Oncogenic pathway-induced fragile sites: a new paradigm for understanding genome instability in cancer

摘要 癌症研究的重大挑战之一是对治疗的反应性存在巨大的异质性， 不同的癌症类型。我们在治疗某些癌症方面取得了很大进展，而其他癌症的预后 仍然令人沮丧。大规模的全基因组序列（WGS）分析已经确定了“断点签名” 不同的癌症类型，可能反映了其潜在的破坏途径的异质性，但药物- gable靶仅在断裂产生致癌融合蛋白的情况下出现。的能力 使用WGS预测被破坏的通路将对癌症诊断和治疗产生高度影响。染色体- 当培养的细胞经历脆性时，一些脆性位点（FS）表现为中期染色体上的间隙和断裂。 复制应力。然而，许多FS不是癌症类型特异性的，并且在癌症中有许多断点热点 是未知的FS，这严重限制了FS字段的影响。因为培养的细胞提供了 前瞻性地剖析引发染色体断裂的机制，并跟踪它们向复杂的 由于结构变异，迫切需要使这些体外系统与癌症更相关。我们的长期 我们的目标是建立一个持续的研究策略，可以预测哪些已知的途径被破坏，在一个给定的 癌症的类型。本提案的总体目标是通过以下方式揭示机制： 这种与癌症相关的细胞通路的扰动在细胞培养物中产生FS的通路特异性模式 并确定这些模式是否可以在癌症中识别出来。我们的中心假设是， 只有在以下情况下，剖析导致癌症断裂点特征的机制的体外系统才变得明显： 从化学诱导的FS转向通过干扰已知的癌症相关途径诱导的FS。 我们已经表明，不同癌基因的过度表达导致FS和前- 初步数据表明了这种情况发生的一些机制。我们的理论是了解癌症- 指定FS的相关机制将填补体外FS与癌症断点之间的差距。这将是 这是从癌症WGS数据中预测中断途径的策略的重要一步，从而提出治疗建议。 治疗以前难治的癌症。Aim 1将使用高吞吐量/分辨率复制和Oligopaints 鉴定下游机制的测定， 延迟表现为FS。目标2将阐明上游机制造成复制延迟和FS在特定的 网站. Aim 3将以前所未有的分辨率映射FS，并挖掘肿瘤测序数据库中的签名， 与癌基因特异性FS相匹配。这一贡献将是重要的，因为能够确定受影响的 仅来自断点签名的途径将暴露肿瘤特异性的精确癌症脆弱性 药拟议的研究是创新的，因为它将振兴金融服务研究的影响，关闭 体外系统和体内癌症之间的差距，同时利用新技术操纵细胞， 他们的基因组不稳定性的标志，并将它们与癌症断点标志相匹配。

ABSTRACT One of the grand challenges in cancer research is the vast heterogeneity in responsiveness to treatment for different cancer types. We have made great strides in treating some cancers, while the prognosis for others remains dismal. Large scale whole genome sequence (WGS) analyses have identified “breakpoint signatures” of different cancer types that presumably reflect heterogeneity in their underlying disrupted pathways but, drug- gable targets have emerged only in cases where the breaks create oncogenic fusion proteins. The ability to predict disrupted pathways using WGS would be highly impactful for cancer diagnosis and treatment. Chromo- some fragile sites (FSs) manifest as gaps and breaks in metaphase chromosomes when cultured cells experi- ence replication stress. However, many FSs are not cancer-type specific and many breakpoint hotspots in cancer are not known FSs, which has severely limited the impact of the FS field. Since cultured cells offer the potential to prospectively dissect mechanisms initiating chromosome breaks and to track their expansion into complex structural variation, there is a critical need to make these in vitro systems more cancer relevant. Our longterm goal is to establish a sustained research strategy that can predict which known pathways are disrupted in a given cancer type from their breakpoint patterns. The overall objective of this proposal is to reveal mechanisms by which perturbation of cancer-relevant cellular pathways produce pathway-specific patterns of FSs in cell culture and determine whether those patterns can be identified in cancers. Our central hypothesis is that the power of in vitro systems to dissect mechanisms leading to cancer breakpoint signatures will become evident only when shifted away from chemically-induced FSs towards FSs induced by perturbing known cancer-relevant pathways. We have shown that overexpression of different oncogenes leads to oncogene-specific spectra of FSs and pre- liminary data suggest some of the mechanisms by which this occurs. Our rationale is that understanding cancer- relevant mechanisms that specify FSs will fill the gap in linking in vitro FSs to cancer breakpoints. This would be a major step toward a strategy to predict disrupted pathways from cancer WGS data, thereby suggesting treat- ments for previously intractable cancers. Aim1 will use high throughput/resolution replication and Oligopaints assays to identify downstream mechanisms distinguishing which of many sites of oncogene-induced replication delay manifest as FSs. Aim2 will elucidate upstream mechanisms causing replication delays and FS at specific sites. Aim3 will map FSs at unprededented resolution and mine tumor sequencing databases for signatures that match those of oncogene-specific FSs. This contribution will be significant because the ability to identify affected pathways solely from breakpoint signatures would expose tumor-specific vulnerabilities for precision cancer medicine. The proposed research is innovative because it will rejuvenate the impact of FS research, closing the gap between in vitro systems and in vivo cancers while leveraging novel technologies to manipulate cells, map their signatures of genome instability and match them to cancer breakpoint signatures.