Abstract 1874: Investigation of the cerebrospinal fluid proteome from central nervous system pediatric tumors using bait loaded hydrogel nanoparticles and mass spectrometry

Abstract

Abstract Central nervous system (CNS) tumors are the second common pediatric malignancies, accounting for approximately 25% of all childhood neoplasms. Cerebrospinal fluid (CSF) is a very valuable source of biomarkers for brain tumors and represents a potential indicator of pathological processes that happen in the CNS. CSF biomarker discovery poses some physiological and technical challenges: low protein levels (total protein concentration 0.3 to 0.7 mg/mL), dynamic range (up to approximately 12 order of magnitude), and the presence of highly abundant proteins masking the less abundant ones. In order to overcome these challenges, we used core-shell capturing hydrogel nanoparticles that can capture, preserve and concentrate candidate low molecular weight, low abundance proteins in solution in one step improving the effective sensitivity of mass-spectrometry by several orders of magnitude. CSF samples from pediatric brain cancer patients (14 medulloblastoma, 4 high-grade glioma, 6 ependimoma, 4 PNET, 2 atypical teratoid rhabdoid tumor) either at initial diagnosis (n=27) or at tumor recurrence (n=3) and 21 non-brain pediatric oncology controls (extra-CNS non Hodgkin lymphoma) were processed with core-shell hydrogel nanoparticles and then analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (MS/MS). We identified 559 non redundant proteins, 147 (26%) of those not present in the public comprehensive CSF proteome database (www.biosino.org). Functional classification analysis performed with IPA Ingenuity System showed that CSF contained proteins normally involved in neurological diseases, developmental disorders, cellular movement, cellular growth and proliferation. Several candidate proteins that show a statistical difference (p-value <0.05, Fisher test) between brain tumor and non-brain oncology controls, were involved in the process of extracellular matrix (ECM) remodeling which has a key role in the transition to invasive cancer and is often an indicator of worse prognosis. Two examples were a) the ECM protein collagen XVIII, which was previously identified in meningioma tissue with a fast progression, and b) procollagen C-endopeptidase enhancer, an extracellular matrix glycoprotein related to tumor growth and angiogenesis. Statistical analysis between non-metastatic and metastatic patient samples also highlighted potentially relevant proteins such as GDNF family receptor α-2 (GFRα2); two other family members GFRα1 and GFRα3 were reported to have a role in tumor growth and invasiveness. In conclusion, combining a unique dataset of CSF from pediatric cancer patients with a novel enabling nanotechnology allowed us to identify important insights for diagnosis, prognosis and molecular stratification of CNS pediatric tumors. Citation Format: Ruben Magni, Paolo Verderio, Lance Liotta, Filippo Spreafico, Maura Massimino, Alessandra Luchini, Italia Bongarzone. Investigation of the cerebrospinal fluid proteome from central nervous system pediatric tumors using bait loaded hydrogel nanoparticles and mass spectrometry. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1874. doi:10.1158/1538-7445.AM2014-1874