Defining HPV integration sites of unknown significance in invasive cervical cancer

项目摘要/摘要 人乳头瘤病毒(HPV)与宿主基因组的整合是 浸润性宫颈癌(ICC)。整合位点的基因组坐标已在 许多肿瘤，但对这些部位顺式基因组变化的性质或 他们可能会如何促进国际刑事法院。利用来自癌症基因组图谱(TCGA)的数据 通过与患者匹配的HPV整合位点的长读测序将定义新的 影响ICC转归的基因/途径。AIM 1将在TCGA中定义HPV整合站点- 使用新开发的HPV DNA捕获进行长读测序的MCW宫颈癌队列。 一旦确定，我们将使用TCGA数据源对每个集成站点进行注释 复杂重排、拷贝数变异、克隆性、杂合性丧失、表观遗传学 签名、基因表达和嵌合体。在此发现的整合位点的特征- 深度注释将使我们能够确定待进一步研究的假定整合驱动基因的优先顺序 在目标2中，当我们将确定一些基因的生物学相关性时，这些基因受到我们的高- 优先HPV整合站点。利用一组可用的宫颈癌细胞株，我们将 描述操纵其功能的基因的功能后果 宫颈癌尚未确定。拟议的研究预计将确定 特定HPV整合位点的下游分子驱动因素，从而揭示了新的ICC特异性 可能作为治疗目标的治疗脆弱性。

PROJECT SUMMARY/ABSTRACT Integration of the human papillomavirus (HPV) into the host genome is a dominant feature of invasive cervical cancer (ICC). Genomic coordinates of integration sites have been identified in many tumors, but little is known about the nature of the cis genomic changes at these sites or how they might promote ICC. Harnessing data from The Cancer Genome Atlas (TCGA) along with patient-matched long-read sequencing of HPV integration sites will define novel genes/pathways affecting ICC outcome. Aim 1 will define HPV integration sites in the TCGA- MCW cervical cancer cohort using newly developed HPV DNA capture for long-read sequencing. Once identified, we will annotate each integration site using TCGA data sources that document complex rearrangements, copy number variation, clonality, loss-of-heterozygosity, epigenetic signature, gene expression, and chimerism. Characteristics of integration sites found by this in- depth annotation will enable us to prioritize putative integration driver genes to be further studied in Aim 2, when we will establish the biological relevance of a few genes influenced by our high- priority HPV integration sites. Using a panel of available cervical cancer cell lines, we will then characterize the functional consequences of manipulating those genes whose functions in cervical cancer have yet to be determined. The proposed study is expected to identify downstream molecular drivers of specific HPV integration sites, thus revealing novel ICC-specific therapeutic vulnerabilities that may be targeted for treatment.