scholarly journals Using weighted gene co-expression network analysis to identify key modules and hub genes in tongue squamous cell carcinoma

Medicine ◽  
2019 ◽  
Vol 98 (37) ◽  
pp. e17100 ◽  
Author(s):  
Ke Yin ◽  
Ying Zhang ◽  
Suxin Zhang ◽  
Yang Bao ◽  
Jie Guo ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Network Analysis ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Tongue Squamous Cell Carcinoma ◽  
Hub Genes

scholarly journals Identification of novel drug candidates for treating tongue squamous cell carcinoma using computational approaches

2021 ◽  
Author(s):  
Yinghua Li ◽  
Zihao Chen ◽  
Lu Chen ◽  
Weizhong Li
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Tumor Grade ◽  
Tongue Squamous Cell Carcinoma ◽  
Hub Genes ◽  
Drug Candidates ◽  
Novel Drug ◽  
Hub Proteins

Abstract BackgroundTongue squamous cell carcinoma (TSCC) is one of the most common oral squamous cell carcinoma (OSCC) with a high occurrence and a poor prognosis, yet its molecular mechanisms are largely unknown and novel drug candidates are needed. The purpose of this study was to construct gene co-expression networks to identify hub proteins significantly associated with tumor grades and the overall survival (OS) of TSCC patients and provide potential drug candidates. MethodsThe mRNA-sequencing and clinical data were obtained from The Cancer Genome Atlas (TCGA) dataset. Weighted gene co-expression network analysis (WGCNA) was used for identifying the co-expression module related to the tumor grade of TSCC. The hub proteins were selected by the interaction number with other proteins, and their correlations with prognosis and tumor grades were calculated. Virtual screening of compounds by the hub protein structures was used to identify the drug candidates. ResultsWGCNA identified ten co-expression modules, in which the brown module consisted of 163 genes was most significantly correlated with the tumor grade. Six hub genes/proteins (BUB1, CCNB2, CDC6, CDC20, CDK1, and MCM2) tended to be in the central hub of the network. And higher expression levels of these hub genes were associated with tumor grades and worse overall survival. Three compounds, targeting hub proteins, demonstrated high binding affinities, favorable pharmacologic properties, and low toxicity. Conclusion The gene co-expression network-based study could provide additional insight into tumorigenesis and progression of TSCC, and our study might provide novel drug candidates.

scholarly journals Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8505 ◽  
Author(s):  
Xuegang Hu ◽  
Guanwen Sun ◽  
Zhiqiang Shi ◽  
Hui Ni ◽  
Shan Jiang
Keyword(s):  
Squamous Cell Carcinoma ◽  
Network Analysis ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Molecular Mechanisms ◽  
Pearson Correlation ◽  
Gene Set Enrichment Analysis ◽  
Hub Genes ◽  
T Stage

Background Oral squamous cell carcinoma (OSCC) is a major lethal malignant cancer of the head and neck region, yet its molecular mechanisms of tumourigenesis are still unclear. Patients and methods We performed weighted gene co-expression network analysis (WGCNA) on RNA-sequencing data with clinical information obtained from The Cancer Genome Atlas (TCGA) database. The relationship between co-expression modules and clinical traits was investigated by Pearson correlation analysis. Furthermore, the prognostic value and expression level of the hub genes of these modules were validated based on data from the TCGA database and other independent datasets from the Gene Expression Omnibus (GEO) database and the Human Protein Atlas database. The significant modules and hub genes were also assessed by functional analysis and gene set enrichment analysis (GSEA). Results We found that the turquoise module was strongly correlated with pathologic T stage and significantly enriched in critical functions and pathways related to tumourigenesis. PPP1R12B, CFD, CRYAB, FAM189A2 and ANGPTL1 were identified and statistically validated as hub genes in the turquoise module and were closely implicated in the prognosis of OSCC. GSEA indicated that five hub genes were significantly involved in many well-known cancer-related biological functions and signaling pathways. Conclusion In brief, we systematically discovered a co-expressed turquoise module and five hub genes associated with the pathologic T stage for the first time, which provided further insight that WGCNA may reveal the molecular regulatory mechanism involved in the carcinogenesis and progression of OSCC. In addition, the five hub genes may be considered candidate prognostic biomarkers and potential therapeutic targets for the precise early diagnosis, clinical treatment and prognosis of OSCC in the future.

Isoliquiritigenin Inhibits Proliferation and Induces Apoptosis in Tongue Squamous Cell Carcinoma by Modulating miR-21/FOXG1 Pathway

2019 ◽  
Vol 17 (4) ◽  
pp. 463-469
Author(s):  
Hou Deqiang ◽  
Gao Yufeng ◽  
Bai Ning ◽  
Dong Yu
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Carcinoma Cells ◽  
Tongue Squamous Cell Carcinoma ◽  
Luciferase Assay ◽  
Forkhead Box ◽  
Proliferation And Apoptosis ◽  
Mrna And Protein Expression ◽  
Induced Apoptosis

Isoliquiritigenin is a flavonoid commonly found in liquorice and has been identified as a potent anti-tumor agent. The aim of this study was to investigate whether isoliquiritigenin regulates the proliferation and apoptosis of tongue squamous cell carcinoma cells by regulating forkhead box G1 expression via miR-21. MTT assay and flow cytometry were used to analyze cell proliferation and apoptosis, respectively. Quantitative real time polymerase chain reaction and western blotting were used to detect mRNA and protein expression levels, respectively. The relationship between miR-21 and forkhead box G1 was detected by dual luciferase assay. Isoliquiritigenin inhibited proliferation and induced apoptosis of tongue squamous cell carcinoma cells, and decreased miR-21 levels and promoted forkhead box G1 expression. Forkhead box G1 was then identified as a target of miR-21 and ISL could promote forkhead box G1 expression by inhibiting miR-21. Further analysis suggested that upregulation of miR-21 improved proliferation and suppressed apoptosis of tongue squamous cell carcinoma cells by inhibiting forkhead box G1 expression. Finally, our results revealed that isoliquiritigenin inhibited proliferation and induced apoptosis of tongue squamous cell carcinoma cells by regulating miR-21. Isoliquiritigenin might act as a novel therapeutic treatment for tongue squamous cell carcinoma cells through up-regulation of forkhead box G1 expression via inhibiting miR-21expression.

Characterization of Healthy and Tumor Oral Cell Lines of Human Origin. The preliminary stage in the assessment of relevant chemical compounds with impact on dentistry

2018 ◽  
Vol 69 (10) ◽  
pp. 2889-2894
Author(s):  
Ion Virgil Corlan ◽  
Adelina Cheveresan ◽  
Delia Berceanu Vaduva ◽  
Cristian Nica ◽  
Alin Faur ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Cell Lines ◽  
Squamous Cell ◽  
Chemical Compounds ◽  
Tongue Squamous Cell Carcinoma ◽  
Gingival Fibroblasts ◽  
Human Origin ◽  
Preliminary Stage

The present study was aimed to evaluate the confluence percentage of three oral cell lines, namely primary gingival keratinocytes (PGK), primary gingival fibroblasts (HGF) and tongue squamous cell carcinoma (SCC-4). All cells have been monitored at different passages for 21 days. Evaluation of confluence percentage reveals the fact that primary gingival keratinocytes and tongue squamous cell carcinoma at small passages requires a period of about two weeks to reach a confluence of approximately 80% while for the gingival fibroblasts a period of about three times smaller is satisfactory.

scholarly journals Prognostic value of MRI-measured tumor thickness in patients with tongue squamous cell carcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ki-Sun Park ◽  
Yangsean Choi ◽  
Jiwoong Kim ◽  
Kook-Jin Ahn ◽  
Bum-soo Kim ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Prognostic Value ◽  
Proportional Hazards ◽  
Correlation Coefficients ◽  
Cox Proportional Hazards ◽  
Tumor Thickness ◽  
Tongue Squamous Cell Carcinoma ◽  
Depth Of Invasion

AbstractThis study aimed to assess the prognostic value of MRI-measured tumor thickness (MRI-TT) in patients with tongue squamous cell carcinoma (SCC). This single-center retrospective cohort study included 133 pathologically confirmed tongue SCC patients between January 2009 and October 2019. MRI measurements of tongue SCC were based on axial and coronal T2-weighted (T2WI) and contrast-enhanced T1-weighted (CE-T1WI) images. Two radiologists independently measured MRI-TT. Intraclass correlation coefficients (ICC) were calculated for inter-rater agreements. Spearman’s rank correlation between MRI-TT and pathologic depth of invasion (pDOI) was assessed. Cox proportional hazards analyses on recurrence-free (RFS) and overall survival (OS) were performed for MRI-TT and pDOI. Kaplan–Meier survival curves were plotted with log-rank tests. The intra- and inter-rater agreements of MRI-TT were excellent (ICC: 0.829–0.897, all P < 0.001). The correlation between MRI-TT and pDOI was good (Spearman’s correlation coefficients: 0.72–0.76, P < 0.001). MRI-TT were significantly greater than pDOI in all axial and coronal T2WI and CE-T1WI (P < 0.001). In multivariate Cox proportional hazards analysis, MRI-TT measured on axial CE-T1WI yielded a significant prognostic value for OS (hazards ratio 2.77; P = 0.034). MRI-TT demonstrated excellent intra- and inter-rater agreements as well as high correlation with pDOI. MRI-TT may serve as a prognostic predictor in patients with tongue SCC.

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