Identification and analysis of genes associated with head and neck squamous cell carcinoma by integrated bioinformatics methods

Yu, Jianhua; Yang, Ya

doi:10.1002/mgg3.857

Cited by 24 publications

(27 citation statements)

References 46 publications

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“…The construction of the gene prediction model has been applied in many tumors, such as esophageal cancer, lung cancer, and thyroid cancer, but there are only few relevant studies on head and neck tumors. In some studies, by comparing three separate comprehensive gene expression omnibus (GEO) databases, researchers claimed that overlapping differentially expressed genes [ 29 ] like SPP1, POSTN, and COL1A2 could be used as potential diagnostic indicators of head and neck carcinoma. However, classical factors of head and neck tumors were not taken into account in the study.…”

Section: Discussionmentioning

confidence: 99%

Novel Prognostic Model Based on Immune Signature for Head and Neck Squamous Cell Carcinoma

Wang

Hua

et al. 2020

BioMed Research International

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Background. Deciphering the immune characteristics within tumors and identifying the immune signals related to the prognostic factor are helpful for the treatment and management of tumor patients. However, systematic analysis of immune signatures in head and neck squamous cell carcinoma (HNSCC) remains largely unstudied. Methods. A total of 718 immune-related genes were extracted from RNA sequencing data from 519 HNSCC patients in the TCGA database, and survival analysis with integrated bioinformatics analyses was performed to build the final predictive prognosis model. Results. The 178 survival-associated genes ( P < 0.05 ) participated in important immune functions, including immune cell activation and migration. Multivariate regression analysis using 93 genes ( P < 0.01 ), together with survival-associated clinicopathological parameters, identified 35 independent prognostic factors. The most significant 8 independent factors were CD3E, CD40LG, TNFRSF4, CD3G, CD5, ITGA2B, ABCB1, and TNFRSF13b. The final prognostic model achieved outstanding predictive efficiency with the highest AUC of 0.963. Conclusion. Our prognostic model based on the immune signature could effectively predict the prognosis of HNSCC patients, providing novel predictive biomarkers and potential therapeutic targets for HNSCC patients.

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Section: Discussionmentioning

confidence: 99%

Novel Prognostic Model Based on Immune Signature for Head and Neck Squamous Cell Carcinoma

Wang

Hua

et al. 2020

BioMed Research International

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“…Many of the members of MMPs family have been investigated as tumor markers, so we further explored the clinical significance of serum MMP3 in NPC. Several studies have reported that the higher MMP3 expression in the stromal compartment compared to normal tissues [10,11,13]. MMP3 is expressed primarily by stromal cells, including fibroblast cell and tumor-infiltrating macrophages.…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have reported that the higher MMP3 expression in the stromal compartment compared to normal tissues 10 , 11 , 13 . MMP3 is expressed primarily by stromal cells, including fibroblast cell and tumor-infiltrating macrophages.…”

Section: Discussionmentioning

confidence: 99%

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Combination of serum matrix metalloproteinase-3 activity and EBV antibodies improves the diagnostic performance of nasopharyngeal carcinoma

Feng

Xing

et al. 2020

J. Cancer

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Objective: Nasopharyngeal carcinoma (NPC) is a malignant head and neck tumor that is highly prevalent in Southeast Asia. The two traditional NPC markers VCA-IgA (EBV viral capsid antigen) and EA-IgA (EBV early antigen) are limited in the screening and diagnosis of NPC. The purpose of present study is to evaluate the diagnostic value of matrix metalloproteinase-3 (MMP3) in NPC. Methods: The levels of 23 secretory MMPs in serum samples from 15 healthy controls and 26 NPC patients were detected by Cytokine Antibody Array 2000. Immunohistochemistry, Real-time PCR and western bolt were used to detect MMP3 mRNA and protein levels in NPC tissues and cell lines. The serum protein levels of MMP3 were further measured by ELISA in healthy control individuals (n = 200) and NPC patients (n = 206). Results: MMP3 can be expressed and secreted by both NPC and fibroblast cell lines, suggesting that the higher expression of MMP3 protein in both tumor nests and stromal of NPC tissues may be the source of circulating MMP3 in NPC patients. Furthermore, we found out both MMP3 concentration and enzymatic activity were significantly increased in the NPC group (n = 206) than the healthy control group (n = 200) (P < 0.001). However, serum MMP3 enzymatic activity, but not MMP3 concentration, was significantly associated with the progression of NPC. In addition, serum MMP3 activity was more valuable in diagnosis of NPC than its concentration (0.86 vs. 0.78, AUC), and MMP3 activity can improve the diagnosis of NPC by combining with EBV-infection biomarkers VCA-IgA and EA-IgA with a sensitivity of 91.5% and a specificity of 92.3%. Conclusions: This study suggested the combination of MMP3 activity and EBV antibodies may be a useful biomarker for screening and diagnosis of NPC.

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“…For data validation, the gene expression profiles of 139 COAD samples from GSE21510 and GSE110224, 1098 LUAD samples from GSE30219, GSE31210, GES3141, GSE37745, GSE50081, and GSE68465, 211 LUSC samples from GSE43580, GSE73403, and GSE67061 and 80 HNSC samples from GSE6631 and GSE13601 were obtained from the GEO data portal 8 and analyzed using R language (Wang et al, 2017;Jin and Yang, 2019;Miao et al, 2019;Yang H. et al, 2019;Gao et al, 2020;Li et al, 2020;Qu et al, 2020). Patients in four cancers were divided into upregulated groups and downregulated groups base on the median expression of SPP1 (Zhao et al, 2018).…”

Section: Correlated Genes In Geomentioning

confidence: 99%

The Significance of Secreted Phosphoprotein 1 in Multiple Human Cancers

Wei

Bian

et al. 2020

Front. Mol. Biosci.

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Malignant tumor represents a major reason for death in the world and its incidence is growing rapidly. Developing the tools for early diagnosis is possibly a promising way to offer diverse therapeutic options and promote the survival chance. Secreted phosphoprotein 1 (SPP1), also called Osteopontin (OPN), has been demonstrated overexpressed in many cancers. However, the specific role of SPP1 in prognosis, gene mutations, and changes in gene and miRNA expression in human cancers is unclear. In this report, we found SPP1 expression was higher in most of the human cancers. Based on Kaplan-Meier plotter and the PrognoScan database, we found high SPP1 expression was significantly correlated with poor survival in various cancers. Using a large dataset of colon adenocarcinoma (COAD), head and neck cancer (HNSC), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC) patients from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, this study identified 22 common genes and 2 common miRNAs. GO, and KEGG paths analyses suggested that SPP1 correlated genes were mainly involved in positive regulation of immune cell activation and infiltration. SPP1-associated genes and miRNAs regulatory networks suggested that their interactions may play a role in the progression of four selected cancers. SPP1 showed significant positive correlation with the immunocyte and immune marker sets infiltrating degrees. All of these data provide strong evidence that SPP1 may promote tumor progress through interacting with carcinogenic genes and facilitating immune cells’ infiltration in COAD, HNSC, LUAD, and LUSC.

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Identification and analysis of genes associated with head and neck squamous cell carcinoma by integrated bioinformatics methods

Cited by 24 publications

References 46 publications

Novel Prognostic Model Based on Immune Signature for Head and Neck Squamous Cell Carcinoma

Novel Prognostic Model Based on Immune Signature for Head and Neck Squamous Cell Carcinoma

Combination of serum matrix metalloproteinase-3 activity and EBV antibodies improves the diagnostic performance of nasopharyngeal carcinoma

The Significance of Secreted Phosphoprotein 1 in Multiple Human Cancers

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