Differential proteomic analysis of actinic keratosis, Bowen’s disease and cutaneous squamous cell carcinoma by label-free LC–MS/MS

Abstract

Our study supports the concept that AK and BD are precursors of cSCC. The identification of proteome changes indicates disruption of repair, pro-apoptotic, and tumor promoting pathways. Our findings will help select targets for classification and treatment.

Data Independent Acquisition Proteomic Analysis Can Discriminate between Actinic Keratosis, Bowen’s Disease, and Cutaneous Squamous Cell Carcinoma

“…We identified promising biomarker candidates that discriminate between AK, BD, and cSCC samples. While analogous changes in several proteins (including SFN, TYMP, TPM3, PARK7, KRT16, NDRG1, and S100A2) were detected in our earlier proteomics study of these lesions (Azimi et al, 2018), the majority of the proteins identified here have not been reported in KSL research. Increased levels of VPS45, TIMM8B, DHPS, and NKTR, and decreased GCSH, distinguished AK from the BD and cSCC lesions.…”

“…In the present study, we employed a SWATH-MS data acquisition method to identify and quantify 3,574 proteins across 93 FFPE samples of KSL subtypes. Using this approach, we identified 72.4% more proteins in KSL samples compared with our previous IDA analyses of the same lesion types (Azimi et al, 2018) (Supplementary Figure S6). This is in line with an earlier study reporting a 77.8% improvement in proteome coverage using SWATH-MS data acquisition mode compared with IDA (Bertrand et al, 2017).…”

“…Molecular pathways disrupted during the progression from normal skin to cSCC Bioinformatics analyses undertaken here and before (Azimi et al, 2018) showed that apoptosis and DNA damage repaireactivities are more active in BD lesions compared with their AK and cSCC counterparts. Interestingly, enhanced pathways in AK lesions included the inhibition of protein kinase R and the regulation of MAPK pathway.…”

“…These proteins were selected as they were found by our proteomic investigation to be diagnostic of actinic keratosis (VPS45), Bowen's disease (PUM2), or cutaneous squamous cell carcinoma (NECTIN2) lesions while having potentially important roles in keratinocytic skin lesion pathophysiology. Microsections of formalin-fixed paraffin-embedded tissue (4 mm thick) from actinic keratosis (n ¼ 5), Bowen's disease (n ¼ 5), and cutaneous squamous cell carcinoma samples (n ¼ 5), and the surrounding normal skin, were cut and processed for immunohistochemistry analysis as described previously (Azimi et al, 2018) with slight modifications. Briefly, histological slides were deparaffinized with xylene (3 treatments; 5 minutes each), then rehydrated in 100%, 95%, and 70% v/v ethanol (5 minutes each) with a final wash with distilled water.…”

“…Mass spectrometry (MS)ebased proteomic analysis is a well-established technique for quantitative analyses of proteins in tumor samples. Using information dependent acquisition (IDA) MS strategies, we previously quantified up to 2,074 proteins from samples of KSLs (Azimi et al, 2019;Azimi et al, 2018;Azimi et al, 2016). Although IDA methods are the gold standard for discovery proteomics, they are limited by the abundances of precursor ions and therefore have reduced depth of proteome coverage (Gillette and Carr, 2013).…”