Open Access

Analysis of transcriptome expression profiling data in oral leukoplakia and early and late‑stage oral squamous cell carcinoma

  • Authors:
    • Lihui Yao
    • Bin Guo
    • Jiannan Wang
    • Jiale Wu
  • View Affiliations

  • Published online on: March 3, 2023     https://doi.org/10.3892/ol.2023.13742
  • Article Number: 156
  • Copyright: © Yao et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

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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April-2023
Volume 25 Issue 4

Print ISSN: 1792-1074
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Spandidos Publications style
Yao L, Guo B, Wang J and Wu J: Analysis of transcriptome expression profiling data in oral leukoplakia and early and late‑stage oral squamous cell carcinoma. Oncol Lett 25: 156, 2023.
APA
Yao, L., Guo, B., Wang, J., & Wu, J. (2023). Analysis of transcriptome expression profiling data in oral leukoplakia and early and late‑stage oral squamous cell carcinoma. Oncology Letters, 25, 156. https://doi.org/10.3892/ol.2023.13742
MLA
Yao, L., Guo, B., Wang, J., Wu, J."Analysis of transcriptome expression profiling data in oral leukoplakia and early and late‑stage oral squamous cell carcinoma". Oncology Letters 25.4 (2023): 156.
Chicago
Yao, L., Guo, B., Wang, J., Wu, J."Analysis of transcriptome expression profiling data in oral leukoplakia and early and late‑stage oral squamous cell carcinoma". Oncology Letters 25, no. 4 (2023): 156. https://doi.org/10.3892/ol.2023.13742