The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma

Abstract

Merkel cell carcinoma (MCC) is a rare but highly aggressive cutaneous neuroendocrine tumor. Merkel cell polyomavirus (MCPyV) may contribute to tumorigenesis in a subset of tumors via inhibition of tumor suppressors such as retinoblastoma (RB1) by mutated viral T-antigens, but the molecular pathogenesis of MCPyV-negative MCC is largely unexplored. Through our MI-ONCOSEQ precision oncology study we performed integrative sequencing on two cases of MCPyV-negative MCC, as well as a validation cohort of 14 additional MCC cases (n=16). In addition to previously identified mutations in TP53, RB1, and PIK3CA, we discovered activating mutations of oncogenes including HRAS and loss-of-function mutations in PRUNE2 and NOTCH family genes in MCPyV-negative MCC. MCPyV-negative tumors also displayed high overall mutation burden (10.09 +/− 2.32 mutations per Mb) and were characterized by a prominent UV-signature pattern with C > T transitions comprising 85% of mutations. In contrast, mutation burden was low in MCPyV-positive tumors (0.40 +/− 0.09 mutations per Mb) and lacked a UV signature. These findings suggest a potential ontologic dichotomy in MCC, characterized by either viral-dependent or UV-dependent tumorigenic pathways.

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

“…More extensive studies are needed to confirm these associations with MCPyV status; however, these and other epidemiologic factors may explain why our rate of detected MCPyV across both modalities is slightly lower than often reported. Our assays were conducted with appropriate controls, and our rate of MCPyV positivity is similar to previous reports from our institution with a variety of detection approaches (6,(37)(38)(39), suggesting that our lower rate of MCPyV positivity in this study is related to the patient cohort rather than technical factors.…”

“…All samples were run in triplicate. The MKL-2 cell line was used as the standard for one viral copy/cell genome, as previously described (6,14). Negative controls included purified, distilled water and DNA from HEK 293 (human embryonic kidney 293) cells.…”

“…To determine regions of MCPyV transcript in highest abundance in MCC, we evaluated previously collected RNAseq data from MCPyV-positive tumors (6). The most consistently detected region was at the 5′ end of LTAg exon 2 (also shared by ALTO and 57kT transcripts) (Supplementary Figure S2) (3,23,24), overlapping with a commonly targeted region for qPCR detection of MCPyV ( Figure 1).…”

“…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).…”

Merkelzellkarzinom: kutane Manifestation einer hochmalignen Prä-/pro-B-Zell-Neoplasie?

“…Etwa 80 % der MZK sind assoziiert mit dem Merkelzell-Polyomavirus (MCPyV), das 2008 identifiziert wurde [15]. Die übri-gen 20 % der MZK sind MCPyV-negativ und zeichnen sich durch charakteristische UV-assoziierte Schäden auf genomischer Ebene aus [16,17] "Prä-/pro-B-Zell"-Hypothese: B-Vorläuferzellen als zellulärer Ursprung der Merkelzellkarzinome Sowohl der morphologisch blastäre Phä-notyp als auch das immunhistochemische Expressionsmuster (TdT-, PAX-5-und CD56-Expression) können da-zu führen, dass v. a. der intermediäre Typ der MZK mit kutanen Manifestationen lymphoproliferativer Neoplasien verwechselt wird [30,31]. Buresh et al [32] …”