IMAT-ITCR Collaboration: Development of a high-resolution mapping platform for HPV DNA integration in premalignant lesions

IMAT-ITCR 合作：开发用于癌前病变中 HPV DNA 整合的高分辨率绘图平台

• 批准号: 10461581
• 负责人: JACK R. LENZ
• 金额: $ 8.4万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-16 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10461581
• 关键词: 2019-nCoV; Address; Administrative Supplement; Affect; Anatomy; Aneuploidy; Benign; Cancer Institute of New Jersey; Carcinoma; Cells; Cervical; Clinical; Cloud Computing; Collaborations; Complex; Computational Biology; Computer software; DNA; DNA Integration; DNA Repair; DNA Structure; DNA Viruses; DNA sequencing; Data; Data Set; Detection; Development; Diagnostic; Family; Fluorescent in Situ Hybridization; Foundations; Gene Amplification; Gene Expression; Genes; Genetic; Genetic Transcription; Genome; Genomics; Genotype-Tissue Expression Project; Goals; Head and Neck Neoplasms; Hepatitis B; Hepatitis C virus; High-Throughput Nucleotide Sequencing; Histologic; Human; Human Genome; Human Papillomavirus; In Situ; Institutes; Laboratories; Length; Lesion; Malignant Neoplasms; Malignant Vaginal Neoplasm; Malignant neoplasm of anus; Malignant neoplasm of cervix uteri; Malignant neoplasm of penis; Malignant neoplasm of vulva; Massive Parallel Sequencing; Medicine; Messenger RNA; Methods; Microscopy; Molecular; Molecular Computations; Mutation; Oncogenic Viruses; Pattern; Play; Process; Proteins; Publishing; RNA; RNA Viruses; Reporting; Residual Tumors; Resolution; Role; Sampling; Scientist; Site; Somatic Mutation; Specificity; Structure; Technology; The Cancer Genome Atlas; Tissues; Transcript; Viral; Viral Genome; Virus; Virus Diseases; Virus Integration; Work; base; cancer genomics; cancer initiation; college; computerized tools; gammaherpesvirus; histopathological examination; human DNA; improved; insight; laboratory equipment; nanopore; neoantigens; neoplastic cell; novel; novel virus; premalignant; reference genome; screening; tool; transcriptome; transcriptome sequencing; transcriptomics; tumor; tumor progression; tumorigenesis; viral DNA; virology

Abstract/Summary Viruses play a role in 10 to 20% of human cancers. Tying specific viruses to human cancers remains a fundamental biomedical and technological problem. One virus family, the human papillomaviruses (HPVs), comprises over 225 known types and causes lesions ranging from benign warts to highly lethal, invasive carcinomas. HPV-induced tumors occur at several anatomical sites including nearly 100% of cervical cancers, 90% of anal cancers, 30 to 60% of head & neck tumors, and roughly one-fourth to one-half of vaginal, vulvar & penile cancers. In most HPV-induced tumors, at least part of the viral DNA genome has become integrated into the human genome, presumably as a consequence of aberrant host cell DNA repair processes. Our laboratory work has been focused on the development of accurate, sensitive, broad specificity technology based on DNA hybridization capture plus massively parallel sequencing to detect and structurally analyze integrated HPV DNA in precancerous lesions and invasive tumors. Ongoing studies are also developing fluorescent microscopy technologies for detection of both integrated HPV DNA and HPV RNA transcripts, as these provide highly specific, potential diagnostic tools to detect the presence of HPV-induced tumor cells, including post-therapy residual disease in clinical samples. Our work encompasses long-range, nanopore DNA sequencing plus RNA sequencing to confirm any complex structural rearrangements of the HPV and human genomes and to elucidate potential viral effects on viral and human gene transcription. Key to these studies has been a very successful, collaborative effort by the Haas group (Broad Institute at MIT) with the Lenz (Albert Einstein College of Medicine) and Montagna (Rutgers Cancer Institute of New Jersey) labs to expand the computational tools of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). This has led to the development of expanded CTAT components for detection of integrated HPV DNA, structural assembly of integrated viral DNA segments, and overall transcriptional analysis of HPV-induced tumors and precancerous lesions. The CTAT-virus insertion finder (CTAT-VIF) is available on GitHub. The IMAT-ITCR collaboration proposed here will substantially expand the ongoing collaboration by pursuing three additional aims. Aim 1 will expand CTAT-VIF to analyze the presence of ~13,000 different viruses and investigate if any viral DNAs are integrated and/or expressed by screening all The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression Project (GTEx) datasets. Aim 2 is to identify and analyze novel virus-human fusion transcripts generated from virus DNA insertions. Aim 3 will broaden our in-situ analysis of HPV- induced cervical cancers and precancerous lesions to include spatial transcriptomic analysis, including expanding CTAT for this technology. These studies should improve computational and laboratory technologies for understanding the roles of viruses in human cancer.

摘要/概要 病毒在10%至20%的人类癌症中发挥作用。将特定的病毒与人类癌症联系起来仍然是一个挑战。 基本的生物医学和技术问题。一个病毒家族，人乳头瘤病毒（HPV）， 包括超过225种已知的类型，并引起从良性疣到高度致命的侵入性 癌HPV诱导的肿瘤发生在几个解剖部位，包括近100%的宫颈癌。 癌症，90%的肛门癌，30%至60%的头颈部肿瘤，以及大约四分之一至一半的阴道癌， 外阴和阴茎癌。在大多数HPV诱导的肿瘤中，至少部分病毒DNA基因组已经成为 整合到人类基因组中，可能是异常宿主细胞DNA修复过程的结果。 我们的实验室工作一直专注于发展准确、灵敏、广泛特异性的技术 基于DNA杂交捕获和大规模并行测序来检测和结构分析 在癌前病变和浸润性肿瘤中整合HPV DNA。正在进行的研究也在发展中 荧光显微镜技术用于检测整合的HPV DNA和HPV RNA转录物， 这些提供了高度特异性的、潜在的诊断工具来检测HPV诱导的肿瘤细胞的存在， 包括临床样品中的治疗后残留疾病。我们的工作包括长距离，纳米孔 DNA测序加RNA测序，以确认HPV的任何复杂结构重排， 人类基因组，并阐明病毒对病毒和人类基因转录的潜在影响。这些的关键 这项研究是哈斯小组（麻省理工学院布罗德研究所）与 伦茨（阿尔伯特爱因斯坦医学院）和蒙塔格纳（罗格斯癌症研究所新泽西）实验室， 扩展Trinity癌症转录组分析工具包（CTAT）的计算工具。这导致 用于检测整合的HPV DNA、结构组装的扩增CTAT组分的开发 整合的病毒DNA片段，以及HPV诱导的肿瘤的总体转录分析， 癌前病变。CTAT-virus insertion finder（CTAT-VIF）可以在GitHub上找到。IMAT-ITCR 这里提出的合作将大大扩大正在进行的合作，通过寻求三个额外的 目标。目标1将扩展CTAT-VIF，以分析约13，000种不同病毒的存在，并调查 通过筛选所有的癌症基因组图谱（TCGA）整合和/或表达任何病毒DNA， Genotype-Tissue Expression Project（GTEx）数据集。目的二是鉴定和分析新型病毒-人 由病毒DNA插入产生的融合转录物。目标3将扩大我们对HPV的原位分析- 诱导宫颈癌和癌前病变，包括空间转录组学分析， 为这项技术扩展CTAT。这些研究将提高计算和实验室 了解病毒在人类癌症中的作用的技术。