Meta-analysis reveals significant association between FOXP3 polymorphisms and susceptibility to Graves' disease

Genetic and Epigenetic Association of FOXP3 with Papillary Thyroid Cancer Predisposition

Papillary thyroid cancer (PTC) is the most common type of thyroid malignancy with an increased female incidence ratio. The specific traits of X chromosome inheritance may be implicated in gender differences of PTC predisposition. The aim of this study was to investigate the association of two X-linked genes, Forkhead Box P3 (FOXP3) and Protein Phosphatase 1 Regulatory Subunit 3F (PPP1R3F), with PTC predisposition and gender disparity. One hundred thirty-six patients with PTC and an equal number of matched healthy volunteers were enrolled in the study. Genotyping for rs3761548 (FOXP3) and rs5953283 (PPP1R3F) was performed using polymerase chain reaction-restriction fragment length polymorphism assay (PCR-RFLP). The methylation status of FOXP3 was assessed using the combined bisulfite restriction analysis (COBRA) method. The SPSS software was used for statistical analyses. Gender stratification analysis revealed that the CA and AA genotypes and the A allele of FOXP3 rs3761548 variant are associated with PTC predisposition only in females. Moreover, different methylation status was observed up to the promoter locus of FOXP3 between PTC female patients, carrying the CA and CC genotype, and controls. Both revealed associations may explain the higher PTC incidence in females through reducing FOXP3 expression as reported in immune related blood cells.

The Role of FOXP3 Polymorphisms in Graves' Disease with or without Ophthalmopathy in a Turkish Population

Objectives

Forkhead box P3 (FOXP3) gene polymorphisms have been evaluated in many autoimmune diseases, including Graves' disease (GD), in different populations. However, those polymorphisms have not been analyzed in GD or Graves' ophthalmopathy (GO) in the Turkish population. In this study, we aimed to evaluate the frequency of FOXP3 polymorphisms in GD with or without ophthalmopathy in a Turkish population.

Materials and Methods

The study included 100 patients with GO, 74 patients with GD without ophthalmopathy, and 100 age- and sex-matched healthy controls. In all study participants, rs3761547 (-3499 A/G), rs3761548 (-3279 C/A), and rs3761549 (-2383 C/T) single nucleotide polymorphisms (SNPs) were detected using the polymerase chain reaction-restriction fragment length polymorphism method. The chi-square test was used to evaluate genotype and allele frequencies. Odds ratios and 95% confidence intervals were calculated for genotype and allele risks.

Results

In the patient group (including GD with or without ophthalmopathy), the rs3761548 AC and AA genotype and rs3761549 CT genotype were significantly more frequent than in the control group (all p<0.05). No genotypic and allelic differences were observed for rs3761547 between the patient and control groups (all p>0.05). There was no statistically significant difference between the GO and GD without ophthalmopathy groups concerning the allele and genotype frequencies of all three FOXP3 SNPs (all p>0.05).

Conclusion

The AC and AA genotypes of rs3761548 (-3279) and CT genotype of rs3761549 (-2383 C/T) were shown to be possible risk factors for GD development in the Turkish population. However, none of the three SNPs was shown to be associated with the development of GO in patients with GD.

Crucial Role of Foxp3 Gene Expression and Mutation in Systemic Lupus Erythematosus, Inferred from Computational and Experimental Approaches

The impaired suppressive function of regulatory T cells is well-understood in systemic lupus erythematosus. This is likely due to changes in Foxp3 expression that are crucial for regulatory T-cell stability and function. There are a few reports on the correlation between the Foxp3 altered expression level and single-nucleotide polymorphisms within the Foxp3 locus. Moreover, some studies showed the importance of Foxp3 expression in the same diseases. Therefore, to explore the possible effects of single-nucleotide polymorphisms, here, we evaluated the association of IVS9+459/rs2280883 (T>C) and -2383/rs3761549 (C>T) Foxp3 polymorphisms with systemic lupus erythematosus. Moreover, through machine-learning and deep-learning methods, we assessed the connection of the expression level of the gene with the disease. Single-nucleotide polymorphisms of Foxp3 (IVS9+459/rs2280883 (T>C) and -2383/rs3761549 (C>T)) were, respectively, genotyped using allele-specific PCR and direct sequencing and polymerase chain reaction-restriction fragment length polymorphism, in 199 systemic lupus erythematosus patients and 206 healthy age- and sex-matched controls. The Statistical Package for the Social Sciences version 19 and Fisher's exact and chi-square tests were used to analyze the data. Moreover, six machine-learning models and two sequential deep-learning models were designed to classify patients from normal people in the E-MTAB-11191 dataset through the expression level of Foxp3 and its correlated genes. The allele and genotype frequencies of both polymorphisms in question were found to be significantly associated with an increased risk of systemic lupus erythematosus. Furthermore, both of the two single-nucleotide polymorphisms were associated with some systemic-lupus-erythematosus-related risk factors. Three SVM models and the logistic regression model showed an 81% accuracy in classification problems. In addition, the first deep-learning model showed an 83% and 89% accuracy for the training and validation data, respectively, while the second model had an 85% and 79% accuracy for the training and validation datasets. In this study, we are prompted to represent the predisposing loci for systemic lupus erythematosus pathogenesis and strived to provide evidence-based support to the application of machine learning for the identification of systemic lupus erythematosus. It is predicted that the recruiting of machine-learning algorithms with the simultaneous measurement of the applied single nucleotide polymorphisms will increased the diagnostic accuracy of systemic lupus erythematosus, which will be very helpful in providing sufficient predictive value about individual subjects with systemic lupus erythematosus.

Association of genetic variations in FoxP3 gene with Graves' disease in a Southwest Chinese Han population

BACKGROUND

Graves' disease (GD) is a T cell-mediated organ-specific autoimmune disease. Forkhead box P3 (FoxP3) is an excellent marker for the induction and development of regulatory T cells (Tregs). Recent studies showed that single-nucleotide polymorphisms (SNPs) in the FoxP3 gene were associated with the increased susceptibility to several autoimmune diseases. In the present study, we investigated the association of FoxP3 gene polymorphisms with GD in a Southwest Chinese Han population.

METHODS

A two-stage case-control study was performed in 890 healthy controls (male, 282; female, 608) and 503 patients with GD (male, 138; female, 365). Four SNPs (rs3761548, rs3761549, rs3761547, and rs2280883) were genotyped by the polymerase chain reaction-restriction fragment length polymorphism assay. The χ2 test was used to compare the genotype distributions and allele frequencies between GD patients and healthy controls.

RESULTS

In the first stage, the significantly increased frequencies of the A allele (p = .031, odds ratio [OR] = 1.635) and AA genotype (p = .023, OR = 3.257), together with a significantly decreased frequency of the C allele (p = .031, OR = 0.611) of FoxP3/rs3761548 were found in female patients with GD. None of the other FoxP3 SNPs was associated with GD susceptibility. Subsequent validation and combination of data confirmed the association between FoxP3/rs3761548 and the female patients with GD (A allele: p < .001, OR = 1.672; AA genotype: p = .005, OR = 2.488; CC genotype: p = .001, OR = 0.622; C allele: p < .001, OR = 0.615, respectively).

CONCLUSION

Our findings suggest that FoxP3/rs3761548 is significantly associated with female GD patients in a Southwest Chinese Han population.

Molecular Mechanisms in Autoimmune Thyroid Disease

The most common cause of acquired thyroid dysfunction is autoimmune thyroid disease, which is an organ-specific autoimmune disease with two presentation phenotypes: hyperthyroidism (Graves-Basedow disease) and hypothyroidism (Hashimoto’s thyroiditis). Hashimoto’s thyroiditis is distinguished by the presence of autoantibodies against thyroid peroxidase and thyroglobulin. Meanwhile, autoantibodies against the TSH receptor have been found in Graves-Basedow disease. Numerous susceptibility genes, as well as epigenetic and environmental factors, contribute to the pathogenesis of both diseases. This review summarizes the most common genetic, epigenetic, and environmental mechanisms involved in autoimmune thyroid disease.

Human forkhead box protein 3 gene variants associated with altered susceptibility to idiopathic recurrent pregnancy loss: A retrospective case-control study

BACKGROUND

The pathogenesis of recurrent pregnancy loss (RPL) is multifactorial and not completely elucidated. Dysregulated immunity was implicated with RPL, in which regulatory T cells (Tregs) are key. As Tregs development and function are regulated by forkhead box P3 (FOXP3) transcription factor, and as FOXP3 expression is genetically determined, a role for FOXP3 polymorphisms in RPL pathogenesis was suggested.

AIM

To investigate the association of rs2294021, rs2232365, rs3761548, and rs141704699 FOXP3 variants with idiopathic RPL in Lebanese women.

METHODS

This retrospective case-control study included 386 RPL cases and 398 age-matched control women. Logistic odds ratios (OR) were estimated with 95% confidence interval after adjustment; a significance value of P<.05 was set.

RESULTS

Significantly lower rs22944021 and rs2232365 minor allele frequency (MAF) was found in patients with idiopathic RPL in comparison with the control group. Furthermore, statistically significantly lower frequency of heterozygous and homozygous rs2294021 and rs2232365 genotypes was seen in controls, while significantly lower rs3761548 heterozygous genotype frequencies were found in the patient group. Obesity, antihypertension treatment, smoking, positive RPL family history, abortion state, and infertility treatment correlated negatively with rs2294021, while rs2232365 negatively correlated with obesity, and rs3761548 negatively correlated with infertility treatment. Marked linkage disequilibrium (LD) was noted among FOXP3 SNPs, with TGCC and CGAC haplotypes being positive, while CAAC, CACC, and TGAC haplotypes being negatively associated with RPL risk. Except for CGAC, the association of these haplotypes with RPL persisted after adjustment.

CONCLUSION

FOXP3 gene variants and haplotypes are associated with altered incidence of RPL, proposing the role of Treg in RPL pathogenesis.