title: 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 ~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 (10 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.
authors.affiliation: Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Department of Dermatology, University of Michigan Health System, Ann Arbor, MI, USA.|Michigan Center for Translational Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Paul W
authors.initials: PW
authors.lastname: Harms
authors.affiliation: Department of Pathology, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Angela M B
authors.initials: AM
authors.lastname: Collie
authors.affiliation: Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Michigan Center for Translational Pathology, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Hovelson
authors.affiliation: Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Michigan Center for Translational Pathology, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Andi K
authors.initials: AK
authors.lastname: Cani
authors.affiliation: Department of Dermatology, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Monique E
authors.initials: ME
authors.lastname: Verhaegen
authors.affiliation: Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Department of Dermatology, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Rajiv M
authors.initials: RM
authors.lastname: Patel
authors.affiliation: Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Department of Dermatology, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Fullen
authors.affiliation: Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Michigan Center for Translational Pathology, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Kei
authors.initials: K
authors.lastname: Omata
authors.affiliation: Department of Dermatology, University of Michigan Health System, Ann Arbor, MI, USA.|Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Andrzej A
authors.initials: AA
authors.lastname: Dlugosz
authors.affiliation: Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Michigan Center for Translational Pathology, University of Michigan Health System, Ann Arbor, MI, USA.|Department of Urology, University of Michigan Health System, Ann Arbor, MI, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Tomlins
authors.affiliation: Department of Pathology, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Billings
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D015266:Carcinoma, Merkel Cell / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D053554:Keratin-20 / Q000235:genetics; D008297:Male; D008875:Middle Aged; D009154:Mutation; D056286:Retinoblastoma Binding Proteins / Q000235:genetics; D012878:Skin Neoplasms / Q000235:genetics*; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D044767:Ubiquitin-Protein Ligases / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; C507499:KRT20 protein, human; D053554:Keratin-20; C000606393:RB1 protein, human; D056286:Retinoblastoma Binding Proteins; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D044767:Ubiquitin-Protein Ligases