Functional annotation of a novel NFKB1 promoter polymorphism that increases risk for ulcerative colitis

Human Molecular Genetics

Volumn 13, Issue 1, 2004, Pages 35-45

  Karban, Amir S ^a   Okazaki, Toshihiko ^a   Panhuysen, Carolien I M ^b   Gallegos, Thomas ^a   Potter, James J ^a   Bailey Wilson, Joan E ^c   Silverberg, Mark S ^d   Duerr, Richard H ^e   Cho, Judy H ^f   Gregersen, Peter K ^g   Wu, Yuqiong ^a   Achkar, Jean Paul ^h   Dassopoulos, Themistocles ^a   Mezey, Esteban ^a   Bayless, Theodore M ^a   Nouvet, Franklin J ^a   Brant, Steven R ^a,i  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^d MOUNT SINAI HOSPITAL   (Canada)

^e UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^f UNIVERSITY OF CHICAGO MEDICAL CENTER   (United States)

^g N Shore Long Island Jewish Res Inst ^*  (United States)

^h LERNER RESEARCH INSTITUTE   (United States)

ⁱ JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; GUANINE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LUCIFERASE; NUCLEAR PROTEIN; NUCLEOTIDE; OLIGONUCLEOTIDE; THYMINE;

COLON; CONTROLLED STUDY; DNA POLYMORPHISM; ENTERITIS; EXON; GENE ACTIVITY; GENE DELETION; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENE REPLICATION; GENE SEQUENCE; GENE TRANSFER; GENETIC ASSOCIATION; GENETIC CODE; GENETIC TRANSFECTION; GENETIC VARIABILITY; HELA CELL; HUMAN; HUMAN CELL; HUMAN TISSUE; ILEUM; JEW; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PEDIGREE; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; REPORTER GENE; REVIEW; RISK ASSESSMENT; ULCERATIVE COLITIS;

BASE SEQUENCE; CASE-CONTROL STUDIES; CHROMOSOMES, HUMAN, PAIR 4; COLITIS, ULCERATIVE; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENE FREQUENCY; HUMANS; LINKAGE (GENETICS); LUCIFERASES; MOLECULAR SEQUENCE DATA; NF-KAPPA B P50 SUBUNIT; OLIGONUCLEOTIDES; PEDIGREE; PLASMIDS; POLYMORPHISM, GENETIC; PROMOTER REGIONS (GENETICS); RISK FACTORS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

INSERTION SEQUENCES;

EID: 0347917295     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddh008     Document Type: Review

References (65)

1. Podolsky, D.K. (1991) Inflammatory bowel disease (1). N. Engl. J. Med., 325, 928-937.
2. Podolsky, D.K. (1991) Inflammatory bowel disease (2). N. Engl. J. Med., 325, 1008-1016.
3. Loftus, E.V., Jr and Sandborn, W.J. (2002) Epidemiology of inflammatory bowel disease. Gastroenterol. Clin. North Am., 31, 1-20.
4. Cho, J.H. and Brant, S.R. (1998) Genetics and genetic markers in IBD. Curr. Opin. Gastroenterol., 14, 283-288.
5. Bayless, T.M., Tokayer, A.Z., Polito, J.M., Quaskey, S.A., Mellits, E.D. and Harris, M.L. (1996) Crohn's disease: concordance for site and clinical type in affected family members-potential hereditary influences. Gastroenterology, 111, 573-579.
6. Orholm, M., Munkholm, P., Langholz, E., Nielsen, O.H., Sorensen, I.A. and Binder, V. (1991) Familial occurrence of inflammatory bowel disease. N. Engl. J. Med., 324, 84-88.
7. Le Beau, M.M., Ito, C., Cogswell, P., Espinosa, R., III, Fernald, A.A. and Baldwin, A.S., Jr (1992) Chromosomal localization of the genes encoding the p50/p105 subunits of NF-kappa B (NFKB2) and the I kappa B/MAD-3 (NFKBI) inhibitor of NF- kappa B to 4q24 and 14q13, respectively. Genomics, 14, 529-531.
8. Mathew, S., Murty, V.V., Dalla-Favera, R. and Chaganti, R.S. (1993) Chromosomal localization of genes encoding the transcription factors, c- rel, NF-kappa Bp50, NF-kappa Bp65, and lyt-10 by fluorescence in situ hybridization. Oncogene, 8, 191-193.
9. Baldwin, A.S., Jr (2001) Series introduction: the transcription factor NF-kappaB and human disease. J. Clin. Invest., 107, 3-6.
10. Chen, F., Castranova, V., Shi, X. and Demers, L.M. (1999) New insights into the role of nuclear factor-kappaB, a ubiquitous transcription factor in the initiation of diseases. Clin. Chem., 45, 7-17.
11. Heron, E., Deloukas, P. and van Loon, A.P. (1995) The complete exon-intron structure of the 156-kb human gene NFKB1, which encodes the p105 and p50 proteins of transcription factors NF- kappa B and I kappa B-gamma: implications for NF-kappa B-mediated signal transduction. Genomics, 30, 493-505.
12. Tak, P.P. and Firestein, G.S. (2001) NF-kappaB: a key role in inflammatory diseases. J. Clin. Invest, 107, 7-11.
13. Finco, T.S. and Baldwin, A.S., Jr. (1995) Mechanistic aspects of NF-kappa B regulation: the emerging role of phosphorylation and proteolysis. Immunity, 3, 263-272.
14. Wang, C.Y., Cusack, J.C., Jr, Liu, R. and Baldwin, A.S., Jr (1999) Control of inducible chemoresistance: enhanced anti-tumor therapy through increased apoptosis by inhibition of NF-kappaB. Nat. Med., 5, 412-417.
15. Barnes, P.J. and Karin, M. (1997) Nuclear factor-kappaB: a pivotal transcription factor in chronic inflammatory diseases. N. Engl. J. Med., 336, 1066-1071.
16. De Bosscher, K., Vanden Berghe, W. and Haegeman, G. (2000) Mechanisms of anti-inflammatory action and of immunosuppression by glucocorticoids: negative interference of activated glucocorticoid receptor with transcription factors. J Neuroimmunol., 109, 16-22.
17. Gerondakis, S., Grossmann, M., Nakamura, Y., Pohl, T. and Grumont, R. (1999) Genetic approaches in mice to understand Rel/NF-kappaB and IkappaB function: transgenics and knockouts. Oncogene, 18, 6888-6895.
18. Schottelius, A.J. and Baldwin, A.S., Jr (1999) A role for transcription factor NF-kappa B in intestinal inflammation. Int. J. Colorectal Dis., 14, 18-28.
19. Rogler, G., Brand, K., Vogl, D., Page, S., Hofmeister, R., Andus, T., Knuechel, R., Baeuerle, P.A., Scholmerich, J. and Gross, V. (1998) Nuclear factor kappaB is activated in macrophages and epithelial cells of inflamed intestinal mucosa. Gastroenterology, 115, 357-369.
20. Schreiber, S., Nikolaus, S. and Hampe, J. (1998) Activation of nuclear factor kappa B inflammatory bowel disease. Gut, 42, 477-484.
21. Bantel, H., Berg, C., Vieth, M., Stolte, M., Kruis, W. and Schulze-Osthoff, K. (2000) Mesalazine inhibits activation of transcription factor NF-kappaB in inflamed mucosa of patients with ulcerative colitis. Am. J. Gastroenterol., 95, 3452-3457.
22. Wahl, C., Liptay, S., Adler, G. and Schmid, R. (1998) Sulfasalazine: a potent and specific inhibitor of nuclear factor kappa B. J. Clin. Invest, 101, 1163-1174.
23. Bonen, D.K., Ogura, Y., Nicolae, D.L., Inohara, N., Saab, L., Tanabe, T., Chen, F.F., Foster, S.J., Duerr, R.H., Brant S.R., et al. (2003) Crohn's disease-associated NOD2 variants share a signaling defect in response to lipopolysaccharide and peptidoglycan. Gastroenterology, 124, 140-146.
24. Hisamatsu, T., Suzuki, M., Reinecker, H.C., Nadeau, W.J., McCormick, B.A. and Podolsky, D.K. (2003) CARD15/NOD2 functions as an antibacterial factor in human intestinal epithelial cells. Gastroenterology, 124, 993-1000.
25. Farmer, M.A., Sundberg, J.P., Bristol, I.J., Churchill, G.A., Li, R., Elson, C.O. and Leiter, E.H. (2001) A major quantitative trait locus on chromosome 3 controls colitis severity in IL-10-deficient mice. Proc. Natl Acad. Sci. USA, 98, 13820-13825.
26. Mahler, M. and Leiter, E.H. (2002) Genetic and environmental context determines the course of colitis developing in EL-10-deficient mice. Inflamm. Bowel Dis., 8, 347-355.
27. Cho, J.H., Nicolae, D.L., Gold, L.H., Fields, C.T., LaBuda, M.C., Rohal, P.M., Pickles, M.R., Qin, L., Fu, Y., Mann, J.S. et al. (1998) Identification of novel susceptibility loci for inflammatory bowel disease on chromosomes 1p, 3q, and 4q: evidence for epistasis between 1p and IBD1. Proc. Natl Acad. Sci. USA, 95, 7502-7507.
28. Hampe, J., Schreiber, S., Shaw, S.H., Lau, K.F., Bridger, S., MacPherson, A.J., Cardon, L.R., Sakul, H., Harris, T.J., Buckler, A. et al. (1999) A genomewide analysis provides evidence for novel linkages in inflammatory bowel disease in a large European cohort. Am. J. Hum. Genet., 64, 808-816.
29. Rioux, J.D., Silverberg, M.S., Daly, M.J., Steinhart, A.H., McLeod, R.S., Griffiths, A.M., Green, T., Brettin, T.S., Stone, V., Bull, S.B. et al. (2000) Genomewide search in Canadian families with inflammatory bowel disease reveals two novel susceptibility loci. Am. J. Hum. Genet., 66, 1863-1870.
30. Brant, S.R., Panhuysen, C.I., Bailey-Wilson, J.E., Rohal, P.M., Lee, S., Mann, J., Ravenhill, G., Kirschner, B.S., Hanauer, S.B., Cho, J.H. et al. (2000) Linkage heterogeneity for the IBD1 locus in Crohn's disease pedigrees by disease onset and severity. Gastroenterology, 119, 1483-1490.
31. Ten, R.M., Paya, C.V., Israel, N., Le Bail, O., Mattei, M.G., Virelizier, J.L., Kourilsky, P. and Israel, A. (1992) The characterization of the promoter of the gene encoding the p50 subunit of NF-kappa B indicates that it participates in its own regulation. EMBO J., 11, 195-203.
32. Cogswell, P.C., Scheinman, R.I. and Baldwin, A.S., Jr (1993) Promoter of the human NF-kappa B p50/p105 gene. Regulation by NF-kappa B subunits and by c-REL. J. Immunol., 150, 2794-2804.
33. Markianos, K., Daly, M.J. and Kruglyak, L. (2001) Efficient multipoint linkage analysis through reduction of inheritance space. Am. J. Hum. Genet., 68, 963-977.
34. Kruglyak, L., Daly, M.J., Reeve-Daly, M.P. and Lander, E.S. (1996) Parametric and nonparametric linkage analysis: a unified multipoint approach. Am. J. Hum. Genet., 58, 1347-1363.
35. Horvath, S., Xu, X. and Laird, N.M. (2001) The family based association test method: strategies for studying general genotype-phenotype associations. Eur. J. Hum. Genet., 9, 301-306.
36. Martin, E.R., Monks, S.A., Warren, L.L. and Kaplan, N.L. (2000) A test for linkage and association in general pedigrees: the pedigree disequilibrium test. Am. J. Hum. Genet., 67, 146-154.
37. Morton, N.E. and Collins, A. (1998) Tests and estimates of allelic association in complex inheritance. Proc. Natl Acad. Sci. USA, 95, 11389-11393.
38. Zuckerman, S.H., Evans, G.F. and Guthrie, L. (2001) Transcriptional and post-transcriptional mechanisms involved in the differential expression of LPS-induced IL-1 and TNF mRNA. Immunology, 74, 460-465.
39. Baer, M., Dillner, A., Schwartz, R.C., Sedon, C., Nedospasov, S. and Johnson, P.F. (1998) Tumor necrosis factor alpha transcription in macrophages is attenuated by an autocrine factor that preferentially induces NF-kappaB p50. Mol. Cell. Biol., 18, 5678-5689.
40. Saban, M.R., Nguyen, N.B., Hammond, T.G. and Saban, R. (2002) Gene expression profiling of mouse bladder inflammatory responses to LPS, substance P, and antigen-stimulation. Am. J. Pathol., 160, 2095-2110.
41. Rich S.S. and Concannon, P. (2002) Challenges and strategies for investigating the genetic complexity of common human diseases. Diabetes, 51, S288-S294.
42. Sha W.C., Liou H.C., Tuomanen E.I. and Baltimore D. (1995) Targeted disruption of the p50 subunit of NF-kappa B leads to multifocal defects in immune responses. Cell, 80, 321-330.
43. Erdman, S., Fox, J.G., Dangler, C.A., Feldman, D. and Horwitz, B.H. (2001) Typhlocolitis in NF-kappa B-deficient mice. J. Immunol., 166, 1443-1447.
44. Ziegler-Heitbrock, H.W., Wedel, A., Schraut, W., Strobel, M., Wendelgass, P., Sternsdorf, T., Bauerle, P.A., Haas, J.G. and Riethmuller, G. (1994) Tolerance to lipopolysaccharide involves mobilization of nuclear factor kappa B with predominance of p50 homodimers. J. Biol. Chem., 269, 17001-17004.
45. Campbell, I.K., Gerondakis, S., O'Donnell, K. and Wicks, I.P. (2000) Distinct roles for the NF-kappaB1 (p50) and c-Rel transcription factors in inflammatory arthritis. J. Clin. Invest., 105, 1799-1806.
46. Agrawal, A., Cha-Molstad, H., Samols, D. and Kushner, I. (2003) Overexpressed nuclear factor-kappaB can participate in endogenous C- reactive protein induction, and enhances the effects of C/EBPbeta and signal transducer and activator of transcription-3. Immunology, 108, 539-547.
47. Wintermeyer, P., Riess, O., Schols, L., Przuntek, H., Miterski, B., Epplen, J.T. and Kruger, R. (2002) Mutation analysis and association studies of nuclear factor-kappaB1 in sporadic Parkinson's disease patients. J. Neural Transm., 109, 1181-1188.
48. Miterski, B., Bohringer, S., Klein, W., Sindern, E., Haupts, M., Schimrigk, S. and Epplen, J.T. (2002) Inhibitors in the NFkappaB cascade comprise prime candidate genes predisposing to multiple sclerosis, especially in selected combinations. Genes Immun., 3, 211-219.
49. Brant, S.R. and Okazaki, T. (2003) The generics of IBD. In Bernstein, C.N. (ed.), The Inflammatory Bowel Disease Yearbook, Remedica, London, pp. 79-128.
50. Louis, E., Satsangi, J., Roussomoustakaki, M., Parkes, M., Fanning, G., Welsh, K. and Jewell, D. (1996) Cytokine gene polymorphisms in inflammatory bowel disease. Gut, 39, 705-710.
51. Carter, M.J., di Giovine, F.S., Jones, S., Mee, J., Camp, N.J., Lobo, A.J. and Duff, G.W. (2001) Association of the interleukin 1 receptor antagonist gene with ulcerative colitis in Northern European Caucasians. Gut, 48, 461-467.
52. Craggs, A., West, S., Curtis, A., Welfare, M., Hudson, M., Donaldson, P. and Mansfield, J. (2001) Absence of a genetic association between IL-1RN and IL-1B gene polymorphisms in ulcerative colitis and Crohn disease in multiple populations from northeast England. Scand. J. Gastroenterol., 36, 1173-1178.
53. De la Concha, E.G., Fernandez-Arquero, M., Lopez-Nava, G., Martin, E., Allcock, R.J., Conejero, L., Paredes, J.G. and Diaz-Rubio, M. (2000) Susceptibility to severe ulcerative colitis is associated with polymorphism in the central MHC gene IKBL. Gastroenterology, 119, 1491-1495.
54. Hegazy, D.M., O'Reilly, D.A., Yang, B.M., Hodgkinson, A.D., Millward, B.A. and Demaine, A.G. (2001) NFkappaB polymorphisms and susceptibility to type 1 diabetes. Genes Immun., 2, 304-308.
55. Gylvin, T., Bergholdt, R., Nerup, J. and Pociot, F. (2002) Characterization of a nuclear-factor-kappa B (NFkappaB) genetic marker in type 1 diabetes (T1DM) families. Genes Immun., 3, 430-432.
56. Ogura, Y., Bonen, D.K., Inohara, N., Nicolae, D.L., Chen, F.F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R.H. et al. (2001) A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature, 411, 603-606.
57. Kruglyak, L., and Nickerson D. (2001) Variation is the spice of life. Nat. Genet., 27, 234-236.
58. Spielman, R.S., McGinnis, R.E. and Ewens, W.J. (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet., 52, 506-516.
59. Curtis, D. and Sham, P.C. (1995) A note on the application of the transmission disequilibrium test when a parent is missing. Am. J. Hum. Genet., 56, 811-812.
60. Lake, S.L., Blacker, D. and Laird, N.M. (2000) Family-based tests of association in the presence of linkage. Am. J. Hum. Genet., 67, 1515-1525.
61. Rosner, B. (1995) Fundamentals of Biostatistics, 4th edn. Duxbury Press, Belmont, CA.
62. Sen, R. and Baltimore, D. (1986) Multiple nuclear factors interact with the immunoglobulin enhancer sequences. Cell, 46, 705-716.
63. Feinberg, A.P. and Vogelstein, B. (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem., 132, 6-13.
64. Potter, J.J., Cheneval, D., Dang, C.V., Resar, L.M., Mezey, E. and Yang, V.W. (1991) The upstream stimulatory factor binds to and activates the promoter of the rat class I alcohol dehydrogenase gene. J. Biol. Chem., 266, 15457-15463.
65. Grentzmann, G., Ingram, J.A., Kelly, P.J., Gesteland, R.F. and Atkins, J.F. (1998) A dual-luciferase reporter system for studying recoding signals. RNA, 4, 479-486.