Towards identification of prognostic gene sets in breast cancer: The E2197 Trial

描述(申请人提供)：随着我们的发展，临床决策将更多地依赖于肿瘤的基因特征，而不是更少地依赖于临床特征。因此，识别和随后验证可用于准确估计乳腺癌复发风险的生物标记物是当务之急。为此，我们的假设是，基于激素受体和HER2状态的乳腺癌亚型具有独特的基因组突变星座，表现为基因表达和蛋白质信号通路的特定变化。我们进一步假设，这些主要的乳腺癌表型包含特定类别的特定信号通路改变，驱动疾病过程本身，最关键的是作为治疗分层和有效药物靶点的生物标记物的候选。我们的总体目标是通过对来自E2197临床试验的福尔马林固定、石蜡包埋(FFPE)肿瘤样本进行分子图谱分析，确定不同患者亚组中的基因集，这些样本将在预测复发方面具有预后价值。ECOG E2197临床试验是一项已完成的第三阶段多点试验，涉及对2952名乳腺癌患者进行随机分组，以比较阿霉素/多西紫杉醇(AT)和阿霉素/环磷酰胺(AC)治疗结节阳性和高风险结节阴性乳腺癌的疗效。我们的主要目标是根据E2197患者不同亚组中预测复发的能力来确定基因。其他目标将包括：1)比较OncotypeDX基因集合的全基因组(WG)-DASL(cDNA-介导性退火、选择和连接)分析中产生的数据与OncotypeDX分析的数据，这将用作WG-DASL平台的验证；2)确定一组最重要的个体基因作为预后标记物；3)比较来自先前研究的OncotypeDX分析的预后价值与本研究中确定的基因组；4)比较从先前研究的371个基因集合中选择的基因与本研究中确定的基因的预后价值；5)比较PAM50基因集与本研究确定的基因的预后价值。为此，我们将从来自E2197的868例FFPE肿瘤标本中提取总RNA，将其分为4个亚组：1)HR+，HER2-；2)HR+，HER2+；3)HR-，HER2+；4)HR-，HER2-和。提取的RNA的表达谱将在WG-DASL平台上执行，该平台将询问24,526个mRNA转录本。一组标志性基因将根据它们预测无复发间期(RFI)作为乳腺癌无癌生存率(BCFs)和总生存率(OS)的主要终点和次要终点的能力而被选择。潜在的生物标志物将通过TaqMan定量实时聚合酶链式反应(qRT-PCR)进行验证。预后生物标记物将在后续研究中进行前瞻性验证。 公共卫生相关性：现有的辅助化疗药物，如阿霉素、多西紫杉醇和环磷酰胺，及其组合，对于大批淋巴结阳性的早期乳腺癌妇女来说是有效的辅助治疗，但许多患者仍然复发并死于他们的疾病。因此，识别和随后验证可用于准确估计乳腺癌复发风险的生物标记物是当务之急。我们的假设是，主要的乳腺癌表型包含特定的信号通路改变，这些改变是特定类别的，驱动疾病过程本身，最关键的是作为治疗分层和有效药物靶点的候选生物标记物。

DESCRIPTION (provided by applicant): As we move forward, clinical decision making will rely more heavily on the genetic characteristics of the tumor and less on the clinical characteristics. Thus, identification and subsequent validation of biomarkers that can be used to accurately estimate the recurrence risk of breast cancer is a high priority. To this end, our hypothesis is that breast cancer subtypes, based upon hormone receptor and HER2 status, possess a unique constellation of genomic mutations that manifest in specific alterations in gene expression and protein signaling pathways. We further hypothesize that these major breast cancer phenotypes, contain specific signaling pathway alterations that are class-specific, drive the disease process itself, and most critically serve as candidates for biomarkers for therapy stratification and effective drug targets. Our overall objective is to identify gene sets within different subgroups of patients through molecular profiling of formalin-fixed, paraffin-embedded (FFPE) tumor samples from the E2197 clinical trial that will have prognostic utility in predicting recurrence. The ECOG E2197 clinical trial is a completed Phase III multisite trial that involved the randomization of patients (2,952) with primary breast cancer to compare the effectiveness of doxorubicin/docetaxel (AT) versus doxorubicin/cyclophosphamide (AC), in treating women with node-positive and high risk node-negative breast cancer. Our primary objective is to identify genes based upon their ability to predict recurrence within the different subgroups of E2197 patients. Additional objectives will involve 1) comparing the data generated in the whole genome (WG)-DASL (cDNA-mediated annealing, selection and ligation) assay for the OncotypeDX set of genes with data from the OncotypeDX assay which will serve as a validation of the WG-DASL platform; 2) defining a set of the most significant individual genes as prognostic markers; 3) comparing the prognostic value of the OncotypeDX assay from a previous study with gene sets determined in this study; 4) comparing the prognostic value of genes selected from a set of 371 genes from a previous study with genes determined in this study; and 5) comparing the prognostic value of the PAM50 gene set with genes determined in this study. Toward that end, total RNA will be prepared from 868 FFPE tumor samples from E2197 classified into 4 patient subgroups as follows: 1) HR+, HER2-; 2) HR+, HER2+; 3) HR-, HER2+; 4) HR-, HER2- and . Expression profiling of the extracted RNA will be performed on the WG-DASL platform which will interrogate 24,526 mRNA transcripts. A signature set of genes will be selected based upon their ability to predict the recurrence-free interval (RFI) as the primary endpoint and secondary endpoints of breast cancer-free survival (BCFS), and overall survival (OS). Potential biomarkers will be validated by TaqMan quantitative real-time polymerase chain reaction (qRT-PCR). Prognostic biomarkers will be prospectively validated in a subsequent study. PUBLIC HEALTH RELEVANCE: Available adjuvant chemotherapies, such as doxorubicin, docetaxel and cyclophosphamide, and combinations thereof, are effective adjuvant treatment for the large population of women with node-positive early-stage breast cancer, but many patients still relapse and die of their disease. Thus, identification and subsequent validation of biomarkers that can be used to accurately estimate the risk of recurrence of breast cancer is a high priority. Our hypothesis is that the major breast cancer phenotypes contain specific signaling pathway alterations that are class-specific, drive the disease process itself, and most critically serve as candidates for biomarkers for therapy stratification and effective drug targets.