A clone's genomic stability as biomarker of its DNA-damage resilience

晚期癌症，包括胃癌和胶质母细胞瘤的治疗中的一个主要问题是不确定 我们预测个别患者对DNA损伤剂的反应，特别是从长远来看。了解这一机制 病人的反应背后，或缺乏反应，将帮助我们摆脱过于简单化的“越多越好”和“一刀切”的观念。 适用于DNA损伤剂的“万能”原则。这将通过允许 我们要找出那些对低剂量的DNA损伤剂比对高剂量的反应更好、更长时间的人。 假设DNA损伤治疗的成功率随着相对增殖率的增加而增加 对于同质肿瘤人群，除了单调的剂量-反应关系外，几乎没有理由假设任何其他因素。但 随着最近范式的转变，大多数癌症实际上是正在进行的进化的DNA马赛克产物，迫切需要 重新考虑DNA损伤治疗管理背后的这些基本原则。作为最早的开发商之一 DNA去卷积方法和可获得多达10,000个细胞转录本的技术 同时，我们已经准备好开始针对DNA损伤治疗的第一个个性化剂量发现策略。我们会 测试DNA损伤对细胞基因组不稳定所带来的非常长期遗产的潜力-作为DNA的新生物标记- 损坏反应。我们的初步研究表明，对于大多数癌症类型，DNA损伤剂会改变克隆人的基因组 不稳定，克隆人屈从于它们可以容忍的基因组不稳定的数量的限制。特别是，我们的结果 显示中度基因组不稳定的患者预后非常差，这种关系只是显而易见的 在治疗天真的患者中，而不是在接受DNA损伤剂治疗的患者中。此外，他们还表明，我们可以 测量每个克隆的基因组不稳定性，基因组极不稳定的克隆通常不会变大。我们的 基因组不稳定而不是增殖率的假设决定了肿瘤对DNA损伤的敏感性 长期的药物，是基于两个意想不到的发现：(I)患者每个肿瘤的基因组不稳定性极高 克隆人有一个特别好的结果。目标1将整合外显子组和单细胞RNA-SEQ数据以表征克隆 并测量它们能容忍多大程度的基因组不稳定。(Ii)基因组不稳定程度低与效益降低有关 来自破坏DNA的毒剂。目标2将使用彗星分析和治疗历史来量化每个克隆的DNA损伤，将其联系起来 克隆人耐受DNA损伤的能力，以及治疗后存活的克隆人基因组不稳定性的变化。这 这将是第一次测试基因组不稳定作为DNA损伤敏感性生物标记物的可能性的研究。我们还将使用 来自这个队列的克隆特定转录本和基因组，用于发现DNA候选生物标记物- 损伤敏感性。该项目的头两年将在季汉礼博士的实验室进行。在这个K99阶段之后，在学习了 为了模拟DNA损伤剂与肿瘤中共存的不同克隆之间的药量学相互作用，Dr。 Andor将继续作为独立研究员。在确定了基因组不稳定的阈值后，克隆 降低了适应性，Andor博士将使这些克隆受到DNA损伤剂的影响，以量化这些克隆随剂量的变化 基因组不稳定以及克隆接近基因组不稳定阈值如何影响其治疗敏感性(R00)。

A main problem in the treatment of advanced cancers, including gastric cancers and glioblastoma, is the incertitude at which we predict how individual patients will respond to DNA-damaging agents, especially on the long run. Knowing the mechanism behind a patient's response, or the lack thereof, will help us depart from the oversimplified “more-is-better” and “one-size- fits-all” principles according to which DNA-damaging agents are administered. This will improve clinical outcome by allowing us to pinpoint those who would respond better and longer to lower doses of DNA-damaging agents, than to higher doses. Under the assumption that the success of DNA-damaging therapy increases with the proliferation rate of a relatively homogeneous tumor population, there was little reason to assume anything other than monotonic dose-response relations. But with the recent paradigm shift that most cancers are in fact DNA mosaic products of ongoing evolution, comes the urgency to reconsider these fundamental principles behind DNA-damaging therapy administration. As the developers of one of the first DNA deconvolution methods and with access to technologies to profile the transcriptomes of up to 10,000 cells simultaneously, we are equipped to embark on first personalized dose-finding strategies for DNA-damaging therapies. We will test the potential of the very long-term legacy that DNA-damage entails on a cell – genomic instability – as new biomarker of DNA- damage response. Our preliminary studies showed that, for most cancer types, DNA-damaging agents change a clone's genomic instability and that clones succumb to a limit in the amount of genomic instability they can tolerate. In particular, our results showed that patients with intermediate genomic instability have a very poor outcome and that this relation is only evident among treatment-naïve patients, but not among patients treated with DNA-damaging agents. Further they show that we can measure genomic instability per clone and that clones with extreme genomic instability typically don't grow large. Our hypothesis that genomic instability, rather than proliferation rate, determines how sensitive a tumor is to DNA damaging agents on the long-term, is founded on two unexpected findings: (i) Patients with extremely high genomic instability per tumor clone have an exceptionally good outcome. Aim 1 will integrate exome- and single cell RNA-seq data to characterize clones and to measure how much genomic instability they can tolerate. (ii) Low genomic instability is associated with reduced benefit from DNA-damaging agents. Aim 2 will use comet assays and treatment history to quantify DNA damage per clone, relating it to the clones' ability to tolerate DNA damage and to changes in the genomic instability of therapy-surviving clones. This would be the first study to test the potential of genomic instability as biomarker of DNA-damage sensitivity. We will also use the clone specific transcriptomes and genomes from this cohort for a discovery study of candidate biomarkers of DNA- damage sensitivity. The first two years of this project will take place in Dr. Hanlee Ji's lab. After this K99 phase, having learned to model pharmakometric interactions between DNA-damaging agents and the diverse clones that coexist in a tumor, Dr. Andor will continue as an independent researcher. Having identified the threshold of genomic instability above which clones have reduced fitness, Dr. Andor will subject these clones to DNA-damaging agents to quantify dose-dependent changes in genomic instability and how a clone's proximity to the genomic instability threshold affects its therapeutic sensitivity (R00).