Experimental validation of 5 in-silico predicted glioma biomarkers

Neuro Oncol. 2013 Dec;15(12):1625-34. doi: 10.1093/neuonc/not124. Epub 2013 Oct 24.


Background: Glioblastoma multiforme (GBM) is a high-grade glioma with poor prognosis. Identification of new biomarkers specific to GBM could help in disease diagnosis. We have developed and validated a bioinformatics method to predict proteins likely to be suitable as glioma biomarkers via a global microarray meta-analysis to identify uncharacterized genes consistently coexpressed with known glioma-associated genes.

Methods: A novel bioinformatics method was implemented called global microarray meta-analysis, using approximately 16,000 microarray experiments to identify uncharacterized genes consistently coexpressed with known glioma-associated genes. These novel biomarkers were validated as proteins highly expressed in human gliomas varying in tumor grades using immunohistochemistry. Glioma gene databases were used to assess delineation of expression of these markers in varying glioma grades and subtypes of GBM.

Results: We have identified 5 potential biomarkers-spondin1, Plexin-B2, SLIT3, fibulin-1, and LINGO1-that were validated as proteins highly expressed on the surface of human gliomas using immunohistochemistry. Expression of spondin1, Plexin-B2, and SLIT3 was significantly higher (P < .01) in high-grade gliomas than in low-grade gliomas. These biomarkers were significant discriminators in grade IV gliomas compared with either grade III or II tumors and also distinguished between GBM subclasses.

Conclusions: This study strongly suggests that this type of bioinformatics approach has high translational potential to rapidly discern which poorly characterized proteins may be of clinical relevance.

Keywords: biomarkers; gene databases; glioblastoma multiforme; gliomas; immunohistochemistry.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms*
  • Biomarkers, Tumor / metabolism*
  • Brain / metabolism
  • Brain Neoplasms / metabolism
  • Brain Neoplasms / pathology
  • Calcium-Binding Proteins / metabolism*
  • Case-Control Studies
  • Extracellular Matrix Proteins / metabolism*
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Glioma / metabolism*
  • Glioma / pathology
  • Humans
  • Membrane Proteins / metabolism*
  • Neoplasm Grading
  • Nerve Tissue Proteins / metabolism*
  • Oligonucleotide Array Sequence Analysis
  • Prognosis


  • Biomarkers, Tumor
  • Calcium-Binding Proteins
  • Extracellular Matrix Proteins
  • LINGO1 protein, human
  • Membrane Proteins
  • Nerve Tissue Proteins
  • SLIT3 protein, human
  • SPON1 protein, human
  • fibulin