Novel Structures of the Human Papilloma Virus Genome in HNSCC

项目摘要 我们试图通过以下方法了解头颈部癌症中人乳头瘤病毒(HPV)基因组的结构 继续我们对来自癌症基因组图谱的DNA序列数据的分析。我们假设 病毒基因组的结构类型决定了疾病的结局。人乳头瘤病毒癌的早期研究 大致假设了三种病毒基因组结构：异构体、整合体和两者的混合体。我们呈现的是 有证据表明情况更加复杂，存在病毒宿主DNA异构体的可能性。这项研究是 关键是因为HPV+口咽癌(OPC)的发病率正在增加，目前被认为 一种流行病；最近的报告显示，这些肿瘤中有80%是HPV+；HPV16存在于90%的 这些。而HPV+OPC患者对化疗的反应更好，5年存活率高出约60% 与HPV阴性的患者相比，有大约20%的HPV+患者对 治疗和/或患有癌症复发，不应接受降级治疗；确定这些 个人是优先事项，这样他们就不会得不到充分的治疗。我们提出并将回答的问题包括： HPV基因组多久整合到人类基因组中并与人类DNA切除一次 改革新的圣公会？ 我们从初步研究中提出了几点意见，与这个问题有关的一点是， 上体HPV基因组可以整合到人类基因组中，随后切除形成新的 带有HPV和人类DNA的圣公会。因此，这种自主复制的分子不仅可以放大 完整的病毒癌基因E6和E7，但也包括可能导致癌症的人类基因/序列 发展。 在HPV+OPC中，切除的HPV结构或HPV基因组的其他结构是预测 疾病结果是什么？ 根据现有样本中确定的HPV基因组结构，我们将初步 调查含有病毒的人类Episome样本的患者是否有更糟糕的疾病结局。 体外HPV16转化的扁桃体细胞是研究HPV+OPC的模型吗？ 我们已经在一些TCGA HPV阳性患者中发现了病毒-人类DNA混合异构体 HNSCC数据。我们想要在原代扁桃体细胞中模拟其中的一些结构。我们建议首先 应用RNA-seq技术分析HPV16转化扁桃体细胞的基因表达。我们将确定a)如果 病毒基因组在这些细胞中的表达类似于在HPV+OPC和b)中观察到的模式。 宿主基因表达模式是否与HPV+OPC相似。如果这些问题的答案是肯定的 那么，将这些细胞作为HPV+OPC转化细胞的模型进行进一步研究是有必要的，包括 将本应用中报道的一些异常的HPV16宿主基因组结构导入细胞。

Project Summary We seek to understand the structure of human papillomavirus (HPV) genomes in head and neck cancers by continuing our analysis of DNA sequence data from The Cancer Genome Atlas. We hypothesize that the type of structure of the viral genome contributes to disease outcome. Previous studies of HPV cancers have broadly assumed three viral genome structures; episomal, integrated, a mixture of both. We present evidence that the situation is more complex, with the possibility of viral-host DNA episomes. This research is critical because the incidence of HPV+ oropharyngeal cancer (OPC) is increasing and is currently considered an epidemic; recent reports have shown that 80% of these tumors are HPV+; HPV16 is present in 90% of these. While HPV+ OPC patients respond better to chemoradiation and have a ~60% higher 5 year survival rate than those who are HPV negative, there is a subset of ~20% HPV+ patients that do not respond well to therapy and/or suffer from cancer recurrence who should not receive de-escalated treatment; identifying these individuals is a priority so that they are not under treated. The questions we are posing and will answer are: How often does the HPV genome integrate into the human genome and excise with human DNA to reform a new episome? We have made several observations from our preliminary studies and one relevant to this question is that the episomal HPV genome can integrate into the human genome and subsequently excise to form a new episome with HPV and human DNA. This autonomously replicating molecule can therefore amplify not only intact viral oncogenes E6 and E7 but also human genes/sequences that may contribute to cancer development. Is the excised HPV structure or other structures of the HPV genome in HPV+ OPC a predictor of disease outcome? Based on the determined structures of the HPV genome in the samples available, we will preliminarily investigate if patients with viral-human episome-containing samples have a worse disease outcome. Are in vitro HPV16 transformed tonsil cells a model for studying HPV+ OPC? We have already identified hybrid viral-human DNA episomes present in some of the TCGA HPV positive HNSCC data. We would like to model some of these structures in primary tonsil cells. We propose to first analyze gene expression from tonsil cells transformed with HPV16 using RNA-seq. We will determine a) if the expression of the viral genome in these cells is similar to the patterns observed in the HPV+ OPC and b) if the host gene expression pattern is similar to that of HPV+ OPC. If the answer to these questions is yes then further studies of these cells as a model for HPV+ OPC transformed cells would be warranted, including transfecting into cells some of the aberrant HPV16-host genome structures reported in this application.