| Literature DB >> 30616520 |
Gui-Cen Liu1, Yun-Fei Zhou1, Xiao-Chao Su1, Jun Zhang2.
Abstract
BACKGROUND: Cervical cancer is the 4th highest cause of female reproductive tract malignancies. Multiple loci have been identified as important determinant factors for tumor susceptibility. In this report, we aimed to explore the roles of gene polymorphisms affecting x-ray repair cross complementing 1 (XRCC1), the tumor protein p53 (TP53), and fibroblast growth factor receptor 3 (FGFR3) in the context of susceptibility to cervical cancer. Additionally, we assessed the impact of single nucleotide polymorphism-single nucleotide polymorphism (SNP-SNP) interaction of these three genes in the context of cervical cancer risk in Chinese women.Entities:
Keywords: Cervical cancer; FGFR3; SNP-SNP interaction; TP53; XRCC1
Mesh:
Substances:
Year: 2019 PMID: 30616520 PMCID: PMC6323714 DOI: 10.1186/s12885-018-5149-0
Source DB: PubMed Journal: BMC Cancer ISSN: 1471-2407 Impact factor: 4.430
Fig. 1schematic illustration for text mining of dominant SNPs related to pathogenesis of cervical cancer, and identified XRCC1, TP53, as well as FGFR3
Fig. 2Network analysis of essential protein from String (a), and pathway analysis for these 62 genes by ClusterProfiler (b)
The genotype distribution and H-W of XRCC1 (rs25487), TP53 (rs1042522) and FGFR3 (rs121913483)
| Variable | Alleles | Phenotype | N | HWE | MAF | M/M (%) | M/m (%) | m/m (%) | M/M +M/m | M/m +m/m | Allele M | Allele m |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs25487 | G > A | Cases | 121 | 0.18 | 0.40 | 47(38.9) | 51(42.1) | 23(19) | 98 | 74 | 145(59.9) | 97(40.1) |
| NC | 118 | 0.15 | 0.25 | 70(59.3) | 38(32.2) | 10(8.5) | 108 | 48 | 178(75.4) | 58(24.6) | ||
| OC | 101 | 0.45 | 0.27 | 55(54.4) | 37(36.6) | 9(9) | 92 | 46 | 147(72.8) | 55(27.2) | ||
| rs1042522 | G > C | Cases | 121 | 0.18 | 0.38 | 50(41.3) | 50(41.3) | 21(17.4) | 100 | 71 | 150(62) | 92(38) |
| NC | 108 | 0.74 | 0.42 | 37(34.3) | 51(47.2) | 20(18.5) | 88 | 71 | 125(57.9) | 91(42.1) | ||
| OC | 99a | 0.07 | 0.44 | 35(35.4) | 40(40.4) | 24(24.2) | 75 | 64 | 110(55.6) | 88(44.4) | ||
| rs121913483 | G > C | Cases | 117 | 117 | 0 | 0 | ||||||
| NC | 113 | 113 | 0 | 0 | ||||||||
| OC | 89 | 89 | 0 | 0 |
N Number, HWE Hardy-Weinberg equilibrium, MAF Minor allele frequency, NC Negative controls, OC Old controls
aThe number of subjects in each group at different sites may be different due to insufficient DNA
The association between gene polymorphism of XRCC1 (rs25487), TP53(rs1042522) and cervical cancer
| Variable | Groups | Co-dominate model | Recessive model | |||||
| OR | 95%CI | OR | 95%CI | |||||
| rs25487 | Cases vs NC | G/A | 0.00* | 2.00 | 1.14–3.50 | 0.02* | 2.54 | 1.15–5.59 |
| A/A | 3.43 | 1.50–7.85 | ||||||
| Cases vs OC | G/A | 0.03* | 1.61 | 0.91–2.87 | 0.03* | 2.40 | 1.06–5.46 | |
| A/A | 3.00 | 1.26–7.10 | ||||||
| NC vs OC | G/A | 0.76 | 0.81 | 0.45–1.43 | 0.91 | 0.95 | 0.37–2.43 | |
| A/A | 0.87 | 0.33–2.30 | ||||||
| rs1042522 | Cases vs NC | G/C | 0.54 | 0.73 | 0.41–1.29 | 0.82 | 0.92 | 0.47–1.82 |
| C/C | 0.78 | 0.37–1.64 | ||||||
| Cases vs OC | G/C | 0.41 | 0.88 | 0.48–1.59 | 0.21 | 0.66 | 0.34–1.27 | |
| C/C | 0.61 | 0.30–1.27 | ||||||
| NC vs OC | G/C | 0.51 | 1.21 | 0.65–2.24 | 0.32 | 0.71 | 0.36–1.39 | |
| C/C | 0.79 | 0.37–1.67 | ||||||
| Variable | Groups | Dominant model | Allele model | |||||
| OR | 95%CI | OR | 95%CI | |||||
| rs25487 | Cases vs NC | 0.00* | 2.30 | 1.37–3.86 | 0.00* | 2.05 | 1.39–3.04 | |
| Cases vs OC | 0.02* | 1.88 | 1.10–3.22 | 0.00* | 1.79 | 1.20–2.67 | ||
| NC vs OC | 0.47 | 0.82 | 0.48–1.40 | 0.53 | 0.87 | 0.57–1.34 | ||
| rs1042522 | Cases vs NC | 0.27 | 0.74 | 0.43–1.27 | 0.37 | 0.84 | 0.58–1.23 | |
| Cases vs OC | 0.37 | 0.78 | 0.45–1.34 | 0.17 | 0.77 | 0.52–1.12 | ||
| NC vs OC | 0.87 | 1.05 | 0.59–1.86 | 0.64 | 0.91 | 0.62–1.34 | ||
OR Odd ratio, CI Confidence interval, NC Negative controls, OC Elderly patients above the age of 80
*indicated p-value< 0.05
The gene - gene interaction of XRCC1 and TP53 in the cervical cancer group and the negative control group
| B | SE | Wald | N | P | OR | 95% CI | ||
|---|---|---|---|---|---|---|---|---|
| Recessive model | ||||||||
| XRCC1 | −0.15 | 0.88 | 0.03 | 1 | 0.86 | 0.86 | 0.15 | 4.79 |
| Tp53 | 0.29 | 0.89 | 0.11 | 1 | 0.75 | 1.33 | 0.24 | 7.56 |
| Tp53-GG/GC by XRCC1-GG/GA | −0.06 | 0.96 | 0.00 | 1 | 0.95 | 0.95 | 0.15 | 6.16 |
| 常数 | 0 | 0.82 | 0 | 1 | 1 | 1 | ||
| Additive model | ||||||||
| Tp53 | 7.71 | 2 | 0.02* | |||||
| Tp53-GC | −1.10 | 0.40 | 7.69 | 1 | 0.01* | 0.33 | 0.15 | 0.72 |
| Tp53-CC | −0.41 | 0.51 | 0.64 | 1 | 0.42 | 0.67 | 0.25 | 1.80 |
| Tp53 * XRCC1 | 10.49 | 4 | 0.03* | |||||
| Tp53-GC by XRCC1-GA | 1.53 | 0.48 | 10.43 | 1 | 0.00* | 4.63 | 1.83 | 11.75 |
| Tp53-GC by XRCC1-AA | 0.80 | 0.58 | 1.93 | 1 | 0.17 | 2.23 | 0.72 | 6.92 |
| Tp53-CC by XRCC1-GA | −0.10 | 0.64 | 0.02 | 1 | 0.88 | 0.91 | 0.26 | 3.20 |
| Tp53-CC by XRCC1-AA | 0.11 | 0.94 | 0.01 | 1 | 0.91 | 1.11 | 0.18 | 6.97 |
| 常数 | 0.30 | 0.22 | 1.93 | 1 | 0.17 | 1.35 | ||
| Dominant model | ||||||||
| XRCC1-GA/AA | 0.71 | 0.27 | 6.84 | 1 | 0.01* | 2.03 | 1.20 | 3.46 |
| Tp53-GC/CC | −0.46 | 0.28 | 2.69 | 1 | 0.10 | 0.63 | 0.37 | 1.09 |
| 常数 | −0.02 | 0.25 | 0.01 | 1 | 0.93 | 0.98 | ||
*indicated p-value< 0.05
The gene - gene interaction of XRCC1 and TP53 in the cervical cancer group and the elderly patients above the age of 80 group
| B | SE | Wald | N | P | OR | 95% CI | ||
|---|---|---|---|---|---|---|---|---|
| Recessive model | ||||||||
| Tp53-GG/GC | 1.34 | 0.55 | 5.85 | 1 | 0.02* | 3.81 | 1.29 | 11.26 |
| Tp53-GG/GC by XRCC1-GG/GA | −1.07 | 0.49 | 4.68 | 1 | 0.03* | 0.34 | 0.13 | 0.90 |
| 常数 | −0.13 | 0.30 | 0.20 | 1 | 0.66 | 0.88 | ||
| Additive model | ||||||||
| XRCC1 | 5.58 | 2 | 0.06 | |||||
| XRCC1-GA | −0.85 | 0.49 | 3.03 | 1 | 0.08 | 0.43 | 0.16 | 1.11 |
| XRCC1-AA | 0.69 | 0.74 | 0.87 | 1 | 0.35 | 1.99 | 0.47 | 8.42 |
| Tp53 | 8.74 | 2 | 0.01* | |||||
| TP53-GC | −1.42 | 0.48 | 8.71 | 1 | 0.00* | 0.24 | 0.10 | 0.62 |
| TP53-CC | −0.81 | 0.57 | 2.07 | 1 | 0.15 | 0.44 | 0.15 | 1.34 |
| Tp53 * XRCC1 | 17.22 | 4 | 0.00* | |||||
| TP53-GC by XRCC1-GA | 2.87 | 0.72 | 16.09 | 1 | 0.00* | 17.61 | 4.34 | 71.50 |
| TP53-GC by XRCC1-AA | 1.22 | 1.05 | 1.34 | 1 | 0.25 | 3.37 | 0.43 | 26.29 |
| TP53-CC by XRCC1-GA | 0.95 | 0.81 | 1.37 | 1 | 0.24 | 2.57 | 0.53 | 12.51 |
| TP53-CC by XRCC1-AA | −0.49 | 1.19 | 0.17 | 1 | 0.68 | 0.62 | 0.06 | 6.32 |
| 常数 | 0.61 | 0.34 | 3.17 | 1 | 0.08 | 1.85 | ||
| Dominant model | ||||||||
| TP53-GC/CC | −0.96 | 0.35 | 7.66 | 1 | 0.01* | 0.39 | 0.20 | 0.76 |
| TP53-GC/CC by XRCC1-GA/AA | 1.29 | 0.37 | 12.54 | 1 | 0.00* | 3.64 | 1.78 | 7.43 |
| 常数 | 0.36 | 0.22 | 2.62 | 1 | 0.11 | 1.43 | ||
*indicated p-value< 0.05
The best model predicted ovarian cancer risk by GMDR
| Model | Training | Testing | Sign test | CV consistency |
|---|---|---|---|---|
| XRCC1 | 0.58 | 0.58 | 7(0.17) | 10/10 |
| XRCC1 TP53 | 0.66 | 0.63 | 10(0.00*) | 10/10 |
| XRCC1 TP53 FGFR3 | 0.66 | 0.63 | 10(0.00*) | 10/10 |
Data was analyzed by GMDR 0.9 with default settings
*indicated p-value< 0.05
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