Metagenomic shotgun microbial sequencing in post-transplant lymphoproliferative disorders (PTLD-MSMS)

移植后淋巴增殖性疾病的宏基因组鸟枪法微生物测序 (PTLD-MSMS)

• 批准号: 10630142
• 负责人: Vikas R. Dharnidharka
• 金额: $ 55.54万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-10 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10630142
• 关键词: Address; Algorithms; Amino Acids; Archives; Belgium; Biological Assay; Biological Markers; Cell Transplantation; Cessation of life; Characteristics; Clinical; Clinical Data; Clinical Pathology; Code; Collection; Communicable Diseases; Complication; Computer software; DNA; DNA Viruses; Data; Databases; Diagnosis; Epidemiology; Etiology; Event; Formalin; Fright; Genes; Genomics; Goals; Grouping; Hematopathology; Human; Human Genome; Human Herpesvirus 4; Immune system; Immunosuppression; International; Knowledge; Literature; Location; Lymphoid Cell; Lymphoproliferative Disorders; Malignant - descriptor; Metagenomics; Morbidity - disease rate; Nucleic Acids; Oncogenes; Oncogenic; Oncogenic Viruses; Oncology; Organ Transplantation; Outcome; Paraffin Embedding; Pathogenicity; Pathologic; Patient Care; Patients; Pennsylvania; Plasma; Prognosis; Publishing; RNA; Registries; Research; Resources; Role; Sample Size; Sampling; Severities; Shotgun Sequencing; Shotguns; Site; Solid; Specialist; Suggestion; Techniques; Technology; Time; Tissue Sample; Tissues; Transplant Recipients; Transplantation; Universities; Variant; Viral; Viral Genome; Virus; Washington; abstracting; analytical tool; cohort; data management; genetic variant; genome sequencing; high risk; human DNA; microbial; microbial genomics; mortality; multidisciplinary; mutant; novel; novel therapeutics; post-transplant; precision medicine; predictive modeling; prognostic index; programs; prospective; reference genome; repository; sample fixation; statistics; tissue archive; tool; transcriptome sequencing; translational genomics; tumor; viral DNA; viral detection; whole genome

Abstract Post-transplant lymphoproliferative disorders (PTLDs) remain a feared malignant complication of transplantation, with high 5-year mortality and morbidity exceeding 50%. About 50-80% of cases are strongly related to the oncogenic Epstein-Barr virus (EBV), a key pathogenic driver. Many knowledge gaps exist in PTLD. Several prognostic indices, comprising multiple clinical, epidemiological and tumor characteristics, including EBV tumor positivity, do not consistently associate with worse patient survival, suggesting an additional role for EBV genome variants or other viral etiologies. However, the precision medicine tools for determining if a viral genome variant is pathogenic are very limited compared to human genome variants. Further, the etiological agent in EBV-negative PTLD is unknown. Using novel recently developed cutting-edge technologies, we can extract viral nucleic acids from formalin-fixed, paraffin-embedded archived PTLD tissues or plasma and sequence multiple viruses simultaneously in unbiased fashion, using metagenomic shotgun sequencing (MSS) and ViroCap™. Based on our preliminary data, we propose a precision medicine translational genomics project to address the following specific aims and close the cited knowledge gaps: 1) Validate our novel observation that PTLD tissue positivity by MSS for anellovirus (and confirmed by other techniques) serves as a biomarker for higher transplant recipient mortality after the diagnosis of PTLD; 2) Determine the role of other oncogenic viruses in EBV-negative PTLD by unbiased MSS of multiple viral groupings, confirmed by other techniques; 3) Develop the necessary computational, algorithmic and software analytic tools required to then determine association of EBV genome variants with worse presentations or outcomes in PTLD. To achieve these aims, we will retrospectively collect PTLD tissues and prospectively collect PTLD tissues/plasma from: 1) cases at Washington University that have occurred after 2015; 2) three USA sites with large transplant programs and existing PTLD collections (Universities of Pennsylvania, Pittsburgh and Stanford; 3) a French national-level PTLD registry that already has extensive clinical data and can obtain archived tissues. In this proposed sample size of adequately powered 630 PTLD cases, we will: a) acquire tissue scrolls from the PTLD samples and transport to Washington University; b) extract the microbial DNA and RNA; c) perform metagenomic shotgun sequencing; and d) validate our novel associations to the clinical data, imported from each of the sites, into an already constructed RedCap database. Our team includes specialists in transplantation, hematopathology, infectious diseases, oncology, genomics, data management and statistics. Our preliminary data, collaborators and local resources are exceptional to accomplish these goals. This study will additionally create the largest-to-date repository of combined PTLD tissue, extracted nucleic acids, and well-annotated clinical and pathological data, for use in further research. Completion of this study will contribute to better patient care and may provide avenues for novel therapies.

抽象的 移植后淋巴增生疾病（PTLD）仍然是错误的恶性并发症 移植，高5年死亡率和发病率超过50％。大约50-80％的案件强烈 与关键致病驱动因素的致癌爱泼斯坦 - 巴尔病毒（EBV）有关。许多知识差距存在 PTLD。几个预后指数，完成了多个临床，流行病学和肿瘤特征， 包括EBV肿瘤阳性，不要始终与患者的生存较差相关，表明 EBV基因组变体或其他病毒病因的其他作用。但是，用于 与人类基因组变体相比，确定病毒基因组变异是否具有致病性。 此外，EBV阴性PTLD中的病因学剂尚不清楚。使用最近开发的尖端 技术，我们可以从福尔马林固定，石蜡包裹的存档PTLD组织中提取病毒核酸 或使用元基因组shot弹枪，或血浆和序列多种病毒仅以公正的方式 测序（MSS）和ViroCap™。根据我们的初步数据，我们提出了一种精确药物 转化基因组学项目旨在解决以下特定目的并缩小引用的知识差距：1） 验证我们的新发现，即MSS对Anellovirus的PTLD组织阳性（并由其他 Techniques）是PTLD诊断后较高移植受者死亡率较高的生物标志物； 2） 通过多种病毒的无偏MSS确定其他致癌病毒在EBV阴性PTLD中的作用 分组，通过其他技术证实； 3）开发必要的计算，算法和软件 然后确定EBV基因组变体与较差的演示或 PTLD的结果。为了实现这些目标，我们将回顾性收集PTLD组织并前瞻性地收集 从：1）华盛顿大学的病例收集PTLD组织/等离子体。 2）三 具有大型移植计划和现有PTLD收藏的美国站点（宾夕法尼亚大学， 匹兹堡和斯坦福； 3）法国国家级PTLD注册中心已经拥有广泛的临床数据，并且 可以获取存档的组织。在此提议的足够供电的630个PTLD案例的样本量中，我们将：a） 从PTLD样品中获取组织卷轴并运输到华盛顿大学； b）提取微生物 DNA和RNA； c）执行宏基因组shot弹枪测序； d）验证我们与 从每个站点进口的临床数据中已构建的REDCAP数据库。我们的团队包括 移植，血症病理学，传染病，肿瘤学，基因组学，数据管理专家 和统计。我们的初步数据，合作者和本地资源是实现这些目的的非凡的 目标。这项研究还将创建合并的PTLD组织的最大至今存储库，提取 核酸以及通知的临床和病理数据，用于进一步研究。完成此操作 研究将有助于更好的患者护理，并可能提供新的疗法。