Analysis of urine tumor nucleic acids for detection and personalized surveillance of bladder cancer

项目概要 膀胱癌 (BC) 是美国第六大常见癌症，是复发率最高的癌症之一 所有实体癌症，并且是从诊断到死亡治疗费用最高的癌症。有显着的 对生物标志物和分子诊断工具的未满足需求，以更好地为各个阶段的决策提供信息 不列颠哥伦比亚省。这包括预测非肌肉侵袭性 (NMIBC) 和 肌层浸润性膀胱癌 (MIBC)，以及提高接受筛查的患者的诊断率 膀胱镜检查检查血尿。我们的长期目标是通过以下方式改善 BC 患者的治疗结果： 分子生物标志物的开发和应用，促进个性化方法 检测和治疗。 尿液是BC诊断发展的一个有吸引力的来源，我们最近开发了一种新策略 检测称为尿液肿瘤 DNA 的尿液肿瘤 DNA 通过深度测序进行癌症个性化分析 （uCAPP-Seq）。我们的初步数据表明 uCAPP-Seq 对以下疾病具有出色的敏感性和特异性： BC 的检测和监视。在这个项目中，我们将前瞻性地收集尿液和其他生物样本 患有 BC 或有 BC 风险的患者，将测试 uCAPP-Seq 在不同临床中的潜在临床效用 场景。我们还将测试是否进一步通过尿 RNA 或 DNA 甲基化分析来增强 uCAPP-Seq 增强性能。我们的中心假设是 uCAPP-Seq 将能够监测 BC NMIBC 和 MIBC 治疗期间和治疗后的反应。此外，我们假设 结合尿液 DNA 突变、DNA 甲基化和尿液 RNA 分析将实现超灵敏 以及 BC 的特异性早期检测。我们提出三个具体目标：1）评估尿肿瘤的价值 DNA 用于高危 NMIBC 患者无创反应评估和监测 卡介苗（BCG）免疫疗法； 2) 确定尿液肿瘤DNA分析是否可以预测 MIBC 患者对新辅助化疗的病理完全缓解； 3) 开发一个 膀胱癌拦截检测 (BCIA) 将 utDNA 突变和甲基化与尿 用于超灵敏检测膀胱癌的 RNA。 成功完成此处提出的研究将为纳入我们的小说奠定基础 基于尿液的生物标志物进入前瞻性临床试验。我们预见我们的方法将允许个性化 改善 BC 患者预后的治疗策略。重要的是，我们的工作将作为证明- 该方法的原理也可应用于其他泌尿生殖系统癌症类型。

PROJECT SUMMARY Bladder cancer (BC) is the sixth most common cancer in the U.S., has one of the highest recurrence rates of all solid cancers, and is the most expensive cancer to treat from diagnosis to death. There are significant unmet needs for biomarkers and molecular diagnostic tools to better inform decision making across all stages of BC. This includes prediction of treatment response in patients with non-muscle invasive (NMIBC) and muscle invasive bladder cancer (MIBC), as well as improving diagnostic yield in patients undergoing screening cystoscopy for hematuria. Our long-term goal is to improve outcomes for BC patients through the development and application of molecular biomarkers that facilitate personalized approaches to detection and treatment. Urine is an attractive source for development of BC diagnostics and we recently developed a novel strategy for detecting urine tumor DNA called urine tumor DNA Cancer Personalized Profiling by Deep Sequencing (uCAPP-Seq). Our preliminary data indicate that uCAPP-Seq has outstanding sensitivity and specificity for detection and surveillance of BC. In this project we will prospectively collect urine and other biospecimens from patients with or at risk for BC and will test the potential clinical utility of uCAPP-Seq in different clinical scenarios. We will also test if augmenting uCAPP-Seq with analysis of urinary RNA or DNA methylation further augments performance. Our central hypothesis is that uCAPP-Seq will enable monitoring of BC responses during and after treatment for NMIBC and MIBC. Furthermore, we hypothesize that combining analysis of urine DNA mutations, DNA methylation, and urine RNA will allow ultrasensitive and specific early detection of BC. We propose three specific aims: 1) To assess the value of urine tumor DNA for non-invasive response assessment and monitoring in patients with high risk NMIBC treated with bacillus Calmette-Guérin (BCG) immunotherapy; 2) To determine if urine tumor DNA analysis can predict pathologic complete responses to neoadjuvant chemotherapy in patients with MIBC; and 3) To develop a Bladder Cancer Interception Assay (BCIA) which integrates utDNA mutations and methylation with urinary RNA for ultra-sensitive detection of bladder cancer. Successful completion of the studies proposed here will serve as a foundation for incorporating our novel urine-based biomarkers into prospective clinical trials. We foresee that our approach will allow personalization of treatment strategies to improve outcomes for BC patients. Importnatly, our work will serve as proof-of- principle for an approach that could also be applied to other genitourinary cancer types.