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

Tarkhan, Amneh H.; AL-Eitan, Laith N.; Alkhatib, Rami; Alghamdi, Mansour A.

doi:10.1016/j.heliyon.2022.e11790

Cited by 1 publication

(1 citation statement)

References 84 publications

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“…However, neither of them detected lncRNAs that were differentially expressed in CA. Although Tarkhan AH and coworkers reported lncRNA profiles in LR-HPV infection in 2022, their specimens were limited to common warts without a larger cohort for validation [ 29 ]. In the present study, we not only revealed transcriptional profiles, including lncRNAs and mRNAs but also analysed the probable regulatory pathway and cis -regulatory mechanism by lncRNAs in CA for the first time, further confirming the sequencing data in larger samples using qRT‒PCR.…”

Section: Discussionmentioning

confidence: 99%

Expression profile of long noncoding RNAs and comprehensive analysis of lncRNA-cisTF-DGE regulation in condyloma acuminatum

Xie,

Wu,

Wang

et al. 2024

BMC Med Genomics

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Objective To identify differentially expressed long noncoding RNAs (lncRNAs) in condyloma acuminatum (CA) and to explore their probable regulatory mechanisms by establishing coexpression networks. Methods High-throughput RNA sequencing was performed to assess genome-wide lncRNA expression in CA and paired adjacent mucosal tissue. The expression of candidate lncRNAs and their target genes in larger CA specimens was validated using real-time quantitative reverse transcriptase polymerase chain reaction (RT‒qPCR). Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used for the functional enrichment analysis of these candidate lncRNAs and differential mRNAs. The coexpressed mRNAs of the candidate lncRNAs, calculated by Pearson’s correlation coefficient, were also analysed using GO and KEGG analysis. In addition, the interactions among differentially expressed lncRNAs (DElncRNAs)-cis-regulatory transcription factors (cisTFs)-differentially expressed genes (DEGs) were analysed and their network was constructed. Results A total of 546 lncRNAs and 2553 mRNAs were found to be differentially expressed in CA compared to the paired control. Functional enrichment analysis revealed that the DEGs coexpressed with DElncRNAs were enriched in the terms of cell adhesion and keratinocyte differentiation, and the pathways of ECM-receptor interaction, local adhesion, PI3K/AKT and TGF-ß signaling. We further constructed the network among DElncRNAs-cisTFs-DEGs and found that these 95 DEGs were mainly enriched in GO terms of epithelial development, regulation of transcription or gene expression. Furthermore, the expression of 3 pairs of DElncRNAs and cisTFs, EVX1-AS and HOXA13, HOXA11-AS and EVX1, and DLX6-AS and DLX5, was validated with a larger number of specimens using RT‒qPCR. Conclusion CA has a specific lncRNA profile, and the differentially expressed lncRNAs play regulatory roles in mRNA expression through cis-acting TFs, which provides insight into their regulatory networks. It will be useful to understand the pathogenesis of CA to provide new directions for the prevention, clinical treatment and efficacy evaluation of CA.

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Section: Discussionmentioning

confidence: 99%