Table 1.
A total of 61 candidate genes selected for siRNA screening followed by MTS assay
| Basis for selection |
MTS assay |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| ID | Gene symbol | IPA Network | Exp-IC50 analysis | SNP-IC50 analysis | Methy-IC50 analysis | SNP-Exp-IC50 analysis | Methy-Exp-IC50 analysis | MDA-MB 231 | Hs578T |
| 1 | ADD1 | 4 | <10−5, <10−27, <10−5, <10−13, <10−4 | ||||||
| 2 | AES | 3 | <10−5 | ||||||
| 3 | AGPAT1 | 3 | <10−4 | resistant | |||||
| 4 | ATP2A3 | 4 | <10−5 | resistant | |||||
| 5 | AUTS2 | 3 | <10−5 | ||||||
| 6 | BAG1 | 1 | <10−5, <10−4, <10−4 | ||||||
| 7 | BAG6 (BAT3) | 1 | <10−4 | ||||||
| 8 | VPS51 (C11orf2) | 2 | <10−5 | resistant | resistant | ||||
| 9 | C14orf105 | 3 | <10−5 | ||||||
| 10 | C16orf58 | 2 | <10−5 | ||||||
| 11 | CCDC88B | 2 | <10−5 | ||||||
| 12 | CD99 | 4 | <10−5 | ||||||
| 13 | CDC25B | 1 | <10−5 | <10−5, <10−27, <10−5, <10−4, <10−5 | resistant | resistant | |||
| 14 | CDC42BPA* | 4 | <10−14, <10−5, <10−2 | resistant | |||||
| 15 | CDK16 (PCTK1) | 1 | <10−4 | <10−5, <10−4, <10−4 | |||||
| 16 | CDK8 | 1 | <10−5 | ||||||
| 17 | CIZ1 | 2 | <10−5 | ||||||
| 18 | CLTB | 1 | <10−4 | ||||||
| 19 | CNNM3 | 4 | <10−5, <10−27, <10−9, <10−18, <10−4 | resistant | resistant | ||||
| 20 | CYB5R2 | 3 | <10−5 | <10−5, <10−27, <10−9, <10−19, <10−5 | |||||
| 21 | CYTH2 (PSCD2) | 4 | <10−5, <10−27, <10−7, <10−11, <10−4 | resistant | |||||
| 22 | DIS3 | 2 | <10−4 | ||||||
| 23 | DUSP5 | 1 | <10−5 | ||||||
| 24 | EPS8 | 4 | <10−5 | <10−5, <10−27, <10−36, <10−44, <10−5 | |||||
| 25 | ESCO1 | 3 | <10−4 | ||||||
| 26 | ESD | 2 | <10−4 | ||||||
| 27 | FAM107B | 3 | <10−5, <10−11, <10−4, <10−7, <10−4 | resistant | resistant | ||||
| 28 | FAM111B | 2 | <10−4 | ||||||
| 29 | FASTK | 3 | <10−5 | ||||||
| 30 | FIBP | 2 | <10−6 | ||||||
| 31 | FXYD5 | 4 | <10−4 | resistant | |||||
| 32 | HOXB2 | 1 | <10−4 | ||||||
| 33 | HOXB7 | 1 | <10−4 | <10−5, <10−27, <10−6, <10−12, <10−4 | resistant | resistant | |||
| 34 | INTS5 | 3 | <10−5 | <10−3, <10−4, <10−5 | resistant | ||||
| 35 | IRF1 | 1 | <10−5, <10−23, <10−7, <10−13, <10−4 | ||||||
| 36 | ITGAL | 1 | <10−5 | ||||||
| 37 | MAP2K6 | 1 | <10−5 | ||||||
| 38 | MED12 | 1 | <10−4 | ||||||
| 39 | MED16 | 1 | <10−4 | ||||||
| 40 | MID1IP1 | 3 | <10−5 | resistant | resistant | ||||
| 41 | NFYC | 3 | <10−5 | ||||||
| 42 | POMP | 3 | <10−5 | resistant | resistant | ||||
| 43 | PPDPF (C20orf149) | 2 | <10−4 | ||||||
| 44 | PPP2R4 | 1 | <10−4 | <10−5, <10−18, <10−4, <10−7, <10−4 | |||||
| 45 | PRDX5 | 3 | <10−4 | ||||||
| 46 | PRKD2 | 4 | <10−5 | resistant | |||||
| 47 | PTP4A2 | 4 | <10−5, <10−4, <10−4, <10−10, <10−4 | ||||||
| 48 | REEP5 | 2 | <10−5, <10−7, <10−5, <10−4, <10−4 | resistant | resistant | ||||
| 49 | SBF1 | 1 | <10−4 | resistant | |||||
| 50 | SCAMP2 | 2 | <10−5 | ||||||
| 51 | SH3BGRL3 | 2 | <10−4, <10−4, <10−4 | resistant | resistant | ||||
| 52 | STARD3 | 3 | <10−4, <10−4, <10−4 | resistant | |||||
| 53 | STUB1 | 1 | <10−4 | resistant | resistant | ||||
| 54 | STX4 | 1 | <10−5 | resistant | resistant | ||||
| 55 | TBCB | 2 | <10−4 | resistant | resistant | ||||
| 56 | TFRC | 1 | <10−5, <10−27, <10−9, <10−17, <10−4 | ||||||
| 57 | THAP7 | 1 | <10−5 | <10−4, <10−4, <10−5 | resistant | ||||
| 58 | TNRC6B | 2 | <10−4 | ||||||
| 59 | TRIO | 4 | <10−5, <10−27, <10−5, <10−9, <10−4 | resistant | |||||
| 60 | USP21 | 4 | <10−6 | <10−5, <10−4, <10−6 | resistant | resistant | |||
| 61 | ZNF496 | 2 | <10−5, <10−27, <10−5, <10−8, <10−4 | resistant | resistant | ||||
Note:P-values under ‘Basis for selection’ indicate the association significance of individual candidate genes with metformin IC50 found by given association analysis. The P-values under ‘SNP-expression-IC50 analysis’ were for SNP-IC50, SNP-expression and expression-IC50 association analyses of individual candidate genes (Supplementary Material, Table S7). The P-values under ‘Methylation-expression-IC50 analysis’ were for Methy1-IC50, Methy1-Exp1, Methy1-Exp2, Exp1-Exp2, and Exp2-IC50 analyses of individual candidate genes (Supplementary Material, Table S11). * CDC42BPA, the P-values were for methylation-expression, methylation-IC50, and expression-IC50 association analyses of CDC42BPA gene. For the MTS assay, ‘resistant’ indicates that the gene knockdown desensitized metformin cytotoxicity when compared with control siRNA. All of the experiments with significant changes were performed in triplicate and were replicated at least three times.