Table 1.
BMI1 knockdown induces an upregulation of critical cell death, growth arrest, and cell differentiation pathways
| Target ID | Definition | Array | p value | qPCR | p value |
|---|---|---|---|---|---|
| HLA cluster | |||||
| HLA-DRB4 | Major histocompatibility complex, class II, DR β4 | 4.291 | 6.3 × 10−5 | 1.945 | 0.0001 |
| HLA-DPA1 | Major histocompatibility complex, class II, DP α1 | 3.186 | 7.6 × 10−5 | 3.575 | 0.0080 |
| HLA-DRA | Major histocompatibility complex, class II, DR α | 2.659 | 2.7 × 10−4 | 4.53 | 0.0368 |
| HLA-DMA | Major histocompatibility complex, class II, DM α | 2.281 | 6.6 × 10−5 | 2.885 | 0.0134 |
| HLA-DMB | Major histocompatibility complex, class II, DM β | 2.119 | 3.3 × 10−5 | n.d. | |
| HOX cluster | |||||
| HOXB5 | Homeo box B5 | 2.331 | 3.4 × 10−4 | n.d. | |
| HOXB2 | Homeo box B2 | 2.134 | 3.33 × 10−4 | n.d. | |
| HOXA9 | Homeo box A9 | 1.962 | 2.46 × 10−4 | n.d. | |
| HOXB7 | Homeo box B7 | 1.715 | 2.10 × 10−3 | n.d. | |
| HOXB8 | Homeo box B8 | 1.621 | 3.02 × 10−4 | n.d. | |
| Notch signaling pathway | |||||
| DLL1 | Delta-like 1 (Drosophila) | 2.507 | 7.1 × 10−5 | n.d. | |
| LFNG | Lunatic fringe homolog (Drosophila) | 2.428 | 1.8 × 10−5 | n.d. | |
| HEY1 | Hairy/enhancer-of-split related with YRPW motif 1 | 2.274 | 1.1 × 10−7 | n.d. | |
| DLK1 | Delta-like 1 homolog (Drosophila) | 2.232 | 6.7 × 10−5 | n.d. | |
| DLL3 | Delta-like 3 (Drosophila) | 2.228 | 1.4 × 10−4 | n.d. | |
| Cell death and growth | |||||
| GADD45G | Growth arrest and DNA-damage-inducible γ | 2.386 | 5.1 × 10−6 | n.d. | |
| EMP1 | Epithelial membrane protein 1 | 2.226 | 4.5 × 10−5 | n.d. | |
| NALP1 | NACHT, leucine rich repeat and PYD containing 1 | 2.078 | 2.2 × 10−5 | n.d. | |
| GAS1 | Growth arrest-specific 1 | 2.061 | 3.4 × 10−4 | n.d. | |
| FOXO3A | Forkhead box O3A | 1.592 | 6.88 × 10−6 | 2.865 | 0.029 |
| CDKN1A | Cyclin-dependent kinase inhibitor 1A (p21, Cip1) | 1.349 | 2.6 × 10−5 | 3.555 | 0.0315 |
| CDKN2C | Cyclin-dependent kinase inhibitor 2C (p18) | 1.320 | 8.6 × 10−4 | 6.840 | 0.0125 |
| Neuronal development and differentiation | |||||
| GABBR2 | GABAB receptor 2 | 6.352 | 2.2 × 10−5 | n.d. | |
| NXPH1 | Neurexophilin 1 | 3.031 | 1.2 × 10−4 | n.d. | |
| EPHA4 | EPH receptor A4 | 2.259 | 9.5 × 10−8 | n.d. | |
| ENC1 | Ectodermal-neural cortex (with BTB-like domain) | 2.181 | 5.0 × 10−4 | n.d. | |
| FHL1 | Four and a half LIM domains 1 | 2.168 | 1.4 × 10−4 | n.d. | |
| Astrocyte phenotype | |||||
| FGFR3 | Fibroblast growth factor receptor 3 | 2.419 | 5.6 × 10−5 | n.d. | |
| GFAP | Glial fibrillary acidic protein | 2.006 | 5.90 × 10−7 | n.d. | |
| Oligodendrocyte phenotype | |||||
| OMG | Oligodendrocyte myelin glycoprotein | 2.042 | 2.1 × 10−8 | n.d. | |
| PDGFRA | Platelet-derived growth factor receptor α | 2.017 | 9.2 × 10−5 | n.d. | |
| Stem cell phenotype | |||||
| NUMBL | Numb homolog (Drosophila)-like | 0.707a | 1.3 × 10−6 | n.d. | |
| CD133 | Prominin 1 (PROM1) | 0.687 | 5.7 × 10−7 | 0.01 | 0.0001 |
| BMI1 | Polycomb group ring finger 4 (PCGF4) | 0.325 | 6.0 × 10−14 | 0.01 | 0.0002 |
GBM cells (from two independent tumors) were infected or not infected with scrambled virus or shBMI1#1. Cells were maintained in culture at high density (2.5 × 104 cells/ml) in neural stem cell media. No relevant differences in gene expression were detected between noninfected and scrambled shRNA-expressing cells. Data were analyzed using the FlexArray software and were expressed as fold change (Array column) over values in scrambled shRNA-infected cells. Data were validated by real-time PCR (qPCR column) for some transcripts. n.d., Not determined.
aValues with underlines are for genes whose expression was downregulated.