title: Proteomics of dedifferentiation of SK-N-BE2 neuroblastoma cells.
abstract: Neuroblastoma develops through processes which include cellular dedifferentiation. Ability of tumors to form spheroids is one of the manifestations of dedifferentiation and carcinogenic transformation. To study mechanisms of dedifferentiation of neuroblastoma cells, we generated spheroids and performed a proteomics study to compare the spheroids with parental SK-N-BE2 cells. We observed that dedifferentiation induced extensive changes in the proteome profiles of the cells, which affected more than 30% of detected cellular proteins. Using mass spectrometry, we identified 239 proteins affected by dedifferentiation into spheroids as compared to the parental cells. These proteins represented such regulatory processes as transcription, cell cycle regulation, apoptosis, cell adhesion, metabolism, intracellular transport, stress response, and angiogenesis. A number of potent regulators of stemness, differentiation and cancer were detected as subnetworks formed by the identified proteins. Our validation tissue microarray study of 30 neuroblastoma cases confirmed that two of the identified proteins, DISC1 and DNA-PKcs, had their expression increased in advanced malignancies. Thus, our report unveiled extensive changes of the cellular proteome upon dedifferentiation of neuroblastoma cells, indicated top subnetworks and clusters of molecular mechanisms involved in dedifferentiation, and provided candidate biomarkers for clinical studies.
authors.affiliation: Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Ravi Kanth Rao
authors.initials: RK
authors.lastname: Saini
authors.affiliation: Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Sanaz
authors.initials: S
authors.lastname: Attarha
authors.affiliation: Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Laboratório Integrado de Microbiologia e Imunorregulação, Universidade Federal da Bahia, Salvador, Brazil.
authors.forename: Claire
authors.initials: C
authors.lastname: da Silva Santos
authors.affiliation: Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; The Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland.
authors.forename: Justyna
authors.initials: J
authors.lastname: Kolakowska
authors.affiliation: Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden. Electronic address: keiko.funa@gu.se.
authors.forename: Keiko
authors.initials: K
authors.lastname: Funa
authors.affiliation: Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Karolinkska University Hospital, Neurocentrum, Stockholm, Sweden; Oranta CancerDiagnostics AB, Uppsala, Sweden. Electronic address: serhiy8085@gmail.com.
authors.forename: Serhiy
authors.initials: S
authors.lastname: Souchelnytskyi
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism; D054337:Cell Dedifferentiation / Q000502:physiology*; D045744:Cell Line, Tumor; D051747:DNA-Activated Protein Kinase / Q000378:metabolism; D006801:Humans; D013058:Mass Spectrometry; D009363:Neoplasm Proteins / Q000378:metabolism*; D014411:Neoplastic Stem Cells / Q000378:metabolism / Q000473:pathology; D009419:Nerve Tissue Proteins / Q000378:metabolism; D058953:Neural Stem Cells / Q000378:metabolism / Q000473:pathology; D009447:Neuroblastoma / Q000378:metabolism* / Q000473:pathology*; D009687:Nuclear Proteins / Q000378:metabolism; D060066:Protein Interaction Maps; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D018874:Spheroids, Cellular / Q000378:metabolism / Q000473:pathology; D046888:Tissue Array Analysis
chemical_list: D014408:Biomarkers, Tumor; C412476:DISC1 protein, human; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D009687:Nuclear Proteins; D020543:Proteome; D051747:DNA-Activated Protein Kinase; C497263:PRKDC protein, human
keywords: DISC1; DNA-PKcs; Dedifferentiation; Neuroblastoma; Proteomics