Network analysis of long non-coding RNA expression profiles in common warts

Amneh H Tarkhan; Laith N Al-Eitan; Rami Q Alkhatib; Mansour A Alghamdi

doi:10.1016/j.heliyon.2022.e11790

Network analysis of long non-coding RNA expression profiles in common warts

Heliyon. 2022 Nov 19;8(11):e11790. doi: 10.1016/j.heliyon.2022.e11790. eCollection 2022 Nov.

Authors

Amneh H Tarkhan¹, Laith N Al-Eitan¹, Rami Q Alkhatib¹, Mansour A Alghamdi^{2

3}

Affiliations

¹ Department of Biotechnology and Genetic Engineering, College of Science and Arts, Jordan University of Science and Technology, Irbid, 22110, Jordan.
² Department of Anatomy, College of Medicine, King Khalid University, Abha, 61421, Saudi Arabia.
³ Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha, 61421, Saudi Arabia.

Abstract

Background: Long non-coding RNAs (lncRNAs) have been the subject of considerable attention in recent years due to their role in gene regulation. However, the function of lncRNAs remains poorly understood, especially in the context of infection with low-risk human papillomaviruses (HPVs). To further understanding on this issue, we investigated lncRNA expression in HPV-induced common warts.

Methods: A publicly available high-throughput sequencing dataset for common warts was downloaded from the Gene Expression Omnibus (GEO). lncRNA profiles were generated using the NetworkAnalyst 3.0 workflow, and a list of differentially expressed (DE) lncRNAs in common warts was identified and inputted into the ENCODE, RegNetwork, DisGeNet, and miRNet platforms.

Results: A total of 54 lncRNAs were revealed to be significantly dysregulated in common warts. Of these 54 lncRNAs, 24 and 30 were upregulated and downregulated, respectively. The most significantly differentially expressed lncRNAs in common warts included the CERNA2, LINC02159, SH3PXD2A-AS1, and UNC5B-AS1 genes.

Conclusion: The current findings suggest that HPV-induced warts impact the host lncRNA transcriptome. To the best of our knowledge, the present study is the first to explore the impact of low-risk HPV infection on lncRNA expression profiles.

Keywords: CERNA2; Human papillomavirus; LINC02159; SH3PXD2A-AS1; UNC5B-AS1; Warts; lncRNA.