Genetic Variants Linked with the Concentration of Sex Hormone-Binding Globulin Correlate with Uterine Fibroid Risk
Abstract
1. Introduction
2. Materials and Methods
2.1. Study Subjects
2.2. Experimental DNA Study (Selection/Genotyping of SHBGcon-Related Genetic Variants)
2.3. Statistical Analysis (SNP–Multi-SNP Association Examined)
2.4. The Evaluation of the Possible Functionality of UF-Correlated Variants: An In Silico Study
3. Results
3.1. Potential Functionality of the UF-Associated Polymorphisms
3.1.1. The Characterization of the Functionality of the Two UF-Causal Loci
3.1.2. The Characterization of the Seven UF-Associated Loci Functionality
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
UF | Uterine fibroids |
SHBG | Sex hormone-binding globulin |
SHBGcon | Sex hormone-binding globulin concentration |
SNP | Single-nucleotide polymorphism |
GWAS | Genome-wide association studies |
BMI | Body mass index |
DNA | Deoxyribonucleic acid |
MB-MDR | Model-based multifactor dimensionality reduction |
MDR | Multifactor dimensionality reduction |
LD | Linkage disequilibrium |
TFs | Transcription factors |
References
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Parameters | Cases (n = 569) ± SD/% (n) |
Controls (n = 973) ± SD/% (n) | p |
---|---|---|---|
Age, years | 43.22 ± 8.35 | 40.26 ± 8.53 | <0.001 |
Height, m | 1.66 ± 0.06 | 1.66 ± 0.06 | >0.05 |
Weight, kg | 76.43 ± 14.35 | 70.54 ± 13.25 | <0.001 |
BMI, kg/m2 | 27.90 ± 5.38 | 25.22 ± 4.52 | <0.001 |
Proportion of the participants by relative BMI, % (n): | |||
underweight (<18.50) | 1.58 (9) | 3.60 (35) | <0.001 |
normal weight (18.50–24.99) | 31.81 (181) | 54.98 (535) | |
overweight (25.00–29.99) | 34.27 (195) | 27.85 (271) | |
obese (>30.00) | 32.34 (184) | 13.57 (132) | |
Family history of UF (mother had UF) | 35.15 (200) | 17.06 (166) | <0.001 |
Married | 85.06 (484) | 85.92 (836) | >0.05 |
Smoking (yes) | 13.71 (78) | 17.06 (166) | >0.05 |
Drinking alcohol (≥7 drinks per week) | 2.99 (17) | 3.08 (30) | >0.05 |
Oral contraceptive use | 9.49 (54) | 10.07 (98) | >0.05 |
Age at first oral contraceptive use (mean, years) | 23.43 ± 2.28 | 23.61 ± 2.34 | >0.05 |
Age at menarche and menstrual cycle | |||
Age at menarche, years | 13.45 ± 1.31 | 13.29 ± 1.26 | >0.05 |
Proportion of the participants by relative age at menarche, % (n) early (<12 years) average (12–14 years) late (>14 years) | 4.62 (26) 80.28 (452) 15.10 (85) | 6.17 (60) 80.06 (779) 13.77 (134) | >0.05 |
Duration of bleeding menstrual (mean, days) | 5.15 ± 1.56 | 4.96 ± 0.95 | >0.05 |
Menstrual cycle length (mean, days) | 28.04 ± 2.15 | 28.18 ± 2.25 | >0.05 |
Reproductive characteristic | |||
Age at first birth (mean, years) | 21.19 ± 2.59 | 21.69 ± 3.48 | >0.05 |
Time since last birth (mean, years) | 15.08 ± 2.28 | 14.31 ± 2.07 | >0.05 |
Gravidity (mean) | 3.34 ± 2.22 | 2.42 ± 1.53 | <0.001 |
No. of births (mean) | 1.46 ± 0.85 | 1.50 ± 0.66 | >0.05 |
No. of spontaneous abortions (mean) | 0.26 ± 0.64 | 0.23 ± 0.50 | >0.05 |
No. of induced abortions (mean) | 1.59 ± 1.65 | 0.66 ± 0.97 | <0.001 |
No. of induced abortions: 0 1 2 3 ≥4 | 31.81 (181) 23.20 (132) 21.62 (123) 12.30 (70) 11.07 (63) | 58.99 (574) 23.74 (231) 10.18 (99) 5.45 (53) 1.64 (16) | <0.001 |
History of infertility | 13.71 (78) | 5.14 (50) | <0.001 |
Gynecological pathologies | |||
Cervical disorders | 26.01 (148) | 25.18 (245) | >0.05 |
History of sexually transmitted diseases | 27.06 (154) | 26.93 (262) | >0.05 |
Chronic endometritis | 10.02 (57) | 5.65 (55) | <0.01 |
Chronic inflammation of adnexa | 34.62 (197) | 31.96 (311) | >0.05 |
Endometrial hyperplasia | 47.10 (268) | - | - |
Endometriosis | 36.38 (207) | - | - |
Adenomyosis | 21.27 (121) | - | - |
SNP, Gene (Chromosome Position (hg38)) | Phenotype | Association (Significance) (Affected Allele) | Reference |
---|---|---|---|
rs17496332 PRMT6 (1p13.3) | SHBG | β = −0.028 (p = 1 × 10−11) (A) | [18] |
rs780093 GCKR (2p23.3) | SHBG | β = −0.032 (p = 2 × 10−16) (T) | [18] |
rs10454142 FOXN2 (2p16.3) | SHBG | β = 0.026 (p = 1 × 10−7) (T) | [18] |
rs3779195 BAIAP2L1 (7q19.3) | SHBG | β = −0.033 (p = 3 × 10−8) (A) | [18] |
β = −2.41 (p = 9 × 10−9) (A) | [21] | ||
rs440837 ZBTB10 (8q19.13) | SHBG | β = −0.030 (p = 3 × 10−9) (A) | [18] |
β = 1.43 (p = 1 × 10−12) (G) | [21] | ||
rs7910927 JMJD1C (10q19.3) | SHBG | β = −0.048 (p = 6 × 10−35) (T) | [18] |
rs4149056 SLCO1B1 (12p12.1) | SHBG | β = 0.029 (p = 2 × 10−8) (T) β = 0.030 (p = 1 × 10−73) (T) β = −1.23 (p = 7 × 10−29) (C) β = −0.065 (p =5 × 10−48) (C) | [18] [20] [21] [22] |
total testosterone | β = 0.028 (p = 5 × 10−10) (C) β = −0.029 (p = 1 × 10−14) (T) | [22] [20] | |
bioavailable testosterone | β = 0.02 (p = 2 × 10−16) (C) β = −0.043 (p = 3 × 10−35) (T) | [21] [20] | |
rs8023580 PPP1R19 (15q26.2) | SHBG | β = −0.03 (p = 8 × 10−12) (T) | [18] |
rs11950660 SHBG (17p13.1) | SHBG | β = 0.103 (p = 2 × 10−106) (T) | [18] |
β = 6.14 (p = 1 × 10−300) (T) | [21] | ||
β = 3.9 (p = 2 × 10−75) (T) | [16] | ||
total testosterone | β = 31.8 (p = 1 × 10−41) (T) | [16] |
SNP | Gene | Minor Allele | n | Allelic Model | Additive Model | Dominant Model | Recessive Model | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
OR | 95%CI | p | OR | 95%CI | p | OR | 95%CI | p | OR | 95%CI | p | ||||||||
L95 | U95 | L95 | U95 | L95 | U95 | L95 | U95 | ||||||||||||
rs17496332 | PRMT6 | G | 1452 | 0.94 | 0.80 | 1.10 | 0.410 | 0.93 | 0.78 | 1.11 | 0.429 | 0.90 | 0.70 | 1.15 | 0.387 | 0.94 | 0.66 | 1.34 | 0.729 |
rs780093 | GCKR | T | 1470 | 1.08 | 0.93 | 1.26 | 0.304 | 1.10 | 0.93 | 1.31 | 0.279 | 1.13 | 0.88 | 1.46 | 0.339 | 1.14 | 0.83 | 1.57 | 0.427 |
rs10454142 | PPP1R21 | C | 1445 | 0.96 | 0.81 | 1.13 | 0.607 | 1.01 | 0.84 | 1.22 | 0.929 | 0.98 | 0.77 | 1.25 | 0.873 | 1.10 | 0.73 | 1.66 | 0.639 |
rs3779195 | BAIAP2L1 | A | 1452 | 1.09 | 0.90 | 1.33 | 0.372 | 1.14 | 0.91 | 1.43 | 0.244 | 1.29 | 1.00 | 1.67 | 0.054 | 0.38 | 0.20 | 0.91 | 0.023 |
rs440837 | ZBTB10 | G | 1423 | 1.06 | 0.88 | 1.26 | 0.539 | 1.11 | 0.91 | 1.36 | 0.292 | 1.01 | 0.78 | 1.29 | 0.963 | 1.93 | 1.17 | 3.14 | 0.010 |
rs7910927 | JMJD1C | T | 1471 | 0.92 | 0.79 | 1.07 | 0.258 | 0.88 | 0.75 | 1.05 | 0.161 | 0.81 | 0.62 | 1.06 | 0.131 | 0.89 | 0.67 | 1.19 | 0.446 |
rs4149056 | SLCO1B1 | C | 1418 | 0.99 | 0.83 | 1.19 | 0.943 | 0.98 | 0.80 | 1.21 | 0.870 | 0.99 | 0.77 | 1.28 | 0.961 | 0.91 | 0.52 | 1.60 | 0.739 |
rs8023580 | NR2F2 | C | 1451 | 0.99 | 0.84 | 1.17 | 0.906 | 1.00 | 0.83 | 1.21 | 0.995 | 1.05 | 0.82 | 1.33 | 0.719 | 0.87 | 0.56 | 1.35 | 0.529 |
rs12150660 | SHBG | T | 1486 | 1.00 | 0.84 | 1.19 | 0.982 | 0.94 | 0.77 | 1.14 | 0.522 | 0.95 | 0.75 | 1.21 | 0.686 | 0.82 | 0.50 | 1.34 | 0.430 |
N | SNP × SNP Interaction Models | MB-MDR Data | GMDR Data (Model Cross-Validation) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NH | betaH | WH | NL | betaL | WL | pperm | OR (95%CI) | TBA | Se | Sp | CVC | ||
Three-order interaction models (p = 4.88 × 10−5) | |||||||||||||
1 | rs8023580 NR2F2-rs7910927 JMJD1C-rs3779195 BAIAP2L1 | 3 | 0.740 | 18.74 | - | - | - | 0.001 | 1.75 (1.37–2.23) | 50.72 | 50.60 | 60.84 | 10/10 |
2 | rs8023580 NR2F2-rs10454142 PPP1R21-rs780093 GCKR | 4 | 0.530 | 16.49 | 3 | −0.549 | 10.45 | 0.01 | 1.76 (1.43–2.18) | 54.51 | 53.08 | 60.95 | 10/10 |
Four-order interaction models (p = 5.86 × 10−8) | |||||||||||||
3 | rs440837 ZBTB10-rs10454142 PPP1R21-rs780093 GCKR-rs17496332 PRMT6 | 7 | 1.168 | 30.61 | 2 | −0.841 | 9.89 | 0.001 | 2.06 (1.67–2.55) | 53.44 | 54.83 | 63.00 | 10/10 |
4 | rs8023580 NR2F2-rs10454142 PPP1R21-rs780093 GCKR-rs17496332 PRMT6 | 5 | 1.380 | 29.41 | 1 | −0.974 | 3.06 | 0.001 | 2.35 (1.90–2.92) | 56.68 | 65.20 | 55.70 | 10/10 |
UF-Causal SNPs and Their Proxy Variants | Haploreg Data | GTE-Portal Data (eQTL, sQTL) | |||
---|---|---|---|---|---|
Epigenetic Modifications (Methylation/Acetylation of Histones) in the Liver Promoter/Enhancer Regions | Transcription Factors | Proteins Bound | Organism | Liver | |
rs440837 [A/G] ZBTB10 | H3K4me1_Enh H3K4me3_Pro H3K27ac_Enh H3K9ac_Pro | Hlx1, Hoxa9, Smad3 | |||
5 proxy variants of rs440837 [A/G] ZBTB10 | H3K4me1_Enh H3K4me3_Pro H3K27ac_Enh H3K9ac_Pro | Pou1f1, Pou3f2, DMRT3, DMRT4, CDP, DMRT5, Smad3, Gfi1, Mrg1: Hoxa9, Sp4, Bbx, Nkx2, Sox, Mef2, Tgif1, CTCF, Mrg, Hoxa9, LXR, Myc, TCF11: MafG, Hlx1 | |||
rs3779195 [T/A] BAIAP2L1 | H3K4me1_Enh H3K4me3_Pro H3K27ac_Enh H3K9ac_Pro | Foxp1 | BAIAP2L1, BRI3, TECPR1, LMTK2, RP11-307C18.1 (eQTL) BAIAP2L1, BRI3, (sQTL) | RP11-307C18.1, BRI3 (eQTL) | |
20 proxy variants of rs3779195 [T/A] BAIAP2L1 | H3K4me1_Enh H3K4me3_Pro H3K27ac_Enh H3K9ac_Pro | ZNF263, Znf143, Zfp161, Zfp105, VDR, TCF12, UF1H3BETA, TCF4, TATA, SP1, STAT, SRF, Sox, Sin3Ak-20, p300, RXRA, Pou6f1, Pou3f2, Pou2f2, PLZF, Pax-6, Pax-4, Pax-2, NRSF, Nrf1, Nr2f2, Nkx3, Nkx2, NF-kappaB, Ncx, MAZR, MZF1:1-4, Myc, Mef2, MAZ, Lhx3, E2F, Lmo2-complex, KAP1, Hoxd10, Hoxa9, Hoxb13, Hoxa4, Hoxa10, HNF4, HNF1, HMGN3, GR, GATA, Foxl1, FAC1, Egr-1, EBF, DMRT4, Dbx1, CTCFL, CHD2, CEBPG, BHLHE40, BATF, BAF155, Bach2, Bach1, Ascl2, Arid3a, AP-2, AP-1 | USF1, SMC3R, AD21, PRDM1, MXI1, GTF2F1, POL24H8, PU1, POL2, MAX, MAFK, CTCF, HDAC2, GABP, CMYC, CEBPB, AP-2-gamma, AP-2-alpha | AC004967.7, ASNS, BAIAP2L1, BRI3, LMTK2, TECPR1, RP11-307C18.1, RP11-307C18.2, RP11-307C18.3, RP11-307C18.4, RP11-307C18.5, RP11-307C18.6, RP11-307C18.7, RP11-307C18.10, RP11-307C18.11 (eQTL) BRI3, TECPR1, BAIAP2L1 (sQTL) |
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Ponomarenko, M.; Reshetnikov, E.; Churnosova, M.; Aristova, I.; Abramova, M.; Novakov, V.; Churnosov, V.; Polonikov, A.; Plotnikov, D.; Churnosov, M.; et al. Genetic Variants Linked with the Concentration of Sex Hormone-Binding Globulin Correlate with Uterine Fibroid Risk. Life 2025, 15, 1150. https://doi.org/10.3390/life15071150
Ponomarenko M, Reshetnikov E, Churnosova M, Aristova I, Abramova M, Novakov V, Churnosov V, Polonikov A, Plotnikov D, Churnosov M, et al. Genetic Variants Linked with the Concentration of Sex Hormone-Binding Globulin Correlate with Uterine Fibroid Risk. Life. 2025; 15(7):1150. https://doi.org/10.3390/life15071150
Chicago/Turabian StylePonomarenko, Marina, Evgeny Reshetnikov, Maria Churnosova, Inna Aristova, Maria Abramova, Vitaly Novakov, Vladimir Churnosov, Alexey Polonikov, Denis Plotnikov, Mikhail Churnosov, and et al. 2025. "Genetic Variants Linked with the Concentration of Sex Hormone-Binding Globulin Correlate with Uterine Fibroid Risk" Life 15, no. 7: 1150. https://doi.org/10.3390/life15071150
APA StylePonomarenko, M., Reshetnikov, E., Churnosova, M., Aristova, I., Abramova, M., Novakov, V., Churnosov, V., Polonikov, A., Plotnikov, D., Churnosov, M., & Ponomarenko, I. (2025). Genetic Variants Linked with the Concentration of Sex Hormone-Binding Globulin Correlate with Uterine Fibroid Risk. Life, 15(7), 1150. https://doi.org/10.3390/life15071150