LT and SOX9 expression are associated with gene sets that distinguish Merkel cell polyomavirus-positive and -negative Merkel cell carcinoma

Abstract

Background: Merkel cell carcinoma (MCC) is an aggressive malignant neuroendocrine tumour. There are two subsets of MCC, one related to Merkel cell polyomavirus (MCPyV) and the other to ultraviolet (UV) radiation. MCPyV-positive and MCPyV-negative MCCs have been considered to be different tumours, since the former type harbours few DNA mutations and is not related to UV radiation, and the latter usually arises in sun-exposed areas and may be found in conjunction with other keratinocytic tumours, mostly squamous cell carcinomas. Two viral oncoproteins, large T antigen (LT, coded by MCPyV_gp3) and small T antigen (sT, coded by MCPyV_gp4), promote different carcinogenic pathways.

Objectives: We hypothesized that the biological behaviours of MCPyV-positive and MCPyV-negative MCCs are different. We aimed to determine which genes are differentially expressed in MCPyV-positive and MCPyV-negative MCC, to describe the mutational burden and the most frequently mutated genes in the two MCC types, and to identify the clinical and molecular factors that may be related to patient survival.

Methods: Ninety-two cases with a diagnosis of MCC were identified from the medical databases of the participating centres.To study gene expression, a customized panel of 172 genes was developed. Gene expression profiling was performed with nCounter Technology (NanoString Technologies, Seattle, WA, USA).For mutational studies, a customized panel of 26 genes was designed. Somatic single nucleotide variants (SNVs) were identified following the best practices GATK workflow for somatic mutations.

Results: The expression of LT enabled the series to be divided into two groups, (LT-positive, n=55; LT-negative, n=37). Genes differentially expressed in LT-negative cases were related to epithelial differentiation, especially SOX9, or proliferation and cell cycle (MYC, CDK6), among others. Congruently, LT displayed lower expression in SOX9-positive cases, and differentially expressed genes in SOX9-positive cases were related to epithelial/squamous differentiation.In LT-positive cases, the mean SNV frequency was 4.3 per case, and 10 per case in LT-negative cases (p=0.03).The expression of SNAI1 (HR=1.046, 95% CI=1.007-1.086, p=0.021) and CDK6 (HR=1.049, 95% CI=1.020-1.080, p=0.001) were identified as risk factors in a multivariate survival analysis.

Conclusions: Tumours with weak expression of LT tend to co-express genes related to squamous differentiation and cell cycle, and to have a higher mutational burden. These findings are congruent with those of earlier studies.