Identification of Novel Oncogenic Signaling Pathways using Viral Perturbations

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Project Summary Merkel cell carcinoma (MCC) is a primary neuroendocrine carcinoma of the skin; a highly aggressive cancer with a 40% 2-year mortality rate. While the incidence of MCC is 25-fold less frequent than melanoma, it is 13-fold more likely to cause death. In a remarkably short time, MCC has gone from an unknown cancer to the poster child for the success of checkpoint blockade therapy (CBT). With the application of powerful new tools to the study of MCC, it can be expected that the next 7 years will continue to bring remarkable new discoveries with the potential to increase our insight not only into this cancer but into many other cancers as well. There are two forms of MCC with different etiologies but nearly identical presentations. Virus-negative (VN) MCC is caused by excessive sunlight exposure resulting in ultraviolet (UV) induced damage to the genome, a pattern typical for other skin cancers including melanoma, squamous cell carcinoma and basal cell carcinoma. In contrast, virus-positive (VP) MCC is caused by integration of the MCPyV viral DNA into the host cell genome with expression of a truncated form of Large T antigen (LT) and an intact Small T antigen (ST). Despite the near identical phenotypes, VN-MCC and VP-MCC have striking differences in their overall genome mutation rate. The VN-MCC has a much higher tumor mutational burden (TMB, median ~ 40 mutations/mB) than VP-MCC (median 2/mB). VN-MCC has near universal inactivation of the RB1 and TP53 tumor suppressor genes as well as in the lysine methyl transferase genes KMT2C and KMT2D (also known as MLL3 and MLL4). In addition, VN-MCC frequently contains amplification of MYCL or MYC. In contrast, VP- MCC can be recognized by the presence of integrated MCPyV genomes, the absence of UV mutation signature, a low TMB, and few if any mutations. Instead, VP-MCC expresses MCPyV LT that functionally inactivates RB while ST recruits MYCL to the EP400 chromatin modifying complex to induce profound changes in gene expressions. These distinctions between VP-MCC and VN-MCC raises the question of what we can learn about each form of MCC that can inform us about the other. We propose that the distinct mechanisms of oncogenesis in VN-MCC and VP-MCC provides us with the unique opportunity to use orthogonal methodologies to gain a clearer insight into MCC. We propose that expression of MCPyV LT and ST is capable of inducing the relevant phenotypic changes observed in VP-MCC that occur through the inactivating mutations of RB1, TP53, and KMT2C/D genes and amplification of MYCL in VN-MCC. Our cancer program has made remarkable progress in distinguishing between VN-MCC and VP-MCC and is now poised to exploit this opportunity to leverage insights gained from each type of MCC to inform the other that will lead to significant insights into this disease. Furthermore, we expect that these insights will provide useful insights into the oncogenic pathways that contribute to other cancer types.