Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
Department of Oncology, Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 61-001 Poznań, Poland.
Biomolecules. 2021 Apr 16;11(4):588. doi: 10.3390/biom11040588.
Selection of optimal control samples is crucial in expression profiling tumor samples. To address this issue, we performed microarray expression profiling of control samples routinely used in head and neck squamous cell carcinoma studies: human bronchial and tracheal epithelial cells, squamous cells obtained by laser uvulopalatoplasty and tumor surgical margins. We compared the results using multidimensional scaling and hierarchical clustering versus tumor samples and laryngeal squamous cell carcinoma cell lines. A general observation from our study is that the analyzed cohorts separated according to two dominant factors: "malignancy", which separated controls from malignant samples and "cell culture-microenvironment" which reflected the differences between cultured and non-cultured samples. In conclusion, we advocate the use of cultured epithelial cells as controls for gene expression profiling of cancer cell lines. In contrast, comparisons of gene expression profiles of cancer cell lines versus surgical margin controls should be treated with caution, whereas fresh frozen surgical margins seem to be appropriate for gene expression profiling of tumor samples.
在肿瘤样本的表达谱分析中，选择最佳的对照样本至关重要。为了解决这个问题，我们对常规用于头颈部鳞状细胞癌研究的对照样本（人支气管和气管上皮细胞、激光悬雍垂腭咽成形术后获得的鳞状细胞和肿瘤手术切缘）进行了微阵列表达谱分析。我们使用多维尺度分析和层次聚类对肿瘤样本和喉鳞状细胞癌细胞系进行了比较。从我们的研究中可以得出一个普遍的观察结果，即分析的队列根据两个主要因素分离：“恶性”，它将对照样本与恶性样本分离，以及“细胞培养-微环境”，它反映了培养和未培养样本之间的差异。总之，我们提倡使用培养的上皮细胞作为癌症细胞系基因表达谱分析的对照。相比之下，癌症细胞系与手术切缘对照的基因表达谱比较应该谨慎对待，而新鲜冷冻的手术切缘似乎适合肿瘤样本的基因表达谱分析。
