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型的供体特异性，基因组方法，以对固体器官移植后的非侵入性，早期诊断排斥反应和移植功能障碍，并解决两个有针对性的主题领域：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。器官移植可挽救末期器官衰竭患者的生命，但是在许多情况下，受体拒绝移植器官，导致威胁生命的情况。先前试图开发关节排斥反应的非侵入性标志物的尝试集中在受体特定的免疫反应上，因此在敏感性和特异性方面具有固有的局限性，尤其是在区分感染和感染方面。我们的新方法是第一个专注于急性排斥的特定捐助者标记的方法。我们将使用高吞吐量的下一代测序来监测接受者血流中无细胞供体DNA与受体DNA的比例，作为排斥的标志。通过有效的基因组移植，以及监测特定于供体的基因组特有的单核苷酸多态性，可以测量移植器官的相对健康，从而可以有效地通过监测器官移植，从而实现了这种方法。理由/假设：在排斥反应期间，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，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； （b）移植功能障碍； （c）慢性拒绝。初步研究：使用来自心脏移植受者的库存血液样本，我们表明供体DNA水平在急性排斥反应发作期间升高，但在没有排斥反应的情况下保持稳定，水平较低。 AIM 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。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，无创分析； （2）最大化对区分供体和受体DNA敏感性的生物信息学算法； （3）定义的单核苷酸多态性（SNP）面板的灵敏度将供体与受体区分开来。 AIM 2：心脏移植后评估供体DNA监测检测临床事件（急性排斥，慢性排斥和移植功能障碍）的效用。我们将对110个连续的心脏移植受者进行前瞻性队列研究，在内膜活检（EMB）程序（EMB）程序（产生1,516二氧化碳/血液）之间收集血液样本，以确定供体：受体DNA比率是否可以在早期阶段和开发疗法的发展阶段检测到置换率。目标3：在肺移植中测试这种方法，并确定供体：受体DNA比是否可以区分由于排斥反应与肺部感染引起的移植功能障碍。如果实现，这些特定目标将为验证研究固体器官移植后的非侵入性，早期检测的非侵入性，早期检测的验证研究提供基础。 公共卫生相关性：器官移植可挽救终末期器官衰竭的患者的生命，但是在许多情况下，移植器官被接收者拒绝，导致危及生命的情况。我们建议开发和测试一种新的和创新的方法，以解决心脏和肺移植后的非侵入性，早期诊断和移植功能障碍。通过简单地监测接受移植后在随访期间出现的供体基因组水平的移植受者的血液，我们希望建立一种诊断工具，该工具有可能每年节省数亿美元的医疗保健费用，并降低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