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Updated: Dec 15, 2025
Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
Published on: February 27, 2015
Investigating proteome changes between primary and metastatic cutaneous squamous cell carcinoma using SWATH mass
Ali Azimi1, Kitty Lo2, Jennifer Kim3
1Centre for Translational Skin Research, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia.
Background:
Cutaneous squamous cell carcinoma (cSCC) is a common malignancy worldwide and the first as the cause of death from keratinocytic carcinomas. Around 5% of primary cSCCs metastasize, leading to a 5-year survival rate of only 11 %.
Objective:
This paper aims to investigate the proteome profile of primary and metastatic cSCC lesions for the identification of potential diagnostic biomarkers and molecular alterations.
Methods:
Liquid chromatography coupled with SWATH-MS workflow was used to analyse the proteome profile of formalin-fixed and paraffin-embedded samples of primary (n = 20) and metastatic cSCC (n = 25) lesions. Statistical and bioinformatics analysis was performed to identify differentially abundant proteins and molecular alterations between the lesions.
Results:
A total of 5037 proteins were identified across the samples of which 19 proteins including ISG15, APOA1 and MARCKS with roles in metastasis were increased and 11 proteins including DMKN, APCS and CST6 decreased in metastatic cSCC lesions relative to the primary phenotypes (adj. p-value <0.05). The proteomic data separated the lesions based on their histopathological diagnosis. Bioinformatics analysis revealed that cell migration, cell survival and immune response are likely activated, and apoptosis is inhibited in metastatic cSCC lesions, indicating increased lesion complexity as the disease progresses from primary to the metastatic phenotype. Two samples were reclassified after PCA analysis.
Conclusion:
SWATH-MS analysis identified important molecular changes between primary and metastatic cSCC samples. Exploring these findings further will allow their translation into the clinic for improved tumour diagnosis, staging and therapeutic intervention.
