Table 3.
Genes upregulated in the MS white matter and gray matter parenchyma.
| Gene | NAWM vs. control WM | Active WM lesion vs. control WM | Chronic active WM lesion rim vs. control WM | Subpial GM lesions vs. control GM |
|---|---|---|---|---|
| TMEM119 | n.s. | n.s. | n.s. | <0.0001 |
| CSF1R | <0.0001 | <0.0001 | n.s. | n.s. |
| TREM2 | <0.0001 | <0.0001 | <0.0001 | n.s. |
| RUNX1 | n.s. | 0.003 | 0.024 | n.s. |
| IRF1 | 0.011 | 0.001 | n.s. | n.s. |
| IRF4 | 0.001 | <0.0001 | 0.005 | n.s. |
| IRF8 | <0.0001 | <0.0001 | <0.0001 | n.s. |
| IFNβ | n.s. | 0.001 | n.s. | <0.0001 |
| STAT1 | n.s. | <0.0001 | n.s. | n.s. |
| STAT2 | n.s. | 0.022 | n.s. | n.s. |
| IFI6 | n.s. | 0.011 | n.s. | n.s. |
| IFI16 | 0.048 | <0.0001 | <0.0001 | <0.0001 |
| MxA | 0.023 | <0.0001 | n.s. | n.s. |
| OAS1 | n.s. | 0.006 | n.s. | n.s. |
| Cathepsin S | <0.0001 | <0.0001 | <0.0001 | <0.0001 |
| CIITA | 0.042 | 0.025 | n.s. | 0.004 |
| RFX5 | 0.001 | <0.0001 | n.s. | n.s. |
| HLA-DRA | <0.0001 | <0.0001 | <0.0001 | <0.0001 |
| CD86 | <0.0001 | <0.0001 | 0.003 | n.s. |
| CD40 | <0.0001 | <0.0001 | 0.003 | 0.02 |
| CD68 | <0.0001 | <0.0001 | <0.0001 | 0.045 |
| MSR1 | <0.0001 | <0.0001 | <0.0001 | n.s. |
| CD163 | n.s. | 0.044 | n.s. | 0.003 |
| Caspase 1 | <0.0001 | <0.0001 | <0.0001 | <0.0001 |
| IL1β | n.s. | n.s. | n.s. | <0.0001 |
| IL10 | <0.0001 | <0.0001 | n.s. | n.s. |
| IL16 | 0.045 | 0.005 | n.s. | n.s. |
| IL18 | <0.0001 | n.s. | n.s. | 0.01 |
| BAFF | n.s. | <0.0001 | n.s. | 0.003 |
| TGFβ1 | 0.03 | <0.0001 | <0.0001 | n.s. |
| TNFR1 | 0.016 | <0.0001 | n.s. | 0.004 |
| TNFR2 | <0.0001 | <0.0001 | 0.035 | n.s. |
| CCL2 | n.s. | 0.022 | n.s. | <0.0001 |
| CCL5 | <0.0001 | <0.0001 | 0.001 | <0.0001 |
| CXCL10 | 0.038 | 0.002 | 0.003 | 0.001 |
| CCR1 | n.s. | <0.0001 | 0.003 | 0.003 |
| CYBA | n.s. | <0.0001 | n.s. | n.s. |
| CYBB | n.s. | <0.0001 | 0.044 | n.s. |
| NRF2 | n.s. | 0.001 | 0.001 | n.s. |
| GPX1 | 0.009 | <0.0001 | 0.006 | 0.006 |
| HMOX1 | n.s. | <0.0001 | n.s. | 0.002 |
| GBP1 | n.s. | 0.001 | 0.022 | n.s. |
| GBP2 | <0.0001 | <0.0001 | <0.0001 | <0.0001 |
| GBP4 | 0.019 | 0.016 | 0.003 | n.s. |
| GBP5 | 0.014 | 0.001 | 0.017 | 0.006 |
| TLR2 | <0.0001 | <0.0001 | 0.001 | n.s. |
| TLR7 | n.s. | <0.0001 | <0.0001 | n.s. |
Gene expression data were obtained in samples microdissected from 5 non-pathological control brains (5 WM and 6 GM areas) and 10 MS brains (14 NAWM, 13 actively demyelinating WM lesions, 8 chronic active WM lesions and 24 subpial chronic GM lesions). Figures represent p values for statistically significant differences in gene expression between control and MS brain parenchymal samples, as assessed by Mann-Whitney test (p < 0.05 without Bonferroni correction; when applying the Bonferroni correction, the significance threshold was p < 0.017); n.s., not significant.