Bioinformatics analysis identifies hub genes and pathways in nasopharyngeal carcinoma

Liu, Kang; Kang, Min; Zhou, Ziyan; Wen, Qiuyuan; Wang, Rensheng

doi:10.3892/ol.2019.10707

Cited by 11 publications

(12 citation statements)

References 66 publications

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“…Moreover, ATAD2 showed expression disturbance in hepatocellular carcinoma, ovarian cancer, stomach cancer, and other cancers (50)(51)(52). The discovery of Liu et al, through bioinformatics analysis, that ATAD2 may take part in the tumorigenesis of NPC is noteworthy (53). This also agrees with our ndings.…”

Section: Discussionsupporting

confidence: 92%

Potential Role of The Upregulation of The Zinc Finger Protein of The Cerebellum 2 In Nasopharyngeal Carcinoma

Peng

Li²,

Ding

et al. 2021

Preprint

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Background: Nasopharyngeal carcinoma (NPC) is a common type of cancer mainly caused by EB virus infection in southern China and Southeast Asia. Zinc finger protein of the cerebellum 2 has been reported to be dysregulated in numerous cancers. However, its role in NPC has not yet been completely investigated. Methods: ZIC2 mRNA expression and clinical role of NPC was explored by Gene Expression Omnibus (GEO) databases and tissue microarrays. Immunohistochemical (IHC) staining was used to assessed the protein expression level of ZIC2 in NPC. Moreover, functional enrichment analyses were performed by the overlapping genes of differentially expressed genes in NPC and ZIC2 related co-expressed genes. Cistrome Data Browser (Cistrome DB) and scatter diagrams displayed the possibility of ATAD2 as a target gene of ZIC2. Last, characteristic phenotype was identified by weighted gene co-expression network analysis (WGCNA).Results: The mRNA expression levels of ZIC2 were significantly increased in NPC within genechips and tissue microarrays (SMD = 2.14; 95% CI = 1.85–2.44). Increased ZIC2 correlated with poor prognosis in NPC patients. The IHC results also showed that ZIC2 protein expression in NPC tissues was remarkably higher than in control tissues. Enrichment analysis showed that genes positively related to ZIC2 are mainly enriched in cell division and in the cell cycle. WGCNA analysis discovered that NPC dataset GSE12452 may be positive correlated with N stage and nagetive correlated with grade. Conclusion: ZIC2 upregulation may promote NPC tumorigenesis through cancer cell proliferation and cell cycle regulation. ATAD2 may produce a marked effect as the downstream target of ZIC2.

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Section: Discussionsupporting

confidence: 92%

Potential Role of The Upregulation of The Zinc Finger Protein of The Cerebellum 2 In Nasopharyngeal Carcinoma

Peng

Li²,

Ding

et al. 2021

Preprint

Self Cite

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“…Over the past few decades, microarray technology established using high-throughput platforms serves as a promising and efficient tool to detect phenotypic characteristics of cancer. [ 6 ] For example, Zhang et al [ 7 ] revealed that 8 genes and immune-related pathways associated with the development of osteosarcoma metastasis by weighted gene co-expression network analysis (WGCNA). Cai et al [ 8 ] and Lu et al [ 9 ] identified 5 hub genes as prognostic biomarkers for breast cancer metastasis by bioinformatics analysis.…”

Section: Introductionmentioning

confidence: 99%

Identification of novel biomarkers and small-molecule compounds for nasopharyngeal carcinoma with metastasis

Liu

et al. 2020

Medicine

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The purpose of this study was to investigate novel biomarkers and potential mechanisms in nasopharyngeal carcinoma (NPC) patients with metastasis. Two microarray datasets (GSE103611 and GSE36682) were obtained from GEO database, differentially expressed genes (DEGs) and differentially expressed miRNA (DEMs) were identified, Gene ontology (GO) as well as Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted with DEGs and DEMs targeted genes. Protein–protein interactions (PPI) network of the DEGs and DEMs targeted genes were constructed, furthermore, Connectivity Map (CMap) database was applied to select the potential drugs with therapeutic effects. Overall, we identified 396 upregulated and 19 downregulated DEGs. Additionally, we identified 1 upregulated DEM, miR-135b, and a downregulated DEM, miR-574-5p. Functional enrichment analysis indicated that both DEGs and DEMs targeted genes participated in biological process (BP) of regulation of transcription from RNA polymerase II promoter, DNA-templated positive regulation of transcription, and Epstein-Barr virus infection signaling pathway. Besides, upregulated EP300 gene was a hub node both in DEGs and DEMs target genes. CMap database analysis indicated that sanguinarine, verteporfin, and chrysin are potential drugs for prevention and treatment of NPC metastasis. In summary, the common hub gene, biological process and pathway identified in the study provided a novel insight into the potential mechanism of NPC metastasis. Furthermore, we identified several possible small molecule compounds for treatment of NPC metastasis.

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“…There were several studies have previously identified many DEGs of NPC through bioinformatical analysis 50 - 52 . Compared with previous studies, the advantages of our study may be summarized as follows: Firstly, these previous reports have only screened core genes for NPC and they did not further evaluate the clinical value of core genes for NPC.…”

Section: Discussionmentioning

confidence: 99%

Screening and bioinformatical analysis of differentially expressed genes in nasopharyngeal carcinoma

Guo¹,

Zheng²,

Liu³

et al. 2021

J. Cancer

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Objective: To identify differentially expressed genes via bioinformatical analysis for nasopharyngeal carcinoma (NPC) and explore potential biomarkers for NPC. Methods: We downloaded the NPC gene expression datasets (GSE40290, GSE53819) and obtained differentially expressed genes (DEGs) via GEO2R. Functional analysis of DEGs was performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In order to explore the interaction of DEGs and screen the core genes, we established protein-protein interaction (PPI) network. Then the expression level, prognostic and diagnostic analysis of the core genes in NPC were performed to reveal their potential effects on NPC. Furthermore, we obtained the transcription factors (TF) and microRNAs of core genes to construct the coregulatory network. Results: We obtained 124 up-regulated genes and 190 down-regulated genes in total. These genes were found to be related to signal transduction, extracellular matrix organization and cell adhesion based on GO analysis. KEGG analysis revealed that the NF-kappa B (NF-κB) signaling pathway, pathways in cancer were mainly enriched signaling pathways. 25 core genes were obtained by constructing PPI network. Then the high expression of 10 core genes in NPC were verified via GEPIA, Oncomine databases and laboratory experiments. The TF-microRNA coregulatory network of the 10 core genes was built. Survival and diagnostic analysis indicated that SPP1 had negative influence on the prognosis of NPC patients based on two datasets and nine up-regulated core genes (FN1, MMP1, MMP3, PLAU, PLAUR, SERPINE1, SPP1, COL8A1, COL10A1) might be diagnostic markers for NPC. Conclusions: Core genes of NPC were screened out by bioinformatical analysis in the present study and these genes may serve as prognostic and diagnostic biomarkers for NPC.

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Bioinformatics analysis identifies hub genes and pathways in nasopharyngeal carcinoma

Cited by 11 publications

References 66 publications

Potential Role of The Upregulation of The Zinc Finger Protein of The Cerebellum 2 In Nasopharyngeal Carcinoma

Potential Role of The Upregulation of The Zinc Finger Protein of The Cerebellum 2 In Nasopharyngeal Carcinoma

Identification of novel biomarkers and small-molecule compounds for nasopharyngeal carcinoma with metastasis

Screening and bioinformatical analysis of differentially expressed genes in nasopharyngeal carcinoma

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