Deep-proteome mapping of WM-266-4 human metastatic melanoma cells: From oncogenic addiction to druggable targets

PLoS One. 2017 Feb 3;12(2):e0171512. doi: 10.1371/journal.pone.0171512. eCollection 2017.

Abstract

Cutaneous melanoma is a malignant tumor of skin melanocytes that are pigment-producing cells located in the basal layer (stratum basale) of epidermis. Accumulation of genetic mutations within their oncogenes or tumor-suppressor genes compels melanocytes to aberrant proliferation and spread to distant organs of the body, thereby resulting in severe and/or lethal malignancy. Metastatic melanoma's heavy mutational load, molecular heterogeneity and resistance to therapy necessitate the development of novel biomarkers and drug-based protocols that target key proteins involved in perpetuation of the disease. To this direction, we have herein employed a nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) proteomics technology to profile the deep-proteome landscape of WM-266-4 human metastatic melanoma cells. Our advanced melanoma-specific catalogue proved to contain 6,681 unique proteins, which likely constitute the hitherto largest single cell-line-derived proteomic collection of the disease. Through engagement of UNIPROT, DAVID, KEGG, PANTHER, INTACT, CYTOSCAPE, dbEMT and GAD bioinformatics resources, WM-266-4 melanoma proteins were categorized according to their sub-cellular compartmentalization, function and tumorigenicity, and successfully reassembled in molecular networks and interactomes. The obtained data dictate the presence of plastically inter-converted sub-populations of non-cancer and cancer stem cells, and also indicate the oncoproteomic resemblance of melanoma to glioma and lung cancer. Intriguingly, WM-266-4 cells seem to be subjected to both epithelial-to-mesenchymal (EMT) and mesenchymal-to-epithelial (MET) programs, with 1433G and ADT3 proteins being identified in the EMT/MET molecular interface. Oncogenic addiction of WM-266-4 cells to autocrine/paracrine signaling of IL17-, DLL3-, FGF(2/13)- and OSTP-dependent sub-routines suggests their critical contribution to the metastatic melanoma chemotherapeutic refractoriness. Interestingly, the 1433G family member that is shared between the BRAF- and EMT/MET-specific interactomes likely emerges as a novel and promising druggable target for the malignancy. Derailed proliferation and metastatic capacity of WM-266-4 cells could also derive from their metabolic addiction to pathways associated with glutamate/ammonia, propanoate and sulfur homeostasis, whose successful targeting may prove beneficial for advanced melanoma-affected patients.

MeSH terms

  • 14-3-3 Proteins / metabolism
  • Ammonia / metabolism
  • Animals
  • Cell Line, Tumor
  • Chromatography, Liquid / methods
  • Drug Resistance, Neoplasm / genetics
  • Female
  • Genetic Heterogeneity
  • Humans
  • Melanins / biosynthesis
  • Melanoma / genetics
  • Melanoma / metabolism*
  • Melanoma, Cutaneous Malignant
  • Mice, SCID
  • Microphthalmia-Associated Transcription Factor / metabolism
  • Middle Aged
  • Neoplasm Proteins / genetics
  • Neoplasm Proteins / metabolism*
  • Neoplasm Transplantation
  • Propionates / metabolism
  • Protein Interaction Maps
  • Proteome* / genetics
  • Proto-Oncogene Proteins B-raf / metabolism
  • Signal Transduction
  • Skin Neoplasms / genetics
  • Skin Neoplasms / metabolism*
  • Tandem Mass Spectrometry / methods

Substances

  • 14-3-3 Proteins
  • Melanins
  • Microphthalmia-Associated Transcription Factor
  • Neoplasm Proteins
  • Propionates
  • Proteome
  • Ammonia
  • Proto-Oncogene Proteins B-raf

Grants and funding

Financial support of the present work was kindly and generously provided by the (a) “European Social Fund UoA - MIS 375784” (European Union and Greek National Funds 2012 - 2015 / “THALIS” Program) and (b) “Bodossaki Foundation Donation Program” 2013 - 2014, Athens, Greece, to DJS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.