Construction of gene expression signatures with RAGE

乳腺癌影响美国八分之一的女性。目前的治疗方案倾向于将手术后辅助化疗扩展到具有更小原始肿瘤的淋巴结阴性患者，即使大多数此类患者似乎并未从此类治疗中获益。定义具有不同肿瘤复发可能性的这些患者亚组的分子特征的建立将是有用的，允许根据患者的预后定制治疗。我们还将建立一种新的全球基因表达分析程序，称为基因表达谱建立早期淋巴结阴性乳腺肿瘤。一组T1N0M0和T2N0M0乳腺肿瘤的回顾性研究，其中20例在5年内复发，20例未复发，将在1期进行研究。该方法将适用于高通量分离和分析技术，多重毛细管电泳，并通过各种手段将通量提高到每周约10，000次测量。将在40个回顾性肿瘤中的每一个中测量一组约3000个基因的表达水平。这些数据将与项目1中使用SAGE对这些肿瘤的子集收集的类似数据相结合。在I期获得的组合的SAGE数据将用于鉴定一组约700个候选特征基因，这些基因在复发性和非复发性肿瘤之间显示出显著的表达差异，或者预期在乳腺肿瘤发生中是重要的。该技术将用于第二阶段，研究这些候选基因在250个T1N0M0和T2N0M0乳腺肿瘤中的表达。随着进一步的SAGE研究（项目1）确定新的候选基因，以及我们对乳腺癌生物学的理解取得进展，将向这一组中添加其他基因。最终，我们希望确定在前瞻性肿瘤组中约1000个基因的表达水平。将鉴定和克隆其表达可能有助于分子特征的新基因。本项目的工作人员将与项目3和数据管理核心中的统计学家、信息科学家和程序员密切合作，分析该数据集的肿瘤人群亚群的分子特征。

Breast cancer affects one in eight women in the United States. Current treatment regimes tend to extend post-surgical adjuvant chemotherapy to lymph node negative patients with ever smaller original tumors, even though the majority of such patients do not appear to benefit from such treatment. The establishment of molecular signatures that define subgroups of these patients with different likelihoods of tumor recurrence would be useful allowing therapy to be tailored of the prognosis of the patient. We will also a novel global gene expression analysis procedure called RAGE to establish gene expression profiles for early node- negative breast tumors. A retrospective group of T1N0M0 and T2N0M0 breast tumors, 20 that have recurred within 5 years and 20 that have not, will be studied in Phase 1. The RAGE method will be adapted to a high throughput separation and analysis technology, multiple capillary electrophoresis, and throughput will be increased through various means to about 10,000 measurements per week. Expression levels of a set of approximately 3000 genes will be measured in each of the 40 retrospective tumors. These data will be combined with analogous data collected in Project 1 using SAGE on a subset of these tumors. The combined RAGE and SAGE data obtained in Phase I will be used to identify a set of approximately 700 candidate signature genes that show significant variance in expression between recurrent and non-recurrent tumors or that are expected to be important in breast tumorigenesis. The RAGE technique will then be used in Phase II to study expression of these candidate genes in a prospective set of 250 T1N0M0 and T2N0M0 breast tumors. Additional genes will be added to this set as new candidate genes are identified by further SAGE studies (Project 1) and as advances in our understanding of the biology of breast cancer are made. Ultimately, we expect to determine expression levels for about 1000 genes in the prospective tumor set. Novel genes whose expression may contribute to molecular signatures will be identified and cloned. Personnel in this Project will work closely with statisticians, information scientists and programmers in Project 3 and in the Data Management Core to analyze this dataset for molecular signatures characteristic of subsets of the tumor population.