Neuroblastoma (AMC, 2012)

Overview

This dataset from the Academic Medical Center Amsterdam encompasses proteomic profiling of neuroblastoma cell lines using label-free LC-MS/MS. The study focused on characterizing extracellular vesicle (EV) proteomes from neuroblastoma cell lines with differing MYCN amplification status and transcriptional programs (adrenergic vs. mesenchymal), using a metabolic labelling strategy (ManNAz/click chemistry) to selectively isolate tumor-derived EVs from native serum.

Composition

  • Three neuroblastoma cell lines: SH-EP2 (mesenchymal, MYCN-non-amplified), SH-SY5Y (adrenergic, MYCN-non-amplified), and Kelly (adrenergic, MYCN-amplified).
  • Survival validation using three publicly available transcriptomic datasets: Kocak (GSE45547; n = 476), Versteeg (GSE16476; n = 88), and NREC (GSE85047; n = 220).
  • DepMap CRISPR dependency screens across >1100 cancer cell lines (37 neuroblastoma lines) used for GJC1 dependency analysis.
  • Cancer type: NBL.

Assays / panels (linked)

  • LC-MS/MS proteomics: Label-free quantitative proteomic profiling of tumor-derived extracellular vesicles.
  • ManNAz metabolic labelling + copper-catalysed click chemistry for selective tumor EV isolation from native serum.

Papers using this cohort

  • PMID:22367537 — Primary proteomic study identifying GJC1 as a neuroblastoma EV surface marker.

Notable findings derived from this cohort

  • GJC1 (connexin 45) identified as a pan-neuroblastoma EV surface marker through LC-MS/MS; high expression correlated with poor overall survival in three independent transcriptomic datasets PMID:22367537.
  • ManNAz labelling selectively isolated tumor-derived EVs from native serum without altering EV composition (94.2% protein overlap, Pearson r = 0.998) PMID:22367537.
  • GJC1 was not detected in EVs from healthy adult donor plasma, suggesting tumor specificity for liquid biopsy applications PMID:22367537.

Sources

This page was processed by entity-page-writer on 2026-05-06.