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

Lin Liu, Lin Liu, Lin Liu, Guangyu Wang, Guangyu Wang, Guangyu Wang, Guangyu Wang, Liguo Wang, Chunlei Yu, Chunlei Yu, Chunlei Yu, Mengwei Li, Mengwei Li, Mengwei Li, Shuhui Song, Shuhui Song, Shuhui Song, Lili Hao, Lili Hao, Lili HaoLina Ma, Lina Ma, Lina Ma, Zhang Zhang, Zhang Zhang, Zhang Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number10
JournalBiology Direct
Volume15
Issue number1
DOIs
StatePublished - Jun 15 2020

Keywords

  • Biomarker
  • Cerebrospinal fluid
  • Glioma
  • Multi-omics
  • PRKCG

ASJC Scopus subject areas

  • Immunology
  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

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