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. 2025 Aug 1:5:1605681.
doi: 10.3389/fbinf.2025.1605681. eCollection 2025.

Bioinformatics analysis of lncRNA and mRNA differentially expressed in patients with cervical cancer

Xiaohua An  1   2 , Xiaoxue Huang  1 , Qiujie Yu  1   2 , Yiyue Tang  3 , Yan Wang  1   2 , Huasu Chen  1   2 , Yafei Zhang  1   2 , Qianhao Huang  1   2 , Yudi Rao  1   2 , Guomei Hu  4 , He Zha  1
Affiliations

Bioinformatics analysis of lncRNA and mRNA differentially expressed in patients with cervical cancer

Xiaohua An et al. Front Bioinform. .

Abstract

To verify the expression profile of long non-coding RNAs (lncRNAs) and mRNAs in cervical cancer, identify their clinical significance in HPV16-associated cervical cancer, and annotate the biological function of mRNAs. Three pairs of cancerous and paracancer tissues were selected in cervical squamous cell carcinoma (IB2 stage), high-throughput sequencing was utilized to determine the expression levels of lncRNAs and mRNAs. The detection results were validated by GEPIA database analysis and RT-qPCR. Functional annotations of differential mRNAs were conducted through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network states. Furthermore, the association between antisense lncRNA and mRNA in cervical cancer was analyzed to predict the biological functions of lncRNA. Finally, recombinant lentivirus CV224-HPV16 E6/E7 was transfected into HcerEpic to establish a stable cell line with overexpressed HPV16 E6/E7, then differential lncRNAs were detected by RT-qPCR. Compared to paracancerous tissues, there were 3,608 lncRNAs significantly upregulated and 4,383 lncRNAs significantly downregulated in cervical cancer tissues (Fold change >2 and P < 0.05). Additionally, 3,666 mRNAs were significantly upregulated, while 2,220 mRNAs were significantly downregulated (Fold change >2 and P < 0.05). GO/KEGG enrichment analysis showed that differentially expressed mRNA played a significant role in cell cycle and cell senescence, and was related to signal pathways such as cAMP and MAPK, forming a complex network among the proteins encoded by these mRNAs. Further analysis indicated that the 20 antisense lncRNAs with the most remarkable differences might exert biological functions by influencing their corresponding mRNAs. The results of RT-qPCR revealed that CDKN2B-AS1, HAGLROS and GATA6-AS1 were potentially regulated by HPV16 E6/E7, which were in accordance with those obtained from chip detection. In this study, differentially expressed lncRNAs associated with HPV16 infection were screened and explored their transcriptional molecular functions and biological pathways, providing a molecular basis for predicting diagnostic markers of cervical cancer.

Keywords: HPV16 E6/E7; cervical cancer; high-throughput sequencing; lncRNA; mRNA.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Differentially expressed lncRNAs in cervical cancer patients. (A) Box plot of the dispersion of the six sets of data for lncRNAs. (B) Volcano plot of lncRNAs with differential expression, with 2-fold upregulated lncRNAs in red and 2-fold downregulated lncRNAs in green. (C) Distribution of lncRNAs in chromosomes.
FIGURE 2
FIGURE 2
GO enrichment analysis of differentially expressed mRNAs in cervical cancer patients. (A) GO function annotation plot for expression of upregulated mRNAs, the horizontal axis indicates GO enrichment entries, the vertical axis indicates the number of genes, and a larger enrichment score indicates a greater degree of enrichment. (B) GO function annotation plot for expression of downregulated mRNAs.
FIGURE 3
FIGURE 3
KEGG enrichment analysis of differentially expressed mRNA in cervical cancer patients. (A) Analysis of enrichment Bubble plot of KEGG signaling pathway expressing upregulated mRNAs: the size of the bubble indicates the number of differentially expressed genes enriched in this pathway, the colors of the bubbles represent the various P-values, and the horizontal axis of the plot shows the enrichment score and the vertical axis the pathway name. The larger the enrichment fraction, the higher the enrichment degree. (B) Enrichment analysis bubble plot of KEGG signaling pathway expressing downregulated mRNAs.
FIGURE 4
FIGURE 4
Interaction analysis between proteins encoded by differentially expressed mRNAs.
FIGURE 5
FIGURE 5
Differential expression of lncRNAs in cervical cancer. (A–E) Indicates the expression of GEPIA database predicted lncRNA CDKN2B-AS1, MIR205HG, HAGLROS, GATA6-AS1, and DICER1-AS1 in cervical cancer tissues and normal tissues, respectively. *P < 0.05.
FIGURE 6
FIGURE 6
Survival curve analysis of differentially expressed lncRNAs. (A–E) Survival curves of patients with cervical cancer with lncRNA CDKN2B-AS1, MIR205HG, HAGLROS, GATA6-AS1, and DICER1-AS1 in the KM-Plotter database.
FIGURE 7
FIGURE 7
Expression of LncRNA in HcerEpic cells and cervical cancer cells. (A–E) RT-qPCR was performed to detect the relative expression of CDKN2B-AS1, MIR205HG, HAGLROS, GATA6-AS1, and DICER1-AS1 in HcerEpic, Hela, SiHa, and C33A cells. *P < 0.05, **P < 0.01, ***P < 0.001.
FIGURE 8
FIGURE 8
Differential expression of lncRNAs in HcerEpic cells overexpressing HPV16 E6/E7. (A) Fluorescence microscopy of HcerEpic cells transfected with lentivirus overexpressing HPV16 E6/E7 to observe the infection efficiency. (B) RT-qPCR to detect the transcription of HPV16 E6/E7 mRNA. (C–E) RT-qPCR to detect CDKN2B-AS1 in HcerEipc cells overexpressing HPV16 E6/E7, relative expression of HAGLROS and GATA6-AS1. *P < 0.05, **P < 0.01, ***P < 0.001.
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References

    1. Akçimen F., Ross J. P., Liao C., Spiegelman D., Dion P. A., Rouleau G. A. (2021). Expanded CAG repeats in ATXN1, ATXN2, ATXN3, and HTT in the 1000 genomes project. Mov. Disord. Official J. Mov. Disord. Soc. 36 (2), 514–518. 10.1002/mds.28341 - DOI - PubMed
    1. Attademo L., Tuninetti V., Pisano C., Cecere S. C., Di Napoli M., Tambaro R., et al. (2020). Immunotherapy in cervix cancer. Cancer Treat. Rev. 90, 102088. 10.1016/j.ctrv.2020.102088 - DOI - PubMed
    1. Bai H., Li X., Wu S. (2023). Up-regulation of long non-coding RNA LOXL1-AS1 functions as an oncogene in cervical squamous cell carcinoma by sponging miR-21. Arch. Physiol. Biochem. 129 (1), 143–147. 10.1080/13813455.2020.1804406 - DOI - PubMed
    1. Bao Z., Yang Z., Huang Z., Zhou Y., Cui Q., Dong D. (2019). LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res. 47 (D1), D1034–D1037. 10.1093/nar/gky905 - DOI - PMC - PubMed
    1. Chen J., Zheng Y., Li L. (2022). LncRNA RPSAP52 regulates miR-423-5p/GSTM1 axis to suppress hypoxia-induced renal proximal tubular epithelial cell apoptosis. Arch. Physiol. Biochem. 128 (4), 1066–1070. 10.1080/13813455.2020.1750657 - DOI - PubMed

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