Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, 751 24, Uppsala, Sweden.
Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Nicolás Cabrera 9, 28049, Madrid, Spain.
Sci Rep. 2021 Apr 7;11(1):7595. doi: 10.1038/s41598-021-87003-6.
Samples in biobanks are generally preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature compound (OCT)-embedding and subsequently frozen. Mass spectrometry (MS)-based analysis of these samples is now available via developed protocols, however, the differences in results with respect to preservation methods needs further investigation. Here we use bladder urothelial carcinoma tissue of two different tumor stages (Ta/T1-non-muscle invasive bladder cancer (NMIBC), and T2/T3-muscle invasive bladder cancer (MIBC)) which, upon sampling, were divided and preserved by FFPE and OCT. Samples were parallel processed from the two methods and proteins were analyzed with label-free quantitative MS. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Multivariate analysis indicates that the preservation method is the main source of variation, but also tumors of different stages could be differentiated. Proteins involved in mitochondrial function were overrepresented in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Concordant results for proteins such as HMGCS2 (uniquely quantified in Ta/T1 tumors), and LGALS1, ANXA5 and plastin (upregulated in T2/T3 tumors) were observed in both FFPE and OCT data, which supports the use of MS technology for biobank samples and encourages the further evaluation of these proteins as biomarkers.
生物银行中的样本通常通过福尔马林固定和石蜡包埋（FFPE）和/或最佳切割温度化合物（OCT）包埋进行保存，随后进行冷冻。现在可以通过开发的方案对这些样本进行基于质谱（MS）的分析，但是，关于保存方法的结果差异需要进一步研究。在这里，我们使用两种不同肿瘤阶段（Ta/T1-非肌肉浸润性膀胱癌（NMIBC）和 T2/T3-肌肉浸润性膀胱癌（MIBC））的膀胱尿路上皮癌组织，在取样后，通过 FFPE 和 OCT 进行分离和保存。从两种方法平行处理样本，并使用无标记定量 MS 分析蛋白质。在 FFPE 和 OCT 样本中分别定量了超过 700 和 1200 种蛋白质。多元分析表明，保存方法是主要的变异来源，但也可以区分不同阶段的肿瘤。在线粒体功能中涉及的蛋白质在 OCT 数据中过度表达，但在 FFPE 数据中缺失，表明这些蛋白质通过 FFPE 保存效果不佳。在 FFPE 和 OCT 数据中观察到 HMGCS2（仅在 Ta/T1 肿瘤中定量）、LGALS1、ANXA5 和 plastin（在 T2/T3 肿瘤中上调）等蛋白质的一致性结果，支持将 MS 技术用于生物银行样本，并鼓励进一步评估这些蛋白质作为生物标志物。
