title: Pediatric Ependymoma: A Proteomics Perspective.
abstract: Proteomics based on high-resolution mass spectrometry (MS) is the tool of choice for the analysis of protein presence, modifications and interactions, with increasing emphasis on the examination of tumor tissues. Application of MS-based proteomics offers a detailed picture of tumor tissue characteristics, facilitating the appreciation of different tumor entities, whilst providing reliable and fast results for therapeutic marker targeting and prognostic factor assessment. Through use of the high analytical resolution of nano-high-pressure liquid chromatography (nanoHPLC) and the high resolution of an Orbitrap Elite mass spectrometer, the present study aimed to provide knowledge on the proteome of the generally unknown entity of pediatric ependymal tumors.
  
  
  
  Ten resected specimens of childhood ependymoma were analyzed through a one-dimensional (1D) nanoLC-MS/MS approach. Method optimization steps were undertaken for both the sample preparation/protein extraction procedure and LC parameters, aiming to achieve the highest possible identification rates.
  
  
  
  Following method optimization, each nanoLC-MS/MS run resulted in identification of more than 5,000 proteins and more than 25,000 peptides for every analyzed sample, thus detailing the greater part of the ependymoma proteome. Identified proteins were found to spread throughout all known tumor categories regarding their molecular function and subcellular localization.
  
  
  
  Through the proposed nanoLC-MS/MS method herein we report, for the firs time, the ependymoma proteome database. A large number of similarities regarding proteome content are revealed compared to other two pediatric brain tumor entities; astrocytomas and medulloblastomas. Furthermore, through our approach, the majority of currently proposed markers for ependymoma (e.g. nucleolin, nestin, Ki67 and laminin subunit A2) as well as all major key players of the phosphoinositide 3-kinase pathway (seemingly implicated in ependymoma), were definitely detected.
authors.affiliation: Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
authors.forename: George Th
authors.initials: GT
authors.lastname: Tsangaris
authors.affiliation: Hematology/Oncology Unit, First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece.
authors.forename: Chrissa
authors.initials: C
authors.lastname: Papathanasiou
authors.affiliation: Department of Neurosurgery, Aghia Sophia Children's Hospital, Athens, Greece.
authors.forename: Panagiotis G
authors.initials: PG
authors.lastname: Adamopoulos
authors.affiliation: Department of Biochemistry and Molecular Biology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece.
authors.forename: Andreas
authors.initials: A
authors.lastname: Scorilas
authors.affiliation: Department of Biochemistry and Molecular Biology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece.
authors.forename: Constantinos E
authors.initials: CE
authors.lastname: Vorgias
authors.affiliation: Department of Neurosurgery, Aghia Sophia Children's Hospital, Athens, Greece.
authors.forename: Neofytos
authors.initials: N
authors.lastname: Prodromou
authors.affiliation: Hematology/Oncology Unit, First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece.
authors.forename: Foteini Tzortzatou
authors.initials: FT
authors.lastname: Stathopoulou
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece.
authors.forename: Dimitrios J
authors.initials: DJ
authors.lastname: Stravopodis
authors.affiliation: Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece atanagnost@bioacademy.gr.
authors.forename: Athanasios K
authors.initials: AK
authors.lastname: Anagnostopoulos
mesh_terms: D001932:Brain Neoplasms / Q000378:metabolism*; D002675:Child, Preschool; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D004806:Ependymoma / Q000378:metabolism*; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D036103:Nanotechnology / Q000379:methods; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D020543:Proteome
keywords: Ependymoma; central nervous system tumors; method development; nanoLC-MS/MS; pediatric brain tumors; proteomics