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: 9816875
• 负责人: Vikas R. Dharnidharka
• 金额: $ 57.93万
• 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 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9816875
• 关键词: Address; Algorithmic Software; Amino Acids; Archives; Belgium; Biological Assay; Biological Markers; Cell Transplantation; Cell Transplants; Cessation of life; Characteristics; Clinical; Clinical Data; Clinical Pathology; Code; Collection; Communicable Diseases; Complication; Computational algorithm; 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; Organ Transplantation; Outcome; Paraffin Embedding; Pathogenicity; Pathologic; Patient Care; Patients; Pennsylvania; Plasma; Publishing; RNA; Registries; Research; Resources; Role; Sample Size; Sampling; Severities; Shotgun Sequencing; Shotguns; Site; Solid; Specialist; Suggestion; Techniques; Technology; Time; Tissue Extracts; Tissue Sample; Tissues; Transplant Recipients; Transplantation; Universities; Variant; Viral; Viral Genome; Virus; Washington; abstracting; analytical tool; base; cohort; data management; genetic variant; genome sequencing; genomic data; high risk; human DNA; indexing; metagenomic sequencing; microbial; mortality; multidisciplinary; mutant; novel; novel therapeutics; oncology; outcome forecast; post-transplant; precision medicine; predictive modeling; prognostic; programs; prospective; reference genome; repository; sample fixation; statistics; 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.

摘要 移植后淋巴增生性疾病(PTLDS)仍然是一种令人恐惧的恶性并发症 移植，5年死亡率高，发病率超过50%。大约50%-80%的病例是强烈的 与致癌的爱泼斯坦-巴尔病毒(EBV)有关，EBV是关键的致病驱动因素。存在着许多知识差距 PTLD。几个预后指数，包括多种临床、流行病学和肿瘤特征， 包括EBV肿瘤阳性在内，并不总是与较差的患者生存相关，这表明 EBV基因组变异或其他病毒病因的额外作用。然而，精准医疗工具 与人类基因组变体相比，确定病毒基因组变体是否具有致病性是非常有限的。 此外，EBV阴性PTLD的病因尚不清楚。使用新近开发的尖端技术 技术，我们可以从福尔马林固定的、石蜡包埋的PTLD存档组织中提取病毒核酸 或血浆，并以无偏见的方式同时对多个病毒进行测序，使用元基因组枪 测序(MS)和病毒壳™。基于我们的初步数据，我们提出了一种精准医学 翻译基因组学项目，以解决以下具体目标并弥合所提到的知识差距：1) 验证了我们的新观察结果，即MSS检测PTLD组织中的花环病毒呈阳性(并得到了其他研究人员的证实 技术)是PTLD诊断后移植受者死亡率较高的生物标志物； 用多个病毒的无偏MS确定其他致癌病毒在EBV阴性PTLD中的作用 分组，通过其他技术确认；3)开发必要的计算、算法和软件 然后需要分析工具来确定EBV基因组变异与较差的呈现或 PTLD的结果。为了达到这些目标，我们将回顾收集PTLD组织，并前瞻性地 收集PTLD组织/血浆来源：1)2015年后发生在华盛顿大学的病例；2)3 拥有大型移植计划和现有PTLD收藏的美国网站(宾夕法尼亚大学， 匹兹堡和斯坦福大学；3)法国国家级PTLD登记，已经有大量的临床数据和 可以获得存档的组织。在这个拟议的630个动力充足的PTLD案例的样本规模中，我们将：a) 从PTLD样本中获取组织卷轴并运往华盛顿大学；b)提取微生物 DNA和RNA；c)执行元基因组鸟枪测序；以及d)验证我们与 从每个站点导入的临床数据，输入已经建立的RedCap数据库。我们的团队包括 移植、血液病理学、传染病、肿瘤学、基因组学、数据管理方面的专家 和统计数据。我们的初步数据、合作者和当地资源都非常出色，能够实现这些目标 目标。这项研究还将创建迄今为止最大的PTLD组织组合库，提取 核酸以及注解良好的临床和病理数据，以供进一步研究使用。完成这项工作 研究将有助于更好地照顾病人，并可能为新的治疗方法提供途径。