| Literature DB >> 32547159 |
Bingqi Wang1, Min Wang1, Xianping Li1, Min Yang1, Lei Liu1.
Abstract
BACKGROUND: Cervical cancer is the fourth most common and fatal tumor among women worldwide. The Wnt/β-catenin signaling pathway was etiologically involved in the cervical cancer model. Herein, we aimed to investigate whether germline genetic variations within the Wnt/β-catenin pathway can be genetic risk factors of cervical cancer. PATIENTS AND METHODS: A total of 305 samples (147 patients, 158 controls) were included. Eight genetic variations located in APC (rs454886), GSK3β (rs3755557), CTNNB1 (rs11564475, rs1798802, rs3864004, rs2293303, and rs4135385), and TCF7L2 (rs7903146) were genotyped via Sanger sequencing. The χ 2 test and non-conditional logistic regression were used in the single-locus analysis. Gene-gene interactions and haplotype construction in case-control samples were performed by the GMDR method and Haploview software, respectively.Entities:
Keywords: APC; CTNNB1; GSK3β; TCF7L2; Wnt/β-catenin signaling pathway; cervical cancer; single nucleotide polymorphism
Year: 2020 PMID: 32547159 PMCID: PMC7247596 DOI: 10.2147/PGPM.S248548
Source DB: PubMed Journal: Pharmgenomics Pers Med ISSN: 1178-7066
SNP Information of Genes Analyzed in This Study
| Gene | SNP ID | Chromosome | Major/Minor Alleles | Position | HWE Test for Controls (P) |
|---|---|---|---|---|---|
| APC | rs454886 | 5:112810420 | G/A | Intron variant | 0.917 |
| GSK3β | rs3755557 | 3:120096110 | T/A | 2KB Upstream variant | 0.242 |
| CTNNB1 | rs11564475 | 3:41238542 | A/G | Intron variant | 0.663 |
| CTNNB1 | rs1798802 | 3:41220488 | G/A | Intron variant | 0.845 |
| CTNNB1 | rs3864004 | 3:41198686 | G/A | Intron variant | 0.683 |
| CTNNB1 | rs4135385 | 3:4123794 | G/A | Intron variant | 0.888 |
| CTNNB1 | rs2293303 | 3:41239336 | C/T | Intron variant | 0.069 |
| TCF7L2 | rs7903146 | 10:112998590 | C/T | Intron variant | 0.396 |
Abbreviations: SNP, single nucleotide polymorphism; HWE, Hardy–Weinberg equilibrium.
Association Between Genotypes Frequencies and Cervical Cancer Risk
| Gene | SNP ID | Model | Frequency, No. (%) | P | OR (95% CI)a | |
|---|---|---|---|---|---|---|
| Cases (n=147) | Controls (n=158) | |||||
| APC | rs454886 | GG | 51 (34.7) | 58 (36.7) | Ref. | Ref. |
| GA | 73 (49.7) | 76 (48.1) | 0.726 | 1.129 (0.684–1.863) | ||
| AA | 23 (15.6) | 24 (15.2) | 0.805 | 1.132 (0.566–2.266) | ||
| Dominant model | / | / | 0.714 | 1.052 (0.564–1.962) | ||
| Recessive model | / | / | 0.912 | 1.129 (0.702–1.814) | ||
| GSK3β | rs3755557 | TT | 114 (77.6) | 118 (74.7) | Ref. | Ref. |
| TA | 31 (21.0) | 39 (24.7) | 0.476 | 1.205 (0.704–2.065) | ||
| AA | 2 (1.4) | 1 (0.6) | 0.543 | 2.090 (0.187–23.382) | ||
| Dominant model | / | / | 0.558 | 0.861 (0.507–1.461) | ||
| Recessive model | / | / | 0.950 | 2.147 (0.193–23.932) | ||
| CTNNB1 | rs11564475 | AA | 112 (76.2) | 122 (77.2) | Ref. | Ref. |
| AG | 33 (22.4) | 33 (20.9) | 0.759 | 0.910 (0.526–1.574) | ||
| GG | 2 (1.4) | 3 (1.9) | 1.000b | 1.199 (0.194–7.403) | ||
| Dominant model | / | / | 0.784 | 0.930 (0.546–1.585) | ||
| Recessive model | / | / | 1.000b | 1.305 (0.213–7.987) | ||
| GG | 85 (57.8) | 73 (46.2) | Ref. | Ref. | ||
| GA | 50 (34.0) | 68 (43.0) | 0.060 | 1.583 (0.978–2.563) | ||
| AA | 12 (8.2) | 17 (10.8) | 0.219 | 0.595 (0.266–1.334) | ||
| Recessive model | / | / | 0.440 | 0.730 (0.336–1.589) | ||
| rs3864004 | GG | 94 (63.9) | 84 (53.2) | Ref. | Ref. | |
| GA | 47 (32.0) | 61 (38.6) | 0.128 | 1.471 (0.908–2.383) | ||
| AA | 6 (4.1) | 13 (8.2) | 0.078 | 0.402 (0.145–1.110) | ||
| Dominant model | / | / | 0.056 | 0.632 (0.399–1.002) | ||
| Recessive model | / | / | 0.134 | 0.471 (0.174–1.275) | ||
| rs4135385 | GG | 46 (31.3) | 43 (27.2) | Ref. | Ref. | |
| GA | 78 (53.1) | 78 (49.4) | 0.800 | 1.059 (0.628–1.787) | ||
| AA | 23 (15.6) | 37 (23.4) | 0.109 | 0.580 (0.297–1.129) | ||
| Dominant model | / | / | 0.434 | 0.822 (0.501–1.349) | ||
| Recessive model | / | / | 0.088 | 0.597 (0.334–1.065) | ||
| rs2293303 | CC | 120 (81.6) | 115 (72.8) | Ref. | Ref. | |
| CT | 24 (16.4) | 36 (22.8) | 0.126 | 1.552 (0.871–2.764) | ||
| TT | 3 (2.0) | 7 (4.4) | 0.192 | 2.495 (0.628–9.921) | ||
| Dominant model | / | / | 0.066 | 1.655 (0.959–2.855) | ||
| Recessive model | / | / | 0.396 | 2.276 (0.576–9.000) | ||
| TCF7L2 | rs7903146 | CC | 140 (0.952) | 142 (0.899) | Ref. | Ref. |
| CT | 6 (0.041) | 15 (0.095) | 0.062 | 2.453 (0.924–6.511) | ||
| TT | 1 (0.007) | 1 (0.006) | 1.000c | 1.087 (0.067–17.679) | ||
| Dominant model | / | / | 0.076 | 2.260 (0.901–5.669) | ||
| Recessive model | / | / | 1.000c | 1.015 (0.063–16.483) | ||
Notes: aAdjusted ORs. bP from continuous correction χ2 test. cP from Fisher’s exact test. P≤0.05 is considered as significant. Bold values indicate significant differences.
Abbreviations: OR, odds ratio; CI, confidence interval.
Association Between Alleles Frequencies and Cervical Cancer Risk
| Gene | SNP ID | Allele | Frequency, No. (%) | P | OR (95% CI) | |
|---|---|---|---|---|---|---|
| Cases (n=147) | Controls (n=158) | |||||
| APC | rs454886 | G | 175 (59.5) | 192 (60.8) | Ref. | Ref. |
| A | 119 (40.5) | 124 (39.2) | 0.755 | 0.950 (0.687–1.314) | ||
| GSK3β | rs3755557 | T | 259 (88.1) | 275 (87.0) | Ref. | Ref. |
| A | 35 (11.9) | 41 (13.0) | 0.689 | 1.103 (0.681–1.786) | ||
| CTNNB1 | rs11564475 | A | 257 (87.4) | 277 (87.7) | Ref. | Ref. |
| G | 37 (12.6) | 39 (12.3) | 0.928 | 0.978 (0.605–1.582) | ||
| rs1798802 | G | 220 (74.8) | 214 (67.7) | Ref. | Ref. | |
| A | 74 (25.2) | 102 (32.3) | 0.053 | 1.417 (0.995–2.018) | ||
| G | 235 (79.9) | 229 (72.5) | Ref. | Ref. | ||
| rs4135385 | G | 170 (57.8) | 164 (51.9) | Ref. | Ref. | |
| A | 124 (42.2) | 152 (48.1) | 0.142 | 1.271 (0.923–1.750) | ||
| C | 264 (89.8) | 266 (84.2) | Ref. | Ref. | ||
| TCF7L2 | rs7903146 | C | 286 (0.973) | 299 (0.946) | Ref. | Ref. |
| T | 8 (0.027) | 17 (0.054) | 0.098 | 2.033 (0.864–4.783) | ||
Notes: P≤0.05 is considered as significant. Bold values indicate significant differences.
Abbreviations: OR, odds ratio; CI, confidence interval.
The Pairwise Linkage Disequilibrium of SNPs in the CTNNB1 Gene
| rs3864004 | rs1798802 | rs4135385 | rs11564475 | rs2293303 | |
|---|---|---|---|---|---|
| rs3864004 | / | 0.980 | 0.984 | 1.000 | 0.982 |
| rs1798802 | / | / | 1.000 | 1.000 | 0.980 |
| rs4135385 | / | / | / | 1.000 | 1.000 |
| rs11564475 | / | / | / | / | 1.000 |
| rs2293303 | / | / | / | / | / |
Note: D’ value is shown above.
Figure 1The linkage disequilibrium estimates in the CTNNB1 gene.
Notes: Each square represents the LD analysis results between two SNP loci. The color ranges from white to red, representing the linkage degree from low to high.
Haplotype Analysis of the CTNNB1 Gene
| Gene | Haplotype | Frequency | P | Pc | |
|---|---|---|---|---|---|
| Cases | Controls | ||||
| 0.419 | 0.452 | 0.389 | 0.114 | 0.455 | |
| 0.162 | 0.170 | 0.155 | 0.614 | 0.995 | |
| 0.129 | 0.102 | 0.155 | 0.051 | 0.234 | |
| 0.125 | 0.126 | 0.123 | 0.928 | 1.000 | |
| 0.107 | 0.099 | 0.114 | 0.540 | 0.982 | |
| 0.053 | 0.051 | 0.054 | 0.878 | 1.000 | |
Notes: The order of haplotype construction: rs3864004, rs1798802, rs4135385, rs11564475 and rs2293303. Only haplotypes with frequency >3% were included in the analysis. Pc: permutation testing with 1000 replications.
The Best SNP–SNP Interaction Models Determined by GMDR
| Model | Training Accuracy | Testing Accuracy | CV Consistency | Pa |
|---|---|---|---|---|
| rs1798802 | 0.5588 | 0.5464 | 8/10 | 0.0547 |
| rs1798802 rs7903146 | 0.5808 | 0.4854 | 5/10 | 0.6230 |
| rs454886 rs3755558 rs1798802 | 0.6135 | 0.5038 | 6/10 | 0.3770 |
Note: aP value adjusted for age.
Figure 2The best three models for predicting the occurrence of cervical cancer (A) one-locus model of rs1798802. (B) Two-loci model of rs1798802-rs7903146. (C) Three-loci model of rs454886-rs3755557-rs1798802. A grid represented an interactive combination. Dark gray and light gray grids presented the high- and low-risk factor combinations, respectively. Left bars within each grid represented case while the right bars represented control.