Table 5. Set of 94 differentially up- or down-regulated genes identified via RNA-sequencing with opposite fold changes in MDA-MB-231 and T47D cells chronically treated with SH-4-54 relative to respective wild-type cells.
Genes containing putative STAT3 or STAT5 binding elements in their promoter region are highlighted in bold. As MYC is a known STAT3/5 target gene, differentially expressed genes regulated by MYC are also indicated in bold. Genes validated by qPCR are further highlighted in grey.
| Gene Symbol | MDA WT vs. Clone #2 Fold Δ | T47D WT vs. Clone #1 Fold Δ | Description |
|---|---|---|---|
| ABCG1 | 0.39 | 1.96 | ATP-Binding Cassette, Sub-Family G (WHITE), Member 1 |
| AC007405.6 | 0.57 | 3.93 | Homo sapiens BAC clone RP11-570C16 |
| AC091801.1 | 18.54 | 0.06 | Homo sapiens chromosome UNK clone RP11-1228A3, SEQUENCING IN PROGRESS, 15 unordered pieces |
| ANKMY2 | 0.34 | 1.56 | Ankyrin Repeat And MYND Domain Containing 2 |
| AREG | 1.88 | 0.22 | Amphiregulin (STAT3 promoter element) |
| ARMCX1 | 0.72 | 1.89 | Armadillo Repeat Containing, X-Linked 1 (STAT1 site in its promoter element) |
| ASH1L | 2.09 | 0.48 | Ash1 (Absent, Small, Or Homeotic)-Like (Drosophila) |
| ATP11A | 1.76 | 0.35 | ATPase, Class VI, Type 11A |
| BCAR3 | 0.34 | 2.00 | Breast Cancer Anti-Estrogen Resistance 3 (STAT5 promoter element) |
| CA12 | 0.75 | 1.67 | Carbonic Anhydrase XII |
| CAMKK1 | 0.59 | 1.59 | Calcium/Calmodulin-Dependent Protein Kinase Kinase 1, Alpha |
| CBX1 | 0.80 | 1.66 | Chromobox Homolog 1 |
| CHAC1 | 0.45 | 2.20 | ChaC Glutathione-Specific Gamma-Glutamylcyclotransferase 1 |
| CILP2 | 2.77 | 0.16 | Cartilage Intermediate Layer Protein 2 |
| CLIC3 | 14.69 | 0.54 | Chloride Intracellular Channel 3 |
| COL5A1 | 2.92 | 0.24 | Collagen, Type V, Alpha 1 |
| CYP4V2 | 0.48 | 3.41 | Cytochrome P450, Family 4, Subfamily V, Polypeptide 2 |
| DNMT3B | 1.33 | 0.63 | DNA (Cytosine-5-)-Methyltransferase 3 Beta |
| EPHA4 | 3.17 | 0.16 | Ephrin receptor 4A (STAT3 promoter element) |
| EREG | 2.77 | 0.02 | Epiregulin; Ligand of the EGF receptor/EGFR and ERBB4 |
| FAM149A | 0.38 | 2.82 | Family With Sequence Similarity 149, Member A |
| FAM185A | 0.60 | 1.74 | Family With Sequence Similarity 185, Member A (MYC-regulated) |
| FAM89A | 0.02 | 6.22 | Family With Sequence Similarity 89, Member A |
| FNBP1L | 0.76 | 1.60 | Formin Binding Protein 1-Like (STAT5 promoter element) |
| GALNT1 | 1.29 | 0.62 | Polypeptide N-Acetylgalactosaminyltransferase 1 |
| GJA1 | 0.71 | 3.52 | Gap Junction Protein, Alpha 1, 43kDa |
| GNG11 | 0.71 | 1.79 | Guanine Nucleotide Binding Protein (G Protein), Gamma 11 (STAT5 promoter element) |
| GPR141 | 0.37 | 8.53 | G Protein-Coupled Receptor 141 |
| GPRC5C | 0.07 | 2.39 | G Protein-Coupled Receptor, Class C, Group 5, Member C |
| GSTM3 | 0.58 | 1.98 | Glutathione S-Transferase Mu 3 (Brain) (STAT5 promoter element) |
| HCAR1 | 2.32 | 0.68 | Hydroxycarboxylic Acid Receptor 1 |
| ID4 | 0.26 | 10.77 | Inhibitor Of DNA Binding 4, Dominant Negative Helix-Loop-Helix Protein |
| IDH1 | 0.57 | 1.66 | Isocitrate Dehydrogenase 1 (NADP+), Soluble (STAT5 promoter element) |
| IFI6 | 1.35 | 0.25 | Interferon, Alpha-Inducible Protein 6 (STAT3 promoter element) |
| IL1R1 | 2.92 | 0.61 | Interleukin 1 Receptor, Type I |
| INPP5E | 1.25 | 0.66 | Inositol Polyphosphate-5-Phosphatase E (MYC-regulated) |
| KRCC1 | 0.61 | 1.61 | Lysine-Rich Coiled-Coil 1 |
| KYNU | 1.35 | 0.60 | Kynureninase |
| LANCL1 | 0.64 | 1.41 | LanC Lantibiotic Synthetase Component C-Like 1 (Bacterial) |
| LCP1 | 4.04 | 0.51 | Lymphocyte Cytosolic Protein 1 (L-Plastin) |
| LEF1 | 0.44 | 4.48 | Lymphoid Enhancer-Binding Factor 1 |
| LINC00665 | 1.63 | 0.64 | Long Intergenic Non-Protein Coding RNA 665 |
| LINC01234 | 11.64 | 0.18 | Long Intergenic Non-Protein Coding RNA 1234 |
| LMO4 | 0.69 | 2.78 | LIM Domain Only 4 (STAT3 promoter element) |
| LYAR | 1.31 | 0.60 | Ly1 Antibody Reactive |
| MAN1C1 | 0.25 | 2.69 | Mannosidase, Alpha, Class 1C, Member 1 |
| MDGA2 | 0.00 | 3.78 | MAM Domain Containing Glycosylphosphatidylinositol Anchor 2 |
| MISP | 2.68 | 0.64 | Mitotic Spindle Positioning |
| MKX | 1.83 | 0.37 | Mohawk Homeobox (STAT5 promoter element) |
| MMD | 0.76 | 1.56 | Monocyte To Macrophage Differentiation-Associated (STAT1 promoter element) |
| MT-CYB | 1.58 | 0.62 | Mitochondrially Encoded Cytochrome B |
| MYC | 0.51 | 2.46 | V-Myc Avian Myelocytomatosis Viral Oncogene Homolog (STAT3 promoter element; regulated by STAT3 and STAT5) |
| NAT8L | 1.63 | 0.61 | N-Acetyltransferase 8-Like (GCN5-Related, Putative) (MYC-regulated) |
| NMB | 3.52 | 0.33 | Neuromedin B |
| NT5DC4 | 0.00 | 143.31 | 5'-Nucleotidase Domain Containing 4 |
| OAT | 0.82 | 1.73 | Ornithine Aminotransferase |
| OLFML2A | 1.48 | 0.50 | Olfactomedin-Like 2A |
| P4HA3 | 35.32 | 0.01 | Prolyl 4-Hydroxylase, Alpha Polypeptide III |
| PCTP | 0.57 | 1.94 | Phosphatidylcholine Transfer Protein |
| PDE9A | 0.00 | 2.94 | Phosphodiesterase 9A (STAT3 & STAT5 promoter elements) |
| PDHB | 0.76 | 1.48 | Pyruvate Dehydrogenase (Lipoamide) Beta (STAT3 promoter element) |
| PHF11 | 1.36 | 0.58 | PHD Finger Protein 11 |
| PON3 | 0.46 | 1.98 | Paraoxonase 3 |
| PPFIA4 | 3.25 | 0.19 | Protein Tyrosine Phosphatase, Receptor Type, F Polypeptide (PTPRF), Interacting Protein (Liprin), Alpha 4 (ERα-regulated) |
| PQLC3 | 0.60 | 1.83 | PQ Loop Repeat Containing 3 |
| PRKACB | 0.38 | 1.59 | Protein Kinase, CAMP-Dependent, Catalytic, Beta (STAT1 promoter element) |
| PSAT1 | 0.55 | 1.76 | Phosphoserine Aminotransferase 1 |
| PTPRS | 1.58 | 0.69 | Protein Tyrosine Phosphatase, Receptor Type, S |
| RAB39A | 2.00 | 0.17 | Member RAS Oncogene Family |
| RNF144B | 0.48 | 2.68 | Ring Finger Protein 144B (STAT5 promoter element) |
| RNF208 | 1.62 | 0.63 | Ring Finger Protein 208 |
| SARS | 0.56 | 1.50 | Seryl-TRNA Synthetase |
| SEC22B | 0.55 | 1.55 | SEC22 Homolog B, Vesicle Trafficking Protein (Gene/Pseudogene) |
| SEMA6B | 1.33 | 0.53 | Sema Domain, Transmembrane Domain (TM), And Cytoplasmic Domain, (Semaphorin) 6B |
| SLC25A24 | 0.74 | 1.70 | Solute Carrier Family 25 (Mitochondrial Carrier; Phosphate Carrier), Member 24 |
| SLC7A11 (xCT) | 0.56 | 3.40 | Solute Carrier Family 7 (Anionic Amino Acid Transporter Light Chain, Xc- System), Member 11 (STAT5 promoter element) |
| SLC9A3R1 | 0.77 | 1.56 | Solute Carrier Family 9, Subfamily A (NHE3, Cation Proton Antiporter 3), Member 3 Regulator 1 |
| SMAD3 | 1.55 | 0.45 | SMAD Family Member 3 (MYC-regulated) |
| SMARCA1 | 0.72 | 1.62 | SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A, Member 1 |
| SNORA22 | 3.81 | 0.22 | Small Nucleolar RNA, H/ACA Box 22 |
| SNORA7B | 1.83 | 0.14 | Small Nucleolar RNA, H/ACA Box 7B |
| SOWAHC | 0.80 | 2.68 | Sosondowah Ankyrin Repeat Domain Family Member C |
| SSR2 | 1.23 | 0.66 | Signal Sequence Receptor, Beta (Translocon-Associated Protein Beta) |
| STEAP1 | 0.64 | 5.04 | Six Transmembrane Epithelial Antigen Of The Prostate 1 |
| STMN3 | 1.67 | 0.44 | Stathmin-Like 3 |
| TENM3 | 2.29 | 0.55 | Teneurin Transmembrane Protein 3 |
| TGFBI | 2.40 | 0.25 | Transforming Growth Factor, Beta-Induced, 68kDa (STAT5 promoter element) |
| TICAM1 | 1.61 | 0.56 | Toll-Like Receptor Adaptor Molecule 1 |
| TMEM108 | 6.73 | 0.40 | Transmembrane Protein 108 |
| TRIB3 | 0.59 | 1.52 | Tribbles Pseudokinase 3 |
| TSKU | 0.70 | 2.08 | Tsukushi, Small Leucine Rich Proteoglycan |
| TSPAN13 | 0.32 | 1.92 | Tetraspanin 13 (MYC-regulated) |
| TSPAN33 | 0.27 | 2.25 | Tetraspanin 33 (STAT1 promoter element) |
| TUB | 0.06 | 2.38 | Tubby Bipartite Transcription Factor |
| VAT1 | 0.79 | 1.55 | Vesicle Amine Transport 1 (MYC-regulated) |