Comprehensive analysis of transcriptome data for identifying biomarkers and therapeutic targets in head and neck squamous cell carcinoma

Yu, Jianhua; Qin, Xing

doi:10.21037/atm.2020.03.30

Cited by 11 publications

(7 citation statements)

References 46 publications

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“…As a pathway to promote cell function, NF−kappa B signaling pathways activation may be related to the synthesis of viral proteins. In summary, the potential host-virus protein interactions may provide us with new ideas and strategies for drug screening and the development of drug-related research in SARS-CoV-2 [ 27 ]. At the same time, based on the PPI network diagram, we used the CytoHubba plug-in to select 12 central genes with high connectivity, all of which occupied the core nodes of the network, suggesting that these central genes might play a pivotal role in the process of infection in the novel coronavirus [ 20 ].…”

Section: Discussionmentioning

confidence: 99%

Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids

et al. 2021

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Background In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people’s health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein–protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in. Results In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients. Conclusions In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.

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Section: Discussionmentioning

confidence: 99%

Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids

et al. 2021

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“…The integration and analysis of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) based on microarray data are helpful to dig out diagnostic biomarkers and therapeutic targets. A study reported that a crucial miRNA-mRNA network involved neck squamous cell carcinoma to explore the underlying regulatory mechanisms [ 11 ]. Another study revealed that candidate miRNA-mRNA regulatory networks could be used to predict radioresistance in nasopharyngeal carcinoma [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatics Analysis of mRNAs and miRNAs for Identifying Potential Biomarkers in Lung Adenosquamous Carcinoma

Nie

Gong

Zhu

et al. 2022

Computational and Mathematical Methods in Medicine

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Background. Lung adenosquamous carcinoma (LASC) is a special type of lung cancer. LASC is a malignant tumor with strong aggressiveness and a poor prognosis. Previous studies have revealed that microRNAs (miRNAs) are widely involved in the development of tumors by targeting mRNA. This study is aimed at identifying the key mRNAs and miRNAs of LASC and constructing miRNA-mRNA networks for deeply comprehending the latent molecular mechanisms. Methods. mRNA dataset (GSE51852) and miRNA dataset (GSE51853) were extracted and downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were picked out by the GEO2R web tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were conducted in the DAVID database. The protein-protein interaction (PPI) network was performed and analyzed by using the STRING database and Cytoscape software, respectively. TransmiR v2.0 was applied to predict potential transcription factors of miRNAs. The target genes of DEMs were predicted in the miRWalk database. Results. In comparison to normal tissues, a total of 1458 DEGs (511 upregulated and 947 downregulated) and 13 DEMs (5 upregulated and 8 downregulated) were screened out in LASC tissues. The PPI network of the DEGs displayed five key modules and seventeen hub genes. Six target genes of the DEMs were predicted, and five essential miRNA-mRNA regulatory pairs were established. Ensuingly, CENPF, one of the target genes, was also the hub genes of GSE51852, which was obtained from MCODE and cytoHubba and regulated by hsa-miR-205. Conclusions. We constructed the miRNA-mRNA regulatory pairs, which are helpful to study the potential regulatory mechanisms and find out promising diagnosis biomarkers and therapeutic targets for LASC.

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“…Jin et al ( 31 ) used functional enrichment analysis to screen genes associated with improving invasive ductal carcinoma treatment and COL4A1 was found to be a key gene that influenced proliferation and invasion of the invasive ductal carcinoma cells. Other studies have shown that COL4A1 is upregulated in head and neck squamous cell carcinoma and may serve as a novel prognostic biomarker for the recurrence of OSCC ( 32 , 33 ), indicating that COL4A1 expression is associated with OSCC. In the present study, COL4A1 was highly expressed in several OSCC cell lines and COL4A expression was highest in SCC-4 cells, which may be associated with the high invasiveness, as well as migration, proliferation and differentiation, of SCC-4 ( 34 , 35 ).…”

Section: Discussionmentioning

confidence: 96%

COL4A1 promotes the proliferation and migration of oral squamous cell carcinoma cells by binding to NID1

Tian

Sun

et al. 2023

Exp Ther Med

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Collagen type IV α1 chain (COL4A1) is a collagen protein that acts as a tumor-promoting factor in several types of cancer. However, the role and the potential mechanisms involving COL4A1 in oral squamous cell carcinoma (OSCC) remain unclear. Using reverse transcription-quantitative PCR and western blotting, the expression levels of COL4A1 and (nidogen-1) NID1 in OSCC cells were assessed. Cell Counting Kit-8, EdU staining and colony formation assays were used to evaluate cell proliferation. Cell migration and invasion were assessed using wound healing and Transwell invasion assays, respectively. The expression levels of proteins involved in epithelial-mesenchymal transition (EMT) were assessed using western blotting. In addition, the association between COL4A1 and NID1 was analyzed using TNMplot and the STRING database and verified by co-immunoprecipitation analysis. COL4A1 expression was found to be significantly increased in OSCC cells. Knockdown of COL4A1 expression decreased SCC-4 cell proliferation, migration and invasion, as well as the progression of EMT. In addition, COL4A1 was shown to be significantly positively associated with NID1 in OSCC and to bind to NID1. NID1 overexpression reversed the inhibitory effects of COL4A1 knockdown on cell proliferation, migration and invasion as well as on the progression of EMT in OSCC cells. In summary, the present findings demonstrated that COL4A1 promoted cell proliferation and migration as well as the progression of EMT in OSCC cells by binding to NID1, highlighting a potential avenue for therapeutic management of OSCC.

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Comprehensive analysis of transcriptome data for identifying biomarkers and therapeutic targets in head and neck squamous cell carcinoma

Cited by 11 publications

References 46 publications

Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids

Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids

Bioinformatics Analysis of mRNAs and miRNAs for Identifying Potential Biomarkers in Lung Adenosquamous Carcinoma

COL4A1 promotes the proliferation and migration of oral squamous cell carcinoma cells by binding to NID1

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