| Literature DB >> 33583939 |
Yuqin Peng1, Bingqian Chen1, Xiaowen Sheng1, Yufeng Qian1.
Abstract
BACKGROUND The IRF5 and TYK2 gene polymorphisms are associated with autoimmune diseases. However, the relationship between the IRF5 and TYK2 gene polymorphisms and RA risk in the Chinese Han population was inconsistent. MATERIAL AND METHODS A total of 578 RA patients (case group) and 578 healthy controls (control group) were assessed in a case-control study. Genotyping of IRF5 (Exon 6 insertion/deletion (in/de), rs2004640, rs2070197, rs10954213) and TYK2 (rs280500, rs280519, rs280521, rs8108236, rs12720253) was performed by direct sequencing method. Data analysis was performed by SHEsis. RESULTS The rs2004640T allele (P=0.0003) and the dominant (P=0.001) and recessive (P=0.01) models of rs2004640 were associated with RA risk after stringent Bonferroni correction (0.05/4). The IRF5 exon 6 (in), rs2070197 and rs10954213 were not associated with RA (P>0.05). Two haplotypes of IRF5 (DTAT and DTGG) were associated with RA susceptibility (P<0.05). In addition, the frequencies of TYK2 rs280500A, rs280521A, and rs8108236A were significantly higher in the RA group compared with the control group (P<0.05). TYK2 rs280500, rs280521, and rs8108236 were associated with RA susceptibility in the dominant model, but the same was not observed for rs280519 and rs12720253 (P<0.05). Furthermore, 3 risk haplotypes (AAAGT, AGGAT, and GAAAT) and a protective haplotype (GAGGT) of TYK2 gene were associated with RA susceptibility (P<0.05). CONCLUSIONS Our results suggest that IRF5 rs2004640, TYK2 rs280500, rs280521, rs8108236, and haplotypes IRF5 (DTAT and DTGG) and TYK2 (AAAGT, AGGAT, GAAAT, and GAGGT) are susceptible factors for RA in a Chinese Han population.Entities:
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Year: 2021 PMID: 33583939 PMCID: PMC7893827 DOI: 10.12659/MSM.928455
Source DB: PubMed Journal: Med Sci Monit ISSN: 1234-1010
Clinical Characteristics of patients with rheumatoid arthritis and healthy controls (n=578).
| Clinical features | Case | Control | p |
|---|---|---|---|
| Male/Female | 51/527 | 55/523 | >0.05 |
| Age (years) | 44.7±12.3 | 45.6±12.8 | >0.05 |
| ESR (mm/h) | 35.1±14.2 | 12.1±8.5 | <0.05 |
| CRP (mg/l) | 26.5±11.2 | 4.7±12.5 | <0.05 |
| HLA-B27+, % | 1/578 (0.17%) | 0/578 (0%) | >0.05 |
| ANA+, % | 102/578 (17.6%) | 0/578 (0%) | <0.05 |
| RF+, % | 224/578 (387%) | 0/578 (0%) | <0.05 |
ANA – antinuclear antibodies; ESR – erythrocyte sedimentation rate; CRP – C-reactive protein; RF – rheumatoid factor. ‘+’ – positive.
Distributions of the genotypes of IRF5 and TYK2 polymorphisms in cases and controls.
| Genes | SNP (A/B) | Genotype (AA/AB/BB) | Genotype frequencies (%) | Power | |||
|---|---|---|---|---|---|---|---|
| Cases | Controls | ||||||
| Exon 6 (D/I) | DD/DI/II | 138/278/162 | 157/288/133 | 0.20, 1.19 [0.91, 1.55] | 0.05, 1.30 [1.00, 1.70] | 95.6 | |
| rs2070197(T/C) | TT/CT/CC | 571/7/0 | 575/3/0 | 0.22, 2.35 [0.60, 9.13] | NA | ||
| rs10954213(A/G) | AA/GA/GG | 277/231/70 | 265/256/57 | 0.48, 0.92 [0.73, 1.16] | 0.22, 1.26 [0.87, 1.82] | ||
| rs2004640(G/T) | GG/GT/TT | 317/232/29 | 371/193/14 | 0.001, 1.49 [1.17, 1.88] | 0.01, 2.30 [1.18, 4.46] | ||
| rs280500(G/A) | GG/AG/AA | 277/260/41 | 347/202/29 | 0.0001, 1.63 [1.29, 2.06] | 0.14, 1.45 [0.89, 2.36] | ||
| rs280519(A/G) | AA/GA/GG | 157/269/152 | 182/270/126 | 0.11, 1.23 [0.96, 1.59] | 0.07, 1.28 [0.98, 1.68] | ||
| rs280521(G/A) | GG/AG/AA | 324/229/25 | 423/140/15 | 1.35e-008, 2.14 [1.67, 2.74] | 0.11, 1.70 [0.89, 3.25] | ||
| rs8108236(G/A) | GG/AG/AA | 311/221/46 | 372/175/31 | 0.0003, 1.55 [1.22, 1.96] | 0.08, 1.53 [0.95, 2.44] | ||
| rs12720253(T/G) | TT/GT/GG | 499/77/2 | 475/101/2 | 0.05, 0.73 [0.53, 1.00] | 1.00, 1.00 [0.14, 7.12] | ||
P – dominant model;
P –recessive model; SNP – single nucleotide polymorphism; OR – odds ratio, 95% CI – 95% confidence intervals, NA – not available; de(D)/in(I) – deletion/insertion; A – allele with major frequency; B – allele with minor frequency.
Figure 1Pairwise linkage disequilibrium of IRF5 and TYK2 single-nucleotide polymorphisms in relation to rheumatoid arthritis. The numbers in the squares refer to the pairwise linkage disequilibrium measured as D’. Haplotype blocks were defined using a setting pairwise D’. (A) Linkage disequilibrium of IRF5 gene. (B) Linkage disequilibrium of TYK2 gene.
The association between the alleles of IRF5 and TYK2 gene polymorphisms and RA risk.
| SNP (A/B) | Position | Case (N=578) | Control (N=578) | P (B vs A+B) | OR (95% CI) | |
|---|---|---|---|---|---|---|
| Exon 6 (D/I) | Exon 6 | 602 | 554 | 0.05 | 0.85 [0.72–0.99] | |
| rs2070197(T/C) | 3′-UTR | 7 | 3 | 0.21 | 2.34 [0.60–9.07] | |
| rs10954213(A/G) | 3′-UTR | 371 | 370 | 0.96 | 1.00 [0.84–1.20] | |
| rs2004640(G/T) | Exon 1 | 290 | 221 | 0.0003 | 1.43 [1.17–1.74] | |
| rs280500(G/A) | 5′ UTR | 342 | 260 | 0.0001 | 1.45 [1.20, 1.75] | |
| rs280519(A/G) | Intron | 573 | 522 | 0.03 | 0.84 [0.71–0.98] | |
| rs280521(G/A) | Intron | 279 | 170 | 1.06e-008 | 1.85 [1.49–2.28] | |
| rs8108236(G/A) | Intron | 313 | 237 | 0.0002 | 1.44 [1.19–1.75] | |
| rs12720253(T/G) | Intron | 81 | 105 | 0.07 | 0.75 [0.56–1.02] |
SNP – single nucleotide polymorphism; OR – odds ratio, 95% CI – 95% confidence intervals; de(D)/in(I) – deletion/insertion; UTR – untranslated region; A – allele with major frequency; B – allele with minor frequency.
Haplotypes structure and frequencies of IRF5 and TYK2 gene polymorphism.
| Genes | Number | Haplotypes | Case | Control | P | OR [95%CI] |
|---|---|---|---|---|---|---|
| IH1 | DTAT | 167 (0.144) | 115 (0.099) | 0.0009 | 1.54 [1.191~1.976] | |
| IH2 | DTAG | 317 (0.274) | 370 (0.320) | 0.02 | 0.81 [0.673~0.962] | |
| IH3 | DTGT | 18 (0.016) | 22 (0.019) | 0.61 | 0.85 [0.455~1.591] | |
| IH4 | DTGG | 48 (0.041) | 95 (0.082) | 4.45e-005 | 0.48 [0.337~0.688] | |
| IH5 | ITAT | 61 (0.052) | 37 (0.032) | 0.01 | 1.69 [1.114~2.572] | |
| IH6 | ITAG | 259 (0.224) | 261 (0.226) | 0.95 | 0.99 [0.817~1.208] | |
| IH7 | ITGT | 44 (0.038) | 46 (0.039) | 0.87 | 0.97 [0.632~1.472] | |
| IH8 | ITGG | 236 (0.204) | 207 (0.179) | 0.12 | 1.18 [0.957~1.449] | |
| TH1 | AAAGT | 43 (0.037) | 14 (0.012) | 9.88e-005 | 3.18 [1.723~5.878] | |
| TH2 | AAGAT | 35 (0.030) | 24 (0.021) | 0.15 | 1.46 [0.866~2.472] | |
| TH3 | AAGGG | 12 (0.011) | 10 (0.009) | 0.66 | 1.20 [0.524~2.753] | |
| TH4 | AAGGT | 83 (0.072) | 80 (0.069) | 0.79 | 1.04 [0.758~1.434] | |
| TH5 | AGAGT | 26 (0.022) | 13 (0.011) | 0.05 | 1.96 [1.005~3.838] | |
| TH6 | AGGAT | 67 (0.058) | 29 (0.025) | 9.82e-005 | 2.35 [1.513~3.667] | |
| TH7 | AGGGT | 73 (0.063) | 80 (0.069) | 0.55 | 0.90 [0.651~1.255] | |
| TH8 | GAAAT | 42 (0.036) | 17 (0.015) | 0.001 | 2.52 [1.427~4.460] | |
| TH9 | GAAGT | 58 (0.050) | 48 (0.042) | 0.34 | 1.21 [0.819~1.789] | |
| TH10 | GAGAT | 71 (0.061) | 87 (0.075) | 0.18 | 0.80 [0.578~1.108] | |
| TH11 | GAGGT | 220 (0.190) | 304 (0.263) | 2.60e-005 | 0.65 [0.538~0.799] | |
| TH12 | GGAAT | 12 (0.011) | 9 (0.008) | 0.55 | 1.29 [0.552~3.032] | |
| TH13 | GGAGT | 56 (0.049) | 54 (0.046) | 0.82 | 1.04 [0.713~1.535] | |
| TH14 | GGGAT | 58 (0.050) | 59 (0.051) | 0.87 | 0.97 [0.668~1.408] | |
| TH15 | GGGGG | 23 (0.020) | 33 (0.029) | 0.41 | 0.92 [0.745~1.126] |
D – deletion; I – insertion; OR – odds ratio; 95% CI – 95% confidence intervals, ‘−‘ – not calculated. a The program, Plink, was used to estimate common (frequency[0.01) haplotypes constructed by the SNPs of IRF5 (exon 6 (in/de), rs2070197, rs10954213, rs2004640) and five SNPs of TYK2 genotyped (rs280500, rs280519, rs280521, rs8108236, rs12720253). b Each haplotype was compared with the other haplotypes combined. c The Bonfferoni correction was applied to correct the p value.
The Hardy-Weinberg equilibrium of IRF5 and TYK2 gene polymorphisms in case and control groups.
| Genes | SNP ID | Position | Case (p) | Control (p) |
|---|---|---|---|---|
| Exon 6 | Exon 6 | 0.38 | 0.96 | |
| rs2070197 | 7: 128948946 | 0.88 | 0.95 | |
| rs10954213 | 7: 128949373 | 0.05 | 0.67 | |
| rs2004640 | 7: 128938247 | 0.10 | 0.06 | |
| rs280500 | 19: 10351402 | 0.06 | 0.95 | |
| rs280519 | 19: 10333933 | 0.09 | 0.71 | |
| rs280521 | 19: 10334392 | 0.05 | 0.40 | |
| rs8108236 | 19: 10326832 | 0.44 | 0.08 | |
| rs12720253 | 19: 10339683 | 0.59 | 0.16 |