| Literature DB >> 34248934 |
Chenxi Liu1, Songxin Yan1, Haizhen Chen1,2, Ziyan Wu3, Liubing Li1, Linlin Cheng1, Haolong Li1, Yongzhe Li1.
Abstract
Objectives: Systemic sclerosis (SSc) is an uncommon autoimmune disease that varies with ethnicity. Single nucleotide polymorphisms (SNPs) in the GTFSI, NFKB1, and TYK2 genes have been reported to be associated with SSc in other populations and in individuals with various autoimmune diseases. This study aimed to investigate the association between these SNPs and susceptibility to SSc in a Chinese Han population. Method: A case-control study was performed in 343 patients with SSc and 694 ethnically matched healthy controls. SNPs in GTF2I, NFKB1, and TYK2 were genotyped using a Sequenom MassArray iPLEX system. Association analyses were performed using PLINK v1.90 software. Result: Our study demonstrated that the GTF2I rs117026326 T allele and the GTF2I rs73366469 C allele were strongly associated with patients with SSc (P = 6.97E-10 and P = 1.33E-08, respectively). Patients carrying the GTF2I rs117026326 TT genotype and the GTF2I rs73366469 CC genotype had a strongly increased risk of SSc (P = 6.25E-09 and P = 1.67E-08, respectively), and those carrying the NFKB1 rs1599961 AA genotype had a suggestively significantly increased risk of SSc (P = 0.014). Moreover, rs117026326 and rs73366469 were associated with SSc in different genetic models (additive model, dominant model, and recessive model) (P < 0.05) whereas rs1599961 was associated with SSc in the dominant genetic model but not in the addictive and recessive models (P = 0.0026). TYK2 rs2304256 was not significantly associated with SSc in this study.Entities:
Keywords: GTF2I; NFKB1; genetic susceptibility; single nucleotide polymorphism; systemic sclerosis
Year: 2021 PMID: 34248934 PMCID: PMC8261294 DOI: 10.3389/fimmu.2021.640083
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
Allele and genotype frequencies in patients with SSc and controls.
| Gene | SNP | Allele Frequency (%) | Genotype Frequency (%) | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Allele | Case/control (%) |
| OR (95%CI) | Genotype | Case/control (%) |
| χ2 | ||
|
| rs117026326 | T | 166/192 (24.6/13.9) |
| 2.22 (1.72-2.86) | TT | 23/10 (6.8/1.4) |
| 37.78 |
| C | 510/1190 (75.4/86.1) | TC | 120/172 (35.5/24.9) | ||||||
| CC | 195/509 (57.7/73.7) | ||||||||
| rs73366469 | C | 181/228 (26.8/16.6) |
| 2.02 (1.58-2.57) | CC | 26/14 (7.7/2.0) |
| 35.82 | |
| T | 495/1148 (73.2/83.4) | TC | 129/200 (38.2/29.1) | ||||||
| TT | 183/474 (54.1/68.9) | ||||||||
|
| rs1599961 | A | 308/560 (40.8/45.3) | 0.086 | 1.19 (0.97-1.46) | AA | 63/124 (18.5/18.1) |
| 8.51 |
| G | 372/814 (59.2/54.7) | AG | 182/312 (53.5/45.4) | ||||||
| GG | 95/251 (28.0/36.5) | ||||||||
|
| rs2304256 | A | 296/626 (45.4/43.5) | 0.592 | 0.95 (0.77-1.56) | AA | 67/140 (19.7/20.3) | 0.599 | 1.03 |
| C | 384/754 (54.6/56.5) | CA | 162/346 (47.7/50.1) | ||||||
| CC | 111/204 (32.6/29.6) | ||||||||
SSc, systemic sclerosis.
Clinical characteristics of patients with SSc and healthy controls.
| SSc Patients | Healthy Controls | |
|---|---|---|
| Number | 342 | 694 |
| Mean age ± SD | 48.1 ± 12.5 | 49.4 ± 11.0 |
| Gender, male/female | 34 /308 | 60/634 |
| dcSSc, n (%) | 21 (6.1%) | – |
| lcSSc, n (%) | 153 (44.7%) | – |
| ILD, n (%) | 219 (64.0%) | – |
| PAH, n (%) | 74 (21.6%) | – |
SSc, systemic sclerosis; ILD, interstitial lung disease; PAH, pulmonary arterial hypertension; dcSSc, diffuse cutaneous systemic sclerosis; lcSSc, limited cutaneous systemic sclerosis.
Characteristics of four SNPs.
| Gene | SNP | Chromosome | Position | Distance to TSS** | Function | Allele | MAF in CHB |
|---|---|---|---|---|---|---|---|
|
| rs117026326 | 7 | 74711703 | 54,040 | intron variant | C>T | 0.117 |
|
| rs73366469* | 7 | 74619286 | 38,394 | regulatory region variant | T>C | 0.155 |
|
| rs1599961 | 4 | 102522412 | 21,083 | intron variant | G>A | 0.388 |
|
| rs2304256 | 19 | 10364976 | 15,700 | missense variant | C>A | 0.456 |
*The distance between rs73366469 and GTF2IRD1 is 1 kb, whereas the distance between rs73366469 and GTF2I is 28 kb. Here, we assign rs73366469 to GTF2I. **TSS, transcription start sites.
Figure 1The genotype distributions of the three significant SNPs [(A) rs117026326, (B) rs73366469, and (C) rs1599961] in the patients with SSc and healthy controls are summarized. ***P < 0.001. *P < 0.05.
Genetic models determined by logistic regression analysis.
| Gene | SNP | Addictive Model | Dominant Model | Recessive Model | |||
|---|---|---|---|---|---|---|---|
|
| OR (95%CI) |
| OR (95%CI) |
| OR (95%CI) | ||
|
| rs117026326 |
| 2.23 (1.72-2.89) |
| 2.25 (1.67-3.05) |
| 6.24 (2.77-14.05) |
| rs73366469 |
| 2.11 (1.64-2.71) |
| 2.01 (1.50-2.69) |
| 5.76 (2.80-11.85) | |
|
| rs1599961 | 0.089 | 1.19 (0.97-1.46) |
| 1.61 (1.18-2.20) | 0.526 | 0.89 (0.61-1.29) |
|
| rs2304256 | 0.591 | 0.95 (0.78-1.16) | 0.292 | 0.85 (0.62-1.15) | 0.786 | 1.05 7(0.74-1.50) |
Associations between SNPs and patients with SSc with different clinical characteristics.
| Clinical characteristics | rs117026326 ( | rs73366469 ( | rs1599961 ( | rs2304256 ( | ||||
|---|---|---|---|---|---|---|---|---|
|
| OR |
| OR |
| OR |
| OR | |
| SSc–ILD vs SSc–non-ILD | 0.129 | 0.74 (0.50–1.09) | 0.179 | 0.77 (0.52–1.13) | 0.083 | 0.72 (0.50–1.04) | 0.426 | 1.15 (0.81–1.63) |
| SSc–ILD vs HC |
| 0.58 (0.44–0.77) |
| 1.66 (1.27–2.17) | 0.307 | 1.12 (0.90–1.38) | 0.97 | 1.00 (0.81–1.25) |
| SSc–non-ILD vs HC |
| 2.38 (1.64–3.46) |
| 2.18 (1.52–3.14) |
| 1.49 (1.09–2.02) | 0.388 | 0.87 (0.64–1.19) |
| SSc–PAH vs SSc–non-PAH | 0.99 | 1.0 (0.63–1.60) | 0.78 | 1.07 (0.67–1.70) | 0.796 | 1.06 (0.69–1.62) | 0.735 | 1.07 (0.71–1.61) |
| SSc–PAH vs HC |
| 2.13 (1.41–3.23) |
| 2.09 (1.40–3.12) | 0.081 | 1.34 (0.96–1.87) | 0.844 | 1.04 (0.74–1.46) |
| SSc–non-PAH vs HC |
| 2.12 (1.51–2.99) |
| 1.96 (1.40–2.73) | 0.074 | 1.28 (0.98–1.67) | 0.788 | 0.96 (0.73–1.27) |
| dcSSc vs lcSSc | 0.601 | 1.23 (0.57–2.68) | 0.68 | 1.17 (0.55–2.50) | 0.448 | 0.77 (0.39–1.51) | 0.134 | 0.61 (0.32–1.16) |
| ATA (+) vs ATA (–) | 0.088 | 0.66 (0.40–1.07) | 0.26 | 0.77 (048–1.22) | 0.72 | 1.09 (0.69–1.70) | 0.67 | 1.10 (0.72–1.67) |
| ACA (+) vs ACA (–) | 0.55 | 0.83 (0.46–1.51) | 0.86 | 0.95 (0.54–1.69) | 0.77 | 0.92 (0.52–1.62) | 0.51 | 0.84 (0.51–1.40) |
SSc, systemic sclerosis; HC, healthy controls; ILD, interstitial lung disease; PAH, pulmonary arterial hypertension; ATA, anti-topoisomerase I antibody; ACA, anti-centromere antibody. *The P value was still < 0.05 after Bonferroni correction.