Bioinformatics and Computational Biology Program, University of North Carolina, Chapel Hill, NC 27599, USA.
Breast Cancer Res Treat. 2012 Jun;133(3):865-80. doi: 10.1007/s10549-011-1846-y. Epub 2011 Nov 3.
Breast cancer is a heterogeneous disease with known expression-defined tumor subtypes. DNA copy number studies have suggested that tumors within gene expression subtypes share similar DNA Copy number aberrations (CNA) and that CNA can be used to further sub-divide expression classes. To gain further insights into the etiologies of the intrinsic subtypes, we classified tumors according to gene expression subtype and next identified subtype-associated CNA using a novel method called SWITCHdna, using a training set of 180 tumors and a validation set of 359 tumors. Fisher's exact tests, Chi-square approximations, and Wilcoxon rank-sum tests were performed to evaluate differences in CNA by subtype. To assess the functional significance of loss of a specific chromosomal region, individual genes were knocked down by shRNA and drug sensitivity, and DNA repair foci assays performed. Most tumor subtypes exhibited specific CNA. The Basal-like subtype was the most distinct with common losses of the regions containing RB1, BRCA1, INPP4B, and the greatest overall genomic instability. One Basal-like subtype-associated CNA was loss of 5q11-35, which contains at least three genes important for BRCA1-dependent DNA repair (RAD17, RAD50, and RAP80); these genes were predominantly lost as a pair, or all three simultaneously. Loss of two or three of these genes was associated with significantly increased genomic instability and poor patient survival. RNAi knockdown of RAD17, or RAD17/RAD50, in immortalized human mammary epithelial cell lines caused increased sensitivity to a PARP inhibitor and carboplatin, and inhibited BRCA1 foci formation in response to DNA damage. These data suggest a possible genetic cause for genomic instability in Basal-like breast cancers and a biological rationale for the use of DNA repair inhibitor related therapeutics in this breast cancer subtype.
乳腺癌是一种具有已知表达定义肿瘤亚型的异质性疾病。DNA 拷贝数研究表明，在基因表达亚型内的肿瘤具有相似的 DNA 拷贝数异常（CNA），并且 CNA 可用于进一步细分表达类别。为了更深入地了解内在亚型的病因，我们根据基因表达亚型对肿瘤进行分类，然后使用一种称为 SWITCHdna 的新方法在下一个验证集中识别 359 个肿瘤中的亚型相关 CNA。使用包含 180 个肿瘤的训练集和 359 个肿瘤的验证集，进行 Fisher 精确检验、卡方近似和 Wilcoxon 秩和检验，以评估按亚型的 CNA 差异。为了评估特定染色体区域缺失的功能意义，通过 shRNA 和药物敏感性敲低个体基因，并进行 DNA 修复焦点测定。大多数肿瘤亚型表现出特定的 CNA。基底样亚型最为独特，常见的 RB1、BRCA1、INPP4B 区域缺失，整体基因组不稳定性最大。一个基底样亚型相关的 CNA 是 5q11-35 的缺失，其中至少包含三个对 BRCA1 依赖性 DNA 修复重要的基因（RAD17、RAD50 和 RAP80）；这些基因通常成对缺失，或者同时缺失三个。这些基因中的两个或三个丢失与基因组不稳定性显著增加和患者预后不良相关。在永生化人乳腺上皮细胞系中，RAD17 或 RAD17/RAD50 的 RNAi 敲低导致对 PARP 抑制剂和卡铂的敏感性增加，并抑制了对 DNA 损伤的 BRCA1 焦点形成。这些数据表明，基底样乳腺癌中基因组不稳定性可能存在遗传原因，并且 DNA 修复抑制剂相关治疗剂在该乳腺癌亚型中具有生物学合理性。
