Identification of a Gene Prognostic Signature for Oral Squamous Cell Carcinoma by RNA Sequencing and Bioinformatics

Objectives. Oral squamous cell carcinoma (OSCC) is the most common oral cancer and has a poor prognosis. We aimed to identify new biomarkers or potential therapeutic targets for OSCC. Materials and Methods. Four pairs of tumor and adjacent normal tissues were collected from OSCC patients, and differ...

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Veröffentlicht in:BioMed research international 2021-04, Vol.2021, p.6657767-14
Hauptverfasser: Zhang, Yang-Yang, Mao, Ming-Hui, Han, Zheng-Xue
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Han, Zheng-Xue
description Objectives. Oral squamous cell carcinoma (OSCC) is the most common oral cancer and has a poor prognosis. We aimed to identify new biomarkers or potential therapeutic targets for OSCC. Materials and Methods. Four pairs of tumor and adjacent normal tissues were collected from OSCC patients, and differentially expressed genes (DEGs) were screened via high-throughput RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to analyze the DEGs. A protein-protein interaction (PPI) network was established with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database and Cytoscape, and two significant clusters were found. Candidate genes were screened by analyzing head and neck squamous cell carcinoma (HNSCC) data from The Cancer Genome Atlas (TCGA). A DEG-based risk model was established to predict the overall survival (OS) of OSCC patients via Kaplan-Meier analysis and the log-rank test. Furthermore, univariate Cox regression analysis was applied to assess associations between potential biomarkers and the overall survival rate. Results. Of 720 total DEGs, fifty-two DEGs in the two subclusters of the PPI network analysis were selected. A risk model was established, and five candidate genes (SPRR2E, ICOS, CTLA4, HTR1D, and CCR4) were identified as biomarkers of OS in OSCC patients. Conclusions. We successfully constructed a prognostic signature to predict prognosis and identified five candidate genes associated with the OS of OSCC patients that are potential tumor biomarkers and targets in OSCC.
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Oral squamous cell carcinoma (OSCC) is the most common oral cancer and has a poor prognosis. We aimed to identify new biomarkers or potential therapeutic targets for OSCC. Materials and Methods. Four pairs of tumor and adjacent normal tissues were collected from OSCC patients, and differentially expressed genes (DEGs) were screened via high-throughput RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to analyze the DEGs. A protein-protein interaction (PPI) network was established with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database and Cytoscape, and two significant clusters were found. Candidate genes were screened by analyzing head and neck squamous cell carcinoma (HNSCC) data from The Cancer Genome Atlas (TCGA). A DEG-based risk model was established to predict the overall survival (OS) of OSCC patients via Kaplan-Meier analysis and the log-rank test. Furthermore, univariate Cox regression analysis was applied to assess associations between potential biomarkers and the overall survival rate. Results. Of 720 total DEGs, fifty-two DEGs in the two subclusters of the PPI network analysis were selected. A risk model was established, and five candidate genes (SPRR2E, ICOS, CTLA4, HTR1D, and CCR4) were identified as biomarkers of OS in OSCC patients. Conclusions. We successfully constructed a prognostic signature to predict prognosis and identified five candidate genes associated with the OS of OSCC patients that are potential tumor biomarkers and targets in OSCC.</description><identifier>ISSN: 2314-6133</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2021/6657767</identifier><identifier>PMID: 33869632</identifier><language>eng</language><publisher>United States: Hindawi</publisher><subject>Analysis ; Bioinformatics ; Biomarkers ; Cancer ; Carcinoma, Squamous Cell - genetics ; Carcinoma, Squamous Cell - pathology ; Care and treatment ; Cluster Analysis ; Computational Biology ; CTLA-4 protein ; Data analysis ; Diagnosis ; Encyclopedias ; Extracellular matrix ; Female ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Ontology ; Gene sequencing ; Genes ; Genetic aspects ; Genetic Association Studies ; Genomes ; Genomics ; Head &amp; neck cancer ; Humans ; Logistic Models ; Male ; Medical prognosis ; Methods ; Middle Aged ; Mouth cancer ; Mouth Neoplasms - genetics ; Mouth Neoplasms - pathology ; Multivariate Analysis ; Network analysis ; Oral cancer ; Oral squamous cell carcinoma ; Peptides ; Prognosis ; Protein interaction ; Protein Interaction Maps - genetics ; Protein-protein interactions ; Proteins ; Rank tests ; Regression analysis ; Ribonucleic acid ; Risk factors ; RNA ; RNA sequencing ; ROC Curve ; Sequence Analysis, RNA ; Software ; Squamous cell carcinoma ; Squamous Cell Carcinoma of Head and Neck - genetics ; Survival ; Survival Analysis ; Therapeutic targets ; Tongue ; Transcription, Genetic ; Tumors ; Values</subject><ispartof>BioMed research international, 2021-04, Vol.2021, p.6657767-14</ispartof><rights>Copyright © 2021 Yang-Yang Zhang et al.</rights><rights>COPYRIGHT 2021 John Wiley &amp; Sons, Inc.</rights><rights>Copyright © 2021 Yang-Yang Zhang et al. 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Oral squamous cell carcinoma (OSCC) is the most common oral cancer and has a poor prognosis. We aimed to identify new biomarkers or potential therapeutic targets for OSCC. Materials and Methods. Four pairs of tumor and adjacent normal tissues were collected from OSCC patients, and differentially expressed genes (DEGs) were screened via high-throughput RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to analyze the DEGs. A protein-protein interaction (PPI) network was established with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database and Cytoscape, and two significant clusters were found. Candidate genes were screened by analyzing head and neck squamous cell carcinoma (HNSCC) data from The Cancer Genome Atlas (TCGA). A DEG-based risk model was established to predict the overall survival (OS) of OSCC patients via Kaplan-Meier analysis and the log-rank test. 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neck cancer</topic><topic>Humans</topic><topic>Logistic Models</topic><topic>Male</topic><topic>Medical prognosis</topic><topic>Methods</topic><topic>Middle Aged</topic><topic>Mouth cancer</topic><topic>Mouth Neoplasms - genetics</topic><topic>Mouth Neoplasms - pathology</topic><topic>Multivariate Analysis</topic><topic>Network analysis</topic><topic>Oral cancer</topic><topic>Oral squamous cell carcinoma</topic><topic>Peptides</topic><topic>Prognosis</topic><topic>Protein interaction</topic><topic>Protein Interaction Maps - genetics</topic><topic>Protein-protein interactions</topic><topic>Proteins</topic><topic>Rank tests</topic><topic>Regression analysis</topic><topic>Ribonucleic acid</topic><topic>Risk factors</topic><topic>RNA</topic><topic>RNA sequencing</topic><topic>ROC Curve</topic><topic>Sequence Analysis, RNA</topic><topic>Software</topic><topic>Squamous cell carcinoma</topic><topic>Squamous Cell Carcinoma of Head and Neck - genetics</topic><topic>Survival</topic><topic>Survival Analysis</topic><topic>Therapeutic targets</topic><topic>Tongue</topic><topic>Transcription, Genetic</topic><topic>Tumors</topic><topic>Values</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Yang-Yang</creatorcontrib><creatorcontrib>Mao, Ming-Hui</creatorcontrib><creatorcontrib>Han, Zheng-Xue</creatorcontrib><collection>Hindawi Publishing Complete</collection><collection>Hindawi Publishing Subscription Journals</collection><collection>Hindawi Publishing Open Access Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health &amp; 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Oral squamous cell carcinoma (OSCC) is the most common oral cancer and has a poor prognosis. We aimed to identify new biomarkers or potential therapeutic targets for OSCC. Materials and Methods. Four pairs of tumor and adjacent normal tissues were collected from OSCC patients, and differentially expressed genes (DEGs) were screened via high-throughput RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to analyze the DEGs. A protein-protein interaction (PPI) network was established with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database and Cytoscape, and two significant clusters were found. Candidate genes were screened by analyzing head and neck squamous cell carcinoma (HNSCC) data from The Cancer Genome Atlas (TCGA). A DEG-based risk model was established to predict the overall survival (OS) of OSCC patients via Kaplan-Meier analysis and the log-rank test. Furthermore, univariate Cox regression analysis was applied to assess associations between potential biomarkers and the overall survival rate. Results. Of 720 total DEGs, fifty-two DEGs in the two subclusters of the PPI network analysis were selected. A risk model was established, and five candidate genes (SPRR2E, ICOS, CTLA4, HTR1D, and CCR4) were identified as biomarkers of OS in OSCC patients. Conclusions. We successfully constructed a prognostic signature to predict prognosis and identified five candidate genes associated with the OS of OSCC patients that are potential tumor biomarkers and targets in OSCC.</abstract><cop>United States</cop><pub>Hindawi</pub><pmid>33869632</pmid><doi>10.1155/2021/6657767</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0003-4379-9089</orcidid><orcidid>https://orcid.org/0000-0002-3157-3413</orcidid><oa>free_for_read</oa></addata></record>
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subjects Analysis
Bioinformatics
Biomarkers
Cancer
Carcinoma, Squamous Cell - genetics
Carcinoma, Squamous Cell - pathology
Care and treatment
Cluster Analysis
Computational Biology
CTLA-4 protein
Data analysis
Diagnosis
Encyclopedias
Extracellular matrix
Female
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Gene Ontology
Gene sequencing
Genes
Genetic aspects
Genetic Association Studies
Genomes
Genomics
Head & neck cancer
Humans
Logistic Models
Male
Medical prognosis
Methods
Middle Aged
Mouth cancer
Mouth Neoplasms - genetics
Mouth Neoplasms - pathology
Multivariate Analysis
Network analysis
Oral cancer
Oral squamous cell carcinoma
Peptides
Prognosis
Protein interaction
Protein Interaction Maps - genetics
Protein-protein interactions
Proteins
Rank tests
Regression analysis
Ribonucleic acid
Risk factors
RNA
RNA sequencing
ROC Curve
Sequence Analysis, RNA
Software
Squamous cell carcinoma
Squamous Cell Carcinoma of Head and Neck - genetics
Survival
Survival Analysis
Therapeutic targets
Tongue
Transcription, Genetic
Tumors
Values
title Identification of a Gene Prognostic Signature for Oral Squamous Cell Carcinoma by RNA Sequencing and Bioinformatics
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