World J Gastroenterol 2017 July 21; 23(27): 4897-4909. DOI: 10.3748/wjg.v23.i27.4897. 

Genetic association and epistatic interaction of the interleukin-10 signaling pathway in pediatric inflammatory bowel disease

Zhenwu Lin1,5, Zhong Wang2, John P Hegarty3, Tony R Lin3, Yunhua Wang1, Sue Deiling3, Rongling Wu2, Neal J Thomas1, Joanna Floros1,4

1 CHILD Research Center, Department of Pediatrics, 2Department of Public Health Science, 3Department of Surgery, 4Department of Obstetrics and Gynecology, the Pennsylvania State University, College of Medicine, Hershey, PA USA;

5 Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA. USA

Authors Z Lin and Z Wang contributed equally to this work.

Correspondence should addressed to: Zhenwu Lin, Department of Pediatrics, the Pennsylvania State

University, College of Medicine, 500 University Drive, Hershey, PA 17033, United States. Email: zxl13@psu.edu

 

Abstract

AIM to study the genetic association and epistatic interaction of the interleukin (IL)-10 and IL 10/STAT3 pathways in pediatric inflammatory bowel disease (IBD).

METHODS A total of 159 pediatric inflammatory IBD patients (Crohn’s disease, n = 136; ulcerative colitis, n = 23) and 129 matched controls were studied for genetic association of selected single nucleotide polymorphisms (SNPs) of the IL-10 gene and the genes IL10RA , IL10RB , STAT3 , and HO1 , from the IL-10/STAT3 signaling pathway. As interactions between SNPs from different loci may significantly affect the associated risk for disease, additive (a) and dominant (d) modeling of SNP interactions was also performed to examine highorder epistasis between combinations of the individual SNPs.

RESULTS The results showed that IL-10 rs304496 was associated with pediatric IBD (P = 0.022), but no association was found for two other IL-10 SNPs, rs1800872 and

rs2034498, or for SNPs in genes IL10RA, IL10RB, STAT3, and HO1. However, analysis of epistatic interaction among these genes showed significant interactions: (1) between two IL-10 SNPs rs1800872 and rs3024496 (additive-additive P = 0.00015, Bonferroni P value (Bp) = 0.003); (2) between IL-10RB rs2834167 and HO1 rs2071746 (dominant-additive, P =

0.0018, Bp = 0.039); and (3) among IL-10 rs1800872, IL10RB rs2834167, and HO1 rs2071746 (additivedominant-additive, P = 0.00015, Bp = 0.005), as well as weak interactions among IL-10 rs1800872, IL-10 rs3024496, and IL-10RA (additive-additive-additive, P = 0.003; Bp = 0.099), and among IL10RA, IL10RB, and HO1 genes (additive-dominant-additive, P = 0.008, Bp = 0.287).

CONCLUSION These results indicate that both the IL-10 gene itself, and through epistatic interaction with genes within the IL-10/STAT3 signaling pathway, contribute to the risk of pediatric IBD.

URL: http://www.wjgnet.com/1007-9327/full/v23/i27/4897.htm DOI: http://dx.doi.org/10.3748/wjg.v23.i27.4897

 

Supplement:

In many human diseases, the mechanisms involved are complex and may include molecular interactions mediated via various pathways including signal transduction pathways. In this paper, in addition to looking at the association of single nucleotide polymorphism (SNP) of IL10 with pediatric IBD, we also studied whether IL10 intragenic (within the same gene) SNP-SNP interactions and intergenic (between two genes or among several genes) IL10 SNPs with SNPs of other genes in the IL10/STAT3 pathway occur, using our recently developed epistatic analysis method [1]. IL10 is an anti-inflammatory cytokine and functions through the IL10/STAT3 pathway. As depicted in Figure, the IL-10 gene binds to receptors IL10RA and IL10RB, and activates Jak1 and Tyk2, leading to the phosphorylation of STAT3. Then the activated STAT3 translocates into nucleus and regulates target gene transcription, such as the HO-1 gene [2], to promote an anti-inflammatory response and thus, control inflammation and protect the intestinal tissue from damage[3]. Two key molecules, IL-10 and STAT3, in this pathway have been identified as IBD-associated genes in children and adults [4-6].

Despite the evidence that IL10 and genes within the IL10/STAT3 signaling pathway play a role in IBD, our knowledge about how they may interact with each other is still limited. Genetic interactions between different loci, such as epistasis, have been thought to be of paramount importance in complex diseases [1, 7]. An epistatic interaction of two or more loci can result in an enhancement of the effect that is beyond the addition of the effects of the individual loci under study or can result in the nullification of the effect of the individual genes.

In this paper, we demonstrate that the following epistatic interactions contribute to pediatric IBD by using four computational epistatic interaction models, additive-additive (aa), additive-dominant (ad), dominant-dominant (dd), and dominant-additive (da) [8].

  1. Contribution of intragenic SNP-SNP interaction to pediatric IBD.

IL10 SNP rs1800872 by itself is not associated with pediatric IBD (p=0.71), but through an intragenic interaction with the rs3024496 (p=0.022) is significantly associated with pediatric IBD (aa model, p=0.00015; shown as solid black arrow between the two SNPs in the figure).

  1. Contribution of intergenic SNP-SNP interaction between two genes to pediatric IBD.

Neither IL10RB rs2834167 nor HO1 rs2071746 is associated with pediatric IBD (p=0.203 and p=0.634, respectively), but through intergenic interaction, the two SNPs are significantly associated with pediatric IBD (da model, p=0.0018; shown as solid red arrow between the two genes in the figure).

  1. Contribution of intergenic SNP-SNP interaction among three genes to pediatric IBD.

The model we used can not only estimate low-order epistasis between a pair of loci, but also detect high-order epistasis among three loci. For example, none of the three SNPs in IL10RB rs2834167, HO1 rs2071746, and IL10 rs1800872 are individually associated with pediatric IBD (p=0.203, p=0.634, and p=0.71, respectively), but through intergenic interaction the three SNPs are significantly associated with pediatric IBD (daa model, p=0.00015; shown as broken red arrow among the three genes in the figure). Another example is where none of the following three SNPs is associated with pediatric IBD, IL10RA rs3135932 (p=0.160), IL10 rs1800872 (p=0.71) and IL10 rs3024496 (p=0.022), but through intergenic interaction, these are significantly associated with pediatric IBD (aaa model, p=0.003; shown as broken black arrow among the three SNPs in the figure).

Human complex diseases are determined by multiple gene interactions and environmental factors. Study of individual or multiple variants within a gene provides significant but limited information in the understanding of mechanisms involved in human disease. The present results show that study of intragenic or intergenic SNP interactions of genes involved in a relevant signaling pathway, can reveal significant associations of genetic variants of the genes in the given pathway; in studies of individual SNP associations, these SNPs were not detected as being significant. Such findings could then focus subsequent functional and/or regulatory studies on the particular genetic variants and potentially use targeted therapies for multiple SNPs of one or more genes. The power of intragenic and/or intergenic SNP-SNP interactions in the discovery of previously undetected genetic variants in human disease associations has also been shown in our published work of case-control and case-trios studies [9, 10].

In summary, SNPs within a single gene or multiple genes via epistatic interactions may be important contributors to human disease expression. Moreover, observations made from epistatic interactions may also help identify future genetic targets for therapy. However, to fully understand the physiological/pathological function of epistatic interactions, and signaling pathways involved in human disease, it is imperative to carry out functional and regulatory studies involving the specific variants.

 

Figure. Summary of genetic contribution of genes in the IL10/STAT3 pathway, via epistatic interaction, to pediatric IBD

 

 

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