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. 2025 Sep 30;18:144. doi: 10.1186/s12920-025-02217-1

Impact of interaction between IL-21 gene variants and smoking status on susceptibility to rheumatoid arthritis

Xiang Lu 1,, Yuan Xue 2, Shanle Yan 1
PMCID: PMC12482331  PMID: 41029746

Abstract

Background

In recent years, interleukin-21 (IL-21) has been found to be a key player in RA pathogenesis and progression, despite accumulating evidence on rheumatoid arthritis (RA) etiology, the precise contribution of IL-21 gene variants interacting with environmental exposures remains unexplored in population-based studies. Therefore, we performed this study to evaluate the impact of gene single nucleotide polymorphisms (SNPs) and their interaction with environment on RA risk.

Methods

In this study, Genomic DNA was extracted from whole blood samples (Invitrogen PureLink™ Genomic DNA Mini Kit), and targeted genotyping of four SNPs (rs2055979, rs12508721, rs2221903 and rs907715) of IL-21 gene was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodology. Genotypic relationship testing in this case-control study was performed by using SNPStats online software (https://www.snpstats.net/), odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. The interaction combinations among four SNPs and environmental factors including smoking and alcohol drinking were screened using generalized multifactor dimensionality reduction (GMDR).

Results

Logistic regression analysis showed that the risks of RA were significantly higher in carriers with rs2055979- CA genotype (OR = 1.63, 95% CI = 1.28–1.97), rs2055979-AA genotype (OR = 2.02, 95% CI = 1.47–2.59), rs2055979-AA + CA genotype (OR = 1.78, 95% CI = 1.32–2.26), compared to carriers with rs2055979-CC genotype. In allele genetic model, rs2055979-A was also associated with increased RA risk (OR = 1.72, 95% CI = 1.39–2.06). However, we did not find any significant association of rs2221903, rs907715 and rs12508721 with RA risk. The GMDR model found a statistically significant two locus model (P = 0.018), including rs2055979 and smoking, indicating that the interaction between rs2055979 and smoking was significantly associated with the risk of RA. Smokers with rs2055979-AA or CA genotype had the highest risk of RA, compared with non-smokers with rs2055979-CC genotype, OR (95% CI) was 3.23 (1.86–4.64).

Conclusions

We found that rs2055979- A allele, gene- environment interaction between rs2055979 and smoking were all correlated with increased RA risk.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-025-02217-1.

Keywords: Smoking, Single nucleotide polymorphisms, Interleukin-21, Rheumatoid arthritis, Interaction

Introduction

Rheumatoid arthritis (RA), a prevalent chronic autoimmune disorder affecting multiple systems, primarily manifests as inflammation targeting smaller joints. This condition progresses with gradual deterioration of joint integrity accompanied by synovitis (joint lining inflammation), culminating in structural deformities and impaired mobility [1, 2]. Worldwide, the prevalence of RA is 0.5%~1% [3]. In the Chinese population, the prevalence of RA is about 0.34% [4], and this value is still increasing [5]. The development and progression of RA are shaped by the synergistic interaction between inherited genetic susceptibility and external environmental triggers [6]. RA belongs to a complex disease involving multiple susceptible genes. Although many biological molecular mechanisms have been proposed, so far, the pathogenesis and specific etiology of RA are still not very clear in this study. It suggests that immune abnormalities may be caused by genetic, epigenetic, environmental, and hormonal interactions, leading to the occurrence of RA [7]. Consequently, systematic elucidation of the dynamic interplay among environmental exposures, genetic predispositions, and stochastic elements holds the key to deciphering the intricate molecular pathways underlying rheumatoid arthritis pathogenesis.

Interleukin-21 (IL-21), a pleiotropic immunomodulator primarily synthesized by activated CD4 + T lymphocytes and natural killer (NK) cells, exerts pleiotropic regulatory effects on both innate and adaptive immunity [8]. This cytokine demonstrates functional dichotomy within the IL-2 cytokine superfamily (including IL-2, IL-4, and IL-15) [9], with which it shares conserved structural domains. The biological activity of IL-21 is mediated through binding to the gamma subunit (γc) of its cognate receptor (IL-21R), which exhibits pan-leukocytic expression patterns. Notably, specialized T cell subsets, particularly Th17, follicular helper T (Tfh), and NKT cells-constitute the predominant cellular sources of IL-21 secretion [10].

In recent years, IL-21 has been found to be a key player in RA pathogenesis and progression [1113]. The IL-21 gene, mapped to chromosomal region 4q27, contains five exons in regions within its genomic structure. And all selected SNPs in this study were located in the intron region. Several single-nucleotide polymorphisms (SNPs) located in IL21 region have proven to be significantly associated with several autoimmune disorders [14, 15], including RA [16, 17]. However, the results obtained from these studies were inconsistent. In addition, the pathogenesis of RA involves complex reasons, including genetic and environmental factors. Previously, several studies reported the impact of smoking on RA pathology [18, 19]. And studies also reported the gene- smoking interaction could influence RA risk in different populations [20, 21]. ‌Despite accumulating evidence on rheumatoid arthritis etiology, the precise contribution of IL-21 genetic variants interacting with environmental exposures remains unexplored in population-based studies. Therefore, the purpose of this study is to evaluate the relationship between IL-21 gene SNPs and RA risk. We also included environmental factors in the interaction analysis models to verify the effect of the interaction between IL-21 gene SNPs and environmental factor on RA risk based on this Chinese Han populations.

Methods

Study population

A total of 816 participants with an average age of 49.5 ± 10.2 years were enrolled in this case- control study, including 406 RA patients and 410 healthy controls from March 2019 to December 2022 in the Fourth Affiliated Hospital of Soochow University hospital in Suzhou city of Jiangsu province and the Shanxi Yuncheng Central Hospital in Yuncheng city of Shanxi province. All participants were selected from RA patients diagnosed by attending physician according to the ACR/EULAR 2010 rheumatoid arthritis classification criteria [22]. RA patients with juvenile idiopathic arthritis or other autoimmune diseases were excluded from the case group. The demographics data including age, gender, BMI and family history, clinical data including RA disease duration, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), rheumatoid factor (RF), anti-cyclic citrullinated peptide (CCP), disease activity score (DAS 28) of all patients were obtained from their medical records. Unrelated controls matching to RA patients regarding age (± 3 years) and sex were selected, while those participants with family history of RA were excluded. Those participants and their first-degree relatives who have a history of RA or any other autoimmune disease were excluded from the control group. All study protocols of the current study were approved by the ethics committee of the Fourth Affiliated Hospital of Soochow University. In this study, PASS 15.0.5 software [23] was used to calculate the sample size. The results showed that the minimum sample size was 401 pairs (power ≥ 0.95, α < 0.05, OR = 2.0, P2 = 0.12). A total of 406 pairs were enrolled in this study. Therefore, the number of RA patients met the requirements for statistical analysis.

The information on smoking and alcohol consumption status were collected by questionnaire. Current alcohol consumers were defined as those who drink more than one drink of any type per month, and current smokers were defined as those who have smoked at least 100 cigarettes and still smoked at the time of the interview [24].

Genotyping methods

A total of four SNPs within IL-21 gene were selected, including: rs2055979, rs12508721, rs2221903 and rs907715, based on HapMap data (http://hapmap.ncbi.nlm.nih.gov/) and dbSNP data (http://www.ncbi.nlm.nih.gov/projects/SNP/) according to the following the criteria: first, minor allele frequency more than 5%; second, it was reported in previous studies on association with RA susceptibility; third, the relationship between this SNP and RA susceptibility remains inconclusive.

Genomic DNA was extracted from peripheral blood samples using a commercial kit (e.g., QIAamp DNA Blood Mini Kit) following the manufacturer’s protocol. Four IL-21 gene SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Primer pairs were designed using Primer3Plus to flank each SNP (Supplementary Table 1), with amplicon sizes ranging 200–400 bp. PCR was performed in 25 µL reactions containing 50–100 ng DNA, 0.4 µM primers, 0.2 mM dNTPs, 1× PCR buffer, and 1 U Taq polymerase. Cycling conditions included initial denaturation (95 °C, 5 min), 35 cycles of denaturation (95 °C, 30 s), annealing (optimized Tm for each primer pair, 30 s), extension (72 °C, 1 min/kb), and final extension (72 °C, 10 min). Amplicons were digested with 5–10 U of restriction enzymes (supplementary Table 1) in 20 µL reactions at manufacturer-specified temperatures for 4 h. Digested products were resolved on 3% agarose gels alongside undigested controls and a 50-bp DNA ladder. Known genotype controls and 10% random replicates were included for validation.

Statistical analysis

In this study, data was calculated by using SPSS version 22.0 (SPSS Inc., Chicago, Ill., USA). Genotype and allele frequencies of rs2055979, rs12508721, rs2221903 and rs907715 were quantified through direct counting methodology, and Hardy–Weinberg equilibrium (HWE) was evaluated by the χ2 test. Odds ratios (ORs) and 95% confidence intervals (CIs) were employed to assess the effects of minor alleles of four SNPs on RA risk. Genotypic relationship testing in this case-control study was performed by using SNPStats online software (https://www.snpstats.net/) under three genetic models (codominant, dominant and allele). A Bonferroni-corrected threshold of P < 0.0125 was considered significant. The interaction combinations among four SNPs and environmental factors including smoking and alcohol drinking were screened using generalized multifactor dimensionality reduction (GMDR) [25]. And the interaction effect was evaluated by dividing participant into four groups according to the rs2055979 genotypes (CC and AA + CA) and smoking status (current or ever and never), OR (95%CI) was calculated for the other three groups compared to never smokers with rs2055979-CC genotype.

Results

A total of 816 participants with an average age of 49.5 ± 10.2 years were enrolled in this case- control study, including 406 RA patients and 410 healthy controls. Table 1 shows the demographics and clinical features of 816 participants grouped by RA patients and control group. The average values of age and body mass index (BMI) and distribution of gender were not significantly different between case and controls. The means of ESR, CRP concentrations and current or ever smoking and alcohol drinking rates were higher in RA patients than in controls.

Table 1.

Demographics and clinical features of 816 participants grouped by RA patients and control group

Variables RA patients
(n = 406)
Normal controls
(n = 410)
p-values
Age (year) (Mean ± SD) 50.2 ± 11.8 48.7 ± 10.6 0.056
Gender, N (%) 0.895
 Male 214 (52.7) 218 (53.2)
 Female 192 (47.3) 192 (46.8)
Current or ever smoking 152 (36.9) 120 (29.3) 0.013
Duration of smoking cessation (years) (Mean ± SD) 4.8 ± 2.5 5.2 ± 2.9 0.114
Current or ever alcohol consumption 171 (42.1) 140 (34.1) 0.019
BMI (kg/m2) (Mean ± SD) 24.3 ± 8.5 23.6 ± 9.0 0.254
ESR (mm/1st hours) (Mean ± SD) 35.2 ± 19.46 18.9 ± 12.4 < 0.001
CRP (mg/mL) (Mean ± SD) 17.6 ± 16.2 1.68 ± 6.8 < 0.001
Family history, N (%) 170 (41.9) 0 (0)
RF (IU\ml) (Mean ± SD) 72.41 ± 32.15
RF positive, N (%) 340 (83.7)
Anti-CCP (U/ml) (Mean ± SD) 147.6 ± 65.7
Anti-CCP positive, N (%) 304 (74.9)
Duration of RA (years) (Mean ± SD) 3.26 ± 0.92
DAS28 score, N (%)
 Low (< 3.2) 112 (27.6)
 Intermediate (3.2–5.1) 160 (39.4)
 High (> 5.1) 134 (33.0)

BMI: body mass index; CRP: C-reactive protein; ESR: Erythrocyte Sedimentation Rate; RF: Rheumatoid Factor; Anti CCP: Anti- Cyclic Citrullinated Peptide; DAS 28: disease activity score

In this study, the distribution of four SNP genotypes in the control group were according to HWE (all P values > 0.05). The frequencies of rs2055979 minor allele (A) were significantly higher in RA patients than those in controls (9.8% and 4.4%). Logistic regression analysis showed that the risks of RA were significantly higher in carriers with rs2055979- CA genotype (OR = 1.63, 95% CI = 1.28–1.97), AA genotype (OR = 2.02, 95% CI = 1.47–2.59), AA + CA genotype (OR = 1.78, 95% CI = 1.32–2.26), compared to carriers with CC genotype. In allele genetic model, rs2055979-A was also associated with increased RA risk (OR = 1.72, 95% CI = 1.39–2.06). However, we did not find any significant association of rs2221903, rs907715 and rs12508721 with RA risk (Table 2).

Table 2.

Genotype and allele frequencies of four SNPs between case and control group

SNP Genotypes and alleles Frequencies N (%) OR (95%CI)* P-values for HWE test P-values for OR
Normal controls
(n = 410)
RA patients
(n = 406)
rs2055979 CC 270 (65.8) 205 (50.5) 1.00
CA 122 (29.8) 161 (39.7) 1.63 (1.28–1.97) 0.0006
AA 18 (4.4) 40 (9.8) 2.02 (1.47–2.59) < 0.001
AA + CA 140 (34.2) 201 (49.5) 1.78 (1.32–2.26) < 0.001
C 662 (80.7) 571 (70.3) 1.00
A 158 (19.3) 241 (29.7) 1.72 (1.39–2.06) < 0.001
HWE test for controls 0.378
rs2221903 TT 242 (59.0) 225 (55.4) 1.00
TC 153 (37.3) 158 (38.9) 1.21 (0.81–1.65) 0.427
CC 15 (3.7) 23 (5.7) 1.47 (0.72–2.23) 0.652
TC + CC 168 (41.0) 181 (44.6) 1.26 (0.79–1.77) 0.604
T 637 (77.7) 608 (74.9) 1.00
C 183 (22.3) 204 (25.1) 1.26 (0.84–1.77) 0.531
HWE test for controls 0.122
rs907715 CC 236 (57.6) 216 (53.2) 1.00
CT 147 (35.8) 153 (37.7) 1.36 (0.86–1.90) 0.486
TT 27 (6.6) 37 (9.1) 1.54 (0.78–2.32) 0.621
CT + TT 174 (42.4) 190 (46.8) 1.39 (0.83–2.01) 0.536
C 619 (75.5) 585 (72.0) 1.00
T 201 (24.5) 227 (28.0) 1.40 (0.87–1.95) 0.503
HWE test for controls 0.528
rs12508721 TT 246 (60.0) 226 (55.7) 1.00
TC 145 (35.4) 152 (37.4) 1.40 (0.90–1.92) 0.284
CC 19 (4.6) 28 (6.9) 1.61 (0.84–2.39) 0.492
CT + TT 164 (40.0) 180 (44.3) 1.44 (0.88–2.04) 0.405
T 637 (77.7) 604 (74.4) 1.00
C 183 (22.3) 208 (25.6) 1.45 (0.92–2.02) 0.382
HWE test for controls 0.686

*Adjusted for age, gender, smoking status, alcohol drinking status and BMI

GMDR was employed to screen IL-21 gene-environment interactions through combinatorial evaluation of rs2069762, rs2221903, rs13143866 and rs907715 variants with environmental factors (smoking and alcohol drinking) on the RA susceptibility (Table 3). We found a statistically significant two-locus model (P = 0.018), which included rs2055979 and smoking. This indicates that the interaction between rs2055979 and smoking was significantly associated with the risk of RA. The Cross-validation consistency of the two-site model was 10/10 and the test accuracy was 0.632.

Table 3.

GMDR analysis on the best interaction models between IL-21 gene SNPs and smoking and alcohol consumption

Locus no. Best combination Cross-validation consistency Testing balanced accuracy p-values*
IL-21 gene-smoking interaction*
2 rs2055979, smoking 10/10 0.632 0.018
3 rs2055979, rs12508721, smoking 7/10 0.607 0.324
4 rs2055979, rs12508721, rs2221903, smoking 6/10 0.532 0.425
5 rs2055979, rs12508721, rs2221903, rs907715, smoking 8/10 0.521 0.182
IL-21 gene-alcohol consumption interaction**
2 rs2055979, alcohol drinking 8/10 0.524 0.256
3 rs2055979, rs12508721, alcohol drinking 6/10 0.518 0.359
4 rs2055979, rs12508721, rs2221903, alcohol drinking 5/10 0.532 0.746
5 rs2055979, rs12508721, rs2221903, rs907715, alcohol drinking 6/10 0.496 0.532

*Adjusted for age, gender, alcohol drinking status and BMI

**Adjusted for age, gender, smoking status and BMI

To test the effect value of this gene- environment interaction, we performed cross analysis according to smoking status (Never and Current or ever) and rs2055979 genotypes (CC and AA or CA), and participants were grouped into four groups, including never smokers with rs2055979- CC genotype, never smokers with rs2055979- AA or CA genotype, current or ever smokers with rs2055979-CC genotype, current or ever smokers with rs2055979-AA or CA genotype. We found that current or ever smokers with rs2055979-AA or CA genotype had the highest risk of RA, compared with never smokers with rs2055979-CC genotype. After covariates adjustment for age, gender, alcohol drinking status and BMI, the OR (95% CI) was 3.23 (1.86–4.64) (Table 4).

Table 4.

Analysis of interaction between rs2055979 and smoking on RA risk by using logistic regression

rs2055979 Smoking OR (95% CI)* P-values
CC Never 1.00
AA + CA Never 1.52 (1.13–1.94) 0.0014
CC Current or ever 1.67 (1.21–2.15) < 0.001
AA + CA Current or ever 3.23 (1.86–4.64) < 0.001
Interaction P- values: 0.041

*Adjusted for age, gender, alcohol drinking status and BMI

Discussion

This research examined the association between four IL-21 gene SNPs and the risk of RA in a Chinese Han population. We found that rs2055979 minor allele (A) was associated with increased RA risk. However, no statistically significant relationship was found between rs2221903, rs907715, rs12508721 and RA risk. The IL-21 gene, mapped to chromosomal region 4q27, contains five exons in regions within its genomic structure. And all selected SNPs in this study were located in the intron region. Previously, several studies reported that SNPs of IL-21 genes were associated with several autoimmune disorders [14, 15] in different populations. Two meta- analyses [16, 17] also reported that IL-21 gene rs6822844 was significantly associated with RA risk. Contrast to rs6822844, less study focused on rs2055979, rs2221903, rs907715 and rs12508721. A case- control study [26] in Mexican populations suggested that IL-21 gene rs2055979 was associated with increased RA risk, but no significant association was found between rs2221903 and RA risk. Hao et al. [27] performed a case-control study in Chinese populations and suggested that rs2055979 was associated with increased RA risk, individuals with the AA genotype exhibit a significantly increased risk of developing rheumatoid arthritis, with a 4.34 times greater likelihood. However, rs2221903 and rs907715 were not correlated with RA risk. Similarly, in an earlier study, a study [28] demonstrated no significant association with RA susceptibility in the Australian population. Although previous studies have investigated the relationship between rs2055979, rs2221903 and rs907715 in different populations, especially the study in Chinese. In terms of rs12508721, Malinowski et al. [29] concluded that no significant relationship existed between rs2221903 variants and RA susceptibility. Compared to the four fore-mentioned studies, our research has the following advantages: first, the sample size of our study was larger than that of the four fore- mentioned studies. Second, rs12508721 was not investigated in previous studies. So, this SNP (rs12508721) was first investigated on this topic in our study, but we concluded that rs12508721 was not associated with RA risk in this population-based case- control study.

The inflammatory environment in RA is shaped by cytokines that are pivotal to immune dysregulation and aberrant autoantibody synthesis [30, 31]. Among these, IL-21 is centrally involved in regulating immune and non-immune cells, with roles spanning CD4 + T-cell activation and proinflammatory cytokine release to support Th17 development [32]. Genetic analysis [26] revealed that the IL-21 gene rs2055979 AA genotype correlated with elevated anti-CCP antibodies in RA. Mechanistically, IL-21 enhances antibody output by stimulating B-cell clonal-expansion and plasma cell formation; however, a causal relationship between this SNP and antibody overproduction remains speculative [33].

RA susceptibility could be mediated through a multifactorial framework, encompassing hereditary components, environmental influences, and their dynamic interplay. Previously, several studies reported the impact of smoking [18, 19] and alcohol drinking [34] on RA pathology. In this study, we found that the current or ever smoking and alcohol drinking rates were higher in RA patients than in controls, which means that the smoking status may be associated with RA risk. So, we performed gene- environment interaction among four SNPs of IL-21 gene, smoking and alcohol drinking status using GMDR model. We found that the interaction between rs2055979 and smoking was significantly associated with the risk of RA. Previously, several studies reported that other genes may interact with smoking to influence RA susceptibility [35, 36]. This is the first study focused on the impact of IL-21 gene- smoking interaction on RA risk. Therefore, RA susceptibility could be influenced by IL-21 gene SNPs, such as rs2055979, however this impact could be influenced by environmental factors, such as smoking status. The RA risk for smokers with rs2055979 minor allele was higher than the sum of subjects with single risk factors (smoking or rs2055979 minor allele). In the verification of RA risk, we should consider not only the single risk factor, but also the synergetic effect among these factors.

This study also has some limitations to explain. Firstly, some serological markers were not measured, including IL-21 levels, ACPA/RF, therefore, it is difficult to explain the effect of rs2055979 on RA mechanism from physiological indicators or serum markers. Secondly, more SNPs of IL-21 genes and more environmental factors should be enrolled in future studies to verify the results obtained in this study. Thirdly, the sex ratio of RA cases is not in line with the routine, which means that the selection bias may exist in this case- control study. The results obtained in this study need to be verified in different populations. Lastly, DAS28 evaluation was not performed for controls, who were normal control without RA, so we could not perform testing on association between IL-21 gene-smoking interaction and DAS28 score, to strengthen the clinical relevance of the findings.

In summary, our findings reveal that both the A allele at the rs2055979 locus of IL-21 gene, and a gene-environment interaction between rs2055979 and smoking behavior demonstrate significant correlations with elevated RA risk. In the future, more functional studies should be performed to investigate the correlation between rs2055979 genotypes and IL-21 expression or B-cell activity. In addition, more environmental factors, such as pollutants or epigenetics should be included in the gene-environment analyses.

Supplementary Information

Supplementary Material 1 (17.9KB, docx)

Acknowledgements

None.

Abbreviations

OR

Odds ratios

CI

Confidence interval

RA

Rheumatoid arthritis

IL-21

Interleukin-21

GMDR

Generalized multifactor dimensionality reduction

SNPs

Single nucleotide polymorphisms

HWE

Hardy-Weinberg equilibrium

BMI

Body mass index

CRP

C-reactive protein

ESR

Erythrocyte Sedimentation Rate

RF

Rheumatoid Factor

Anti CCP

Anti Cyclic Citrullinated Peptide

Author contributions

All authors have read and approved the manuscript. Xiang Lu: guarantor of integrity of the entire study, study design, literature research, data acquisition, manuscript review; Yuan Xue: study concepts, experimental studies, manuscript editing; Shanle Yan: definition of intellectual content, statistical analysis and manuscript preparation.

Funding

Not applicable.

Data availability

The datasets generated and/or analyzed during the current study are available from the corresponding author on reasonable request.

Declarations

Ethical approval and consent to participate

Each participant understood the process of the study and signed a written informed consent before the start of the study. All study protocols of the current study were approved by the ethics committee of the Fourth Affiliated Hospital of Soochow University (2025-251185). All methods were performed in accordance with the Declaration of Helsinki.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary Material 1 (17.9KB, docx)

Data Availability Statement

The datasets generated and/or analyzed during the current study are available from the corresponding author on reasonable request.


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