Volume 7, Issue 1, June 2019, Page: 5-10
Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach
Sevgi Kalkanli Tas, Department of Immunology, Faculty of Medicine, University of Health Sciences, Istanbul, Turkey
Eylem Cagiltay, Department of Endocrinology, Sultan Abdulhamid Han Training & Research Hospital, Istanbul, Turkey
Duygu Kirkik, Department of Medical Biology, Faculty of Medicine, University of Health Sciences, Istanbul Turkey
Nevin Kalkanli, Department of Dermatology, Ozel Diyarlife Hospital, Diyarbakir, Turkey
Received: Jun. 27, 2019;       Accepted: Jul. 17, 2019;       Published: Jul. 30, 2019
DOI: 10.11648/j.cbb.20190701.12      View  104      Downloads  29
Abstract
Tumor Necrosis Factor Ligand Superfamily Member4 (TNFSF4) has a huge family of physically homologous transmembrane proteins that regulate various functions in responding cells containing proliferation, differentiation, apoptosis, and inflammatory gene expression. TNFSF4 can play significant role in inflammatory diseases that its polymorphisms of the TNFSF4 gene are mostly related with Sjogren's syndrome, and systemic lupus erythematosus (SLE). The aim of this study is to investigate the genetic variations that may alter the expression, function and role of the TNFSF4 by using in silico methods. Single Nucleotide Polymorphisms (SNPs) on TNFSF4 are analyzed by GeneMania, SIFT, PolyPhen2, UTRscan programme, U.S. National Library of Medicine Database, ClinVar. 37 variants of TNFSF4 were found that among these 9 missense, 8 coding synonymous, 1 coding, 1 splice-3, 1 UTR-3, 11 intron, 5 UTR-5 variants. Moreover, two of them SNPs that these are rs199835957, rs372063551 were detected probably damaging by PolyPhen2 and they should be noted that vital candidates in causing diseases related to TNFSF4 and they were identified missense variants that weren’t reported in ClinVar. In the future, genes of TNFSF4, TNFSFR and CD40 may be studied on polymorphisms with experimental analysis in order to contribute to science by helping to identify disease pathogenesis.
Keywords
AITD, SLE, TNFSF4, Bioinformatics, in silico
To cite this article
Sevgi Kalkanli Tas, Eylem Cagiltay, Duygu Kirkik, Nevin Kalkanli, Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach, Computational Biology and Bioinformatics. Vol. 7, No. 1, 2019, pp. 5-10. doi: 10.11648/j.cbb.20190701.12
Copyright
Copyright © 2019 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Reference
[1]
Croft M. The Role of TNF Superfamily Members in T-cell Function and Diseases. Nat Rev Immunol. 9 (4): pp. 271-85.
[2]
Ward KL, Lin WW, Sedy JS, Ware CF. The TNF Receptor Superfamily in Costimulating and Coinhibitory Responses. Immunity. 44 (5): pp. 1005–1019. 2016.
[3]
Croft M. et al. TNF Superfamily in Inflammatory Disease: Translating Basic Insights. Trends Immunol. 33 (3): pp. 144-52. 2012.
[4]
Sonar S, Lal G. Role of Tumor Necrosis Factor Superfamily in Neuroinflammation and Autoimmunity. Front Immunol. 6: pp. 364. 2015.
[5]
Cheng J. et al. Association between TNFSF4 tagSNPs and Myocardial Infarction in a Chinese Han Population. Genet. Mol. Res. 14 (2): pp. 6136-6145. 2015.
[6]
Liu Y. et al. Genetic Risk of TNFSF4 and FAM167A-BLK Polymorphisms in Children with Asthma and Allergic Rhinitis in a Han Chinese Population. Journal of Asthma. 53 (6): pp. 567-575. 2016.
[7]
Lu S. et al. Association of TNFSF4 Polymorphisms with Vogt-Koyanagi-Harada and Behcet's Disease in Han Chinese. Sci Rep, 6. 2016.
[8]
Gupta V. et al. Association of ITGAM, TNFSF4, TNFAIP3 and STAT4 Gene Polymorphisms with Risk of Systemic Lupus Erythematosus in a North Indian Population. Lupus, 27 (12): pp. 1973-1979. 2018.
[9]
Brix TH, Hegedus L. Twin Studies as a Model for Exploring the Aetiology of Autoimmune Thyroid Disease. Clin Endocrinol (Oxf). pp. 76 (4): 457-64. 2012.
[10]
Hollowell JG. et. al. Serum TSH, T (4), and Thyroid Antibodies in the United States Population (1988 to 1994): National Health and Nutrition Examination Survey (NHANES III). J Clin Endocrinol Metab. 87 (2): 489-99. 2002.
[11]
Tomer Y. Mechanisms of Autoimmune Thyroid Diseases: from Genetics to Epigenetics, Annu. Rev. Pathol. 9 147e156. 2014.
[12]
Javinani A, Ganjouei AA, Aslani S, Jamshidi A, Mahmoudi M. Exploring the Etiopathogenesis of Systemic Lupus Erythematosus: a Genetic Perspective. Immunogenetics. 2019.
[13]
Rees F, Doherty M, Grainge MJ, Lanyon P, Zhang W, The Worldwide Incidence and Prevalence of Systemic Lupus Erythematosus: a Systematic Review of Epidemiological Studies. Rheumatology (Oxford) 56: 1945–1961. 2017.
[14]
Rajasekaran R. et al. Computational and Structural Investigation of Deleterious Functional SNPs in Breast Cancer BRCA2 Gene. Chinese Journal of Biotechnology. 24( 5): pp. 851-6. 2008.
[15]
Montojo J. et al. GeneMANIA: Fast Gene Network Construction and Function Prediction for Cytoscape. F1000Res. 3: pp. 153. 2014.
[16]
Ng PC, Henikoff S. Predicting Deleterious Amino acid Substitutions. Genome Res. 11 (5): p. 863-74. 2001.
[17]
Ng PC, Henikoff S. SIFT: Predicting Amino acid Changes that Affect Protein Function. Nucleic Acids Res. 31 (13): p. 3812-3814. 2003.
[18]
Ng PC, Henikoff S. Predicting the Effects of Amino acid Substitutions on Protein Function. Annual Review of Genomics and Human Genetics. 7: p. 61-80. 2006.
[19]
Richard AC. et al. Targeted Genomic Analysis Reveals Widespread Autoimmune Disease Association with Regulatory Variants in the TNF Superfamily Cytokine Signalling Network. Genome Med. 2016.
[20]
Serin EAR. et al. Learning from Co-expression Networks: Possibilities and Challenges. Frontiers in Plant Science, 2016.
[21]
Zhu LJ. et al. Altered Expression of TNF-alpha Signaling Pathway Proteins in Systemic Lupus Erythematosus. Journal of Rheumatology. 37 (8): p. 1658-1666. 2010.
[22]
Weinberger P. et al. Cell Cycle M-Phase Genes Are Highly Upregulated in Anaplastic Thyroid Carcinoma. Thyroid. 27 (2): p. 236-252. 2017.
[23]
Leonardi A. et al. Endoplasmic Reticulum Stress Causes Thyroglobulin Retention in This Organelle and Triggers Activation of Nuclear Factor-kappa B via Tumor Necrosis Factor Receptor-associated factor 2. Endocrinology. 143 (6): p. 2169-2177. 2002.
[24]
Wigren M. et al. Cardiovascular Disease in Systemic Lupus Erythematosus is Associated with Increased Levels of Biomarkers Reflecting Receptor-activated Apoptosis. Atherosclerosis. 270: p. 1-7. 2018.
[25]
Kutukculer N. et al. CD4+CD25+Foxp3+ T regulatory cells, Th1 (CCR5, IL-2, IFN-gamma) and Th2 (CCR4, IL-4, Il-13) Type Chemokine Receptors and Intracellular Cytokines in Children with Common Variable Immunodeficiency. Int J Immunopathol Pharmacol. 29 (2): p. 241-51. 2016.
Browse journals by subject