| Literature DB >> 36246885 |
Weixing Qu1, Fuzhou Zhang2, Yongyi Cheng1, Jing Li1, Jiancheng Zhou1.
Abstract
Background: Bladder cancer is the most common leading cause of mortality around the world. Previous studies have indicated that genetic factors are significantly associated with bladder cancer progression-for instance, the CYP2C8 gene is involved in bladder cancer progression. However, little is known about the impact of CYP2C8 genetic polymorphisms on bladder cancer risk. We aimed to detect the association between CYP2C8 variations and bladder cancer susceptibility.Entities:
Keywords: CYP2C8; bladder cancer; case–control study; genetic variants; susceptibility
Mesh:
Substances:
Year: 2022 PMID: 36246885 PMCID: PMC9554954 DOI: 10.3389/fendo.2022.989030
Source DB: PubMed Journal: Front Endocrinol (Lausanne) ISSN: 1664-2392 Impact factor: 6.055
Primers used in this study.
| SNP_ID | 2nd-PCRP | 1st-PCRP | UEP-DIR | UEP SEQ |
|---|---|---|---|---|
| rs1934953 | ACGTTGGATGCTTGTTTCCTGTTCCAAGCC | ACGTTGGATGAGAGAGTGTATGACCAGAGC | F | AAGCCTGATATTCCATGA |
| rs1934951 | ACGTTGGATGGTTGGAATTTACATGGCACC | ACGTTGGATGATGGGTGTTAAGAGTGGTGC | R | GGGGCTGGTAGAATTGCTATTT |
| rs2275620 | ACGTTGGATGCATCTTGTGTTGTTAGAGGG | ACGTTGGATGCCCCAAGGTAAGCTTGTTTC | F | ccAACCAAACCAGCACTC |
| rs17110453 | ACGTTGGATGACACTGATTTCCCTCAAGGT | ACGTTGGATGCTGTGATGATGGAGAAACAC | R | cgGATTTCCCTCAAGGTCATAAA |
SNP, single-nucleotide polymorphisms; PCRP, polymerase chain reaction primer; UEP-DIR, unextended primer sequence direction; UEP SEQ, unextended mini-sequencing primer sequence.
1st-PCRP, first PCR primer; 2nd-PCRP, second PCR primer.
Characteristics of bladder cancer patients and healthy controls in this study.
| Characteristics | Cases ( | Controls ( |
|
|---|---|---|---|
| Age, years (mean ± SD) | 64.40 ± 10.99 | 63.92 ± 6.62 | 0.549 |
| >65 | 103 (47%) | 197 (36%) | |
| ≤65 | 114 (53%) | 353 (64%) | |
| Gender |
| ||
| Male | 175 (81%) | 379 (69%) | |
| Female | 42 (19%) | 171 (31%) | |
| Clinical stage | |||
| I/II | 68 (31%) | ||
| III/IV | 86 (40%) | ||
| Missing | 63 (29%) | ||
p <0.05 indicates statistical significance.
The p-value was calculated by Student’s t-test.
The p-value was calculated by χ2 test. The bold values mean statistically significant.
Basic information and allele frequencies of CYP2C8 SNPs.
| SNP ID | Chromosome position | Role | Alleles (minor/major) | MAF | O (HET) | E (HET) |
| |
|---|---|---|---|---|---|---|---|---|
| Case | Control | |||||||
| rs1934953 | chr10: 95037713 | Intron | T/C | 0.364 | 0.420 | 0.533 | 0.498 | 0.123 |
| rs1934951 | chr10: 95038791 | Intron | T/C | 0.294 | 0.313 | 0.486 | 0.475 | 0.590 |
| rs2275620 | chr10: 95042841 | Intron | T/A | 0.290 | 0.316 | 0.525 | 0.494 | 0.167 |
| rs17110453 | chr10: 95069772 | 3′UTR | C/A | 0.297 | 0.339 | 0.433 | 0.451 | 0.345 |
p-values were calculated by exact test. p <0.05 indicates statistical significance.
SNP, single-nucleotide polymorphisms; MAF, minor allele frequency; HWE, Hardy–Weinberg equilibrium.
Association analysis between CYP2C8 SNPs and bladder cancer risk.
| SNP ID | Model | Geno type | Case | Control | Without adjusted | With adjusted | ||
|---|---|---|---|---|---|---|---|---|
| OR (95% CI) |
| OR (95% CI) |
| |||||
| rs1934953 | Allele | C | 282 | 585 | 1 | |||
| T | 152 | 515 | 0.61 (0.49–0.77) |
| ||||
| Codominant | CC | 80 | 146 | 1 | 1 | |||
| CT | 122 | 293 | 0.76 (0.54–1.07) | 0.119 | 0.74 (0.53–1.05) | 0.096 | ||
| TT | 15 | 111 | 0.68 (0.46–0.99) | 5.59E-06 | 0.26 (0.14–0.47) |
| ||
| Dominant | CC | 80 | 146 | 1 | 1 | |||
| TC-TT | 137 | 403 | 0.62 (0.44–0.86) | 0.005 | 0.62 (0.44–0.86) |
| ||
| Recessive | CC-TC | 202 | 439 | 1 | 1 | |||
| TT | 15 | 111 | 0.29 (0.17–0.52) | 2.09E-05 | 0.31 (0.18–0.55) |
| ||
| Log-additive | – | – | – | 0.58 (0.45–0.74) | 1.19E-05 | 058 (0.45–0.75) |
| |
| rs1934951 | Allele | C | 253 | 670 | 1 | |||
| T | 181 | 424 | 1.13 (0.90–1.42) | 0.288 | ||||
| Codominant | CC | 55 | 202 | 1 | 1 | |||
| CT | 143 | 266 | 1.97 (1.38–2.83) | 2.19E-04 | 1.96 (1.37–2.82) |
| ||
| TT | 19 | 79 | 0.88 (0.49–1.58) | 0.677 | 0.94 (0.52–1.69) | 0.82 | ||
| Dominant | CC | 55 | 202 | 1 | 1 | |||
| TC-TT | 162 | 345 | 1.73 (1.21–2.45) | 0.002 | 1.74 (1.22–2.48) |
| ||
| Recessive | CC-TC | 198 | 468 | 1 | 1 | |||
| TT | 19 | 79 | 0.57 (0.34–0.96) | 0.036 | 0.60 (0.35–1.03) | 0.064 | ||
| Log-additive | – | – | – | 1.15 (0.90–1.46) | 0.258 | 0.58 (0.92–1.51) | 0.189 | |
| rs2275620 | Allele | A | 260 | 608 | 1 | |||
| T | 174 | 490 | 0.83 (0.66–1.04) | 0.107 | ||||
| Codominant | AA | 57 | 160 | 1 | 1 | |||
| AT | 146 | 288 | 1.42 (0.99–2.04) | 0.056 | 1.38 (0.96–1.99) | 0.081 | ||
| TT | 14 | 101 | 0.39 (0.21–0.73) | 3.60E-03 | 0.40 (0.21–0.76) |
| ||
| Dominant | AA | 57 | 160 | 1 | 1 | |||
| TA-TT | 160 | 389 | 1.16 (0.81–1.65) | 0.426 | 1.14 (0.80–1.62) | 0.482 | ||
| Recessive | AA-TA | 203 | 448 | 1 | 1 | |||
| TT | 14 | 101 | 0.31 (0.17–0.55) | 6.84E-05 | 0.32 (0.18–0.58) |
| ||
| Log-additive | – | – | – | 0.80 (0.63–1.03) | 0.080 | 0.81 (0.63–1.04) | 0.092 | |
| rs17110453 | Allele | A | 275 | 722 | 1 | |||
| C | 159 | 378 | 1.10 (0.88–1.39) | 0.401 | ||||
| Codominant | AA | 71 | 242 | 1 | 1 | |||
| AC | 133 | 238 | 1.91 (1.36–2.67) | 1.96E-04 | 1.89 (1.35–2.67) |
| ||
| CC | 13 | 70 | 0.63 (0.33–1.21) | 0.167 | 0.66 (0.34–1.27) | 0.213 | ||
| Dominant | AA | 71 | 242 | 1 | 1 | |||
| CA-CC | 146 | 308 | 1.62 (1.16–2.25) | 0.004 | 1.63 (1.16–2.27) |
| ||
| Recessive | AA-CA | 204 | 480 | 1 | 1 | |||
| CC | 13 | 70 | 0.44 (0.24–0.81) | 0.008 | 1.46 (0.25–0.85) |
| ||
| Log-additive | – | – | – | 1.11 (0.83–1.41) | 0.386 | 1.13 (0.83–1.44) | 0.334 | |
p <0.05 indicates statistical significance.
CI, confidence interval; OR, odds ratio; SNP, single-nucleotide polymorphism.
p‐values were calculated by logistic regression analysis without adjustment.
p‐values were calculated by logistic regression analysis with adjustment for age and gender. The bold values mean statistically significant.
Association of CYP2C8 SNPs with the risk of bladder cancer stratified by age.
| SNP | Model | Allele/genotype | Case | Control | OR (95% CI) |
| Case | Control | OR (95% CI) |
|
|---|---|---|---|---|---|---|---|---|---|---|
|
|
|
| ||||||||
| rs1934953 | Allele | C | 128 | 199 | 1 | 154 | 386 | 1 | ||
| T | 78 | 195 | 0.62 (0.44–0.88) |
| 74 | 320 | 0.58 (0.42–0.79) |
| ||
| Codominant | CC | 34 | 49 | 1 | 46 | 97 | 1 | |||
| CT | 60 | 101 | 0.79 (0.45–1.40) | 0.425 | 62 | 192 | 0.74 (0.46–1.19) | 0.212 | ||
| TT | 9 | 47 | 0.29 (0.12–0.69) |
| 6 | 64 | 0.25 (0.10–0.63) |
| ||
| Dominant | CC | 34 | 49 | 1 | 46 | 97 | 1 | |||
| TC-TT | 69 | 148 | 0.64 (0.37–1.11) | 0.108 | 68 | 256 | 0.62 (0.39–1.00) |
| ||
| Recessive | CC-TC | 94 | 150 | 1 | 108 | 289 | 1 | |||
| TT | 9 | 47 | 0.34 (0.16–0.74) |
| 6 | 64 | 0.30 (0.12–0.73) |
| ||
| Log-additive | – | – | – | 0.59 (0.40–0.87) |
| – | – | 0.59 (0.41–0.84) |
| |
| rs1934951 | Allele | C | 118 | 234 | 1 | 135 | 436 | 1 | ||
| T | 88 | 156 | 1.12 (0.79–1.58) | 0.521 | 93 | 268 | 1.12 (0.83–1.52) | 0.464 | ||
| Codominant | CC | 25 | 72 | 1 | 30 | 130 | 1 | |||
| CT | 68 | 90 | 2.17 (1.21–3.86) |
| 75 | 176 | 1.87 (1.13–3.11) |
| ||
| TT | 10 | 33 | 0.88 (0.37–2.10) | 0.776 | 9 | 46 | 1.12 (0.48–2.62) | 0.794 | ||
| Dominant | CC | 25 | 72 | 1 | 30 | 130 | 1 | |||
| TC-TT | 78 | 123 | 1.82 (1.04–3.19) |
| 84 | 222 | 1.74 (1.06–2.86) |
| ||
| Recessive | CC-TC | 93 | 162 | 1 | 123 | 276 | 1 | |||
| TT | 10 | 33 | 0.53 (0.25–1.15) | 0.110 | 9 | 46 | 0.75 (0.34–1.62) | 0.461 | ||
| Log-additive | – | – | – | 1.13 (0.77–1.64) | 0.538 | – | – | 1.27 (0.89–1.81) | 0.196 | |
| rs2275620 | Allele | A | 117 | 209 | 1 | 143 | 399 | 1 | ||
| T | 89 | 183 | 0.87 (0.62–1.22) | 0.417 | 85 | 307 | 0.77 (0.57–1.05) | 0.099 | ||
| Codominant | AA | 24 | 54 | 1 | 33 | 106 | 1 | |||
| AT | 69 | 101 | 1.47 (0.81–2.66) | 0.207 | 77 | 187 | 1.32 (0.80–2.17) | 0.280 | ||
| TT | 10 | 41 | 0.58 (0.24–1.38) | 0.218 | 4 | 60 | 0.25 (0.08–0.77) |
| ||
| Dominant | AA | 24 | 54 | 1 | 33 | 106 | 1 | |||
| TA-TT | 79 | 142 | 1.22 (0.68–2.18) | 0.505 | 81 | 247 | 1.08 (0.66–1.77) | 0.759 | ||
| Recessive | AA-TA | 93 | 155 | 1 | 110 | 293 | 1 | |||
| TT | 10 | 41 | 0.44 (0.21–0.94) |
| 4 | 60 | 0.21 (0.07–0.61) |
| ||
| Log-additive | – | – | – | 0.85 (0.58–1.26) | 0.425 | – | – | 0.77 (0.54–1.11) | 0.156 | |
| rs17110453 | Allele | A | 125 | 253 | 1 | 150 | 469 | 1 | ||
| C | 81 | 141 | 1.16 (0.82–1.65) | 0.395 | 78 | 237 | 1.03 (0.75–1.41) | 0.859 | ||
| Codominant | AA | 30 | 85 | 1 | 41 | 157 | 1 | |||
| AC | 65 | 83 | 1.96 (1.13–3.39) |
| 68 | 155 | 1.93 (1.19–3.12) |
| ||
| CC | 8 | 29 | 0.67 (0.27–1.69) | 0.398 | 5 | 41 | 0.56 (0.20–1.55) | 0.265 | ||
| Dominant | AA | 30 | 85 | 1 | 41 | 157 | 1 | |||
| CA-CC | 73 | 112 | 1.62 (0.95–2.76) | 0.074 | 73 | 196 | 1.64 (1.03–2.62) |
| ||
| Recessive | AA-CA | 95 | 168 | 1 | 109 | 312 | 1 | |||
| CC | 8 | 29 | 0.45 (0.19–1.05) | 0.065 | 5 | 41 | 0.39 (0.15–1.03) | 0.058 | ||
| Log-additive | – | – | – | 1.07 (0.74–1.57) | 0.714 | – | – | 1.14 (0.80–1.61) | 0.467 | |
p-values were calculated by logistic regression adjusted by age and gender. p <0.05 indicates statistical significance.The bold values mean statistically significant.
Figure 1SNP–SNP interaction map. Values in nodes represent the information gains of individual attribute (main effects). Values between nodes are information gains of each pair of attributes (interaction effects). Blue and green with negative percent entropy indicate redundancy or independence.
Analysis of the SNP–SNP interaction models with the multifactor dimensionality reduction method.
| Model | Training bal. acc. | Testing bal. acc. | CVC | OR (95% CI) |
|
|---|---|---|---|---|---|
| rs17110453 | 0.6246 | 0.6083 | 9/10 | 2.81 (1.77–4.46) |
|
| rs1934953, rs1934951 | 0.6798 | 0.6242 | 6/10 | 5.61 (3.29–9.59) |
|
| rs1934953, rs2275620, rs17110453 | 0.7162 | 0.6561 | 7/10 | 6.75 (4.06–11.23) |
|
| rs1934953, rs1934951, rs2275620, rs17110453 | 0.7272 | 0.6720 | 10/10 | 7.64 (4.56–12.77) |
|
p-values were calculated by χ2 test. p <0.05 indicates statistical significance.
Bal. Acc., balanced accuracy; CVC, cross-validation consistently.The bold values mean statistically significant.