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. 2025 Aug 4;16(1):1462.
doi: 10.1007/s12672-025-02922-4.

Uncovering biomarkers and pathways in oral squamous cell carcinoma through integrated lncRNA-mRNA regulatory network analysis

ShiWei Liu #  1 , Jin Li #  1 , Qing Shao #  2 , JuFeng Chen  1 , Chen Zou  2 , YiLong Ai  3
Affiliations

Uncovering biomarkers and pathways in oral squamous cell carcinoma through integrated lncRNA-mRNA regulatory network analysis

ShiWei Liu et al. Discov Oncol. .

Abstract

Objective: This study aimed to identify potential biomarkers and elucidate molecular mechanisms in oral squamous cell carcinoma (OSCC) by leveraging an integrated bioinformatics approach.

Methods: We conducted high-throughput RNA sequencing on OSCC and adjacent normal tissues to profile mRNA and lncRNA expression. Differentially expressed genes were identified and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. A competing endogenous RNA (ceRNA) network was constructed, and protein-protein interaction (PPI) networks were analyzed using STRING and Cytoscape software. Hub genes were identified using the Cytohubba plug-in in Cytoscape.

Results: Our analysis identified 5362 differentially expressed mRNAs and 2801 differentially expressed lncRNAs. GO analysis revealed that dysregulated mRNAs were associated with system development and responses to organic substances. At the same time, lncRNAs were enriched in muscle system processes and cell-cell signaling. KEGG pathway analysis highlighted cancer-related pathways, including cytokine-cytokine receptor interactions and the NF-kappa B signaling pathway. The constructed ceRNA network highlighted key regulatory nodes, including hub genes IGF2BP1, CLDN6, and HLA-G, which may play pivotal roles in OSCC.

Conclusions: This study provides a comprehensive lncRNA-mRNA regulatory network and identifies biomarkers that could advance OSCC therapeutic strategies. The findings offer new insights into OSCC pathogenesis and potential targets for clinical application.

Keywords: Bioinformatics; CeRNA network; LncRNA; Oral squamous cell carcinoma; mRNA.

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Conflict of interest statement

Declarations. Consent for publication: Informed consent was obtained from all individual participants included in the study. Ethical approval: All procedures performed in studies involving human participants were in accordance with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. This study is approved by the Ethics Committee of Foshan First People’s Hospital. Written informed consent was obtained. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Identification of differential expression mRNAs and lncRNAs inRNA-seq. A Box plot of gene expression FPKM distribution in samples. B PCA results for the RNA-seq data. C Volcano plot of differential expression mRNAs. D Volcano plot of differential expression lncRNAs. E Heatmap of differential expression mRNAs. F Heatmap of differential expression lncRNAs. N normal, T tumor
Fig. 2
Fig. 2
Functional analysis of differential expression mRNAs. A GO analysis of differential expression mRNAs. B KEGG pathway analysis of differential expression mRNAs
Fig. 3
Fig. 3
Functional analysis of differential expression lncRNAs. A GO analysis of differential expression lncRNAs. B KEGG pathway analysis of differential expression lncRNAs
Fig. 4
Fig. 4
Construction of deferential expression lncRNA–mRNA co-expression network. Green ovals depict the representation of key genes; blue ovals represent differential expression mRNAs; differential expression lncRNAs are indicated by red diamonds
See this image and copyright information in PMC

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References

    1. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. 10.3322/caac.21660. - PubMed
    1. Ferreira AK, Carvalho SH, Granville-Garcia AF, Sarmento DJ, Agripino GG, Abreu MH, Melo MC, Caldas AD Jr, G P Godoy. Survival and prognostic factors in patients with oral squamous cell carcinoma. Med Oral Patol Oral Cir Bucal. 2021;26(3):e387–92. 10.4317/medoral.24242. - PMC - PubMed
    1. Weckx A, Grochau KJ, Grandoch A, Backhaus T, Zoller JE, Kreppel M. Survival outcomes after surgical treatment of oral squamous cell carcinoma. Oral Dis. 2020;26(7):1432–9. 10.1111/odi.13422. - PubMed
    1. Dik EA, Willems SM, Ipenburg NA, Adriaansens SO, Rosenberg AJ, van Es RJ. Resection of early oral squamous cell carcinoma with positive or close margins: relevance of adjuvant treatment in relation to local recurrence: margins of 3 mm as safe as 5 mm. Oral Oncol. 2014;50(6):611–5. 10.1016/j.oraloncology.2014.02.014. - PubMed
    1. Chinn SB, Myers JN. Oral cavity carcinoma: current management, controversies, and future directions. J Clin Oncol. 2015;33(29):3269–76. 10.1200/JCO.2015.61.2929. - PMC - PubMed

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