| Literature DB >> 28386271 |
L Dziki1, A Dziki1, M Mik1, I Majsterek2, J Kabzinski2.
Abstract
Polymorphisms in DNA repair genes may affect the activity of the BER (base excision repair) and NER (nucleotide excision repair) systems. Using DNA isolated from blood taken from patients (n = 312) and a control group (n = 320) with CRC, we have analyzed the polymorphisms of selected DNA repair genes and we have demonstrated that genotypes 51Gln/His and 148Asp/Glu of APEX gene and 23Gly/Ala of XPA gene may increase the risk of colorectal cancer. At the same time analyzing the gene-gene interactions, we suggest the thesis that the main factor to be considered when analyzing the impact of polymorphisms on the risk of malignant transformation should be intergenic interactions. Moreover, we are suggesting that some polymorphisms may have impact not only on the malignant transformation but also on the stage of the tumor.Entities:
Year: 2017 PMID: 28386271 PMCID: PMC5366231 DOI: 10.1155/2017/3840243
Source DB: PubMed Journal: Gastroenterol Res Pract ISSN: 1687-6121 Impact factor: 2.260
The refSNP and thermal conditions used in the PCR reaction.
| Gene |
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| ERCC4 |
|---|---|---|---|---|---|
| Polymorphism | 51Gln/His | 64Ile/Val | 148Asp/Glu | 23Gly/Ala | 689Ser/Arg |
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| refSNP | rs1048945 | rs2307486 | rs1130409 | rs1800975 | rs149364215 |
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| Thermal conditions | (1) 95°C, 10 min | ||||
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| Dyes | ROX, HEX, FAM | ||||
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| Ref dye | ROX | ||||
The distribution of genotypes and allele frequencies and the analysis of the odds ratio (OR) for 51Gln/His polymorphism of APEX gene in patients with colorectal cancer (CRC) and the control group.
| Genotype/allele | Patients ( | Controls ( | OR (95% CI) |
|
|---|---|---|---|---|
| Gln/Gln | 69 | 92 | 1 (ref) | — |
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| His/His | 36 | 49 | 0.979 (0.576–1.667) | 0.920 |
| Gln | 344 | 345 | 1 (ref) | — |
| His | 278 | 259 | 1.077 (0.859–1.349) | 0.522 |
∗Genotype distribution in the Hardy-Weinberg equilibrium, χ2 = 0.125.
Values set in italics denote statistical significance.
The distribution of genotypes and allele frequencies and the analysis of the odds ratio (OR) for 148Asp/Glu polymorphism of APEX gene in patients with colorectal cancer (CRC) and the control group.
| Genotype/allele | Patients ( | Controls ( | OR (95% CI) |
|
|---|---|---|---|---|
| Asp/Asp | 51 | 88 | 1 (ref) | — |
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| Glu/Glu | 21 | 55 | 0.659 (0.358–1.212) | 0.179 |
| Asp | 339 | 334 | 1 (ref) | — |
| Glu | 279 | 268 | 1.026 (0.819–1.285) | 0.823 |
∗Genotype distribution in the Hardy-Weinberg equilibrium, χ2 = 0.277.
Values set in italics denote statistical significance.
The distribution of genotypes and allele frequencies and the analysis of the odds ratio (OR) for 23Gly/Ala polymorphism of XPA gene in patients with colorectal cancer (CRC) and the control group.
| Genotype/allele | Patients ( | Controls ( | OR (95% CI) |
|
|---|---|---|---|---|
| Gly/Gly | 31 | 95 | 1 (ref) | — |
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| Ala/Ala | 16 | 59 | 0.831 (0.419–1.649) | 0.597 |
| Gly | 325 | 340 | 1 (ref) | — |
| Ala | 295 | 268 | 1.152 (0.920–1.442) | 0.218 |
∗Genotype distribution in the Hardy-Weinberg equilibrium, χ2 = 0.988.
Values set in italics denote statistical significance.
The distribution of genotypes and allele frequencies and the analysis of the odds ratio (OR) for 64Ile/Val polymorphism of APEX gene in patients with colorectal cancer (CRC) and the control group.
| Genotype/allele | Patients ( | Controls ( | OR (95% CI) |
|
|---|---|---|---|---|
| Ile/Ile | 93 | 78 | 1 (ref) | — |
| Ile/Val | 148 | 159 | 0.781 (0.537–1.136) | 0.195 |
| Val/Val | 66 | 67 | 0.826 (0.525–1.301) | 0.409 |
| Ile | 334 | 315 | 1 (ref) | — |
| Val | 280 | 293 | 0.901 (0.720–1.128) | 0.365 |
∗Genotype distribution in the Hardy-Weinberg equilibrium, χ2 = 0.408.
The distribution of genotypes and allele frequencies and the analysis of the odds ratio (OR) for 689Ser/Arg polymorphism of ERCC4 gene in patients with colorectal cancer (CRC) and the control group.
| Genotype/allele | Patients ( | Controls ( | OR (95% CI) |
|
|---|---|---|---|---|
| Ser/Ser | 93 | 101 | 1 (ref) | — |
| Ser/Arg | 155 | 160 | 1.052 (0.736–1.505) | 0.777 |
| Arg/Arg | 61 | 43 | 1.541 (0.952–2.493) | 0.078 |
| Ser | 341 | 362 | 1 (ref) | — |
| Arg | 277 | 246 | 1.195 (0.953–1.499) | 0.123 |
∗Genotype distribution in the Hardy-Weinberg equilibrium, χ2 = 0.107.
The distribution of genotypes and the analysis of the odds ratio (OR) for gene-gene interactions in analyzed polymorphisms in patients with colorectal cancer (CRC) and the control group. Shown are only pairs that modulate the risk at a statistically significant level. All partial results for the gene-gene interaction are shown in the supplementary materials.
| Gene-gene interaction | Genotype | Patients | Controls | OR (95% CI) |
|
|---|---|---|---|---|---|
| 51Gln/His APEX-64Ile/Val APEX | Gln/His-Val/Val | 55 | 32 | 2.266 (1.120–4.585) | 0.022 |
| 51Gln/His APEX-148Asp/Glu APEX | Gln/His-Asp/Glu | 174 | 102 | 2.003 (1.091–3.676) | 0.023 |
| Gln/His-Glu/Glu | 8 | 26 | 0.361 (0.137–0.951) | 0.036 | |
| His/His-Asp/Asp | 6 | 28 | 0.252 (0.089–0.714) | 0.007 | |
| 51Gln/His APEX-23Gly/Ala XPA | Gln/His-Gly/Gly | 6 | 35 | 0.220 (0.078–0.622) | 0.003 |
| Gln/His-Gly/Ala | 193 | 98 | 2.532 (1.362–4.707) | 0.003 | |
| His/His-Gly/Ala | 30 | 8 | 4.821 (1.835–12.670) | 0.001 | |
| 51Gln/His APEX-689Ser/Arg ERCC4 | Gln/His-Arg/Arg | 39 | 24 | 2.464 (1.247–4.870) | 0.009 |
| 64Ile/Val APEX-148Asp/Glu APEX | Ile/Val-Asp/Asp | 10 | 27 | 0.403 (0.170–0.955) | 0.036 |
| Val/Val-Asp/Glu | 59 | 18 | 3.567 (1.765–7.211) | 0.0003 | |
| 64Ile/Val APEX-23Gly/Ala XPA | Ile/Val-Gly/Gly | 9 | 37 | 0.269 (0.103–0.700) | 0.006 |
| Ile/Val-Ala/Ala | 6 | 23 | 0.288 (0.097–0.859) | 0.022 | |
| Val/Val-Gly/Ala | 62 | 14 | 4.895 (2.093–11.445) | 0.0001 | |
| 148Asp/Glu APEX-23Gly/Ala XPA | Asp/Asp-Gly/Ala | 26 | 58 | 0.399 (0.176–0.902) | 0.025 |
| Asp/Glu-Gly/Gly | 8 | 46 | 0.155 (0.056–0.424) | 0.0001 | |
| Asp/Glu-Gly/Ala | 218 | 81 | 2.392 (1.164–4.915) | 0.015 | |
| 148Asp/Glu APEX-689Ser/Arg ERCC4 | Asp/Asp-Ser/Arg | 21 | 48 | 0.844 (0.370–1.924) | 0.689 |
| Asp/Asp-Arg/Arg | 13 | 13 | 1.929 (0.707–5.263) | 0.198 | |
| Asp/Glu-Ser/Ser | 69 | 49 | 2.716 (1.293–5.704) | 0.007 | |
| 23Gly/Ala XPA-689Ser/Arg ERCC4 | Gly/Ala-Ser/Ser | 76 | 57 | 2.333 (1.061–5.131) | 0.032 |
| Gly/Ala-Ser/Arg | 135 | 77 | 3.068 (1.431–6.577) | 0.003 | |
| Gly/Ala-Arg/Arg | 47 | 16 | 5.141 (2.073–12.749) | 0.0003 |
Analysis of correlation of selected polymorphisms with the state of tumor according to classification of American Joint Committee on Cancer.
| 51Gln/His polymorphism of APEX gene | ||||||||||
| Genotype | Patients ( | II° versus I° | III° + IV° versus I° | III° + IV° versus II° | ||||||
| I° | II° | III° | IV° | OR (95% CI) |
| OR (95% CI) |
| OR (95% CI) |
| |
| Gln/Gln | 24 | 21 | 19 | 5 | 1 (ref) | — | 1 (ref) | — | 1 (ref) | — |
| Gln/His | 57 | 94 | 48 | 7 | 1.885 (0.963–3.690) | 0.062 | 0.965 (0.491–1.898) | 0.920 | 0.512 (0.261–1.004) | 0.049 |
| His/His | 19 | 15 | 2 | 0 | 0.902 (0.369–2.209) | 0.823 | — | — | — | — |
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| 64Ile/Val polymorphism of APEX | ||||||||||
| Genotype | Patients ( | II° versus I° | III° + IV° versus I° | III° + IV° versus II° | ||||||
| I° | II° | III° | IV° | OR (95% CI) |
| OR (95% CI) |
| OR (95% CI) |
| |
| Ile/Ile | 41 | 32 | 19 | 1 | 1 (ref) | — | 1 (ref) | — | 1 (ref) | — |
| Ile/Val | 64 | 51 | 28 | 5 | 1.021 (0.566–1.843) | 1.000 | 1.057 (0.536–2.086) | 0.862 | 1.035 (0.509–2.105) | 0.920 |
| Val/Val | 33 | 17 | 14 | 2 | 0.660 (0.313–1.391) | 0.273 | 0.994 (0.446–2.215) | 1.000 | 1.506 (0.623–3.638) | 0.362 |
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| 148Asp/Glu polymorphism of APEX | ||||||||||
| Genotype | Patients ( | II° versus I° | III° + IV° versus I° | III° + IV° versus II° | ||||||
| I° | II° | III° | IV° | OR (95% CI) |
| OR (95% CI) |
| OR (95% CI) |
| |
| Asp/Asp | 29 | 17 | 5 | 0 | 1 (ref) | — | 1 (ref) | — | 1 (ref) | — |
| Asp/Glu | 98 | 133 | 5 | 1 |
|
| — | — | — | — |
| Glu/Glu | 16 | 5 | 0 | 0 | 0.533 (0.166–1.716) | 0.288 | — | — | — | — |
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| 23Gly/Ala polymorphism of XPA gene | ||||||||||
| Genotype | Patients ( | II° versus I° | III° + IV° versus I° | III° + IV° versus II° | ||||||
| I° | II° | III° | IV° | OR (95% CI) |
| OR (95% CI) |
| OR (95% CI) |
| |
| Gly/Gly | 17 | 9 | 5 | 0 | 1 (ref) | — | 1 (ref) | — | 1 (ref) | — |
| Gly/Ala | 87 | 165 | 9 | 2 |
|
| — | — | — | — |
| Ala/Ala | 11 | 5 | 0 | 0 | 0.859 (0.227–3.248) | 0.823 | — | — | — | — |
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| 689Ser/Arg polymorphism of ERCC4 | ||||||||||
| Genotype | Patients ( | II° versus I° | III° + IV° versus I° | III° + IV° versus II° | ||||||
| I° | II° | III° | IV° | OR (95% CI) |
| OR (95% CI) |
| OR (95% CI) |
| |
| Ser/Ser | 49 | 31 | 9 | 4 | 1 (ref) | — | 1 (ref) | — | 1 (ref) | — |
| Ser/Arg | 83 | 52 | 16 | 4 | 0.990 (0.561–1.747) | 1.000 | 0.908 (0.415–1.986) | 0.806 | 0.795 (0.356–1.776) | 0.578 |
| Arg/Arg | 32 | 24 | 3 | 2 | 1.186 (0.592–2.374) | 0.632 | 0.589 (0.192–1.811) | 0.351 | 0.431 (0.137–1.352) | 0.143 |
Values set in italics denote statistical significance.