Int J Med Sci 2020; 17(2):191-206. doi:10.7150/ijms.39261 This issue
1. Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
2. Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
3. Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
4. Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
5. Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital, Jordan University of Science and Technology, Irbid 22110, Jordan
Epigenetic alteration of host DNA is a common occurrence in both low- and high-risk human papillomavirus (HPV) infection. Although changes in promoter methylation have been widely studied in HPV-associated cancers, they have not been the subject of much investigation in HPV-induced warts, which are a temporary manifestation of HPV infection. The present study sought to examine the differences in promoter methylation between warts and normal skin. To achieve this, DNA was extracted from 24 paired wart and normal skin samples and inputted into the Infinium MethylationEPIC BeadChip microarray. Differential methylation analysis revealed a clear pattern of hyper- and hypomethylation in warts compared to normal skin, and the most differentially methylated promoters were found within the EIF3EP2, CYSLTR1, C10orf99, KRT6B, LAMA4, and H3F3B genes as well as the C9orf30 pseudogene. Moreover, pathway analysis showed that the H3F3A, CDKN1A, and MAPK13 genes were the most common regulators among the most differentially methylated promoters. Since the tissue samples were excised from active warts, however, this differential methylation could either be a cellular response to HPV infection or an HPV-driven process to establish the wart and/or promote disease progression. Conclusively, it is apparent that HPV infection alters the methylation status of certain genes to possibly initiate the formation of a wart and maintain its presence.
Keywords: wart, HPV, methylation, promoter, epigenetics
Epigenetics is the study of heritable changes in gene expression that are not caused by changes to the DNA sequence itself, but by covalent modifications such as DNA methylation (DNA-M) . Mammalian DNA-M, which primarily involves the addition of a methyl group to a cytosine base in a CpG dinucleotide, results in increased gene expression when it occurs at higher levels within the gene's body instead of its promoter region . On a similar note, promoter methylation is of particular epigenetic importance because the vast majority of those located upstream of a gene contain a CpG island, the latter of which is a region with a high concentration of CpG sites . In contrast to the hypermethylated CpG sites scattered throughout the human genome, CpG islands are not methylated, and the methylation of CpG islands initiates remodeling mechanisms that ultimately result in gene silencing [4, 5].
The methylation status of promoters is integral to maintaining normal expression levels of the genes they regulate. In fact, promoter hypermethylation is a key part of cancer development and progression, as it results in the silencing of tumor suppressor gene expression . In addition, host promoter hypermethylation has also been implicated in infections by both oncogenic and non-oncogenic viruses such as the human papillomaviruses (HPV) . HPV comprises a family of double-stranded DNA viruses that exclusively infect the basal epithelium of the skin and mucosa . The majority of HPV infections are asymptomatic and resolve without the need for medical intervention but, depending on the individual and the HPV type, can also result in a number of malignancies and dermatological diseases . One such condition is the wart, which arises due to the benign proliferation of HPV-infected epithelial keratinocytes . The most prevalent type of wart is the common wart, which accounts for nearly 70% of all cutaneous warts encountered in clinical settings . As a result of their benign nature, common warts are subject to a much lesser degree of scrutiny than other HPV-associated diseases.
The impermanent nature of cutaneous warts strongly suggests that epigenetic changes are involved in the mechanism of wart formation and their eventual disappearance. However, a paucity of information exists regarding the methylation status of cutaneous warts, especially in the context of the promotor regions. Therefore, the primary objective of the current study was to provide an exploratory survey of the genome-wide changes in promoter methylation patterns in cutaneous warts compared to healthy skin.
Ethical approval to conduct this study was obtained from Jordan University of Science and Technology's (JUST) Institutional Review Board (IRB). Twelve Arab males presenting with common warts were recruited from the general population after providing written informed consent. Shave biopsies of common warts and adjacent normal skin were performed, allowing paired tissue samples (wart and normal skin) to be obtained from each participant.
A QIAamp DNA Mini Kit (Qiagen, Germany) was used to perform DNA extraction, and optional RNase A digestion was incorporated. DNA purity and integrity were determined by means of the BioTek PowerWave XS2 Spectrophotometer (BioTek Instruments, Inc., USA) and agarose gel electrophoresis, respectively. Genomic DNA that fulfilled our standards for quality and quantity were shipped on dry ice to the Australian Genome Research Facility (AGRF) in Melbourne, where the quality was further ascertained by the QuantiFluor® dsDNA System (Promega, USA). The Zymo EZ DNA Methylation Kit (Zymo Research, USA) was utilized in order to perform bisulfite conversion on the 24 samples. Lastly, the samples were inputted into the Infinium MethylationEPIC BeadChip microarray (Illumina, USA) for a genome-wide interrogation of over 850,000 CpG sites.
RnBeads, a computational R package, was adapted to process and analyze the raw intensity data (IDAT files) from the BeadChip . Quality control, preprocessing, batch effects adjustment, and normalization were carried out on all probes and samples according to the RnBeads package pipeline.
The mean of the mean β (mean.mean β) values of all the interrogated CpG sites in each promoter were computed. The distribution of CpG sites per promoter is shown in Figure 1, while Figure 2 depicts the distribution of CpG sites across promoters. DM for each promoter was calculated using the following three measures: the mean.mean β difference between warts (W) and normal skin (NS), the log2 of the mean quotient in β means across all CpG sites in a promoter, and the adjusted combined p-value of all CpG sites in the promoter using a limma statistical test [12, 13]. Furthermore, these three measures were used to create a combined ranking, in which promoters that exhibit more DM are assigned a lower combined rank . Promoters were sorted from smallest to largest using the combined rank score, and the top-ranking 1000 DM promoters were selected for further analysis. In order to correct for multiple testing, the Benjamini-Hochberg procedure was utilized to set the false discovery rate (FDR) at 5%.
Enrichment analysis for gene ontology (GO) terms associated with the top-ranking 500 DM promoters was performed using the GO consortium .
A signaling network of the top-ranking 1000 DM promoters was investigated using the SIGnaling Network Open Resource (SIGNOR) 2.0 . Due to the large number of connections, the type of relation was selected to only include 'direct' interactions with a relaxed layout and a score of '0.0'.
Based on all methylation values of the top-ranking 1000 DM promoters, the 24 samples showed an expected clustering pattern, as samples with similar methylation patterns or phenotypes tended to cluster together (Figure 3). In addition, the dimension reduction test was applied to the dataset using multidimensional scaling (MDS) and principal component analysis (PCA) in order to inspect for a strong signal in the methylation values of the samples (Figures 4 and 5). MDS and PCA confirmed that the difference between wart (W) and normal skin (NS) samples predominated the analysis.
Distribution of CpG sites per promoter.
Distribution of CpG sites across promoters. The relative coordinates of 0 and 1 correspond to the start and end coordinates of promoters. Coordinates smaller than 0 and greater than 1 denote flanking regions normalized by region length.
Heatmap showing the hierarchical clustering of samples displaying only the top-ranking 1000 most variable promoters with the highest variance across all samples. Clustering utilized complete linkage and Manhattan distance. The top x-axis shows the normal skin (NS) and wart (W) samples, while the bottom x-axis shows the patient identification number. Values of 0 (red color) and 1 (purple color) indicate decreased and increased methylation, respectively.
Two-dimensional scatterplot illustrating sample positions after the application of Kruskal's non-metric multidimensional scaling based on the matrix of average methylation and Manhattan distance.
Two-dimensional scatterplot showing sample positions after principal component analysis.
44,929 genomic identifiers passed the quality control and pre-processing steps, including some identifiers that did not map to gene symbols or which were not assigned (NA). Genomic identifiers without symbols were then removed, leaving 27,790 with symbols. The list of DM promoters in warts was limited to the top-ranking 1000 DM promoters using the combined rank score. Using this scoring method, a total of 576 and 424 promoters were found to be hypomethylated and hypermethylated, respectively, in warts (W) compared to normal skin (NS), with a mean β difference =>0.064 and =< -0.064 and p-value =< 0.001 (adjusted p-value =<0.007) (Figure 6). Among the 576 hypomethylated promoters, the β difference ranged from -0.064 to -0.458, while the mean β difference ranged between 0.064 and 0.367 for the 424 hypermethylated promoters. The log2 of the quotient in methylation between warts and normal skin had a maximum value of 1.633 and minimum value of -1.924 (Figure 7). The top-ranking 100 DM promoters with the lowest combined rank score are shown in Table 1.
Gene ontology (GO) enrichment analysis of biological process (BP) and molecular function (MF) was conducted on the top-ranking 500 DM hypermethylated promoters (Figure 8, Figure 9, Table 2, and Table 3) and the top-ranking 500 DM hypomethylated promoters (Figure 10, Figure 11, Table 4, and Table 5).
Signaling network analysis of the top-ranking 1000 DM promoters illustrated that several promoter genes were common regulators of this gene network, with a minimum of 7 direct connectivities each. These promoter genes include H3F3A, CDKN1A, MAPK13, IKBKG, CAPN2, CAMKK1 and CUL1 (Figure 12). Moreover, H3F3A was found to be the most common regulator when the signaling network analysis was carried out on the top 100 DM promoters.
To the best of the authors' knowledge, this is the first study to investigate the genome-wide changes in promoter methylation patterns associated with HPV-induced cutaneous warts. The present findings provide an exploratory analysis that creates clear lines of future research on this topic, especially with regard to validation studies involving larger sample sizes.
In the present study, the most differentially methylated (DM) promoter in warts compared to normal skin was found within the eukaryotic translation initiation factor 3 subunit E pseudogene 2 (EIF3EP2) gene, a pseudogene with no function or association previously reported in the literature. Likewise, little is known about the second most DM gene in warts, the chromosome 9 open reading frame 30 (C9orf30) pseudogene. In contrast, the third most DM gene is the protein-coding cysteinyl leukotriene receptor 1 (CYSLTR1) gene, which is normally involved in allergic and hypersensitive reactions . Variation in the CYSLTR1 gene modulates asthma risk as well as adenoid hypertrophy progression, and it has been implicated in the disease outcome of colorectal, prostate, and squamous cell carcinoma [17-21]. Moreover, CYSLTR1 is highly expressed in the normal human skin epidermis, but its expression was found to be even higher in atopic dermatitis . Table 2 depicts all the protein-coding genes containing DM promoters from among the top-ranking 100 listed in Table 1.
Two-dimensional scatterplot of the top-ranking 1000 DM promoters. The mean.mean β values of normal skin (NS) and warts (W) are shown on the x-axis and y-axis, respectively. The methylation β values range from 0 (unmethylated) to 1 (methylated).
Volcano plot of the promoter differential methylation quantified by the log2 of the quotient in mean.mean methylation and adjusted combined p-value between warts (W) and normal skin (NS). The color scale represents the combined ranking.
The 100 top-ranking promoters based on combined ranking score.
|Gene||Gene symbol||Category||RNA class||Chromosome||mean.mean β value (NS)||mean.mean β value (W)||mean.mean β value diff. |
|mean.mean. quot.log2||comb.p.val||comb.p.adj. (FDR)||Combined rank|
|ENSG00000207258||RF00019||RNA gene||Y RNA||1||0.508||0.192||-0.315||-1.356||6.373E-10||4.522E-07||62|
|ENSG00000283664; ENSG00000265375||MIR4679-1; MIR4679-2||RNA gene||miRNA||10||0.353||0.589||0.236||0.722||1.858E-10||1.756E-07||410|
|ENSG00000265462; ENSG00000266758||MIR3680-1; MIR3680-2||RNA gene||miRNA||16||0.383||0.630||0.247||0.705||8.156E-10||5.161E-07||438|
Word cloud illustrating the significant biological processes (BP) associated with the top-ranking 500 hypermethylated promoters.
Word cloud illustrating the significant molecular functions (MF) associated with the top-ranking 500 hypermethylated promoters.
Word cloud illustrating the significant biological processes (BP) associated with the top-ranking 500 hypomethylated promoters.
Function and clinical relevance of the protein-coding genes containing the most differentially methylated promoters in warts
|Gene symbol||Gene name||Main physiological function|
|CYSLTR1||Cysteinyl leukotriene receptor 1||Mediates bronchoconstriction|
|C10orf99||Chromosome 10 Open Reading Frame 99||Mediates recruitment of lymphocytes to epithelia|
|KRT6B||Keratin 6B||Epithelial wound repair and inflammation|
|KLK2||Kallikrein Related Peptidase 2||Sperm liquefication|
|LAMA4||Laminin Subunit Alpha 4||Cell adhesion, differentiation, and migration|
|ALPK2||Alpha Kinase 2||Unknown|
|METTL7A||Methyltransferase Like 7A||Unknown|
|HSD17B14||17β-Hydroxysteroid dehydrogenase type 14||Steroid metabolism|
|H3F3B||H3 Histone Family Member 3B||Found at sites of nucleosomal displacement|
|MST1L||Macrophage Stimulating 1 Like||Unknown|
|LTC4S||Leukotriene C4 Synthase||Involved in cysteinyl leukotriene biosynthesis|
|IZUMO1||Izumo sperm-egg fusion 1||Essential for fusion and binding of sperm and egg|
|FOLR3||Folate receptor 3||Mediate delivery of 5-methyltetrahydrofolate to cell interior|
|FXYD1||FXYD Domain Containing Ion Transport Regulator 1||Regulates ion channel activity|
|KRTAP2-4||Keratin Associated Protein 2-4||Involved in hair formation|
|KRTAP4-8||Keratin Associated Protein 4-8||Involved in hair formation|
|ADH7||Alcohol dehydrogenase 7||Functions in retinoic acid synthesis|
|KRT75||Keratin 75||Involved in hair and nail formation|
|FAM25A||Family with sequence similarity 25 member A||Unknown|
|ADIPOR2||Adiponectin receptor 2||Regulates glucose and lipid metabolism|
GO enrichment analysis showing the significant biological processes (BP) of the top 500 hypermethylated promoters.
|GO:0009913||0||11.3215||2.1081||19||328||epidermal cell differentiation|
|GO:0042742||0||8.0356||1.5624||11||239||defense response to bacterium|
|GO:0006959||0||6.7129||1.4905||9||228||humoral immune response|
|GO:0051707||0||3.5529||5.4585||17||835||response to other organism|
|GO:0009607||1e-04||3.3622||5.7461||17||879||response to biotic stimulus|
|GO:0050832||1e-04||17.986||0.2549||4||39||defense response to fungus|
|GO:0090630||3e-04||9.5433||0.5753||5||88||activation of GTPase activity|
|GO:0061844||5e-04||11.8647||0.3726||4||57||antimicrobial humoral immune response mediated by antimicrobial peptide|
|GO:0009605||8e-04||2.5057||8.646||19||1419||response to external stimulus|
|GO:0051674||8e-04||2.378||10.0018||21||1530||localization of cell|
|GO:0031338||0.001||9.819||0.4445||4||68||regulation of vesicle fusion|
|GO:0002376||0.0014||2.0026||18.1078||31||2770||immune system process|
|GO:0002523||0.0018||38.6782||0.0654||2||10||leukocyte migration involved in inflammatory response|
|GO:1904995||0.0022||34.3786||0.0719||2||11||negative regulation of leukocyte adhesion to vascular endothelial cell|
|GO:0045104||0.0023||12.6396||0.2615||3||40||intermediate filament cytoskeleton organization|
|GO:0032119||0.0027||30.9389||0.0784||2||12||sequestering of zinc ion|
|GO:0030856||0.003||5.4424||0.9806||5||150||regulation of epithelial cell differentiation|
|GO:0034497||0.0032||28.1246||0.085||2||13||protein localization to phagophore assembly site|
|GO:0032101||0.0034||2.6778||4.8571||12||743||regulation of response to external stimulus|
|GO:0022408||0.0036||5.2242||1.0198||5||156||negative regulation of cell-cell adhesion|
|GO:0006928||0.0045||1.979||13.0285||23||1993||movement of cell or subcellular component|
|GO:0045087||0.0051||2.4353||5.7853||13||885||innate immune response|
|GO:0021660||0.0065||Inf||0.0065||1||1||rhombomere 3 formation|
|GO:0021666||0.0065||Inf||0.0065||1||1||rhombomere 5 formation|
|GO:0034516||0.0065||Inf||0.0065||1||1||response to vitamin B6|
|GO:0043420||0.0065||Inf||0.0065||1||1||anthranilate metabolic process|
|GO:0045660||0.0065||Inf||0.0065||1||1||positive regulation of neutrophil differentiation|
|GO:0072046||0.0065||Inf||0.0065||1||1||establishment of planar polarity involved in nephron morphogenesis|
|GO:0072740||0.0065||Inf||0.0065||1||1||cellular response to anisomycin|
|GO:1905716||0.0065||Inf||0.0065||1||1||negative regulation of cornification|
|GO:0006950||0.008||1.6938||24.6188||36||3766||response to stress|
|GO:1903036||0.0081||7.7836||0.4118||3||63||positive regulation of response to wounding|
|GO:0050729||0.0082||5.354||0.791||4||121||positive regulation of inflammatory response|
|GO:0030539||0.0082||16.2749||0.1373||2||21||male genitalia development|
|GO:1902807||0.0087||5.2634||0.8041||4||123||negative regulation of cell cycle G1/S phase transition|
|GO:0045606||0.0098||14.7231||0.1504||2||23||positive regulation of epidermal cell differentiation|
Word cloud illustrating the significant molecular functions (MF) associated with the top-ranking 500 hypomethylated promoters.
Pathway signaling network generated from the top-ranking 1000 DM promoters.
GO enrichment analysis showing the significant molecular functions (MF) of the top 500 hypermethylated promoters.
|GO:0050786||0||99.375||0.0655||4||11||RAGE receptor binding|
|GO:0017137||1e-04||7.2337||1.0653||7||179||Rab GTPase binding|
|GO:0035662||1e-04||340.8367||0.0179||2||3||Toll-like receptor 4 binding|
|GO:0050544||3e-04||113.5986||0.0298||2||5||arachidonic acid binding|
|GO:0005200||4e-04||8.9173||0.613||5||103||structural constituent of cytoskeleton|
|GO:0036041||0.0022||34.0653||0.0714||2||12||long-chain fatty acid binding|
|GO:0001856||0.006||Inf||0.006||1||1||complement component C5a binding|
|GO:0005130||0.006||Inf||0.006||1||1||granulocyte colony-stimulating factor receptor binding|
|GO:0036458||0.006||Inf||0.006||1||1||hepatocyte growth factor binding|
|GO:0047888||0.006||Inf||0.006||1||1||fatty acid peroxidase activity|
|GO:1901567||0.0096||14.7995||0.1488||2||25||fatty acid derivative binding|
GO enrichment analysis showing the significant biological processes (BP) of the top 500 hypomethylated promoters.
|GO:1901750||0||102.821||0.0789||4||8||leukotriene D4 biosynthetic process|
|GO:0006751||0||82.2519||0.0888||4||9||glutathione catabolic process|
|GO:0006691||0||21.5282||0.2861||5||29||leukotriene metabolic process|
|GO:0046456||1e-04||12.589||0.4538||5||46||icosanoid biosynthetic process|
|GO:0051572||3e-04||203.1707||0.0296||2||3||negative regulation of histone H3-K4 methylation|
|GO:0006575||4e-04||4.9708||1.7363||8||176||cellular modified amino acid metabolic process|
|GO:0072268||6e-04||101.5793||0.0395||2||4||pattern specification involved in metanephros development|
|GO:0048762||9e-04||4.3203||1.9829||8||201||mesenchymal cell differentiation|
|GO:0072081||9e-04||67.7154||0.0493||2||5||specification of nephron tubule identity|
|GO:0040012||0.0012||2.2988||9.4409||20||957||regulation of locomotion|
|GO:0030155||0.0015||2.5831||6.2347||15||632||regulation of cell adhesion|
|GO:0030334||0.0016||2.3435||8.2867||18||840||regulation of cell migration|
|GO:0051893||0.0018||8.3709||0.5229||4||53||regulation of focal adhesion assembly|
|GO:0017144||0.0018||2.3773||7.6948||17||780||drug metabolic process|
|GO:0048293||0.002||40.6244||0.0691||2||7||regulation of isotype switching to IgE isotypes|
|GO:0086036||0.002||40.6244||0.0691||2||7||regulation of cardiac muscle cell membrane potential|
|GO:0032412||0.002||3.7493||2.269||8||230||regulation of ion transmembrane transporter activity|
|GO:0033598||0.0023||12.7584||0.2664||3||27||mammary gland epithelial cell proliferation|
|GO:0071493||0.0026||33.8516||0.0789||2||8||cellular response to UV-B|
|GO:1902041||0.0027||7.455||0.582||4||59||regulation of extrinsic apoptotic signaling pathway via death domain receptors|
|GO:0016064||0.0031||5.4155||0.9865||5||100||immunoglobulin mediated immune response|
|GO:0033689||0.0033||29.0139||0.0888||2||9||negative regulation of osteoblast proliferation|
|GO:0045869||0.0033||29.0139||0.0888||2||9||negative regulation of single stranded viral RNA replication via double stranded DNA intermediate|
|GO:0070383||0.0033||29.0139||0.0888||2||9||DNA cytosine deamination|
|GO:0072048||0.0033||29.0139||0.0888||2||9||renal system pattern specification|
|GO:0051270||0.0034||2.1328||9.579||19||971||regulation of cellular component movement|
|GO:0043001||0.0035||10.9332||0.3058||3||31||Golgi to plasma membrane protein transport|
|GO:0032409||0.0035||3.421||2.4761||8||251||regulation of transporter activity|
|GO:0071526||0.0038||10.5555||0.3157||3||32||semaphorin-plexin signaling pathway|
|GO:0043648||0.0038||5.1432||1.0358||5||105||dicarboxylic acid metabolic process|
|GO:0046087||0.0041||25.3857||0.0987||2||10||cytidine metabolic process|
|GO:0030307||0.0048||4.0729||1.5587||6||158||positive regulation of cell growth|
|GO:0034754||0.0049||4.8503||1.095||5||111||cellular hormone metabolic process|
|GO:0060766||0.005||22.5637||0.1085||2||11||negative regulation of androgen receptor signaling pathway|
|GO:0007045||0.0056||6.0251||0.7103||4||72||cell-substrate adherens junction assembly|
|GO:0001867||0.006||20.3061||0.1184||2||12||complement activation, lectin pathway|
|GO:0016554||0.006||20.3061||0.1184||2||12||cytidine to uridine editing|
|GO:0046133||0.006||20.3061||0.1184||2||12||pyrimidine ribonucleoside catabolic process|
|GO:0072520||0.006||20.3061||0.1184||2||12||seminiferous tubule development|
|GO:0048513||0.0067||1.5794||33.344||47||3380||animal organ development|
|GO:0032101||0.0068||2.1741||7.3298||15||743||regulation of response to external stimulus|
|GO:0001838||0.007||4.4295||1.1937||5||121||embryonic epithelial tube formation|
|GO:0045995||0.007||4.4295||1.1937||5||121||regulation of embryonic development|
|GO:0010566||0.007||18.459||0.1282||2||13||regulation of ketone biosynthetic process|
|GO:0002699||0.007||3.7491||1.6869||6||171||positive regulation of immune effector process|
|GO:0016053||0.0076||2.6059||4.0447||10||410||organic acid biosynthetic process|
|GO:0045668||0.0076||8.0512||0.4045||3||41||negative regulation of osteoblast differentiation|
|GO:0050772||0.0077||5.4604||0.7793||4||79||positive regulation of axonogenesis|
|GO:1901888||0.0081||5.3882||0.7892||4||80||regulation of cell junction assembly|
|GO:0000722||0.0081||16.9197||0.1381||2||14||telomere maintenance via recombination|
|GO:0042446||0.0084||5.3179||0.7991||4||81||hormone biosynthetic process|
|GO:0001667||0.0085||2.56||4.1137||10||417||ameboidal-type cell migration|
|GO:0030278||0.0092||3.5327||1.7856||6||181||regulation of ossification|
|GO:0010959||0.0092||2.6793||3.5317||9||358||regulation of metal ion transport|
|GO:1904062||0.0094||2.8684||2.9299||8||297||regulation of cation transmembrane transport|
|GO:0000415||0.0099||Inf||0.0099||1||1||negative regulation of histone H3-K36 methylation|
|GO:0003147||0.0099||Inf||0.0099||1||1||neural crest cell migration involved in heart formation|
|GO:0030209||0.0099||Inf||0.0099||1||1||dermatan sulfate catabolic process|
|GO:0035713||0.0099||Inf||0.0099||1||1||response to nitrogen dioxide|
|GO:0044345||0.0099||Inf||0.0099||1||1||stromal-epithelial cell signaling involved in prostate gland development|
|GO:0046901||0.0099||Inf||0.0099||1||1||tetrahydrofolylpolyglutamate biosynthetic process|
|GO:0048694||0.0099||Inf||0.0099||1||1||positive regulation of collateral sprouting of injured axon|
|GO:0050928||0.0099||Inf||0.0099||1||1||negative regulation of positive chemotaxis|
|GO:0060598||0.0099||Inf||0.0099||1||1||dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis|
|GO:0061713||0.0099||Inf||0.0099||1||1||anterior neural tube closure|
|GO:0061767||0.0099||Inf||0.0099||1||1||negative regulation of lung blood pressure|
|GO:0071250||0.0099||Inf||0.0099||1||1||cellular response to nitrite|
|GO:0071954||0.0099||Inf||0.0099||1||1||chemokine (C-C motif) ligand 11 production|
|GO:0072168||0.0099||Inf||0.0099||1||1||specification of anterior mesonephric tubule identity|
|GO:0072169||0.0099||Inf||0.0099||1||1||specification of posterior mesonephric tubule identity|
|GO:0072184||0.0099||Inf||0.0099||1||1||renal vesicle progenitor cell differentiation|
|GO:0072259||0.0099||Inf||0.0099||1||1||metanephric interstitial fibroblast development|
|GO:0090246||0.0099||Inf||0.0099||1||1||convergent extension involved in somitogenesis|
|GO:0098749||0.0099||Inf||0.0099||1||1||cerebellar neuron development|
|GO:1900281||0.0099||Inf||0.0099||1||1||positive regulation of CD4-positive, alpha-beta T cell costimulation|
|GO:1904328||0.0099||Inf||0.0099||1||1||regulation of myofibroblast contraction|
|GO:1904635||0.0099||Inf||0.0099||1||1||positive regulation of glomerular visceral epithelial cell apoptotic process|
|GO:1904877||0.0099||Inf||0.0099||1||1||positive regulation of DNA ligase activity|
|GO:1905580||0.0099||Inf||0.0099||1||1||positive regulation of ERBB3 signaling pathway|
|GO:1905943||0.0099||Inf||0.0099||1||1||negative regulation of formation of growth cone in injured axon|
|GO:2000080||0.0099||Inf||0.0099||1||1||negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation|
|GO:2000184||0.0099||Inf||0.0099||1||1||positive regulation of progesterone biosynthetic process|
|GO:2000572||0.0099||Inf||0.0099||1||1||positive regulation of interleukin-4-dependent isotype switching to IgE isotypes|
GO enrichment analysis showing the significant molecular functions (MF) of the top 500 hypomethylated promoters.
|GO:0036374||0||105.3038||0.0575||3||6||glutathione hydrolase activity|
|GO:0047844||0.0019||41.8516||0.0671||2||7||deoxycytidine deaminase activity|
|GO:0000979||0.0045||9.855||0.3354||3||35||RNA polymerase II core promoter sequence-specific DNA binding|
|GO:0004126||0.0057||20.9195||0.115||2||12||cytidine deaminase activity|
|GO:0050681||0.0075||8.0828||0.4025||3||42||androgen receptor binding|
|GO:0031492||0.0091||7.5041||0.4312||3||45||nucleosomal DNA binding|
|GO:0004326||0.0096||Inf||0.0096||1||1||tetrahydrofolylpolyglutamate synthase activity|
|GO:0004441||0.0096||Inf||0.0096||1||1||inositol-1,4-bisphosphate 1-phosphatase activity|
|GO:0008725||0.0096||Inf||0.0096||1||1||DNA-3-methyladenine glycosylase activity|
|GO:0008829||0.0096||Inf||0.0096||1||1||dCTP deaminase activity|
|GO:0008841||0.0096||Inf||0.0096||1||1||dihydrofolate synthase activity|
|GO:0031962||0.0096||Inf||0.0096||1||1||mineralocorticoid receptor binding|
|GO:0034512||0.0096||Inf||0.0096||1||1||box C/D snoRNA binding|
|GO:0043916||0.0096||Inf||0.0096||1||1||DNA-7-methylguanine glycosylase activity|
|GO:0050649||0.0096||Inf||0.0096||1||1||testosterone 6-beta-hydroxylase activity|
|GO:0052821||0.0096||Inf||0.0096||1||1||DNA-7-methyladenine glycosylase activity|
|GO:0052822||0.0096||Inf||0.0096||1||1||DNA-3-methylguanine glycosylase activity|
|GO:0052829||0.0096||Inf||0.0096||1||1||inositol-1,3,4-trisphosphate 1-phosphatase activity|
|GO:0086038||0.0096||Inf||0.0096||1||1||calcium:sodium antiporter activity involved in regulation of cardiac muscle cell membrane potential|
|GO:0031625||0.0096||2.8578||2.9417||8||307||ubiquitin protein ligase binding|
Pathway signaling network generated from the top-ranking 100 DM promoters.
Among the protein-coding genes, C10orf99 and KRT6B promoters exhibited high levels of differential methylation in warts. The chromosome 10 open reading frame 99 (C10orf99) gene encodes for an antimicrobial peptide that is widely expressed in the skin and digestive tract . In a pathologic context, C10orf99 was determined to contribute to psoriasis development by promoting keratinocyte proliferation [24, 25]. Likewise, the keratin 6B (KRT6B) gene encodes for a type II keratin that is normally present in mammalian epithelial cells and is rapidly induced in human keratinocytes after skin wounding . KRT6B has been identified as a potential biomarker for differentiating between lung adenocarcinoma and lung squamous cell carcinoma, and its increased expression is associated with lower disease-free survival rates in young breast cancer patients [27, 28]. Mutations in the KRT6B gene result in an autosomal dominant skin disorder known as pachyonychia congenita, which involves plantar keratoderma and pain alongside thickened toenails . In contrast, two of the most differentially methylated protein-coding promoters, namely the kallikrein related peptidase 2 (KLK2) and Izumo sperm-egg fusion 1 (IZUMO1) genes, are integral for sperm function. KLK2 over-expression has been associated with the promotion of prostate cancer cell growth .
As previously mentioned, the ephemeral nature of warts hints towards the involvement of an epigenetic component. Correspondingly, some of the most DM promoters were found within the laminin subunit alpha 4 (LAMA4) and H3 histone family member 3B (H3F3B) genes, which are responsible for cell differentiation and nucleosomal displacement, respectively [31, 32]. In certain breast cancer subtypes, increased LAMA4 expression was noted to contribute to the chromatin remodeling mechanisms that are a part of cancer progression . Moreover, atypical HF3B expression was reported to be associated with colorectal cancer and chondroblastoma [34, 35]. On a similar note, epigenetic modifications have been linked to changes in metabolism in a number of different non-communicable diseases, including cancer and diabetes . In the present study, promoters were differentially methylated within the 17β-hydroxysteroid dehydrogenase type 14 (HSD17B14), leukotriene C4 synthase (LTC4S), folate receptor 3 (FOLR3), alcohol dehydrogenase 7 (ADH7), and adiponectin receptor 2 (ADIPOR2) genes that are involved in steroid, eicosanoid, folate, retinol, and glucose and lipid metabolism, respectively [37-41]. Like the CYSLTR1 gene, LTC4S polymorphisms were associated with asthma risk and drug responsiveness in different ethnic populations [42-45].
Pathway analysis demonstrated that the most common regulator among the top-ranking 1000 DM promoters was the H3 histone family member 3A (H3F3A) gene. Like the H3F3B gene, H3F3A encodes for a histone variant and is involved in transcriptional regulation . Aberrant H3F3A expression has been associated with the promotion of pediatric and adolescent cancers as well as lung cancer cell migration [46, 47]. The second most common regulator was the cyclin dependent kinase inhibitor 1A (CDKN1A) gene, which is mostly involved in CDK2 inhibition and is a primary target of p53 activity . The CDKN1A gene was associated with better patient survival in HPV-related oropharyngeal squamous cell carcinoma . The third most common regulator in HPV-induced warts is the mitogen-activated protein kinase 13 (MAPK13) gene. MAPK13 is a member of the MAP kinase family and functions to regulate cellular responses to a range of different stimuli, especially in the context of keratinocyte apoptosis and skin homeostasis . Analysis of genome-wide promoter methylation revealed that MAPK13 was hypermethylated in the majority of primary and metastatic melanomas . MAPK13 was also found to be hypermethylated in esophageal squamous cell carcinoma .
In summary, it is apparent that HPV-induced warts possess certain patterns of promoter methylation that could be responsible for their formation and maintenance. One limitation of the current study is that it is not possible at this stage to determine whether the differential methylation occurred as a result of the host cells' response to infection or due to HPV-driven processes responsible for wart formation and progression. Future research is required in order to assess the functional and clinical importance of the hypo- and hypermethylated promoter sites as well as to determine the exact nature of this differential methylation.
This work was supported by the Deanship of Research at Jordan University of Science and Technology under grant number 184/2017. The authors would like to express their gratitude to King Khalid University, Saudi Arabia, for providing administrative and technical support.
Ethical approval was obtained from the Jordan University of Science and Technology (JUST) IRB committee (Ref. # 19/105/2017). All participants gave written informed consent before participating in this study.
The authors have declared that no competing interest exists.
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Corresponding author: Email: lneitanedu.jo