Genome-wide DNA methylation profi le and expression of TLR2, TLR9, IL4, IL13 genes in pediatric patients with atopic dermatitis


Introduction. Atopic dermatitis (AD) is a multifactorial disease, resulted from complex interactions between genetic and environmental factors. Epigenetic mechanisms involved in the gene expression regulationmay clarify how environmental exposure affects the risk of allergy development.

The aim of this study is to conduct a comprehensive analysis of the immune mechanisms (methylome; gene expression profile of TLR2, TLR9, IL4, IL13) locally and systematically in pediatric patients with moderate and severe AD.

Material and methods. With the use of DNA new generation sequencing technology (Oxford Nanopore Technologies Ltd) we performed a DNA methylation genome-wide study in atopic patients’ biopsies. At the same time the expression level for genes TLR2, TLR9, IL4, IL13 was assessed in the skin and mononuclear blood cells using real-time polymerase chain reaction.

Results. Targeted gene expression analysis revealed a significant (p ≤ 0.017) increase in the levels of TLR2, TLR9, IL4, IL13 expression in the blood of patients with AD compared with the group of comparison, as well as a decrease (p ≤ 0.05) in the levels of TLR2, TLR9, IL4 expression in affected skin compared to the group of comparison. We detected loci that were differentially methylated in atopic patients and healthy donors.

Conclusion. It is important to have a complete understanding of the AD pathogenic mechanisms. New insights on epigenetic and immunological markers associated with the risk of AD development will help to create new prognostic approaches in the management of patients with atopic pathology.

Keywords:atopic dermatitis; innate immunity; cytokines; Toll-like receptors; gene expression; methylation

For citation: Bystritskaya E.P., Murashkin N.N., Materikin A.I., Naumova E.A., Svitich O.A. Genome-wide DNA methylation profile and expression of TLR2, TLR9, IL4, IL13 genes in pediatric patients with atopic dermatitis. Immunologiya. 2022; 43 (3): 255–65. DOI: (in Russian)

Funding. The study had no sponsor support.

Conflict of interests. Authors declare no conflict of interests.

Authors’ contribution. The concept and design of the study, analysis of results – Svitich O.A., Murashkin N.N.; providing a database of clinical samples from patients – Materikin A.I.; bioinformatic processing of sequencing data, interpretation of the statistical analysis results – Naumova E.A.; conducting the experimental part of the research, statistical analysis and interpretation of its results – Bystritskaya E.P.


1.Atopic dermatitis: clinical recommendaitions. 2020. URL: (in Russian)

2.Luger T., Adaskevich U., Anfilova M., Dou X., Murashkin N.N., Namazova-Baranova L., Nitochko O., Reda A., Svyatenko T. V., Tamay Z., Tawara M., Vishneva E. A., Vozianova S., Wang H., Zhao Z. Practical algorithm to inform clinical decision-making in the topical treatment of atopic dermatitis. J Dermatol. 2021; 48 (8): 1139–48. DOI:

3.Tham E.H, Leung D.Y. Mechanisms by which atopic dermatitis predisposes to food allergy and the atopic march. Allergy Asthma Immunol Res. 2019; 11 (1): 4–15. DOI:

4.Kubanov A.A., Namazova-Baranova L.S., Khaitov R.M., Ilina N.I., Alekseeva E.A., Ambarchian E.T., Artemieva S.I., Arshins- kiy M.I., Astafieva N.G., Vishneva E.A., Volnukchin V.A., Danili- cheva I.V., Elisutina O.G., Epishev R.V., Zhestkov A.V., Zhilova M.B., Zhukova O.V., Zaslavsky D.V., Znamenskaya L.F., Karamova A.E., Korotky N.G., Kokchan M.M., Kruglova L.S., Kungurov N.V., Le- vina J.G., Lvov A.N., Materikin A.I., Mishina O.S., Monakhov K.N., Murashkin N.N., Nenasheva N.M., Pampura A.N., Plakhova X.I., Potekaev N.N., Prytulо O.A., Raznatovskiy К.I., Sapuntsova S.G., Selimzianova L.R., Skorokhodkina O.V., Fedenko E.S., Fomina D.S., Frigo N.V., Frolova Z.V., Khaitov M.R., Chikin V.V. Atopic dermatitis. Russian Journal of Allergy. 2021; 18 (3): 44–92. DOI: (in Russian)

5.Elisyutina O.G., Fedenko E.S., Boldyreva M.N., Gudima G.O. Characteristics of immune response and role of cytokines in atopic dermatitis. Russian Journal of Allergy. 2015; (1): 3–14. (in Russian)

6.Ahn K., Kim B.E., Kim J., Leung D.Y. Recent advances in atopic dermatitis. Curr Opin Immunol. 2020; 66: 14–21. DOI:

7.Sun L., Liu W., Zhang L.-J. The role of toll-like receptors in skin host defense, psoriasis, and atopic dermatitis. J Immunol Res. 2019; 2019: 1824624. DOI:

8.Novak N., Yu C.-F., Bussmann C., Maintz L., Peng W.-M., Hart J., Hagemann T., Diaz-Lacava A., Baurecht H.J., Klopp N., Wagenpfeil S., Behrendt H., Bieber T., Ring J., Illig T., Weidinger S. Putative association of a TLR9 promoter polymorphism with atopic eczema: TLR9 polymorphisms and atopic eczema. Allergy. 2007; 62 (7): 766–72. DOI:

9.Potaczek D., Nastalek M., Okumura K., Wojas-Pelc A., Undas A., Nishiyama C. An association of TLR2-16934A>T polymorphism and severity/phenotype of atopic dermatitis: TLR2-16934A>T polymorphism and AD severity/phenotype. J Eur Acad Dermatol Venereol. 2011; 25 (6): 715–21. DOI: 03812.x

10.Elisyutina O.G., Fedenko E.S., Boldyreva M.N., Gudima G.O. Genetic aspects of immunopathogenesis of atopic dermatitis. Immunologiya. 2015; 36 (2): 122–8. (in Russian)

11.Ghosh D., Bernstein J.A., Khurana Hershey G.K., Rothenberg M.E., Mersha T.B. Leveraging multilayered «omics» data for atopic dermatitis: a road map to precision medicine. Front Immunol. 2018; 9: 2727. DOI:

12.Timoshenko D.O., Kofiadi I.A., Gudima G.O., Kurbacheva O.M. Epigenetics of bronchial asthma. Immunologiya. 2021; 42 (2): 93–101. DOI: (in Russian)

13.Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001; 25 (4): 402–8. DOI:

14.Ligation sequencing gDNA (SQK-LSK109). URL:

15.PycoMeth. URL:

16.Unguryanu T.N., Grjibovski A.M. Analysis of three independent groups using non-parametric Kruskal–Wallis test in stata software. Ekologiya cheloveka. 2014; (6): 55–8. (in Russian)

17.Kruskal-Wallis Test Calculator. URL:

18.Iwamoto K., Nümm T.J., Koch S., Herrmann N., Leib N., Bieber T. Langerhans and inflammatory dendritic epidermal cells in atopic dermatitis are tolerized toward TLR2 activation. Allergy. 2018; 73 (11): 2205–13. DOI:

19.Jiao D., Wong C.-K., Qiu H.-N., Dong J., Cai Z., Chu M., Hon K. L., Tsang M.S., Lam C.W. NOD2 and TLR2 ligands trigger the activation of basophils and eosinophils by interacting with dermal fibroblasts in atopic dermatitis-like skin inflammation. Cell Mol Immunol. 2016; 13 (4): 535–50. DOI:

20.Merkushova E.D., Khasanova E.M., Gankovskaya L.V. Hyperexpression of NLRP1 inflammasome complex genes and cytokines IL-1β, IL-18 in bioptates of lesion and healthy skin of patients with psoriasis. Immunologiya. 2021; 42 (1): 21–8. DOI: (in Russian)

21.Moriwaki M., Iwamoto K., Niitsu Y., Matsushima A., Yanase Y., Hisatsune J., Sugai M., Hide M. Staphylococcus aureus from atopic dermatitis skin accumulates in the lysosomes of keratinocytes with induction of IL-1α secretion via TLR9. Allergy. 2019; 74 (3): 560–71. DOI:

22.Yu Y., Lin D., Cai X., Cui D., Fang R., Zhang W., Yu B., Wang X. Enhancement of chemokine mRNA expression by toll-like receptor 2 stimulation in human peripheral blood mononuclear cells of patients with atopic dermatitis. Biomed Res Int. 2020; 2020: 1497175. DOI:

23.Ricciardolo FLM., Bertolini F., Carriero V. The role of dupilumab in severe asthma. Biomedicines. 2021; 9 (9): 1096. DOI:

24.Kozlov V.A. Methylation of cellular DNA and pathology of the organism. Medical Immunology. 2008; 10 (4-5): 307–18. (in Russian)

25.Sobolev V., Bystritskaya E., Svitich O. Epigenetic studies of atopic dermatitis. In: atopic dermatitis – essential issues. Pereira C., ed. IntechOpen, 2021. DOI:

26.Han J., Park S. G., Bae J. B., Choi J., Lyu J. M., Park S. H., Kim H. S., Kim Y. J., Kim S., Kim T. Y. The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis. Biochem Biophys Res Commun. 2012; 422 (1): 157–63. DOI:

27.Rodríguez E., Baurecht H., Wahn A.F., Kretschmer A., Hotze M., Zeilinger S., Klopp N., Illig T., Schramm K., Prokisch H., Kühnel B., Gieger C., Harder J., Cifuentes L., Novak N., Weidinger S. An integrated epigenetic and transcriptomic analysis reveals distinct tissue-specific patterns of DNA methylation associated with atopic dermatitis. J Invest Dermatol. 2014; 134 (7): 1873–83. DOI:

28.Olisova O.Y., Kochergin N.G., Kayumova L.N., Zavary- kina T.M., Dmitriev A.A., Asanov A.Y. Skin DNA methylation profile in atopic dermatitis patients: A case-control study. Exp Dermatol. 2020; 29 (2): 184–9. DOI:

Musa R. Khaitov

Corresponding member of Russian Academy of Sciences, MD, Professor, Director of the NRC Institute of Immunology FMBA of Russia

Medicine today

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