study revealed Plectin 1 as a candidate gene within the 8q24.3 amplicon. Integration of copy number and transcriptomic data also revealed enrichment of genes within pathways leading to activation of NF-kappa B, WNT signaling and RNA splicing. Using a complementary bioinformatics approach, additional novel mutations in known dominant UM driver genes (GNAQ, GNA11, BAP1, SF3B1, EIFIAX and CYSLTR2) were identified and an accurate estimate of the frequencies of mutations in each gene were obtained. Finally, integration of data obtained from CNAs with mutational and transcriptome data reveled homozygous deletions, protein damaging mutations and gene fusions that targeted chromatin modifiers, and specifically genes encoding components of the human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling complex. Genes from the BAF complex (ARID1A and ARID1B) and the PBAF complex (PHF10) were subjected to functional loss through CNAs, gene fusions and mutations. Two of these chromatin modifiers (ARID1B and PHF10) map to chromosome 6q whose loss is associated with metastasis in a subset of UMs, and an ARID1B fusion is found in a tumour with a BAP1 mutation that subsequently underwent metastasis. In conclusion, this study provides a comprehensive overview of the landscape of genomic alterations in UM, identifying candidate genes in regions of CNAs and providing further insights into the altered pathways of tumour development and progression.Open Acces

Mutant MYO1F alters the mitochondrial network and induces tumor proliferation in thyroid cancer

Familial aggregation is a significant risk factor for the development of thyroid cancer and Familial Non-Medullary Thyroid Cancer (FNMTC) accounts for 5-7% of all NMTC. Whole Exome Sequencing analysis in the family affected by FNMTC with oncocytic features where our group previously identified a predisposing locus on chromosome 19p13.2, revealed a novel heterozygous mutation (c.400G>A, NM_012335; p.Gly134Ser) in exon 5 of MYO1F, mapping to the linkage locus. In the thyroid FRTL-5 cell model stably expressing the mutant MYO1F p.Gly134Ser protein we observed an altered mitochondrial network, with increased mitochondrial mass and a significant increase of both intracellular and extracellular Reactive Oxygen Species, compared to cells expressing the wild-type protein or carrying the empty vector. The mutation conferred a significant advantage in colony formation, invasion and anchorage independent growth. These data were corroborated by in vivo studies in zebrafish, since we demonstrated that the mutant MYO1F p.Gly134Ser, when overexpressed, can induce proliferation in whole vertebrate embryos, compared to the wild-type one. MYO1F screening in additional 192 FNMTC families identified another variant in exon 7, which leads to exon skipping, and is predicted to alter the ATP-binding domain in MYO1F. Our study identified for the first time a role for MYO1F in NMTC. This article is protected by copyright. All rights reserved

Integrative Copy Number Analysis of Uveal Melanoma Reveals Novel Candidate Genes Involved in Tumorigenesis Including a Tumor Suppressor Role for PHF10/BAF45a

Uveal melanoma is a primary malignancy of the eye with oncogenic mutations in , and additional mutations in (usually associated with LOH of Chr 3), , or . There are other characteristic chromosomal alterations, but their significance is not clear. To investigate genes driving chromosomal alterations, we integrated copy number, transcriptome, and mutation data from three cohorts and followed up key findings. We observed significant enrichment of transcripts on chromosomes 1p, 3, 6, 8, and 16q and identified seven shared focal copy number alterations (FCNAs) on Chr 1p36, 2q37, 3, 6q25, 6q27, and 8q24. Integrated analyses revealed clusters of genes in focal copy number regions whose expression was associated with metastasis and worse overall survival. This included genes from Chr 1p36, 3p21, and 8q24.3. At Chr 6q27, we identified two tumors with homozygous deletion of and one with a frameshift mutation with concomitant loss of the wild-type allele. Downregulation of in uveal melanoma cell lines and tumors altered a number of biological pathways including development and adhesion. These findings provide support for a role for as a novel tumor suppressor at Chr 6q27. Integration of copy number, transcriptome, and mutation data revealed novel candidate genes playing a role in uveal melanoma pathogenesis and a potential tumor suppressor role for

Driver Mutations in Uveal Melanoma: Associations With Gene Expression Profile and Patient Outcomes

Frequent mutations have been described in the following 5 genes in uveal melanoma (UM): BAP1, EIF1AX, GNA11, GNAQ, and SF3B1. Understanding the prognostic significance of these mutations could facilitate their use in precision medicine. To determine the associations between driver mutations, gene expression profile (GEP) classification, clinicopathologic features, and patient outcomes in UM. Retrospective study of patients with UM treated by enucleation by a single ocular oncologist between November 1, 1998, and July 31, 2014. Clinicopathologic features, patient outcomes, GEP classification (class 1 or class 2), and mutation status were recorded. The study cohort comprised 81 participants. Their mean age was 61.5 years, and 37% (30 of 81) were female. The GEP classification was class 1 in 35 of 81 (43%), class 2 in 42 of 81 (52%), and unknown in 4 of 81 (5%). BAP1 mutations were identified in 29 of 64 (45%), GNAQ mutations in 36 of 81 (44%), GNA11 mutations in 36 of 81 (44%), SF3B1 mutations in 19 of 81 (24%), and EIF1AX mutations in 14 of 81 (17%). Sixteen of the mutations in BAP1 and 6 of the mutations in EIF1AX were previously unreported in UM. GNAQ and GNA11 mutations were mutually exclusive. BAP1, SF3B1, and EIF1AX mutations were almost mutually exclusive with each other. Using multiple regression analysis, BAP1 mutations were associated with class 2 GEP and older patient. EIF1AX mutations were associated with class 1 GEP and the absence of ciliary body involvement. SF3B1 mutations were associated with younger patient age. GNAQ mutations were associated with the absence of ciliary body involvement and greater largest basal diameter. GNA11 mutations were not associated with any of the analyzed features. Using Cox proportional hazards modeling, class 2 GEP was the prognostic factor most strongly associated with metastasis (relative risk, 9.4; 95% CI, 3.1-28.5) and melanoma-specific mortality (relative risk, 15.7; 95% CI, 3.6-69.1) (P < .001 for both). After excluding GEP class, the presence of BAP1 mutations was the factor most strongly associated with metastasis (relative risk, 10.6; 95% CI, 3.4-33.5) and melanoma-specific mortality (relative risk, 9.0; 95% CI, 2.8-29.2) (P < .001 for both). BAP1, SF3B1, and EIF1AX mutations occur during UM tumor progression in an almost mutually exclusive manner and are associated with different levels of metastatic risk. These mutations may have value as prognostic markers in UM

Abstract 3390: Clonal evolution in uveal melanoma

Abstract Introduction: Uveal melanoma is the most common primary cancer of the eye and frequently gives rise to lethal metastatic disease. Uveal melanoma can be divided into two prognostic subgroups based on gene expression profiling: class 1 (low metastatic risk) and class 2 (high metastatic risk). Uveal melanoma is also notable for a characteristic set of driver mutations that cluster into two groups. The first group consists of mutually exclusive gain-of-function mutations in members of the Gαq signaling pathway (GNAQ, GNA11, CYSLTR2 and PLCB4), which are present in almost all uveal melanomas. These mutations are not prognostic, and are thought to represent initiating events that are insufficient alone to cause full malignant transformation. The second group consists of near-mutually exclusive mutations in BAP1, SF3B1, and EIF1AX. These are thought to occur later in tumor progression and are prognostic of patient outcome. These molecular features are associated with characteristic chromosome copy number variations (CNV). The purpose of this study was to investigate the life history of primary uveal melanomas by inferring the intratumoral evolution of these genetic events. Methods: Exome or whole genome sequencing data from 151 primary uveal melanomas were evaluated with a new bioinformatic pipeline for calling mutations and CNVs. Data from this analysis were used in downstream subclonality algorithms to determine intratumor evolutionary patterns within individual tumor samples. Results: A Gαq mutation was found in 98.7% of tumors, which were all mutually exclusive with each other. BAP1 mutations were found in 46%, SF3B1 mutations in 23%, and EIF1AX mutations in 14% of tumors, all of which were mutually exclusive with each other except for 4 cases. We identified novel driver mutations in 20% of the remaining tumors. In most samples that contained a BAP1 or SF3B1 mutation, this driver mutation and associated CNVs were present in 100% of tumor cells. However, in 14% of cases with BAP1 mutations, 100% of tumor cells exhibited monosomy 3, but a BAP1 mutation was present in a smaller subclone, suggesting that the BAP1 mutation occurred after the loss of chromosome 3. In tumors with EIF1AX mutations, this mutation was consistently found in 100% of tumor cells, with 6p gain being found in a smaller subclone in 45% of cases, suggesting that 6p gain usually occurs after the EIF1AX mutation in this subgroup of tumors. Conclusions: The driver mutations and associated CNVs that are characteristic of uveal melanoma occur very early in tumor evolution and are followed by the accumulation of silent passenger mutations, consistent with a punctuated evolution model in which an initial “big bang” is followed by neutral non-Darwinian evolution. These unexpected findings alter prevailing theories of uveal melanoma progression, and could have a significant impact on patient management. Citation Format: Matthew G. Field, Hima Anbunathan, Michael A. Durante, Louie Cai, Karam Alawa, Christina L. Decatur, Stefan Kurtenbach, Anne Bowcock, J. William Harbour. Clonal evolution in uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3390. doi:10.1158/1538-7445.AM2017-3390</jats:p

Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma

Uveal melanoma is the most common primary cancer of the eye and often results in fatal metastasis. Here, we describe mutations occurring exclusively at arginine-625 in splicing factor 3B subunit 1 (SF3B1) in low-grade uveal melanomas with good prognosis. Thus, uveal melanoma is among a small group of cancers associated with SF3B1 mutation, and these mutations denote a distinct molecular subset of uveal melanomas

Integrated genomics point to immune vulnerabilities in pleural mesothelioma.

Funder: Libor Fund grant from the UK Department of Health, by the British Lung Foundation and by the Asmarley FoundationFunder: UK Medical Research CouncilPleural mesothelioma is an aggressive malignancy with limited effective therapies. In order to identify therapeutic targets, we integrated SNP genotyping, sequencing and transcriptomics from tumours and low-passage patient-derived cells. Previously unrecognised deletions of SUFU locus (10q24.32), observed in 21% of 118 tumours, resulted in disordered expression of transcripts from Hedgehog pathways and the T-cell synapse including VISTA. Co-deletion of Interferon Type I genes and CDKN2A was present in half of tumours and was a predictor of poor survival. We also found previously unrecognised deletions in RB1 in 26% of cases and show sub-micromolar responses to downstream PLK1, CHEK1 and Aurora Kinase inhibitors in primary mesothelioma cells. Defects in Hippo pathways that included RASSF7 amplification and NF2 or LATS1/2 mutations were present in 50% of tumours and were accompanied by micromolar responses to the YAP1 inhibitor Verteporfin. Our results suggest new therapeutic avenues in mesothelioma and indicate targets and biomarkers for immunotherapy