BACKGROUND Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin caused by either the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet-induced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep sequencing studies of MCC have identified significant differences between the number and types of point mutations, copy number alterations, and structural variants between virus-positive and virus-negative tumors. However, it has been challenging to reliably distinguish between virus positive and UV damaged MCC. METHODS In this study, we assembled a cohort of 71 MCC patients and performed deep sequencing with OncoPanel, a clinically implemented, next-generation sequencing assay targeting over 400 cancer-associated genes. To improve the accuracy and sensitivity for virus detection compared to traditional PCR and IHC methods, we developed a hybrid capture baitset against the entire MCPyV genome and software to detect integration sites and structure. RESULTS Sequencing from this approach revealed distinct integration junctions in the tumor genome and generated assemblies that strongly support a model of microhomology-initiated hybrid, virus-host, circular DNA intermediate that promotes focal amplification of host and viral DNA. Using the clear delineation between virus-positive and virus-negative tumors from this method, we identified recurrent somatic alterations common across MCC and alterations specific to each class of tumor, associated with differences in overall survival. Finally, comparing the molecular and clinical data from these patients revealed a surprising association of immunosuppression with virus-negative MCC and significantly shortened overall survival. CONCLUSIONS These results demonstrate the value of high-confidence virus detection for identifying molecular mechanisms of UV and viral oncogenesis in MCC. Furthermore, integrating these data with clinical data revealed features that could impact patient outcome and improve our understanding of MCC risk factors.

中文翻译：

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病毒阳性和病毒阴性默克尔细胞癌的临床和分子特征。


背景默克尔细胞癌（MCC）是一种高度侵袭性的皮肤神经内分泌癌，由默克尔细胞多瘤病毒（MCPyV）的整合和病毒T抗原的表达或过度阳光照射对肿瘤基因组造成的紫外线损伤引起。越来越多的 MCC 深度测序研究发现，病毒阳性和病毒阴性肿瘤之间的点突变数量和类型、拷贝数改变和结构变异之间存在显着差异。然而，可靠地区分病毒阳性 MCC 和紫外线损伤 MCC 一直具有挑战性。方法 在这项研究中，我们汇集了 71 名 MCC 患者，并使用 OncoPanel 进行深度测序，OncoPanel 是一种针对 400 多个癌症相关基因的临床实施的下一代测序测定法。与传统 PCR 和 IHC 方法相比，为了提高病毒检测的准确性和灵敏度，我们开发了针对整个 MCPyV 基因组的混合捕获诱饵组和用于检测整合位点和结构的软件。结果 这种方法的测序揭示了肿瘤基因组中不同的整合连接，并生成了强烈支持微同源性杂交、病毒-宿主、环状 DNA 中间体模型的组装体，该模型促进宿主和病毒 DNA 的局部扩增。利用这种方法对病毒阳性和病毒阴性肿瘤之间的清晰划分，我们确定了 MCC 中常见的复发性体细胞改变以及每类肿瘤特有的改变，这些改变与总生存率的差异相关。 最后，比较这些患者的分子和临床数据揭示了免疫抑制与病毒阴性 MCC 之间存在令人惊讶的关联，并显着缩短了总生存期。结论 这些结果证明了高置信度病毒检测对于识别 MCC 中紫外线和病毒肿瘤发生的分子机制的价值。此外，将这些数据与临床数据整合揭示了可能影响患者结果并提高我们对 MCC 风险因素的理解的特征。