Abstract NG07: Genomic and transcriptomic analysis reveals incremental disruption of key signaling pathways during melanoma evolution

Thousands of tumors have been sequenced through large-scale genomic profiling efforts, and from these studies the mutational drivers of most tumor subtypes have been catalogued. Nevertheless, the order in which these mutations occur is poorly understood. This is because most tumors are sequenced at a late stage, revealing only the aftermaths of the evolutionary processes that led to their transformation. A better understanding of tumor evolution would reveal biomarkers for progression and identify crucial steps in tumorigenesis, which could be subject to future treatments. In order to delineate the evolution of melanoma, we identified cases of melanomas that were adjacent to their intact, remnant precursors (e.g. a melanoma adjacent to a nevus from which it originated). We separately microdissected the precursor and descendent areas from these cases and performed matched DNA- and RNA- sequencing on the microdissected tissues. From these data, we were able to infer the order of genetic alterations that occur during the evolution of each melanoma and the transcriptomic changes that accompanied these mutations. In total, we analyzed 230 histopathologically distinct areas (normal, precursor, and descendent tissues) from 82 patients. Somatic alterations known to activate MAP-kinase signaling occurred at the earliest stages and continued to accumulate as individual tumors evolved, indicating that MAPK signaling ramps up during progression. TERT promoter mutations were detectable in 52% of intermediate stage lesions and 85% of melanomas, regardless of tumor thickness. Telomerase expression strongly correlated with the presence of a promoter mutation, confirming that telomerase is upregulated early during progression. The transition from the benign to the malignant state was marked by the emergence of mutations affecting genes involved in chromatin remodeling and accompanied by downregulation of genes modulated by polycomb repressive complex-2 (PRC2). Mono-allelic inactivation of G1/S checkpoint genes were occasionally found in earlier histopathologic stages, whereas bi-allelic alterations, predicted to ablate checkpoint function, occurred at or after the transition to invasive melanoma. p53- and PI3-kinase pathway mutations appeared later, only becoming evident in thicker primary melanomas. Comparisons between paired primary melanomas and metastases did not reveal oncogenic alterations specifically associated with metastatic progression. The types of somatic alterations further revealed the mutational forces that shaped each melanoma during its progression. Point mutations with signatures of UV-radiation induced DNA damage were more common in the trunks of the phylogenetic trees and tended to occur prior to the transition to invasive melanoma. In contrast, copy number alterations were more branchial and tended to occur at or after the transition to invasive melanoma. In aggregate, these patterns indicate that UV radiation is the predominant mutagen shaping melanocytic neoplasms until the transition to invasive melanoma, at which point chromosomal instability prevails. Overall, this study delineates the sequential order in which key signaling pathways are disrupted during melanoma evolution, highlighting replicative senescence, G1/S arrest, and chromatin organization as barriers that have to be overcome for the transition to melanoma, whereas amplification of MAPK signaling and inactivation of the p53 and PI3-kinase pathways are associated with the progression to more advanced primaries. Citation Format: A. Hunter Shain, Nancy M. Joseph, Richard Yu, Jamal Benhamida, Shanshan Liu, Tarl Prow, Beth Ruben, Jeffrey North, Laura Pincus, Iwei Yeh, Robert Judson, Boris C. Bastian. Genomic and transcriptomic analysis reveals incremental disruption of key signaling pathways during melanoma evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr NG07.