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

项目总结 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 都是实体癌症，是从确诊到死亡治疗费用最高的癌症。有重要的 对生物标志物和分子诊断工具的需求尚未得到满足，以更好地为所有阶段的决策提供信息 公元前。这包括对非肌肉侵袭性(NMIBC)和 肌肉浸润性膀胱癌(MIBC)，以及提高接受筛查患者的诊断率 血尿的膀胱镜检查。我们的长期目标是通过 促进个性化治疗的分子生物标记物的开发和应用 检测和治疗。 尿液是发展BC诊断的一个有吸引力的来源，我们最近开发了一种新的策略来 深层测序法检测尿液肿瘤DNA肿瘤DNA肿瘤个体化指征 (uCAPP-Seq)。我们的初步数据表明，uCAPP-Seq具有显著的敏感性和特异性 BC的检测和监测。在这个项目中，我们将前瞻性地收集尿液和其他生物样本 并将测试uCAPP-Seq在不同临床中的潜在临床效用 场景。我们还将测试是否通过进一步分析尿液RNA或DNA甲基化来增强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 联合分析尿液DNA突变、DNA甲基化和尿液RNA将使超敏 以及特定的BC早期检测。我们提出了三个具体目标：1)评估尿路肿瘤的价值 DNA在高危NMIBC患者治疗中的无创性反应评估和监测 卡介苗(BCG)免疫治疗；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反应；以及3)发展成 尿液中整合utDNA突变和甲基化的膀胱癌截获试验 用于膀胱癌超灵敏检测的RNA。 这里提出的研究的成功完成将成为纳入我们小说的基础 以尿液为基础的生物标志物进入预期的临床试验。我们预见到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，我们的工作将成为- 一种也可以应用于其他泌尿生殖系癌症类型的方法的原则。

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.