Leveraging canine spontaneous cancer to optimize the power of blood biopsy

项目总结 最近的技术进步推动了新的、侵入性更小的评估方法的发展 肿瘤基因组。特别是，利用循环中的肿瘤DNA(CtDNA)由 正在死亡的癌细胞，对筛查有癌症风险的人，确定这些患者具有潜在的效用 可能在治疗后复发，识别可操作的突变以计划治疗和表征肿瘤 基因组进化。然而，仍然存在一些挑战，包括需要标准化收集和 处理程序，优化测序/分析平台，并将ctDNA产生的数据与 病人的结果。例如，诸如一天中的时间或用于采血的静脉(中央与 外周)可能会影响ctDNA产量和分析的重复性。此外，在评估常见问题时， 突变可以很容易地使用ctDNA(即肺癌中的EGFR突变)、低风险的肿瘤类型 突变负担和/或大的结构变异(缺失/倒置)仍然更难表征。 最后，对人类患者进行前瞻性抽样以评估血液活检的预测价值需要 相对较长的时间线(年)。虽然这样的研究可能是理想的小鼠癌症模型， 疾病进展迅速，血液容量有限，重复采样可能很困难，而且存在问题 以准确概括治疗反应和耐药的周期。有趣的是，宠物狗自发地 患上在临床病程、分子水平上与人类相似的癌症 调节失调和基因组改变，因此它们代表了改善血液活检的独特模式 性能和应用。因为宠物狗还会接受标准的治疗(化学/放射/免疫疗法)。 在经历一个压缩的疾病时间线后，关键信息通常可以相当快地获得。冲向 为此，我们已经产生了初步数据，表明ctDNA在患有癌症的狗身上很容易检测到， 可以检测到与肿瘤中的基因变化一致的基因变化，并且治疗有一个变量 对ctDNA水平的影响。这项建议的目的是在这些发现的基础上为狗提供证书 将癌症作为血液活检的相关工具，并使用该模型来优化和推进 它适用于人类患者。具体地说，我们将确定各种因素如何影响ctDNA产量， 评估肿瘤和ctDNA序列数据的一致性，开发和实施诊断突变小组 用于患者筛查，并进行纵向研究以跟踪最小残留疾病和 旧病复发。为了便于快速临床翻译研究结果，我们选择了具有基因组图谱的犬癌。 与人类等同的疾病：尿路上皮癌(BRAF V595E)、肥大细胞瘤(KIT内部串联 复制)、骨肉瘤(大型结构变异)、淋巴瘤(Myc扩增、TRAF3突变)和 血管肉瘤(P53、PIK3CA突变)。通过这项工作创建的工具也将具有持续使用的实用程序 作为未来犬转化性癌症的研究，从而支持这一模型系统的继续发展。

PROJECT SUMMARY Recent technological advances have driven the development of novel, less invasive approaches for assessing the tumor genome. In particular, the “blood biopsy” which leverages circulating tumor DNA (ctDNA) released by dying cancer cells, has potential utility for screening individuals at risk for cancer, determining those patients likely to relapse post treatment, identifying actionable mutations to plan treatment and characterizing tumor genome evolution. However, several challenges remain including the need to standardize collection and processing procedures, optimize sequencing/analysis platforms, and correlate data generated from ctDNA with patient outcomes. For example, factors such as time of day or vein used for blood collection (central vs. peripheral) may influence ctDNA yields and reproducibility of the assay. Moreover, while evaluation for common mutations can readily be performed using ctDNA (i.e., EGFR mutations in lung cancer), tumor types with low mutation burden and/or large structural variants (deletions/inversions) remain more difficult to characterize. Finally, prospective sampling of human patients to assess the predictive value of blood biopsy requires a relatively long timeline (years). While such studies would presumably be ideal in murine cancer models where disease progression is rapid, blood volumes are limited, repeated sampling can be difficult, and it is problematic to accurately recapitulate cycles of treatment response and resistance. Interestingly, pet dogs spontaneously develop cancers that closely mirror their human counterparts with respect to clinical course, molecular dysregulation and genomic alterations, and as such they represent a unique model for improving blood biopsy performance and application. Because pet dogs receive standard treatment (chem/radiation/immunotherapy) yet experience a compressed disease timeline, critical information can typically be obtained quite rapidly. Toward that end, we have generated preliminary data demonstrating that ctDNA is readily detectable in dogs with cancer, that genetic changes concordant with those in the tumor can be detected, and that treatment has a variable impact on ctDNA levels. The purpose of this proposal is to build upon these findings to credential dogs with cancer as a relevant tool for blood biopsy advancement and use this model to optimize and advance its application to human patients. Specifically, we will determine how various factors affect ctDNA yield, assess concordance of tumor and ctDNA sequence data, develop and implement a diagnostic mutation panel for patient screening, and conduct longitudinal studies to track both minimal residual disease and likelihood of relapse. To facilitate rapid clinical translation of findings, we selected canine cancers with genomic landscapes that have human equivalents: urothelial carcinoma (BRAF V595E), mast cell tumor (KIT internal tandem duplication), osteosarcoma (large structural variants), lymphoma (Myc amplification, TRAF3 mutation) and hemangiosarcoma (p53, PIK3CA mutation). Tools created through this work will have utility for ongoing as well as future canine translational cancer research, thereby supporting continued development of this model system.