Identification of the potential biomarkers in patients with glioma: a weighted gene co-expression network analysis

Chen, Ting‐Yu; Liu, Yang; Liang, Chen; Luo, Jianxun; Chao, Zhang; Shen, Xianfeng

doi:10.1093/carcin/bgz194

Cited by 22 publications

(21 citation statements)

References 68 publications

(68 reference statements)

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“…Moreover, higher IKBIP expression indicated a significantly shorter survival for patients with glioma, across different WHO grades. These findings suggested that IKBIP played a vital role in the malignant progression of gliomas, in line with the results of a previous WGCNA study [ 7 ]. Understanding the molecular mechanism of IKBIP in glioma may provide a novel therapeutic target to overcome this fatal disease.…”

Section: Discussionsupporting

confidence: 91%

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IKBIP is a novel EMT-related biomarker and predicts poor survival in glioma

Yang¹,

Wang

et al. 2021

Translational Neuroscience

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Background In cancer, kappa B-interacting protein (IKBIP) has rarely been reported. This study aimed at investigating its expression pattern and biological function in brain glioma at the transcriptional level. Methods We selected 301 glioma patients with microarray data from CGGA database and 697 glioma patients with RNAseq data from TCGA database. Transcriptional data and clinical data of 998 samples were analyzed. Statistical analysis and figure generating were performed with R language. Results We found that IKBIP expression showed positive correlation with WHO grade of glioma. IKBIP was increased in isocitrate dehydrogenase (IDH) wild type and mesenchymal molecular subtype of glioma. Gene ontology analysis demonstrated that IKBIP was profoundly associated with extracellular matrix organization, cell–substrate adhesion and response to wounding in both pan-glioma and glioblastoma. Subsequent gene set enrichment analysis revealed that IKBIP was particularly correlated with epithelial-to-mesenchymal transition (EMT). To further elucidate the relationship between IKBIP and EMT, we performed gene set variation analysis to screen the EMT-related signaling pathways and found that IKBIP expression was significantly associated with PI3K/AKT, hypoxia and TGF-β pathway. Moreover, IKBIP expression was found to be synergistic with key biomarkers of EMT, especially with N-cadherin, vimentin, snail, slug and TWIST1. Finally, higher IKBIP indicated significantly shorter survival for glioma patients. Conclusions IKBIP was associated with more aggressive phenotypes of gliomas. Furthermore, IKBIP was significantly involved in EMT and could serve as an independent prognosticator in glioma.

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Section: Discussionsupporting

confidence: 91%

“…Heretofore, the biological function of IKBIP in malignancies has been rarely reported. Only one study [ 7 ], through weighted gene co-expression network analysis (WGCNA), preliminarily revealed IKBIP as a potential hub gene in gliomagenesis. However, the role of IKBIP in glioma still remains largely unclear.…”

Section: Introductionmentioning

confidence: 99%

IKBIP is a novel EMT-related biomarker and predicts poor survival in glioma

Yang¹,

Wang

et al. 2021

Translational Neuroscience

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“…10 Moreover, higher IKBIP expression indicated a significantly shorter survival for patients with glioma, across different WHO grades. These findings suggested that IKBIP played a vital role in the malignant progression of gliomas, in line with what Chen et al found in their WGCNA study [7] . Understanding the molecular mechanism of IKBIP in glioma may provide a novel therapeutic target to overcome this fatal disease.…”

Section: Discussionsupporting

confidence: 89%

“…Heretofore, the biological function of IKBIP in malignancies has been rarely reported. Only one study [7] , through weighted gene co-expression network analysis (WGCNA), preliminarily revealed IKBIP as a potential hub gene in gliomagenesis. However, the role of IKBIP in 4 glioma still remains largely unclear.…”

Section: Introductionmentioning

confidence: 99%

IKBIP is a novel EMT-related biomarker and predicts poor survival in glioma

Yang¹,

Wang

et al. 2020

Preprint

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Purpose I kappa B-interacting protein (IKBIP) in cancer has rarely been reported.This study aimed at investigating its expression pattern and biological function in brain glioma at transcriptional level. MethodsWe selected 301 glioma patients with microarray data from CGGA database and 697 glioma patients with RNAseq data from TCGA database. Transcriptome data and clinical data of 998 samples were analyzed. Statistical analysis and figure generating were performed with R language. ResultsWe found that IKBIP expression showed positive correlation with WHO grade of glioma. IKBIP was increased in IDH wildtype and mesenchymal molecular subtype of glioma. Gene ontology analysis demonstrated that IKBIP was profoundly associated with extracellular matrix organization, cell-substrate adhesion and response to wounding in both pan-glioma and glioblastoma. Subsequent GSEA analysis revealed that IKBIP was particularly correlated with epithelial-to-mesenchymal transition (EMT). To further elucidate the relationship between IKBIP and EMT, we performed GSVA analysis to screen the EMT-related signaling pathways, and found that IKBIP expression was significantly associated with PI3K/AKT, hypoxia and TGF-β pathway. Moreover, IKBIP expression was found to be synergistic with key biomarkers of EMT, especially with N-cadherin, vimentin, snail, slug and TWIST1.Finally, higher IKBIP indicated significantly shorter survival for glioma patients.Conclusions IKBIP was associated with more aggressive phenotypes of gliomas. 3 Furthermore, IKBIP was significantly involved in EMT and could serve as an independent prognosticator in glioma.

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“…Since it was first proposed, WGCNA has been extensively applied in subsequent studies on the gene coexpression relationships across glioma subtypes to identify key genes and pathways associated with the occurrence, progression, and survival of GBM (e.g., [ 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 ]).…”

Section: Network Discovery In Glioblastomamentioning

confidence: 99%

The Role of Network Science in Glioblastoma

Lopes

Martins

Vinga

et al. 2021

Cancers

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Network science has long been recognized as a well-established discipline across many biological domains. In the particular case of cancer genomics, network discovery is challenged by the multitude of available high-dimensional heterogeneous views of data. Glioblastoma (GBM) is an example of such a complex and heterogeneous disease that can be tackled by network science. Identifying the architecture of molecular GBM networks is essential to understanding the information flow and better informing drug development and pre-clinical studies. Here, we review network-based strategies that have been used in the study of GBM, along with the available software implementations for reproducibility and further testing on newly coming datasets. Promising results have been obtained from both bulk and single-cell GBM data, placing network discovery at the forefront of developing a molecularly-informed-based personalized medicine.

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Identification of the potential biomarkers in patients with glioma: a weighted gene co-expression network analysis

Cited by 22 publications

References 68 publications

IKBIP is a novel EMT-related biomarker and predicts poor survival in glioma

IKBIP is a novel EMT-related biomarker and predicts poor survival in glioma

IKBIP is a novel EMT-related biomarker and predicts poor survival in glioma

The Role of Network Science in Glioblastoma

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