Novel Structures of the Human Papilloma Virus Genome in HNSCC

项目摘要 我们试图了解人乳头瘤病毒（HPV）基因组在头颈癌的结构， 继续我们对癌症基因组图谱中的DNA序列数据的分析。我们假设 病毒基因组的结构类型有助于疾病的结果。HPV癌症的既往研究 广泛地假设了三种病毒基因组结构：游离型、整合型、两者的混合。我们提出 有证据表明情况更为复杂，可能存在病毒宿主DNA附加体。本研究是 关键是因为HPV+口咽癌（OPC）的发病率正在增加，目前被认为是 流行病;最近的报告显示，80%的这些肿瘤是HPV+; HPV 16存在于90%的 这些.而HPV+ OPC患者对放化疗的反应更好，5年生存率高约60%， 与HPV阴性患者相比，约20%的HPV+患者对HPV阴性患者的反应不佳。 治疗和/或患有癌症复发，不应接受降级治疗;识别这些 个人是一个优先事项，使他们不会受到治疗。我们提出并将回答的问题是： HPV基因组多久整合到人类基因组中并与人类DNA一起切除， 改革一个新的附加体？ 我们从初步研究中得出了几个观察结果，其中一个与这个问题有关的是， 附加型HPV基因组可以整合到人类基因组中，随后切除以形成新的 附加体与HPV和人类DNA。因此，这种自主复制的分子不仅可以扩增 完整的病毒癌基因E6和E7，以及可能导致癌症的人类基因/序列 发展 HPV+ OPC中切除的HPV结构或HPV基因组的其他结构是否是 疾病结局？ 根据现有样本中确定的HPV基因组结构，我们将初步 研究含有病毒-人游离体样品的患者是否具有更差的疾病结果。 体外HPV 16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阳性的细胞中发现了杂交病毒-人DNA附加体。 HNSCC数据。我们想在初级扁桃体细胞中模拟这些结构。我们建议首先 使用RNA-seq分析来自用HPV 16转化的扁桃体细胞的基因表达。我们将确定a）如果 这些细胞中病毒基因组的表达与HPV+ OPC中观察到的模式相似，和B） 如果宿主基因表达模式与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转化细胞的模型的进一步研究将是必要的，包括 将本申请中报道的一些异常HPV 16宿主基因组结构引入细胞中。

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.