Despite the histologic benign presentation of JORRP, disease management remains a medical challenge due to its aggressive clinical course and high propensity for recurrence [11]. Identifying the pivotal genes and regulatory pathways of JORRP is therefore crucial to explore the progression and effective treatment. In this study, we performed comprehensive bioinformatics analysis using gene expression profiles of three JORRP tissues and two adjacent non-tumor tissues to identify potential biomarkers and understand the molecular mechanisms behind them.
Our study found a total of 1795 DEGs associated with JORRP, including 876 up-regulated genes and 919 down-regulated genes. In GO analysis, the up-regulated DEGs were mainly involved in cornification and cell cycle, while the down-regulated DEGs were mainly associated with cell projection organization and cilium movement -related genes. KEGG enrichment analysis showed that upregulated DEGs were mainly enriched in cell cycle, steroid biosynthesis, and HIF-1 signaling pathways. Down-regulated DEGs were closely associated with metabolism of xenobiotics by cytochrome P450, Chemical carcinogenesis, Drug metabolism -cytochrome P450,Retinol metabolism.
We then performed PPI network construction and hub genes screening using STRING and Cytoscape software, the 10 identified hub genes were VEGFA, CDH1, CDK1, IL1B, KIF11, HIF1A, ASPM, AURKA, CENPE, and MKI67. Notably, the expression levels of all 10 genes were upregulated compared to the adjacent normal tissue. After further GO and KEGG enrichment analysis, hub genes were significantly enriched in spindle organization, cancer-related pathways, Th17 cell differentiation, and HIF-1 signaling pathway.
In KEGG analysis of differentially expressed genes, Metabolism of xenobiotics by cytochrome P450 signaling pathway expression was significantly downregulated.Cytochrome P450 (CYP) is a membrane-associated blood protein, expressed in almost all tissues and organs [12]. It plays an imporant role in tumor cell metabolism by participating in endogenous signaling pathways [13]. Previous studies have shown that the expression of CYPs are usually abnormal in tumor cells compared to adjacent normal tissues, and altered activity of CYPs often leads to subsequent tumor recurrence and poor prognosis [14].
The nodal degree of vascular endothelial growth factor A (VEGFA) is at the top of the PPI network with 111, which belongs to the core of the PPI network. VEGFA was first identified as an endothelial cell-specific mitogen and angiogenic inducer that promotes neovascularization by regulating endothelial cell activity and integrity [15]. By activating the VEGF pathway, tumor angiogenesis improves the blood supply and enriches the nutritional source of tumors. VEGFA not only stimulates angiogenesis, but also promotes tumor survival, growth, and metastasis [16]. A series of studies have shown that VEGFA is highly expressed in tumors such as cutaneous squamous cell carcinoma, hepatocellular carcinoma, ovarian cancers, cervical cancers, renal cell carcinoma, and colon cancers, leading to proliferation, differentiation, migration, and invasion of cancer cells [17–22]. A study by Rahbar R. et al. evaluated the role of VEGFA and its receptors in RRP, where VEGFA was highly expressed in the epithelial cells of RRP and had a direct impact on the formation of the RRP vascular stroma [23]. Furthermore, it has been shown that high expression of VEGFA in papillomas correlated with high severity and malignant progression of RRP [24].
Calmodulin-1 (cadherin-1, CDH1) is a calcium-dependent transmembrane molecule localized to epithelial cells, mediates adhesion between adjacent cells and encodes E-cadherin [25]. As an epithelial-mesenchymal transition (EMT)-associated protein, E-cadherin is involved in epithelial cell adhesion and bridging granule attachment and plays an important role in the maintenance of cell morphology, cell motility and cell adhesion [26]. In previous studies, CDH1 was usually considered as a tumor suppressor gene, the downregulation or loss of E-cadherin was associated with infiltration and metastasis of many malignancies [27]. However, it has also been shown that CDH1 and its encoded E-cadherin have pro-cancer activity [28]. In our study, CDH1 showed upregulation,which may be a marker of JORRP progression.
Cyclin-dependent kinase1 (CDK1), also known as cytokine cyclin 2 (CDC2), is one of a family of protein kinases that drive the major events of the cell cycle in eukaryotic cells [29]. In addition to its involvement in cell cycle regulation, CDK1 plays an instrumental role in gene transcription, protein translation, chromatin structural remodeling, cell division and migration, protein secretion, and other important molecular processes [30, 31]. CDK1 is highly expressed in most malignancies, exacerbates the proliferation of malignant cells, and is associated with poor prognosis [32]. Numerous studies have shown that inhibition of CDK1 is an efficient anti-cancer strategy and CDK1 has the potential to serve as a target for the treatment of different types of cancers [33]. The study by Farooq et al. found that CDK1 interacts with HPV oncoproteins and is enriched in the cell cycle and cellular oncogenic pathways [34], which may provide inspiration for molecular studies of JORRP.
Interleukin-1β (IL1B) is mainly produced and secreted by immune cells, epithelial cells, and cancer cells [35], regulating the expression of several inflammatory genes [36]. During tumor development, IL1B plays a central role in angiogenesis, endothelial cell activation, and tumor cell proliferation [37]. It has been demonstrated that as a potent activator of adaptive immune responses to viral infections, the biological activity of IL1B is increased in HPV-infected skin [38], which may provide new directions for the prevention and treatment of HPV infections.
Hypoxia-inducible factor 1 subunit alpha (HIF1A) is a key regulator required for tumor cell adaptation to hypoxia [39] and mediates multiple functional pathways during tumor development, including metabolic regulation, angiogenesis, cell survival, and inflammatory regulation [40, 41].
The other five hub genes are KIF11, ASPM, AUKRA, CENPE, and MKI67, which drive mitosis and regulate cell cycle progression [42–46], thereby regulating tumor cell proliferation and influencing tumor development.
There are a couple of limitations of this study. First, only three JORRP tissues and two adjacent non-tumor tissues were used for bioinformatics analysis in this study, in future, experimental validation based on larger sample sizes is needed to guarantee more accurate findings. In the second place, this study only used bioinformatics analysis to reveal potential biomarkers of JORRP, and further experiments are needed to confirm the role of these genes and related pathways.