Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas

• Published in: Journal of clinical virology 2011-11, Vol.52 (3), p.272-275
• Main Authors: Lee, Sherry, Paulson, Kelly G, Murchison, Elizabeth P, Afanasiev, Olga K, Alkan, Can, Leonard, J. Helen, Byrd, David R, Hannon, Gregory J, Nghiem, Paul
• Format: Article
• Language: English
• Subjects: Allergy and Immunology; Base Sequence; Biological and medical sciences; Carcinoma, Merkel Cell - diagnosis; Carcinoma, Merkel Cell - genetics; Carcinoma, Merkel Cell - pathology; Carcinoma, Merkel Cell - virology; DNA, Viral - biosynthesis; Fundamental and applied biological sciences. Psychology; Human viral diseases; Humans; Infectious Disease; Infectious diseases; MCV-miR-M1; Medical sciences; Merkel cell carcinoma; Merkel cell polyomavirus; Merkel cell polyomavirus - genetics; Microbiology; MicroRNA; MicroRNAs - biosynthesis; MicroRNAs - genetics; Miscellaneous; Polyomavirus Infections - genetics; Polyomavirus Infections - pathology; Polyomavirus Infections - virology; Real-Time Polymerase Chain Reaction; RNA, Viral - biosynthesis; Sequence Alignment; Sequence Analysis, RNA; Tumors; Viral diseases; Virology
• ISSN: 1386-6532; 1873-5967
• DOI: 10.1016/j.jcv.2011.08.012

Abstract Background Merkel cell polyomavirus (MCPyV) is present in approximately 80% of human Merkel cell carcinomas (MCCs). A previous in silico prediction suggested MCPyV encodes a microRNA (miRNA) that may regulate cellular and viral genes. Objectives To determine the presence and prevalence of a putative MCPyV-encoded miRNA in human MCC tumors. Study design Over 30 million small RNAs from 7 cryopreserved MCC tumors and 1 perilesional sample were sequenced. 45 additional MCC tumors were examined for expression of an MCPyV-encoded mature miRNA by reverse transcription real-time PCR. Results An MCPyV-encoded mature miRNA, “MCV-miR-M1-5p”, was detected by direct sequencing in 2 of 3 MCPyV-positive MCC tumors. Although a precursor miRNA, MCV-miR-M1, had been predicted in silico and studied in vitro by Seo et al., no MCPyV-encoded miRNAs have been directly detected in human tissues. Importantly, the mature sequence of MCV-miR-M1 found in vivo was identical in all 79 reads obtained but differed from the in silico predicted mature miRNA by a 2-nucleotide shift, resulting in a distinct seed region and a different set of predicted target genes. This mature miRNA was detected by real-time PCR in 50% of MCPyV-positive MCCs ( n = 38) and in 0% of MCPyV-negative MCCs ( n = 13). Conclusions MCV-miR-M1-5p is expressed at low levels in 50% of MCPyV-positive MCCs. This virus-encoded miRNA is predicted to target genes that may play a role in promoting immune evasion and regulating viral DNA replication.