Combining global genome and transcriptome approaches to identify the candidate genes of small-effect quantitative trait loci in collagen-induced arthritis

Arthritis Research and Therapy

Volumn 9, Issue , 2007, Pages

  Yu, Xinhua ^a   Bauer, Kristin ^a   Koczan, Dirk ^a   Thiesen, Hans Jürgen ^a   Ibrahim, Saleh M ^a  

^a UNIVERSITY OF ROSTOCK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COLLAGEN; TRANSCRIPTOME;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTHRITIS; ARTICLE; CONTROLLED STUDY; DISEASE SEVERITY; DNA MICROARRAY; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC LINKAGE; GENETIC SCREENING; GENOME; IMMUNIZATION; LINKAGE ANALYSIS; MOUSE; NONHUMAN; PROGENY; QUANTITATIVE TRAIT LOCUS; ANIMAL; COMPARATIVE STUDY; DBA MOUSE; GENE EXPRESSION PROFILING; GENETIC MARKER; GENETICS; METHODOLOGY; SPECIES DIFFERENCE;

ANIMALS; ARTHRITIS, EXPERIMENTAL; GENE EXPRESSION PROFILING; GENETIC MARKERS; GENOME; LINKAGE (GENETICS); MICE; MICE, INBRED DBA; QUANTITATIVE TRAIT LOCI; SPECIES SPECIFICITY;

EID: 33847242646     PISSN: 14786354     EISSN: 14786362     Source Type: Journal    
DOI: 10.1186/ar2108     Document Type: Article

References (35)

1. Amos CI Chen WV Lee A Li W Kern M Lundsten R Batliwalla F Wener M Remmers E Kastner DA High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33 Genes Immun 2006 7 277-286 10.1038/sj.gene.6364295 16691188
2. Cornelis F Faure S Martinez M Prud'homme JF Fritz P Dib C Alves H Barrera P de Vries N Balsa A New susceptibility locus for rheumatoid arthritis suggested by a genome-wide linkage study Proc Natl Acad Sci USA 1998 95 10746-10750 27966 9724775 10.1073/pnas.95.18.10746
3. Jawaheer D Seldin MF Amos CI Chen WV Shigeta R Monteiro J Kern M Criswell LA Albani S Nelson JL A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases Am J Hum Genet 2001 68 927-936 1275647 11254450 10.1086/319518
4. Jawaheer D Seldin MF Amos CI Chen WV Shigeta R Etzel C Damle A Xiao X Chen D Lum RF Screening the genome for rheumatoid arthritis susceptibility genes: A replication study and combined analysis of 512 multicase families Arthritis Rheum 2003 48 906-916 10.1002/art.10989 12687532
5. Choi SJ Rho YH Ji JD Song GG Lee YH Genome scan meta-analysis of rheumatoid arthritis Rheumatology (Oxford) 2006 45 166-170 10.1093/ rheumatology/kei128 16278286
6. Gregersen PK Silver J Winchester RJ Genetic susceptibility to rheumatoid arthritis and human leukocyte antigen class II polymorphism. The role of shared conformational determinants Am J Med 1988 85 17-19 10.1016/ 0002-9343(88)90374-9 3059797
7. Suzuki A Yamada R Chang X Tokuhiro S Sawada T Suzuki M Nagasaki M Nakayama-Hamada M Kawaida R Ono M Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis Nat Genet 2003 34 395-402 10.1038/ ng1206 12833157
8. Kochi Y Yamada R Suzuki A Harley JB Shirasawa S Sawada T Bae SC Tokuhiro S Chang X Sekine A A functional variant in FCRL3, encoding Fc receptor-like 3, is associated with rheumatoid arthritis and several autoimmunities [erratum appears in Nat Genet 2005, 37:652] Nat Genet 2005 37 478-485 1362949 15838509 10.1038/ng1540
9. Begovich AB Carlton VE Honigberg LA Schrodi SJ Chokkalingam AP Alexander HC Ardlie KG Huang Q Smith AM Spoerke JM A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis Am J Hum Genet 2004 75 330-337 1216068 15208781 10.1086/422827
10. Bauer K Yu X Wernhoff P Koczan D Thiesen HJ Ibrahim SM Identification of new quantitative trait loci in mice with collagen-induced arthritis Arthritis Rheum 2004 50 3721-3728 10.1002/art.20624 15529344
11. Todd JA Aitman TJ Cornall RJ Ghosh S Hall JR Hearne CM Knight AM Love JM McAleer MA Prins JB Genetic analysis of autoimmune type 1 diabetes mellitus in mice Nature 1991 351 542-547 10.1038/351542a0 1675432
12. Korstanje R Paigen B From QTL to gene: The harvest begins Nat Genet 2002 31 235-236 10.1038/ng0702-235 12089518
13. Flint J Valdar W Shifman S Mott R Strategies for mapping and cloning quantitative trait genes in rodents Nat Rev Genet 2005 6 271-286 10.1038/ nrg1576 15803197
14. Glazier AM Nadeau JH Aitman TJ Finding genes that underlie complex traits Science 2002 298 2345-2349 10.1126/science.1076641 12493905
15. Thornton S Sowders D Aronow B Witte DP Brunner HI Giannini EH Hirsch R DNA microarray analysis reveals novel gene expression profiles in collagen-induced arthritis Clin Immunol 2002 105-155 168 10.1006/ clim.2002.5227 12482389
16. Ibrahim SM Koczan D Thiesen HJ Gene-expression profile of collagen-induced arthritis J Autoimmun 2002 18 159-167 10.1006/ jaut.2001.0580 11908948
17. Heller RA Schena M Chai A Shalon D Bedilion T Gilmore J Woolley DE Davis RW Discovery and analysis of inflammatory disease-related genes using cDNA microarrays Proc Natl Acad Sci USA 1997 94 2150-2155 20056 9122163 10.1073/pnas.94.6.2150
18. Bovin LF Rieneck K Workman C Nielsen H Sorensen SF Skjodt H Florescu A Brunak S Bendtzen K Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor Immunol Lett 2004 93 217-226 10.1016/j.imlet.2004.03.018 15158620
19. Devauchelle V Marion S Cagnard N Mistou S Falgarone G Breban M Letourneur F Pitaval A Alibert O Lucchesi C DNA microarray allows molecular profiling of rheumatoid arthritis and identification of pathophysiological targets Genes Immunity 2004 5 597-608 10.1038/ sj.gene.6364132 15496955
20. Batliwalla FM Baechler EC Xiao X Li W Balasubramanian S Khalili H Damle A Ortmann WA Perrone A Kantor AB Peripheral blood gene expression profiling in rheumatoid arthritis Genes Immunity 2005 6 388-397 10.1038/ sj.gene.6364209 15973463
21. Gierer P Ibrahim S Mittlmeier T Koczan D Moeller S Landes J Gradl G Vollmar B Gene expression profile and synovial microcirculation at early stages of collagen-induced arthritis Arthritis Res Ther 2005 7 R868-R876 1175036 15987489 10.1186/ar1754
22. Adarichev VA Vermes C Hanyecz A Mikecz K Bremer EG Glant TT Gene expression profiling in murine autoimmune arthritis during the initiation and progression of joint inflammation Arthritis Res Ther 2005 7 R196-R207 1065315 15743466 10.1186/ar1472
23. Manly KF Cudmore RH Jr Meer JM Map Manager QTX, cross-platform software for genetic mapping Mamm Genome 2001 12 930-932 10.1007/ s00335-001-1016-3 11707780
24. Li C Wong WH Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection Proc Natl Acad Sci USA 2001 98 31-36 14539 11134512 10.1073/pnas.011404098
25. Wang Y Kristan J Hao L Lenkoski CS Shen Y Matis LA A role for complement in antibody-mediated inflammation: C5-deficient DBA/1 mice are resistant to collagen-induced arthritis J Immunol 2000 164 4340-4347 10754334
26. Lander ES Botstein D Mapping mendelian factors underlying quantitative traits using RFLP linkage maps Genetics 1989 121-185 199 1203601 2563713
27. Adarichev VA Valdez JC Bardos T Finnegan A Mikecz K Glant TT Combined autoimmune models of arthritis reveal shared and independent qualitative (binary) and quantitative trait loci J Immunol 2003 170 2283-2292 12594249
28. Yang HT Jirholt J Svensson L Sundvall M Jansson L Pettersson U Holmdahl R Identification of genes controlling collagen-induced arthritis in mice: Striking homology with susceptibility loci previously identified in the rat J Immunol 1999 163 2916-2921 10453039
29. Otto JM Chandrasekeran R Vermes C Mikecz K Finnegan A Rickert SE Enders JT Glant TT A genome scan using a novel genetic cross identifies new susceptibility loci and traits in a mouse model of rheumatoid arthritis J Immunol 2000 165 5278-5286 11046062
30. Ensembl http://www.ensembl.org
31. Yu X Bauer K Wernhoff P Koczan D Moller S Thiesen HJ Ibrahim SM Fine mapping of collagen-induced arthritis quantitative trait loci in an advanced intercross line J Immunol 2006 177 7042-7049 17082620
32. Kumar S Boehm J Lee JC p38 MAP kinases: Key signalling molecules as therapeutic targets for inflammatory diseases Nat Rev Drug Discov 2003 2 717-726 10.1038/nrd1177 12951578
33. Nishikawa M Myoui A Tomita T Takahi K Nampei A Yoshikawa H Prevention of the onset and progression of collagen-induced arthritis in rats by the potent p38 mitogen-activated protein kinase inhibitor FR167653 Arthritis Rheum 2003 48 2670-2681 10.1002/art.11227 13130488
34. Yao Z Cui Y Watford WT Bream JH Yamaoka K Hissong BD Li D Durum SK Jiang Q Bhandoola A Stat5a/b are essential for normal lymphoid development and differentiation Proc Natl Acad Sci USA 2006 103 1000-1005 1327727 16418296 10.1073/pnas.0507350103
35. Snow JW Abraham N Ma MC Herndier BG Pastuszak AW Goldsmith MA Loss of tolerance and autoimmunity affecting multiple organs in STAT5A/ 5B-deficient mice J Immunol 2003 171 5042-5050 14607901