Detection of single-nucleotide polymorphisms in the intron 9 region of the nucleotide oligomerization domain-1 gene in ulcerative colitis patients of North India

J Gastroenterol Hepatol. 2012 Jan;27(1):96-103. doi: 10.1111/j.1440-1746.2011.06832.x.

Abstract

Background and aim: The nucleotide-binding oligomerization domain-1 (NOD1) gene encodes a pattern recognition receptor that senses pathogens. NOD1/caspase recruitment domain (CARD4) signaling leads to the activation of nuclear factor-kB, and plays an important role in innate immunity. Certain polymorphisms and mutations in NOD1/CARD4 might result in a dysfunctional innate immune response during bacterial recognition, which might have direct implications in inflammatory bowel disease (IBD) pathogenesis.

Methods: We carried out a systemic analysis for the presence of polymorphic variants in the intron 9 region of the leucine-rich repeat (LRR) domain encompassing the exon-intron boundaries of the NOD1 gene. To detect unknown single-nucleotide polymorphisms, we used the denaturing high-performance liquid chromatography (DHPLC) screening technique and validated our data by restriction fragment length polymorphism and direct sequencing.

Result: Genotype and allele frequencies showed significant differences in their distribution. The mutations discriminating alleles in the intron 9 region of the LRR domain of the NOD1 gene were correctly predicted by DHPLC technique and statistically verified in IBD and non-IBD individuals. Of the seven mutations detected, only four showed a significant association with disease activity. Mutations detected earlier in the exon 6 region of NOD1 were also used for the haplotype analysis. The GTTG haplotype was found to be significantly overrepresented in ulcerative colitis (UC) patients, as compared to the controls (P = 3.3726E(-6) ).

Conclusion: Our study has revealed a polymorphism association in the LRR domain of the NOD1 gene with the severity of UC disease. This might be due to disruption of the LRR region critical for NOD1-mediated bacterial sensing. A gene-wide, haplotype-based approach shows that GTTG haplotype carriers are overrepresented in UC patients, and that could increase the risk of the disease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Analysis of Variance
  • Base Sequence
  • Case-Control Studies
  • Chi-Square Distribution
  • Chromatography, High Pressure Liquid
  • Colitis, Ulcerative / ethnology
  • Colitis, Ulcerative / genetics*
  • DNA Mutational Analysis
  • Female
  • Gene Frequency
  • Genetic Predisposition to Disease
  • Haplotypes
  • Humans
  • India
  • Introns*
  • Linkage Disequilibrium
  • Male
  • Middle Aged
  • Molecular Sequence Data
  • Mutation
  • Nod1 Signaling Adaptor Protein / genetics*
  • Phenotype
  • Polymerase Chain Reaction
  • Polymorphism, Restriction Fragment Length
  • Polymorphism, Single Nucleotide*
  • Predictive Value of Tests
  • Reproducibility of Results
  • Risk Assessment
  • Risk Factors
  • Severity of Illness Index
  • White People / genetics
  • Young Adult

Substances

  • NOD1 protein, human
  • Nod1 Signaling Adaptor Protein