Prioritizing genes of potential relevance to diseases affected by sex hormones: An example of Myasthenia Gravis

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Kaur, Mandeep ^a   Schmeier, Sebastian ^a   MacPherson, Cameron R ^a   Hofmann, Oliver ^a   Hide, Winston A ^a   Taylor, Stephen ^b   Willcox, Nick ^c   Bajic, Vladimir B ^a  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN; GENE PRODUCT; HLA DR ANTIGEN; HLA G ANTIGEN; MICROTUBULE PROTEIN; PROTEIN TAP2; PROTEIN TUBB; SEX HORMONE; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ADOLESCENT; ADULT; ANALYTIC METHOD; ARTICLE; AUTOIMMUNE DISEASE; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; GENE IDENTIFICATION; GENE LOCATION; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC LINKAGE; GENETIC RISK; GENOMICS; HORMONE ACTION; HORMONE DETERMINATION; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; MYASTHENIA GRAVIS; ONSET AGE; RISK ASSESSMENT; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; SYSTEMS BIOLOGY; THYMUS;

ESTROGENS; GENE EXPRESSION REGULATION; GONADAL STEROID HORMONES; HUMANS; MYASTHENIA GRAVIS; SYSTEMS BIOLOGY; THYMUS GLAND;

EID: 57249105129     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-481     Document Type: Article

References (50)

1. Bodmer WF Models and mechanisms for HLA and disease associations J Exp Med 1980, 152:353s-357s. 6774043
2. McDevitt HO Bodmer WF HL-A, immune-response genes, and disease Lancet 1974, 1:1269-1275. 10.1016/S0140-6736(74)90021-X 4134154
3. Whitacre CC Sex differences in autoimmune disease Nat Immunol 2001, 2:777-780. 10.1038/ni0901-777 11526384
4. Traherne JA Horton R Roberts AN Miretti MM Hurles ME Stewart CA Ashurst JL Atrazhev AM Coggill P Palmer S Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history PLoS Genet 2006, 2:e9. 1331980 16440057 10.1371/journal.pgen.0020009
5. Gregersen JW Kranc KR Ke X Svendsen P Madsen LS Thomsen AR Cardon LR Bell JI Fugger L Functional epistasis on a common MHC haplotype associated with multiple sclerosis Nature 2006, 443:574-577. 17006452
6. Friese MA Fugger L Autoreactive CD8+ T cells in multiple sclerosis: A new target for therapy? Brain 2005, 128:1747-1763. 10.1093/brain/awh578 15975943
7. Janer M Cowland A Picard J Campbell D Pontarotti P Newsom-Davis J Bunce M Welsh K Demaine A Wilson AG A susceptibility region for myasthenia gravis extending into the HLA-class I sector telomeric to HLA-C Hum Immunol 1999, 60:909-917. 10.1016/S0198-8859(99)00062-2 10527401
8. Vandiedonck C Giraud M Garchon HJ Genetics of autoimmune myasthenia gravis: The multifaceted contribution of the HLA complex J Autoimmun 2005, 25(Suppl):6-11. 10.1016/j.jaut.2005.09.010 16260117
9. Giraud M Taubert R Vandiedonck C Ke X Levi-Strauss M Pagani F Baralle FE Eymard B Tranchant C Gajdos P An IRF8-binding promoter variant and AIRE control CHRNA1 promiscuous expression in thymus Nature 2007, 448:934-937. 10.1038/nature06066 17687331
10. Safar D Aime C Cohen-Kaminsky S Berrih-Aknin S Antibodies to thymic epithelial cells in myasthenia gravis J Neuroimmunol 1991, 35:101-110. 10.1016/0165-5728(91)90165-4 1720131
11. Shiono H Roxanis I Zhang W Sims GP Meager A Jacobson LW Liu JL Matthews I Wong YL Bonifati M Scenarios for autoimmunization of T and B cells in myasthenia gravis Ann N Y Acad Sci 2003, 998:237-256. 10.1196/ annals.1254.026 14592881
12. Meraouna A Cizeron-Clairac G Panse RL Bismuth J Truffault F Tallaksen C Berrih-Aknin S The chemokine CXCL13 is a key molecule in autoimmune myasthenia gravis Blood 2006, 108:432-440. 1847364 16543475 10.1182/ blood-2005-06-2383
13. Le Panse R Cizeron-Clairac G Bismuth J Berrih-Aknin S Microarrays Reveal Distinct Gene Signatures in the Thymus of Seropositive and Seronegative Myasthenia Gravis Patients and the Role of CC Chemokine Ligand 21 in Thymic Hyperplasia The Journal of Immunology 2006, 177:7868-7879. 1892191 17114458
14. Sims GP Shiono H Willcox N Stott DI Somatic hypermutation and selection of B cells in thymic germinal centers responding to acetylcholine receptor in myasthenia gravis J Immunol 2001, 167:1935-1944. 11489973
15. MacLennan IC Germinal centers Annu Rev Immunol 1994, 12:117-139. 10.1146/ annurev.iy.12.040194.001001 8011279
16. Vincent A Leite MI Farrugia ME Jacob S Viegas S Shiraishi H Benveniste O Morgan BP Hilton-Jones D Newsom-Davis J Myasthenia gravis seronegative for acetylcholine receptor antibodies Ann N Y Acad Sci 2008, 1132:84-92. 10.1196/annals.1405.020 18567857
17. Willcox N Leite MI Kadota Y Jones M Meager A Subrahmanyam P Dasgupta B Morgan BP Vincent A Autoimmunizing mechanisms in thymoma and thymus Ann N Y Acad Sci 2008, 1132:163-173. 10.1196/annals.1405.021 18567866
18. Yamanouchi J Rainbow D Serra P Howlett S Hunter K Garner VE Gonzalez-Munoz A Clark J Veijola R Cubbon R et al. Interleukin-2 gene variation impairs regulatory T cell function and causes autoimmunity Nat Genet 2007, 39:329-337. 10.1038/ng1958 17277778
19. Leite MI Jones M Strobel P Marx A Gold R Niks E Verschuuren JJ Berrih-Aknin S Scaravilli F Canelhas A et al. Myasthenia gravis thymus: complement vulnerability of epithelial and myoid cells, complement attack on them, and correlations with autoantibody status Am J Pathol 2007, 171:893-905. 1959483 17675582 10.2353/ajpath.2007.070240
20. Martinez-Martinez P Losen M Duimel H Frederik P Spaans F Molenaar P Vincent A De Baets MH Overexpression of rapsyn in rat muscle increases acetylcholine receptor levels in chronic experimental autoimmune myasthenia gravis Am J Pathol 2007, 170:644-657. 1851878 17255332 10.2353/ajpath.2007.060676
21. Donmez B Ozakbas S Oktem MA Gedizlioglu M Coker I Genc A Idiman E HLA genotypes in Turkish patients with myasthenia gravis: Comparison with multiple sclerosis patients on the basis of clinical subtypes and demographic features Hum Immunol 2004, 65:752-757. 10.1016/ j.humimm.2004.05.004 15301866
22. Graham RR Ortmann W Rodine P Espe K Langefeld C Lange E Williams A Beck S Kyogoku C Moser K et al. Specific combinations of HLA-DR2 and DR3 class II haplotypes contribute graded risk for disease susceptibility and autoantibodies in human SLE Eur J Hum Genet 2007, 15:823-830. 10.1038/sj.ejhg.5201827 17406641
23. Ansar AS Penhale WJ Talal N Sex hormones, immune responses, and autoimmune diseases. Mechanisms of sex hormone action Am J Pathol 1985, 121:531-551. 1887926 3907369
24. Vijayan N Vijayan VK Dreyfus PM Acetylcholinesterase activity and menstrual remissions in myasthenia gravis J Neurol Neurosurg Psychiatry 1977, 40:1060-1065. 492903 599353 10.1136/jnnp.40.11.1060
25. Leker RR Karni A Abramsky O Exacerbation of myasthenia gravis during the menstrual period J Neurol Sci 1998, 156:107-111. 10.1016/ S0022-510X(98)00031-8 9559997
26. Verthelyi D Sex hormones as immunomodulators in health and disease Int Immunopharmacol 2001, 1:983-993. 10.1016/S1567-5769(01)00044-3 11407317
27. Suenaga R Evans MJ Mitamura K Rider V Abdou NI Peripheral blood T cells and monocytes and B cell lines derived from patients with lupus express estrogen receptor transcripts similar to those of normal cells J Rheumatol 1998, 25:1305-1312. 9676761
28. Kramer PR Wray S Beta-estradiol regulates expression of genes that function in macrophage activation and cholesterol homeostasis J Steroid Biochem Mol Biol 2002, 81:203-216. 10.1016/S0960-0760(02)00065-1 12163132
29. Staples JE Gasiewicz TA Fiore NC Lubahn DB Korach KS Silverstone AE Estrogen receptor alpha is necessary in thymic development and estradiol-induced thymic alterations J Immunol 1999, 163:4168-4174. 10510352
30. Nancy P Berrih-Aknin S Differential estrogen receptor expression in autoimmune myasthenia gravis Endocrinology 2005, 146:2345-2353. 1839841 15661863 10.1210/en.2004-1003
31. Gregersen PK Lee HS Batliwalla F Begovich AB autoimmunity Semin Immunol 2006, 18:214-223. 10.1016/j.smim.2006.03.009 16731003
32. Dennis G Jr Sherman BT Hosack DA Yang J Gao W Lane HC Lempicki RA DAVID: Database for Annotation, Visualization, and Integrated Discovery Genome Biol 2003, 4:3. 12734009 10.1186/gb-2003-4-5-p3
33. van Driel MA Cuelenaere K Kemmeren PP Leunissen JA Brunner HG Vriend G GeneSeeker: Extraction and integration of human disease-related information from web-based genetic databases Nucleic Acids Res 2005, 33:W758-W761. 1160196 15980578 10.1093/nar/gki435
34. Lopez-Bigas N Ouzounis CA Genome-wide identification of genes likely to be involved in human genetic disease Nucleic Acids Res 2004, 32:3108-3114. 434425 15181176 10.1093/nar/gkh605
35. Adie E Adams R Evans K Porteous D Pickard B Speeding disease gene discovery by sequence based candidate prioritization BMC Bioinformatics 2005, 6:55. 1274252 15766383 10.1186/1471-2105-6-55
36. Perez-Iratxeta C Wjst M Bork P Andrade MA G2D: A tool for mining genes associated with disease BMC Genet 2005, 6:45. 1208881 16115313 10.1186/ 1471-2156-6-45
37. Adie EA Adams RR Evans KL Porteous DJ Pickard BS SUSPECTS: Enabling fast and effective prioritization of positional candidates Bioinformatics 2006, 22:773-774. 10.1093/bioinformatics/btk031 16423925
38. Turner FS Clutterbuck DR Semple CA POCUS: Mining genomic sequence annotation to predict disease genes Genome Biol 2003, 4:R75. 329128 14611661 10.1186/gb-2003-4-11-r75
39. Tiffin N Adie E Turner F Brunner HG van Driel MA Oti M Lopez-Bigas N Ouzounis C Perez-Iratxeta C Andrade-Navarro MA et al. Computational disease gene identification: A concert of methods prioritizes type 2 diabetes and obesity candidate genes Nucleic Acids Res 2006, 34:3067-3081. 1475747 16757574 10.1093/nar/gkl381
40. Lombard Z Tiffin N Hofmann O Bajic VB Hide W Ramsay M Computational selection and prioritization of candidate genes for fetal alcohol syndrome BMC Genomics 2007, 8:389. 2194724 17961254 10.1186/ 1471-2164-8-389
41. Hill M Beeson D Moss P Jacobson L Bond A Corlett L Newsom-Davis J Vincent A Willcox N Early-onset myasthenia gravis: A recurring T-cell epitope in the adult-specific acetylcholine receptor epsilon subunit presented by the susceptibility allele HLA-DR52a Ann Neurol 1999, 45:224-231. 10.1002/1531-8249(199902)45:2<224::AID-ANA13>3.0.CO;2-B 9989625
42. Yu D Cook MC Shin DM Silva DG Marshall J Toellner KM Havran WL Caroni P Cooke MP Morse HC Axon growth and guidance genes identify T-dependent germinal centre B cells Immunol Cell Biol 2008, 86:3-14. 10.1038/ sj.icb.7100123 17938642
43. Bajic VB Tan SL Chong A Tang S Strom A Gustafsson JA Lin CY Liu ET Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes Nucleic Acids Research 2003, 31:3605-3607. 168924 12824376 10.1093/nar/gkg517
44. Tang S Zhang Z Tan SL Tang MH Kumar AP Ramadoss SK Bajic VB KBERG: KnowledgeBase for Estrogen Responsive Genes Nucleic Acids Res 2007, 35:D732-D736. 1669744 17090589 10.1093/nar/gkl816
45. Jin VX Sun H Pohar TT Liyanarachchi S Palaniswamy SK Huang TH Davuluri RV ERTargetDB: An integral information resource of transcription regulation of estrogen receptor target genes J Mol Endocrinol 2005, 35:225-230. 10.1677/jme.1.01839 16216904
46. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Gene Ontology: Tool for the unification of biology Nature Genetics 2000, 25:25-29. 10.1038/75556 10802651
47. Lie BA Thorsby E Several genes in the extended human MHC contribute to predisposition to autoimmune diseases Curr Opin Immunol 2005, 17:526-531. 16054351
48. Kelso J Visagie J Theiler G Christoffels A Bardien S Smedley D Otgaar D Greyling G Jongeneel CV McCarthy MI et al. eVOC: A controlled vocabulary for unifying gene expression data Genome Res 2003, 13:1222-1230. 403650 12799354 10.1101/gr.985203
49. Kruger A Hofmann O Carninci P Hayashizaki Y Hide W Simplified ontologies allowing comparison of developmental mammalian gene expression Genome Biol 2007, 8;R229. 2246303 17961239 10.1186/gb-2007-8-10-r229
50. Safran M Solomon I Shmueli O Lapidot M Shen-Orr S Adato A Ben Dor U Esterman N Rosen N Peter I et al. GeneCards 2002: Towards a complete, object-oriented, human gene compendium Bioinformatics 2002, 18:1542-1543. 10.1093/bioinformatics/18.11.1542 12424129