背景:液体活检和动态跟踪循环肿瘤DNA(ctDNA)中的体细胞突变可以深入了解癌症演变的动力学和肿瘤内异质性,从而促进治疗抗性。然而,识别和跟踪体细胞拷贝数改变(SCNA)的动态变化,与不良预后和转移有关,使用ctDNA是具有挑战性的。胰腺腺癌是一种在其进化过程中被认为具有早期断点事件的疾病。导致早期健身高峰,具有最小的进一步亚克隆进化。
方法:探讨SCNA在胰腺癌演变中的作用,我们对前瞻性纳入临床试验的24例转移性疾病患者(包括8例患者来源的异种移植物(PDX))的55个纵向无细胞DNA(cfDNA)样本进行了全外显子组测序.我们开发了一种方法,循环肿瘤DNA的非整倍体(ACT-Discover),利用配对肿瘤活检或PDX的单倍型定相,以更高的灵敏度鉴定cfDNA中的SCNA。
结果:在47个可评价的cfDNA样品中的28个中观察到SCNA。在这些事件中,30%只能通过利用ACT-Discover中利用的单倍型感知方法来识别。PDX肿瘤的特殊纯度使等位基因失衡的基因组区域几乎完全定相,突出了PDX的重要辅助功能。最后,虽然胰腺癌进化的经典模型强调早期的重要性,同质躯体事件是癌症发展的关键要求,ACT-Discover确定了SCNA的实质性异质性,包括平行的焦点和手臂级别的事件,影响个体肿瘤内不同的亲本等位基因。的确,在整个疾病过程中,在肿瘤中发现了SCNA的持续获取,包括在未经治疗的转移性肿瘤内。
结论:这项工作证明了单倍型定相研究cfDNA样本基因组变异的能力,并揭示了未发现的肿瘤内异质性,具有重要的科学和临床意义。ACT-Discover的实施可能会从现有的队列中获得重要的见解,或支持未来的前瞻性研究,以寻求通过液体活检来表征肿瘤演变的景观。
Liquid biopsies and the dynamic tracking of somatic mutations within circulating tumour DNA (ctDNA) can provide insight into the dynamics of cancer evolution and the intra-tumour heterogeneity that fuels treatment resistance. However, identifying and tracking dynamic changes in somatic copy number alterations (SCNAs), which have been associated with poor outcome and metastasis, using ctDNA is challenging. Pancreatic adenocarcinoma is a disease which has been considered to harbour early punctuated events in its evolution, leading to an early fitness peak, with minimal further subclonal evolution.
To interrogate the role of SCNAs in pancreatic adenocarcinoma cancer evolution, we applied whole-exome sequencing of 55 longitudinal cell-free DNA (cfDNA) samples taken from 24 patients (including 8 from whom a patient-derived xenograft (PDX) was derived) with metastatic disease prospectively recruited into a clinical trial. We developed a method, Aneuploidy in Circulating Tumour DNA (ACT-Discover), that leverages haplotype phasing of paired tumour biopsies or PDXs to identify SCNAs in cfDNA with greater sensitivity.
SCNAs were observed within 28 of 47 evaluable cfDNA samples. Of these events, 30% could only be identified by harnessing the haplotype-aware approach leveraged in ACT-Discover. The exceptional purity of PDX tumours enabled near-complete phasing of genomic regions in allelic imbalance, highlighting an important auxiliary function of PDXs. Finally, although the classical model of pancreatic cancer evolution emphasises the importance of early, homogenous somatic events as a key requirement for cancer development, ACT-Discover identified substantial heterogeneity of SCNAs, including parallel focal and arm-level events, affecting different parental alleles within individual tumours. Indeed, ongoing acquisition of SCNAs was identified within tumours throughout the disease course, including within an untreated metastatic tumour.
This work demonstrates the power of haplotype phasing to study genomic variation in cfDNA samples and reveals undiscovered intra-tumour heterogeneity with important scientific and clinical implications. Implementation of ACT-Discover could lead to important insights from existing cohorts or underpin future prospective studies seeking to characterise the landscape of tumour evolution through liquid biopsy.