Next generation sequencing of Cytokeratin 20-negative Merkel cell carcinoma reveals ultraviolet-signature mutations and recurrent TP53 and RB1 inactivation

Abstract

Merkel cell carcinoma is a rare but highly aggressive cutaneous neuroendocrine carcinoma. Cytokeratin-20 (CK20) is expressed in approximately 95% of Merkel cell carcinomas and is useful for distinction from morphologically similar entities including metastatic small cell lung carcinoma. Lack of CK20 expression may make diagnosis of Merkel cell carcinoma more challenging, and has unknown biological significance. Approximately 80% of CK20-positive Merkel cell carcinomas are associated with the oncogenic Merkel cell polyomavirus. Merkel cell carcinomas lacking Merkel cell polyomavirus display distinct genetic changes from Merkel cell polyomavirus-positive Merkel cell carcinoma, including RB1 inactivating mutations. Unlike CK20-positive Merkel cell carcinoma, the majority of CK20-negative Merkel cell carcinomas are Merkel cell polyomavirus-negative, suggesting CK20-negative Merkel cell carcinomas predominantly arise through virus-independent pathway(s) and may harbor additional genetic differences from conventional Merkel cell carcinoma. Hence, we analyzed 15 CK20-negative Merkel cell carcinoma tumors (ten Merkel cell polyomavirus-negative, four Merkel cell polyomavirus-positive, and one undetermined) using the Ion Ampliseq Comprehensive Cancer Panel, which assesses copy number alterations and mutations in 409 cancer-relevant genes. Twelve tumors displayed prioritized high-level chromosomal gains or losses (average 1.9 per tumor). Non-synonymous high confidence somatic mutations were detected in 14 tumors (average 11.9 per tumor). Assessing all somatic coding mutations, an ultraviolet-signature mutational profile was present, and more prevalent in Merkel cell polyomavirus-negative tumors. Recurrent deleterious tumor suppressor mutations affected TP53 (9/15, 60%), RB1 (3/15, 20%), and BAP1 (2/15, 13%). Oncogenic activating mutations included PIK3CA (3/15, 20%), AKT1 (1/15, 7%)) and EZH2 (1/15, 7%). In conclusion, CK20-negative Merkel cell carcinoma display overlapping genetic changes with CK20-positive Merkel cell carcinoma, including RB1 mutations restricted to Merkel cell polyomavirus-negative tumors. However, some CK20-negative Merkel cell carcinomas harbor mutations not previously described in Merkel cell carcinoma. Hence, CK20-negative Merkel cell carcinomas harbor diverse oncogenic drivers which may represent therapeutic targets in individual tumors.

Metastatic Merkel cell carcinoma response to nivolumab

“…Mutational load was not examined in this case. However, based on recent genomic findings in MCPyV-negative tumors, we would predict this MCPyV-negative case to display a high mutational burden with associated neoantigens that may result in susceptibility to immunotherapy [11, 19].

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“…Pathology demonstrated morphologic and immunohistochemical (strongly cytokeratin-20, neuron specific enolase and CD56 positive and thyroid transcription factor-1 negative) findings in both lesions consistent with MCC. Polymerase chain reaction performed on deoxyribonucleic acid extracted from formalin-fixed, paraffin-embedded tumor tissue alongside appropriate controls using a previously described protocol demonstrated that the tumor lacked detectable Merkel cell polyomavirus (MCPyV) large T antigen and small T antigen [10, 11]. Staging fluorodeoxyglucose-positron emission tomography/computed tomography (FDG-PET/CT) revealed lesions in right upper lung, right upper back, right axilla and right adrenal gland consistent with metastatic disease (Fig.…”

Neurofilament is superior to cytokeratin 20 in supporting cutaneous origin for neuroendocrine carcinoma

“…For 22 MCC cases from 14 unique patients, the results of MCPyV immunohistochemistry previously performed for other studies were available. 2,35,36 The SmCC cohort consisted of 61 tumours from 60 unique patients, with primary sites including lung (27), bladder (18), cervix (3), gastrointestinal tract (3), sinonasal tract (2), ovary (3), breast (1), prostate (1), thymus (1) and larynx (1). Five negative lymph nodes from non-MCC cases served as negative controls.…”

Cytokeratin 20 negative Merkel cell carcinoma consistent with negative Merkel cell polyomavirus

“…Harms et al reported that 80% of CK20-positive MCC patients were associated with MCPyV oncogenes. Next-generation sequencing techniques were used to show the presence of virus-independent mechanisms such as BAP1, or TP53 and RB1 inactivation in CK20-negative MCC patients, and were able to interpret these as findings of CK20 negativity in MCC to date [10].…”