Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
PLoS One. 2012;7(12):e51719. doi: 10.1371/journal.pone.0051719. Epub 2012 Dec 17.
In breast cancer, the basal-like subtype has high levels of genomic instability relative to other breast cancer subtypes with many basal-like-specific regions of aberration. There is evidence that this genomic instability extends to smaller scale genomic aberrations, as shown by a previously described micro-deletion event in the PTEN gene in the Basal-like SUM149 breast cancer cell line.
We sought to identify if small regions of genomic DNA copy number changes exist by using a high density, gene-centric Comparative Genomic Hybridizations (CGH) array on cell lines and primary tumors. A custom tiling array for CGH (244,000 probes, 200 bp tiling resolution) was created to identify small regions of genomic change, which was focused on previously identified basal-like-specific, and general cancer genes. Tumor genomic DNA from 94 patients and 2 breast cancer cell lines was labeled and hybridized to these arrays. Aberrations were called using SWITCHdna and the smallest 25% of SWITCHdna-defined genomic segments were called micro-aberrations (<64 contiguous probes, ~ 15 kb).
Our data showed that primary tumor breast cancer genomes frequently contained many small-scale copy number gains and losses, termed micro-aberrations, most of which are undetectable using typical-density genome-wide aCGH arrays. The basal-like subtype exhibited the highest incidence of these events. These micro-aberrations sometimes altered expression of the involved gene. We confirmed the presence of the PTEN micro-amplification in SUM149 and by mRNA-seq showed that this resulted in loss of expression of all exons downstream of this event. Micro-aberrations disproportionately affected the 5' regions of the affected genes, including the promoter region, and high frequency of micro-aberrations was associated with poor survival.
Using a high-probe-density, gene-centric aCGH microarray, we present evidence of small-scale genomic aberrations that can contribute to gene inactivation. These events may contribute to tumor formation through mechanisms not detected using conventional DNA copy number analyses.
在乳腺癌中，与其他乳腺癌亚型相比，基底样亚型具有更高水平的基因组不稳定性，并且存在许多基底样特异性的畸变区域。有证据表明，这种基因组不稳定性扩展到较小规模的基因组畸变，如先前在基底样 SUM149 乳腺癌细胞系中描述的 PTEN 基因的微缺失事件所示。
我们试图通过使用高密度、基因特异性比较基因组杂交（CGH）阵列在细胞系和原发性肿瘤中鉴定是否存在小区域的基因组 DNA 拷贝数变化。创建了用于 CGH 的定制平铺阵列（244,000 个探针，200 bp 平铺分辨率），以识别小区域的基因组变化，这些变化集中在先前鉴定的基底样特异性和一般癌症基因上。94 名患者和 2 个乳腺癌细胞系的肿瘤基因组 DNA 被标记并杂交到这些阵列上。使用 SWITCHdna 调用畸变，并且将 SWITCHdna 定义的基因组片段的最小 25%称为微畸变（<64 个连续探针，约 15 kb）。
我们的数据表明，原发性乳腺癌肿瘤基因组经常包含许多小尺度的拷贝数增益和丢失，称为微畸变，其中大多数使用典型密度全基因组 aCGH 阵列是无法检测到的。基底样亚型表现出这些事件的最高发生率。这些微畸变有时会改变涉及基因的表达。我们证实了 SUM149 中存在 PTEN 微扩增，并通过 mRNA-seq 显示，这导致该事件下游的所有外显子表达缺失。微畸变不成比例地影响受影响基因的 5'区域，包括启动子区域，并且微畸变的高频率与不良预后相关。
使用高探针密度、基因特异性 CGH 微阵列，我们提供了小尺度基因组畸变的证据，这些畸变可能导致基因失活。这些事件可能通过常规 DNA 拷贝数分析未检测到的机制促进肿瘤形成。
