The association of polymorphic loci affecting sex hormone-binding globulin levels with the risk of isolated uterine myoma

Uterine fibroids are benign tumors originating from smooth muscle tissue and are the most common neoplasms in women of reproductive age [1–3]. The pathogenesis of these diseases is multifactorial and involves a complex interplay between hormonal, genetic, and environmental factors [4–6].

More than ten genome-wide association studies (GWAS) have investigated the genetic determinants of uterine fibroid development. These studies have identified several dozen risk loci associated with the disease in genes involved in sex hormone metabolism (ESR1, FSHB, etc.) [7–10]. However, currently available GWAS data explain only a small proportion (≈13%) of the heritability of uterine fibroids [8], underscoring the need for further genetic investigations.

The role of sex hormones, such as estrogen and testosterone, in uterine fibroid development is well established [11–13]. The pathophysiological effects of these hormones in the body, including uterine fibroids, largely depend on sex hormone-binding globulin (SHBG) [14, 15]. SHBG regulates the levels of free, and therefore bioactive, fractions of testosterone (80% bound by SHBG) [11] and estrogen (38% bound by SHBG) [16] in circulation. These free fractions, accounting for approximately 2% of estrogens and 1% of testosterone, exert biological activity in the female body [11, 16]. SHBG concentration is genetically determined, and numerous GWAS have addressed this [17–23]. However, the role of polymorphisms in genes that determine SHBG concentration in uterine fibroid development remains unclear.

This study aimed to evaluate the role of polymorphic variants of genes associated with SHBG levels in the development of isolated uterine fibroids.

Materials and methods

The study group included 192 patients with uterine fibroids, and the control group comprised 973 healthy women. Participants were recruited at the Perinatal Center (Department of Gynecology) of St. Ioasaph Belgorod Regional Clinical Hospital between 2008 and 2013. The patient group consisted of women with a confirmed diagnosis of uterine fibroids and without other hyperplastic diseases of the pelvic organs, such as genital endometriosis, adenomyosis, or endometrial hyperplasia. The control group included women without benign proliferative disorders of the reproductive system based on clinical and instrumental findings. All women enrolled in the study were of Russian ethnicity, born and residing in the Central region of Russia, and were unrelated to each other [24].

Compared with the control group, patients with uterine fibroids had a significantly higher mean age (p<0.001) and body mass index (BMI) (p<0.001). They also had a significantly higher frequency of previous pregnancies (p<0.001), induced abortions (p<0.001), and chronic endometritis (p=0.04) (Table 1). The Research Ethics Committee of the Belgorod State National Research University reviewed and approved this study.

Molecular genetic analysis was performed on four gene loci associated with SHBG levels: rs8023580 [T/C] NR2F2 (15q), rs3779195 [T/A] BAIAP2L1 (7q), rs7910927 [G/T] JMJD1C (10q), and rs4149056 [T/C] SLCO1B1 (12q). SNPs were selected based on the following criteria [25, 26]: (1) association with SHBG levels according to GWAS data; (2) significant regulatory relevance (epigenetic effects and influence on gene transcription); and (3) minor allele frequency of ≥5%.

Biological material for the study (DNA samples) was obtained from the biobank of the Department of Medical and Biological Disciplines of Belgorod State National Research University (storage temperature: -80°C). Genotyping of the four SHBG-associated gene loci was performed using CFX-96 thermal cyclers with the TaqMan probes. DNA amplification kits (for each SNP) were developed by Test-Gen LLC (Ulyanovsk, Russia). The DNA sample concentrations ranged from 10 to 20 ng/μL. Genotyping quality was assessed by testing for Hardy–Weinberg equilibrium for all four SNPs in both the uterine fibroid and control groups. The agreement between the observed and expected heterozygosity (Ho/He) was evaluated.

Statistical analysis

Statistical analysis of the medical-biological and clinical-anamnestic data was performed using Statistica software. The normality of the distribution of all continuous variables was initially assessed using the Shapiro–Wilk test. As none of the continuous variables followed a normal distribution, they are presented as the median (Me) and interquartile range (Q1; Q3) and were compared using the Mann–Whitney U test. Categorical variables are summarized as counts (n) and percentages (%). A comparative analysis of these variables, as well as an assessment of the differences between the observed and expected genotype distributions (for Hardy–Weinberg equilibrium), was conducted using Pearson's χ² test. Differences were considered statistically significant at p<0.05. The association between polymorphic loci of SHBG candidate genes and the development of isolated uterine fibroids was analyzed using gPLINK software (logistic regression method) [27]. The presence and direction of associations were evaluated under four genetic models (allelic, additive, dominant, and recessive) based on odds ratios (OR) and 95% confidence intervals (95% CI) calculated for each model. Covariates (age, BMI, number of pregnancies and induced abortions, and history of chronic endometritis) were included in the analyses, and a permutation test (p_perm) was applied to address multiple comparisons [28]. A p_perm<0.05 was considered statistically significant. For the molecular genetic marker rs3779195 BAIAP2L1 [T/A] (7q), which is associated with the development of isolated uterine fibroids, and for 20 SNPs in strong linkage disequilibrium with it (linkage strength parameters r²=0.81–1.00 and D'=0.94–1.00), the predicted functional potential was evaluated using in silico data analysis [29]. The HaploReg [accessed July 13, 2025] [30] and GTEx portal [accessed July 13, 2025] [31] tools were used for this analysis.

Results

The distribution of all four analyzed SNPs in both the isolated uterine fibroids group (p_HWE≥0.093) and the control group (p_HWE≥0.060) was consistent with Hardy–Weinberg equilibrium (p>0.05) (Table 2). The minor allele frequencies at the examined loci ranged from 0.199 to 0.464 in patients with isolated uterine fibroids and from 0.176 to 0.496 in the control group (Table 2).

An association was identified between the polymorphic locus rs3779195 of the BAIAP2L1 gene [T/A] and the development of isolated uterine fibroids (Table 2). Under the dominant model, the A allele of rs3779195 BAIAP2L1 [T/A] was associated with an increased risk of isolated uterine fibroids (AA+TA genotypes were observed in 66 [38.15%] patients and 285 [31.08%] women in the control group; OR=1.44, 95% CI 1.00–2.06, p=0.049, p_perm=0.049).

In silico analysis (using HaploReg and GTEx Portal) indicated that the rs3779195 [T/A] polymorphism in BAIAP2L1, along with 20 SNPs in strong linkage disequilibrium, was associated with interactions between this genomic region and 68 transcription factors (at 17 loci) and 18 regulatory proteins (at 4 loci). They are also linked to transcriptional regulation (eQTL) of 15 genes and alternative splicing (sQTL) of 3 genes (BRI3, TECPR1, BAIAP2L1) in organs/tissues directly related to the pathophysiology of uterine fibroids: ovaries (eQTL – RP11-307C18.1), adipose tissue (eQTL – BRI3, RP11-307C18.1; sQTL – BRI3), brain (eQTL – BHLHA15, RP11-307C18.1; sQTL – TECPR1, BRI3), adrenal glands (eQTL – RP11-307C18.1), thyroid gland (eQTL – BAIAP2L1, RP11-307C18.1, TECPR1, BHLHA15, LMTK2; sQTL – BRI3), blood (eQTL – TECPR1, RP11-307C18.1), and skeletal muscle (eQTL – BRI3, RP11-307C18.1, ASNS, BAIAP2L1; sQTL – BRI3), among others.

The polymorphic locus rs3779195 [T/A] in BAIAP2L1 and several SNPs in linkage disequilibrium with it are predicted to have important functional significance in the liver, which is the primary site of SHBG synthesis. These SNPs are located within DNA regions characterized by various epigenetic histone modifications (acetylation/methylation) marking promoters (three SNPs), enhancers (ten SNPs), active promoters (six SNPs), and active enhancers (eight SNPs). Furthermore, in the liver, rs3779195 [T/A] BAIAP2L1 and 17 linked SNPs were associated with the expression of two genes: BRI3 and RP11-307C18.1. Notably, the A allele of rs3779195 [T/A] BAIAP2L1, which is associated with an increased risk of isolated uterine fibroids (OR = 1.44), is linked to the elevated expression of BRI3 (NES = 0.87) and reduced transcription of RP11-307C18.1 (NES=-0.54) in the liver.

The protein product of the BAIAP2L1 gene (brain-specific angiogenesis inhibitor 1–associated protein 2-like protein 1, also known as insulin receptor tyrosine kinase substrate [IRTKS]) participates in several biologically important processes, including cell morphogenesis and migration (participation in plasma membrane protrusion formation and actin assembly), as well as proliferation and apoptosis (via activation of EGFR–ERK, PI3K/AKT, and other signaling pathways) [32–34]. These processes play a critical role in oncogenesis [33, 34], including malignant neoplasms of the female reproductive system (e.g., ovarian cancer) [32]. Notably, positive genetic correlations have been reported between uterine fibroids and ovarian cancer [35], suggesting that BAIAP2L1 may be one of the genes underlying these correlations.

Interestingly, several SNPs in linkage disequilibrium with rs3779195 [T/A] BAIAP2L1 are associated with SHBG concentrations and sex hormone levels according to GWAS data: SHBG – rs112758337 (linkage parameters D'=1.00; r²=0.96), rs1688606 (D'=1.00; r²=0.96), and rs4268041 (D'=1.00; r²=0.99) [19]; total testosterone – rs1635612 (D'=1.00; r²=0.96) [19] and rs35903783 (D'=1.00; r²=0.41) [22]. Thus, the genomic region encompassing SNP rs3779195 [T/A] BAIAP2L1, owing to its predicted pronounced functional significance (epigenetic and eQTL effects) in the liver (the principal organ of SHBG synthesis), likely plays an important role in the regulation of SHBG and testosterone levels in the body, thereby influencing the risk of uterine fibroid development.

Two previously published GWAS demonstrated an association between the A allele of rs3779195 [T/A] BAIAP2L1 and low SHBG concentrations [18, 19]. In the present study, we showed that the A allele of the rs3779195 [T/A] BAIAP2L1 polymorphism, previously linked to lower SHBG concentrations in GWAS, is involved in the development of isolated uterine fibroids and represents a risk factor for their occurrence (OR=1.44). A potential mechanism underlying the association between SHBG (and, accordingly, the rs3779195 [T/A] BAIAP2L1 polymorphism associated with SHBG levels) and the formation of isolated uterine fibroids may be related to its role in estrogen transport. Published data indicate that approximately 38% of circulating estrogens are bound to SHBG, whereas only approximately 2% circulate in a free form. These free estrogens exert biological activity in women [36]. Thus, SHBG regulates the concentration of biologically active estrogens in the blood by modulating their bioavailability; lower SHBG levels result in higher concentrations of active estrogens and more pronounced phenotypic effects [37, 38]. Estradiol, a well-established driver of tumor growth, stimulates the proliferation of fibroid cells [12].

Conclusion

The findings of this study suggest an association between the rs3779195 [T/A] BAIAP2L1 polymorphism and the development of isolated uterine fibroids. The A allele of rs3779195 [T/A] BAIAP2L1 was associated with an increased risk of isolated uterine fibroids (OR=1.44). The rs3779195 [T/A] BAIAP2L1 polymorphism and 20 single nucleotide polymorphisms (SNPs) in linkage disequilibrium with it are located in genomic regions that are functionally significant in various organs and tissues related to the pathophysiology of uterine fibroids.