title: Functional classification of cellular proteome profiles support the identification of drug resistance signatures in melanoma cells.
abstract: Drug resistance is a major obstacle in melanoma treatment. Recognition of specific resistance patterns, the understanding of the patho-physiology of drug resistance, and identification of remaining options for individual melanoma treatment would greatly improve therapeutic success. We performed mass spectrometry-based proteome profiling of A375 melanoma cells and HeLa cells characterized as sensitive to cisplatin in comparison to cisplatin resistant M24met and TMFI melanoma cells. Cells were fractionated into cytoplasm, nuclei and secretome and the proteome profiles classified according to Gene Ontology. The cisplatin resistant cells displayed increased expression of lysosomal as well as Ca²⁺ ion binding and cell adherence proteins. These findings were confirmed using Lysotracker Red staining and cell adhesion assays with a panel of extracellular matrix proteins. To discriminate specific survival proteins, we selected constitutively expressed proteins of resistant M24met cells which were found expressed upon challenging the sensitive A375 cells. Using the CPL/MUW proteome database, the selected lysosomal, cell adherence and survival proteins apparently specifying resistant cells were narrowed down to 47 proteins representing a potential resistance signature. These were tested against our proteomics database comprising more than 200 different cell types/cell states for its predictive power. We provide evidence that this signature enables the automated assignment of resistance features as readout from proteome profiles of any human cell type. Proteome profiling and bioinformatic processing may thus support the understanding of drug resistance mechanism, eventually guiding patient tailored therapy.
authors.affiliation: Department of Dermatology, Medical University of Vienna, Vienna, Austria.
authors.forename: Verena
authors.initials: V
authors.lastname: Paulitschke
authors.forename: Verena
authors.initials: V
authors.lastname: Haudek-Prinz
authors.forename: Johannes
authors.initials: J
authors.lastname: Griss
authors.forename: Walter
authors.initials: W
authors.lastname: Berger
authors.forename: Thomas
authors.initials: T
authors.lastname: Mohr
authors.forename: Hubert
authors.initials: H
authors.lastname: Pehamberger
authors.forename: Rainer
authors.initials: R
authors.lastname: Kunstfeld
authors.forename: Christopher
authors.initials: C
authors.lastname: Gerner
mesh_terms: D045744:Cell Line, Tumor; D002945:Cisplatin / Q000627:therapeutic use; D019295:Computational Biology; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D006367:HeLa Cells; D006801:Humans; D013058:Mass Spectrometry; D008545:Melanoma / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D009363:Neoplasm Proteins / Q000145:classification* / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*; D059467:Transcriptome / Q000187:drug effects
chemical_list: D009363:Neoplasm Proteins; D002945:Cisplatin