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.

项目概要/摘要 这种 UH2/UH3 组合应用的目标是开发一种经济高效、快速的测试，可以 迅速转化为临床并最终用于重新利用 FDA 批准的一类结直肠药物 癌症 (CRC) EGFR 抑制剂 (EGFRi) 疗法（西妥昔单抗和帕尼单抗）迄今为止仅呈阴性。 EGFr 反应的遗传预测因子（突变型 KRAS/NRAS）目前已应用于临床 将 EGFRi 的使用限制于野生型 RAS/RAF 亚群，最近又仅限于“左侧”病变。 我们最近报道了 APC 的一个新的预后作用，该作用与突变等位基因的数量和 与其他突变基因（例如 KRAS 和 TP53）的关联（Nat Commun，2016）。 研究表明，突变型 APC (A) 基因型与突变型 TP53 (P) 相结合，与 测量西妥昔单抗敏感性（CTX-S）的基因表达特征这些数据引发了争议。 假设突变 APC + TP53 (AP) 基因型在一起——比单独的任一突变基因更有效 (A_ / _P) 或野生型 AP (_ _)——可能在积极预测 EGFRi 结果方面发挥新作用（Nat Commun， 正在审查中，2018 年）。这一假设基于我们最近在队列中进行的 3 个关键观察。 TCGA 数据中： (1) CTX-S评分在WT和MUT KRAS肿瘤中均显着较高：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) MSI肿瘤（西妥昔单抗高度耐药）中几乎不存在AP突变。 这些发现具有两个潜在的高影响力的临床意义：（1）它们重新定义了患者选择 该策略进一步限制 EGFRi 疗法仅适用于携带 AP 突变的野生型 RAS/RAF 患者，从而 提高缓解率；（2）它们可以扩大治疗大量患者的机会 先前排除的 KRAS/NRAS 突变患者，其左、右 CRC 均存在 AP 突变。 这些突变的测试已经开发出来并经过临床验证，这些药物的使用可以扩大 约 25% 的患者增加，包括更多的一线患者 对于绝大多数 CRC 患者，AP。 与 KRAS/NRAS 癌基因不同，A 和 P 都是肿瘤。 抑制基因可能具有大量必须检测的失活突变。 改变临床实践和护理标准的机会，最终通过新的方法改善结直肠癌结果 测试。 在 LabCorp CAP/CLIA 环境中，我们计划开发一种新的高度敏感、特异且具有成本效益的方法 靶向 DNA 测序“测定”来检测主要基因 APC、TP53、 来自福尔马林固定石蜡包埋 (FFPE) 组织样本的 KRAS、BRAF、NRAS。 在该提案的 UH2 阶段，一种新的 FFPE 靶向 DNA 测序分析具有更大的潜力 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本： (1) 将使用各种天然和工程细胞系来确保分析灵敏度、特异性和 再现性。 (2) ~100 个不同年龄、质量、肿瘤异质性的福尔马林固定石蜡包埋 (FFPE) 样本， 等级和阶段与来自同一样品的最高质量“黄金标准”新鲜冷冻 (FF) 样品相匹配 起源肿瘤将用于评估检测性能。 在UH3阶段，我们计划对UH2阶段开发的测试进行临床验证，以提供 有证据表明 AP 突变的存在可以预测 EGFRi 反应，从而转化为临床改善 在这里，我们将展示 APC 和 TP53 基因型的测定以及已经测定的结果。 作为 SOC (KRAS/NRAS/BRAF) 执行，可以进行临床验证（即用于预测西妥昔单抗 敏感性/反应）使用来自以下来源的人体样本： (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相关联。 (2) 历史性 NCI 试验 (CALGB 80203)，其中患者接受西妥昔单抗治疗，但未进行测序。