Vanderbilt University, Department of Surgery, Nashville, 37232, USA.
Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.
Sci Rep. 2016 Sep 14;6:33273. doi: 10.1038/srep33273.
Defining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed, Paraffin-Embedded (FFPE). NanoString nCounter® and Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE samples. In this study, to evaluate the gene expression of frozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR < 0.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P < 0.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, one of the six multi-gene signatures (P < 0.05) but no individual gene was associated with survival outcomes. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients.
定义能够预测 II-III 期结直肠癌 (CRC) 复发的分子特征仍然是癌症研究中的一个挑战。大多数可用的临床样本都是福尔马林固定、石蜡包埋 (FFPE) 的。NanoString nCounter® 和 Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) 是两个用于 FFPE 样本高通量基因表达谱分析的商业化平台。在这项研究中，为了评估冷冻组织衍生的预后特征在 FFPE CRC 样本中的基因表达，我们使用这两个平台测量了 42 个 FFPE CRC 样本中 516 个已发表的冷冻组织衍生的预后特征基因的表达。基于 HTA 平台衍生的数据，我们确定了与生存结果相关的基因（99 个单个基因，FDR<0.05）和基因集（六个报告的多基因特征中有四个，有足够信息进行评估，P<0.05）表达差异。使用 nCounter 平台衍生的数据，六个多基因特征之一（P<0.05）但没有单个基因与生存结果相关。我们的研究表明，足够高质量的 RNA 可以从 FFPE 肿瘤组织中获得，以检测 CRC 患者的冷冻组织衍生的预后基因表达特征。
