Int J Med Sci 2020; 17(2):191-206. doi:10.7150/ijms.39261

Research Paper

Epigenome-wide analysis of common warts reveals aberrant promoter methylation

Laith N. AL-Eitan1,2✉, Mansour A. Alghamdi3, Amneh H. Tarkhan1, Firas A. Al-Qarqaz4,5

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

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Citation:
AL-Eitan LN, Alghamdi MA, Tarkhan AH, Al-Qarqaz FA. Epigenome-wide analysis of common warts reveals aberrant promoter methylation. Int J Med Sci 2020; 17(2):191-206. doi:10.7150/ijms.39261. Available from http://www.medsci.org/v17p0191.htm

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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