Table 3.
Expression changes of the DEGs affected by gefitinib in colon and SI organoids.
| Gene Symbol | Pathways Involved/Function | Expression in Treated Colon/SI Cells (Adjusted p-Value) * | Remarks |
|---|---|---|---|
| DEGs with same trend in colon and SI organoids | |||
| AREG | Interaction with EGFR to promote growth of epithelial cells | ↓ (9.7 × 10−8)/↓ (6.5 × 10−7) | |
| AURKA | DNA repair; Cell cycle | ↓ (3.9 × 10−6)/↓ (0.04) | |
| BAX | Induction of apoptosis | ↑ (1.5 × 10−4)/↑ (1.0) | Activated in gefitinib treated gallbladder cancer cells [31] |
| BCL2L11 (BIM) | Induction of apoptosis | ↑ (2.1 × 10−5)/↑ (1.1 × 10−8) | ↑ linked to higher sensitivity to gefitinib in NSCLC [32] |
| BTG2 | Cell cycle arrest (G1/S) | ↑ (5.5 × 10−29)/↑ (7.1 × 10−6) | |
| c-MYC | Cell cycle progression | ↓ (8.1 × 10−30)/↓ (1.7 × 10−10) | |
| CCND1 | Cell cycle/proliferation | ↓ (0.03)/↓ (2.8 × 10−32) | ↓ in gefitinib treated IEC [33] |
| CCNG1 | Cell cycle arrest | ↓ (5.5 × 10−6)/↓ (1.0) | |
| CCNG2 | Cell cycle arrest | ↑ (1.0)/↑ (0.004) | |
| CDH1 | E-cadherin; cell adhesion molecule | ↓ (8.5 × 10−8)/↓ (1.5 × 10−5) | ↓ in TKI-treated IEC [33,34] |
| DDB2 | DNA repair | ↑ (0.13)/↑ (1.4 × 10−4) | |
| FGF19 | Cell growth, tissue repair, effects on glucose and lipid metabolism | ↓ (9.6 × 10−9)/↓ (0.02) | ↓ in chronic diarrhoea [35] |
| ITGB1 | β1-integrin; cell adhesion, embryogenesis, homeostasis, tissue repair, immune response | ↓ (8.3 × 10−17)/↓ (1.0) | ↓ in TKI-treated IEC [34] |
| MUC20 | Suppressor of MET signalling/proliferation | ↑ (9.0 × 10−9)/↑ (0.005) | |
| MYBL2 | Cell cycle/proliferation | ↓ (1.0)/↓ (6.1 × 10−4) | |
| PCNA | DNA repair | ↑ (1.4 × 10−8)/↑ (1.0) | |
| PERP | Apoptosis effector; epithelial integrity and cell-cell adhesion | ↓ (1.7 × 10−16)/↓ (0.03) | |
| SFN | Cell cycle arrest (G2/M) | ↓ (1.1 × 10−7)/↓ (0.04) | |
| SUSD6 (KIAA0247) | Suppressor of cell growth; activator of apoptosis | ↑ (8.8 × 10−6)/↑ (1.0) | |
| TLR2 | Inflammatory signals | ↑ (0.005)/↑ (1.0) | |
| TNFRSF10 (TRAIL-R2) | Induction of apoptosis | ↓ (0.007)/↓ (1.0) | |
| TNS3 | Cell motility/migration | ↑ (6.5 × 10−14)/↑ (1.0) | |
| TNS4 | Cell motility/migration | ↓ (0.01)/↓ (5.8 × 10−8) | |
| DEGs with opposite trend in colon and SI organoids | |||
| ABCA1 | Efflux of cholesterol | ↑ (0.02)/↓ (1.0) | |
| c-FOS | Cell cycle progression | ↓ (3.2 × 10−6)/↑ (1.0) | |
| CYP51A1 | Cholesterol biosynthesis | ↓ (1.4 × 10−22)/↑ (2.2 × 10−8) | |
| DTX3 | Regulator of Notch signalling | ↑ (0.03)/↓ (1.0) | |
| FUCA1 | Degradation of glycoproteins and glycolipids | ↓ (8.7 × 10−7)/↑ (1.0) | |
| HMGCR | Cholesterol biosynthesis | ↓ (4.5 × 10−11)/↑ (7.4 × 10−4) | |
| HMGCS1 | Cholesterol biosynthesis | ↓ (1.6 × 10−4 )/↑ (0.004) | |
| PEPCK | Glucose metabolism | ↓ (3.1 × 10−6)/↑ (1.0) | |
| PRKAB1 | AMPK-mediated metabolism | ↑ (7.9 × 10−10)/↓ (0.008) | |
| SESN1 | DNA damage and oxidative stress response; translation control | ↑ (1.4 × 10−7)/↓ (1.0) | |
Legend: * adjusted p-values (in brackets) above 0.05 were considered as not significant; ↑—upregulated; ↓—downregulated; IEC—intestinal epithelial cells; NSCLC—non-small cell lung cancer.