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International Journal of Medical Sciences logoLink to International Journal of Medical Sciences
. 2020 Jan 14;17(2):191–206. doi: 10.7150/ijms.39261

Epigenome-wide analysis of common warts reveals aberrant promoter methylation

Laith N AL-Eitan 1,2,✉, Mansour A Alghamdi 3, Amneh H Tarkhan 1, Firas A Al-Qarqaz 4,5
PMCID: PMC6990892  PMID: 32038103

Abstract

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

Introduction

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) 1. 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 2. 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 3. 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 6. In addition, host promoter hypermethylation has also been implicated in infections by both oncogenic and non-oncogenic viruses such as the human papillomaviruses (HPV) 7. HPV comprises a family of double-stranded DNA viruses that exclusively infect the basal epithelium of the skin and mucosa 8. 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 9. One such condition is the wart, which arises due to the benign proliferation of HPV-infected epithelial keratinocytes 10. The most prevalent type of wart is the common wart, which accounts for nearly 70% of all cutaneous warts encountered in clinical settings 11. 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.

Materials and Methods

Study participants

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.

Whole genome bisulfite sequencing

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.

Data processing

RnBeads, a computational R package, was adapted to process and analyze the raw intensity data (IDAT files) from the BeadChip 12. Quality control, preprocessing, batch effects adjustment, and normalization were carried out on all probes and samples according to the RnBeads package pipeline.

Differential methylation and statistical analysis

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 12. 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%.

Figure 1.

Figure 1

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Distribution of CpG sites per promoter.

Figure 2.

Figure 2

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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.

Gene ontology enrichment analysis

Enrichment analysis for gene ontology (GO) terms associated with the top-ranking 500 DM promoters was performed using the GO consortium 14.

Signaling pathway analysis

A signaling network of the top-ranking 1000 DM promoters was investigated using the SIGnaling Network Open Resource (SIGNOR) 2.0 15. 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'.

Results

Sample clustering based on methylation data

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.

Figure 3.

Figure 3

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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.

Figure 4.

Figure 4

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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.

Differential methylation of promoters

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.

Figure 6.

Figure 6

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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).

Figure 7.

Figure 7

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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.

Table 1.

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.
(W-NS)		 mean.mean. quot.log2 comb.p.val comb.p.adj. (FDR) Combined rank
ENSG00000224674 EIF3EP2 Pseudogene 2 0.611 0.154 -0.458 -1.924 7.832E-16 3.519E-11 1
ENSG00000263368 AC069366.1 Pseudogene antisense 17 0.206 0.573 0.367 1.431 1.336E-13 2.001E-09 14
ENSG00000173198 CYSLTR1 Protein coding X 0.166 0.520 0.353 1.580 1.671E-11 4.415E-08 17
ENSG00000266228 MIR3611 RNA gene miRNA 10 0.403 0.128 -0.275 -1.584 1.083E-11 3.744E-08 27
ENSG00000267125 AC012615.3 RNA gene 19 0.192 0.465 0.273 1.280 3.531E-13 3.410E-09 29
ENSG00000270808 AC022400.4 Pseudogene lncRNA 10 0.691 0.295 -0.396 -1.202 1.686E-10 1.756E-07 40
ENSG00000241114 AC008280.2 Pseudogene 2 0.383 0.129 -0.254 -1.503 1.876E-10 1.756E-07 47
ENSG00000272156 AC008280.3 RNA gene 2 0.383 0.129 -0.254 -1.503 1.876E-10 1.756E-07 47
ENSG00000207258 RF00019 RNA gene Y RNA 1 0.508 0.192 -0.315 -1.356 6.373E-10 4.522E-07 62
ENSG00000226545 AL357552.1 Pseudogene 1 0.508 0.192 -0.315 -1.356 6.373E-10 4.522E-07 62
ENSG00000270002 AC022028.2 RNA gene 10 0.458 0.199 -0.259 -1.056 5.656E-10 4.246E-07 70
ENSG00000227096 HMGB3P8 Pseudogene 10 0.653 0.246 -0.408 -1.376 1.138E-09 6.141E-07 82
ENSG00000250532 AC021180.1 RNA gene 4 0.621 0.233 -0.388 -1.378 1.576E-09 7.956E-07 89
ENSG00000254653 AC024475.1 RNA gene 11 0.228 0.440 0.212 1.071 1.411E-10 1.756E-07 99
ENSG00000265503 MIR1269B RNA gene miRNA 17 0.346 0.141 -0.205 -1.239 1.140E-09 6.141E-07 109
ENSG00000238024 DDX39BP2 Pseudogene 6 0.326 0.124 -0.202 -1.323 1.391E-09 7.248E-07 113
ENSG00000273044 AL022334.2 RNA gene 22 0.243 0.481 0.238 0.956 1.766E-10 1.756E-07 119
ENSG00000234105 AC009468.2 RNA gene 7 0.576 0.307 -0.269 -0.961 3.100E-09 1.151E-06 121
ENSG00000188373 C10orf99 Protein coding 10 0.400 0.202 -0.198 -0.982 5.786E-10 4.262E-07 124
ENSG00000271597 AC112230.1 Pseudogene lncRNA 2 0.306 0.594 0.287 0.933 3.019E-09 1.151E-06 136
ENSG00000271265 AL355297.3 RNA gene lncRNA 6 0.347 0.667 0.320 0.924 1.317E-11 3.856E-08 145
ENSG00000244286 ITGB5-AS1 RNA gene ncRNA 3 0.202 0.393 0.190 1.223 8.912E-12 3.640E-08 152
ENSG00000226403 AL392089.1 RNA gene 9 0.080 0.269 0.189 1.633 1.086E-12 6.969E-09 154
ENSG00000234936 AC010883.1 RNA gene 2 0.288 0.498 0.210 0.909 2.020E-11 4.908E-08 158
ENSG00000203527 Z99756.1 RNA gene ncRNA 22 0.385 0.198 -0.187 -0.906 5.290E-09 1.674E-06 161
ENSG00000242147 AL365356.5 RNA gene ncRNA 10 0.334 0.148 -0.186 -1.263 3.506E-11 7.161E-08 166
ENSG00000270781 AC091133.5 Pseudogene 17 0.416 0.219 -0.197 -0.896 4.980E-10 3.925E-07 170
ENSG00000250282 AC002401.2 RNA gene 17 0.225 0.443 0.217 0.894 3.488E-09 1.234E-06 174
ENSG00000255158 AC131934.1 RNA gene 11 0.299 0.590 0.291 0.977 1.016E-08 2.625E-06 174
ENSG00000232486 AL592437.2 Pseudogene 9 0.666 0.354 -0.312 -0.892 1.930E-09 8.758E-07 175
ENSG00000262067 AC120057.1 Pseudogene lncRNA 17 0.505 0.171 -0.333 -1.505 1.139E-08 2.816E-06 181
ENSG00000266258 LINC01909 RNA gene ncRNA 18 0.629 0.299 -0.330 -1.048 1.479E-08 3.408E-06 195
ENSG00000257496 AC025031.1 RNA gene 12 0.217 0.397 0.180 0.982 1.649E-08 3.703E-06 200
ENSG00000185479 KRT6B Protein-coding 12 0.340 0.166 -0.174 -1.045 7.004E-11 1.124E-07 216
ENSG00000270255 AC009884.2 Pseudogene 8 0.279 0.529 0.250 0.900 2.221E-08 4.587E-06 217
ENSG00000167751 KLK2 Protein coding 19 0.328 0.136 -0.192 -1.214 2.772E-08 5.463E-06 227
ENSG00000268518 AC020909.2 RNA gene 19 0.432 0.238 -0.194 -0.839 2.897E-11 6.197E-08 229
ENSG00000243795 LINC02044 RNA gene ncRNA 3 0.387 0.663 0.276 0.825 1.229E-11 3.856E-08 246
ENSG00000267632 AC067852.3 RNA gene lncRNA 17 0.402 0.719 0.316 0.821 1.561E-10 1.756E-07 254
ENSG00000259265 AC027088.3 RNA gene 15 0.362 0.195 -0.167 -0.918 2.209E-08 4.587E-06 260
ENSG00000264733 MIR4718 RNA gene miRNA 16 0.342 0.176 -0.166 -0.922 1.674E-09 8.164E-07 263
ENSG00000253630 AC026407.1 Pseudogene antisense 5 0.537 0.301 -0.236 -0.815 1.148E-09 6.141E-07 264
ENSG00000228918 LINC01344 RNA gene ncRNA 1 0.180 0.346 0.166 0.908 4.232E-10 3.475E-07 264
ENSG00000232878 DPYD-AS1 RNA gene ncRNA 1 0.572 0.387 -0.185 -0.815 4.216E-08 7.523E-06 265
ENSG00000112769 LAMA4 Protein coding 6 0.325 0.512 0.187 0.810 3.888E-08 7.072E-06 269
ENSG00000237126 AC073254.1 RNA gene 2 0.368 0.202 -0.166 -0.835 1.684E-08 3.745E-06 270
ENSG00000256746 AC018410.1 RNA gene ncRNA 11 0.344 0.536 0.192 0.807 2.084E-09 9.002E-07 271
ENSG00000232560 C21orf37 RNA gene ncRNA 21 0.300 0.495 0.195 0.805 5.048E-08 8.338E-06 274
ENSG00000198796 ALPK2 Protein coding 18 0.165 0.329 0.163 0.924 1.006E-08 2.622E-06 286
ENSG00000185432 METTL7A Protein coding 12 0.389 0.673 0.283 0.795 7.318E-13 5.480E-09 286
ENSG00000087076 HSD17B14 Protein coding 19 0.145 0.346 0.201 1.168 5.925E-08 9.251E-06 287
ENSG00000239255 AC007620.1 Pseudogene 3 0.347 0.575 0.227 1.085 6.353E-08 9.775E-06 292
ENSG00000230403 LINC01066 RNA gene ncRNA 13 0.475 0.302 -0.173 -0.902 8.129E-08 1.192E-05 306
ENSG00000132475 H3F3B Protein coding 17 0.173 0.358 0.184 1.003 8.349E-08 1.218E-05 308
ENSG00000258274 AC012085.2 RNA gene ncRNA 12 0.415 0.624 0.208 0.785 6.143E-11 1.062E-07 308
ENSG00000244167 AC005532.2 Pseudogene lncRNA 7 0.488 0.281 -0.207 -0.775 4.380E-08 7.657E-06 324
ENSG00000266740 MIR4708 RNA gene miRNA 14 0.240 0.416 0.177 0.771 4.844E-10 3.887E-07 328
ENSG00000258657 AL136018.1 RNA gene 14 0.448 0.234 -0.213 -0.946 1.163E-07 1.588E-05 329
ENSG00000186715 MST1L Protein coding 1 0.300 0.145 -0.156 -1.006 6.774E-11 1.124E-07 335
ENSG00000253543 AC083923.1 Pseudogene 8 0.277 0.121 -0.156 -1.127 6.441E-10 4.522E-07 339
ENSG00000261095 AC136285.1 RNA gene ncRNA 16 0.487 0.272 -0.215 -0.958 1.368E-07 1.803E-05 341
ENSG00000213316 LTC4S Protein coding 5 0.211 0.365 0.154 1.075 1.025E-08 2.631E-06 348
ENSG00000267299 AC011444.3 RNA gene 19 0.141 0.300 0.159 0.752 2.936E-08 5.687E-06 352
ENSG00000234502 FYTTD1P1 Pseudogene 9 0.361 0.180 -0.182 -0.969 1.678E-07 2.118E-05 356
ENSG00000265666 RARA-AS1 RNA gene ncRNA 17 0.189 0.339 0.151 0.868 1.088E-07 1.501E-05 370
ENSG00000182264 IZUMO1 Protein coding 19 0.308 0.468 0.160 0.737 3.157E-08 5.910E-06 376
ENSG00000254113 AC090193.2 RNA gene 8 0.243 0.419 0.177 0.736 1.371E-08 3.276E-06 378
ENSG00000204933 CD177P1 Pseudogene 19 0.375 0.607 0.232 0.733 2.798E-09 1.103E-06 382
ENSG00000110203 FOLR3 Protein coding 11 0.536 0.357 -0.180 -0.746 1.990E-07 2.311E-05 387
ENSG00000266964 FXYD1 Protein coding 19 0.299 0.452 0.154 0.731 3.068E-09 1.151E-06 391
ENSG00000221857 AC020907.2 RNA gene 19 0.299 0.452 0.154 0.731 3.068E-09 1.151E-06 391
ENSG00000213417 KRTAP2-4 Protein coding 17 0.471 0.309 -0.163 -0.855 2.328E-07 2.604E-05 401
ENSG00000254853 AP004247.1 Pseudogene 11 0.247 0.100 -0.147 -1.221 3.631E-09 1.265E-06 410
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
ENSG00000261257 AP000821.1 RNA gene lncRNA 11 0.394 0.543 0.149 0.746 2.524E-07 2.757E-05 411
ENSG00000204880 KRTAP4-8 Protein coding 17 0.356 0.198 -0.158 -0.823 2.945E-07 3.114E-05 425
ENSG00000215930 MIR942 RNA gene miRNA 1 0.410 0.266 -0.144 -0.782 8.361E-09 2.305E-06 427
ENSG00000271680 AC098935.2 Pseudogene antisense 1 0.244 0.100 -0.144 -1.211 4.741E-08 7.978E-06 428
ENSG00000258380 AL356805.1 RNA gene 14 0.292 0.435 0.144 1.043 2.010E-08 4.354E-06 432
ENSG00000249717 AC110760.2 RNA gene ncRNA 4 0.480 0.694 0.213 0.707 5.817E-08 9.171E-06 436
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
ENSG00000263361 MIR378H RNA gene miRNA 5 0.411 0.268 -0.143 -0.731 7.162E-08 1.080E-05 443
ENSG00000249483 AC026726.1 RNA gene lncRNA 5 0.114 0.257 0.142 0.852 1.524E-08 3.459E-06 446
ENSG00000227735 CYCSP5 Pseudogene antisense 1 0.212 0.070 -0.142 -1.478 2.842E-09 1.110E-06 449
ENSG00000267130 AC008738.2 RNA gene 19 0.163 0.310 0.146 0.698 3.087E-08 5.835E-06 449
ENSG00000269480 AC020913.2 RNA gene 19 0.388 0.226 -0.162 -0.755 4.211E-07 3.933E-05 481
ENSG00000260673 AL034376.1 RNA gene 6 0.392 0.254 -0.139 -0.703 8.046E-08 1.187E-05 482
ENSG00000261392 AC087190.2 RNA gene 16 0.735 0.481 -0.255 -0.681 2.657E-07 2.869E-05 488
ENSG00000196344 ADH7 Protein coding 4 0.290 0.152 -0.138 -0.936 2.488E-07 2.740E-05 488
ENSG00000170454 KRT75 Protein coding 12 0.467 0.293 -0.175 -0.729 4.448E-07 4.087E-05 489
ENSG00000254175 IGLVI-42 Pseudogene 22 0.232 0.095 -0.137 -1.201 1.475E-10 1.756E-07 498
ENSG00000254073 IGLVVII-41-1 Pseudogene 22 0.232 0.095 -0.137 -1.201 1.475E-10 1.756E-07 498
ENSG00000253947 AC008705.1 RNA gene 5 0.393 0.582 0.189 0.677 1.507E-08 3.438E-06 498
ENSG00000275874 PICSAR RNA gene ncRNA 21 0.467 0.318 -0.150 -0.675 2.541E-07 2.757E-05 503
ENSG00000233930 KRTAP5-AS1 RNA gene ncRNA 11 0.162 0.298 0.136 0.944 1.138E-08 2.816E-06 503
ENSG00000188100 FAM25A Protein coding 10 0.389 0.254 -0.135 -0.688 1.426E-07 1.862E-05 509
ENSG00000261078 AC009118.1 RNA gene 16 0.250 0.115 -0.135 -1.008 2.220E-08 4.587E-06 513
ENSG00000259195 AC021739.1 Pseudogene 15 0.284 0.149 -0.134 -0.927 4.219E-08 7.523E-06 519
ENSG00000260905 AC009021.1 RNA gene 16 0.616 0.384 -0.232 -0.667 8.523E-08 1.235E-05 523
ENSG00000006831 ADIPOR2 Protein coding 12 0.721 0.501 -0.220 -0.667 1.007E-07 1.410E-05 527
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Gene ontology enrichment analysis

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).

Figure 8.

Figure 8

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Word cloud illustrating the significant biological processes (BP) associated with the top-ranking 500 hypermethylated promoters.

Figure 9.

Figure 9

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Word cloud illustrating the significant molecular functions (MF) associated with the top-ranking 500 hypermethylated promoters.

Table 2.

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
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Table 3.

GO enrichment analysis showing the significant biological processes (BP) of the top 500 hypermethylated promoters.

GOMFID P-value Odds ratio ExpCount Count Size Term
GO:0009913 0 11.3215 2.1081 19 328 epidermal cell differentiation
GO:0043588 0 9.3276 2.6737 20 409 skin development
GO:0070268 0 14.8063 0.7126 9 110 cornification
GO:0031424 0 13.9409 0.664 8 111 keratinization
GO:0060429 0 3.7163 8.1779 25 1251 epithelium development
GO:0042742 0 8.0356 1.5624 11 239 defense response to bacterium
GO:0030154 0 2.5597 26.423 49 4042 cell differentiation
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:0070488 0 Inf 0.0131 2 2 neutrophil aggregation
GO:0031581 0 58.5596 0.0719 3 11 hemidesmosome assembly
GO:0009607 1e-04 3.3622 5.7461 17 879 response to biotic stimulus
GO:0048731 1e-04 2.1729 30.6198 50 4684 system development
GO:0050832 1e-04 17.986 0.2549 4 39 defense response to fungus
GO:0032502 2e-04 2.0271 40.0921 59 6133 developmental process
GO:0016477 2e-04 2.639 9.1062 21 1393 cell migration
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:0007155 9e-04 2.4699 8.6421 19 1322 cell adhesion
GO:0031338 0.001 9.819 0.4445 4 68 regulation of vesicle fusion
GO:0097530 0.001 7.0599 0.7648 5 117 granulocyte migration
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:0030595 0.0019 4.9654 1.2943 6 198 leukocyte chemotaxis
GO:0040011 0.002 2.1602 11.4792 22 1756 locomotion
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:0030593 0.0025 7.5626 0.5687 4 87 neutrophil chemotaxis
GO:0003334 0.0027 30.9389 0.0784 2 12 keratinocyte development
GO:0032119 0.0027 30.9389 0.0784 2 12 sequestering of zinc ion
GO:0008219 0.0029 2.0056 14.1398 25 2163 cell death
GO:0030856 0.003 5.4424 0.9806 5 150 regulation of epithelial cell differentiation
GO:0018119 0.0032 28.1246 0.085 2 13 peptidyl-cysteine S-nitrosylation
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:0006935 0.0049 2.8124 3.8177 10 584 chemotaxis
GO:0045087 0.0051 2.4353 5.7853 13 885 innate immune response
GO:0003336 0.0065 Inf 0.0065 1 1 corneocyte desquamation
GO:0021593 0.0065 Inf 0.0065 1 1 rhombomere morphogenesis
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:0033037 0.0065 Inf 0.0065 1 1 polysaccharide localization
GO:0034516 0.0065 Inf 0.0065 1 1 response to vitamin B6
GO:0035644 0.0065 Inf 0.0065 1 1 phosphoanandamide dephosphorylation
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
GO:0001775 0.0099 2.0563 8.459 16 1294 cell activation
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Figure 10.

Figure 10

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Word cloud illustrating the significant biological processes (BP) associated with the top-ranking 500 hypomethylated promoters.

Figure 11.

Figure 11

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Word cloud illustrating the significant molecular functions (MF) associated with the top-ranking 500 hypomethylated promoters.

Table 4.

GO enrichment analysis showing the significant molecular functions (MF) of the top 500 hypermethylated promoters.

GOMFID P-value Odds ratio ExpCount Count Size Term
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:0045294 0.0019 37.8526 0.0655 2 11 alpha-catenin binding
GO:0036041 0.0022 34.0653 0.0714 2 12 long-chain fatty acid binding
GO:0008146 0.0035 10.7307 0.3035 3 51 sulfotransferase activity
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:0030429 0.006 Inf 0.006 1 1 kynureninase activity
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:0061981 0.006 Inf 0.006 1 1 3-hydroxykynureninase activity
GO:1901567 0.0096 14.7995 0.1488 2 25 fatty acid derivative binding
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Table 5.

GO enrichment analysis showing the significant biological processes (BP) of the top 500 hypomethylated promoters.

GOMFID P-value Odds ratio ExpCount Count Size Term
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:0022612 0.0012 5.4916 1.1739 6 119 gland morphogenesis
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:0035148 0.003 4.523 1.4107 6 143 tube formation
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:0001756 0.0041 6.6105 0.6511 4 66 somitogenesis
GO:0009972 0.0041 25.3857 0.0987 2 10 cytidine deamination
GO:0046087 0.0041 25.3857 0.0987 2 10 cytidine metabolic process
GO:0035510 0.0041 10.2031 0.3255 3 33 DNA dealkylation
GO:0048870 0.0043 1.8716 15.0936 26 1530 cell motility
GO:0070988 0.0048 6.3043 0.6807 4 69 demethylation
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:0060429 0.0058 1.9184 12.3412 22 1251 epithelium development
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:0090382 0.0076 8.0512 0.4045 3 41 phagosome maturation
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
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Pathway analysis

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.

Figure 12.

Figure 12

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Pathway signaling network generated from the top-ranking 1000 DM promoters.

Discussion

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 16. 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 22. Table 2 depicts all the protein-coding genes containing DM promoters from among the top-ranking 100 listed in Table 1.

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 23. 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 26. 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 29. 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 30.

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 33. 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 36. 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 46. 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 48. The CDKN1A gene was associated with better patient survival in HPV-related oropharyngeal squamous cell carcinoma 49. 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 50. Analysis of genome-wide promoter methylation revealed that MAPK13 was hypermethylated in the majority of primary and metastatic melanomas 51. MAPK13 was also found to be hypermethylated in esophageal squamous cell carcinoma 52.

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.

Figure 5.

Figure 5

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Two-dimensional scatterplot showing sample positions after principal component analysis.

Figure 13.

Figure 13

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Pathway signaling network generated from the top-ranking 100 DM promoters.

Table 6.

GO enrichment analysis showing the significant molecular functions (MF) of the top 500 hypomethylated promoters.

GOMFID P-value Odds ratio ExpCount Count Size Term
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:0003940 0.0096 Inf 0.0096 1 1 L-iduronidase activity
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
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Acknowledgments

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.

Ethics Committee Approval and Patient Consent

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.

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