Functional variants of OCTN cation transporter genes are associated with Crohn disease

Abstract

Crohn disease is a chronic, inflammatory disease of the gastrointestinal tract. A locus of ∼250 kb at 5q31 (IBD5) 1,2 was previously associated with susceptibility to Crohn disease, as indicated by increased prevalence of a risk haplotype of 11 single-nucleotide polymorphisms 3 among individuals with Crohn disease, but the pathogenic lesion in the region has not yet been identified. We report here that two variants in the organic cation transporter cluster at 5q31 (a missense substitution in SLC22A4 and a G→C transversion in the SLC22A5 promoter) form a haplotype associated with susceptibility to Crohn disease. These variants alter transcription and transporter functions of the organic cation transporters and interact with variants in another gene associated with Crohn disease, CARD15, to increase risk of Crohn disease. These results suggest that SLC22A4, SLC22A5 and CARD15 act in a common pathogenic pathway to cause Crohn disease.By resequencing the five genes in the IBD5 interval, we identified ten new single-nucleotide polymorphisms (SNPs; Supplementary Table 1 online), including two in the organic cation transporter (OCTN) gene cluster (SLC22A4 and SLC22A5, encoding OCTN1 and OCTN2, respectively) that are predicted to have functional effects. The first is a C→T substitution in SLC22A4 exon 9 (1672C→T; numbered according to the cDNA sequence for SLC22A4 in GenBank) that causes the amino acid substitution L503F. Leucine or isoleucine is conserved at this position in most OCTNs and other related transporters 4 (Fig. 1a), and its substitution with phenylalanine is predicted computationally (by PolyPhen 5 , TMHMM2 (ref. 6) and PHAT transmembrane database 7 ) to be nonconservative. The second SNP is a G→C transversion in the SLC22A5 promoter (-207G→C), which disrupts a heat shock element (HSE) 207 bp upstream of the start codon (Fig. 1b).1672C→T and -207G→C are in strong linkage disequilibrium and create a two-allele risk haplotype (TC) enriched in individuals with Crohn disease (frequency = 0.54 in affected individuals versus 0.42 in controls, P = 0.0003;

Spontaneous development of intestinal and colonic atrophy and inflammation in the carnitine-deficient jvs (OCTN2−/−) mice

“…Some studies have reported that OCTN1 is capable of mediating carnitine uptake [6], but we could not reproduce these results in our laboratory using cloned rat and human OCTN1 (unpublished data). ATB 0,+ is a low-affinity transporter for carnitine [47].…”

“…These studies included diverse populations and originated from Canada [6,13,14], the UK [15][16][17][18], Germany [19], New Zealand [20], Spain [21], Italy [22,23], Belgium [24], Greece [25], Sweden [26] and Japan [27,28]. One Japanese and another Hungarian study with a small number of subjects found no association between OCTN 1&2 transporter polymorphisms and CD [28,29]; thus there could be ethnic differences in IBD5 locus mutations and propensity for Crohn's disease [7].…”

“…Both these mutations are in strong linkage disequilibrium and create a two-allele risk haplotype. These mutations have been shown to cause a reduced carnitine uptake by OCTN1 and a reduced expression of OCTN2 in in-vitro experiments, thus potentially causing tissue carnitine deficiency [6]. These association studies suggest that carnitine transport deficiency might play a role in the pathogenesis of Crohn's disease.…”

Association of ATG16L1 and IRGM genes polymorphisms with inflammatory bowel disease: a meta-analysis approach

“…Although the aetiology of these diseases is not fully understood, there is strong support for a genetic component based on findings of familial aggregation, higher concordance in monozygotic twins and ethnic differences in disease prevalence. 1,2 To date, different genetic studies have shown several genes playing a relevant role in these diseases, including NOD2/CARD15, 3 DGL5, 4 SLC22A4 and SLC22A5, 5,6 TNFSF15, 7,8 NOD1/CARD4 7 and IL23R. 9,10 NOD2/CARD15 is likely to be the major genetic factor contributing to CD.…”

Evaluation of AGR2 and AGR3 as candidate genes for inflammatory bowel disease

“…10,11 Genetic linkage studies in IBD provide a thorough proof for a genetic background, 12 and the first disease gene (NOD2 or CARD15) has been identified for CD. [13][14][15][16][17] Genome-wide linkage analyses in large patient cohorts of different ethnic backgrounds have defined IBD susceptibility loci located on chromosomes 3, 6, 7, 12 and 16. 12,18-20 Recently, mutations in the murine Anterior Gradient 2 (AGR2) gene have been associated with a spontaneous phenotype characterized by diarrhea and goblet cell dysfunction resembling pathological changes seen in human UC (European patent WO2004056858).…”