CLINCIAL VALIDATION OF APC AND TP53 AS BIOMARKERS FOR CETUXIMAB RESPONSE

APC 和 TP53 作为西妥昔单抗反应生物标志物的临床验证

• 批准号: 10381742
• 负责人: TIMOTHY J YEATMAN
• 金额: $ 29.88万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-03 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10381742
• 关键词: APC gene; Age; Alleles; Archives; BRAF gene; Biological Assay; Biological Markers; Cancer and Leukemia Group B; Caring; Cell Line; Certification; Cetuximab; Clinic; Clinical; Clinical Trials; Code; Colorectal Cancer; Consensus Sequence; Cyclophosphamide; DNA sequencing; Data; Drug Utilization; Engineering; Ensure; Environment; Epidermal Growth Factor Receptor; Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor; FDA approved; Formalin; Freezing; Funding; Gene Expression Profile; Gene Frequency; Genes; Genotype; Gold; Human; In Vitro; KRAS2 gene; Knowledge; Laboratories; Left; Lesion; Measures; Modeling; Molecular; Mutate; Mutation; Mutation Detection; Negative Finding; Observational Study; Oncogenes; Outcome; Paraffin Embedding; Patient Recruitments; Patient Selection; Patients; Performance; Pharmacologic Substance; Phase; Publishing; Ras/Raf; Reporting; Reproducibility; Research Personnel; Resistance; Role; Sampling; Sensitivity and Specificity; Side; TP53 gene; Testing; The Cancer Genome Atlas; Therapeutic; Tissue Sample; Translating; Treatment outcome; Tumor Suppressor Genes; Validation; Work; aged; base; cancer genetics; clinical practice; cohort; colon cancer patients; colorectal cancer treatment; cost effective; experience; genetic predictors; improved; indexing; inhibitor therapy; metastatic colorectal; mutant; panitumumab; prognostic; rapid test; response; therapeutic target; tumor; tumor heterogeneity

PROJECT SUMMARY/ABSTRACT The objective of this combined UH2/UH3 application is to develop a cost-effective, rapid, test that can be rapidly translated to the clinic and ultimately be used to re-purpose a class of FDA-approved colorectal cancer (CRC) EGFR inhibitor (EGFRi) therapeutics (cetuximab and panitumumab). To date, only negative genetic predictors (mutant KRAS/NRAS) of EGFRi response have been employed clinically, currently restricting EGFRi use to wild-type RAS/RAF subpopulations, and more recently, just to “left-sided” lesions. We recently reported a new prognostic role for APC that relates to the number of alleles mutated and to the association with other mutant genes such as KRAS and TP53 (Nat Commun, 2016). Further analysis also revealed that mutant APC (A) genotypes, in combination with mutant TP53 (P), are strongly correlated with a gene expression signature measuring cetuximab sensitivity (CTX-S). These data led to the provocative hypothesis that mutant APC + TP53 (AP) genotypes together---more so than either mutant gene alone (A_ / _P), or wild-type AP (_ _)---may have a new role in positively-predicting EGFRi outcomes (Nat Commun, Under Review, 2018). This hypothesis is based on 3 key observations we have recently made in our cohort and in TCGA data: (1) CTX-S scores are significantly higher in: AP > A_ / _P > _ _ tumors in both WT and MUT KRAS tumors; (2) AP mutations are more frequent in Left (cetuximab-sensitive) > Right (cetuximab-resistant) CRC; (3) AP mutations are almost non-existent in MSI tumors (highly cetuximab-resistant). These findings have two potentially high-impact clinical implications: (1) they re-define the patient selection strategy by further restricting EGFRi therapies to wild-type RAS/RAF patients harboring AP mutations, thereby increasing response rates; (2) they could expand the therapeutic opportunity to treat a substantial number of previously-excluded mutant KRAS/NRAS patients who have AP mutations in both left and right CRCs. If the test for these mutations is developed and clinically validated, the utilization of these drugs could be expanded to ~25% more patients, including more first-line patients. For the vast majority of CRC patients, AP mutations are not assessed in current practice. Unlike KRAS/NRAS oncogenes, both A and P are tumor suppressor genes that can have a multitude of inactivating mutations that must be detected. Thus, there is an opportunity to change clinical practice and standards of care to ultimately improve CRC outcomes with a new test. In the LabCorp CAP/CLIA environment, we plan to develop a new highly sensitive, specific and cost-effective targeted DNA-sequencing “assay” to detect mutations in the coding regions of the principal genes APC, TP53, KRAS, BRAF, NRAS from formalin fixed paraffin embedded (FFPE) tissue samples. In the UH2 Phase of this proposal, a new FFPE targeted DNA sequencing assay, with greater potential to accurately detect mutations at low allelic frequencies, will be analytically validated with the following approaches so that it can be offered in a CAP/CLIA laboratory for testing clinical samples: (1) A variety of cell lines, both native and engineered, will be used to ensure analytic sensitivity, specificity, and reproducibility. (2) ~100 formalin fixed paraffin embedded (FFPE) samples of variable age, quality, tumor heterogeneity, grade, and stage matched to the highest quality, “gold standard” fresh frozen (FF) samples from the same originating tumor will be used to assess assay performance. In the UH3 Phase, we plan to perform clinical validation of the test developed in the UH2 Phase to provide evidence that the presence of AP mutations may predict EGFRi responses translating into improved clinical outcomes. Here, we will demonstrate that assay of APC and TP53 genotypes along with those already performed as SOC (KRAS/NRAS/BRAF) can be clinically validated (i.e. used to predict cetuximab sensitivity/response) using human samples derived from: (1) a retrospective CRC observational study relating CRC genetics to predicted cetuximab sensitivity. (2) a historical NCI trial (CALGB 80203) where patients were treated with cetuximab but were not sequenced.

项目总结/摘要 这种UH 2/UH 3组合应用的目的是开发一种具有成本效益的快速测试， 迅速转化为临床，并最终用于重新利用一类FDA批准的结直肠癌 癌症（CRC）EGFR抑制剂（EGFRi）治疗（西妥昔单抗和帕尼单抗）。迄今为止，只有负 EGFRi应答的遗传预测因子（突变型KRAS/NRAS）目前已在临床上使用 限制EGFRi用于野生型RAS/RAF亚群，最近仅用于“左侧”病变。 我们最近报道了APC的一个新的预后作用，它与突变等位基因的数量和 与其他突变基因如KRAS和TP 53相关（Nat Commun，2016）。进一步分析还 突变型APC（A）基因型与突变型TP 53（P）基因型的结合，与 测量西妥昔单抗敏感性的基因表达特征（CTX-S）。这些数据引发了 假设突变APC + TP 53（AP）基因型一起-比单独的突变基因（A_ / _P）或野生型AP（_ _）--可能在阳性预测EGFRi结果中具有新的作用（Nat Commun， 2018年）。这一假设基于我们最近在队列中进行的3项关键观察 在TCGA数据中： (1)CTX-S评分在WT和MUT KRAS肿瘤中均显著高于AP > A_ / _P > _ _肿瘤; (2)AP突变在左（西妥昔单抗敏感）>右（西妥昔单抗耐药）CRC中更常见; (3)AP突变在MSI肿瘤中几乎不存在（高度西妥昔单抗耐药）。 这些发现有两个潜在的高影响力的临床意义：（1）他们重新定义病人的选择 通过进一步将EGFRi疗法限制于携带AP突变的野生型RAS/RAF患者， 提高反应率;（2）它们可以扩大治疗机会，以治疗大量的 之前排除的突变型KRAS/NRAS患者，在左侧和右侧CRC中均存在AP突变。如果 这些突变的测试开发和临床验证，这些药物的使用可以扩大 增加约25%的患者，包括更多的一线患者。对于绝大多数CRC患者，AP 在目前的实践中没有评估突变。与KRAS/NRAS癌基因不同，A和P都是肿瘤基因。 抑制基因可能具有大量必须检测的失活突变。因此， 有机会改变临床实践和护理标准，最终改善CRC结果， test. 在LabCorp CAP/CLIA环境中，我们计划开发一种新的高度敏感，特异性和成本效益高的 靶向DNA测序“测定法”检测主要基因APC，TP 53， 福尔马林固定石蜡包埋（FFPE）组织样本的KRAS、BRAF、NRAS。 在该提案的UH 2阶段，一种新的FFPE靶向DNA测序检测方法，具有更大的潜力， 准确检测低等位基因频率的突变，将通过以下方法进行分析验证 方法，以便可以在CAP/CLIA实验室中提供用于测试临床样品的方法： (1)将使用各种天然和工程化的细胞系来确保分析灵敏度、特异性和特异性。 再现性 (2)约100份福尔马林固定石蜡包埋（FFPE）样本，年龄、质量、肿瘤异质性各不相同， 等级和阶段匹配的最高质量，“黄金标准”新鲜冷冻（FF）样品来自相同的 起源肿瘤将用于评估测定性能。 在UH 3阶段，我们计划对UH 2阶段开发的测试进行临床确认，以提供 证据表明AP突变的存在可以预测EGFRi反应转化为改善的临床 结果。在这里，我们将证明APC和TP 53基因型的测定沿着那些已经被证实的基因型。 作为SOC（KRAS/NRAS/BRAF）进行，可进行临床验证（即用于预测西妥昔单抗 灵敏度/响应），使用源自以下的人样品： (1)一项回顾性CRC观察性研究，将CRC遗传学与预测的西妥昔单抗敏感性联系起来。 (2)一项历史性NCI试验（CALGB 80203），患者接受西妥昔单抗治疗，但未进行测序。