Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling

Biol Direct. 2020 Jun 15;15(1):10. doi: 10.1186/s13062-020-00264-5.


Background: Glioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies have led to massive multi-omics datasets, there lacks of comprehensive integration of glioma datasets for uncovering candidate biomarker genes.

Results: In this study, we collected a large-scale assemble of multi-omics multi-cohort datasets from worldwide public resources, involving a total of 16,939 samples across 19 independent studies. Through comprehensive molecular profiling across different datasets, we revealed that PRKCG (Protein Kinase C Gamma), a brain-specific gene detectable in cerebrospinal fluid, is closely associated with glioma. Specifically, it presents lower expression and higher methylation in glioma samples compared with normal samples. PRKCG expression/methylation change from high to low is indicative of glioma progression from low-grade to high-grade and high RNA expression is suggestive of good survival. Importantly, PRKCG in combination with MGMT is effective to predict survival outcomes in a more precise manner.

Conclusions: PRKCG bears the great potential for glioma diagnosis, prognosis and therapy, and PRKCG-like genes may represent a set of important genes associated with different molecular mechanisms in glioma tumorigenesis. Our study indicates the importance of computational integrative multi-omics data analysis and represents a data-driven scheme toward precision tumor subtyping and accurate personalized healthcare.

Keywords: Biomarker; Cerebrospinal fluid; Glioma; Multi-omics; PRKCG.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers, Tumor / analysis*
  • Brain Neoplasms / genetics*
  • Brain Neoplasms / metabolism
  • Computational Biology*
  • Gene Expression
  • Glioma / genetics*
  • Glioma / metabolism
  • Humans
  • Methylation
  • Protein Kinase C / genetics*
  • Protein Kinase C / metabolism


  • Biomarkers, Tumor
  • protein kinase C gamma
  • Protein Kinase C