| Literature DB >> 26573232 |
Lina Wu1, Lu Yao2, Hong Zhang1, Tao Ouyang2, Jinfeng Li2, Tianfeng Wang2, Zhaoqing Fan2, Tie Fan2, Benyao Lin2, C Cameron Yin3, Yuntao Xie2.
Abstract
Breast cancer is believed to result from the interplay of genetic and non-genetic risk factors, and individual genetic variation may influence the efficacy of chemotherapy. Here we conducted a genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with response to anthracycline- and taxane-based neoadjuvant chemotherapy in breast cancer patients. In the discovery stage, we divided 92 patients who received anthracycline-based neoadjuvant chemotherapy into 2 groups according to pathologic response and performed a genome-wide study using Affymetrix SNP6.0 genechip. Of 389,795 SNPs associated with pathologic complete response (pCR), we identified 2 SNPs, rs6044100 and rs1799937, that were significantly associated with pCR after neoadjuvant chemotherapy. In the validation stage, genotype analysis of samples from an independent cohort of 401 patients who received anthracycline-based neoadjuvant regimens and 467 patients who received taxane-based regimens was performed using sequencing analysis. We found that only SNP rs1799937, located in the WT1 gene, was associated with pCR after anthracycline-based neoadjuvant therapy (AA vs GG; odds ratio [OR], 2.81; 95% confidence interval [CI], 1.13-6.98; P < 0.05) but not after taxane-based neoadjuvant therapy (AA vs GG; OR, 0.85; 95% CI, 0.36-2.04; P = 0.72). These results suggest that WT1 may be a potential target of anthracycline-based neoadjuvant therapy for breast cancer.Entities:
Keywords: WT1; anthracycline; breast cancer; neoadjuvant chemotherapy; rs1799937
Mesh:
Substances:
Year: 2016 PMID: 26573232 PMCID: PMC4826264 DOI: 10.18632/oncotarget.5837
Source DB: PubMed Journal: Oncotarget ISSN: 1949-2553
Patient characteristics
| Characteristic | No. of patients | Discoverycohort ( | Validation cohort | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Anthracycline ( | Taxane ( | ||||||||
| % | % | % | % | ||||||
| Age (years) | |||||||||
| ≤ 50 | 571 | 59.5 | 65 | 70.7 | 250 | 62.3 | 256 | 54.8 | 0.006 |
| > 50 | 389 | 40.5 | 27 | 29.3 | 151 | 37.7 | 211 | 45.2 | |
| Tumor size | |||||||||
| ≤ 2cm | 381 | 40.0 | 22 | 23.9 | 147 | 37.3 | 212 | 45.5 | < 0.001 |
| > 2cm | 571 | 60.0 | 70 | 76.1 | 247 | 62.7 | 254 | 54.5 | |
| Unknown | 8 | 0 | 7 | 1 | |||||
| Tumor grade | |||||||||
| I | 95 | 10.3 | 6 | 6.7 | 45 | 11.6 | 44 | 9.8 | 0.21 |
| II | 691 | 74.7 | 68 | 76.4 | 277 | 71.2 | 346 | 77.4 | |
| III | 139 | 15.0 | 15 | 16.9 | 67 | 17.2 | 57 | 12.8 | |
| Unknown | 35 | 3 | 12 | 20 | |||||
| Lymph node involvement | |||||||||
| Negative | 525 | 55.4 | 63 | 69.2 | 230 | 57.6 | 232 | 50.7 | 0.002 |
| Positive | 423 | 44.6 | 28 | 30.8 | 169 | 42.4 | 226 | 49.3 | |
| Unknown | 12 | 1 | 2 | 9 | |||||
| Estrogen receptor status | |||||||||
| Negative | 377 | 39.4 | 44 | 48.4 | 155 | 38.8 | 178 | 38.2 | 0.18 |
| Positive | 579 | 60.6 | 47 | 51.6 | 244 | 61.2 | 288 | 61.8 | |
| Unknown | 4 | 1 | 2 | 1 | |||||
| Progesterone receptor status | |||||||||
| Negative | 479 | 50.2 | 51 | 56.7 | 206 | 51.6 | 222 | 47.7 | 0.23 |
| Positive | 475 | 49.8 | 39 | 43.3 | 193 | 48.4 | 243 | 52.3 | |
| Unknown | 6 | 2 | 2 | 2 | |||||
| HER2 status | |||||||||
| Negative | 694 | 72.4 | 56 | 61.5 | 296 | 73.8 | 342 | 73.4 | 0.05 |
| Positive | 264 | 27.6 | 35 | 38.5 | 105 | 26.2 | 124 | 26.6 | |
| Unknown | 2 | 1 | 0 | 1 | |||||
| Surgery type | |||||||||
| BCS | 406 | 42.3 | 51 | 55.4 | 171 | 42.6 | 184 | 39.4 | 0.017 |
| Mastectomy | 554 | 57.7 | 41 | 44.6 | 230 | 57.4 | 283 | 60.6 | |
| Chemotherapy cycles | |||||||||
| ≥ 4 | 897 | 93.4 | 92 | 100.0 | 361 | 90.0 | 444 | 95.1 | < 0.001 |
| < 4 | 63 | 6.6 | 0 | 0.0 | 40 | 10.0 | 23 | 4.9 | |
| Adjuvant chemotherapy | |||||||||
| No | 332 | 34.6 | 15 | 16.3 | 113 | 28.2 | 204 | 43.7 | < 0.001 |
| Yes | 628 | 65.4 | 77 | 83.7 | 288 | 71.8 | 263 | 56.3 | |
| Adjuvant endocrine therapy | |||||||||
| No | 395 | 41.1 | 35 | 38.0 | 162 | 40.4 | 198 | 42.4 | 0.68 |
| Yes | 565 | 58.9 | 57 | 62.0 | 239 | 59.6 | 269 | 57.6 | |
| Pathologic complete response | |||||||||
| non-pCR | 788 | 82.1 | 62 | 67.4 | 339 | 84.5 | 387 | 82.9 | < 0.001 |
| pCR | 172 | 17.9 | 30 | 32.6 | 62 | 15.5 | 80 | 17.1 | |
HER2, human epidermal growth factor receptor 2; BCS, breast-conserving surgery; pCR, pathologic complete response
A P value < 0.05 was considered statistically significant.
Figure 1Scatter plot of P values (shown as -log10) in association test of 389,795 single nucleotide polymorphismalleles with pathologic response status at the end of anthracycline-based neoadjuvant chemotherapy in discovery cohort of 92 breast cancer patients. Colors indicate chromosomes
SNPs significantly associated with breast cancer in patients who received anthracycline-based CTF chemotherapy regimens in discovery cohort
| MAF | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| SNP | Minor allele | Chr. | Position | Gene | Location | pCR | non-pCR | OR (95%CI) | |
| rs6135795 | G | 20 | 16534948 | KIF16B | Intron | 0.62 | 0.28 | 4.07 (2.11–7.83) | 1.61 × 10−5 |
| rs4748316 | T | 10 | 16779881 | RSU1 | Intron | 0.48 | 0.18 | 4.17 (2.10–8.27) | 2.55 × 10−5 |
| rs6686072 | C | 1 | 57936193 | DAB1 | Intron | 0.40 | 0.13 | 4.33 (2.07–9.06) | 4.98 × 10−5 |
| rs687660 | A | 11 | 70111532 | PPFIA1 | Upstream | 0.32 | 0.08 | 5.10 (2.19–11.87) | 5.97 × 10−5 |
| rs3102072 | A | 1 | 20964066 | PINK1 | Intron | 0.62 | 0.31 | 3.61 (1.89–6.90) | 7.39 × 10−5 |
| rs9806453 | G | 15 | 60943845 | RORA | Intron | 0.67 | 0.37 | 3.46 (1.80–6.64) | 1.43 × 10−4 |
| rs6075070 | G | 20 | 16536424 | KIF16B | Intron | 0.42 | 0.16 | 3.80 (1.87–7.72) | 1.44 × 10−4 |
| rs4811431 | T | 20 | 52031569 | TSHZ2 | Intron | 0.28 | 0.08 | 4.88 (2.02–11.77) | 1.78 × 10−4 |
| rs4580153 | T | 16 | 81817239 | PLCG2 | Intron | 0.32 | 0.10 | 4.17 (1.86–9.35) | 2.84 × 10−4 |
| rs12481468 | C | 20 | 43532438 | YWHAB | intron | 0.22 | 0.04 | 6.14(2.07–18.20) | 3.16 × 10−4 |
| rs1004895 | A | 20 | 16540600 | KIF16B | Intron | 0.40 | 0.16 | 3.54 (1.74–7.22) | 3.38 × 10−4 |
| rs32496 | A | 5 | 55641639 | MAP3K1 | Upstream | 0.68 | 0.40 | 3.24 (1.68–6.23) | 3.38 × 10−4 |
| rs16944877 | C | 12 | 115459615 | TBX3 | Upstream | 0.35 | 0.13 | 3.77 (1.77–8.04) | 3.74 × 10−4 |
| rs12530912 | G | 7 | 116127529 | CAV2 | Intron | 0.28 | 0.08 | 4.35 (1.85–10.25) | 3.96 × 10−4 |
| rs17191246 | C | 15 | 60386336 | ANXA2 | Downstream | 0.27 | 0.08 | 4.49 (1.85–10.90) | 4.56 × 10−4 |
| rs10443217 | G | 1 | 57979666 | DAB1 | Intron | 0.38 | 0.14 | 3.64 (1.73–7.66) | 4.58 × 10−4 |
| rs1620195 | T | 12 | 32084747 | H3F3C | Upstream | 0.42 | 0.18 | 3.37 (1.68–6.76) | 4.58 × 10−4 |
| rs10493224 | A | 1 | 57938752 | DAB1 | Intron | 0.25 | 0.07 | 4.67 (1.85–11.77) | 5.14 × 10−4 |
| rs4833326 | C | 4 | 126424441 | FAT4 | Downstream | 0.67 | 0.40 | 3.00 (1.57–5.74) | 7.41 × 10−4 |
| rs1467089 | T | 8 | 49960530 | SNAI2 | Upstream | 0.40 | 0.17 | 3.27 (1.61–6.62) | 7.52 × 10−4 |
| rs12151836 | G | 2 | 86601052 | KDM3A | Upstream | 0.28 | 0.09 | 3.92 (1.70–9.04) | 8.24 × 10−4 |
| rs17588172 | G | 7 | 116154015 | CAV2 | Downstream | 0.28 | 0.09 | 3.92 (1.70–9.04) | 8.24 × 10−4 |
| rs4631527 | G | 9 | 110270036 | KLF4 | Upstream | 0.57 | 0.31 | 2.93 (1.55–5.57) | 8.29 × 10−4 |
| rs10857592 | C | 10 | 49732975 | ARHGAP22 | Intron | 0.24 | 0.07 | 4.46 (1.75–11.36) | 9.02 × 10−4 |
| rs1080954 | T | 20 | 16506016 | KIF16B | Intron | 0.47 | 0.23 | 3.01 (1.55–5.85) | 9.07 × 10−4 |
| rs3821629 | C | 3 | 25620132 | RARB | Intron | 0.52 | 0.27 | 2.94 (1.54–5.62) | 9.17 × 10−4 |
| rs3019286 | A | 8 | 99895405 | STK3 | Intron | 0.60 | 0.34 | 2.89 (1.53–5.48) | 9.59 × 10−4 |
| rs12039126 | A | 1 | 56681381 | PPAP2B | Downstream | 0.27 | 0.08 | 4.00 (1.69–9.49) | 9.73 × 10−4 |
| rs7307249 | G | 12 | 117077849 | MAP1LC3B2 | Downstream | 0.37 | 0.15 | 3.28 (1.59–6.78) | 9.80 × 10−4 |
| rs527912 | A | 1 | 20934283 | CDA | Intron | 0.43 | 0.20 | 3.06 (1.55–6.03) | 9.85 × 10−4 |
SNP, single nucleotide polymorphism; CTF, 5-fluorouracil, pirarubicin, and cyclophosphamide; Chr., chromosome; MAF, minor allele frequency; pCR, pathologic complete response; OR, odds ratio; CI, confidence interval
A P value < 0.05 was considered statistically significant.
The two SNPs examined in the validation phase were marked by bold.
SNPs for which homozygosity was significantly associated with pCR in the discovery cohort
| SNP | Genotype | No. ( | % | Pathologic response | ||||
|---|---|---|---|---|---|---|---|---|
| non-pCR ( | pCR ( | |||||||
| No. | % | No. | % | |||||
| rs1799937 | A A | 10 | 10.9 | 4 | 40.0 | 6 | 60.0 | 0.002 |
| G A | 34 | 37.0 | 18 | 52.9 | 16 | 47.1 | ||
| G G | 48 | 52.2 | 40 | 83.3 | 8 | 16.7 | ||
| rs6044100 | C C | 55 | 59.8 | 46 | 83.6 | 9 | 16.4 | < 0.001 |
| T C | 30 | 32.6 | 14 | 46.7 | 16 | 53.3 | ||
| T T | 7 | 7.6 | 2 | 28.6 | 5 | 71.4 | ||
SNP, single nucleotide polymorphism; pCR, pathologic complete response
A P value < 0.05 was considered statistically significant
AA vs GG in rs11799937
CC vs TT in rs6044100.
Associations between SNP genotypes and pCR in 401 validation cohort patients who underwent anthracycline-based (CTF) chemotherapy. Two SNPs were examined
| SNP | Genotype | No. ( | % | Pathologic response | OR (95%CI) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| non-pCR ( | pCR ( | |||||||||
| No. | % | No. | % | |||||||
| rs1799937 | A A | 30 | 7.5 | 22 | 73.3 | 8 | 26.7 | 0.035 | 2.81(1.13–6.98) | 0.026 |
| G A | 153 | 38.2 | 124 | 81 | 29 | 19 | 1.81(1.01–3.23) | 0.046 | ||
| G G | 218 | 54.4 | 193 | 88.5 | 25 | 11.5 | ||||
| rs6044100 | C C | 224 | 57.3 | 190 | 84.8 | 34 | 15.2 | 0.86 | 0.78(0.30–2.03) | 0.60 |
| T C | 135 | 34.5 | 113 | 83.7 | 22 | 16.3 | 0.84(0.31–2.29) | 0.74 | ||
| T T | 32 | 8.2 | 26 | 81.2 | 6 | 18.8 | ||||
| Unknown | 10 | 10 | 0 | |||||||
SNP, single nucleotide polymorphism; pCR, pathologic complete response; CTF, 5-fluorouracil, pirarubicin, and cyclophosphamide; OR, odds ratio; CI, confidence interval
A P value of < 0.05 was considered statistically significant.
AA vs GG
AG vs GG
CC vs TT
CT vs TT.
Associations between SNP genotypes and pCR in 467 validation cohort patients who underwent taxane-based chemotherapy
| SNP | Genotype | No.( | % | Pathologic response | OR (95%CI) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| non-pCR | pCR | |||||||||
| No. ( | % | No.( | % | |||||||
| rs1799937 | A A | 41 | 8.8 | 34 | 82.9 | 7 | 17.1 | 0.34 | 0.85 (0.36–2.04) | 0.72 |
| G A | 185 | 39.6 | 159 | 85.9 | 26 | 14.1 | 0.68 (0.40–1.14) | 0.14 | ||
| G G | 241 | 51.6 | 194 | 80.5 | 47 | 19.5 | ||||
pCR, pathologic complete response; SNP, single nucleotide polymorphism; OR, odds ratio; CI, confidence interval
A P value of < 0.05 was considered statistically significant.
AA vs GG
GA vs GG.
Figure 2Kaplan-Meier estimates of recurrence-free survival (RFS) and distant recurrence-free survival (DRFS) by rs1799937 genotype and neoadjuvant chemotherapy regimen
Panel A. 10-year RFS by rs1799937 genotype in patients receiving anthracycline-based regimen. Panel B. 10-year DRFS by rs1799937 genotype in patients receiving anthracycline-based regimen. Panel C. 10-year RFS by rs1799937 genotype in patients receiving taxane-based regimen. Panel D. 10-year DRFS by rs1799937 genotype in patients receiving taxane-based regimen.