Abstract
Background: Isocitrate dehydrogenase (IDH) mutant is one of the most robust and important genetic aberrations in glioma. However, the underlying regulation mechanism of long non-coding RNA (lncRNA) in IDH mutant glioma has not been systematically portrayed.Methods:In this work, 775 IDH mutant glioma samples with transcriptome data, including 167 samples from the Chinese Glioma Genome Atlas (CGGA) RNAseq dataset, 390 samples from The Cancer Genome Atlas (TCGA) dataset, 79 samples from GSE16011 dataset, and 139 samples from CGGA microarray dataset, were enrolled. R language and GraphPad Prism software were applied for the statistical analysis and graphical work.Results: By comparing the differentially lncRNA genes between IDH mutant and IDH wild-type glioma samples, a four-lncRNA (JAG1, PVT1, H19, and HAR1A) signature was identified in IDH mutant glioma patients. The signature model was established based on the expression level and the regression coefficient of the four lncRNA genes. IDH mutant glioma samples could be successfully stratified into low-risk and high-risk groups in CGGA RNAseq, TCGA, GSE16011, and CGGA microarray databases. Meanwhile, multivariate Cox analysis showed that the four-lncRNA signature was an independent prognostic biomarker after adjusting for other clinicopathologic factors. Moreover, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the immune response and cellular metabolism were significantly associated with the four-lncRNA risk signature.Conclusion: Taken together, the four-lncRNA risk signature was identified as a novel prognostic marker for IDH mutant glioma patients and may potentially lead to improvements in the lives of glioma patients.
Highlights
Long non-coding RNAs, which are initially regarded as spurious transcriptional noise, are recently reported to play roles in cellular development, cell metabolism, and posttranscriptional modification [1]
By comparing the differentially Long non-coding RNAs (lncRNAs) genes between Isocitrate dehydrogenase (IDH) mutant and IDH wild-type glioma samples, a four-lncRNA (JAG1, Plasmacytoma variant translocation 1 (PVT1), H19, and Highly Accelerated Region 1A (HAR1A)) signature was identified in IDH mutant glioma patients
The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the immune response and cellular metabolism were significantly associated with the four-lncRNA risk signature
Summary
Long non-coding RNAs (lncRNAs), which are initially regarded as spurious transcriptional noise, are recently reported to play roles in cellular development, cell metabolism, and posttranscriptional modification [1]. Many reports were proposed to investigate the molecular mechanism of lncRNA and its impact on cancer development. The lncRNA HOX Transcript Antisense RNA (HOTAIR), which regulates the transcriptional silencing of EZH2 and the epigenetic modification of H3K27, is reported as a negative prognostic factor in breast cancer and colon cancer [3, 4]. The aberrant expressions of lncRNA in IDH mutant glioma remain unknown. Isocitrate dehydrogenase (IDH) mutant is one of the most robust and important genetic aberrations in glioma. The underlying regulation mechanism of long non-coding RNA (lncRNA) in IDH mutant glioma has not been systematically portrayed
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