title: Large-scale proteomic characterization of melanoma expressed proteins reveals nestin and vimentin as biomarkers that can potentially distinguish melanoma subtypes.
abstract: Melanoma is an aggressive type of skin cancer, which accounts for only 4% of skin cancer cases but causes around 75% of skin cancer deaths. Currently, there is a limited set of protein biomarkers that can distinguish melanoma subtypes and provide an accurate prognosis of melanoma. Thus, we have selected and profiled the proteomes of five different melanoma cell lines from different stages of progression in comparison with a normal melanocytes using tandem mass spectrometry. We also profiled the proteome of a solid metastatic melanoma tumor. This resulted in the identification of 4758 unique proteins, among which ∼200-300 differentially expressed proteins from each set were found by quantitative proteomics. Correlating protein expression with aggressiveness of each melanoma cell line and literature mining resulted in the final selection of six proteins: vimentin, nestin, fibronectin, annexin A1, dipeptidyl peptidase IV, and histone H2A1B. Validation of nestin and vimentin using 40 melanoma samples revealed pattern of protein expression can help predict melanoma aggressiveness in different subgroups of melanoma. These results, together with the combined list of 4758 expressed proteins, provide a valuable resource for selecting melanoma biomarkers in the future for the clinical and research community.
authors.affiliation: Department of Cell Biology, Center for Vascular Biology, University of Connecticut Health Center , 263 Farmington Avenue, Farmington, Connecticut 06030, United States.
authors.forename: Veneta
authors.initials: V
authors.lastname: Qendro
authors.forename: Deborah H
authors.initials: DH
authors.lastname: Lundgren
authors.forename: Karim
authors.initials: K
authors.lastname: Rezaul
authors.forename: Forrest
authors.initials: F
authors.lastname: Mahony
authors.forename: Nicholas
authors.initials: N
authors.lastname: Ferrell
authors.forename: Andrew
authors.initials: A
authors.lastname: Bi
authors.forename: Ardian
authors.initials: A
authors.lastname: Latifi
authors.forename: Daniyal
authors.initials: D
authors.lastname: Chowdhury
authors.forename: Steven
authors.initials: S
authors.lastname: Gygi
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Haas
authors.forename: Lori
authors.initials: L
authors.lastname: Wilson
authors.forename: Michael
authors.initials: M
authors.lastname: Murphy
authors.forename: David K
authors.initials: DK
authors.lastname: Han
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis / Q000378:metabolism; D006801:Humans; D008544:Melanocytes / Q000378:metabolism; D008545:Melanoma / Q000378:metabolism* / Q000473:pathology; D064231:Nestin / Q000032:analysis / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D012016:Reference Values; D015203:Reproducibility of Results; D012878:Skin Neoplasms / Q000378:metabolism* / Q000473:pathology; D053719:Tandem Mass Spectrometry / Q000379:methods; D046888:Tissue Array Analysis; D014746:Vimentin / Q000032:analysis / Q000378:metabolism*
chemical_list: D014408:Biomarkers, Tumor; C577484:NES protein, human; D064231:Nestin; D014746:Vimentin
keywords: biomarkers; melanoma; nestin; proteomics; quantitative proteomics; spectral counting; vimentin