Development of a Multi-Virus, Whole Genome Sequencing Platform for Post-Transplantation Virus Characterization

开发用于移植后病毒表征的多病毒全基因组测序平台

• 批准号: 9225020
• 负责人: Benjamin Pinsky
• 金额: $ 23.55万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-04 至 2019-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9225020
• 关键词: Address; Adenoviruses; Affect; Antiviral Agents; Antiviral Therapy; BK Virus; CD8-Positive T-Lymphocytes; Cell Therapy; Cellular Immunity; Child health care; Clinical; Clinical Trials; Clinical Virology; Collaborations; Communicable Diseases; Cytomegalovirus; Cytotoxic T-Lymphocytes; DNA sequencing; Data; Defect; Detection; Development; Discipline; Disease; Drug resistance; Epidemiology; Epitopes; Escape Mutant; Exposure to; Genomics; Genotype; Goals; Graft Rejection; Healthcare; Human Herpesvirus 4; Human Herpesvirus 6; Immune; Immune response; Immunocompromised Host; Immunology; Immunosuppression; Immunotherapy; Informatics; Infusion procedures; Institution; Kidney Transplantation; Lead; Methodology; Methods; Mission; Morbidity - disease rate; Mutation; Opportunistic Infections; Outcome; Patients; Pharmaceutical Preparations; Population; Population Dynamics; Protocols documentation; Public Health; Recurrence; Research; Risk; Sampling; T cell therapy; T-Lymphocyte; T-Lymphocyte Epitopes; Testing; Therapeutic; Toxic effect; Transplant Recipients; Transplantation; Treatment Failure; United States National Institutes of Health; Variant; Viral Genome; Viremia; Virus; Virus Diseases; Work; alternative treatment; base; clinically relevant; deep sequencing; design; genetic variant; genome sequencing; genome-wide; hematopoietic cell transplantation; improved; innovation; insight; mortality; next generation sequencing; novel; novel therapeutics; pressure; response; sequencing platform; success; tool; viral DNA; viral detection; viral transmission; virus genetics; whole genome

PROJECT SUMMARY Novel T-cell immunotherapies that infuse multi-virus-specific, cytotoxic T-cells to boost the host immune response against viruses may be a promising treatment option for persistent viral infections in transplant recipients. However, causes of T-cell therapy failures in early clinical trials are not yet fully understood and virus-specific causes for treatment failures are currently not known. With advances in next-generation sequencing, whole genome sequencing of the most clinically relevant viruses in transplantation for virus escape mutant detection is now possible, though methodologies and informatics pipelines have yet to be established. The objective of this proposal is to develop an efficient sequencing method that provides genome-wide data on five of the most common viruses targeted by multi-virus cytotoxic T-cell therapies: adenovirus (ADV), BK virus (BKV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesvirus-6 (HHV-6) to facilitate the detection of virus escape mutants as a potential cause of T-cell therapy failure and define virus genetic changes in response to immune pressure. The central hypothesis is that therapeutic strategies that enhance the host immune response against viruses, such as the infusion of virus-specific cytotoxic T-cells, will promote the emergence of escape mutants and result in treatment failure and persistent viremia. We plan to test the central hypothesis and accomplish the objectives of this proposal by pursuing these specific aims: 1) Develop and validate a whole genome sequencing platform for ADV, CMV, EBV, and HHV-6; and 2) Define virus responses to T-cell therapy in transplant recipients with persistent viremia. Under the first aim, a novel design that uses bait enrichment for targeted virus DNA sequencing will be used and informatics pipeline validated, to accompany BKV whole genome sequencing capabilities recently established by our group. Under the second aim, the platform will be used to define changes in the virus repertoire in transplant recipients with recurrent or persistent viremia after receipt of virus-specific T-cell immunotherapy. The significance of this work is needed application to emerging clinical trials evaluating the efficacy of novel immune-based therapies in transplant recipients at institutions worldwide. The proposed research is innovative, in the applicant's opinion, because it enables whole genome sequencing of five of the most important viruses causing disease in transplant recipients, not yet available, that can be easily and broadly applied for characterization of these viruses in transplantation and other immunocompromised states. Such depth of virus characterization offers the ability to evaluate dynamic changes in the virus repertoire to both immunomodulating and antiviral therapies in various disease states. Thus, the proposed work is expected to open new research horizons not previously attainable and improve the management of these pervasive viral infections.

项目摘要 新型的T细胞免疫疗法注入多病毒特异性的细胞毒性T细胞，以增强宿主免疫 对病毒的反应可能是持续性病毒感染的有前途的治疗选择 移植接受者。但是，在早期临床试验中导致T细胞疗法失败的原因尚未完全 目前尚不清楚理解的治疗失败的病毒特异性原因。随着进步 下一代测序，最相关病毒中最相关病毒的整个基因组测序 尽管方法论和 信息管道尚未建立。该提案的目的是发展有效 测序方法可提供有关五种最常见病毒的全基因组数据 多病毒细胞毒性T细胞疗法：腺病毒（ADV），BK病毒（BKV），巨细胞病毒（CMV）， 爱泼斯坦 - 巴尔病毒（EBV）和人疱疹病毒6（HHV-6），以促进病毒逃生的检测 突变体是T细胞治疗衰竭的潜在原因，并定义了病毒遗传变化 免疫压力。中心假设是增强宿主免疫的治疗策略 对病毒的反应，例如输注病毒特异性细胞毒性T细胞，将促进 逃生突变体的出现并导致治疗衰竭和持续性病毒血症。我们计划测试 中央假设并通过追求这些特定目标来实现该提议的目标：1） 为ADV，CMV，EBV和HHV-6开发和验证整个基因组测序平台；和2） 定义病毒对持续病毒血症的移植受者中T细胞治疗的反应。在第一个 Aim，一种新型设计，将使用诱饵富集进行靶向病毒DNA测序，并且将使用 信息管道已验证，最近伴随BKV全基因组测序功能 由我们的小组建立。在第二个目标下，该平台将用于定义 在接受病毒特异性后复发或持续性病毒血症的移植受者中的病毒曲目 T细胞免疫疗法。这项工作的意义需要应用于新兴的临床试验 评估新型免疫疗法在机构移植受者中的疗效 全世界。申请人认为，拟议的研究具有创新性，因为它可以使整个 五种最重要病毒的基因组测序，导致移植受者疾病，而不是 但是可用，可以轻松而广泛地应用于这些病毒的表征 移植和其他免疫功能低下的状态。这种病毒特征的深度提供了 能够评估病毒曲目的动态变化对免疫调节和抗病毒的能力 各种疾病状态的疗法。因此，预计拟议的工作将开放新的研究 地平线以前无法达到并改善这些普遍病毒感染的管理。