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

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.

• Authors: Lin Liu, Guangyu Wang, Liguo Wang, Chunlei Yu, Mengwei Li, Shuhui Song, Lili Hao, Lina Ma, Zhang Zhang
• Journal: Biology direct (Biol Direct) Vol. 15 Issue 1 Pg. 10 (06 15 2020) ISSN: 1745-6150 [Electronic] England
• PMID: 32539851 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

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

Topics

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