A biobanking turning-point in the use of formalin-fixed, paraffin tumor blocks to unveil kinase signaling in melanoma

Abstract

A biobanking turning-point in the use of formalin-fixed, paraffin tumor blocks to unveil kinase signaling in melanoma Dear Editor, Malignant melanoma (MM) is one of the most aggressive human solid tumors, and it is associated with the highest mortality of all skin cancers. 1 Aberrant patterns of protein expression and posttranslational modifications (PTMs) have been linked to MM pathogenesis, 2 which has promoted large-scale proteomics studies.Our study establishes a novel proteomics strategy that provides validity for formalin-fixed and paraffin-embedded (FFPE) tumors as a novel source for phosphoprotein mapping in MM.This constitutes an important future clinical resource for discovering novel biomarkers and refining therapeutic approaches for MM treatment.Most of the MM proteomic analyses using patient samples to date have been conducted on fresh frozen tumors (FFT).However, FFT specimens are difficult to preserve with a limited number of samples in biobanks compared to FFPE tissues.3 Roughly 500 million FFPE cancer tissues are stored in biobank archives linked to relevant clinical information.4 This represents a precious resource for the elucidation of novel molecular mechanisms and new biomarkers for MM, as well as a potential tool for personalized treatment monitoring.So far, a comparison between the proteomics profiles of FFPE tumor blocks and FFT in the context of MM has not been addressed.Only a few studies have focused on FFPE samples to explore the MM proteome, but none of these has evaluated the preservation of PTMs, such as phosphorylation.5 This is important since alterations in the phosphorylation status of the tumor are linked to the activation of oncogenic pathways.6 Here, we analyzed tumor samples derived from 11 patients diagnosed with MM.After surgical removal, all