Dataset Information

Bioinformatic Analysis of Plus Gene Expression Related to Progression from Leukoplakia to Oral Squamous Cell Carcinoma.

ABSTRACT:

Introduction

Leukoplakia is one of the most frequently found lesions in the oral cavity, with a probability of 17 to 24% of becoming malignant cells in a period of 30 years.

Objective

To identify differentially expressed gene profiles of leukoplakia and its progression to oral squamous cell carcinoma, essential for the discovery of new biomarkers to predict and prevent the presence of diseases in the oral cavity.

Methods

Initially, gene profiles of GSE85514 and GSE160042 from the Gene Expression Omnibus database were used. Differentially expressed genes were identified using GEO2R. The CLUEGO plugin in Cytoscape was used for DEG functionality and enrichment analysis. Finally, a protein-protein interaction (PPI) network was constructed using Cytoscape from data collected online from the STRING server.

Results

According to the MCC algorithm, the 10 most found gene sequences were HNRNPU, SMC1A, PAFAH1B1, EHMT1, SPTBN4, OLFM1, NCAM1, SF3B3, FGF2, and UBE2I; with HNRNPU, SMC1A, and PAFAH1B1 being the most representative of the modules.

Conclusions

We were able to describe the gene sequences that promote the progression from leukoplakia to oral squamous cell carcinoma. Within these genes, the HNRNPU, SMC1A, and PAFAH1B1 constitute the main promising therapeutic targets to counteract the progression of oral cancer, they could also be important biomarkers for the diagnosis and classification of the disease.

SUBMITTER: Guzman De Avila J

PROVIDER: S-EPMC9930946 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Publications

Bioinformatic Analysis of Plus Gene Expression Related to Progression from Leukoplakia to Oral Squamous Cell Carcinoma.

Guzman De Avila Jaime J Silvera-Redondo Carlos C Alviz-Amador Antistio A

Asian Pacific journal of cancer prevention : APJCP 20221101 11

<h4>Introduction</h4>Leukoplakia is one of the most frequently found lesions in the oral cavity, with a probability of 17 to 24% of becoming malignant cells in a period of 30 years.<h4>Objective</h4>To identify differentially expressed gene profiles of leukoplakia and its progression to oral squamous cell carcinoma, essential for the discovery of new biomarkers to predict and prevent the presence of diseases in the oral cavity.<h4>Methods</h4>Initially, gene profiles of GSE85514 and GSE160042 fr ...[more]

PMID: 36444596

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Project description:The present study screened, potential prognostic biomarkers for oral carcinogenesis. The GSE85195 dataset, which consisted of oral leukoplakia (OL) and early and late-stage oral squamous cell carcinoma (OSCC) samples, was used. The differentially expressed genes (DEGs) in early OSCC vs. OL, late OSCC vs. OL and late OSCC vs. early OSCC groups were screened using the limma package in R. The Short Time-series Expression Miner software package was used to cluster DEGs with similar expression patterns in the course of disease progression (from OL to early and then late-stage OSCC). Moreover, the Database for Annotation, Visualization and Integrated Discovery online analysis tool was used to perform Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. A protein-protein interaction (PPI) network was also constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Reverse transcription-quantitative PCR was performed to assess the mRNA expression levels of hub node genes in clinical samples, and receiver operating characteristic curve analysis was performed to assess the prognostic value of the hub genes. A total of 4,595, 6,042 and 2,738 DEGs were screened in the early OSCC vs. OL, late OSCC vs. OL and late OSCC vs. early OSCC groups, respectively. A total of 665 overlapping genes were identified when the screened DEGs were compared. Cluster 1 and cluster 7 were identified as the significant clusters, which contained 496 and 341 DEGs, respectively. A PPI network was constructed with 440 interaction pairs. There were five differentially expressed hub nodes identified in different stages from OL to OSCC. The results of the present study indicated that fibronectin 1, signal transducer and activator of transcription 1, collagen type II α1 chain, collagen type X α1 chain and collagen type IV α6 chain might serve as independent diagnostic factors for OL and OSCC, and as prognostic biomarkers for OL carcinogenesis.

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Dataset Information

Bioinformatic Analysis of Plus Gene Expression Related to Progression from Leukoplakia to Oral Squamous Cell Carcinoma.

Introduction

Objective

Methods

Results

Conclusions

Publications

Bioinformatic Analysis of Plus Gene Expression Related to Progression from Leukoplakia to Oral Squamous Cell Carcinoma.

Similar Datasets

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