Table II.
List of differentially expressed proteins in in situ vs. invasive melanoma formalin-fixed, paraffin-embedded tissues.
| A, Upregulated proteins in invasive melanoma vs. in situ melanoma | |||||
|---|---|---|---|---|---|
| Gene name | Protein identification | Peptide count | Confidence scorea | ANOVA (P-value) | Fold-change |
| PEBP1 | Phosphatidylethanolamine-binding protein 1 | 2 | 118.45 | 0.0000 | 4.04 |
| HNRNPK | Heterogeneous nuclear ribonucleoprotein K | 4 | 273.85 | 0.0002 | 4.63 |
| EEF2 | Elongation factor 2 | 7 | 418.22 | 0.0002 | 5.50 |
| HSP90B1 | Endoplasmin | 3 | 221.46 | 0.0003 | 2.57 |
| PSAP | Proactivator polypeptide | 2 | 92.05 | 0.0005 | 5.83 |
| HSP90AB1 | Heat shock protein HSP 90-beta | 4 | 300.79 | 0.0006 | 2.58 |
| HSPA5 | 78 kDa glucose-regulated protein | 3 | 176.94 | 0.0007 | 2.45 |
| PPIA | Peptidyl-prolyl cis-trans isomerase A | 3 | 258.37 | 0.0008 | 2.91 |
| FLNA | Filamin-A | 5 | 260.43 | 0.0010 | 5.75 |
| PGK1 | Phosphoglycerate kinase 1 | 4 | 328.39 | 0.0012 | 2.80 |
| TPI1 | Triosephosphate isomerase | 2 | 185.99 | 0.0014 | 3.98 |
| GSTP1 | Glutathione S-transferase P | 4 | 301.10 | 0.0014 | 2.61 |
| VCP | Transitional endoplasmic reticulum ATPase | 3 | 238.53 | 0.0015 | 2.53 |
| KRT31 | Keratin, type I cuticular Ha1 | 3 | 150.13 | 0.0015 | 22.11 |
| YWHAB | 14-3-3 protein beta/alpha | 3 | 278.01 | 0.0016 | 1.65 |
| PKM | Pyruvate kinase isozymes M1/M2 | 6 | 405.02 | 0.0024 | 3.78 |
| FBN1 | Fibrillin-1 | 4 | 245.97 | 0.0030 | 9.02 |
| FABP5 | Fatty acid-binding protein, epidermal | 3 | 179.44 | 0.0047 | 4.03 |
| PLEC | Plectin | 3 | 175.04 | 0.0050 | 2.85 |
| MDH2 | Malate dehydrogenase, mitochondrial | 3 | 181.57 | 0.0053 | 2.52 |
| COL6A1 | Collagen alpha-1(VI) chain | 6 | 444.60 | 0.0053 | 3.83 |
| PDIA3 | Protein disulfide-isomerase A3 | 2 | 116.05 | 0.0054 | 3.27 |
| RPS12 | 40S ribosomal protein S12 | 2 | 99.78 | 0.0061 | 2.98 |
| ACTB | Actin, cytoplasmic 1 | 9 | 640.45 | 0.0066 | 3.14 |
| PCBP1 | Poly(rC)-binding protein 1 | 3 | 183.71 | 0.0067 | 2.54 |
| TUBB2B | Tubulin beta-2B chain | 7 | 487.19 | 0.0073 | 6.87 |
| GAPDH | Glyceraldehyde-3-phosphate dehydrogenase | 3 | 290.29 | 0.0075 | 2.64 |
| OLFML1 | Olfactomedin-like protein 1 | 3 | 180.42 | 0.0078 | 2.86 |
| PRDX6 | Peroxiredoxin-6 | 2 | 125.87 | 0.0086 | 3.32 |
| LGALS1 | Galectin-1 | 2 | 122.70 | 0.0088 | 5.05 |
| VIM | Vimentin | 4 | 257.04 | 0.0097 | 2.16 |
| TUBA1A | Tubulin alpha-1A chain | 2 | 152.25 | 0.0098 | 2.77 |
| TUBA4A | Tubulin alpha-4A chain | 3 | 232.50 | 0.0103 | 2.58 |
| ENO1 | Alpha-enolase | 4 | 352.14 | 0.0105 | 1.46 |
| COL6A2 | Collagen alpha-2(VI) chain | 4 | 330.08 | 0.0111 | 2.23 |
| DPYSL2 | Dihydropyrimidinase-related protein 2 | 3 | 284.36 | 0.0113 | 2.06 |
| FASN | Fatty acid synthase | 6 | 441.55 | 0.0134 | 3.19 |
| YWHAE | 14-3-3 protein epsilon | 2 | 135.71 | 0.0135 | 8.98 |
| PLIN3 | Perilipin-3 | 2 | 115.71 | 0.0150 | 1.66 |
| ACTC1 | Actin, alpha cardiac muscle 1 | 5 | 258.90 | 0.0150 | 1.91 |
| TUBB | Tubulin beta chain | 7 | 505.61 | 0.0151 | 1.81 |
| AMBP | Protein AMBP | 2 | 123.71 | 0.0155 | 2.56 |
| ALDOA | Fructose-bisphosphate aldolase A | 2 | 223.37 | 0.0161 | 1.85 |
| ALB | Serum albumin | 20 | 1632.42 | 0.0162 | 3.94 |
| PDIA6 | Protein disulfide-isomerase A6 | 2 | 125.31 | 0.0162 | 2.29 |
| HSPD1 | 60 kDa heat shock protein, mitochondrial | 2 | 197.72 | 0.0166 | 2.66 |
| YWHAZ | 14-3-3 protein zeta/delta | 3 | 166.90 | 0.0171 | 2.95 |
| HLA-A | Human leukocyte antigen class I | 2 | 150.32 | 0.0195 | 7.68 |
| ACTN1 | Alpha-actinin-1 | 3 | 167.03 | 0.0197 | 4.05 |
| UBA1 | Ubiquitin-like modifier-activating enzyme 1 | 2 | 106.53 | 0.0200 | 1.81 |
| ACTN4 | Alpha-actinin-4 | 4 | 284.64 | 0.0226 | 4.13 |
| SERPINF1 | Pigment epithelium-derived factor | 2 | 130.19 | 0.0247 | 2.24 |
| CALM1 | Calmodulin | 3 | 286.87 | 0.0255 | 1.55 |
| NPM1 | Nucleophosmin | 2 | 154.40 | 0.0278 | 2.32 |
| YWHAQ | 14-3-3 protein theta | 2 | 125.98 | 0.0287 | 7.12 |
| TUBB4A | Tubulin beta-4A chain | 7 | 497.08 | 0.0307 | 3.63 |
| CLEC3B | Tetranectin | 2 | 114.64 | 0.0319 | 4.37 |
| ACSL1 | Long-chain-fatty-acid-CoA ligase 1 | 2 | 120.91 | 0.0327 | 3.10 |
| HNRNPA2B1 | Heterogeneous nuclear ribonucleoproteins A2/B1 | 2 | 204.90 | 0.0350 | 2.17 |
| COL14A1 | Collagen alpha-1(XIV) chain | 2 | 147.41 | 0.0375 | 2.20 |
| IGHG3 | Ig gamma-3 chain C region | 2 | 128.39 | 0.0402 | 1.54 |
| TF | Serotransferrin | 7 | 626.01 | 0.0405 | 3.70 |
| BGN | Biglycan | 2 | 119.89 | 0.0433 | 2.49 |
| EZR | Ezrin | 2 | 111.07 | 0.0458 | 12.78 |
| B, Downregulated proteins in invasive melanoma vs. in situ melanoma | |||||
| Gene name | Protein identification | Peptide count | Confidence scorea | ANOVA (P-value) | Fold-change |
| HRNR | Hornerin | 2 | 144.28 | 0.0003 | 7.24 |
| ITIH1 | Inter-alpha-trypsin inhibitor heavy chain H1 | 3 | 219.20 | 0.0021 | 1.78 |
| DSP | Desmoplakin | 16 | 956.60 | 0.0030 | 6.70 |
| KRT9 | Keratin, type I cytoskeletal 9 | 31 | 3005.85 | 0.0030 | 4.25 |
| KRT1 | Keratin, type II cytoskeletal 1 | 34 | 2801.68 | 0.0042 | 3.04 |
| DCD | Dermcidin | 2 | 136.27 | 0.0047 | 4.12 |
| LGALS7 | Galectin-7 | 3 | 395.32 | 0.0058 | 1.78 |
| CAT | Catalase | 3 | 223.78 | 0.0089 | 1.62 |
| ATP5A1 | ATP synthase subunit alpha, mitochondrial | 3 | 258.83 | 0.0101 | 2.11 |
| IGHA1 | Ig alpha-1 chain C region | 2 | 188.63 | 0.0108 | 2.24 |
| CALML5 | Calmodulin-like protein 5 | 2 | 175.25 | 0.0113 | 3.72 |
| KRT2 | Keratin, type II cytoskeletal 2 epidermal | 24 | 2034.24 | 0.0113 | 3.23 |
| KRT10 | Keratin, type I cytoskeletal 10 | 19 | 1719.86 | 0.0147 | 2.54 |
| FLG2 | Filaggrin-2 | 2 | 129.72 | 0.0229 | 2.75 |
| HSPB1 | Heat shock protein beta-1 | 2 | 125.22 | 0.0242 | 1.61 |
| MSN | Moesin | 2 | 109.96 | 0.0479 | 2.09 |
a
Confidence score obtained from Mascot. ANOVA, analysis of variance.