Ribeiro Franclim R, Henrique Rui, Hektoen Merete, Berg Marianne, Jerónimo Carmen, Teixeira Manuel R, Lothe Ragnhild A
Department of Genetics, Portuguese Oncology Institute--Porto, Portugal.
Mol Cancer. 2006 Sep 4;5:33. doi: 10.1186/1476-4598-5-33.
In order to gain new insights into the molecular mechanisms involved in prostate cancer, we performed array-based comparative genomic hybridization (aCGH) on a series of 46 primary prostate carcinomas using a 1 Mbp whole-genome coverage platform. As chromosomal comparative genomic hybridization (cCGH) data was available for these samples, we compared the sensitivity and overall concordance of the two methodologies, and used the combined information to infer the best of three different aCGH scoring approaches.
Our data demonstrate that the reliability of aCGH in the analysis of primary prostate carcinomas depends to some extent on the scoring approach used, with the breakpoint estimation method being the most sensitive and reliable. The pattern of copy number changes detected by aCGH was concordant with that of cCGH, but the higher resolution technique detected 2.7 times more aberrations and 15.2% more carcinomas with genomic imbalances. We additionally show that several aberrations were consistently overlooked using cCGH, such as small deletions at 5q, 6q, 12p, and 17p. The latter were validated by fluorescence in situ hybridization targeting TP53, although only one carcinoma harbored a point mutation in this gene. Strikingly, homozygous deletions at 10q23.31, encompassing the PTEN locus, were seen in 58% of the cases with 10q loss.
We conclude that aCGH can significantly improve the detection of genomic aberrations in cancer cells as compared to previously established whole-genome methodologies, although contamination with normal cells may influence the sensitivity and specificity of some scoring approaches. Our work delineated recurrent copy number changes and revealed novel amplified loci and frequent homozygous deletions in primary prostate carcinomas, which may guide future work aimed at identifying the relevant target genes. In particular, biallelic loss seems to be a frequent mechanism of inactivation of the PTEN gene in prostate carcinogenesis.
为了深入了解前列腺癌相关的分子机制，我们使用1 Mbp全基因组覆盖平台，对46例原发性前列腺癌进行了基于芯片的比较基因组杂交（aCGH）分析。由于这些样本已有染色体比较基因组杂交（cCGH）数据，我们比较了两种方法的灵敏度和总体一致性，并利用综合信息推断三种不同aCGH评分方法中最佳的一种。
我们的数据表明，aCGH在原发性前列腺癌分析中的可靠性在一定程度上取决于所使用的评分方法，断点估计法是最敏感和可靠的。aCGH检测到的拷贝数变化模式与cCGH一致，但更高分辨率的技术检测到的畸变多2.7倍，基因组失衡的癌多15.2%。我们还表明，使用cCGH时一些畸变一直被忽视，如5q、6q、12p和17p的小缺失。后者通过靶向TP53的荧光原位杂交得到验证，尽管只有一例癌在该基因中有一个点突变。令人惊讶的是，在10q缺失的病例中，58%的病例在10q23.31处出现了包含PTEN基因座的纯合缺失。
我们得出结论，与先前建立的全基因组方法相比，aCGH可显著提高癌细胞中基因组畸变的检测率，尽管正常细胞的污染可能会影响某些评分方法的灵敏度和特异性。我们的工作描绘了原发性前列腺癌中反复出现的拷贝数变化，揭示了新的扩增位点和频繁的纯合缺失，这可能为未来旨在鉴定相关靶基因的工作提供指导。特别是，双等位基因缺失似乎是前列腺癌发生过程中PTEN基因失活的常见机制。
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