Discovery proteomics reveals potential protein signature associated with malignant phenotype acquisition in pleomorphic adenoma

Abstract

Objective:To analyze the proteomic profile of salivary pleomorphic adenoma (PA) and carcinoma ex pleomorphic adenoma (CXPA) samples and correlate them with the malignant transformation of the PA. Materials and methods:Thirty samples (10 PA, 16 CXPA, and 4 residual PA) were microdissected and submitted to liquid chromatography-tandem mass spectrometry (LC-MS/MS). The proteomic data and protein identification were analyzed through LC-MS/MS spectra using the MaxQuant software. Results:The proteomic analysis identified and quantified a total of 240 proteins in which 135 were found in PA, residual PA, and CXPA. The shared proteins were divided into six subgroups, and the proteins that showed statistically significant differences (p > 0.05) and fold-change > or <2.5 in one subgroup to another subgroup were included. Seven proteins (Apolipoprotein A-I-APOA1, haptoglobin-HP, protein of the synaptonemal complex 1-SYCP1, anion transport protein of band 3-SLC4A1, subunit μ1 of AP-1 complex-AP1M1, beta subunit of hemoglobin-HBB, and dermcidin-DCD) were classified as potential protein signatures, being HP, AP1M1, and HBB with higher abundance for PA to residual PA, APOA1 with higher abundance for PA to

Malignant phenotype acquisition in pleomorphic adenoma: An exclusive proteins analysis

“…In our analysis, 39 proteins were identified in the PA, 4 in the residual PA, and 17 in the CXPA. Although fresh tissue is known to yield greater protein detection, our work using the same cohort could reach satisfactory results using FFPE tissues (de Lima-Souza, Scarini, Lavareze, Emerick, Crescencio, et al, 2022).…”

“…Recently, we published an article that provided new proteomics insight associated with malignant phenotype acquisition in pleomorphic adenoma (PA) (de Lima-Souza, Scarini, Lavareze, Emerick, Crescencio, et al, 2022). In proteomics studies, the "exclusive" proteins are defined as the most abundant proteins in one group when compared to another.…”

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Dear Editor,Recently, we published an article that provided new proteomics insight associated with malignant phenotype acquisition in pleomorphic adenoma (PA) (de Lima-Souza, Scarini, Lavareze, Emerick, Crescencio, et al, 2022). In proteomics studies, the "exclusive" proteins are defined as the most abundant proteins in one group when compared to another.Most studies focus their results on shared proteins, but the "exclusive" proteins must be taken into consideration as they have important structural and functional roles (Salmon et al, 2013).

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Clinical applications of mass spectrometry‐based proteomics in cancer: Where are we?

“…Protein signatures are often converted to MRM-based assays to capitalize on their clinical utility. A few such signatures have been identified and proposed for development to clinical use, but many more are required [34,35].…”

ProInfer: An interpretable protein inference tool leveraging on biological networks

“…The process of estimating the optimal set of proteins given acquired spectra is known as the protein inference problem [5][6][7]. Quantitative analysis is then performed to identify phenotype-specific proteins [8], obtain their function annotation [9] and determine potential applications in clinical [10] and medical settings [11] (Fig 1A).…”