Cutaneous squamous cell carcinoma (cSCC), premalignant actinic keratosis (AK) and Bowen’s disease (BD) are highly prevalent, heterogeneous keratinocytic skin lesions (KSLs). Discrepancies between clinical presentations and histologic analyses of KSLs frequently lead to misdiagnoses or delayed diagnoses. Biomarkers that can accurately stratify KSLs by their malignant potential are urgently needed to support a paradigm shift in skin cancer care to personalised, precision medicine. In this thesis, a liquid chromatography tandem mass spectrometry (MS) platform was employed to conduct comprehensive proteomic profiling of formalin-fixed and paraffin embedded samples of normal skin and KSLs. Using complementary MS approaches, namely information dependent acquisition (IDA) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS), 3574 proteins were quantified overall allowing the identification of novel protein signatures for KSL subtypes. Proteomic findings were further investigated in silico using transcriptome databases, and several interesting targets were confirmed by immunohistochemistry. Distinct proteome profiles corresponding to subcategories of cSCC and precursor lesions were found, demonstrating the potential of MS-based approaches to deliver reliable diagnostics and disease staging. The bioinformatic analysis provided new insights into molecular pathways disrupted in different KSLs. The successful application of a non-invasive tape-stripping method for proteome sampling of KSLs was also demonstrated.
This work represents the most comprehensive proteome study of KSLs to date. The identification of deferentially altered proteins and molecular pathways between subtypes of KSLs will inform the development of diagnostic, therapeutic and disease staging strategies. Further exploration and implementation of the approaches described herein could have a major impact on patient outcomes and reduce the cost burden of KSLs.