Molecular Characteristics of Conjunctival Melanoma Using Whole-Exome Sequencing

Abstract

onjunctival melanoma (CM) is a rare but potentially deadly ocular malignant condition, with a 10-year disease-specific mortality of 9% to 35%. 1 Primary treatment of CM consists of local surgical excision with wide margins and adjuvant therapy (cryotherapy, brachytherapy, and/or topical application of mitomycin C). However, regional and systemic metastasis occurs in approximately 30% of patients within 3 years, and there are no effective treatments for metastatic disease. 1 Conjunctival melanoma appears to be a distinct entity compared with other mucosal melanomas. In contrast to these malignant conditions, CM incidence is often associated with UV sunlight exposure. Conjunctival melanoma is also associated with a higher 5-year survival rate (86%) compared with melanomas of the gastrointestinal tract (4%-33%), urogenital tract (7%-22%), and respiratory mucosal tissues (0%-31%); this difference is possibly related to earlier detection or differences in the innate aggressiveness of the tumor. 2 The molecular attributes of CM remain poorly characterized, which is a problem that has hindered the development of novel therapies. One study 3 reported mutations in BRAF and NRAS in 29% and 18% of CMs, respectively, but the technology used in this study did not allow for a comprehensive assessment of driver mutations, chromosome copy number aberrations (CNAs), and mutational signatures. In the present study, whole-exome sequencing (WES) permits more comprehensive characterization of the molecular biology of CM. MethodsFive formalin-fixed, paraffin-embedded, archival CM specimens were selected based on the availability of sufficient tissue for testing. Tumor DNA was extracted from all 5 and prepared for WES. Ethical approval was obtained from the University of Miami institutional review board for this study, IMPORTANCE Conjunctival melanoma (CM) is a highly aggressive ocular cancer for which treatment options are limited; the molecular pathogenesis is poorly understood. OBJECTIVE To identify the molecular characteristics of CM using next-generation whole-exome sequencing (WES).DESIGN, SETTING, AND PARTICIPANTS Whole-exome sequencing was performed on tumor DNA extracted from the archived specimens of 5 patients with CM who had been treated with surgical excision between 2006 and 2011. These samples were analyzed at a tertiary academic ocular oncology referral center using a customized bioinformatic pipeline.MAIN OUTCOMES AND MEASURES Sample analyses were designed to detect driver mutations, chromosome copy number aberrations, and mutation signatures. RESULTSThe study's 5 patients ranged in age from 51 to 77 years. Four of the 5 were female, and all were white. Mutations were detected in known oncogenes, including BRAF, NRAS, NF1, EGFR, ALK, TERT, and APC. None of the mutations associated with uveal melanoma were found. All samples demonstrated a C→T mutation signature typical of UV-induced DNA damage. The most common CNA was a gain in chromosome 6p. CONCLUSIONS AND RELEVANCEIn these 5 patients, WES allowed identification of m...

Conjunctival melanoma copy number alterations and correlation with mutation status, tumor features, and clinical outcome

“…Amplifications of 6p21‐25 were found in up to 61% of CoM in our cohort. Regional chr 6p amplification was previously identified by our group and others (Griewank et al, ; Lake et al, ; Swaminathan et al, ), and has also been documented in CM (Höglund et al, ). The Histone Cluster 1 (6p22.2) was the most common amplification in our study, which is implicated in various cancers and is thought to impact epigenetic and post‐transcriptional modification (King, Waxman, & Stauss, ), but was not associated with the clinical outcome in the current study.…”

“…In CoM, such mutations are reported in 8%–54%, 0%–18%, 0%–11%, and 32%, respectively (Beadling et al, ; El‐Shabrawi, Radner, Muellner, Langmann, & Hoefler, ; Gear, Williams, Kemp, & Roberts, ; Goldenberg‐Cohen et al, ; Griewank et al, ; Lake et al, ; Larsen et al, ; Populo, Soares, Rocha, Silva, & Lopes, ; Scholz et al, ; Spendlove et al, ). Whole exome sequencing on a relatively small series of 5 CoMs identified mutually exclusive NF1 , BRAF , and NRAS driver mutations in 20%, 60%, and 20% of samples, respectively, alongside other individual cancer‐associated and epigenetic regulator mutations, such as those of EGFR and the TERT promoter (Swaminathan et al, ). Most recently, a larger study using next‐generation sequencing discovered mutations of NF1 in 21 of 63 (33%) CoMs, BRAF in 16 (25%), NRAS in 11 (17%), and KRAS in a single sample (Scholz et al, ).…”

Clinical features and survival outcomes of ocular melanoma in a multi-ethnic Asian cohort

“…This is similar to previous studies on UM in Chinese and Koreans which reported an earlier age of presentation for UM (mean age 48 to 53 years) 11,13 compared to Caucasians (mean age 60 years) 9 . For CM, Chinese and Indian patients also have a younger age at presentation (mean age 43 to 54 years) 15,17 compared to Caucasians (mean age 55 to 65 years) 6 . Survival analysis in our study was focused on patients with non-metastatic disease as tumour behaviour and prognostic factors of primary non-metastatic and metastatic disease differ greatly 20 .…”

“…The most common symptom at presentation was blurring of vision, which is consistent with previous studies in Caucasian cohorts 27,28 . Previous studies have similarly indicated that the majority of UM patients are symptomatic at the time of diagnosis 4 while CM is often asymptomatic 6 . UM is more likely to affect vision especially if within the visual axis as opposed to tumours arising from the bulbar conjunctiva, the most common location of CM.…”

The 2018 World Health Organization Classification of Cutaneous, Mucosal, and Uveal Melanoma: Detailed Analysis of 9 Distinct Subtypes Defined by Their Evolutionary Pathway

“…151 In contrast, conjunctival melanomas are probably a mixture of high-CSD melanoma, having evidence of solar elastosis and genomic changes indicative of high UV exposure, and of low-CSD melanomas. 152,153 Pathway VII: Melanoma Arising in a Congenital Nevus…”