Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues

The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.

结直肠癌（colorectal cancer, CRC）II期与III期患者的预后评估仍是临床难题，原因在于难以筛选出适用于临床样本检测的稳定生物标志物。目前已发表的结直肠癌基因特征大多基于新鲜冰冻结直肠组织构建，但冰冻组织的采集在常规外科病理实践中并不具备可行性。因此，若要开发优于标准病理分期的结肠癌预后检测手段，需针对福尔马林固定石蜡包埋（formalin-fixed paraffin-embedded, FFPE）组织进行设计。NanoString nCounter®平台是一款专为FFPE来源样本开发的基因表达分析工具。本研究基于多项已发表的基于微阵列的结肠癌新鲜冰冻组织预后基因特征，定制了一套nCounter®编码集，并利用该平台系统比较了FFPE组织与匹配的冰冻组织微阵列数据的基因表达情况。研究结果显示，两种平台的基因表达呈现中等程度相关性，同时发现了一小部分基因可作为结肠癌预后候选生物标志物，这类基因在FFPE组织切片中可被有效检测与定量。