Interlocking core regulatory circuits enable viral hijacking in Merkel cell carcinoma

Merkel Cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer. The conditions and cell type(s) of MCC are unknown. Virus positive MCC (VP-MCC) is driven by T antigens expressed from integrated Merkel cell polyomavirus (MCPyV). We found that VP-MCC required lineage-specific neuroendocrine transcription factors (TFs), including ATOH1, INSM1, ISL1, LHX3, POU4F3, and SOX2 that were central to core regulatory (CR) transcriptional circuitry. MCPyV small T antigen and host CR TFs co-bound VP-MCC super enhancers while T antigen expression was directly regulated by LHX3 and ISL1, establishing an interlocking network between host CR circuitry and the oncovirus. Moreover, MCPyV integration sites were enriched near VP- MCC super enhancers, further suggesting a functional relationship between viral oncogenesis and core neuroendocrine circuitry. Overall design: Genome-wide profiles for histone marks, DNase hypersensitivity, transcription factors, and 3D loops of active chromatin (AQuA-HiChIP).