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Biyoinformatik yöntemler yardımıyla, CD40 polimorfizmlerinin tespiti ve olası hastalıklarla ilişkinin araştırılması

Year 2020, Volume 1, Issue 4, 83 - 92, 18.12.2020
https://doi.org/10.47582/jompac.769064

Abstract

Giriş: Cluster of differentiation 40 olgun B hücreleri, monositler, dendritik hücreler ve sinyal iletimi ile ilgili epitel hücrelerde bulunan ve hücre aktivasyonuna, çoğalmasına, yapışmasına veya farklılaşmasına yol açan tip I transmembran proteinidir ve cluster of differentiation 40; B hücreli kronik lenfositik lösemiler, lenfomalar ve bazı karsinomlarda eksprese edilir. Bu çalışmada amaç; cluster of differentiation 40’ın biyoinformatik yöntemler yardımıyla tek nükleotid değişimlerinin bulunması ve olası hastalıklarla ilişkilerinin araştırılmasıdır. Gereç ve Yöntem: Çalışmamızda; cluster of differentiation 40’ın olası genlerle ilişkisini araştırmak için GeneMANIA, benzer fonksiyona sahip muhtemel ilişkili dizileri seçmek için SIFT, popülasyonlara özel değişikleri analiz etmek ve şüpheli tek nükleotid değişimlerinin tespiti için Exome Variant Server, 3’UTR tek nükleotid değişimlerinin miRNA bağlanması üzerindeki etkisini tahmin etmek için mr tek nükleotid değişimlerinin Software, tek nükleotid değişimlerde untranslated bölgelerin analizi için UTRscan, proteindeki potansiyel ubikuitinasyon bölgesinin tahmini için UbPred ve protein domainin fonksiyonel karakterizasyonunu tanımlamak için Prosite kullanıldı. Bulgular: Çalışmamızda farklılaşma 40 geni kümesi için toplam 85 adet tek nükleotid polimorfizmi ve rs147677886, rs11569321, rs7273698, rs11086998 ve rs139300926 şüpheli tek nükleotid polimorfizmleri olarak tespit edildi. Ayrıca, bu tek nükleotid polimorfizmleri multipl skleroz (MS), romatoid artrit (RA) ve Kawasaki hastalığı ile bağlantılı olabilir. Sonuç: Biyoinformatik yöntemlerle tespit ettiğimiz 40 farklılaşma gen kümesinin tek nükleotid polimorfizmleri ile ilgili literatürde şu anda herhangi bir çalışma bulunmamaktadır. Gelecekte bu çalışmayı laboratuvarda deneysel olarak değerlendirmeyi ve popülasyona özel çalışmalara katkı sağlamayı hedefliyoruz.

References

  • Kooten C, Banchereau J. Functions of CD40 on B cells, dendritic cells and other cells. Curr Opin Immunol 1997; 9: 3: 330-7
  • Kawabe T, Matsushima M, Hashimoto N, et al. CD40/CD40 ligand interactions in immune responses and pulmonary immunity. Nagoya J MedSci 2011; 73: 3: 69-8.
  • Elgueta R, Micah J. Benson, et al. Molecular mechanism and function of CD40/CD40L engagement in the immune system. Immunol Rev 2009; 229: 1.
  • Davies C, Mak W, Young S, et al. TRAF6 Is Required for TRAF2-Dependent CD40 signal transduction in nonhemopoietic cells. Mol Cell Biol 2005; 25: 22: 9806-19.
  • Ghezala A, Frieling J, Paris D, et al. CD40 promotion of amyloid beta production occurs via the NF-kappaB pathway. Eur J Neurosci 2007;25: 6: 1685-95.
  • Charles AJ, Travers P, Walport M, et al. Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001. ISBN-10: 0-8153-3642-X.
  • Kawabe T, Naka T, Yoshida K, et al. The immune responses in CD40-deficient mice:impaired immunoglobulin classs witching and germinal center formation. Immunity 1994; 1: 3: 167-8.
  • Chatzigeorgiou A, Lyberi M, Chatzilymperis G, et al. CD40/CD40L signaling and its implication in health and disease”. Biofactors 2009; 35: 6: 474-3.
  • Carlring J, Altaher HM, Clark S, et al. CD154-CD40 interactions in the control of murine B cell hematopoiesis. J Leukoc Biol 2011; 89: 5: 697-06.
  • Zhang SQ, Han JW, Sun LD, et al. A single-nucleotide polymorphism of the TNFSF4 gene is associated with systemic lupus erythematosus in Chinese Han Population. Rheumatol Int 2011; 31: 227-31.
  • Zhu Y, Wang J, Feng X. CTLA-4 SNPs (CT60A/G, -1722T/C, -1661G/A, and -318C/T) and systemic lupus erythematosus: a meta-analysis. Crit Rev Eukaryot Gene Expr 2014; 24: 89-100.
  • Orozco G, Eyre S, Hinks A, et al. Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study. Ann Rheum Dis 2010; 69: 813-16.
  • Raychaudhuri S, Remmers EF, Lee AT, et al. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet 2008; 40: 1216-23.
  • Burdon KP, Langefeld CD, Beck SR, et al. Variants of the CD40 gene but not of the cd40l gene are associated with coronary artery calcification in the diabetes heart study (DHS). Am Heart J 2006; 151: 706-11.
  • Chen F, Hou S, Jiang Z, et al. CD40 polymorphisms in han chinese patients with fuch uveitis syndrome. Mol Vis 2011; 17: 2469-72
  • Yan JC, Ma GS, Wu ZG et al. ıncreased levels of CD40-CD40 ligand system in patients with essential hypertension. Clin Chim Acta 2005; 355: 191-6.
  • Li M, Sun H, Liu S, et al. CD40 C/T-1 polymorphism plays different roles in graves’ disease and hashimoto’s thyroiditis: a meta-analysis. Endocr J 2012; 59: 1041-50.
  • Zhang B, Wu T, Song C, et al. Association of CD40–1C/T polymorphism with cerebral ınfarction susceptibility and its effect on CD40L in chinese population. Int Immuno pharmacol 2013; 16: 461-5.
  • Büküm E, Düzgün A, Karkucak M, et al. Mide kanserli hastalarda siklin D1 (G870A) gen polimorfizminin araştırılması. Konuralp Tıp Derg 2013; 5: 1: 18-2.
  • Li B, Krishnan VG, Mort ME, et al. Automated inference of molecular mechanisms of disease from amino acid substitutions. 2009; 25: 21: 2744-0.
  • Radivojac, P, Vacic V, Haynes C, et al. Identification analysis and prediction of protein ubiquitination sites. Proteins. 2010; 78: 2: 365-80.

Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods

Year 2020, Volume 1, Issue 4, 83 - 92, 18.12.2020
https://doi.org/10.47582/jompac.769064

Abstract

Introduction: Cluster of differentiation 40 is a type I transmembrane protein present on B cells, macrophages, dendritic cells, and endothelial cells, which leads to cell activation, proliferation, adhesion or differentiation. Previous studies have been shown that cluster of differentiation 40 polymorphisms have an effect on some autoimmune diseases. The purpose of this study is to investigate all single nucleotide polymorphisms found on cluster of differentiation 40 gene and their relationship with possible diseases by bioinformatics methods. Material and Method: In our study, while GeneMANIA was used to investigate the relationship between cluster of differentiation 40 gene with other genes, SIFT was employed to select sequences with similar functions as cluster of differentiation 40 gene. Exome cariant server was used for the detection of changes between populations and suspected single nucleotide polymorphisms. Mr single nucleotide polymorphisms Software was used to predict the effect of binding of 3’untranslated regions single nucleotide polymorphisms to miRNA. In order to analyze the untranslated regions on single nucleotide polymorphisms, UTRscan tool was used. UbPred was used for the estimation of the potential ubiquitination site on proteins, and Prosite was used to define the functional characterization of the protein domain. Results: In our study, a total of 85 single nucleotide polymorphisms were found for cluster of differentiation 40 gene, and rs147677886, rs11569321, rs7273698, rs11086998, and rs139300926 were detected as suspected single nucleotide polymorphisms. Moreover, these single nucleotide polymorphisms may be associated with multiple sclerosis (MS), rheumatoid arthritis (RA), and Kawasaki disease. Conclusion: Currently, there are no studies in the literature about single nucleotide polymorphisms of cluster of differentiation 40 gene that we detected by bioinformatics methods. In the future, we aim to evaluate this study experimentally in the laboratory and contribute to population-specific studies.

References

  • Kooten C, Banchereau J. Functions of CD40 on B cells, dendritic cells and other cells. Curr Opin Immunol 1997; 9: 3: 330-7
  • Kawabe T, Matsushima M, Hashimoto N, et al. CD40/CD40 ligand interactions in immune responses and pulmonary immunity. Nagoya J MedSci 2011; 73: 3: 69-8.
  • Elgueta R, Micah J. Benson, et al. Molecular mechanism and function of CD40/CD40L engagement in the immune system. Immunol Rev 2009; 229: 1.
  • Davies C, Mak W, Young S, et al. TRAF6 Is Required for TRAF2-Dependent CD40 signal transduction in nonhemopoietic cells. Mol Cell Biol 2005; 25: 22: 9806-19.
  • Ghezala A, Frieling J, Paris D, et al. CD40 promotion of amyloid beta production occurs via the NF-kappaB pathway. Eur J Neurosci 2007;25: 6: 1685-95.
  • Charles AJ, Travers P, Walport M, et al. Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001. ISBN-10: 0-8153-3642-X.
  • Kawabe T, Naka T, Yoshida K, et al. The immune responses in CD40-deficient mice:impaired immunoglobulin classs witching and germinal center formation. Immunity 1994; 1: 3: 167-8.
  • Chatzigeorgiou A, Lyberi M, Chatzilymperis G, et al. CD40/CD40L signaling and its implication in health and disease”. Biofactors 2009; 35: 6: 474-3.
  • Carlring J, Altaher HM, Clark S, et al. CD154-CD40 interactions in the control of murine B cell hematopoiesis. J Leukoc Biol 2011; 89: 5: 697-06.
  • Zhang SQ, Han JW, Sun LD, et al. A single-nucleotide polymorphism of the TNFSF4 gene is associated with systemic lupus erythematosus in Chinese Han Population. Rheumatol Int 2011; 31: 227-31.
  • Zhu Y, Wang J, Feng X. CTLA-4 SNPs (CT60A/G, -1722T/C, -1661G/A, and -318C/T) and systemic lupus erythematosus: a meta-analysis. Crit Rev Eukaryot Gene Expr 2014; 24: 89-100.
  • Orozco G, Eyre S, Hinks A, et al. Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study. Ann Rheum Dis 2010; 69: 813-16.
  • Raychaudhuri S, Remmers EF, Lee AT, et al. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet 2008; 40: 1216-23.
  • Burdon KP, Langefeld CD, Beck SR, et al. Variants of the CD40 gene but not of the cd40l gene are associated with coronary artery calcification in the diabetes heart study (DHS). Am Heart J 2006; 151: 706-11.
  • Chen F, Hou S, Jiang Z, et al. CD40 polymorphisms in han chinese patients with fuch uveitis syndrome. Mol Vis 2011; 17: 2469-72
  • Yan JC, Ma GS, Wu ZG et al. ıncreased levels of CD40-CD40 ligand system in patients with essential hypertension. Clin Chim Acta 2005; 355: 191-6.
  • Li M, Sun H, Liu S, et al. CD40 C/T-1 polymorphism plays different roles in graves’ disease and hashimoto’s thyroiditis: a meta-analysis. Endocr J 2012; 59: 1041-50.
  • Zhang B, Wu T, Song C, et al. Association of CD40–1C/T polymorphism with cerebral ınfarction susceptibility and its effect on CD40L in chinese population. Int Immuno pharmacol 2013; 16: 461-5.
  • Büküm E, Düzgün A, Karkucak M, et al. Mide kanserli hastalarda siklin D1 (G870A) gen polimorfizminin araştırılması. Konuralp Tıp Derg 2013; 5: 1: 18-2.
  • Li B, Krishnan VG, Mort ME, et al. Automated inference of molecular mechanisms of disease from amino acid substitutions. 2009; 25: 21: 2744-0.
  • Radivojac, P, Vacic V, Haynes C, et al. Identification analysis and prediction of protein ubiquitination sites. Proteins. 2010; 78: 2: 365-80.

Details

Primary Language English
Subjects Health Care Sciences and Services
Journal Section Research Articles [en] Araştırma Makaleleri [tr]
Authors

Duygu KIRKIK> (Primary Author)
University of Health Sciences
0000-0003-1417-6915
Türkiye


Faruk Berat AKÇEŞME>
UNIVERSITY OF HEALTH SCIENCES
0000-0002-6285-8577
Türkiye


Sevgi KALKANLI>
UNIVERSITY OF HEALTH SCIENCES
Türkiye

Publication Date December 18, 2020
Published in Issue Year 2020, Volume 1, Issue 4

Cite

Bibtex @research article { jompac769064, journal = {Journal of Medicine and Palliative Care}, eissn = {2717-7505}, address = {Kırıkkale Üniversitesi Tıp Fakültesi, İç Hastalıkları Anabilim Dalı}, publisher = {MediHealth Academy Yayıncılık}, year = {2020}, volume = {1}, number = {4}, pages = {83 - 92}, doi = {10.47582/jompac.769064}, title = {Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods}, key = {cite}, author = {Kırkık, Duygu and Akçeşme, Faruk Berat and Kalkanlı, Sevgi} }
APA Kırkık, D. , Akçeşme, F. B. & Kalkanlı, S. (2020). Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods . Journal of Medicine and Palliative Care , 1 (4) , 83-92 . DOI: 10.47582/jompac.769064
MLA Kırkık, D. , Akçeşme, F. B. , Kalkanlı, S. "Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods" . Journal of Medicine and Palliative Care 1 (2020 ): 83-92 <https://dergipark.org.tr/en/pub/jompac/issue/58401/769064>
Chicago Kırkık, D. , Akçeşme, F. B. , Kalkanlı, S. "Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods". Journal of Medicine and Palliative Care 1 (2020 ): 83-92
RIS TY - JOUR T1 - Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods AU - DuyguKırkık, Faruk BeratAkçeşme, SevgiKalkanlı Y1 - 2020 PY - 2020 N1 - doi: 10.47582/jompac.769064 DO - 10.47582/jompac.769064 T2 - Journal of Medicine and Palliative Care JF - Journal JO - JOR SP - 83 EP - 92 VL - 1 IS - 4 SN - -2717-7505 M3 - doi: 10.47582/jompac.769064 UR - https://doi.org/10.47582/jompac.769064 Y2 - 2020 ER -
EndNote %0 Journal of Medicine and Palliative Care Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods %A Duygu Kırkık , Faruk Berat Akçeşme , Sevgi Kalkanlı %T Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods %D 2020 %J Journal of Medicine and Palliative Care %P -2717-7505 %V 1 %N 4 %R doi: 10.47582/jompac.769064 %U 10.47582/jompac.769064
ISNAD Kırkık, Duygu , Akçeşme, Faruk Berat , Kalkanlı, Sevgi . "Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods". Journal of Medicine and Palliative Care 1 / 4 (December 2020): 83-92 . https://doi.org/10.47582/jompac.769064
AMA Kırkık D. , Akçeşme F. B. , Kalkanlı S. Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods. J Med Palliat Care / JOMPAC / jompac. 2020; 1(4): 83-92.
Vancouver Kırkık D. , Akçeşme F. B. , Kalkanlı S. Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods. Journal of Medicine and Palliative Care. 2020; 1(4): 83-92.
IEEE D. Kırkık , F. B. Akçeşme and S. Kalkanlı , "Detection of CD40 polymorphisms and investigation of their relationship with possible diseases by bioinformatics methods", Journal of Medicine and Palliative Care, vol. 1, no. 4, pp. 83-92, Dec. 2020, doi:10.47582/jompac.769064




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