Table 1. MELK gene copies and RNA expression in breast cancer cell lines.
| Organ of origin and molecular subtype | Cell line | MELK FISH | MELK mRNA | ||||||
|---|---|---|---|---|---|---|---|---|---|
| (qRT-PCR) | |||||||||
| MELK/cell1 | CEP9/cell1 | MELK/CEP9 | Major clone MELK:CEP9 (%)3 | Interpretation4 | RQ5 | SD | Interpretation6 | ||
| Ratio2 | |||||||||
| Breast cancer | HCC70 | 8.9 | 10.6 | 0.8 | 9:10–15 (55%) | High unbalanced polysomy | 381.55 | 25.73 | High |
| BT549 | 6.4 | 7.7 | 0.8 | 6:8 (19%), 8:9 (15%) | High unbalanced polysomy | N/D | N/D | N/D | |
| UACC3199 | 4.0 | 4.0 | 1.0 | 4:4 (65%) | High balanced polysomy | 86.04 | 8.27 | High | |
| Triple-negative | HCC1187 | 3.0 | 2.9 | 1.0 | 3:3 (90%) | Low balanced polysomy | 57.38 | 4.87 | High |
| /Basal | MDAMB231 | 3.2 | 3.1 | 1.0 | 3:3 (85%) | Low balanced polysomy | 44.18 | 3.87 | Moderate |
| (ER-/PR-/HER2-) | HCC1954 | 3.1 | 3.8 | 0.8 | 3:4 (80%) | Low unbalanced polysomy | 41.29 | 2.06 | Moderate |
| BT20 | 2.0 | 3.0 | 0.7 | 2:3 (82%) | SA, unbalanced disomy | 38.36 | 3.12 | Moderate | |
| HCC1937 | 3.8 | 3.8 | 1.0 | 4:4 (63%) | High balanced polysomy | 34.51 | 9.63 | Moderate | |
| HCC1500 | 2.0 | 2.1 | 1.0 | 2:2 (80%) | Disomy balanced | 29.11 | 1.86 | Moderate | |
| Breast Cancer | HCC1428 | 3.8 | 3.8 | 1.0 | 4:4 (73%) | High balanced polysomy | 50.78 | 2.86 | High |
| Luminal A | T47D | 2.0 | 1.2 | 1.7 | 2:1 (77%) | SA, CEP9 hemizygous deletion | 27.43 | 1.71 | Moderate |
| (ER+/PR+/HER2-) | MCF7 | 3.0 | 3.0 | 1.0 | 3:3 (80%) | Low balanced polysomy | 12.90 | 1.02 | Low |
| Breast cancer | ZR7530 | 3.0 | 3.0 | 1.0 | 3:3 (88%) | Low balanced polysomy | 19.05 | 0.75 | Low |
| Luminal B | |||||||||
| (ER+/PR+/HER2+) | |||||||||
| Breast cancer | HCC2185 | 29.1 | 5.3 | 5.5 | - | High ampl; CEP9 high polysomy | 265.44 | 16.2 | High |
| HER2+ | HCC202 | 3.0 | 5.1 | 0.6 | 3:5 (58%) | Unbalanced polysomy | 28.07 | 1.10 | Moderate |
| ER-/PR-/HER2+) | SKBR3 | 3.1 | 3.0 | 1.1 | 3:3 (80%) | Low balanced polysomy | 5.09 | 0.43 | Low |
| Normal breast | HMEC | N/D | N/D | N/D | N/D | qRT-PCR Control | 1.00 | 0.04 | Baseline |
| Normal lymphoblasts | GM14667 | 2.0 | 2.0 | 1.0 | 2:2 (90%) | FISH Control | N/D | N/D | N/D |
1mean copies of MELK or chromosome 9 centromere enumeration probe (CEP9) per cell
2 mean gene to chromosome ratio per cell
3 most representative clone of cells with given copies of MELK and CEP9 per cell
4FISH interpretation: Amplification (Ampl), MELK to CEP9 ratio ≥ 2.0; polysomy, MELK and CEP9 copy number ≥3; balanced polysomy, equal copy number gain; unbalanced polysomy, unequal copy number gain; low polysomy, copy number >2 and ≤ 3; high polysomy, copy number ≥4; SA, structural alterations, rearrangements of chromosome 9 resulting in MELK loss, duplication or translocation
5RQ: Relative Quantification, mRNA value relative to HMEC control (2-ddCt method)
6qRT-PCR interpretation: High (RQ ≥ 50), moderate (20 ≤ RQ <50) or low (1 < RQ < 20) expression
N/D, no data