High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms

摘要: Merkel Cell Polyomavirus (MCPyV) is the etiological agent of majority Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express oncogenes. Which molecular mechanisms promote integration, if distinct integration patterns exist, and occurs preferentially at loci with specific chromatin states unknown. We here combined short long-read (nanopore) next-generation sequencing present first high-resolution analysis site structure in MCC cell lines as well primary tumor material. We find two main types structure: Linear chromosomal breakpoints map closely together, complex exhibit local amplification genomic sequences flanking DNA. Sequence suggests linear are produced during replication by defective/linear into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest mediated microhomology-mediated break-induced replication, MMBIR. Furthermore, we show ChIP-Seq RNA-Seq preferably integrates open provide evidence oncogene expression driven promoter region, rather than transcription from juxtaposed promoters. Taken explain characteristics may also a model for other oncogenic viruses such papillomaviruses.