Table 3.
MS signature genes counter-regulated by interferon treatmenta
| Gene symbol | Fold change (P-value) |
Gene name | Gene function | Validated | |
|---|---|---|---|---|---|
| MS versus Ctrl | IFN versus untreated | ||||
| PARK7 | 1.239 (2 × 10−7) | 0.873 (0.001) | Parkinson protein 7 | Mitochondrial oxidative stress, TRAIL-induced cell death (65); mutated form causes early-onset Parkinson disease (66); previously linked to MS (34–36) | Yes |
| CSNK2B | 1.207 (9 × 10−8) | 0.895 (0.002) | Casein kinase 2, beta polypeptide | Anti-viral response (67), Wnt signaling (68); susceptibility region for rheumatoid arthritis (69) | No |
| USE1 | 1.163 (2 × 10−7) | 0.943 (0.039) | Unconventional SNARE in the ER 1 homolog | Localizes to the endoplasmatic reticulum (ER) and Golgi | Yes |
| S100A11 | 1.201 (2 × 10−7) | 0.919 (0.008) | S100 calcium binding protein A11 | Interleukin signaling (70) | No |
| LST1 | 1.275 (1 × 10−7) | 0.874 (0.002) | Leukocyte-specific transcript 1 | Myeloid transmembrane protein, expression increased in rheumatoid arthritis and up-regulated by LPS, IFN-gamma and bacterial infection (71) | Yes |
| FCGRT | 1.126 (1 × 10−5) | 0.905 (2 × 10−5) | Fc fragment of IgG, receptor, transporter, alpha | Binds to, and increases the stability of, IgG in serum (72) | Yes |
| GMFG | 1.160 (1 × 10−4) | 0.908 (0.007) | Glia maturation factor, gamma | Hematopoietic cell development (73) | Yes |
| MRFAP1 | 1.134 (6 × 10−7) | 0.938 (0.007) | Morf4 family associated protein 1 | Uncertain | No |
| COX4I1 | 1.225 (3 × 10−9) | 0.914 (0.006) | Cytochrome c oxidase subunit IV isoform 1 | Oxidative phosphorylation | Yes |
| C19orf43 | 1.159 (4 × 10−6) | 0.941 (0.033) | Open reading frame 43 (Chr 19) | Uncertain | Yes |
| PSMA7 | 1.129 (3 × 10−6) | 0.947 (0.019) | Proteasome subunit, alpha type, 7 | Component of proteasome; among others, functions in cell cycle and viral replication (74) | No |
aCtrl, control; IFN, interferon; TRAIL, tumor necrosis factor-related apoptosis-inducing ligand; Wnt, wingless-related MMTV integration site; LPS, lipopolysaccharide. Validated, also found to be down-regulated in publicly available data sets measuring gene expression before and after administration of IFN (see Materials and Methods).