CANCER GENOMICS & PROTEOMICS 13: 453-466 (2016) doi:10.21873/cgp.20008
In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue 1Department
2School
ALI AZIMI1, KIMBERLEY L. KAUFMAN2,3, MARINA ALI1, STEVEN KOSSARD4 and PABLO FERNANDEZ-PENAS1
of Dermatology, Westmead Hospital, The University of Sydney, Westmead, NSW, Australia; of Molecular Bioscience, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia; 3Brain and Mind Centre, The University of Sydney, Camperdown, NSW, Australia; 4Dermatopathology, Skin and Cancer Foundation Australia, Darlinghurst, NSW, Australia
Abstract. 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
In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue 1Department
2School
ALI AZIMI1, KIMBERLEY L. KAUFMAN2,3, MARINA ALI1, STEVEN KOSSARD4 and PABLO FERNANDEZ-PENAS1
of Dermatology, Westmead Hospital, The University of Sydney, Westmead, NSW, Australia; of Molecular Bioscience, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia; 3Brain and Mind Centre, The University of Sydney, Camperdown, NSW, Australia; 4Dermatopathology, Skin and Cancer Foundation Australia, Darlinghurst, NSW, Australia
Abstract. 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
