Human intelectin-1 (ITLN1) genetic variation and intestinal expression

Eric B Nonnecke,Carol A De La Motte,Patricia A Castillo,Charles L Bevins,Mark A Underwood,Laura L Kiessling,Faisal Almalki,Amanda E Dugan,Bo Shen,Bo Lönnerdal,Wuyuan Lu,Weirong Yuan,Malin E V Johansson,Edward J Hollox

doi:10.1038/s41598-021-92198-9

Abstract

Intelectins are ancient carbohydrate binding proteins, spanning chordate evolution and implicated in multiple human diseases. Previous GWAS have linked SNPs in ITLN1 (also known as omentin) with susceptibility to Crohn's disease (CD); however, analysis of possible functional significance of SNPs at this locus is lacking. Using the Ensembl database, pairwise linkage disequilibrium (LD) analyses indicated that several disease-associated SNPs at the ITLN1 locus, including SNPs in CD244 and Ly9, were in LD. The alleles comprising the risk haplotype are the major alleles in European (67%), but minor alleles in African superpopulations. Neither ITLN1 mRNA nor protein abundance in intestinal tissue, which we confirm as goblet-cell derived, was altered in the CD samples overall nor when samples were analyzed according to genotype. Moreover, the missense variant V109D does not influence ITLN1 glycan binding to the glycan β-D-galactofuranose or protein–protein oligomerization. Taken together, our data are an important step in defining the role(s) of the CD-risk haplotype by determining that risk is unlikely to be due to changes in ITLN1 carbohydrate recognition, protein oligomerization, or expression levels in intestinal mucosa. Our findings suggest that the relationship between the genomic data and disease arises from changes in CD244 or Ly9 biology, differences in ITLN1 expression in other tissues, or an alteration in ITLN1 interaction with other proteins.

Highlights

Intelectins are ancient carbohydrate binding proteins, spanning chordate evolution and implicated in multiple human diseases
We found by direct sequence analysis of PCR products that the Genome-wide association studies (GWAS)-identified single nucleotide polymorphisms (SNPs), rs2274910 (T/C), located in intron 3 of ITLN1, was associated with rs2274907 (A/T), which encodes a missense variant in exon 4, where valine is substituted with aspartic acid at amino acid position 109 (V109D)[1,30]
Various GWAS investigations have identified SNPs at the ITLN1 locus as risk alleles for Crohn’s d isease[1,23,24,25,26,27]. We observed that these SNPs are in linkage disequilibrium (LD), forming a risk haplotype that extends into the adjacent CD244 and Ly9 genes

Summary

Introduction

Intelectins are ancient carbohydrate binding proteins, spanning chordate evolution and implicated in multiple human diseases. Intelectins are multimeric, secreted proteins that exhibit calcium-dependent carbohydrate binding, and each monomer is comprised of a fibrinogen-related domain and C-terminal glycan-binding domain[4,5,6] Both preservation across evolution and abundant expression at mucosal surfaces suggest important function of these lectins in innate immunity[4]. Within β-D-galactofuranose, ITLN1 binds to the exocyclic vicinal 1,2-diol, a chemical moiety present on other microbial carbohydrate-containing structures, such as Kdo[2] (Di[3-deoxy-D-manno-octulosonic acid]) of lipopolysaccharide[6,20,21,22] This carbohydrate specificity suggests microbial pattern recognition binding for ITLN1, in its otherwise elusive role in innate immunity[6,19,20]. We further characterize the ITLN1 locus in the context of IBD-associated SNPs, examine the intestinal expression and glycan binding of ITLN1 associated with risk and non-risk alleles, and localize ITLN1 protein expression to goblet cells of the human small and large intestine

Methods

Results

Conclusion