Functional annotation of a novel NFKB1 promoter polymorphism that increases risk for ulcerative colitis.
Nuclear Factor-kappaB (NF-kappaB) is a major transcription regulator of immune response, apoptosis and cell-growth control genes, and is upregulated in inflammatory bowel disease (IBD), both ulcerative colitis (UC) and Crohn's disease. The NFKB1 gene encodes the NF-kappaB p105/p50 isoforms. Genome-wide screens in IBD families show evidence for linkage on chromosome 4q where NFKB1 maps. We sequenced the NFKB1 promoter, exon 1 and all coding exons in 10 IBD probands and two controls, and identified six nucleotide variants, including a common insertion/deletion promoter polymorphism (-94ins/delATTG). Using pedigree-based transmission disequilibrium tests, we observed modest evidence for linkage disequilibrium (LD), independent of linkage, between the -94delATTG allele and UC in 131 out of 235 IBD pedigrees with UC offspring (P=0.047-0.052). This allele was also more frequent in the 156 non-Jewish UC probands from the 235 IBD pedigrees than in 149 non-Jewish controls (P=0.015). The -94delATTG association with UC was replicated in a second set of 258 unrelated, non-Jewish UC cases and 653 new, non-Jewish controls (P=0.021). Nuclear proteins from normal human colon tissue and colonic cell lines, but not ileal tissue, showed significant binding to -94insATTG but not to -94delATTG containing oligonucleotides. NFKB1 promoter/exon 1 luciferase reporter plasmid constructs containing the -94delATTG allele and transfected into either HeLa or HT-29 cell lines showed less promoter activity than comparable constructs containing the -94insATTG allele. Therefore, we have identified the first potentially functional polymorphism of NFKB1 and demonstrated its genetic association with a common human disease, ulcerative colitis.
Karban
Amir S
AS
Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Room B136, Baltimore, MD 21231, USA.
Okazaki
Toshihiko
T
Panhuysen
Carolien I M
CI
Gallegos
Thomas
T
Potter
James J
JJ
Bailey-Wilson
Joan E
JE
Silverberg
Mark S
MS
Duerr
Richard H
RH
Cho
Judy H
JH
Gregersen
Peter K
PK
Wu
Yuqiong
Y
Achkar
Jean-Paul
JP
Dassopoulos
Themistocles
T
Mezey
Esteban
E
Bayless
Theodore M
TM
Nouvet
Franklin J
FJ
Brant
Steven R
SR
D001483:Base Sequence; D016022:Case-Control Studies; D002894:Chromosomes, Human, Pair 4 / Q000235:genetics*; D003093:Colitis, Ulcerative / Q000235:genetics*; D024202:Electrophoretic Mobility Shift Assay; D005787:Gene Frequency; D008040:Genetic Linkage / Q000235:genetics; D006801:Humans; D008156:Luciferases / Q000378:metabolism; D008969:Molecular Sequence Data; D052002:NF-kappa B p50 Subunit; D009841:Oligonucleotides / Q000378:metabolism; D010375:Pedigree; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic / Q000235:genetics; D012307:Risk Factors; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
D052002:NF-kappa B p50 Subunit; C489548:NFKB1 protein, human; D009841:Oligonucleotides; D014157:Transcription Factors; D008156:Luciferases