A model of phenotypic susceptibility to tuberculosis: Deficient in silico selection of Mycobacterium tuberculosis epitopes by HLA alleles

Sarcoidosis Vasculitis and Diffuse Lung Diseases

Volumn 25, Issue 1, 2008, Pages 21-28

  Contini, S ^a   Pallante, M ^a   Vejbaesya, S ^b   Park, M H ^c   Chierakul, N ^b   Kim, H S ^c   Saltini, C ^a   Amicosante, Massimo ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b MAHIDOL UNIVERSITY   (Thailand)

^c Seoul National University Hospital   (South Korea)

Author keywords

Epitope prediction; HLA; Sarcoid like granulomas; Susceptibility; T cell response; Tuberculosis

Indexed keywords

BERYLLIUM;

ALLELE; ANTIGEN PRESENTATION; ARTICLE; BINDING AFFINITY; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; EPITOPE MAPPING; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; HLA SYSTEM; HUMAN; HYPERSENSITIVITY REACTION; MAJOR CLINICAL STUDY; MYCOBACTERIUM TUBERCULOSIS; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; SARCOIDOSIS; T LYMPHOCYTE; TUBERCULOSIS;

ALLELES; DNA, BACTERIAL; EPITOPES; GENETIC PREDISPOSITION TO DISEASE; GENOME, BACTERIAL; HLA-DR ANTIGENS; HUMANS; MYCOBACTERIUM TUBERCULOSIS; PHENOTYPE; T-LYMPHOCYTES; TUBERCULOSIS;

EID: 56349086631     PISSN: 11240490     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (49)

1. Grigg ER: The Arcana of Tuberculosis. Am. Rev. Tuberc. 1958, 78: 426-53.
2. Vidal SM, Malo D, Vogan K, Skamene E, Gros P: Natural resistance to infection with intracellular parasites: isolation of a candidate for Bcg. Cell 1993, 73: 469-85.
3. Bellamy R, Ruwende C, Corrah T, McAdam KP, Whittle HC, Hill AV: Variations in the NRAMP1 gene and susceptibility to tuberculosis in West Africans. N Engl J Med 1998, 338: 640-4.
4. Greenwood CM, Fujiwara TM, Boothroyd LJ, Miller MA, Frappier D, Fanning EA, Schurr E, Morgan K: Linkage of tuberculosis to chromosome 2q35 loci, including NRAMP1, in a large aboriginal Canadian family. Am J Hum Genet 2000, 67: 405-16.
5. Newport MJ, Huxley CM, Huston S, Hawrylowicz CM, Oostra BA, Williamson R, Levin M: A mutation in the interferon-gamma-receptor gene and susceptibility to mycobacterial infection. N Engl J Med 1996, 335: 1941-9.
6. Jouanguy E, Altare F, Lamhamedi S, Revy P, Emile JF, Newport M, Levin M, Blanche S, Seboun E, Fischer A, Casanova JL: Interferon-gamma-receptor deficiency in an infant with fatal bacille Calmette-Guerin infection. N Engl J Med 1996, 335: 1956-61.
7. Altare F, Durandy A, Lammas D, Emile JF, Lamhamedi S, Le Deist F, Drysdale P, Jouanguy E, Doffinger R, Bernaudin F, Jeppsson O, Gollob JA, Meinl E, Segal AW, Fischer A, Kumararatne D, Casanova JL: Impairment of mycobacterial immunity in human interleukin-12 receptor deficiency. Science 1998, 280: 1432-5.
8. de Jong R, Altare F, Haagen IA, Elferink DG, Boer T, van Breda Vriesman PJ, Kabel PJ, Draaisma JM, van Dissel JT, Kroon FP, Casanova JL, Ottenhoff TH: Severe mycobacterial and Salmonella infections in interleukin-12 receptor-deficient patients. Science 1998, 280: 1435-8.
9. Baghdadi JE, Orlova M, Alter A, Ranque B, Chentoufi M, Lazrak F, Archane MI, Casanova JL, Benslimane A, Schurr E, Abel L: An autosomal dominant major gene confers predisposition to pulmonary tuberculosis in adults. J Exp Med 2006, 203: 1679-1684.
10. Kettaneh A, Seng L, Tiev KP, Toledano C, Fabre B, Cabane J: Human leukocyte antigens and susceptibility to tuberculosis: a meta-analysis of case-control studies. Int J Tuberc Lung Dis 2006, 10: 717-25.
11. Ghodke Y, Joshi K, Chopra A, Patwardhan B: HLA and disease. Eur J Epidemiol. 2005, 20: 475-88.
12. Davenport MP, Quinn CL, Valsasnini P, Sinigaglia F, Hill AV, Bell JI: Analysis of peptide-binding motifs for two disease associated HLA-DR13 alleles using an M13 phage display library. Immunology 1996, 88: 482-486.
13. Mallios RR: Predicting class II MHC/peptide multi-level binding with an iterative stepwise discriminant analysis meta-algorithm. Bioinformatics 2001, 17: 942-8.
14. Germain RN: MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation. Cell 1994, 76: 287-99.
15. Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sabin U, Braxenthaler M, Gallazzi F, Protti MP, Sinigaglia F, Hammer J: Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol 1999, 17: 555-61.
16. Scherer A, Frater J, Oxenius A, Agudelo J, Price DA, Gunthard HF, Barnardo M, Perrin L, Hirschel B, Phillips RE, McLean AR; Swiss HIV: Quantifiable cytotoxic T lymphocyte responses and HLA-related risk of progression to AIDS. Proc Natl Acad Sci U S A 2004, 101: 12266-70.
17. Stunz L, Karr RW, Anderson R: HLA-DRB1 and -DRB4 genes are differentially regulated at the transcriptional level. J Immunol 1989, 143: 3081-86.
18. Berdoz J, Gorski J, Termijtelen A, Dayer J, Irle C, Schendel D, Mach B: Constitutive and induced expression of the individual HLA-DR h and a chain loci in different cell types. J Immunol 1987, 139: 1336-41.
19. Cotner T, Charbonneau H, Mellins E, Pious D: mRNA abundance, rather than differences in subunit assembly, determine expression of HLA-DRh1 and DRh3 molecules. J Biol Chem 1996, 264: 11107-11.
20. De Groot AS, Bosma A, Chinai N, Frost J, Jesdale BM, Gonzalez MA, Martin W, Saint-Aubin C: From genome to vaccine: in silico predictions, ex vivo verification. Vaccine 2001, 19: 4385-95.
21. Vejbaesya S, Chierakul N, Luangtrakool K, Srinak D, Stephens HA: Associations of HLA class II alleles with pulmonary tuberculosis in Thais. Eur J Immunogenet 2002, 29: 431-4.
22. Kim HS, Park MH, Song EY, Park H, Kwon SY, Han SK, Shim YS: Association of HLA-DR and HLA-DQ genes with susceptibility to pulmonary tuberculosis in Koreans: preliminary evidence of associations with drug resistance, disease severity, and disease recurrence. Hum Immunol 2005, 66: 1074-81.
23. Amicosante M, Berretta F, Rossman M, Butler RH, Rogliani P, van den Berg-Loonen E, Saltini C: Identification of HLA-DRPhebeta47 as the susceptibility marker of hypersensitivity to beryllium in individuals lacking the berylliosis-associated supratypic marker HLA-DPGlubeta69. Respir Res 2005, 6: 94.
24. Marsh SGE: Nomenclature for factors of the HLA system, update January 1998. Tissue Antigens 1998, 51: 582-3.
25. Marsh SG: WHO Nomenclature Committee for Factors of the HLA System. Nomenclature for factors of the HLA system, update September 2006. Tissue Antigens 2006, 68: 540-2.
26. Wilson CC, Palmer B, Southwood S, Sidney J, Higashimoto Y, Appella E, Chesnut R, Sette A, Livingston BD: Identification and anti-genicity of broadly cross-reactive and conserved human immunodeficiency virus type 1-derived helper T-lymphocyte epitopes. J Virol 2001, 75: 4195-207.
27. Singh H, Raghava GP: ProPred: prediction of HLA-DR binding sites. Bioinformatics 2001, 17: 1236-7.
28. Uma H, Selvaraj P, Reetha AM, Xavier T, Prabhakar P, Narayanan PR: Influence of HLA-DR antigens on lymphocyte response to Mycobacterium tuberculosis culture filtrate antigens and mitogens in pulmonary tuberculosis. Tuber Lung Dis 1999, 79: 199-206.
29. Sriram U, Selvaraj P, Kurian SM, Reetha AM, Narayanan PR: HLA-DR2 subtypes & immune responses in pulmonary tuberculosis. Indian J Med Res 2001, 113: 117-24.
30. Comstock GW: Tuberculosis in twins: a re-analysis of the Prophit survey. Am Rev Respir Dis 1978, 117: 621-4.
31. Delgado JC, Baena A, Thim S, Goldfeld AE: Aspartic acid homozygosity at codon 57 of HLA-DQ beta is associated with susceptibility to pulmonary tuberculosis in Cambodia. J Immunol 2006, 176: 1090-7.
32. Czaja AJ, Donaldson PT. Genetic susceptibilities for immune expression and liver cell injury in autoimmune hepatitis. Immunol Rev. 2000; 174: 250-9.
33. Embil J, Warren P, Yakrus M, Stark R, Corne S, Forrest D, Hershfield E: Pulmonary Illness Associated With Exposure to Mycobacterium-avium Complex in Hot Tub Water: Hypersensitivity Pneumonitis or Infection? Chest 1997; 111: 813-6.
34. Khan IUH, Selvaraju SB, Yadav JS: Occurrence and characterization of multiple novel genotypes of Mycobacterium immunogenum and Mycobacterium chelonae in metalworking fluids. FEMS Microbiology Ecology 2005, 54: 329-38.
35. Fujita J, Ohtsuki Y, Suemitsu I, Shigeto E, Yamadori I, Obayashi Y, Miyawaki H, Dobashi N, Matsushima T, Takahara J: Pathological and radiological changes in resected lung specimens in Mycobacterium avium intracellulare complex disease. Eur Respir J 1999; 13: 535-40.
36. Kubo K, Yamazaki Y, Hanaoka M, Nomura H, Fujimoto K, Honda T, Ota M, Kamijou Y. Analysis of HLA antigens in Mycobacterium avium-intracellulare pulmonary infection. Am J Respir Crit Care Med 2000, 161: 1368-71.
37. Van?k J, Schwarz J: Demonstration of acid-fast rods in sarcoidosis. Am Rev Respir Dis 1970, 101: 395-400.
38. Almenoff PL, Johnson A, Lesser M, Mattman LH: Growth of acid fast L forms from the blood of patients with sarcoidosis. Thorax 1996, 51: 530-3.
39. Mangiapan G, Hance AJ. Mycobacteria and sarcoidosis: an overview and summary of recent molecular biological data. Sarcoidosis 1995, 12: 20-37.
40. Drake WP, Dhason MS, Nadaf M, Shepherd BE, Vadivelu S, Hajizadeh R, Newman LS, Kalams SA: Cellular recognition of Mycobacterium tuberculosis ESAT-6 and KatG peptides in systemic sarcoidosis. Infect Immun 2007, 75: 527-30.
41. Dubaniewicz A, Trzonkowski P, Dubaniewicz-Wybieralska M, Dubaniewicz A, Singh M, MyÊliwski A: Mycobacterial heat shock protein-induced blood T lymphocytes subsets and cytokine pattern: comparison of sarcoidosis with tuberculosis and healthy controls. Respirology 2007, 12: 346-54.
42. Allen SS, Evans W, Carlisle J, Hajizadeh R, Nadaf M, Shepherd BE, Pride DT, Johnson JE, Drake WP: Superoxide dismutase A antigens derived from molecular analysis of sarcoidosis granulomas elicit systemic Th-1 immune responses. Respir Res 2008; 9: 36.
43. Dubaniewicz A, Dubaniewicz-Wybieralska M, Sternau A, Zwolska Z, Izycka-Swieszewska E, Augustynowicz-Kopec E, Skokowski J, Singh M, Zimnoch L: Mycobacterium tuberculosis complex and mycobacterial heat shock proteins in lymphnode tissue from patients with pulmonary sarcoidosis. J Clin Microbiol 2006, 44: 3448-51.
44. Song Z, Marzilli L, Greenlee BM, Chen ES, Silver RF, Askin FB, Teirstein AS, Zhang Y, Cotter RJ, Moller DR: Mycobacterial catalase-peroxidase is a tissue antigen and target of the adaptive immune response in systemic sarcoidosis. J Exp Med 2005, 201: 755-67.
45. Kettaneh A, Seng L, Tiev KP, Toledano C, Fabre B, Cabane J: Human leukocyte antigens and susceptibility to tuberculosis: a meta-analysis of case-control studies. Int J Tuberc Lung Dis 2006, 10: 717-25.
46. Seitzer U, Gerdes J, Müller-Quernheim J: Evidence for disease phenotype associated haplotypes (DR.TNF) in sarcoidosis. Sarcoidosis Vasc Diffuse Lung Dis 2001, 18: 279-83.
47. Rutherford RM, Brutsche MH, Kearns M, Bourke M, Stevens F, Gilmartin JJ: HLA-DR2 predicts susceptibility and disease chronicity in Irish sarcoidosis patients. Sarcoidosis Vasc Diffuse Lung Dis 2004, 21: 191-8.
48. Burgner D, Jamieson SE, Blackwell JM: Genetic susceptibility to infectious diseases: big is beautiful, but will bigger be even better? Lancet Infect Dis 2006, 6: 653-63.
49. Rollenhagen C, Sörensen M, Rizos K, Hurvitz R, Bumann D: Antigen selection based on expression levels during infection facilitates vaccine development for an intracellular pathogen. Proc Natl Acad Sci U S A 2004, 101: 8739-44.