SIRT1 Gene Polymorphisms and the Risk of Vitiligo: Molecular Association and in Silico Approach

Yıl 2023, , 1 - 8, 28.04.2023

Oktay Kuru , Nilgün Solak Tekin , Ümmühani Özel Türkcü , Sevim Karakaş Çelik , Tuba Edgünlü

https://doi.org/10.29058/mjwbs.1223300

Öz

Aim: The aim of our study is to analyze the SIRT1 gene rs2273773, rs7895833 and rs7069102
polymorphisms and the association of SIRT1 gene and interacting genes with vitiligo disease by
molecular and in silico methods.
Material and Methods: The study group consisted of 78 vitiligo patients and 85 unrelated healthy
controls. SIRT1 polymorphisms were determined using the Polymerase chain reaction confronting twopair
primers (PCR-CTPP) method. In addition, other genes with which the SIRT1 gene interacts and
gene ontology (GO) were determined using the GeneMANIA and GeneCodis 4 tools, respectively.
Results: We have determined a significant difference in genotypes of rs7895833 in SIRT1 gene.
Especially, the AG genotype was observed more in the group with vitiligo. It was determined that the
rs7895833 G allele had a protective effect in terms of vitiligo (p=0.001). Intergene interaction analysis
was also performed by in silico method, and it was shown that SIRT 1 is co-expressed with 16 genes
and shares an area with only 12 genes physically interacting with 19 genes. We showed gene ontology
and pathway analyzed with all relevant genes. It was determined that especially apoptosis and systemic
sclerosis were associated with these genes.
Conclusion: The SIRT1 rs7895833 SNP genotype and allele frequencies of vitiligo patients are
significantly different from healthy controls. Our study shows that the rs7895833 polymorphism of the
SIRT1 gene may be associated with vitiligo susceptibility. Considering the role of sirtuin and related
genes, especially in the apoptotic pathway, its effect on vitiligo can be further investigated to elucidate
the molecular aspect of the disease.

Anahtar Kelimeler

Gene polymorphism, In silico, SIRT1, Vitiligo

Destekleyen Kurum

Muğla Sıtkı Koçman Üniversitesi Bilimsel Araştırma Projeleri Birimi

Proje Numarası

13/114

Teşekkür

We thank to Çilem Özdemir for the support in performing the in silico analysis, interpretation of digital data for risk relation and for the contribution in structural design of the present manuscript. Çilem Özdemir'e in silico analizin yapılmasında, dijital verilerin risk ilişkisi için yorumlanmasında verdiği destek ve bu yazının yapısal tasarımına yaptığı katkı için teşekkür ederiz.

SIRT1 Gen Polimorfizmleri ve Vitiligo Riski İlişkisi: Moleküler ve “in Siliko” Yaklaşım

Öz

Amaç: Çalışmamızın amacı, SIRT1 geni rs2273773, rs7895833 ve rs7069102 polimorfizmlerinin ve
SIRT1 geni ile etkileşimli genlerin vitiligo hastalığı ile ilişkilisinin moleküler ve in silico yöntemler ile
analizini yapmaktır
Gereç ve Yöntemler: Çalışma grubu 78 vitiligo hastası ve 85 sağlıklı kontrol katılımcısını kapsamaktadır. SIRT1 polimorfizmleri, iki çift
primer (PCR-CTPP) yöntemiyle karşılıklı Polimeraz zincir reaksiyonu kullanılarak belirlendi. Ayrıca SIRT1 geninin etkileştiği diğer genler ve
gen ontolojisi (GO) sırasıyla GeneMANIA ve GeneCodis 4 araçları kullanılarak belirlendi.
Bulgular: SIRT1 geninde rs7895833 genotipinin analiz edilen gruplar arasında anlamlı bir farklılık gösterdiğini belirledik. Özellikle AG
genotipi vitiligolu grupta daha fazla gözlendi. rs7895833 G allellin vitiligo açısından koruyucu bir etki gösterdiği tespit edilmiştir (p=0.001). In
silico yöntemle genler arası etkileşim analizi de yapılarak SIRT 1'in 16 gen ile birlikte eksprese edildiğini ve 19 gen ile sadece 12 gen fiziksel
etkileşimi olan bir alanı paylaştığı gösterildi. İlgili tüm genlerle analiz edilen gen ontolojisini ve yolunu gösterdik. Özellikle apoptoz ve sistemik
sklerozun bu genlerle ilişkili olduğunu belirlendi.
Sonuç: Vitiligo hastalarının SIRT1 rs7895833 SNP genotipi ve allel frekansları, sağlıklı kontrollerden önemli ölçüde farklıdır. Çalışmamız,
SIRT1 geninin rs7895833 polimorfizmiyle vitiligo duyarlılığının ilişkili olabileceğini göstermektedir. Sirtuin ve ilgili genlerin özellikle apoptotik
yolaktaki görevleri göz önüne alındığında vitiligoya etkisi, hastalığın moleküler yönünü aydınlatmak için daha fazla araştırılabilir

Anahtar Kelimeler

Gen polimorfizmi, In silico, SIRT1, Vitiligo

Proje Numarası

13/114

Kaynakça

• 1. Turkcu UO, Tekin NS, Edgunlu TG, Karakas SÇ, Oner S. The association of FOXO3A gene polymorphisms with serum FOXO3A levels and oxidative stress markers in vitiligo patients. Gene 2014;536(1):129-134.
• 2. Bergqvist C, Ezzedine K. Vitiligo: A review. Dermatology 2020;236(6):571-592.
• 3. Çelik SK, Tekin NS, Genç GÇ, Edgünlü T, Türkcü ÜÖ, Dursun A. Investigation of genetic variations of IL17 for vitiligo disease. Kuwait Medical Journal 2019;51(3):283-289.
• 4. Kundu RV, Mhlaba JM, Rangel SM, Le Poole IC. The convergence theory for vitiligo: A reappraisal. Exp Dermatol 2019;28(6):647-655.
• 5. Kutlubay Z, Karakus O, Engin B, Serdaroglu S. Vitiligo as an autoimmune disease. J Turk Acad Dermatol 2012;6(2):1262.
• 6. Preyat N, Leo O. Sirtuin deacylases: A molecular link between metabolism and immunity. J Leukoc Biol 2013;93(5):669-680.
• 7. Vachharajani VT, Liu T, Wang X, Hoth JJ, Yoza BK, McCall CE. Sirtuins link inflammation and metabolism. J Immunol Res 2016;8167273.
• 8. Bordone L, Guarente L. Calorie restriction, SIRT1 and metabolism: Understanding longevity. Nat Rev Mol Cell Biol 2005;6(4):298-305.
• 9. Hirschey MD. Old enzymes, new tricks: Sirtuins are NAD+- dependent de-acylases. Cell Metab 2011;14(6):718-719.
• 10. Grimaldi B, Nakahata Y, Kaluzova M, Masubuchi S, Sassone- Corsi P. Chromatin remodeling, metabolism and circadian clocks: The interplay of CLOCK and SIRT1. Int J Biochem Cell Biol 2009;41(1):81-86.
• 11. Kauppinen A, Suuronen T, Ojala J, Kaarniranta K, Salminen A. Antagonistic crosstalk between NF-κB and SIRT1 in the regulation of inflammation and metabolic disorders. Cell Signal 2013;25(10):1939-1948.
• 12. Yang H, Bi Y, Xue L, Wang J, Lu Y, Zhang Z, Chen X, Chu Y, Yang R, Wang R, Liu G. Multifaceted modulation of SIRT1 in cancer and inflammation. Crit Rev Oncog 2015;20(1-2):49-64.
• 13. Jin Q, Yan T, Ge X, Sun C, Shi X, Zhai Q. Cytoplasm‐localized SIRT1 enhances apoptosis. J Cell Physiol 2007;213(1):88-97.
• 14. Xu C, Wang L, Fozouni P, Evjen G, Chandra V, Jiang J, Lu C, Nicastri M, Bretz C, Winkler JD, Amaravadi R, Garcia BA, Adams PD, Ott M, Tong W, Johansen T, Dou Z, Berger SL. SIRT1 is downregulated by autophagy in senescence and ageing. Nat Cell Biol 2020;22(10):1170-1179.
• 15. Bielach-Bazyluk A, Zbroch E, Mysliwiec H, Rydzewska- Rosolowska A, Kakareko K, Flisiak I, Hryszko T. Sirtuin 1 and skin: Implications in intrinsic and extrinsic aging-a systematic review. Cells 2021;10(4):813.
• 16. Tanno M, Sakamoto J, Miura T, Shimamoto K, Horio Y. Nucleocytoplasmic shuttling of the NAD+-dependent histone deacetylase SIRT1. J Biol Chem 2007;282(9):6823-6832.
• 17. Kwon HS, Ott M. The ups and downs of SIRT1. Trends Biochem Sci 2008;33(11):517-525.
• 18. Ulu İ, Çakmak Genç G, Karakaş Çelik S. Sirtuin 1 ve sirtuin 2’nin tip 2 diyabet ile ilişkisi. Turk J Diab Obes 2021;5(1):81-88.
• 19. Li X. SIRT1 and energy metabolism. Acta Biochim Biophys Sin 2013;45(1):51-60.
• 20. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q. The geneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 2010;38(Web Server issue):W214-220.
• 21. Gilani N, Belaghi RA, Aftabi Y, Faramarzi E, Edgünlü T, Somi MH. Identifying potential miRNA biomarkers for gastric cancer diagnosis using machine learning variable selection approach. Front Genet 2021;12:779455.
• 22. Benavente CA, Schnell SA, Jacobson EL. Effects of niacin restriction on sirtuin and PARP responses to photodamage in human skin. PLoS One 2012;7(7):e42276.
• 23. Becatti M, Fiorillo C, Barygina V, Cecchi C, Lotti T, Prignano F, Silvestro A, Nassi P, Taddei N. SIRT1 regulates MAPK pathways in vitiligo skin: Insight into the molecular pathways of cell survival. J Cell Mol Med 2014;18(3):514-529.
• 24. CaoCao C, Lu S, Kivlin R, Wallin B, Card E, Bagdasarian A, Tamakloe T, Wang WJ, Song X, Chu WM, Kouttab N, Xu A, Wan Y. SIRT1 confers protection against UVB- and H2O2- induced cell death via modulation of p53 and JNK in cultured skin keratinocytes. J Cell Mol Med 2009;13:3632-3643.
• 25. Lee JH, Moon JH, Nazim UM, Lee YJ, Seol JW, Eo SK, Lee JH, Park SY. Melatonin protects skin keratinocyte from hydrogen peroxide-mediated cell death via the SIRT1 pathway. Oncotarget 2016;7(11):12075-12088.
• 26. Becatti M, Barygina V, Emmi G, Silvestri E, Taddei N, Lotti T, Fiorillo C. SIRT1 activity is decreased in lesional psoriatic skin. Intern Emerg Med 2016;11(6):891-893.
• 27. Ming M, Zhao B, Shea CR, Shah P, Qiang L, White SR, Sims DM, He YY. Loss of sirtuin 1 (SIRT1) disrupts skin barrier integrity and sensitizes mice to epicutaneous allergen challenge. J Allergy Clin Immunol 2015;135(4):936-945.
• 28. Pektas SD, Dogan G, Edgunlu TG, Karakas-Celik S, Ermis E, Tekin NS. The role of forkhead box class O3A and SIRT1 gene variants in early-onset psoriasis. Indian J Dermatol 2018;63(3):208-214.
• 29. Arora AK, Kumaran MS. Pathogenesis of vitiligo: An update. Pigment international 2017;4(2):65-77.
• 30. Sahoo A, Lee B, Boniface K, Seneschal J, Sahoo SK, Seki T, Wang C, Das S, Han X, Steppie M, Seal S, Taieb A, Perera RJ. MicroRNA-211 regulates oxidative phosphorylation and energy metabolism in human vitiligo. J Invest Dermatol 2017;137(9):1965-1974.
• 31. Xie H, Zhou F, Liu L, Zhu G, Li Q, Li C, Gao T. Vitiligo: How do oxidative stress-induced autoantigens trigger autoimmunity? J Dermatol Sci 2016;81(1):3-9.
• 32. Seneschal J, Boniface K, D’Arino A, Picardo M. An update on vitiligo pathogenesis. Pigment Cell Melanoma Res 2021;34(2):236-243.
• 33. Yi X, Guo W, Shi Q, Yang Y, Zhang W, Chen X, Kang P, Chen J, Cui T, Ma J, Wang H, Guo S, Chang Y, Liu L, Jian Z, Wang L, Xiao Q, Li S, Gao T, Li C. SIRT3-dependent mitochondrial dynamics remodeling contributes to oxidative stress-induced melanocyte degeneration in vitiligo. Theranostics 2019;9(6):1614-1633.
• 34. Tsuj G, Okiyama N, Villarroel VA, Katz SI. Histone deacetylase 6 inhibition impairs effector CD8 T-cell functions during skin inflammation. J Allergy Clin Immunol 2015;135(5):1228-1239.
• 35. Salem MM, Shalbaf M, Gibbons NC, Chavan B, Thornton JM, Schallreuter KU. Enhanced DNA binding capacity on upregulated epidermal wild‐type p53 in vitiligo by H2O2‐mediated oxidation: A possible repair mechanism for DNA damage. FASEB J 2009;23(11):3790-3807.
• 36. Becatti M, Prignano F, Fiorillo C, Pescitelli L, Nassi P, Lotti T, Taddei N. The involvement of Smac/DIABLO, p53, NF-kB, and MAPK pathways in apoptosis of keratinocytes from perilesional vitiligo skin: Protective effects of curcumin and capsaicin. Antioxid Redox Signal 2010;13:1309-1321.