Département de Dermatologie, hôpital saint Louis Paris, Paris, France.
PLoS One. 2012;7(1):e29143. doi: 10.1371/journal.pone.0029143. Epub 2012 Jan 17.
The source tissue for biomarkers mRNA expression profiling of tumors has traditionally been fresh-frozen tissue. The adaptation of formalin-fixed, paraffin-embedded (FFPE) tissues for routine mRNA profiling would however be invaluable in view of their abundance and the clinical information related to them. However, their use in the clinic remains a challenge due to the poor quality of RNA extracted from such tissues. Here, we developed a method for the selection of melanoma archival paraffin-embedded tissues that can be reliably used for transcript biomarker profiling. For that, we used qRT-PCR to conduct a comparative study in matched pairs of frozen and FFPE melanoma tissues of the expression of 25 genes involved in angiogenesis/tumor invasion and 15 housekeeping genes. A classification method was developed that can select the samples with a good frozen/FFPE correlation and identify those that should be discarded on the basis of paraffin data for four reference genes only. We propose therefore a simple and inexpensive assay which improves reliability of mRNA profiling in FFPE samples by allowing the identification and analysis of "good" samples only. This assay which can be extended to other genes would however need validation at the clinical level and on independent tumor series.
肿瘤标志物 mRNA 表达谱分析的原始组织通常是新鲜冷冻组织。然而，考虑到福尔马林固定、石蜡包埋（FFPE）组织的丰富程度及其相关的临床信息，如果能将其用于常规 mRNA 分析将是非常有价值的。然而，由于从这些组织中提取的 RNA 质量较差，它们在临床上的应用仍然是一个挑战。在这里，我们开发了一种选择黑色素瘤存档石蜡包埋组织的方法，这些组织可以可靠地用于转录生物标志物分析。为此，我们使用 qRT-PCR 对冷冻和 FFPE 黑色素瘤组织中 25 个参与血管生成/肿瘤侵袭的基因和 15 个管家基因的表达进行了配对比较研究。开发了一种分类方法，可以选择与冷冻组织相关性良好的样本，并仅根据 4 个参考基因的石蜡数据来识别和丢弃那些应该丢弃的样本。因此，我们提出了一种简单且廉价的检测方法，通过仅识别和分析“良好”的样本，提高了 FFPE 样本中 mRNA 分析的可靠性。然而，这种可以扩展到其他基因的检测方法需要在临床水平和独立的肿瘤系列中进行验证。
