Table 1.
Expression of HFD-induced genes in breast cancer subtypes and association with breast cancer prognosis
| Gene a | Basal-like b | HER2 c | Luminal A d | Luminal B e | Normal-like f | Survival association g |
|---|---|---|---|---|---|---|
| MMP12 | 0.17 | -0.13* | -0.24* | -0.19* | -0.33* | Poor prognosis |
| GPNMB | -0.01 | 0.00 | -0.18* | -0.06 | -0.11 | Poor prognosis |
| CTSL | 0.07 | 0.04 | -0.16* | -0.03* | -0.18* | Poor prognosis |
| ITGAX | 0.00 | 0.07* | 0.04 | 0.05 | 0.05 | - |
| LILRB4 | 0.10 | 0.02 | -0.15* | -0.04* | -0.22* | Poor prognosis |
| TM7SF1 | -0.18 | 0.05* | 0.05* | 0.01* | -0.03* | - |
| DNMT3A | 0.09 | 0.03 | -0.08* | 0.00* | -0.10* | Poor prognosis |
| TYROBP | 0.06 | 0.01 | -0.05* | -0.01 | -0.13* | - |
| DIO1 | -0.21 | -0.18 | -0.04* | -0.01* | -0.07* | - |
| SLC11A1 | 0.14 | 0.01* | -0.10* | -0.03* | -0.15* | Poor prognosis |
| GALNS | 0.05 | 0.03* | 0.01 | 0.03 | 0.01 | - |
| NCF2 | 0.11 | 0.01* | -0.15* | -0.04* | -0.16* | Poor prognosis |
| PTPNS1 | 0.23 | 0.00* | -0.15* | -0.08* | -0.14* | Poor prognosis |
| LGALS3 | -0.07 | 0.04* | -0.03 | -0.01* | 0.04* | - |
| MTHFS | -0.02 | 0.00 | 0.02 | 0.05* | -0.07 | - |
| IL1RN | 0.00 | -0.17* | -0.13* | -0.11 | -0.05 | - |
| CTSS | 0.12 | -0.04* | -0.17* | -0.06* | -0.20* | - |
| WBSCR5 | 0.03 | 0.01 | 0.00 | 0.00 | -0.06* | - |
| PRKCD | -0.05 | 0.02* | 0.03* | 0.04* | -0.02 | - |
| CAPG | 0.09 | -0.03* | -0.06* | 0.01* | -0.07* | - |
| CD68 | 0.06 | 0.09 | -0.02* | 0.02 | -0.01* | - |
| ITGB2 | 0.11 | 0.04 | -0.09* | -0.03* | -0.11* | Poor prognosis |
| CSTB | 0.18 | 0.02* | -0.04* | -0.03* | -0.07* | Poor prognosis |
| ATF3 | 0.01 | -0.13* | -0.12* | -0.09* | 0.01 | - |
| CSF2RA | 0.01 | -0.01 | -0.02 | -0.01 | -0.11* | - |
| WFS1 | -0.20 | 0.00* | 0.03* | 0.06* | -0.02* | - |
| PPGB1 | 0.00 | 0.07* | -0.05* | 0.02 | -0.07* | Poor prognosis |
| ADAM8 | 0.12 | 0.02* | -0.09* | -0.06* | -0.25* | Poor prognosis |
| CCRL2 | 0.06 | 0.07 | -0.01 | 0.02 | -0.06* | - |
| VTN | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | - |
| RGS1 | 0.04 | 0.01 | -0.03* | -0.04* | -0.13* | - |
| FCGR3 | 0.09 | 0.06 | -0.03* | 0.03* | -0.08* | Poor prognosis |
| EMR1 | 0.06 | -0.03 | 0.01 | 0.00* | 0.03 | - |
| ARPC2 | 0.06 | 0.03 | -0.06* | -0.03* | -0.03* | - |
| ESD | -0.04 | -0.04 | 0.02* | -0.01 | 0.08* | Good prognosis |
| VAMP4 | 0.06 | 0.05 | 0.05 | 0.05 | -0.03 | - |
| CDKN1C | -0.05 | -0.05 | -0.05 | -0.12 | 0.13* | - |
| HEXB | -0.04 | 0.00 | -0.02 | -0.02 | -0.03 | - |
| NAGLU | -0.01 | 0.05* | 0.02 | 0.04* | 0.12* | - |
| KCNH2 | 0.00 | -0.29* | -0.21* | -0.15* | -0.32* | - |
| MSTF1 | 0.02 | 0.03 | 0.04* | 0.04* | 0.04 | - |
aHFD induced genes (Luitjen et al.) that were present in the NKI human breast cancer data set as described in the Methods. b-fAverage gene expression among 5 different human breast cancer subtypes for these genes (Tumors: basal-like n = 46; HER2 n = 49; luminal A n = 88; luminal B n = 81; normal-like n = 31). gTotal of 13 genes associated with poor prognosis and 1 gene associated with good prognosis based on Kaplan Meier survival analysis for the indicated gene with 295 BC samples from the NKI dataset as described in the Materials and Methods. The plots for the genes that were significantly associated with prognosis are depicted in Figure 1 of this manuscript. *Gene expression statistically different with respect to basal-like subtype (False discovery Rate [FDR] < 0.01).