title: NKX2-3 variant rs11190140 is associated with IBD and alters binding of NFAT.
abstract: NKX2-3 SNP rs11190140 is associated with inflammatory bowel disease (IBD). The T allele is over-transmitted in IBD and the C allele represents a potential CpG methylation site. We hypothesize that genetic variation and/or methylation of SNP rs11190140 may play a role in NKX2-3 gene expression by affecting transcription factor binding. We studied 233 IBD cases and 250 unrelated healthy individuals from an IBD population from central Pennsylvania and performed genotype analyses of the genetic variation and methylation status analysis using PCR-based RFLP. For transcription factor binding, nuclear extracts from human B cells were incubated with biotin-labeled oligonucleotide sequences of the NKX2-3 promoter region containing the genetic variation of T, non-methylated C or methylated C at rs11190140, followed by biotin pull-down and Western blot analysis for transcription factors SP1, NFAT1, NF-κB, and ETS-1. In case-control analysis, the genetic variation was significantly associated with IBD (OR=0.503, 95% CI=0.330-0.764, p<0.001). Methylation status analyses revealed that the C allele is subject to modification by DNA methylation. transcription factor binding assay indicated distinct differential binding of NFAT1 to the NKX2-3 promoter sequence, with higher binding to those with non-methylated and methylated C than to T. The binding of NFAT1 to the NKX2-3 promoter region with rs1190140 was confirmed by ChIP assay. We speculate that the rs11190140 may regulate NKX2-3 expression and have a role in IBD pathogenesis.
authors.affiliation: Department of Surgery, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
authors.forename: Gerrit
authors.initials: G
authors.lastname: John
authors.forename: John P
authors.initials: JP
authors.lastname: Hegarty
authors.forename: Wei
authors.initials: W
authors.lastname: Yu
authors.forename: Arthur
authors.initials: A
authors.lastname: Berg
authors.forename: Danielle M
authors.initials: DM
authors.lastname: Pastor
authors.forename: Ashley A
authors.initials: AA
authors.lastname: Kelly
authors.forename: Yunhua
authors.initials: Y
authors.lastname: Wang
authors.forename: Lisa S
authors.initials: LS
authors.lastname: Poritz
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Walter A
authors.initials: WA
authors.lastname: Koltun
authors.forename: Zhenwu
authors.initials: Z
authors.lastname: Lin
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001483:Base Sequence; D015153:Blotting, Western; D016022:Case-Control Studies; D019175:DNA Methylation / Q000235:genetics; D005260:Female; D005787:Gene Frequency / Q000235:genetics; D020022:Genetic Predisposition to Disease; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D050778:NFATC Transcription Factors / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*; D055815:Young Adult
chemical_list: D018398:Homeodomain Proteins; D050778:NFATC Transcription Factors; C494006:NFATC2 protein, human; C534957:NKX2-3 protein, human; D014157:Transcription Factors