Basic Study
Copyright ©The Author(s) 2017.
World J Gastroenterol. Jul 21, 2017; 23(27): 4897-4909
Published online Jul 21, 2017. doi: 10.3748/wjg.v23.i27.4897
Table 1 Study samples
SamplenSex, nRace, nAge at diagnosis
IBD159Male, 85; female, 74White, 153; black, 613.1
CD136Male, 77; female, 59White, 130; black, 613.1
CCFA118Male, 65; female, 53White, 112; black, 613.0
Hershey18Male, 12; female, 6White, 1813.4
UC23Male, 9; female, 14White, 2313.3
CCFA10Male, 5; female, 5White, 1012.9
Hershey13Male, 4; female, 9White, 1313.6
Control129Male, 65; female, 64White, 121; black, 7; unknown, 117.5
Table 2 Study single nucleotide polymorphisms for IL-10, IL10RA, IL10RB, STAT3 and HO1 genes
GeneSNP IDChromosomal positionVariationGene locationDisease implicationRef.
IL-10rs1800872206946407C-592>A5'-upstreamassociated with IBD[37]
rs3024498206941529c.T>C3'-untralated regionassociated with colorectal cancer[41]
rs3024496206941864A>G3'-untralated regionassociated with IBD and colorectal cancer, with decreased IL-10, with increased IgE levels[37-39,41]
IL10RArs3135932117864063c.A247>G, p.Ser159Glycoding regionmutations (other than the studied SNP) associated with pediatric IBD[7,10,12]
IL10RBrs283416734640788c.A>G, p.Lys(A)47Glu(G)coding regionmutations (other than the studied SNP) associated with pediatric IBD[7-11]
STAT3rs744166404514201A>GIntron 1 (closer to exon2)associated with IBD[20]
HO1rs20717463577672A413>T5'-upstreamno association with IBD, associated with asthma and allergy, anti-inflammation, anti-oxidant[30,31]
Table 3 PCR-RFLP method for genotyping IL-10, IL10RA, IL10RB, STAT3 and HO1 genes
GeneSNP IDVariantPCR amplification
RFLP
Primers1Product, bpRestriction enzymeRecognition site
IL-10rs1800872G>TIL-2f: 5'-AACTTAGGCAGTCACCTTAGG-3'149ScaIT yes; G No
IL-2r: 5'-CATCCTGTGACCCCTCCAGT-3'
rs3024498T>CIL-5f: 5'-GCTCCtTGGTTTCTCTTCCTA AG-3'137HpyCH4VC yes; T No
IL-5r: 5'-AGAAGCTTCCATTCCAAGCC TGA-3'
rs3024496A>GIL-4f: 5'-GTATCAGAGGTAATAAATATTCcAT-3'178NlaIIIG yes; A No
IL-4r: 5'-TAGAAGCATACATGACAATGAAG-3'
IL10RArs3135932A>GRA3f: 5'-CCCGCAAATGACACATATGgA-3'172MnIG yes; A No
RA3r: 5'-AGTTCCCAATGGCACACAAGG-3'
IL10RBrs2834167A>GRB3f: 5'-GCCATAGAGGAGAACCAAGTG-3'206CarIG yes; A No
RB3r: 5'-GCTGTGAAAGTCAGGTTCTCTT-3'
STAT3rs744166A>GST2f: 5'-CAGGAGTGCCAACATTGAGAG-3'106AluIA yes; G No
ST2r: 5'-G TAATGTCTTGAGGGAATCGAG-3'
HO1rs2071746A>THO4f: 5'-TCAGCAGAGGATTCCAGCAGG-3'110BfaIA yes; T No
TG-3' HO4r: 5'-AGGCAGCGCTGCTCAGAGCAC-3'
Table 4 Genetic association of IL-10, IL10RA, IL10RB, STAT3 and HO1 genes with pediatric inflammatory bowel disease
GeneSNP IDGenotypeDisease, nControl, nOR95%CIP value
IL-10rs1800872CC89780.8630.564-1.3130.71
CA6850
AA21
C allele246206
A allele7252
rs3024498CC86770.8300.552-1.2440.616
CT6547
TT85
C allele237201
T allele8157
rs3024496AA57271.4871.055-2.0990.022
AG6969
GG3333
A allele183123
G allele185135
IL10RArs3135932AA108850.9250.595-1.4330.160
AG3940
GG124
A allele255210
G allele6348
IL10RBrs2834167AA91641.3180.884-1.9680.203
AG6660
GG25
A allele248188
G allele7070
STAT3rs744166GG64490.9430.662-1.3400.352
AG6663
AA2917
A allele194161
G allele12497
HO1rs2071746AA32300.9570.680-1.3480.634
AT9671
TT3128
A allele158131
T allele160127
Table 5 Epistatic interaction between two single nucleotide polymorphisms in three IL-10 single nucleotide polymorphisms studied
Epistatic modelrs3024496, P = 0.022, Bp = 0.0226rs3024498, P = 0.616; Bp = 1
rs1800872, P = 0.71; Bp = 1aaP = 0.00015; Bp = 0.003P = 0.638; Bp = 1
adP = 0.057; Bp = 1P = 0.605; Bp = 1
daP = 0.010; Bp = 0.216P = 0.977; Bp = 1
ddP = 0.239; Bp = 1P = 0.049; Bp = 1
rs3024496, P = 0.022, Bp = 0.0226aaP = 0.371; Bp = 1
adP = 0.222; Bp = 1
daP = 0.167; Bp = 1
ddP = 0.584; Bp = 1
Table 6 Gene-gene interaction between IL-10 with IL10RA, IL10RB, STAT3, or HO1 in pediatric inflammatory bowel disease
GeneSNPEpistatic modelIL10RA rs3135932, P = 0.160; Bp = 1IL10RB rs2834167, P = 0.203; Bp = 1STAT3 rs744166, P = 0.352; Bp = 1HO1 rs2071746, P = 0.634; Bp = 1
IL-10rs1800872aaP = 0.046; Bp = 1P = 0.029; Bp = 1P = 0.248; Bp = 1P = 0.910; Bp = 1
adP = 0.739; Bp = 1P = 0.107; Bp = 1P = 0.954; Bp = 1P = 0.617; Bp = 1
daP = 0.056; Bp = 1P = 0.376; Bp = 1P = 0.117; Bp = 1P = 0.569; Bp = 1
ddP = 0.126; Bp = 1P = 0.168; Bp = 1P = 0.036; Bp = 1P = 0.671; Bp = 1
rs3024498aaP = 0.330; Bp = 1P = 0.062; Bp = 1P = 0.143; Bp = 1P = 0.898; Bp = 1
adP = 0.068; Bp = 1P = 0.629; Bp = 1P = 0.032; Bp = 1P = 0.840; Bp = 1
daP = 0.884; Bp = 1P = 0.307; Bp = 1P = 0.316; Bp = 1P = 0.607; Bp = 1
ddP = 0.265; Bp = 1P = 0.644; Bp = 1P = 0.029; Bp = 1P = 0.790; Bp = 1
rs3024496aaP = 0.021; Bp = 0.433P = 0.425; Bp = 1P = 0.538; Bp = 1P = 0.346; Bp = 1
adP = 0.020; Bp = 0.426P = 0.495; Bp = 1P = 0.306; Bp = 1P = 0.741; Bp = 1
daP = 0.081; Bp = 1P = 0.189; Bp = 1P = 0.234; Bp = 1P = 0.297; Bp = 1
ddP = 0.967; Bp = 1P = 0.570; Bp = 1P = 0.402; Bp = 1P = 0.457; Bp = 1
IL10RBrs2834167aaP = 0.403; Bp = 1P = 0.251; Bp = 1P = 0.128; Bp = 1
adP = 0.384; Bp = 1P = 0.956; Bp = 1P = 0.369; Bp = 1
daP = 0.518; Bp = 1P = 0.776; Bp = 1P = 0.0018; Bp = 0.039
ddP = 0.176; Bp = 1P = 0.072; Bp = 1P = 0.289; Bp = 1
Table 7 Epistatic interaction among the two IL-10 single nucleotide polymorphisms, rs1800872 and rs3024496, and IL10RA, IL10RB, STAT3, or HO1
Epistatic modelIL10RA rs3135932, P = 0.16; Bp = 1IL10RB rs2834167, P = 0.203; Bp = 1STAT3 rs744166, P = 0.352; Bp = 1HO1 rs2071746, P = 0.634; Bp = 1
Two IL-10 SNPs: rs1800872 and rs3024496 aa: P = 0.0002; Bp = 0.003aaaP = 0.003; Bp = 0.099P = 0.080; Bp = 1P = 0.175; Bp = 1P = 0.216; Bp = 1
aadP = 0.130; Bp = 1P = 0.340; Bp = 1P = 0.920; Bp = 1P = 0.140; Bp = 1
Table 8 Epistatic interaction of IL10RB and HO1 with IL-10 (three single nucleotide polymorphisms), IL10RA, or STAT3
Epistatic modelIL-10 rs1800872, P = 0.71; Bp = 1IL-10 rs3024498, P = 0.616; Bp = 21IL-10 rs3024496, P = 0.022; Bp = 0.0226IL10RA rs3135932, P = 0.16; Bp = 1STAT3 rs744166, P = 0.352; Bp = 1
aa IL10RB rs2834167 and HO1 rs2071746aaaP = 0.029;P = 0.545;P = 0.255;P = 0.023;P = 0.049;
Bp = 1Bp = 1Bp = 1Bp = 0.820Bp = 1
aadP = 0.127;P = 0.240;P = 0.928;P = 0.193;P = 0.554;
Bp = 1Bp = 1Bp = 1Bp = 1Bp = 1
ad IL10RB rs2834167 and HO1 rs2071746adaP = 0.394;P = 0.824;P = 0.242;P = 0.444;P = 0.436;
Bp = 1Bp = 1Bp = 1Bp = 1Bp = 1
addP = 0.976;P = 0.406;P = 0.327;P = 0.644;P = 0.649;
Bp = 1Bp = 1Bp = 1Bp = 1Bp = 1
da IL10RB rs2834167 and HO1 rs2071746daaP = 0.00015;P = 0.489;P = 0.047;P = 0.008;P = 0.014;
Bp = 0.005Bp = 1Bp = 1Bp = 0.287Bp = 0.491
dadP = 0.072;P = 0.140;P = 0.388;P = 0.205;P = 0.977;
Bp = 1Bp = 1Bp = 1Bp = 1Bp = 1
dd IL10RB rs2834167 and HO1 rs2071746ddaP = 0.199;P = 0.808;P = 0.568;P = 0.766;P = 0.4731;
Bp = 1Bp = 1Bp = 1Bp = 1Bp = 1
dddP = 0.694;P = 0.958;P = 0.007;P = 0.181;P = 0.057;
Bp = 1Bp = 1Bp = 0.242Bp = 1Bp = 1