Mutational landscape of MCPyV-positive and MCPyV-negative Merkel cell carcinomas with implications for immunotherapy

Abstract

Merkel cell carcinoma (MCC) is a rare but highly aggressive cutaneous neuroendocrine carcinoma, associated with the Merkel cell polyomavirus (MCPyV) in 80% of cases. To define the genetic basis of MCCs, we performed exome sequencing of 49 MCCs. We show that MCPyV-negative MCCs have a high mutation burden (median of 1121 somatic single nucleotide variants (SSNVs) per-exome with frequent mutations in RB1 and TP53 and additional damaging mutations in genes in the chromatin modification (ASXL1, MLL2, and MLL3), JNK (MAP3K1 and TRAF7), and DNA-damage pathways (ATM, MSH2, and BRCA1). In contrast, MCPyV-positive MCCs harbor few SSNVs (median of 12.5 SSNVs/tumor) with none in the genes listed above. In both subgroups, there are rare cancer-promoting mutations predicted to activate the PI3K pathway (HRAS, KRAS, PIK3CA, PTEN, and TSC1) and to inactivate the Notch pathway (Notch1 and Notch2). TP53 mutations appear to be clinically relevant in virus-negative MCCs as 37% of these tumors harbor potentially targetable gain-of-function mutations in TP53 at p.R248 and p.P278. Moreover, TP53 mutational status predicts death in early stage MCC (5-year survival in TP53 mutant vs wild-type stage I and II MCCs is 20% vs. 92%, respectively; P = 0.0036). Lastly, we identified the tumor neoantigens in MCPyV-negative and MCPyV-positive MCCs. We found that virus-negative MCCs harbor more tumor neoantigens than melanomas or non-small cell lung cancers (median of 173, 65, and 111 neoantigens/sample, respectively), two cancers for which immune checkpoint blockade can produce durable clinical responses. Collectively, these data support the use of immunotherapies for virus-negative MCCs.

Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay

“…Although reports on prognostic significance have been mixed regarding whether the presence of MCPyV detection is associated with improved outcome, a recent large prospective study of 282 cases using multimodal MCPyV detection with qPCR and IHC demonstrated significantly better outcome for MCPyV-positive tumors (28). In addition, the presence of MCPyV may influence tumor sensitivity to immunotherapy and targeted therapy (5,29,30). Hence, detection of MCPyV in MCC tumors has diagnostic and prognostic utility and may have a future role in guiding management.…”

“…MCPyV is a DNA virus that likely mediates tumorigenesis via large T antigen (LTAg) binding to the tumor suppressor RB1 and small T antigen (sTAg) upregulation of oncoprotein stability and mTOR activation (1,2). Unlike MCPyV-positive tumors, MCPyV-negative MCC tumors display high mutation burdens, TP53 and RB1 mutations, and UV-signature mutational profiles, suggesting a molecular dichotomy between MCPyV-positive and MCPyV-negative tumors that may have translational relevance (4)(5)(6)(7).…”

Rationale For Immune-Based Therapies in Merkel Polyomavirus-Positive and -Negative Merkel Cell Carcinomas

“…Specifically, several recent studies have shown that MCPyV-negative MCCs have a very high mutation burden (median 1,121 somatic single nucleotide variants per exome). These are dominated by C > T transitions, characteristic of UV-induced DNA damage [88][89][90]. This UV-induced signature was not observed in MCPyV-positive tumors and the mutation burden was 19-fold lower (median 12.5 somatic single nucleotide variants per exome) indicating that these tumor types arise through distinct mechanisms [88][89][90].…”

“…Conversely, several others have reported no significant survival difference between the two groups [85][86][87]. Importantly, genetic analysis indicates that these two subsets are etiologically distinct [88][89][90]. Specifically, several recent studies have shown that MCPyV-negative MCCs have a very high mutation burden (median 1,121 somatic single nucleotide variants per exome).…”

“…Strikingly, on average, MCPyV-negative tumors were found to contain more tumor neoantigens than either melanomas or nonsmall-cell lung cancers suggesting that these virus-negative MCCs have the potential to be highly immunogenic [88]. Furthermore, among virus-negative tumors, a subset expressed PD-L1 and these PD-L1-positive tumors harbor a higher mutational burden as compared with PD-L1-negative tumors, which may reflect immune recognition within these tumors [89].…”