Leveraging canine spontaneous cancer to optimize the power of blood biopsy

项目摘要 最近的技术进步推动了新的、侵入性较小的方法的发展， 肿瘤基因组特别是，利用由肿瘤细胞释放的循环肿瘤DNA（ctDNA）的“血液活检”， 死亡的癌细胞，具有潜在的实用性，用于筛查有癌症风险的个体， 治疗后可能复发，识别可操作的突变以计划治疗并表征肿瘤 基因组进化然而，仍然存在一些挑战，包括需要使收集标准化， 处理程序，优化测序/分析平台，并将ctDNA生成的数据与 患者结局。例如，一天中的时间或用于血液采集的静脉（中心vs. 外周的）可能影响ctDNA产率和测定的再现性。此外，虽然评价共同 突变可以容易地使用ctDNA进行（即，肺癌中的EGFR突变），低 突变负荷和/或大的结构变体（缺失/倒位）仍然更难以表征。 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一个 相对较长的时间轴（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，血容量有限，重复采样可能很困难，并且存在问题 以准确地概括治疗反应和耐药性的周期。有趣的是，宠物狗自发地 发展癌症，密切反映他们的人类同行方面的临床过程，分子 因此，它们代表了改善血液活检的独特模型 性能和应用。因为宠物狗接受标准治疗（化学/放射/免疫疗法）， 在经历压缩的疾病时间轴的情况下，通常可以相当迅速地获得关键信息。朝向 为此，我们已经产生了初步数据，证明ctDNA在患有癌症的狗中是容易检测到的， 可以检测到与肿瘤中的遗传变化一致的遗传变化， 影响ctDNA水平。这项建议的目的是建立在这些调查结果的证书狗 癌症作为血液活检进展的相关工具，并使用该模型优化和推进 应用于人类患者。具体来说，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面板 进行患者筛查，并进行纵向研究，以跟踪微小残留疾病和 复发为了促进研究结果的快速临床转化，我们选择了具有基因组景观的犬癌症， 具有人类等同物：尿路上皮癌（BRAF V595 E）、肥大细胞瘤（KIT内部串联 重复）、骨肉瘤（大结构变体）、淋巴瘤（Myc扩增、TRAF 3突变）和 血管肉瘤（p53，PIK 3CA突变）。通过这项工作创建的工具也将具有持续的实用性 作为未来的犬转化癌研究，从而支持该模型系统的持续发展。

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.