Abstract 2221: Whole transcriptome sequencing reveals oncogenic fusions in melanoma
Authors: Darabi Sourat , Elliott Andrew , Braxton David R. , Zeng Jia , Poorman Kelsey , Swensen Jeffrey , Gibney Geoffrey T. , Moser Justin C. , Phung Thuy , Atkins Michael B. , In Gino K. , Korn Wolfgang Michael , Eisenberg Burton L. , Demeure Michael J. 
Published: July 2021

Introduction: Oncogenic gene fusions are frequently identified in different cancers; however, the exact incidence of oncogenic fusions in melanoma is not well defined. Several targeted therapies are approved and considered the standard of care for patients whose solid or hematologic tumors harbor particular gene fusions, but their role as targets in melanoma also remains undelineated. We sought to determine the prevalence of oncogenic fusions in metastatic or locally advanced melanoma.

Methods: We retrospectively analyzed data from formalin-fixed paraffin-embedded (FFPE) tumor samples sent to a commercial CLIA-certified laboratory (Caris Life Sciences) from February 2019 to July 2020. Samples were profiled by next-generation sequencing of a 592-gene DNA panel, whole transcriptome sequencing, and immunohistochemistry (IHC).

Results: Melanoma specimens were analyzed from 1,255 subjects, of whom 478 (38.1%) were female and 777 (61.9%) were male, with a median age of 67 years. Of these specimens, 780 (63.1%) were from metastatic sites. We identified 33 (2.6%) cases with in-frame oncogenic fusions (14 novel) including 21 BRAF fusions and 4 RAF1 fusions, as well as fusions involving PRKCA (n=4), TERT (n=2), AXL (n=1), and FGFR3 (n=1). PD-L1 expression by IHC (SP142 or 28-8 antibody) was detected in 512 (42.5%) specimens, including 10 (32.3%) of the fusion-positive tumors, while 572 (47.4%) specimens were TMB-High (≥10 mutations/Mb), including 11 (33.3%) of the fusion-positive tumors, suggesting these patients may respond to immunotherapy. We identified 796 (63.4%) cases with RAS/RAF pathogenic or likely pathogenic mutations, including 373 (30.0%) BRAF p.V600X mutations. With the exception of a single BRAF p.S467L (Class 3, “kinase-dead”) mutation, the absence of BRAF mutations in BRAF fusion-positive tumors suggests these fusions are oncogenic drivers. However, tumors harboring PRKCA and TERT fusions were each detected with at least one MAPK pathway co-alteration (NRAS, NF1, or BRAF p.V600E mutation). Fusion transcripts with unknown pathogenicity were also detected in 668 (53.2%) cases. RNA expression analysis of key molecular pathways (including Wnt/β-catenin, PI3K/AKT/MTOR, DNA repair, INFG, and JAK/STAT) showed a high degree of variability among fusion-positive tumors and other mutational subgroups, which may reflect the heterogeneity common to melanoma, prior treatments or development of various resistance mechanisms.

Conclusions: Oncogenic gene fusions are rare in melanoma when compared with other genetic variants. We identified potentially actionable fusions as well as co-alterations in fusion-positive cases, with notably mutual exclusivity of BRAF fusions and p.V600X mutations. The data suggest that targetable variants, including oncogenic fusions, may be identified in melanoma with comprehensive tumor profiling and provide patients with personalized treatment or clinical trial options.

Citation Format: Sourat Darabi, Andrew Elliott, David R. Braxton, Jia Zeng, Kelsey Poorman, Jeffrey Swensen, Geoffrey T. Gibney, Justin C. Moser, Thuy Phung, Michael B. Atkins, Gino K. In, Wolfgang Michael Korn, Burton L. Eisenberg, Michael J. Demeure. Whole transcriptome sequencing reveals oncogenic fusions in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2221.