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

致癌途径诱导的脆弱位点：了解癌症基因组不稳定性的新范例

• 批准号: 10589809
• 负责人: David M Gilbert
• 金额: $ 50.49万
• 依托单位: SAN DIEGO BIOMEDICAL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-03-10 至 2027-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10589809
• 关键词: Address; Affect; Aphidicolin; Appearance; Architecture; Biological Assay; CCNE1 gene; Cancer Biology; Cell Culture Techniques; Cells; Chemicals; Chimeric Proteins; Chromosomal Breaks; Chromosome Fragile Sites; Chromosomes; Complex; Cultured Cells; DNA Sequence; Data; Development; Evolution; Frequencies; Genetic Transcription; Genomic Instability; Genomics; Goals; Health; Heterogeneity; Hot Spot; Human; In Vitro; Link; Location; Malignant Neoplasms; Maps; Metaphase; Methods; Minority; Mitosis; Monitor; Oncogenes; Oncogenic; Pathway interactions; Pattern; Pharmaceutical Preparations; Prognosis; Rejuvenation; Replication Initiation; Research; Resolution; Role; S phase; Sequence Analysis; Site; Specific qualifier value; Specificity; Stress; Structure; System; Testing; Variant; anticancer research; cancer diagnosis; cancer therapy; cancer type; clinically relevant; druggable target; experience; improved; in vivo; innovation; molecular sequence database; new technology; novel strategies; overexpression; precision oncology; prediction algorithm; prospective; replication stress; response; stressor; tumor; tumor progression; whole genome

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.

抽象的 癌症研究的巨大挑战之一是对治疗的反应存在巨大的异质性。 不同的癌症类型。我们在治疗某些癌症方面取得了长足进步，而其他癌症的预后 仍然惨淡。大规模全基因组序列（WGS）分析已识别出“断点特征” 不同癌症类型的研究可能反映了其潜在被破坏途径的异质性，但是，药物 只有在断裂产生致癌融合蛋白的情况下，山墙靶标才会出现。有能力 使用全基因组测序预测被破坏的通路将对癌症诊断和治疗产生巨大影响。铬- 当培养的细胞经历某些脆弱位点（FS）时，其表现为中期染色体中的间隙和断裂。 ence 复制压力。然而，许多 FS 并不具有癌症类型特异性，而且癌症中存在许多断点热点 都是未知的FS，这严重限制了FS领域的影响。由于培养细胞具有潜力 前瞻性地剖析启动染色体断裂的机制并追踪它们扩展到复杂的 由于结构变异，迫切需要使这些体外系统与癌症更加相关。我们的长期 目标是建立一个持续的研究策略，可以预测在给定的情况下哪些已知的途径被破坏 根据断点模式判断癌症类型。该提案的总体目标是通过以下方式揭示机制： 癌症相关细胞通路的扰动会在细胞培养物中产生通路特异性的 FS 模式 并确定是否可以在癌症中识别出这些模式。我们的中心假设是 只有当以下情况时，用于剖析导致癌症断点特征的机制的体外系统才会变得明显： 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会导致 FS 和预癌基因特异性谱。 初步数据表明了这种情况发生的一些机制。我们的理由是了解癌症—— 指定 FS 的相关机制将填补将体外 FS 与癌症断点联系起来的空白。这将是 这是朝着从癌症 WGS 数据中预测中断途径的策略迈出的重要一步，从而建议治疗 以前顽固性癌症的治疗。 Aim1 将使用高通量/分辨率复制和 Oligopaints 鉴定下游机制的测定，区分癌基因诱导复制的许多位点中的哪些位点 延迟表现为 FS。 Aim2 将阐明在特定情况下导致复制延迟和 FS 的上游机制 网站。 Aim3 将以前所未有的分辨率绘制 FS 图谱，并挖掘肿瘤测序数据库中的特征 与癌基因特异性 FS 相匹配。这一贡献将是巨大的，因为能够识别受影响的 仅来自断点特征的通路将暴露精准癌症的肿瘤特异性漏洞 药品。拟议的研究具有创新性，因为它将重振 FS 研究的影响，结束 体外系统和体内癌症之间的差距，同时利用新技术来操纵细胞，绘制地图 他们的基因组不稳定性特征并将其与癌症断点特征相匹配。