Table 3. Known STAT3/1 regulated genes regulated by C188-9 treatment of UM-SCC-17B xenografts in nude mice.
| Sl | Gene | ID | Description | Fold Change | Regulation by STAT3 | Regulation by IFN/STAT1 | References |
|---|---|---|---|---|---|---|---|
| Downregulated Genes | |||||||
| 1 | SPOCK3 | NM_001251967.1 | sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3 | −5.1 | Pos | - | [52] |
| 2 | SFRP1 | NM_003012.4 | secreted frizzled-related protein 1 | −2.6 | Pos | - | [53] |
| 3 | UPK1B | NM_006952 | uroplakin 1B | −1.9 | Pos | - | [54] |
| 4 | SCARA3 | NM_182826.1 | scavenger receptor class A, member 3 | −1.8 | Pos | - | [55] |
| 5 | CALML3 | NM_005185.2 | calmodulin-like 3 | −1.7 | Pos | - | [53] |
| 6 | MMP10 | NM_002425 | matrix metallopeptidase 10 (stromelysin 2) | −1.7 | Pos | - | [56] |
| 7 | SLPI | NM_003064 | secretory leukocyte peptidase inhibitor | −1.6 | Pos | - | [57] |
| 8 | CCND3 | NM_001081636 | similar to Cyclin D3; cyclin D3 | −1.6 | Pos | - | [58] |
| 9 | IFIT1 | NM_001548 | interferon-induced protein with tetratricopeptide repeats 1 | −2.5 | Pos | Pos | [20, 59, 60] |
| 10 | ISG15 | NM_005101 | ISG15 ubiquitin-like modifier | −2.3 | Pos | Pos | [60, 61] |
| 11 | NNMT | NM_006169 | nicotinamide N-methyltransferase | −2.3 | Pos | Pos | [62, 63] |
| 12 | OAS1 | NM_002534 | 2,5-oligoadenylate synthetase 1, 40/46kDa | −2.1 | Pos | Pos | [20, 53, 59, 64] |
| 13 | IFI6 | NM_022873 | interferon, alpha-inducible protein 6 | −2.1 | Pos | Pos | [11, 65] |
| 14 | USP18 | NM_017414 | ubiquitin specific peptidase 18 | −1.9 | Pos | Pos | [20, 64, 66] |
| 15 | MX1 | NM_002462 | myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) | −1.9 | Pos | Pos | [20, 53, 62] |
| 16 | OAS2 | NM_016817 | 2-5-oligoadenylate synthetase 2, 69/71kDa | −1.8 | Pos | Pos | [59, 60] |
| 17 | IFI27 | NM_005532 | interferon, alpha-inducible protein 27 | −1.7 | Pos | Pos | [53, 62, 67] |
| 18 | DDX58 | NM_014314 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 | −1.7 | Pos | Pos | [60, 68] |
| 19 | CLU | NM_001171138 | clusterin | −1.7 | Pos | Pos | [69, 70] |
| 20 | SERPINB3 | NM_006919 | serpin peptidase inhibitor, clade B (ovalbumin), member 3 | −1.6 | Pos | Pos | [67, 71] |
| 21 | IFITM1 | NM_003641 | interferon induced transmembrane protein 1 | −1.5 | Pos | Pos | [53, 72] |
| 22 | IFI35 | NM_005533 | interferon-induced protein 35 | −1.9 | Pos | Pos | [20, 62, 73] |
| 23 | PSMB9 | NM_002800 | proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2) | −1.6 | Pos | Pos | [62, 73, 74] |
| 24 | IFITM3 | NM_021034 | interferon induced transmembrane protein 3 | −1.5 | Pos | Pos | [75, 76] |
| 25 | OASL | NM_003733 | 2-5-oligoadenylate synthetase-like | −2.6 | Neg | Pos | [61, 67] |
| 26 | IFIT3 | NM_001549 | interferon-induced protein with tetratricopeptide repeats 3 | −2.5 | Neg | Pos | [59, 67] |
| 27 | IFI44L | NM_006820 | interferon-induced protein 44-like | −2.3 | Neg | Pos | [59, 64, 67] |
| 28 | PLSCR1 | NM_021105 | phospholipid scramblase 1 | −1.8 | Neg | Pos | [20, 62, 67] |
| 29 | MX2 | NM_002463 | myxovirus (influenza virus) resistance 2 (mouse) | −1.8 | Neg | Pos | [77] |
| 30 | HERC5 | NM_016323 | hect domain and RLD 5 | −1.7 | Neg | Pos | [67, 78] |
| 31 | IRF7 | NM_004029 | interferon regulatory factor 7 | −1.7 | Neg | Pos | [20, 62, 67] |
| 32 | IFI44 | NM_006417 | interferon-induced protein 44 | −1.7 | Neg | Pos | [64, 67] |
| 33 | TRIM22 | NM_006074 | tripartite motif containing 22 | −1.7 | Neg | Pos | [64, 67] |
| 34 | SAMD9 | NM_017654 | sterile alpha motif domain containing 9 | −1.7 | Neg | Pos | [64, 67] |
| 35 | SP110 | NM_004509 | SP110 nuclear body protein | −1.6 | Neg | Pos | [64, 67] |
| 36 | HERC6 | NM_017912 | hect domain and RLD 6 | −1.6 | Neg | Pos | [67, 79] |
| 37 | IFIT5 | NM_012420 | interferon-induced protein with tetratricopeptide repeats 5 | −1.6 | Neg | Pos | [67, 80] |
| 38 | UBE2L6 | NM_004223 | ubiquitin-conjugating enzyme E2L 6 | −1.5 | Neg | Pos | [62, 67] |
| 39 | PCDH17 | NM_001040429 | protocadherin 17 | −3.7 | - | Pos | [81] |
| 40 | CCNA1 | NM_001111046 | Cyclin A1 | −2.3 | - | Pos | [20] |
| 41 | IFIT2 | NM_001547 | interferon-induced protein with tetratricopeptide repeats 2 | −2.2 | - | Pos | [62] |
| 42 | EPSTI1 | NM_033255 | Epithelial Stromal Interaction 1 (Breast) | −2.2 | - | Pos | [64] |
| 43 | BATF2 | NM_138456 | basic leucine zipper transcription factor, ATF-like 2 | −2.1 | - | Pos | [62] |
| 44 | CMPK2 | NM_207315 | cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial | −2.1 | - | Pos | [81] |
| 45 | GBP1 | NM_002053 | guanylate binding protein 1, interferon-inducible, 67kDa | −1.7 | - | Pos | [62] |
| 46 | TYMP | NM_001953 | thymidine phosphorylase | −1.7 | - | Pos | [82] |
| 47 | LY6E | NM_002346 | lymphocyte antigen 6 complex, locus E | −1.5 | - | Pos | [83] |
| 48 | KRT15 | NM_002275 | keratin 15 | −2.1 | - | Pos | [84, 85] |
| Upregulated Genes | |||||||
| 1 | NPTX2 | NM_002523 | Neuronal pentraxin II | 6.5 | Neg | - | [86] |
| 2 | SLC2A3 | NM_006931 | solute carrier family 2 (facilitated glucose transporter), member 3 | 5.9 | Neg | - | [86] |
| 3 | CCL2 | NM_002982 | chemokine (C-C motif) ligand 2 | 5.1 | Neg | - | [86] |
| 4 | PTGS2 | NM_000963 | prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) | 4.4 | Neg | - | [86] |
| 5 | ANPEP | NM_001150 | alanyl (membrane) aminopeptidase | 3.7 | Neg | - | [86] |
| 6 | IGFBP3 | NM_000598 | insulin-like growth factor binding protein 3 | 3.3 | Neg | - | [1] |
| 7 | CXCL3 | NM_002090 | Chemokine (C-X-C motif) ligand 3 | 2.6 | Neg | - | [86] |
| 8 | TNC | NM_011607 | tenascin C | 2.9 | Neg | - | [86] |
| 9 | AKAP12 | NM_005100 | A kinase (PRKA) anchor protein 12 | 2.9 | Neg | - | [86] |
| 10 | CXCL2 | NM_009140 | chemokine (C-X-C motif) ligand 2 | 2.9 | Neg | - | [86] |
| 11 | SMAD9 | NM_019483 | MAD homolog 9 (Drosophila) | 2.7 | Neg | - | [86] |
| 12 | THBS1 | NM_003246 | thrombospondin 1 | 2.2 | Neg | - | [86] |
| 13 | CCL20 | NM_004591.2 | chemokine (C-C motif) ligand 20 | 2.1 | Neg | - | [53] |
| 14 | IER3 | NM_003897 | Immediate early response 3 | 2.0 | Neg | - | [86] |
| 15 | FOS | NM_005252 | v-fos FBJ murine osteosarcoma viral oncogene homolog | 2.0 | Neg | - | [86] |
| 16 | VEGFA | NM_001171623 | vascular endothelial growth factor A | 2.0 | Neg | - | [86] |
| 17 | EGR1 | NM_001964 | early growth response 1 | 2.0 | Neg | - | [86] |
| 18 | NEDD9 | NM_001142393 | neural precursor cell expressed, developmentally down-regulated 9 | 1.9 | Neg | - | [86] |
| 19 | ATF3 | NM_001674 | activating transcription factor 3 | 1.9 | Neg | - | [86] |
| 20 | FOSB | NM_006732 | FBJ murine osteosarcoma viral oncogene homolog B | 1.9 | Neg | - | [86] |
| 21 | PHLDA1 | NM_007350 | Pleckstrin homology-like domain, family A, member 1 | 1.8 | Neg | - | [86] |
| 22 | EREG | NM_001432 | Epiregulin | 1.8 | Neg | - | [86] |
| 23 | NOTCH4 | NM_010929 | Notch gene homolog 4 (Drosophila) | 1.8 | Neg | - | [86] |
| 24 | NR4A2 | NM_006186 | nuclear receptor subfamily 4, group A, member 2 | 1.8 | Neg | - | [86] |
| 25 | STC1 | NM_003155 | stanniocalcin 1 | 1.8 | Neg | - | [86] |
| 26 | SLC4A7 | NM_001258379 | solute carrier family 4, sodium bicarbonate cotransporter, member 7 | 1.8 | Neg | - | [86] |
| 27 | ADM | NM_001124 | adrenomedullin | 1.8 | Neg | - | [86] |
| 28 | COL5A1 | NM_000093 | collagen, type V, alpha 1 | 1.7 | Neg | - | [86] |
| 29 | SLC2A1 | NM_006516 | solute carrier family 2 (facilitated glucose transporter), member 1 | 1.7 | Neg | - | [86] |
| 30 | VLDLR | NM_003383 | very low density lipoprotein receptor | 1.7 | Neg | - | [86] |
| 31 | PDK1 | NM_002610 | pyruvate dehydrogenase kinase, isozyme 1 | 1.7 | Neg | - | [86] |
| 32 | SERTAD2 | NM_014755 | SERTA domain containing 2 | 1.6 | Neg | - | [86] |
| 33 | HK2 | NM_000189 | hexokinase 2 | 1.6 | Neg | - | [86] |
| 34 | NAV1 | NM_173437 | neuron navigator 1 | 1.6 | Neg | - | [86] |
| 35 | SLC7A11 | NM_014331 | Solute carrier family 7, (cationic amino acid transporter, y+ system) member 11 | 1.6 | Neg | - | [86] |
| 36 | HSPG2 | NM_005529.5 | heparan sulfate proteoglycan 2 | 1.5 | Neg | - | [26] |
| 37 | TGFBR3 | NM_011578 | transforming growth factor, beta receptor III | 1.5 | Neg | Neg | [20, 86] |
| 38 | ALDH3A1 | NM_000691 | aldehyde dehydrogenase family 3, subfamily A1 | 2.6 | Pos | - | [86] |
| 39 | NRP2 | NM_201266 | neuropilin 2 | 1.9 | - | Pos | [62] |
| 40 | COL16A1 | NM_001856 | collagen, type XVI, alpha 1 | 1.8 | - | Pos | [62] |
| 41 | CYP1B1 | NM_000104 | cytochrome P450, family 1, subfamily B, polypeptide 1 | 2.0 | - | Pos | [62] |
| 42 | DYNC1H1 | NM_001376 | dynein, cytoplasmic 1, heavy chain 1 | 1.5 | - | Pos | [62] |
RNA-sequence data was analyzed as stated in methods. Identification of all differentially expressed genes was based on a cutoff false detection rate fdr < 0.01, and a fold change FC > 1.5. The absolute value of FC is the magnitude of up- or down-regulation for each gene/homolog after C188-9 treatment. FC > 1.5 indicates up-regulation, and < −1.5 indicates down-regulation. The genes in this table are arranged in decreasing order of FC, which are shown in column 5. It also shows literature info on whether a gene is reported to be positively (Pos) or negatively (Neg) regulated by STAT3 (Column 5) and/or STAT1 (Column 6).