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Polyomavirus and neuroendocrine regulomes converge to establish tumor dependencies

ABSTRACT: Merkel Cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer often driven by Merkel cell polyomavirus T antigens. The epigenomic mechanisms driving MCC are poorly understood. We show that virus positive MCC (VP-MCC) super enhancer networks are committed to and controlled by lineage-specific neuroendocrine transcription factors (TFs) including LHX3, ISL1, ATOH1, INSM1, SOX2 and POU4F3. These VP-MCC TFs are central to core regulatory (CR) transcriptional circuitry, essential for growth, and co-bind enhancers with polyomavirus small T antigen. We establish that T antigen expression is directly regulated by LHX3 and ISL1, establishing a positive feedback autoregulatory circuitry for a neuroendocrine state.

ORGANISM(S): Homo sapiens

PROVIDER: GSE147406 | GEO | 2021/01/01

REPOSITORIES: GEO

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Project description:Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine tumor with high mortality rates. Merkel cell polyomavirus (MCPyV), identified in the majority of MCC, may drive tumorigenesis via viral T antigens. However, mechanisms underlying pathogenesis in MCPyV-negative MCC remain poorly understood. To nominate genes contributing to pathogenesis of MCPyV-negative MCC, we performed DNA microarray analysis on 30 MCCs. MCPyV status of MCCs was determined by PCR for viral DNA and RNA. 1593 probe-sets were differentially expressed between MCPyV-negative and -positive MCC, with significant differential expression defined as at least 2-fold change in either direction and p-value of ≤ 0.05. MCPyV-negative tumors showed decreased RB1 expression, whereas MCPyV-positive tumors were enriched for immune response genes. Validation studies included immunohistochemistry demonstration of decreased RB protein expression in MCPyV-negative tumors and increased peritumoral CD8+ T lymphocytes surrounding MCPyV-positive tumors. In conclusion, our data suggest that loss of RB1 expression may play an important role in tumorigenesis of MCPyV-negative MCC. Functional and clinical validation studies are needed to determine whether this tumor suppressor pathway represents an avenue for targeted therapy. We used microarrays to characterize global gene expression patterns related to Merkel cell polyomavirus status in Merkel cell carcinoma. Furthermore, we compared Merkel cell carcinoma to less aggressive primary cutaneous carcinomas. We utilized flash-frozen tumor tissue from primary Merkel cell carcinomas, metastatic Merkel cell carcinomas, primary cutaneous squamous cell carcinomas, and basal cell carcinomas. Merkel cell carcinoma cell lines, which represent a pure population of tumor cells, were also included. Merkel cell polyomavirus status was determined at the DNA and RNA level using multiple primers for viral T-antigen and capsid protein sequences. This Series represents two analyses - one with new Samples normalized together, and another with some of the new Samples re-normalized with Samples previously submitted under Series GSE13355. The latter group contain 'renormalized' in the titles.

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Polyomavirus and neuroendocrine regulomes converge to establish tumor dependencies

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