Molecular Analysis of NeoAdjuvant Platinum in Triple Negative Breast Cancer

描述（由申请人提供）：本申请涉及广泛的挑战领域（04）临床研究，以及特定的挑战主题04- gm -101：个性化药物反应和毒性。挑战和潜在影响：乳腺癌的全球发病率为每年1,151,298例，是最常见的癌症，也是妇女癌症死亡的第二大原因（每年46.5万例）。三阴性乳腺癌（TNBC）的定义是雌激素受体（ER）、孕激素受体（PR）和人表皮生长因子受体2 （HER-2）缺乏表达，占所有乳腺癌的15-20%，临床结果较差，部分原因是缺乏现有的靶向治疗。目前，对于治疗此类患者的最佳化疗方案尚无共识。临床前数据表明，由于brca相关的DNA修复缺陷，尤其是同源重组缺陷，TNBC可能对铂基化疗敏感。因此，我们假设基因表达变化将在局部晚期三阴性乳腺癌患者中确定，这些患者与铂类化疗的病理和/或临床完全缓解有关。本研究的目的是评估在接受新辅助铂类化疗的TNBC患者中，与病理（pCR）和临床完全缓解（cCR）相关的基因表达谱和/或拷贝数变异，以确定可靠的生物标志物用于反应预测。方法：为了解决这一挑战，我们回顾性分析了1999年1月至2008年6月在迈阿密大学西尔维斯特综合癌症中心/杰克逊纪念医院接受新辅助化疗的674例局部晚期乳腺癌（LABC）患者。其中125例（18.5%）患者经组织病理学证实为TNBC。所有患者均接受新辅助铂盐治疗。病理完全缓解（pCR）被严格定义为乳腺和腋窝无残留侵袭性疾病。根据Kaplan-Meier （K-M）分析计算RFS和OS估计值。患者年龄中位数为50岁（28-86岁），60%为绝经前患者，54%为西班牙裔，34%为非洲裔，其余为白种人。发病时TNM分期分布：T1 0.9%, T2 5.2%, T3 53.4%, T4 40.5%, N0 25.0%, N1 36.2%, N2 35.4%, N3 3.4%, M0 100%，炎性乳腺癌11%，中位肿瘤大小9.5cm。随访时间为0.2至8.9年。125例患者中有42例（34%;95% CI 26-42%）检测到pCR。在实现pCR的患者亚组中，K-M分析的中位RFS尚未达到，而非pCR的中位RFS为2.6年（P=0.0002）。此外，获得pCR的患者有显著更高的生存期（中位生存期未达到vs. 5.1年，pCR vs.非pCR； P=0.001）。迄今为止，这是最大的单一机构队列报道的局部晚期TNBC患者统一使用铂类化疗方案治疗。为了验证我们的假设，我们将完成以下具体目标：目的一：确定局部晚期三阴性BC样本中病理完全应答者和无应答者之间基因表达的全基因组差异。目的2：在未表现出pCR的患者的局部晚期三阴性BC样本中，鉴定临床完全应答者和无应答者之间基因表达的全基因组差异。目的3：研究可能与基因表达差异相关的染色体改变。从历史上看，表达阵列技术的使用一直依赖于新鲜冷冻肿瘤组织中完整RNA的可用性，因此不可能对许多大型回顾性队列进行带注释的临床随访研究。然而，使用一种创新的方法，我们最近成功地测试了一种新型阵列探针，这种探针专门用于检测来自迈阿密大学样本的FFPE乳腺肿瘤材料中部分降解的RNA。使用极端3'序列的问题集减轻了以前的技术限制，因此被认为是高度创新的。重要的是，高密度阵列CGH技术与表达阵列数据的整合是新颖的（据我们所知，这是第一个在铂治疗的局部晚期三阴性乳腺癌队列中进行的研究）。这种方法将允许识别特定拷贝数变异和杂合性损失，以及它们与基因表达变化的关系。我们的最终目标将是进一步了解疾病的生物学，并开发预测性生物标志物，以有效治疗TNBC亚组，否则预后不良。

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (04) Clinical Research, and specific Challenge topic 04-GM-101: Personalized drug response and toxicity. The Challenge and Potential Impact: With a global incidence of 1,151,298 each year, breast cancer is the most frequently diagnosed cancer and the second leading cause of cancer death (465,000/year) in women. Triple-negative breast cancer (TNBC), defined by lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2), accounts for 15-20% of all breast cancers and is associated with poor clinical outcome, in part due to the lack of available targeted treatments. Currently, there is no consensus regarding optimal chemotherapy regimens for the treatment of such patients. Preclinical data suggests that TNBC may be sensitive to platinum-based chemotherapy because of deficiencies in BRCA-associated DNA repair, especially defective homologous recombination. We therefore hypothesize that gene expression changes will be identified in locally advanced triple negative breast cancer patients which are associated with pathological and/or clinical complete response to platinum-based chemotherapy. The aim of this study is to evaluate gene expression profiles and/or copy number variation associated with pathologic (pCR) and clinical complete response (cCR), in patients with TNBC treated with neoadjuvant platinum-based chemotherapy, in order to identify robust biomarkers for response prediction. The Approach: In order to address this challenge, we retrospectively reviewed 674 patients with locally advanced breast cancer (LABC) who received neoadjuvant chemotherapy between January 1999 and June 2008 at the University of Miami Sylvester Comprehensive Cancer Center/Jackson Memorial Hospital. Of these, 125 (18.5%) patients had histopathologic confirmation of TNBC. All patients received neoadjuvant platinum salts. Pathologic complete response (pCR) was strictly defined as no residual invasive disease in breast and axilla. RFS and OS estimates were calculated according to Kaplan-Meier (K-M) analysis. Patient demographics indicate a median age of 50 years (range 28-86 years), 60% premenopausal, 54% Hispanic, 34% African descent, and the remainder Caucasian. The TNM stage distribution at presentation: T1 0.9%, T2 5.2%, T3 53.4%, T4 40.5%, N0 25.0%, N1 36.2%, N2 35.4%, N3 3.4%, M0 100%, inflammatory breast cancer 11%, median tumor size = 9.5cm. Follow up duration ranged from 0.2 to 8.9 years. pCR was observed in 42 of 125 patients (34%; 95% CI 26-42%). Median RFS by K-M analysis has not yet been reached in the subgroup of patients achieving a pCR, while the median RFS for non-pCR was 2.6 years (P=0.0002). Moreover, patients achieving pCR had significantly higher OS (median OS not reached vs. 5.1 years, pCR vs. non-pCR, respectively; P=0.001). To date, this is the largest reported single institution cohort of locally advanced TNBC uniformly treated with platinum-based chemotherapy regimens. In order to test our hypothesis, we will complete the following specific aims: Aim I: Identify genome-wide differences in gene expression between pathological complete responders and non-responders in locally advanced triple negative BC samples. Aim 2: Identify genome-wide differences in gene expression between clinical complete responders and nonresponders among locally advanced triple negative BC samples from patients which do not exhibit pCR. Aim 3: Investigate possible chromosomal alterations associated with gene expression differences. The use of expression array technology historically has been dependent upon the availability of intact RNA from fresh frozen tumor tissue for analysis, thus study of the many large retrospective cohorts with annotated clinical follow-up has not been possible. However, using an innovative approach we have recently successfully tested novel array probes specifically designed to detect partially degraded RNA from FFPE breast tumor material from samples at the University of Miami. The use of a probeset with extreme 3' sequence mitigates this previous technical limitation, and thus is considered highly innovative. Importantly, integration of high density array CGH technology with the expression array data is novel (to our knowledge, the first study in a well characterized platinum-treated locally advanced triple negative breast cancer cohort). This approach will allow identification of specific copy number variations and loss of heterozygosity, and their relation to gene expression changes. Our eventual goal will be to develop further understanding of biology of disease, and develop predictive biomarkers, for effective treatment for the subgroup of TNBC, who otherwise have poor prognosis. PUBLIC HEALTH RELEVANCE: With a global incidence of 1,151,298 each year, breast cancer is the most frequently diagnosed cancer and the second leading cause of cancer death (465,000/year) in women. Triple-negative breast cancer (TNBC), defined by lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2), accounts for 15-20% of all breast cancers and is associated with poor clinical outcome, in part due to the lack of available targeted treatments. Currently, there is no consensus regarding optimal chemotherapy regimens for the treatment of such patients. Preclinical data suggests that TNBC may be sensitive to platinum-based chemotherapy because of deficiencies in BRCA-associated DNA repair, especially defective homologous recombination. We therefore hypothesize that gene expression changes will be identified in locally advanced triple negative breast cancer patients which are associated with pathological and/or clinical complete response to platinum-based chemotherapy. The aim of this study is to evaluate gene expression profiles and/or copy number variation associated with pathologic (pCR) and clinical complete response (cCR), in patients with TNBC treated with neoadjuvant platinum-based chemotherapy, in order to identify robust biomarkers for response prediction