Table 2.
The Genetic Profile of wt-PAI-1-expressing MDA-MB-435 Cells
| Genes upregulateda | |||||
|---|---|---|---|---|---|
| Wt-PAI-1- expressing MDA-MB- 435:MDA- MB-435 Neo |
MDA-MB- 435:MDA- MB-435 Neo |
UG Cluster |
Gene Symbol |
Gene | Function |
| 18.63 | 1.22 | Hs.414795 | SERPINE1 | serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (PAI-1) | Serine protease inhibitor; PAI-1 |
| 5.67 | 0.96 | Hs.12379 | ELAVL1 | ELAV | RNA transporter/stabilizer; upregulation results in unstable mRNA in breast cancer |
| 4.45 | 0.71 | Hs.149609 | ITGA5 | integrin, alpha 5 (fibronectin receptor, alpha polypeptide) | Adhesion/cell surface mediated signaling; interacts with uPAR; IGF-1 decreases its adhesion strength in breast cancer |
| 4.08 | 1.23 | Hs.414332 | OAS2 | 2’-5’-oligoadenylate synthase 2, 69/71 kDa | Antiviral activity of interferons |
| 3.77 | 0.86 | Hs.194710 | GCNT3 | glucosaminyl (N-acetyl) transferase 3, mucin type | Inflammation/immune system |
| 3.64 | 0.83 | Hs.201641 | BASP1 | brain abundant, membrane attached signal protein | Regulate actin cytoskeleton/neuronal outgrowth in mammory gland |
| 3.62 | 1.38 | Hs.111779 | SPARC | secreted protein, acidic, cysteine-rich (osteonectin) | Extracellular matrix, adhesion; increased expression in breast cancer; also associated with increased cell motility |
| 3.52 | 1.16 | Hs.519385 | FOXD1 | forkhead box D1 | Involved in the increase in PAI-1 gene expression |
| 3.5 | 1.19 | Hs.173894 | CSF1 | colony stimulating factor 1 (macrophages) | Regulate differentiation, activity, survival of osteoclasts and monocytes/macrophages; role in monocyte/macrophage mediated tumor angiogenesis |
| 3.15 | 0.97 | Hs.22265 | PPM2C | protein phosphatase 2C, magnesium - dependent, catalytic subunit | Mitochondrial enzyme regulated by insulin |
| 2.96 | 0.87 | Hs.262960 | TRPC4 | transient receptor potential cation channel, subfamily C, member 4 | Component of Ca2+ signaling pathway; activated by EGFR stimulation |
| 2.96 | 0.86 | Hs.528634 | OAS3 | 2’-5’-oligoadenylate synthetase 3, 100kDa | Antiviral activity of interferons |
| 2.94 | 0.96 | Hs.525392 | SYNE2 | spectrin repeat containing, nuclear envelope 2 | Nuclear envelope scaffolding |
| 2.91 | 0.95 | Hs.517601 | RAC2 | Ras-related C3 botulimun toxin substrate 2 (rho family, small GTP binding protein Rac2) | Ras superfamily GTPase involved in cell growth, cytoskeletal reorganization, and protein kinase activation |
| 2.83 | 1.27 | Hs.78068 | CPZ | carboxypeptidase Z | Member of metallocarboxypeptidase gene family; associated with extracellular matrix and Wnt binding |
| 2.73 | 0.83 | Hs.184907 | GPR1 | G protein-coupled receptor 1 | Senescence associated gene |
| 2.72 | 0.86 | Hs.464779 | NPC1 | Niemann-Pick disease, type C1 | Lysosomal membrane protein involved in cholesterol trafficking associated with drug clearance in the cell |
| 2.66 | 0.97 | Hs.468410 | EPAS1 | endothelial PAS domain protein 1 | Hypoxia induced protein involved in angiogenesis; regulates PAI-1 and VEGF gene expression |
| 2.65 | 0.87 | Hs.249125 | TLX3 | T-cell Leukemia, homeobox 3 | Involved in autonomic nervous system development; gene rearrangement (t(5;14)) upregulated in acute lymphoblastic leukemia |
| 2.63 | 0.95 | Hs.144795 | KCNMA1 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1 | Component of a conductance, voltage, and Ca2+ sensitive channel |
| 2.61 | 1.36 | Hs.13155 | ITGB5 | integrin, beta 5 | Adhesion to extracellular matrix; cell migration |
| 2.58 | 0.79 | Hs.474751 | MYH9 | myosin, heavy polypeptide 9, non-muscle | Cytoskeleton and cell migration |
| 2.57 | 1.24 | Hs.226755 | YWHAH | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide | 14-3-3 protein involved in signal transduction; found to be bound to gremlin 1, which is upregulated in numerous carcinomas including breast |
| 0.29 | 0.85 | Hs.522555 | APOD | apolipoprotein D | Regulate both proliferation and cell migration in response to growth factors |
| 0.41 | 1.04 | Hs.318894 | GPR126 | G protein-coupled receptor 126 | G-protein coupled receptor involved in cell adhesion |
| 0.42 | 1.14 | HS.9914 | FST | follistatin | Downregulated in cancer; inhibits activin, a member of the TGF-beta superfamily involved in regulating proliferation |
| 0.44 | 1.39 | Hs.25597 | ELOVL1 | elongation of very long chain fatty acids (FEN/Elo2, SUR4/Elo3, yeast)-like 2 | Unknown |
| 0.47 | 0.78 | Hs.368226 | SOX6 | SRY (sex determining region Y)-box 6 | Transcription factor involved in various developmental processes; upregulated in gliomas and not other cancers |
The MDA-MB-435 cell line was transfected using pcDNA3.1 vectors (Invitrogen) containing wt PAI-1 using Effectene (Qiagen) according to manufacturer's instructions.73,75,76 Clones were selected for resistance to neomycin analogue, G418 (Invitrogen). In collaboration with the Microarray Core Facility at NHGRI, a cDNA microarray was used to compare the gene expression profiles among the parental MDA-MB-435, Neomycin vector control MDA-MB-435 (MDA-MB-435 Neo), and wt-PAI-1-expressing MDA-MB-435 cells. A standard human chip was used that contains over 29,000 elements: 28,200 human sequence verified clones and 800 controls. These genes represent over 24,400 unique Unigene clusters. One sample of RNA was labeled with Cy3 and the other with Cy5. The mixture of the two-labeled RNAs was competitively hybridized to a glass slide containing the cDNAs. For analysis, only genes in which the ratio between MDA-MB-435 and MDA-MB-435 Neo was between 0.7–1.4 were considered. From this list of genes the above tables were generated that list the genes upregulated ≥2.5 fold and those genes that are reduced by ≤0.5 compared to the MDA-MB-435 Neo cells.