Table S1.
Relative changes in expression of select genes up-regulated in MDA cells cultured for 72 h in hanging drops or sorted from 3D cocultures of MSCs and MDA cells
| Gene name | Fold change in 3D MDA at 72 h (relative to MDA control) | Fold change in 3D MDA sorted from MDA/MSC cocultures (relative to MDA control) |
| Cytokines/chemokines (inflammatory response) | ||
| CSF3 (GCSF) | 1.6 | 384 |
| CXCL8 (IL8) | 7.1 | 1,466 |
| CXCL2 | 1.8 | 107 |
| PTGS2 (COX2) | 3.7 | 207 |
| IL6 | −1.7 | 31 |
| CXCL1 | 3.8 | 191 |
| IL1A | 1.1 | 52 |
| CCL20 | 2.5 | 110 |
| IL1B | 1.4 | 25 |
| Cell survival (drug/stress resistance) | ||
| IFI6 | 2.2 | 786 |
| SAT1 | 2.9 | 85 |
| IER3 | −1.4 | 7.6 |
| Cell growth (anticancer/senescence) | ||
| EGR1 | −1.4 | 28 |
| ZFP36 (TTP) | −2 | 17 |
| SERPINE1 | −6.2 | 26 |
| SPINT1 | 1.6 | 25 |
| TFPI2 | −1.2 | 12 |
| Transcription factors (stress response) | ||
| FOSB | −2.1 | 19 |
| JUNB | −1.2 | 15 |
| JUN | −2.3 | 7.1 |
| NAMPT | 3.7 | 41 |
| NFKBIZ | 4.2 | 42 |
| NR4A2 | 1.4 | 14 |
| CEBPB | 1.2 | 12 |
| Other | ||
| IFI27 | 1.2 | 31 |
| SLC6A14 | 1.1 | 26 |
| HIST2H2BE | −2.3 | 9.4 |
| TNFAIP3 | 1.7 | 31 |
| MX1 | 1.2 | 25 |
| IFI44L | 2.5 | 36 |
| CD74 | 9.5 | 143 |
| CCNL1 | 1.9 | 35 |
| LAMC2 | 1.1 | 16 |
| OAS2 | 1.9 | 23 |
| TGFβI | −1.8 | 5.6 |
The results are compared with MDA cells cultured as monolayers (MDA control). Most genes in the list were up-regulated at least 10-fold in MDA cells from cocultures relative to 3D MDA cells. Of the genes with highest up-regulation, many are involved in inflammatory and stress responses, promote cell survival, and/or have tumor-suppressive activities.