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.

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“…Proteome profiling. For proteome profiling, two-dimensional gel electrophoresis, gel image analysis and MALDI TOF mass spectrometry were used, as described earlier (36). In brief, cells were solubilized in urea-containing buffer for isoelectrofocusing.…”

“…Protein identification. Protein spots were excised from the gels, destained and subjected to in-gel digestion with trypsin (modified, sequence grade porcine, Promega, Madison, WI, USA), as described earlier (36). Tryptic peptides were concentrated and desalted by C18 ZipTip's.…”