Assessment of the 2-D Gel-Based Proteomics Application of Clinically Archived Formalin-Fixed Paraffin Embedded Tissues
Assessment of the 2-D Gel-Based Proteomics Application of Clinically Archived Formalin-Fixed Paraffin Embedded Tissues
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DOI：
10.1007/s10930-014-9545-2
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发表时间：
2014-04-01
期刊：
影响因子：
3
通讯作者：
Polenakovic, Momir
中科院分区：
文献类型：
--
作者：
Davalieva, Katarina;Kiprijanovska, Sanja;Polenakovic, Momir
医院组织库拥有大量有价值的疾病样本以及匹配的回顾性临床信息。福尔马林固定石蜡包埋 (FFPE) 组织中疾病生物标志物的检测和表征将极大地帮助了解疾病机制，并有助于诊断和预后标志物的开发。在本研究中，评估了在基于二维 (2-D) 凝胶的蛋白质组学中使用从临床存档的 FFPE 组织中提取的全长蛋白质的可能性。该评估是根据两种类型的肿瘤组织（乳腺和前列腺）和两种提取方案进行的。通过两种提取方案获得的 FFPE 提取物的二维模式与匹配的冷冻组织提取物的比较表明，来自冷冻组织的蛋白质只有 7-10% 可以与来自 FFPE 组织的蛋白质相匹配。 2-D FFPE 图谱中的大多数斑点的 pl 为 4-6，而 pl 高于 6 的蛋白质百分比比新鲜/冷冻组织低 3-5 倍。尽管 FFPE 图谱中检测到的斑点数量比匹配的新鲜/冷冻图谱少三倍，但 FFPE 中 67-78% 的蛋白质斑点无法与新鲜/冷冻组织图谱中的相应斑点匹配，表明存在不可逆的蛋白质修饰。总之，目前的 FFPE 提取方法无法完全逆转交联复合物并克服蛋白质碎片，阻碍了这些样品在基于二维凝胶的蛋白质组学研究中的有效使用。
Hospital tissue repositories possess a vast and valuable supply of disease samples with matched retrospective clinical information. Detection and characterization of disease biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues will greatly aid the understanding of the diseases mechanisms and help in the development of diagnostic and prognostic markers. In this study, the possibility of using full-length proteins extracted from clinically archived FFPE tissues in two-dimensional (2-D) gel-based proteomics was evaluated. The evaluation was done based on two types of tumor tissues (breast and prostate) and two extraction protocols. The comparison of the 2-D patterns of FFPE extracts obtained by two extraction protocols with the matching frozen tissue extracts showed that only 7-10 % of proteins from frozen tissues can be matched to proteins from FFPE tissues. Most of the spots in the 2-D FFPE's maps had pl 4-6, while the percentages of proteins with pl above 6 were 3-5 times lower in comparison to the fresh/frozen tissue. Despite the three-fold lower number of the detected spots in FFPE maps compared to matched fresh/frozen maps, 67-78 % of protein spots in FFPE could not be matched to the corresponding spots in the fresh/frozen tissue maps indicating irreversible protein modifications. In conclusion, the inability to completely reverse the cross-linked complexes and overcome protein fragmentation with the present day FFPE extraction methods stands in the way of effective use of these samples in 2-D gel based proteomics studies.