Construction of lncRNA‐associated ceRNA networks to identify prognostic lncRNA biomarkers for glioblastoma

Liu, Zhendong; Wang, Xiaoxiong; Yang, Guangchao; Chen, Zhong; Zhang, Ruotian; Ye, Junyi; Zhong, Yingqiang; Hu, Junlong; Beylerli, Ozal

doi:10.1002/jcb.29625

Cited by 30 publications

(20 citation statements)

References 35 publications

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“…In current study, hsa‐miR‐21‐5p was involved in the regulation of CDK4 and MYC, which known to be detected in the GBM development. Six lncRNA‐related ceRNA combined with four small molecule compounds were considered to help identify the regulatory functions of lncRNAs in the pathogenesis of GBM 53 . Via recruiting EZH2, LncRNA HOTAIR modulated the chromatin architecture 54 .…”

Section: Discussionmentioning

confidence: 99%

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme

Jiang

Zhong

Chen

et al. 2020

J Cellular Molecular Medi

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Glioblastoma multiforme (GBM) is a very serious mortality of central nervous system cancer. The microarray data from http://GSE2223, http://GSE4058, http://GSE4290, http://GSE13276, http://GSE68848 and http://GSE70231 (389 GBM tumour and 67 normal tissues) and the RNA‐seq data from TCGA‐GBM dataset (169 GBM and five normal samples) were chosen to find differentially expressed genes (DEGs). RRA (Robust rank aggregation) method was used to integrate seven datasets and calculate 133 DEGs (82 up‐regulated and 51 down‐regulated genes). Subsequently, through the PPI (protein‐protein interaction) network and MCODE/ cytoHubba methods, we finally filtered out ten hub genes, including FOXM1, CDK4, TOP2A, RRM2, MYBL2, MCM2, CDC20, CCNB2, MYC and EZH2, from the whole network. Functional enrichment analyses of DEGs were conducted to show that these hub genes were enriched in various cancer‐related functions and pathways significantly. We also selected CCNB2, CDC20 and MYBL2 as core biomarkers, and further validated them in CGGA, HPA and CCLE database, suggesting that these three core hub genes may be involved in the origin of GBM. All these potential biomarkers for GBM might be helpful for illustrating the important role of molecular mechanisms of tumorigenesis in the diagnosis, prognosis and targeted therapy of GBM cancer.

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Section: Discussionmentioning

confidence: 99%

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme

Jiang

Zhong

Chen

et al. 2020

J Cellular Molecular Medi

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“…The mechanism of lncRNAs as ceRNAs in GBM have been attracted many researchers [45,46]. Therefore, we constructed an immune ceRNA network by predicting the targeting relationship between lncRNA-miRNA and miRNA-mRNA.…”

Section: Discussionmentioning

confidence: 99%

LINC01268 and CTB-31O20.2 as Prognostic and Functional Protective Immune Related lncRNAs in Glioblastoma

D¹,

Yang²,

Meng³

et al. 2021

Preprint

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Glioblastoma (GBM) is the most common and deadly tumor in the central nervous system. Recent studies illuminated that long noncoding RNAs (lncRNAs) serve as competitive endogenous RNAs (ceRNAs) and play an important role in GBM by regulating immune responses. Here, GBM datasets from TCGA database were analyzed to obtain 356 significantly differentially expressed lncRNAs (DE-lncRNAs), 4951 DE-mRNAs, and 34 DE-miRNAs in GBM, respectively. For mRNAs, 369 DE-mRNAs were identified as immune-related genes in Immport database. For DE-lncRNAs, univariate analysis identified 39 DE-lncRNAs with prognostic significance, and 9 DE-lncRNAs are included in ImmLnc database. Then, combined analysis was conducted, by integrating 9 immune related DE-lncRNAs, 369 immune related DE-mRNAs and 34 DE-miRNAs, and generated a ceRNA network composed of 2 upregulated lncRNAs (LINC01268 and CTB-31O20.2), 3 downregulated miRNAs and 5 upregulated mRNAs. Then we focused on LINC01268 and CTB-31O20.2, and Kaplan-Meier survival, univariate and multivariate Cox regression analysis showed that LINC01268 and CTB-31O20.2 serve as independent protective prognostic markers in GBM. Finally, LINC01268 and CTB-31O20.2 overexpression was conducted in GBM cell U251. CCK8, transwell and scratch healing assay indicated that LINC01268 and CTB-31O20.2 inhibits GBM cell line U251 proliferation, invasion and migration. To sum up, LINC01268 and CTB-31O20.2 are independent prognostic immune related markers, and reduces cancer cell proliferation and metastasis in GBM.

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“…Potential small-molecule drugs with an inhibitory effect on CKAP2L were identified in CMap when P < 0.05 and enrichment < −0.8. Finally, the 3D and 2D structures of these drugs and their molecular formulas were obtained from the PubChem database ( https://pubchem.ncbi.nlm.nih.gov/ ) [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

CKAP2L, as an Independent Risk Factor, Closely Related to the Prognosis of Glioma

Zhu

Zheng

et al. 2021

BioMed Research International

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Recent studies have found that cytoskeleton-associated protein 2 like (CKAP2L), an important oncogene, is involved in the biological behavior of many malignant tumors, but its function in the malignant course of glioma has not been confirmed. The main purpose of this study was to clarify the relationship between prognostic clinical characteristics of glioma patients and CKAP2L expression using data collected from the GEPIA, HPA, CGGA, TCGA, and GEO databases. CKAP2L expression was significantly increased in glioma. Further, Kaplan-Meier plots revealed that increased expression of CKAP2L was associated with shorter survival time of glioma patients in datasets retrieved from multiple databases. Cox regression analysis indicated that CKAP2L can serve as an independent risk factor but also has relatively reliable diagnostic value for the prognosis of glioma patients. The results of gene set enrichment analysis suggested that CKAP2L may play a regulatory role through the cell cycle, homologous recombination, and N-glycan biosynthesis cell signaling pathways. Several drugs with potential inhibitory effects on CKAP2L were identified in the CMap database that may have therapeutic effects on glioma. Finally, knockdown of CKAP2L inhibited the proliferation and invasion of cells by reducing the expression level of cell cycle-related proteins. This is the first study to demonstrate that high CKAP2L expression leads to poor prognosis in glioma patients, providing a novel target for diagnosis and treatment of glioma.

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Construction of lncRNA‐associated ceRNA networks to identify prognostic lncRNA biomarkers for glioblastoma

Cited by 30 publications

References 35 publications

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme

LINC01268 and CTB-31O20.2 as Prognostic and Functional Protective Immune Related lncRNAs in Glioblastoma

CKAP2L, as an Independent Risk Factor, Closely Related to the Prognosis of Glioma

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