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)

基本信息

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
项目类别：
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

项目摘要

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殖性疾病（PTLD）仍然是一种令人担忧的恶性并发症移植，5年死亡率高，发病率超过50%，约50-80%的病例严重。与致癌性 Epstein-Barr 病毒 (EBV) 相关，这是一种关键的致病驱动因素。 PTLD。几个预后指标，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率相关，这表明 EBV 基因组变异或其他病毒病因的额外作用然而，精准医学工具。与人类基因组变异相比，确定病毒基因组变异是否致病的能力非常有限。此外，EBV 阴性 PTLD 的病因尚不清楚。技术，我们可以从福尔马林固定、石蜡包埋的存档 PTLD 组织中提取病毒核酸或血浆并使用宏基因组猎枪以无偏见的方式同时对多种病毒进行测序基于我们的初步数据，我们提出了一种精准医疗。转化基因组学项目旨在解决以下具体目标并缩小引用的知识差距：1) 验证我们的新观察结果，即 MSS 对指环病毒的 PTLD 组织呈阳性（并得到其他人的证实）技术）作为 PTLD 诊断后较高移植受者死亡率的生物标志物；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，通过其他技术确认；3) 开发必要的计算、算法和软件需要分析工具来确定 EBV 基因组变异与较差表现或症状的关联为了实现这些目标，我们将回顾性收集 PTLD 组织并前瞻性地收集。从以下来源收集 PTLD 组织/血浆：1) 2015 年之后发生在华盛顿大学的病例；2) 三个；美国拥有大型移植项目和现有 PTLD 馆藏的站点（宾夕法尼亚大学、匹兹堡和斯坦福大学；3) 法国国家级 PTLD 注册中心，已经拥有广泛的临床数据和在这个建议的 630 个 PTLD 病例的样本量中，我们将：从 PTLD 样本中获取组织卷轴并运送至华盛顿大学 b) 提取微生物； DNA 和 RNA；c) 进行宏基因组鸟枪测序；d) 验证我们与我们的团队包括从每个站点导入已构建的 RedCap 数据库的临床数据。移植、血液病理学、传染病、肿瘤学、基因组学、数据管理专家我们的初步数据、合作者和当地资源非常适合实现这些目标。这项研究还将创建迄今为止最大的提取的组合 PTLD 组织存储库。核酸以及注释良好的临床和病理数据，用于完成这项工作。研究将有助于更好的患者护理，并可能为新疗法提供途径。