Research Article: Activating Killer-cell Immunoglobulin-like Receptor genes confer risk for Crohn’s disease in children and adults of the Western European descent: Findings based on case-control studies

Date Published: June 13, 2019

Publisher: Public Library of Science

Author(s): Suzanne Samarani, David R. Mack, Charles N. Bernstein, Alexandre Iannello, Olfa Debbeche, Prevost Jantchou, Christophe Faure, Colette Deslandres, Devendra K. Amre, Ali Ahmad, Gualtiero I. Colombo.


Killer-cell Immunoglobulin-like Receptor (KIR) genes encode receptors, which are mainly expressed on, and control functional activities of, Natural Killer (NK) cells. There exist six distinct activating KIR genes in humans, who differ from one another with respect to the repertoire of these genes. Because activated NK cells can potentially cause tissue destruction, we hypothesized that variation in the inherited activating KIR genes in humans is associated with their innate susceptibility/resistance to developing Crohn disease (CD).

We performed case control studies on three independent Canadian CD patient cohorts (all of the Western European descent): two comprising children (Montreal having 193 cases and 245 controls, and Ottawa having 93 cases and 120 controls) and the third one comprising predominantly adults (Winnipeg having 164 cases and 200 controls). We genotyped cases and controls for activating KIR genes by PCR with gene-specific primers and investigated associations between the genes and cases using unconditional logistic regression.

We observed strong associations between all the six KIR genes and CD in Ottawa children, with the strongest risk observed for the KIR2DS1 (p = 1.7 x10-10). Associations between all but the KIR2DS2 were replicated in the Montreal cohort with the strongest association evident for the KIR2DS5 (8.0 x 10−10). Similarly associations between five genes were observed in the adult Winnipeg cohort. In this cohort, strongest associations were evident with the KIR2DS5 (8.75 x 10−8). An overall analysis for all cohorts showed strong associations with four of the genes, with the strongest association evident for the KIR2DS5 (p = 1.35 x 10−17). In the combined analysis for four KIR genes, individuals carrying one or more of the KIR genes were at significantly higher risks for acquiring CD (p = 3.5 x 10−34).

Activating KIR genes are associated with risk for developing CD in both children and adults.

Partial Text

Crohn’s Disease (CD), a type of inflammatory bowel disease (IBD), is a chronic, relapsing and remitting disease of the gastrointestinal tract. Considered a disease commonly affecting children and young adults, it is one of the most prevalent gastrointestinal tract diseases in the industrialized world. In North America alone, it affects one in three hundred children and its incidence appears to be on the rise in the developing countries; reviewed in [1,2]. As no cure for the disease exists, morbidity from the disease is quite high in particular in children who suffer from numerous consequences such as frequent surgery, growth impairment and psychosocial distress [2,3]. Deciphering the etio-pathogenesis of the disease is the focus of ongoing research.

The clinical and demographic characteristics of the CD cases are shown in Table 1. Based on 26 null markers, we found no evidence of population stratification in any of the 3 cohorts (λ = 1.0, 1.02 and 1.0 respectively for the Ottawa, Montreal and Manitoba cohorts). As the laboratory methods utilized could not distinguish between those who had one or two genes, tests for Hardy-Weinberg could not be implemented. Initially we conducted this study in the Ottawa cohort of Canadian children of Caucasian ancestry. Initially we conducted this study in the Ottawa cohort of Canadian children of Caucasian ancestry. As shown in Table 2, the frequencies of most of the activating KIR genes were significantly higher (p≤0.001) in the cases than in the controls suggesting that the inheritance of these genes enhanced risk for developing CD. The gene that posed the maximum risk in this population was KIR2DS1 (OR = 7.2, 95% CI = 3.78–13.7, p-value = 1.7 x 10−10). The gene rank in conferring the CD risk was 2DS1>2DS2 >2DS4>2DS3>2DS5>3DS1.

To the best of our knowledge, this is the first study implicating multiple activating KIR genes in enhancing the risk for developing CD both in children and adults of the white origin. It is noteworthy that the magnitudes of the associations noted here for most of the genes are comparable to the ones reported earlier for NOD2 and IL23R, which represent the most strongly associated genes with CD [15,16]. So far, a few studies have investigated potential associations between KIR genes and susceptibility/resistance to developing CD. In one study, Wilson et al [43] examined associations between KIR genes and CD in a Brazilian white population comprising of 137 CD patients and 250 healthy unrelated individuals. Although no independent effects with either of the KIR genes were observed, some interactions between the KIR genes and their HLA ligand genes were noted. Jones et al [44] showed that the KIR2DS2 gene was associated with enhanced risk for Ulcerative Colitis (the other less severe type of IBD) but not for CD in white adults (of the Western European descent). Similarly, Hollenbach et al [45] did not find any association of activating or inhibitory KIR genes with CD in a North American population. More recently, Saito et al [46] investigated KIR variability in a relatively small number (fifty) of Japanese CD patients and 325 healthy controls. They found no significant association of any KIR gene with the disease, however, the frequency of KIR2DS3 was significantly increased and that of KIR2DS4 was decreased in UC patients. In this regard, a recent meta-analysis of five published studies [47] reported a negative association of one KIR gene (KIR2DS3) with CD risk. Of relevance here is a published meta-analysis of GWAS by Jostins et al [4]. They identified several SNPs in significant associations with both CD and UC. The eQTL analysis showed that one of the SNPs, rs11672983, was associated with the expression of genes within the KIR gene complex. In line with this finding, Lopez-Hernandez et al. [48] identified KIR2DS1 and KIR2DS5 as significant risk factors in Spanish IBD patients. Taken together, the studies suggest that imbalances between activating and inhibitory KIR genes and their ligands may explain, at least in part, the pathogenesis of the inflammatory bowel diseases. Our results are in concordance with these conclusions and suggest a stronger role of activating KIR genes in conferring CD risk. Since the inhibitory KIR-HLA genotypes with different inhibitory potentials for NK cells (e.g., KIR2L2/3-HLA-C1 vs KIR2DL1-HLA-C2) have been differentially associated with human diseases including CD [28,29,45,46], we are currently investigating whether inhibitory KIR genes and their cognate MHC class I alleles show any association with CD in our cohorts.