Received on February 23, 2006
Accepted on May 23, 2006

Proteomics and Protein Markers

Identification of Apolipoprotein A-II in Cerebrospinal Fluid of Pediatric Brain Tumor Patients by Protein Expression Profiling

¹ Erasmus MC--Sophia Children's Hospital--University Medical Center Rotterdam, Department of Pediatric Oncology and Hematology, Rotterdam, The Netherlands
² Ciphergen Biosystems Inc., Fremont, CA
³ Erasmus MC--University Medical Center Rotterdam, Department of Clinical Chemistry, Rotterdam, The Netherlands
⁴ Erasmus MC--University Medical Center Rotterdam, Department of Pathology, Rotterdam, The Netherlands
⁵ Erasmus MC--University Medical Center Rotterdam, Department of Neuro-oncology, Rotterdam, The Netherlands, Rotterdam, The Netherlands

^* To whom correspondence should be addressed. E-mail: m.l.denboer{at}erasmusmc.nl.

Background: Our aim was to detect differences in protein expression profiles in cerebrospinal fluid (CSF) from pediatric patients with and without brain tumors.

Methods: We used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry and Q10 ProteinChip arrays to compare protein expression profiles in CSF from 32 pediatric brain tumor patients and 70 pediatric control patients. A protein with high discriminatory power was isolated and identified by subsequent anion-exchange and reversed-phase fractionation, gel electrophoresis, and mass spectrometry. The identity of the protein was confirmed by Western blotting and immunohistochemistry.

Results: Of the 247 detected protein peak clusters, 123 were differentially expressed between brain tumor and control patients with a false discovery rate of 1%. Double-loop classification analysis gave a mean prediction accuracy of 88% in discriminating brain tumor patients from control patients. From the 123 clusters, a highly overexpressed protein peak cluster (M_r 17 000) in CSF from brain tumor patients was selected for further analysis and identified as apolipoprotein A-II. Apolipoprotein A-II expression in CSF was correlated with the CSF albumin concentration, suggesting that the overexpression of apolipoprotein A-II is related to a disrupted blood-brain barrier.

Conclusions: SELDI-TOF mass spectrometry can successfully find differentially expressed proteins in CSF of pediatric brain tumor and control patients. Apolipoprotein A-II is highly overexpressed in CSF of pediatric brain tumor patients, which most likely is related to a disrupted blood-brain barrier. Ongoing studies are aimed at finding subtype specific proteins in larger groups of pediatric brain tumor patients.