Association of Cytotoxic T-Lymphocyte Antigen-4 Gene Polymorphism with Type 1 Diabetes Mellitus: In silico Analysis of Biological Features of CTLA-4 Protein on Ethiopian Population

References

• Giacco F, Brownlee M, Holt RI, Cockram C, Flyvbjerg A, Goldstein BJ. Textbook of Diabetes. Wiley; 2010.
   Google Scholar
• Worede A, Alemu S, Gelaw YA, Abebe M. The prevalence of impaired fasting glucose and undiagnosed diabetes mellitus and associated risk factors among adults living in a rural Koladiba town, northwest Ethiopia. BMC Res Notes. 2017;10(1):251. doi:10.1186/s13104-017-2571-3
   PubMed Web of Science ®Google Scholar
• Guja C, Marshall S, Welsh K, et al. The study of CTLA-4 and vitamin D receptor polymorphisms in the Romanian type 1 diabetes population. J Cellular Mol Med. 2002;6(1):75–81. doi:10.1111/j.1582-4934.2002.tb00312.x
   Web of Science ®Google Scholar
• Tesfaye T, Shikur B, Shimels T, Firdu N. Prevalence and factors associated with diabetes mellitus and impaired fasting glucose level among members of federal police commission residing in Addis Ababa, Ethiopia. BMC Endocr Disord. 2016;16(1):68. doi:10.1186/s12902-016-0150-6
   PubMed Web of Science ®Google Scholar
• Kanazawa Y, Motohashi Y, Yamada S, et al. Frequency of CTLA-4 gene CT60 polymorphism may not be affected by vitamin D receptor gene Bsm I polymorphism or HLA DR9 in autoimmune-related type 1 diabetes in the Japanese. Ann N Y Acad Sci. 2006;1079(1):251–256. doi:10.1196/annals.1375.038
   Web of Science ®Google Scholar
• Bouqbis L, Izaabel H, Akhayat O, et al. Association of the CTLA4 promoter region (− 1661G allele) with type 1 diabetes in the South Moroccan population. Genes Immun. 2003;4(2):132. doi:10.1038/sj.gene.6363933
   PubMed Web of Science ®Google Scholar
• Bilous R, Donnelly R. Handbook of Diabetes. John Wiley & Sons; 2010.
   Google Scholar
• White PT. HANDBOOK OF DIABETES. Br J Gen Pract. 1993;43(373):355.
   Google Scholar
• Powers MA. Handbook of Diabetes Nutritional Management. Aspen Publishers; 1987.
   Google Scholar
• Ann Kelly M, Rees SD, Barnett AH, Bain SC. Molecular genetics of type 1 diabetes. In: DeFronzo RA, Ferrannini E, Zimmet P, Alberti KG, editors. International Textbook of Diabetes Mellitus. Chichester, UK: John Wiley & Sons, Ltd; 2015:454–466.
   Google Scholar
• Haller K, Kisand K, Nemvalts V, Laine AP, Ilonen J, Uibo R. Type 1 diabetes is insulin −2221 MspI and CTLA-4 +49 A/G polymorphism dependent. Eur J Clin Invest. 2004;34(8):543–548. doi:10.1111/j.1365-2362.2004.01385.x
   Web of Science ®Google Scholar
• Barani M, Sargazi S, Mohammadzadeh V, et al. Theranostic advances of bionanomaterials against gestational diabetes mellitus: a preliminary review. JFB. 2021;12(4):54. doi:10.3390/jfb12040054
   Web of Science ®Google Scholar
• Hossain MS, Roy AS, Islam MS. In silico analysis predicting effects of deleterious SNPs of human RASSF5 gene on its structure and functions. Sci Rep. 2020;10(1):14542. doi:10.1038/s41598-020-71457-1
   PubMed Web of Science ®Google Scholar
• Ide A, Kawasaki E, Abiru N, et al. Association between IL-18 gene promoter polymorphisms and CTLA-4 gene 49A/G polymorphism in Japanese patients with type 1 diabetes. J Autoimmun. 2004;22(1):73–78. doi:10.1016/j.jaut.2003.10.001
   PubMed Web of Science ®Google Scholar
• Fajardy I, Vambergue A, Stuckens C, Weill J, Danze PM, Fontaine P. CTLA-4 49 A/G dimorphism and type 1 diabetes susceptibility: a French case-control study and segregation analysis. Evidence of a maternal effect: CTLA-4 dimorphism and type 1 diabetes. Eur J Immunol. 2002;29(3):251–257. doi:10.1046/j.1365-2370.2002.00309.x
   Web of Science ®Google Scholar
• Teft WA, Kirchhof MG, Madrenas J. A molecular perspective of CTLA-4 FUNCTION. Annu Rev Immunol. 2006;24(1):65–97. doi:10.1146/annurev.immunol.24.021605.090535
   PubMed Web of Science ®Google Scholar
• Jonson C-O, Lernmark Å, Ludvigsson J, Rutledge EA, Hinkkanen A, Faresjö M. The importance of CTLA-4 polymorphism and human leukocyte antigen genotype for the induction of diabetes-associated cytokine response in healthy school children. Pediatr Diabetes. 2007;8(4):185–192. doi:10.1111/j.1399-5448.2007.00245.x
   Web of Science ®Google Scholar
• Khan MY, Riaz R, Malik SA, Ali M, Afzal MS. Association of CTLA-4 polymorphisms and autoimmune type-1 diabetes mellitus susceptibility in Pakistani population. Turkish J Biochem. 2018;43(2):173–175. doi:10.1515/tjb-2017-0079
   Google Scholar
• Ahmed NS. CTLA4 gene polymorphisms associated with insulin dependent diabetes mellitus (IDDM) type I in Iraqi population. Iraqi J Cancer Med Genet. 2018;5(2):1–4.
   Google Scholar
• Alam S, Sayem M, Hasan MK, Sharmin Z, Pavel MA, Hossain MF. Prediction of deleterious single nucleotide polymorphisms in human p53 gene. Preprint. Bioinformatics. 2018. doi:10.1101/408476
   Google Scholar
• Hassan MM, Omer SE, Khalf-allah RM, Mustafa RY, Ali IS, Mohamed SB. Bioinformatics approach for prediction of functional coding/noncoding simple polymorphisms (SNPs/Indels) in human BRAF gene. Adv Bioinformatics. 2016;2016:1–15. doi:10.1155/2016/2632917
   Google Scholar
• Tavares NA, Santos MMS, Moura R, et al. Association of TNF-α, CTLA4, and PTPN22 polymorphisms with type 1 diabetes and other autoimmune diseases in Brazil. Genet Mol Res. 2015;14(4):18936–18944. doi:10.4238/2015.December.28.42
   Web of Science ®Google Scholar
• Mosaad YM, Elsharkawy AA, El-Deek BS. Association of CTLA-4 (+49A/G) gene polymorphism with type 1 diabetes mellitus in Egyptian children. Immunol Invest. 2012;41(1):28–37. doi:10.3109/08820139.2011.579215
   Web of Science ®Google Scholar
• World Health Organizations. Global Burden of Diabetes. World Health Organizations. 2021.
   Google Scholar
• Wolde HF, Derso T, Biks GA, et al. High hidden burden of diabetes mellitus among adults aged 18 years and above in urban northwest Ethiopia. J Diabetes Res. 2020;2020:1–9. doi:10.1155/2020/9240398
   Web of Science ®Google Scholar
• Silver B, Ramaiya K, Andrew SB, et al. EADSG guidelines: insulin therapy in diabetes. Diabetes Ther. 2018;9(2):449–492. doi:10.1007/s13300-018-0384-6
   PubMed Web of Science ®Google Scholar
• Wondemagegn AT, Bizuayehu HM, Abie DD, Ayalneh GM, Tiruye TY, Tessema MT. Undiagnosed diabetes mellitus and related factors in East Gojjam (NW Ethiopia) in 2016: a community-based study. J Public Health Res. 2017;6(1). doi:10.4081/jphr.2017.834
   Web of Science ®Google Scholar
• Sahile AT, Bekele GE. Prevalence of diabetes mellitus and associated factors in Addis Ababa public health facilities, Addis Ababa, Ethiopia, 2016. Diabetes Metab Syndr Obes. 2020;13:501–508. doi:10.2147/DMSO.S237995
   PubMed Web of Science ®Google Scholar
• Balcha SA, Phillips DIW, Trimble ER. Type 1 diabetes in a resource-poor setting: malnutrition related, malnutrition modified, or just diabetes? Curr Diab Rep. 2018;18(7):47. doi:10.1007/s11892-018-1003-7
   PubMed Web of Science ®Google Scholar
• Habtewold TD, Tsega WD, Wale BY. Diabetes mellitus in outpatients in Debre Berhan Referral Hospital, Ethiopia. J Diabetes Res. 2016;2016:1–6. doi:10.1155/2016/3571368
   Web of Science ®Google Scholar
• Tsega G, Getaneh G, Taddesse G, Alam K. Are Ethiopian diabetic patients protected from financial hardship? PLoS One. 2021;16(1):e0245839. doi:10.1371/journal.pone.0245839
   PubMed Web of Science ®Google Scholar
• Nisticò L, Buzzetti R, Pritchard LE, et al. The CTLA-4 gene region of chromosome 2q33 is linked to, and associated with, type 1 diabetes. Hum Mol Genet. 1996;5(7):1075–1080. doi:10.1093/hmg/5.7.1075
   PubMed Web of Science ®Google Scholar
• CSA. Summary and Statistical Report of the 2007 Population and Housing Census Addis Ababa, Ethiopia. Population and Housing Census Commission. 2008:57–60.
   Google Scholar
• World Health Organization. Global Report on Diabetes. Geneva: World Health Organization; 2016.
   Google Scholar
• García-Alegría AM, Anduro-Corona I, Pérez-Martínez CJ, Guadalupe Corella-Madueño MA, Rascón-Durán ML, Astiazaran-Garcia H. Quantification of DNA through the NanoDrop spectrophotometer: methodological validation using standard reference material and Sprague Dawley rat and human DNA. Int J Anal Chem. 2020;2020:1–9. doi:10.1155/2020/8896738
   Web of Science ®Google Scholar
• Choura M, Rebaï A. Applications of computational tools to predict functional SNPs effects in human ErbB genes. J Recept Signal Transduct. 2009;29(5):286–291. doi:10.1080/10799890902911948
   PubMed Web of Science ®Google Scholar
• Arshad M, Bhatti A, John P, Zhang Y. Identification and in silico analysis of functional SNPs of human TAGAP protein: a comprehensive study. PLoS One. 2018;13(1):e0188143. doi:10.1371/journal.pone.0188143
   PubMed Web of Science ®Google Scholar
• Mah JTL, Low ESH, Lee E. In silico SNP analysis and bioinformatics tools: a review of the state of the art to aid drug discovery. Drug Discov Today. 2011;16(17–18):800–809. doi:10.1016/j.drudis.2011.07.005
   Web of Science ®Google Scholar
• Capriotti E, Fariselli P. PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. Nucl Acids Res. 2017;45(W1):W247–W52. doi:10.1093/nar/gkx369
   PubMed Web of Science ®Google Scholar
• Capriotti E, Calabrese R, Fariselli P, Martelli P, Altman RB, Casadio R. WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genom. 2013;14(Suppl 3):S6. doi:10.1186/1471-2164-14-S3-S6
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Zhang M, Huang C, Wang Z, Lv H, Li X. In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract. BMC Mol and Cell Biol. 2020;21(1):12. doi:10.1186/s12860-020-00252-7
   PubMed Web of Science ®Google Scholar
• Pejaver V, Urresti J, Lugo-Martinez J, et al. MutPred2: inferring the molecular and phenotypic impact of amino acid variants. preprint. Bioinformatics. 2017. doi:10.1093/bioinformatics/btx272
   Web of Science ®Google Scholar
• Kalia N, Sharma A, Kaur M, Kamboj SS, Singh J. A comprehensive in silico analysis of non-synonymous and regulatory SNPs of human MBL2 gene. SpringerPlus. 2016;5(1):811. doi:10.1186/s40064-016-2543-4
   PubMedGoogle Scholar
• Saeed NA, Hamzah IH, Ali ANM, Abuderman AA. Prediction of single nucleotide polymorphisms (SNPs) in apolipoprotein E gene and their possible associations with a deleterious effect on the structure and functional properties: an in silico approach. Netw Model Anal Health Inform Bioinform. 2018;7(1):16. doi:10.1007/s13721-018-0178-9
   Web of Science ®Google Scholar
• Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10(6):845–858. doi:10.1038/nprot.2015.053
   PubMed Web of Science ®Google Scholar
• Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinform. 2008;9(1):40. doi:10.1186/1471-2105-9-40
   PubMed Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinform. 2010;11(1):548. doi:10.1186/1471-2105-11-548
   PubMed Web of Science ®Google Scholar
• Berezin C, Glaser F, Rosenberg J; Berezin CeaC. The identification of functionally and structurally important residues in protein sequences. Bioinformatics. 2004;20:1322–1324. doi:10.1093/bioinformatics/bth070
   PubMed Web of Science ®Google Scholar
• Dallakyan S, Olson AJ. Small-molecule library screening by docking with PyRx. Methods Mol Biol. 2015;1263:243–250.
   PubMedGoogle Scholar
• Fatih Ç, Doğa T, Deniz Ö, Sema A, Olcay Y. CTLA-4 (+49A/G) polymorphism and type-1 diabetes in Turkish children. J Clin Res Pediatr Endocrinol. 2013;5(1):40–43. doi:10.4274/Jcrpe.879
   Web of Science ®Google Scholar
• Osei-Hyiaman D, Hou L, Zhiyin R, et al. Association of a novel point mutation (C159G) of the CTLA4 gene with type 1 diabetes in West Africans but not in Chinese. Diabetes. 2001;50(9):2169–2171. doi:10.2337/diabetes.50.9.2169
   Web of Science ®Google Scholar
• Philip B, Isabel W. Association of cytotoxic T lymphocyte-associated antigen 4 gene single nucleotide polymorphism with type 1 diabetes mellitus in Madurai population of Southern India. Indian J Hum Genet. 2011;17(2):85. doi:10.4103/0971-6866.86189
   Google Scholar
• Van der Auwera BJ, Vandewalle CL, Schuit FC, et al. CTLA‐4 gene polymorphism confers susceptibility to insulin‐dependent diabetes mellitus (IDDM) independently from age and from other genetic or immune disease markers. Clin Exp Immunol. 1997;110(1):98–103. doi:10.1111/j.1365-2249.1997.t01-1-512-ce1410.x
   Web of Science ®Google Scholar
• Bobby Koeleman HMS. Association of CTLA-4 polymorphisms with type 1 diabetes in the Egyptian Population. J Diabetes Metab. 2013;04(07). doi:10.4172/2155-6156.1000291
   Google Scholar
• Jin P, Xiang B, Huang G, Zhou Z. The association of cytotoxic T-lymphocyte antigen-4+ 49A/G and CT60 polymorphisms with type 1 diabetes and latent autoimmune diabetes in Chinese adults. J Endocrinol Invest. 2015;38(2):149–154. doi:10.1007/s40618-014-0162-x
   Web of Science ®Google Scholar
• Fajardy I, Vambergue A, Stuckens C, Weill J, Danze PM, Fontaine P. CTLA‐4 49 A/G dimorphism and type 1 diabetes susceptibility: a French case–control study and segregation analysis. Evidence of a maternal effect. Eur J Immunol. 2002;29(3):251–257.
   Web of Science ®Google Scholar
• Cosentino A, Gambelunghe G, Tortoioli C, Falorni A. CTLA-4 gene polymorphism contributes to the genetic risk for latent autoimmune diabetes in adults. Ann N Y Acad Sci. 2006;958(1):337–340. doi:10.1111/j.1749-6632.2002.tb03000.x
   Google Scholar
• Benmansour J, Stayoussef M, Al-Jenaidi FA, et al. Association of single nucleotide polymorphisms in cytotoxic T-lymphocyte antigen 4 and susceptibility to autoimmune type 1 diabetes in tunisians. CVI. 2010;17(9):1473–1477. doi:10.1128/CVI.00099-10
   Web of Science ®Google Scholar
• Padma-Malini R, Rathika C, Ramgopal S, et al. Associations of CTLA4 +49 A/G dimorphism and HLA-DRB1*/DQB1* alleles with type 1 diabetes from South India. Biochem Genet. 2018;56(5):489–505. doi:10.1007/s10528-018-9856-7
   Web of Science ®Google Scholar
• Balic I, Angel B, Codner E, Carrasco E, Pérez-Bravo F. Association of CTLA-4 polymorphisms and clinical-immunologic characteristics at onset of type 1 diabetes mellitus in children. Hum Immunol. 2009;70(2):116–120. doi:10.1016/j.humimm.2008.12.007
   Web of Science ®Google Scholar
• Kamel AM, Mira MF, Mossallam GI, et al. Lack of association of CTLA-4 +49 A/G polymorphism with predisposition to type 1 diabetes in a cohort of Egyptian families. Egypt J Med Hum Genet. 2014;15(1):25–30. doi:10.1016/j.ejmhg.2013.09.002
   Google Scholar
• Tawfik M, Abou El-Ella S, Abouzouna Z. Association of CTLA-4 (+49A/G) gene polymorphism with type 1 diabetes mellitus in Egyptian children. Menoufia Med J. 2016;29(1):100. doi:10.4103/1110-2098.178996
   Google Scholar
• Wang J, Liu L, Ma J, Sun F, Zhao Z, Gu M. Common variants on cytotoxic T lymphocyte antigen-4 polymorphisms contributes to type 1 diabetes susceptibility: evidence based on 58 studies. PLoS One. 2014;9(1):e85982. doi:10.1371/journal.pone.0085982
   Web of Science ®Google Scholar
• Lemos MC, Coutinho E, Gomes L, et al. The CTLA4 +49 A/G polymorphism is not associated with susceptibility to type 1 diabetes mellitus in the Portuguese population. Int J Immunogenet. 2009;36(3):193–195. doi:10.1111/j.1744-313X.2009.00844.x
   Web of Science ®Google Scholar
• Majaliwa ES, Elusiyan BEJ, Adesiyun OO, et al. Type 1 diabetes mellitus in the African population: epidemiology and management challenges. Acta Biomed. 2008;79(3):255–259.
   PubMedGoogle Scholar
• Fernández-Mestre M, Sánchez K, Balbás O, et al. Influence of CTLA-4 gene polymorphism in autoimmune and infectious diseases. Hum Immunol. 2009;70(7):532–535. doi:10.1016/j.humimm.2009.03.016
   Web of Science ®Google Scholar
• Dunlavy DM, O’Leary DP, Klimov D, Thirumalai D. HOPE: a homotopy optimization method for protein structure prediction. J Comput Biol. 2005;12(10):1275–1288. doi:10.1089/cmb.2005.12.1275
   Web of Science ®Google Scholar
• Hea A, Abadi S, Martz E. ConSurf: improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucl Acids Res. 2016;44:W344–W350. doi:10.1093/nar/gkw408
   Web of Science ®Google Scholar
• Zhang YS. TM-align: a protein structure alignment algorithm based on the TMscore. Nucleic Acids Res. 2005;33:2302–2309. doi:10.1093/nar/gki524
   PubMed Web of Science ®Google Scholar
• Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461. doi:10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Gough SCL, Walker LSK, Sansom DM. CTLA4 gene polymorphism and autoimmunity. Immunol Rev. 2005;204(1):102–115. doi:10.1111/j.0105-2896.2005.00249.x
   Web of Science ®Google Scholar
• Thi-Qar IIN. Investigate the relation between CTLA-4 gene polymorphisms and insulin dependent diabetes mellitus (IDDM) type I in Thi-Qar Population. Int J Med Pharm Sci. 2014;4(6):45–54.
   Google Scholar