Table 1.
Induced gene expression by PDS cultures is linked to clinico-pathological characteristics of the original tumor. Table shows p-values when the entire PDSs cohort was analysed together (all), and subdivided by ERα-status (ERα-, ERα-negative; ERα+, ERα-positive). Clinico-pathological features analysed: grade, ERα-status, PR (progesterone receptor)-status and metastasis in lymph nodes (LN). Data was analysed using SPSS statistics (IBM). Non-parametric Mann-Whitney U and Kruskall-Wallis statistical test were performed for assessment of clinico-pathological variables relationship with individual gene expression in PDSs. p-value < 0.05 were considered significant (* p-value < 0.05, ** p-value < 0.01). Significant p-values after Benjamini-Hochberg corrections (§ α = 0.15) are indicated. Detailed information in Supplementary Table S4.
| All | ER+ | ER− | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Grade | ERα | PR | LN | Grade | PR | LN | Grade | PR | LN | |||
| MCF7 | Proliferation | MKI67 | 0.893 | 0.135 | 0.075 | 0.721 | 0.632 | 0.538 | 0.495 | 0.955 | 0.068 | 0.421 |
| CCNA2 | 0.933 | 0.300 | 0.032 * | 0.560 | 0.607 | 0.196 | 0.975 | 0.737 | 0.035 * | 0.080 | ||
| CCNB2 | 0.321 | 0.925 | 0.214 | 0.112 | 0.109 | 0.188 | 0.353 | 0.263 | 0.261 | 0.083 | ||
| EMT | VIM | 0.291 | 0.624 | 0.703 | 0.604 | 0.304 | 0.400 | 0.525 | 0.434 | 0.888 | 0.573 | |
| SNAI1 | 0.015 *§ | 0.132 | 0.241 | 0.547 | 0.019 *§ | 0.641 | 0.231 | 0.502 | 0.888 | 0.237 | ||
| SNAI2 | 0.01 *§ | 0.760 | 0.153 | 0.945 | 0.005 **§ | 0.204 | 0.800 | 1.000 | 0.206 | 0.633 | ||
| FOSL1 | 0.052 | 0.487 | 0.170 | 0.047 * | 0.025 *§ | 0.269 | 0.134 | 0.695 | 0.888 | 0.474 | ||
| Pluripotency | NANOG | 0.679 | 0.960 | 0.359 | 0.769 | 0.712 | 0.211 | 0.481 | 1.000 | 0.399 | 0.965 | |
| POU5F1 | 0.236 | 0.970 | 0.725 | 0.511 | 0.141 | 0.578 | 0.299 | 0.371 | 0.673 | 0.408 | ||
| NEAT1 | 0.174 | 0.682 | 0.457 | 0.148 | 0.120 | 0.575 | 0.135 | 0.146 | 0.673 | 0.762 | ||
| SOX2 | 0.571 | 0.017 * | 0.492 | 0.715 | 0.438 | 0.952 | 0.721 | 0.655 | 0.160 | 0.947 | ||
| BCSC | CD44 | 0.108 | 0.345 | 0.966 | 0.201 | 0.131 | 0.700 | 0.436 | 0.867 | 0.261 | 0.237 | |
| ABCG2 | 0.140 | 0.759 | 0.226 | 0.754 | 0.074 | 0.370 | 0.316 | 0.911 | 0.035 * | 0.327 | ||
| ALDH1A3 | 0.03 *§ | 0.874 | 0.528 | 0.833 | 0.014 *§ | 0.627 | 0.875 | 0.955 | 0.574 | 0.395 | ||
| T-47D | Proliferation | MKI67 | 0.260 | 0.258 | 0.118 | 0.609 | 0.451 | 0.322 | 0.330 | 0.01 *§ | 0.673 | 0.633 |
| CCNA2 | 0.342 | 0.627 | 0.416 | 0.781 | 0.626 | 0.749 | 0.616 | 0.034 * | 0.261 | 0.829 | ||
| CCNB2 | 0.024 * | 0.360 | 0.637 | 0.858 | 0.064 | 0.357 | 0.837 | 0.434 | 0.261 | 0.744 | ||
| EMT | VIM | 0.004 **§ | 0.113 | 0.262 | 0.424 | 0.026 * | 0.490 | 0.333 | 0.314 | 0.574 | 0.829 | |
| SNAI1 | 0.865 | 0.524 | 0.893 | 0.117 | 0.797 | 0.947 | 0.157 | 0.823 | 0.261 | 0.515 | ||
| SNAI2 | 0.734 | 0.618 | 0.888 | 0.530 | 0.796 | 0.884 | 0.374 | 0.602 | 1.000 | |||
| FOSL1 | 0.705 | 0.211 | 0.056 | 0.320 | 0.930 | 0.015 *§ | 0.889 | 0.399 | 0.136 | 0.036 * | ||
| Pluripotency | NANOG | 0.427 | 0.668 | 0.579 | 0.671 | 0.306 | 0.941 | 0.386 | 0.678 | 0.655 | 0.673 | |
| POU5F1 | 0.264 | 0.390 | 0.092 | 0.075 | 0.429 | 0.256 | 0.046 * | 0.314 | 0.122 | 0.897 | ||
| NEAT1 | 0.198 | 0.859 | 0.001 **§ | 0.086 | 0.098 | 0.005 **§ | 0.083 | 0.911 | 0.049 * | 0.897 | ||
| SOX2 | 0.303 | 0.950 | 0.811 | 0.956 | 0.316 | 0.696 | 0.868 | 1.000 | 0.655 | 0.321 | ||
| BCSC | CD44 | 0.062 | 0.137 | 0.070 | 0.590 | 0.185 | 0.230 | 0.988 | 0.737 | 0.779 | 0.146 | |
| ABCG2 | 0.476 | 0.546 | 0.638 | 0.431 | 0.418 | 0.911 | 0.402 | 0.146 | 0.325 | 0.897 | ||
| ALDH1A3 | 0.328 | 0.063 | 0.132 | 0.024 * | 0.348 | 0.324 | 0.034 * | 0.219 | 0.261 | 0.460 | ||
| MDA-MB-231 | Proliferation | MKI67 | 0.875 | 0.131 | 0.078 | 0.855 | 0.975 | 0.352 | 0.426 | 0.676 | 0.187 | 0.559 |
| CCNA2 | 0.383 | 0.089 | 0.176 | 0.599 | 0.672 | 0.512 | 0.511 | 0.552 | 0.923 | 0.779 | ||
| CCNB2 | 0.307 | 0.769 | 0.383 | 0.979 | 0.219 | 0.197 | 0.813 | 0.381 | 0.791 | 0.710 | ||
| EMT | VIM | 0.274 | 0.186 | 0.770 | 0.285 | 0.423 | 0.259 | 0.125 | 0.305 | 1.000 | 0.620 | |
| SNAI1 | 0.512 | 0.559 | 0.345 | 0.730 | 0.378 | 0.157 | 0.505 | 0.305 | 0.923 | 0.620 | ||
| SNAI2 | 0.712 | 0.511 | 0.166 | 0.691 | 0.451 | 0.435 | 0.320 | 0.933 | 0.264 | 0.535 | ||
| FOSL1 | 0.825 | 0.719 | 0.962 | 0.255 | 0.771 | 0.763 | 0.426 | 0.933 | 0.923 | 0.710 | ||
| Pluripotency | NANOG | 0.846 | 0.489 | 0.929 | 0.878 | 0.919 | 0.941 | 0.511 | 0.800 | 0.198 | 0.259 | |
| POU5F1 | 0.503 | 0.579 | 0.514 | 0.783 | 0.540 | 0.710 | 0.324 | 0.933 | 0.549 | 0.318 | ||
| NEAT1 | 0.972 | 0.927 | 0.098 | 0.669 | 0.994 | 0.102 | 0.921 | 0.476 | 0.132 | 0.128 | ||
| SOX2 | 0.690 | 0.960 | 0.138 | 0.213 | 0.715 | 0.107 | 0.148 | 0.476 | 0.549 | 0.902 | ||
| BCSC | CD44 | 0.605 | 0.105 | 0.369 | 0.846 | 0.671 | 0.787 | 0.833 | 0.790 | 1.000 | 0.740 | |
| ABCG2 | 0.598 | 0.633 | 0.778 | 0.359 | 0.648 | 0.823 | 0.328 | 0.933 | 0.264 | 0.902 | ||
| ALDH1A3 | 0.156 | 0.612 | 0.478 | 0.818 | 0.284 | 0.435 | 0.640 | 0.371 | 0.429 | 0.831 | ||