Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma

Abstract

Background Merkel cell carcinoma (MCC) is a rare but aggressive skin cancer with limited treatment possibilities. Merkel cell tumors display with neuroendocrine features and Merkel cell polyomavirus (MCPyV) infection in the majority (80%) of patients. Although loss of histone H3 lysine 27 trimethylation (H3K27me3) has been shown during MCC tumorigenesis, epigenetic dysregulation has largely been overlooked. Methods We conducted global DNA methylation profiling of clinically annotated MCC primary tumors, metastatic skin tumors, metastatic lymph node tumors, paired normal tissues, and two human MCC cell lines using the Illumina Infinium EPIC DNA methylation BeadArray platform. Results Significant differential DNA methylation patterns across the genome are revealed between the four tissue types, as well as based on MCPyV status. Furthermore, 964 genes directly regulated by promoter or gene body DNA methylation were identified with high enrichment in neuro-related pathways. Finally, our findings suggest that loss of H3K27me3 occupancy in MCC is attributed to KDM6B and EZHIP overexpression as a consequence of promoter DNA hypomethylation. Conclusions We have demonstrated specific DNA methylation patterns for primary MCC tumors, metastatic MCCs, and adjacent-normal tissues. We have also identified DNA methylation markers that not only show potential diagnostic or prognostic utility in MCC management, but also correlate with MCC tumorigenesis, MCPyV expression, neuroendocrine features, and H3K27me3 status. The identification of DNA methylation alterations in MCC supports the need for further studies to understand the clinical implications of epigenetic dysregulation and potential therapeutic targets in MCC.

Epigenetic Dysregulations in Merkel Cell Polyomavirus-Driven Merkel Cell Carcinoma

“…One study found an association between hypomethylation at PD-1 gene in relation to patient outcome, when used as prognostic marker [ 119 ], while a lack of diagnostic significance has been reported for several candidate genes, such as p14 ARF /CDKN2A , MGMT , PTCH1, and members of the RASSF family [ 113 , 115 , 116 , 117 , 118 ]. The potential diagnostic and prognostic utility of KDM6B gene hypomethylation in MCPyV-driven MCC management has also been pointed out [ 121 ]. No data have been reported on DNA methylation as a therapy target for MCPyV-driven MCC.…”

“…A recent analysis reported hypermethylation of RASSF2/-5C/-10 genes ranging from 7-23% in MCCs and absent in normal tissues, while no correlation between RASSFs methylation status and MCC characteristics (primary vs. metastatic), or MCPyV-positivity, was found [ 116 ]. The DNA methylation profile has been recently investigated in MCPyV-positive and -negative primary and metastatic MCC tumors and cell lines compared with paired normal tissues [ 121 ]. Specific DNA methylation patterns exhibiting potential clinical relevance for MCC management and correlating with MCC onset, MCPyV gene expression, neuroendocrine features, and H3K27me3 status have been described [ 121 ].…”

“…The DNA methylation profile has been recently investigated in MCPyV-positive and -negative primary and metastatic MCC tumors and cell lines compared with paired normal tissues [ 121 ]. Specific DNA methylation patterns exhibiting potential clinical relevance for MCC management and correlating with MCC onset, MCPyV gene expression, neuroendocrine features, and H3K27me3 status have been described [ 121 ]. In particular, hypomethylation at Lysine Demethylase 6B (KDM6B), a gene involved in the negative regulation of H3K27me3 [ 150 , 151 ], has been hypothesized to prompt KDM6B overexpression in MCPyV-driven MCC, ultimately leading to a global reduction of H3K27me3 [ 121 ].…”

DNA-methylation patterns imply a common cellular origin of virus- and UV-associated Merkel cell carcinoma

“…Secondly, the direct use of tumor samples would certainly have advantages; however, cell lines are extremely useful for determining cell origin patterns as they do not suffer from sample impurity. Two recent studies addressed differences in DNA-methylation between VP- and UV-MCCs using either MCC tissue or cell lines [ 56 , 57 ]. Consistent with the here reported results, both studies found a relatively low number of DMPs (470 and 2260) with the majority of DMPs being hypomethylated in VP-MCC samples in these reports as well.…”

“…Consistent with the here reported results, both studies found a relatively low number of DMPs (470 and 2260) with the majority of DMPs being hypomethylated in VP-MCC samples in these reports as well. However, neither group inferred tissue of origin signatures since clustering of MCC with samples from dermis, epidermis, and nerve tissues resulted in a clear separation of MCC tissues or because MCC cell lines clustered together with other neuroendocrine entities [ 56 , 57 ]. The PCA derived scoring of the present study allowed conclusion on the tissue of origin by deconvolution of the data into its underlying components, exploiting the purity of cell lines.…”