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

TL;DR

This study identifies thousands of lncRNAs and mRNAs that are differentially expressed in cervical cancer, linking them to HPV16 infection and key biological processes like cell cycle and signaling pathways.

Contribution

The study provides new insights into the role of lncRNAs and mRNAs in HPV16-associated cervical cancer and identifies potential diagnostic markers.

Findings

3,608 lncRNAs were upregulated and 4,383 were downregulated in cervical cancer tissues compared to paracancerous tissues.

Differentially expressed mRNAs were enriched in cell cycle, cell senescence, and pathways like cAMP and MAPK.

CDKN2B-AS1, HAGLROS, and GATA6-AS1 were potentially regulated by HPV16 E6/E7, suggesting their role in cervical cancer progression.

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.

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