Proteomic Biomarkers for Urothelial Cancer Based on the Tissue Preservation Methods - Expert Commentary

Two key methods to preserve tumor tissues in biobanks are broadly adopted: formalin-fixation and paraffin-embedding (FFPE) and optimal cutting-temperature compound (OCT)- embedding and subsequent freezing, of the tissue specimens. Multiple proteins can be quantified simultaneously from the same sample using mass spectrometry (MS). However, applying MS to FFPE and OCT samples carries several technical challenges such as background artifacts from embedding materials and protein alteration. The differences in the. quality of retrieved protein expression data from FFPE compared to matched OCT samples are not well-characterized.

A recent study published by Valdés et al. in Scientific Reports investigated the differences in MS-based analysis of bladder urothelial carcinoma tissue samples using the two different preservation methods. The authors analyzed nine pairs of urothelial carcinoma tissue tumors at various disease stages (Ta/T1 and T2/T3). A higher number of proteins could be quantified in OCT-preserved samples compared to FFPE-preserved samples for all the tumors (1511 versus 947 proteins). This, in part, is attributed to difficulties in removing paraffin and reversing formalin fixation.

The authors conducted a principal component analysis to define the contribution of the two preservation methods or the tumor stage to the observed variation in protein expression. They have found that the choice of the preservation method contributed more to variation than tumor stage. The investigators identified proteins uniquely upregulated in T2 and T 3 tumors, including Galectin-1 (LGALS1 or GAL1), plastin, and Annexin A5 (ANXA5) and proteins upregulated in Ta/T1, including the HMGCS2 protein. Several important proteins were upregulated in OCT samples but were not quantified in FFPE samples, such as TES (Testin) and DDX21 protein. These data support the feasibility of using MS to interrogate tumor tissues stored in biobanks and the potential for developing proteomic biomarkers in urothelial cancer patients.

Written by: Bishoy M. Faltas, MD, Director of Bladder Cancer Research, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York City, New York


  1. Valdés A, Bitzios A, Kassa E, Shevchenko G, Falk A, Malmström P-U, et al. Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer. Sci Rep. 2021;11(1):1–12. PMID: 33828141

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