Linkage disequilibrium with HLA-DRB1-DQB1 haplotypes explains the association of TNF-308G>A variant with type 1 diabetes in a Brazilian cohort

Gene

Volumn 568, Issue 1, 2015, Pages 50-54

  Patente, Thiago A ^a   Monteiro, Maria B ^a   Vieira, Suzana M ^b   Rossi da Silva, Maria E ^a   Nery, Márcia ^a   Queiroz, Márcia ^a   Azevedo, Mirela J ^c   Canani, Luis H ^c   Parisi, Maria C ^d   Pavin, Elizabeth J ^d   Mainardi, Débora ^a   Javor, Juraj ^e   Velho, Gilberto ^f   Coimbra, Cássio N ^g   Corrêa Giannella, Maria Lúcia ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b HOSPITAL DO SERVIDOR PÚBLICO ESTADUAL DE SÃO PAULO   (Brazil)

^c HOSPITAL DE CLÍNICAS DE PORTO ALEGRE   (Brazil)

^d UNIVERSITY OF CAMPINAS   (Brazil)

^e Bratislava   (Slovakia)

^f CENTRE DE RECHERCHE DES CORDELIERS   (France)

^g Universidade Santo Amaro UNISA   (Brazil)

Author keywords

Single nucleotide polymorphism; TNFHLA; Type 1A diabetes

Indexed keywords

HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN; TUMOR NECROSIS FACTOR; HLA DQ ANTIGEN; HLA-DQB1 ANTIGEN; TNF PROTEIN, HUMAN; TUMOR NECROSIS FACTOR ALPHA;

ADULT; AFRICAN; ALLELE; ARTICLE; BRAZILIAN; CAUCASIAN; CODOMINANCE; COHORT ANALYSIS; CONTROLLED STUDY; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HLA SYSTEM; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; BRAZIL; CASE CONTROL STUDY; DOMINANT GENE; GENETIC PREDISPOSITION; GENETICS; MIDDLE AGED; SINGLE NUCLEOTIDE POLYMORPHISM; YOUNG ADULT;

ADULT; BRAZIL; CASE-CONTROL STUDIES; DIABETES MELLITUS, TYPE 1; FEMALE; GENES, DOMINANT; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; HLA-DQ BETA-CHAINS; HLA-DRB1 CHAINS; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; TUMOR NECROSIS FACTOR-ALPHA; YOUNG ADULT;

EID: 84930872714     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2015.05.017     Document Type: Article

References (30)

1. Aly T.A., Ide A., Jahromi M.M., Barker J.M., Fernando M.S., Babu S.R., et al. Extreme genetic risk for type 1A diabetes. Proc. Natl. Acad. Sci. U. S. A. Sep 19 2006, 103(38):14074-14079. (PubMed PMID: 16966600. Epub 2006/09/13. eng).
2. Bouqbis L., Akhayat O., Garchon H.J., Calafell F., Izaabel H. TNFA-TNFB haplotypes modify susceptibility to type I diabetes mellitus independently of HLA class II in a Moroccan population. Tissue Antigens Jan 2003, 61(1):72-79. (PubMed PMID: 12622777).
3. Cox A., Gonzalez A.M., Wilson A.G., Wilson R.M., Ward J.D., Artlett C.M., et al. Comparative analysis of the genetic associations of HLA-DR3 and tumour necrosis factor alpha with human IDDM. Diabetologia May 1994, 37(5):500-503. (PubMed PMID: 8056188. Epub 1994/05/01. eng).
4. Das S.N., Baniasadi V., Kapuria V. Association of -308 TNF-alpha promoter polymorphism with type 1 diabetes in North Indians. Int. J. Immunogenet. Dec 2006, 33(6):411-416. (PubMed PMID: 17117950. Epub 2006/11/23. eng).
5. Deja G., Jarosz-Chobot P., Polanska J., Siekiera U., Malecka-Tendera E. Is the association between TNF-alpha-308 A allele and DMT1 independent of HLA-DRB1, DQB1 alleles?. Mediat. Inflamm. 2006, 2006(4):19724. (PubMed PMID: 17047287. Epub 2006/10/19. eng).
6. Deng G.Y., Maclaren N.K., Huang H.S., Zhang L.P., She J.X. No primary association between the 308 polymorphism in the tumor necrosis factor alpha promoter region and insulin-dependent diabetes mellitus. Hum. Immunol. Feb 1996, 45(2):137-142. (PubMed PMID: 8882412. Epub 1996/02/01. eng).
7. Eizirik D.L., Mandrup-Poulsen T. A choice of death-the signal-transduction of immune-mediated beta-cell apoptosis. Diabetologia Dec 2001, 44(12):2115-2133. (PubMed PMID: 11793013. Epub 2002/01/17. eng).
8. Excoffier L., Lischer H.E. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. May 2010, 10(3):564-567. (PubMed PMID: 21565059. Epub 2011/05/14. eng).
9. Faul F., Erdfelder E., Buchner A., Lang A.G. Statistical power analyses using G*Power 3.1: tests for correlation and regression analyses. Behav. Res. Methods Nov 2009, 41(4):1149-1160. (PubMed PMID: 19897823).
10. Feng R.N., Li Y., Sun C.H. TNF 308G/A polymorphism and type 1 diabetes: a meta-analysis. Diabetes Res. Clin. Pract. Jul 2009, 85(1):e4-e7. (PubMed PMID: 19477545. Epub 2009/05/30. eng).
11. Gamble D.R. The epidemiology of insulin dependent diabetes with particular reference to the relationship of virus infection to its etiology. Epidemiol. Rev. 1980, 2:49-70. (PubMed PMID: 7000538).
12. Green E.A., Eynon E.E., Flavell R.A. Local expression of TNFalpha in neonatal NOD mice promotes diabetes by enhancing presentation of islet antigens. Immunity Nov 1998, 9(5):733-743. (PubMed PMID: 9846494. Epub 1998/12/10. eng).
13. Javor J., Ferencik S., Bucova M., Stuchlikova M., Martinka E., Barak L., et al. Polymorphisms in the genes encoding TGF-beta1, TNF-alpha, and IL-6 show association with type 1 diabetes mellitus in the Slovak population. Arch. Immunol. Ther. Exp. Oct 2010, 58(5):385-393. (PubMed PMID: 20686866. Epub 2010/08/06. eng).
14. Krikovszky D., Vasarhelyi B., Toth-Heyn P., Korner A., Tulassay T., Madacsy L. Association between G-308A polymorphism of the tumor necrosis factor-alpha gene and 24-hour ambulatory blood pressure values in type 1 diabetic adolescents. Clin. Genet. Dec 2002, 62(6):474-477. (PubMed PMID: 12485196. Epub 2002/12/18. eng).
15. Kroeger K.M., Carville K.S., Abraham L.J. The -308 tumor necrosis factor-alpha promoter polymorphism effects transcription. Mol. Immunol. Apr 1997, 34(5):391-399. (PubMed PMID: 9293772. Epub 1997/04/01. eng).
16. Kumar R., Goswami R., Agarwal S., Israni N., Singh S.K., Rani R. Association and interaction of the TNF-alpha gene with other pro- and anti-inflammatory cytokine genes and HLA genes in patients with type 1 diabetes from North India. Tissue Antigens Jun 2007, 69(6):557-567. (PubMed PMID: 17498265. Epub 2007/05/15. eng).
17. Lehuen A., Diana J., Zaccone P., Cooke A. Immune cell crosstalk in type 1 diabetes. Nat. Rev. Immunol. Jul 2010, 10(7):501-513. (PubMed PMID: 20577267. Epub 2010/06/26. eng).
18. Li Z., Zhang Z., He Z., Tang W., Li T., Zeng Z., et al. A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers: update of the SHEsis (http://analysis.bio-x.cn). Cell Res. Apr 2009, 19(4):519-523. (PubMed PMID: 19290020. Epub 2009/03/18. eng).
19. Louis E., Franchimont D., Piron A., Gevaert Y., Schaaf-Lafontaine N., Roland S., et al. Tumour necrosis factor (TNF) gene polymorphism influences TNF-alpha production in lipopolysaccharide (LPS)-stimulated whole blood cell culture in healthy humans. Clin. Exp. Immunol. Sep 1998, 113(3):401-406. (PubMed PMID: 9737669. Epub 1998/09/16. eng).
20. Miller S.A., Dykes D.D., Polesky H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. Feb 11 1988, 16(3):1215. (PubMed PMID: 3344216. Epub 1988/02/11. eng).
21. Morran M.P., Omenn G.S., Pietropaolo M. Immunology and genetics of type 1 diabetes. Mt Sinai J. Med. Aug 2008, 75(4):314-327. (PubMed PMID: 18729178. Epub 2008/08/30. eng).
22. Newton D.J., Bowen-Jones D., Crosby I., Barnes R.M., Flanagan B.F. TNFB gene polymorphism in insulin-dependent diabetes mellitus: association with HLA-DR alleles. Eur. J. Immunogenet. Feb 1998, 25(1):39-41. (PubMed PMID: 9587743. Epub 1998/05/20. eng).
23. Noble J.A., Valdes A.M. Genetics of the HLA region in the prediction of type 1 diabetes. Curr. Diab. Rep. Dec 2011, 11(6):533-542. (PubMed PMID: 21912932. Epub 2011/09/14. eng).
24. Noble J.A., Valdes A.M., Lane J.A., Green A.E., Erlich H.A. Linkage disequilibrium with predisposing DR3 haplotypes accounts for apparent effects of tumor necrosis factor and lymphotoxin-alpha polymorphisms on type 1 diabetes susceptibility. Hum. Immunol. Dec 2006, 67(12):999-1004. (PubMed PMID: 17174749. Epub 2006/12/19. eng).
25. Pociot F., Wilson A.G., Nerup J., Duff G.W. No independent association between a tumor necrosis factor-alpha promoter region polymorphism and insulin-dependent diabetes mellitus. Eur. J. Immunol. Nov 1993, 23(11):3050-3053. (PubMed PMID: 8223882. Epub 1993/11/01. eng).
26. Redondo M.J., Yu L., Hawa M., Mackenzie T., Pyke D.A., Eisenbarth G.S., et al. Heterogeneity of type I diabetes: analysis of monozygotic twins in Great Britain and the United States. Diabetologia Mar 2001, 44(3):354-362. (PubMed PMID: 11317668. Epub 2001/04/25. eng).
27. Todd J.A. Etiology of type 1 diabetes. Immunity Apr 23 2010, 32(4):457-467. (PubMed PMID: 20412756. Epub 2010/04/24. eng).
28. Torn C., Hillman M., Sanjeevi C.B., Landin-Olsson M. Polymorphisms of TNF microsatellite marker a and HLA-DR-DQ in diabetes mellitus-a study in 609 Swedish subjects. Hum. Immunol. Jul 2006, 67(7):527-534. (PubMed PMID: 16829307. Epub 2006/07/11. eng).
29. Wilson A.G., di Giovine F.S., Blakemore A.I., Duff G.W. Single base polymorphism in the human tumour necrosis factor alpha (TNF alpha) gene detectable by NcoI restriction of PCR product. Hum. Mol. Genet. Aug 1992, 1(5):353. (PubMed PMID: 1363876. Epub 1992/08/01. eng).
30. Wilson A.G., Symons J.A., McDowell T.L., McDevitt H.O., Duff G.W. Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc. Natl. Acad. Sci. U. S. A. Apr 1 1997, 94(7):3195-3199. (PubMed PMID: 9096369. Epub 1997/04/01. eng).