Novel Structures of the Human Papilloma Virus Genome in HNSCC

HNSCC 中人乳头瘤病毒基因组的新结构

• 批准号: 9332364
• 负责人: BRAD E. WINDLE
• 金额: $ 22.88万
• 依托单位: VIRGINIA COMMONWEALTH UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9332364
• 关键词: Affect; Alpha Cell; Biological Models; Cancer Patient; Cells; Complex; DNA; DNA Sequence; DNA Sequence Analysis; DNA Structure; DNA sequencing; Data; Data Analyses; Development; Diagnostic; Disease; Disease Management; Disease Outcome; Epidemic; Episome; Experimental Models; Future; Gene Expression; Gene Expression Profile; Genes; Genome; Genomics; Growth; Head and Neck Cancer; Head and Neck Squamous Cell Carcinoma; High-Throughput RNA Sequencing; Human; Human Genome; Human Papillomavirus; Human papillomavirus 16; Hybrids; In Vitro; Incidence; Individual; Malignant Neoplasms; Mediating; Modeling; Oral; Outcome; Patients; Pattern; Performance; Public Health; Reporting; Research; Risk; Sampling; Sequence Analysis; Structure; Study models; Survival Rate; The Cancer Genome Atlas; Thinking; Tonsil; Viral; Viral Genome; Viral Oncogene; base; cancer recurrence; cell immortalization; cell transformation; chemoradiation; high throughput analysis; human DNA; human data; immortalized cell; insight; integration site; keratinocyte; malignant oropharynx neoplasm; novel; transcriptome sequencing; tumor; tumorigenesis; whole genome

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.

项目摘要 通过 继续我们对癌症基因组图集的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结果。先前对HPV癌症的研究 广泛地假设了三个病毒基因组结构；偶发，整合，两者的混合物。我们在场 证据表明这种情况更为复杂，可能会出现病毒宿主DNA发作。这项研究是 至关重要，因为HPV+口咽癌（OPC）的发生率正在增加，目前被认为 流行;最近的报道表明，这些肿瘤中有80％为HPV+。 HPV16存在于90％ 这些。虽然HPV+ OPC患者对化学放疗的反应较好，并且5年生存率高约60％ 比率比HPV负的率，〜20％HPV+患者的子集对 治疗和/或患有癌症复发，不应接受降级治疗；识别这些 个人是优先事项，因此他们没有受到治疗。我们提出的问题和会回答的是： HPV基因组多久将其整合到人类基因组中，并与人DNA进行切除至 改革新的情节？ 我们已经从初步研究中进行了一些观察，与这个问题有关的一个是 偶发性HPV基因组可以整合到人类基因组中，然后切除以形成新的 HPV和人类DNA的sistome。因此，这种自主复制分子不仅可以扩大 完整的病毒性癌基因E6和E7，但也可能导致癌症的人类基因/序列 发展。 是HPV+ OPC中HPV基因组的HPV结构或其他结构的预测因子 疾病结果？ 基于可用样品中HPV基因组的确定结构，我们将初步 调查含有病毒式围激体样本的患者是否患有较差的疾病结果。 体外HPV16是否转化了扁桃体细胞研究HPV+ OPC的模型？ 我们已经确定了一些TCGA HPV阳性中存在的混合病毒 - 人类DNA插发事件 HNSCC数据。我们想在原代扁桃体细胞中对其中一些结构进行建模。我们建议先 分析使用RNA-Seq从HPV16转化的扁桃体细胞的基因表达。我们将确定a）是否 这些细胞中病毒基因组的表达与HPV+ OPC和B中观察到的模式相似 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是 然后，将有必要将这些细胞作为HPV+ OPC转化细胞的模型的进一步研究，包括 转染到细胞中，该应用中报道的一些异常的HPV16-HOST基因组结构。