Harnessing treatment-induced tumor evolution and collateral sensitivities using a human rectal cancer co-clinical platform

项目摘要/摘要 局部进展期直肠癌，定义为扩散至淋巴或整个直肠壁 厚度，每年在超过15,000名美国患者中被诊断出来。局部晚期直肠的标准治疗 美国的癌症包括手术切除前的化疗和放射治疗(化学放疗，CRT 整个直肠。患者可能会经历手术后的不良后果，如永久性的 结肠造口或肛门直肠功能改变。有鉴于此，许多正在进行的研究都集中在避免 对可能仅用CRT治愈的患者亚组进行手术干预。在手术时，10- 30%的肿瘤通过CRT根治(即，它们表现出病理上的完全反应)，而其他 肿瘤几乎没有反应。这种反应的可变性并不完全被理解，但可能与 一个肿瘤可能包含许多不同的肿瘤细胞亚群，这些亚群都具有不同的基因类型 和表观遗传(或非遗传)特征。这些不同的亚群和可变的遗传/表观遗传学 功能可以相互作用，导致一个动态和演变的肿瘤细胞网络，但人们对此知之甚少。在一个 癌症的数量不断增加，有证据支持治疗诱导进化的出现 “陷阱”，或“侧支敏感性”，对一种疗法的耐药性会导致对另一种疗法的敏感性。 这种情况是否发生在直肠癌中，以及如何将其运用到治疗策略中，目前尚不清楚。致信地址 在这些问题上，选择一个具有代表性的实验模型至关重要。因此，目前的提案 利用已经建立的联合临床渠道，患者提取的肿瘤样本用于 生成配对的、特定于患者的器官移植模型和异种移植模型。两种广泛的分析方法将是 确定CRT诱导的肿瘤演变的趋势，并阐明潜在的协同治疗方法 改善CRT响应。特定目标1将使用基因组、表观基因组和 单细胞图谱技术，包括结合单细胞RNA-SEQ和谱系的先进方法 追踪。特定目标2采用创新的迭代配对CRISPR/高通量药物筛选方法 目的：明确CRT治疗直肠癌的侧支敏感性变化。为了验证这两个目标的发现， 先进的患者来源的直肠癌器官和异种移植模型将被使用。研究，科学 指导和职业发展将由一个由导师和合作者组成的专家小组以及 有组织的培训计划。这两个目标的成功实现将由专业知识和现有的 共同导师实验室的筛查和基因组基础设施，并利用独特的联合临床 已经由密切的机构合作者建立的平台。这项研究将建立一种由患者衍生的 质疑CRT诱导的肿瘤进化的平台，建立促进成功的科学利基 在向科学独立过渡的过程中。

PROJECT SUMMARY/ABSTRACT Locally advanced rectal cancer, defined by spread to lymph nodes or extension through the full rectal wall thickness, is diagnosed in over 15,000 US patients yearly. Standard treatment for locally advanced rectal cancer in the US involves chemotherapy and radiation therapy (chemoradiation, CRT) prior to surgical removal of the entire rectum. Patients may experience undesirable post-surgical consequences such as permanent colostomy or altered anorectal function. In light of this, much ongoing research focuses on strategies to avoid surgical intervention in the subset of patients who might be cured with CRT alone. At the time of surgery, 10- 30% of tumors are eradicated by CRT (i.e., they demonstrate a pathologic complete response) while other tumors show little to no response. This variability in response is incompletely understood, but likely relates to the fact that one tumor may contain numerous different tumor cell subpopulations, all with different genotypes and epigenetic (or non-genetic) features. These diverse subpopulations and variable genetic/epigenetic features can interact, resulting in a dynamic and evolving tumor cell network that is poorly understood. In an increasing number of cancers, there is evidence supporting the emergence of treatment-induced evolutionary “traps,” or “collateral sensitivities”, where resistance to one therapy results in sensitivity to another therapy. Whether this occurs in rectal cancer, and how to leverage it into treatment strategies, is unclear. To address these questions, it is crucial to select a representative experimental model. Thus, the current proposal leverages an already-established co-clinical pipeline from which patient derived tumor samples are used to generate paired, patient-specific organoid and xenograft models. Two broad analytic approaches will be undertaken to identify trends in CRT-induced tumor evolution and elucidate potential synergistic approaches to improve CRT response. Specific Aim 1 will dissect CRT-induced changes using genomic, epigenomic, and single cell profiling techniques, including an advanced method combining single cell RNA-seq with lineage tracing. Specific Aim 2 employs an innovative iterative paired CRISPR/high throughput drug screen approach to identify evolving collateral sensitivities in CRT-treated rectal cancer. To validate the findings in both Aims, advanced patient-derived rectal cancer organoid and xenograft models will be utilized. Research, scientific instruction, and career development will be supported by an expert panel of mentors and collaborators and a structured training plan. Successful completion of both Aims will be promoted by the expertise and existing screening and genomic infrastructure in the co-mentors’ laboratories and leverages a unique co-clinical platform already established by close institutional collaborators. This research will establish a patient-derived platform for interrogating CRT-induced tumor evolution, establishing a scientific niche to facilitate success during the transition to scientific independence.