In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

Cancer Genomics - Proteomics

ALI AZIMI²  KIMBERLEY L. KAUFMAN³  MARINA ALI²  PABLO FERNANDEZ-PENAS²  STEVEN KOSSARD¹ 

[1] ermatopathology, Skin and Cancer Foundation Australia, Darlinghurst, NSW, Australiaermatopathology, Skin and Cancer Foundation Australia, Darlinghurst, NSW, Australiaermatopathology, Skin and Cancer Foundation Australia, Darlinghurst, NSW, Australia;epartment of Dermatology, Westmead Hospital, The University of Sydney, Westmead, NSW, Australiaepartment of Dermatology, Westmead Hospital, The University of Sydney, Westmead, NSW, Australiaepartment of Dermatology, Westmead Hospital, The University of Sydney, Westmead, NSW, Australia;chool of Molecular Bioscience, Faculty of Science, The University of Sydney, Camperdown, NSW, Australiarain and Mind Centre, The University of Sydney, Camperdown, NSW, Australiachool of Molecular Bioscience, Faculty of Science, The University of Sydney, Camperdown, NSW, Australiachool of Molecular Bioscience, Faculty of Science, The University of Sydney, Camperdown, NSW, Australiarain and Mind Centre, The University of Sydney, Camperdown, NSW, Australiarain and Mind Centre, The University of Sydney, Camperdown, NSW, Australiachool of Molecular Bioscience, Faculty of Science, The University of Sydney, Camperdown, NSW, Australiarain and Mind Centre, The University of Sydney, Camperdown, NSW, Australia

关键词: Cutaneous squamous cell carcinoma;    formalin-fixed paraffin embedded;    laser capture microdissection;    proteomics;    label-free mass spectrometry;   

DOI  :  

来源: Delinasios GJ CO

【 摘 要 】

Background: Cutaneous squamous cell carcinoma (cSCC) is a common type of skin cancer but there are no comprehensive proteomic studies on this entity. Materials and Methods: We employed liquid chromatography coupled with tandem mass spectrometry (MS/MS) using formalin-fixed paraffin-embedded (FFPE) cSCC material to study the tumor and normal skin tissue proteomes. Ingenuity Pathway Analysis (IPA) was used to interpret the role of altered proteins in cSCC pathophysiology. Results were validated using the Human Protein Atlas and Oncomine database in silico. Results: Of 1,310 unique proteins identified, expression of an average of 144 and 88 proteins were significantly (p<0.05) increased and decreased, respectively, in the tumor samples compared to their normal counterparts. IPA analysis revealed disruptions in proteins associated with cell proliferation, apoptosis, and migration. In silico analysis confirmed that proteins corresponding to 12 antibodies, and genes corresponding to 18 proteins were differentially expressed between the two categories, validating our proteomic measurements. Conclusion: Label-free MS-based proteomics is useful for analyzing FFPE cSCC tissues.

【 授权许可】

Unknown