Genome Transplant Dynamics: non-invasive sequencing-based diagnosis of rejection

基因组移植动力学：基于非侵入性测序的排斥反应诊断

• 批准号: 8047524
• 负责人: STEPHEN R QUAKE
• 金额: $ 246.39万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-30 至 2013-09-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8047524
• 关键词: Acute; Address; Algorithms; Apoptosis; Area; Base Sequence; Basic Science; Bioinformatics; Biopsy; Blood; Blood Circulation; Blood specimen; Bronchiolitis Obliterans; Cells; Chest; Chronic; Clinical; Cohort Studies; Coronary artery; DNA; DNA Sequence; Detection; Development; Diagnosis; Diagnostic; Early Diagnosis; Endothelial Cells; Event; Foundations; Functional disorder; Future; Genome; Genomics; Goals; Graft Rejection; Health; Health Care Costs; Healthcare; Heart Transplantation; Heart-Lung Transplantation; Immune response; Infection; Injury; Life; Lung; Lung Transplantation; Measurement; Measures; Medical; Methods; Monitor; Morbidity - disease rate; Non-Invasive Cancer Detection; Organ; Organ Transplantation; Patients; Pattern; Procedures; Relative (related person); Resources; Sensitivity and Specificity; Serum; Single Nucleotide Polymorphism; Solid; Staging; Stream; Syndrome; Techniques; Testing; Thick; Translating; Transplant Recipients; Transplantation; Ultrasonography; Vascular Diseases; allograft rejection; base; cost; design; end-stage organ failure; follow-up; graft function; heart allograft; high throughput technology; innovation; lung injury; mortality; next generation; novel; novel strategies; prevent; prospective; public health relevance; tool; validation studies

DESCRIPTION (provided by applicant): Our goal is to develop and test a novel donor-specific, genomic approach to the non-invasive, early diagnosis of rejection and graft dysfunction after solid organ transplantation, and addresses two targeted thematic areas: 1) Applying Genomics and Other High Throughput Technologies; 2) Translating Basic Science Discoveries into New and Better Treatments. Organ transplantation saves the lives of patients with end-stage organ failure, yet in many cases, the transplanted organ is rejected by the recipient, causing a life-threatening situation. Previous attempts to develop a non-invasive marker of graft rejection have focused on recipient-specific immune responses, and thus have inherent limitations in sensitivity and specificity, especially for distinguishing rejection from infection. Our novel approach is the first to focus on a donor-specific marker of acute rejection. We will use high throughput next generation sequencing to monitor the proportion of cell-free donor DNA to recipient DNA, in the recipient's blood stream as a marker of rejection. This approach is enabled by the fact that an organ transplant is also effectively a genome transplant, and by monitoring single nucleotide polymorphisms that are specific to the donor's genome one can measure the relative health of the transplanted organ. RATIONALE/HYPOTHESIS: during rejection, apoptosis of donor cells releases donor DNA into the recipient circulation; this DNA can be distinguished from recipient DNA and quantified using high-throughput sequencing techniques; and dynamic changes in donor DNA levels will predict (a) acute rejection; (b) graft dysfunction; and (c) chronic rejection. PRELIMINARY STUDIES: using banked blood samples from heart transplant recipients, we showed that donor DNA levels rise during episodes of acute rejection but remain at stable, low levels in the absence of rejection. AIM 1: Develop a donor DNA monitoring approach for the non-invasive detection of allograft rejection. We will develop and test: (1) next generation DNA sequencing methods to perform low cost, noninvasive analysis of donor DNA load; (2) bioinformatic algorithms that maximize the sensitivity to discriminate donor and recipient DNA; (3) sensitivity of a defined single nucleotide polymorphism (SNP) panel that differentiates donor from recipient. AIM 2: Evaluate the utility of donor DNA monitoring for detection of clinical events (acute rejection, chronic rejection, and graft dysfunction) after heart transplantation. We will conduct a prospective cohort study of 110 consecutive heart transplant recipients, collecting blood samples during and between endomyocardial biopsy (EMB) procedures (yielding 1,516-paired EMB/blood) to determine whether donor:recipient DNA ratio can detect rejection in its early stages and before the development of graft dysfunction. AIM 3: Test this approach in lung transplantation and determine whether donor:recipient DNA ratio can differentiate between graft dysfunction due to rejection versus pulmonary infection. If achieved, these specific aims will provide the foundation for validation studies of a donor-specific, genome-based approach to non-invasive, early detection of rejection after solid organ transplantation. PUBLIC HEALTH RELEVANCE: Organ transplantation saves the lives of patients with end-stage organ failure, yet in many cases, the transplanted organ is rejected by the recipient, causing a life-threatening situation. We propose to develop and test a new and innovative approach to the non-invasive, early diagnosis of rejection and graft dysfunction after heart and lung transplantation. By simply monitoring the blood of a transplant recipient for level of the donor genome appearing during follow-up after receiving a transplant, we hope to establish a diagnostic tool that has potential to save hundreds of millions of dollars in health care costs annually, and reduce patient morbidity and mortality.

描述（由申请人提供）：我们的目标是开发和测试一种新的供体特异性基因组方法，以非侵入性地早期诊断实体器官移植后的排斥反应和移植物功能障碍，并解决两个目标主题领域：1）应用基因组学和其他高通量技术； 2) 将基础科学发现转化为新的、更好的治疗方法。器官移植可以挽救终末期器官衰竭患者的生命，但在许多情况下，移植的器官会被受体排斥，导致危及生命的情况。以前开发移植排斥的非侵入性标记物的尝试主要集中在受体特异性免疫反应上，因此在敏感性和特异性方面存在固有的局限性，特别是在区分排斥和感染方面。我们的新方法是第一个关注急性排斥的供体特异性标记物的方法。我们将使用高通量下一代测序技术来监测受者血流中无细胞供体 DNA 与受者 DNA 的比例，作为排斥反应的标志。这种方法的实现是因为器官移植实际上也是基因组移植，并且通过监测供体基因组特有的单核苷酸多态性，人们可以测量移植器官的相对健康状况。基本原理/假设：在排斥过程中，供体细胞的凋亡将供体 DNA 释放到受体循环中；该 DNA 可以与受体 DNA 区分开来，并使用高通量测序技术进行定量；供体 DNA 水平的动态变化将预测 (a) 急性排斥反应； (b) 移植物功能障碍； (c) 慢性排斥反应。初步研究：使用心脏移植受者的储存血液样本，我们发现供体 DNA 水平在急性排斥反应期间升高，但在没有排斥反应的情况下保持稳定的低水平。目标 1：开发一种供体 DNA 监测方法，用于非侵入性检测同种异体移植排斥反应。我们将开发和测试：（1）下一代 DNA 测序方法，对供体 DNA 负载进行低成本、非侵入性分析； (2) 生物信息算法，最大限度地提高区分供体和受体 DNA 的灵敏度； (3) 区分供体和受体的确定的单核苷酸多态性 (SNP) 组的敏感性。目标 2：评估供体 DNA 监测在检测心脏移植后临床事件（急性排斥、慢性排斥和移植物功能障碍）方面的效用。我们将对 110 名连续心脏移植受者进行一项前瞻性队列研究，在心内膜心肌活检 (EMB) 程序期间和之间收集血液样本（产生 1,516 对 EMB/血液），以确定供体：受体 DNA 比率是否可以检测早期排斥反应以及在移植物功能障碍发生之前。目标 3：在肺移植中测试这种方法，并确定供体：受体 DNA 比率是否可以区分由于排斥和肺部感染引起的移植功能障碍。如果实现，这些具体目标将为验证研究奠定基础，验证供体特异性、基于基因组的方法，以非侵入性、早期检测实体器官移植后的排斥反应。 公共卫生相关性：器官移植可以挽救终末期器官衰竭患者的生命，但在许多情况下，移植的器官会被接受者排斥，从而导致危及生命的情况。我们建议开发和测试一种新的创新方法，对心肺移植后的排斥反应和移植物功能障碍进行非侵入性早期诊断。通过简单地监测移植受者的血液，了解移植后随访期间出现的供体基因组水平，我们希望建立一种诊断工具，有可能每年节省数亿美元的医疗保健费用，并减少患者的发病率和死亡率。

项目成果

Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection.

• DOI: 10.1126/scitranslmed.3007803
• 发表时间: 2014-06-18
• 期刊: Science translational medicine
• 影响因子: 17.1
• 作者: De Vlaminck I;Valantine HA;Snyder TM;Strehl C;Cohen G;Luikart H;Neff NF;Okamoto J;Bernstein D;Weisshaar D;Quake SR;Khush KK
• 通讯作者: Khush KK

Personalized treatment in heart transplantation.

心脏移植的个体化治疗。

• DOI: 10.1097/mot.0000000000000406
• 发表时间: 2017
• 期刊: Current opinion in organ transplantation
• 影响因子: 2.2
• 作者: Khush,KiranK

Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy study.

• DOI: 10.1371/journal.pmed.1001890
• 发表时间: 2015-10
• 期刊: PLoS medicine
• 影响因子: 15.8
• 作者: Vollmers C;De Vlaminck I;Valantine HA;Penland L;Luikart H;Strehl C;Cohen G;Khush KK;Quake SR
• 通讯作者: Quake SR

Use of donor-derived-cell-free DNA as a marker of early allograft injury in primary graft dysfunction (PGD) to predict the risk of chronic lung allograft dysfunction (CLAD).

• DOI: 10.1016/j.healun.2021.02.008
• 发表时间: 2021-06
• 期刊: The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation
• 作者: Keller M;Bush E;Diamond JM;Shah P;Matthew J;Brown AW;Sun J;Timofte I;Kong H;Tunc I;Luikart H;Iacono A;Nathan SD;Khush KK;Orens J;Jang M;Agbor-Enoh S
• 通讯作者: Agbor-Enoh S