title: Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence.
abstract: Expression of the BRAF(V600E) oncoprotein is known to cause benign lesions, such as melanocytic nevi (moles). Despite the oncogenic function of mutant BRAF, these lesions are arrested by a cell-autonomous mechanism called oncogene-induced senescence. Infrequently, nevi can progress to malignant melanoma, through mechanisms that are incompletely understood. To gain more insight into this vital tumor-suppression mechanism, we performed a mass-spectrometry-based screening of the proteome and phosphoproteome in cycling and senescent cells and in cells with abrogated senescence. Proteome analysis of senescent cells revealed the up-regulation of established senescence biomarkers, including specific cytokines, but also several proteins not previously associated with senescence, including extracellular matrix-interacting. Using both general and targeted phosphopeptide enrichment by Ti(4+)-IMAC and phosphotyrosine antibody enrichment, we identified over 15,000 phosphorylation sites. Among the regulated phosphorylation sites we encountered components of the interleukin, BRAF/MAPK, and CDK-retinoblastoma pathways and several other factors. The extensive proteome and phosphoproteome dataset of BRAF(V600E)-expressing senescent cells provides molecular clues as to how oncogene-induced senescence is initiated, maintained, or evaded, serving as a comprehensive proteomic basis for functional validation.
authors: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶Center for Biomedical Genetics, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors: Erik L
authors: EL
authors: de Graaf
authors: ‖Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors: Joanna
authors: J
authors: Kaplon
authors: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors: Houjiang
authors: H
authors: Zhou
authors: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶Center for Biomedical Genetics, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors: Albert J R
authors: AJ
authors: Heck
authors: ‖Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands m.altelaar@uu.nl d.peeper@nki.nl.
authors: Daniel S
authors: DS
authors: Peeper
authors: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; m.altelaar@uu.nl d.peeper@nki.nl.
authors: A F Maarten
authors: AF
authors: Altelaar
mesh_terms: D002460:Cell Line; D016922:Cellular Senescence; D030541:Databases, Genetic; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009857:Oncogenes; D010766:Phosphorylation; D040901:Proteomics / Q000379:methods*; D048493:Proto-Oncogene Proteins B-raf / Q000378:metabolism; D015398:Signal Transduction
chemical_list: C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf