Detection of Colorectal Cancer Adaptive Mutability May Justify Combination of Targeted- and Immune-Therapies

结直肠癌适应性突变的检测可能证明靶向治疗和免疫治疗相结合的合理性

• 批准号: 10289627
• 负责人: TIMOTHY J YEATMAN
• 金额: $ 6.88万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-20 至 2022-04-16
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10289627
• 关键词: BRAF gene; Biological Assay; Biological Markers; Biological Sciences; Cancer Etiology; Cancer cell line; Cell Line; Cells; Cessation of life; Colorectal Cancer; Combined Modality Therapy; Complex; DNA; DNA Repair Gene; DNA sequencing; Data; Dependence; Diagnosis; Drug Tolerance; Drug resistance; Epidermal Growth Factor Receptor; Exposure to; Gene Expression Profile; Gene Frequency; Genes; Genetic; Genome; Immune; Immune checkpoint inhibitor; Immunotherapy; Individual; KRAS2 gene; Lead; MEKs; Measurable; Measures; Mediating; Microsatellite Instability; Mismatch Repair; Molecular; Molecular Target; Mutate; Mutation; Oncogenes; Organoids; Pathway interactions; Patients; Pharmaceutical Preparations; Phenotype; Polymerase; Population; Probability; Ras Inhibitor; Ras Signaling Pathway; Ras/Raf; Reactive Oxygen Species; Reporting; Resistance; Signal Pathway; Signal Transduction; Solid; Technology; Testing; Time; base; biological adaptation to stress; biomarker-driven; cancer cell; checkpoint therapy; clinical predictors; colon cancer cell line; colorectal cancer screening; detection limit; experimental study; gene panel; genetic variant; genome-wide; genotoxicity; homologous recombination; immune checkpoint; immunogenicity; improved; inhibitor/antagonist; mutant; mutational status; neoantigens; novel; novel therapeutics; patient subsets; predicting response; predictive marker; repair enzyme; resistance mechanism; response; sound; targeted agent; targeted treatment; therapeutic target; transcriptome sequencing; tumor

PROJECT SUMMARY/ABSTRACT Colorectal cancer (CRC) is a major cause of cancer deaths which is curable if detected early. Unfortunately, many CRC tumors are diagnosed at more advanced stages where cure rates remain low with 20% five-year survival. The EGFR/RAS signaling pathway is a strong driver of CRC when constitutively activated via mutations (KRAS ~40%, BRAF ~10%, NRAS ~5%), but targeted molecular inhibitors, when used alone (EGFRi, BRAFi, MEKi or ERKi), have yielded disappointing survival benefit. To date, it remains difficult to identify the subset of patients who will meaningfully benefit from EGFR/RAS pathway-targeted therapies, likely due to complex resistance mechanisms. A widely held view is that resistance to targeted therapies is due to pre-existence of rare, drug-resistant mutant cells (subclones) that expand and repopulate the tumor following initial successful treatment leading to permanent, clonal resistance. Recently, however, adaptive mutability (AM) of CRC in response to targeted therapies has been reported as a novel, early resistance mechanism. This hypothesis proposes that blocking critical, hard-wired signaling pathways causes a “stress” reaction characterized by the of genotoxic, reactive oxygen species (ROS) and the suppression of DNA mismatch repair enzymes. These early drug-induced changes effectively cause a sub-clonal, hypermutable state that facilitates the eventual emergence of permanently drug-resistant clones. Microsatellite instability (MSI) and other mutator states (i.e. POLE-mutated tumors) are now known to provide a greater probability of checkpoint inhibitor responses. Thus, we hypothesize that the AM induced by EGFR/RAS pathway inhibitors may lead to rapid, sub-clonal, enhanced mutability, and a higher load of neoantigens producing an “MSI-like” state. This hypermutability, if detectable, would portend the higher likelihood of response to checkpoint inhibitors. Traditional analysis of tumor mutation burden (TMB) by NGS assessment of a cancer gene panel would not likely detect genome-wide sub-clonal TMB (scTMB). Standard TMB assays detect bountiful, clonally-expanded mutations fixed in the tumor from the time of its founding. Conversely, we propose that the mutations resulting from a rapid, drug-induced mutator phenotype will likely be present at low variant allele frequencies (i.e. subclonal) that are below the limit of detection of standard NGS approaches. In this proposal, we will test the hypothesis that scTMB occurs in response to targeted therapies, and can be detected using an ultrasensitive and highly specific genome-wide Duplex DNA sequencing assay as an indicator (biomarker) of a mutator state induced by targeted therapies. We propose that the presence of scTMB would predict responses to checkpoint inhibitors, and suggest a benefit to targeted therapies combined with checkpoint inhibitors. These studies will lead to a better molecular understanding of the newly identified “adaptive mutability” resistance mechanism, and potentially provide a solid rationale for the use of combination targeted- and immune-therapies in biomarker-selected patient subpopulations to improve response.

项目摘要/摘要 结直肠癌（CRC）是癌症死亡的主要原因，如果早期检测到可以治愈。很遗憾， 许多CRC肿瘤在更高级的阶段被诊断为较低，五年五年 生存。当通过突变持续激活时，EGFR/RAS信号通路是CRC的强大驱动力 （KRAS 〜40％，BRAF〜10％，NRAS〜5％），但单独使用时具有靶向分子抑制剂（Egfri，Brafi， Meki或Erki）产生了令人失望的生存收益。迄今为止，很难识别 将有意义地受益于EGFR/RAS途径靶向疗法的患者，这可能是由于复杂的 电阻机制。一个广泛认为的观点是，对靶向疗法的抗性是由于先前存在的 最初成功后，罕见的，耐药的突变细胞（亚克隆）扩展和重新填充肿瘤 治疗导致永久性克隆耐药性。然而，最近，CRC的适应性可突变性（AM） 据报道，对靶向疗法的反应是一种新型的早期抗性机制。这个假设 阻止临界，硬连线信号通路的建议会导致以OF为特征的“应力”反应 遗传毒性，活性氧（ROS）和DNA错配修复酶的抑制。这些早 药物诱导的变化有效地引起了亚克隆的，超切的状态，可促进最终出现 永久性耐药克隆。微卫星不稳定性（MSI）和其他突变态（即极线突变 现在已知肿瘤提供更大的检查点抑制剂反应的可能性。那我们假设 EGFR/RAS途径抑制剂诱导的AM可能会导致快速，亚连锁，增强的可突变性和 较高的新抗原产生“ MSI状”状态。如果检测到这种超显性，则将预示 对检查点抑制剂的响应可能性较高。肿瘤突变的传统分析伯嫩（TMB） 通过NGS评估癌症基因面板，不太可能检测到全基因组亚共子TMB（SCTMB）。 标准TMB测定从肿瘤中固定在肿瘤中的广阔的，克隆膨胀的突变。 成立。相反，我们提出突变是由快速，药物诱导的突变表型引起的 可能以低于检测极限的低变异等位基因频率（即亚克隆）存在 标准NGS方法。在此提案中，我们将检验以下假设：SCTMB发生在 靶向疗法，可以使用超敏感和高度特异性基因组双链DNA检测 测序测定作为靶向疗法引起的突变态的指标（生物标志物）。我们提出了这一点 SCTMB的存在将预测对检查点抑制剂的响应，并提出针对目标的好处 疗法结合检查点抑制剂。这些研究将使人们对 新确定的“适应性突变性”抗性机制，并有可能为 在生物标志物选择的患者亚群中使用靶向和免疫疗法以改善 回复。