A Noninvasive Integrated Genomic Approach for Early Cancer Detection and Risk Stratification after Transplantation

项目摘要/摘要 实体器官移植受者是研究致癌病毒之间联系的理想人群。 感染和癌症是由于预防同种异体移植排斥所需的深度免疫抑制所致，这 增加他们发生感染和癌症等临床并发症的风险。我们的长期目标是 以移植为模型系统，研究免疫抑制、感染和癌症之间的关系。 我们的中心假设是，新的癌症风险生物标志物，如检测循环中的肿瘤DNA， 循环中无细胞DNA的测序和详细的免疫图谱可以用于早期癌症检测，以 确定恶变之前的病毒体的变化，并全面量化 免疫抑制。我们将通过三个具体目标来验证我们的假设：(1)评估循环中的肿瘤DNA 用于移植后恶性肿瘤的早期检测，重点是移植后淋巴组织增生性疾病 精神障碍(PTLDS)。我们将评估CAPP-Seq的性能，这是一种早期癌症的超灵敏检测方法 斯坦福大学对2000多名心肺移植受者的现有队列进行了检测 和6个合作站点。我们将对PTLDS患者进行研究，以(A)确定新出现的体细胞的动力学 肿瘤发生前的变异，(B)定义了通过以下方式准确早期预测癌症风险的窗口 循环肿瘤DNA，以及(C)这些发现与致癌病毒的扩张和免疫系统有关 压制。类似的探索性分析将在移植后肺和结直肠的患者中进行。 癌症。(2)分析无细胞DNA中的肿瘤病毒，并评估整合部位的致癌风险 预测者。为了区分恶变前嗜瘤病毒的特征，我们将丰富 肿瘤病毒无细胞DNA能够通过深度测序识别人：病毒基因融合，并将 确定阅读覆盖率是与基因组整合一致还是与自由DNA一致。然后我们会做侧写 来自原发肿瘤的DNA和无细胞DNA，并将比较肿瘤亚型中整合部位的覆盖率。(3) 量化免疫抑制、病毒感染和癌症发展之间的关系。我们会 在移植后的特定时间点执行新的免疫图谱分析，并将结果关联 出现急性排斥反应、机会性感染和癌症。具体地说，我们将测量循环 AnelloVirus负载，将从RNA-seq推断免疫细胞亚群，并将对B细胞抗体重链进行排序。 我们将确定这些结果与注射免疫抑制的关系，并将建立数学模型 预测临床并发症风险的模型。这一贡献意义重大，因为了解了 与癌症风险和早期检测相关的分子特征可能导致新的方法来预防、监测 治疗恶性疾病。我们的创新方法，其中我们将使用由我们的 小组研究非常高风险的移植患者队列，将为旨在预防的研究奠定基础 以及早期发现癌症，作为改善临床结果的一种手段。

PROJECT SUMMARY/ABSTRACT Solid organ transplant recipients are an ideal population in which to study the link between oncogenic viral infections and cancer due to the deep immunosuppression required to prevent allograft rejection, which increases their risk of developing clinical complications such as infections and cancer. Our long-term goal is to study the relations among immunosuppression, infections, and cancer using transplantation as a model system. Our central hypothesis is that novel biomarkers of cancer risk such as detection of circulating tumor DNA, sequencing of circulating cell-free DNA, and detailed immune profiling can be used for early cancer detection, to identify changes in the virome that precede malignant transformation, and to quantify overall immunosuppression. We will test our hypothesis via three specific aims: (1) To evaluate circulating tumor DNA for early detection of post-transplant malignancies, focusing on post-transplant lymphoproliferative disorders (PTLDs). We will evaluate the performance of CAPP-Seq, an ultra-sensitive assay for early cancer detection, in existing cohorts of over 2000 heart and lung transplant recipients followed at Stanford University and 6 collaborating sites. We will study patients with PTLDs to (a) determine the kinetics of emerging somatic variants preceding tumor development, (b) define the window for accurate early prediction of cancer risk via circulating tumor DNA, and (c) relate these findings to oncotropic viral expansion and immune system suppression. Similar exploratory analyses will be performed in patients with post-transplant lung and colorectal cancers. (2) To profile oncoviruses in cell-free DNA and evaluate integration sites as cancer risk predictors. To distinguish features in the oncotropic virome preceding malignant transformation, we will enrich oncoviral cell-free DNA to enable identification of human:virus gene fusion by deep sequencing, and will determine whether read coverage is consistent with genome integration or with free DNA. We will then profile DNA from primary tumors and cell-free DNA, and will compare integration site coverage in tumor subtypes. (3) To quantify associations among immunosuppression, viral infection and cancer development. We will perform novel immune profiling assays at defined time points following transplantation and will correlate results with development of acute rejection, opportunistic infections, and cancer. Specifically, we will measure circulating Anellovirus load, will infer immune cell subsets from RNA-seq, and will sequence the B-cell antibody heavy chain. We will determine how these results relate to administered immunosuppression, and will build mathematical models to predict risk of clinical complications. This contribution is significant because knowledge of the molecular signatures associated with cancer risk and early detection may lead to novel ways to prevent, monitor, and treat malignant disease. Our innovative approach, in which we will employ novel methods developed by our group to study a very high-risk transplant patient cohort, will lay the foundation for studies aimed at prevention and early detection of cancer as a means of improving clinical outcomes.