Table 1.
Identified proteins in breast cancer cells (MCF-7) and normal breast epithelial cells (MCF10A) with or without exogenous zinc exposure.
| Spot ID | Identified proteins | Gene ID | Protein accession | Theoretical MW (kDa)/pI | Observed MW (KDa)/pI | PLGS score | Matched peptides | Sequence coverage (%) | (Fold change/p value) | Molecular functions | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MCF-7 T0/MCF10A T0 | MCF-7 T120/MCF10A T120 | MCF-7 T120/MCF-7 T0 | MCF10A T120/MFC10A T0 | ||||||||||
| 1 | 14-3-3 protein σ | SFN | P31947 | 27.8/4.5 | 27.9/4.5 | 2586 | 24 | 44 | (0.5/0.02) ↓ | I | |||
| 2 | 14-3-3 protein θ | YWHAQ | P27348 | 27.8/4.5 | 29.0/4.7 | 10806 | 14 | 43 | (0.4/0.003) ↓ | (0.3/0.0001) ↓ | II | ||
| 3 | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4 | Q5VWC4 | 41.1/4.5 | 62.0/4.6 | 1085 | 22 | 23 | (0.2/0.003) ↓ | III | |||
| 4 | 39S ribosomal protein L12 mitochondrial | MRPL12 | P52815 | 21.3/9.2 | 17.7/5.3 | 4066 | 8 | 30 | (0.7/0.03) ↓ | IV | |||
| 5 | 60S acidic ribosomal protein P0 | RPLP0 | A0A024RBS2 | 34.3/5.6 | 42.0/5.6 | 588 | 6 | 16 | (0.3/0.002) ↓ | V | |||
| 6 | α-Smooth muscle actin 2 | ACTA2 | D2JYH4 | 42.0/5.1 | 44.4/5.2 | 6831 | 22 | 28 | (6.8/0.0003) ↑ | (0.3/0.003) ↓ | VI | ||
| 7 | Actin cytoplasmic 1 | ACTB | P60709 | 41.7/5.1 | 59.6/5.3 | 17835 | 27 | 60 | (0.3/0.0004) ↓ | VII | |||
| 8 | Actinin α1 isoform CRA a | ACTN1 | A0A024R694 | 103.0/5.1 | 156.6/5.5 | 35257 | 64 | 45 | (1.9/0.02) ↑ | VIII | |||
| 9 | Adenosylhomocysteinase | AHCY | A0A384MTQ3 | 47.7/5.9 | 50.1/6.0 | 911 | 24 | 19 | (0.5/0.04) ↓ | III | |||
| 10 | Annexin | ANXA8L1 | A0A075B752 | 40.7/5.6 | 35.2/5.6 | 623 | 8 | 17 | (0.1/0.04) ↓ | VIII | |||
| 11 | Annexin A1 | ANXA1 | P04083 | 38.7/6.6 | 36.0/6.6 | 21563 | 27 | 62 | (0.2/0.03) ↓ | VIII | |||
| 12 | Annexin A5 | ANXA5 | P08758 | 35.9/4.7 | 29.0/5.0 | 3292 | 8 | 20 | (0.5/0.03) ↓ | (4.4/0.02) ↑ | VIII | ||
| 13 | Calmodulin-1 | CALM1 | P0DP23 | 17.0/3.9 | 13.9/3.3 | 1613 | 6 | 41 | (0.2/0.006) ↓ | VIII, III | |||
| 14 | Cathepsin D | CTSD | A0A1B0GW44 | 43.7/6.1 | 30.2/5.4 | 1908 | 11 | 19 | (8.4/0.0001) ↑ | (3.3/0.007) ↑ | III | ||
| 15 | Cytochrome b5 type B | CYB5B | O43169 | 16.3/4.7 | 18.2/3.7 | 867 | 3 | 17 | (4.2/0.0003) ↑ | VIII | |||
| 16 | D-3-Phosphoglycerate dehydrogenase | PHGDH | A0A286YF22 | 55.9/6.3 | 69.2/6.7 | 4302 | 8 | 16 | (2.0/0.02) ↑ | (0.8/0.04) ↓ | (1.4/0.02) ↑ | III | |
| 17 | Dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) isoform CRA a | DLST | A0A024R6C9 | 48.7/9.3 | 62.0/6.0 | 1601 | 4 | 10 | (2.6/0.01) ↑ | III | |||
| 18 | Dynactin 2 (P50) isoform CRA c | DCTN2 | A0A384MDU9 | 44.2/4.9 | 59.2/5.2 | 6320 | 21 | 52 | (0.4/0.03) ↓ | (0.7/0.04) ↓ | VII | ||
| 19 | Elongation factor 1 δ | EEF1D | A0A087X1X7 | 69.2/6.8 | 42.0/4.3 | 52531 | 21 | 25 | (0.7/0.001) ↓ | V | |||
| 20 | Elongation factor Tu | TUFM | A0A384ME17 | 49.8/7.4 | 50.1/7.0 | 2644 | 49 | 36 | (5.2/0.01) ↑ | (0.5/0.003) ↓ | (0.5/0.01) ↓ | (1.4/0.02) ↑ | V |
| 21 | Exosome complex component MTR3 | EXOSC6 | Q5RKV6 | 28.2/6.0 | 32.4/5.9 | 350 | 4 | 17 | (0.5/0.04) ↓ | IV | |||
| 22 | F-Actin-capping protein subunit β | CAPZB | A0A384MR50 | 30.6/5.6 | 28.5/5.7 | 1812 | 10 | 26 | (3.0/0.0003) ↑ | (2.4/0.03) ↑ | VI | ||
| 23 | ATP-dependent RNA helicase DDX1 | DDX1 | A0A087X2G1 | 73.9/7.6 | 136.2/8.1 | 298 | 19 | 12 | (1.4/0.04) ↑ | III | |||
| 24 | Adenylosuccinate lyase | ADSL | A0A1B0GTJ7 | 54.4/6.7 | 67.2/7.6 | 584 | 4 | 8 | (0.3/0.002) ↓ | (0.4/0.005) ↓ | III | ||
| 25 | FUBP1 | FUBP1 | A0A1Z1G4M2 | 67.6/7.9 | 89.5/8.2 | 372 | 5 | 9 | (2.1/0.02) ↑ | II | |||
| 26 | Peptidyl-prolyl cis-trans isomerase FKBP4 | FKBP4 | Q02790 | 51.8/5.2 | 62.0/5.6 | 32827 | 47 | 65 | (1.9/0.01) ↑ | (2.5/0.003) ↑ | IX | ||
| 27 | Glutathione S-transferase Mu 3 | GSTM3 | P21266 | 26.5/5.2 | 26.9/5.4 | 8436 | 20 | 54 | (3.0/0.04) ↑ | (5.0/0.005) ↑ | III | ||
| 28 | Glutathione S-transferase P | GSTP1 | P09211 | 23.3/5.3 | 24.6/5.6 | 12769 | 31 | 66 | (0.2/0.002) ↓ | III | |||
| 29 | Glutathione synthetase | GSS | P48637 | 52.4/5.6 | 62.0/5.6 | 11269 | 26 | 57 | (1.5/0.04) ↑ | III | |||
| 30 | Inorganic pyrophosphatase | PPA1 | Q15181 | 32.6/5.4 | 37.8/5.5 | 957 | 4 | 11 | (2.5/0.03) ↑ | III | |||
| 31 | Heat shock protein 90 kDa alpha (cytosolic) class B member 1 isoform CRA a | HSP90AB1 | A0A024RD80 | 83.2/4.8 | 143.0/5.4 | 5834 | 28 | 33 | (0.5/0.0006) ↓ | IX | |||
| 32 | Heat shock protein β 1 | HSPB1 | P04792 | 22.8/6.0 | 26.0/5.9 | 46679 | 22 | 78 | (3.5/0.002) ↑ | (0.2/0.002) ↓ | IX | ||
| 33 | Pyruvate dehydrogenase E1 component subunit α | PDHA1 | A0A024RBX9 | 43.3/8.0 | 50.1/6.5 | 373 | 3 | 6 | (1.7/0.04) ↑ | III | |||
| 34 | Heterogeneous nuclear ribonucleoproteins C1/C2 | HNRNPC | B2R5W2 | 31.9/4.9 | 40.8/5.0 | 7292 | 24 | 43 | (8.0/0.0002) ↑ | (0.5/0.009) ↓ | X, IV | ||
| 35 | High mobility group protein B1 | HMGB1 | A0A024RDR0 | 24.9/5.5 | 23.5/6.3 | 3179 | 8 | 26 | (1.9/0.03) ↑ | X | |||
| 36 | Histidine-tRNA ligase cytoplasmic | HARS1 | P12081 | 57.4/5.6 | 62.0/5.8 | 3224 | 15 | 25 | (1.5/0.04) ↑ | III | |||
| 37 | Histone H4 | HIST1H4J | B2R4R0 | 11.4/11.8 | 18.2/5.7 | 897 | 4 | 36 | (2.5/0.007) ↑ | (1.9/0.001) ↑ | VII, X | ||
| 38 | Heat shock 70 kDa protein 1A | HSPA1A | A0A1U9X7W4 | 70.0/5.3 | 89.5/5.5 | 29565 | 38 | 49 | (1.7/0.02) ↑ | IX | |||
| 39 | Inosine-5′-monophosphate dehydrogenase | IMPDH | A0A384N6C2 | 55.8/6.5 | 69.2/7.0 | 3921 | 8 | 14 | (0.6/0.04) ↓ | (1.5/0.005) ↑ | III | ||
| 40 | L-Lactate dehydrogenase B chain | LDHB | P07195 | 36.6/5.6 | 38.9/5.7 | 6282 | 11 | 28 | (0.6/0.004) ↓ | III | |||
| 41 | C-1-Tetrahydrofolate synthase, cytoplasmic | MTHFD1 | A0A024R652 | 101.5/6.8 | 156.6/7.8 | 342 | 18 | 18 | (0.5/0.04) ↓ | XI, V | |||
| 42 | Myosin regulatory light chain 12A | MYL12A | J3QRS3 | 20.4/4.4 | 17.3/4.8 | 1142 | 5 | 29 | (0.4/0.0003) ↓ | VIII | |||
| 43 | NADH dehydrogenase (ubiquinone) iron-sulfur protein 3 mitochondrial | NDUFS3 | O75489 | 30.2/7.4 | 29.0/5.7 | 1561 | 5 | 20 | (2.5/0.0004) ↑ | III | |||
| 44 | Nucleoside diphosphate kinase | NME | A0A384MTW7 | 17.1/5.8 | 19.1/5.8 | 3957 | 6 | 30 | (2.8/0.01) ↑ | (1.7/0.03) ↑ | III | ||
| 45 | Perilipin | PLIN | A0A140VJN8 | 46.9/5.1 | 55.1/5.1 | 3760 | 11 | 32 | (0.1/0.005) ↓ | XII | |||
| 46 | Plastin 3 | PLS3 | P13797 | 70.8/5.3 | 92.2/5.6 | 4429 | 20 | 31 | (1.8/0.04) ↑ | VIII | |||
| 47 | Actin γ | ACTG2 | P63267 | 41.9/5.2 | 47.1/5.1 | 11163 | 11 | 30 | (5.2/0.001) ↑ | VII | |||
| 48 | Proliferating cell nuclear antigen | PCNA | P12004 | 28.8/4.4 | 36.0/4.7 | 3412 | 13 | 44 | (1.5/0.004) ↑ | (0.6/0.02) ↓ | X | ||
| 49 | Peroxiredoxin 6 | PRDX6 | A0A024R938 | 25.0/6.0 | 26.0/6.3 | 2521 | 26 | 34 | (1.9/0.04) ↑ | III | |||
| 50 | Proteasome subunit β type 6 | PSMB6 | P28072 | 25.3/4.6 | 21.4/4.9 | 1361 | 5 | 21 | (1.4/0.04) ↑ | (0.3/0.03) ↓ | III | ||
| 51 | Protein S100A2 | S100A2 | P29034 | 11.0/4.5 | 12.0/4.5 | 2026 | 3 | 18 | (0.04/0.004) ↓ | (0.08/0.01) ↓ | (0.4/0.02) ↓ | VIII | |
| 52 | Cytochrome c oxidase subunit 6B1 | COX6B1 | P14854 | 10.2/6.9 | 12.4/5.9 | 833 | 8 | 28 | (1.9/0.02) ↑ | (0.7/0.04) ↓ | XII | ||
| 53 | Protein S100A13 | S100A13 | Q99584 | 11.5/5.8 | 13.1/5.7 | 9088 | 17 | 60 | (4.1/0.001) ↑ | (4.0/0.0002) ↑ | VIII | ||
| 54 | Protein SET | SET | Q01105 | 33.5/4.0 | 50.1/4.4 | 8811 | 16 | 34 | (0.2/0.0009) ↓ | (0.2/0.0001) ↓ | IX, X | ||
| 55 | Radixin | RDX | B0YJ88 | 68.5/6.0 | 110.1/6.3 | 5828 | 28 | 36 | (1.3/0.02) ↑ | (0.3/0.0004) ↓ | (1.6/0.004) ↑ | VI | |
| 56 | Rho GDP-dissociation inhibitor 1 | ARHGDIA | P52565 | 23.2/4.8 | 26.8/5.1 | 1996 | 8 | 28 | (0.6/0.04) ↓ | III | |||
| 57 | 40S ribosomal protein SA | RPSA | A0A024R2L6 | 32.8/4.6 | 47.1/5.1 | 2510 | 8 | 16 | (4.4/0.0005) ↑ | VII | |||
| 58 | 60S acidic ribosomal protein P2 | RPLP2 | A0A024RCA7 | 11.7/4.2 | 15.9/4.3 | 8497 | 11 | 77 | (0.7/0.004) ↓ | V | |||
| 59 | Serine/threonine-protein kinase PAK 2 | PAK2 | Q13177 | 58.0/5.6 | 73.4/5.8 | 2239 | 17 | 28 | (0.5/0.03) ↓ | III | |||
| 60 | Serpin B5 | SERPINB5 | A0A024R2B6 | 42.1/5.6 | 45.7/5.8 | 2466 | 15 | 38 | (0.2/0.0007) ↓ | III | |||
| 61 | START domain-containing 10 isoform CRA a | STARD10 | A0A024R5L8 | 33.0/6.7 | 39.8/6.0 | 1134 | 5 | 20 | (3.1/0.002) ↑ | XIII | |||
| 62 | Stathmin | STMN1 | P16949 | 17.3/5.7 | 16.5/5.7 | 8524 | 12 | 53 | (0.4/0.002) ↓ | VII | |||
| 63 | SUMO-1 activating enzyme subunit 1 isoform CRA b | SAE1 | A0A024R0R4 | 38.4/5.0 | 42.0/5.4 | 3930 | 11 | 28 | (0.1/0.03) ↓ | III | |||
| 64 | T-Complex protein 1 subunit α | TCP1 | P17987 | 60.3/5.7 | 75.5/5.8 | 4508 | 17 | 30 | (0.4/0.008) ↓ | IX | |||
| 65 | T-Complex protein 1 subunit γ | CCT3 | B3KX11 | 57.9/6.5 | 89.5/6.1 | 1050 | 17 | 23 | (0.8/0.02) ↓ | IX | |||
| 66 | T-Complex protein 1 subunit θ | CCT8 | P50990 | 59.6/5.3 | 73.4/5.6 | 1289 | 15 | 28 | (0.2/0.03) ↓ | IX | |||
| 67 | Thioredoxin | TXN | H9ZYJ2 | 11.7/4.6 | 14.5/5.1 | 1389 | 15 | 34 | (1.4/0.0004) ↑ | III | |||
| 68 | Torsin-1A-interacting protein 1 | TOR1AIP1 | A0A0A0MSK5 | 52.4/6.6 | 75.5/6.1 | 1086 | 9 | 21 | (0.2/0.001) ↓ | (2.3/0.0005) ↑ | III | ||
| 69 | Transitional endoplasmic reticulum ATPase | VCP | P55072 | 89.3/5.0 | 132.3/5.4 | 2552 | 27 | 28 | (0.6/0.01) ↓ | V, III | |||
| 70 | Triosephosphate isomerase | TPI1 | P60174 | 30.8/5.6 | 25.5/7.7 | 4224 | 8 | 32 | (3.0/0.002) ↑ | (3.8/0.03) ↑ | III | ||
| 71 | Tubulin alpha-1C chain | TUBA1C | Q9BQE3 | 50.1/4.8 | 14.8/5.3 | 1665 | 4 | 12 | (0.2/0.0001) ↓ | (0.2/00) ↓ | (3.1/0.03) ↑ | VII | |
| 72 | Tumour protein D53 | TPD52L1 | E9PNK6 | 18.7/5.5 | 19.1/5.6 | 1601 | 3 | 9 | (4.8/0.0005) ↑ | (13.6/0.001) ↑ | II | ||
| 73 | Tumour protein D54 | TPD52L2 | A0A087WYR3 | 23.8/6.1 | 27.9/5.2 | 3042 | 11 | 38 | (2.5/0.04) ↑ | II | |||
| 74 | Vesicle amine transport protein 1 | VAT1 | A0A024R1Z6 | 41.9/5.9 | 57.5/6.0 | 5485 | 12 | 21 | (0.7/0.04) ↓ | III | |||
Note. MW stands for molecular weight, kDa for kilo Dalton, pI for isoelectric point, PLGS for ProteinLynx Global Server, T0 for 0 min or without zinc exposure (control), T120 for 120 min, ↑ for upregulation, ↓ for downregulation, MCF-7 for breast cancer cells, and MCF10A for breast normal epithelial cells. The PLGS score, protein accession, theoretical MW/pI, matched peptides, and sequence coverage (%) were obtained using ProteinLynx Global Server (PLGS) software (version 3.0, Waters Corporation, USA) and the UniProt (Homo sapiens, human) database. Gene ID was derived from UniProt database. The observed MW and pI were calculated according to the protein standards. The fold changes and p values were acquired from the quantitative analysis of the gel images (each group n = 3) by Delta2D software (version 4.0.8, DECODON Gmbh, Germany). MCF-7 T0/MCF10A T0 is the expression fold change of the proteins in MCF-7 cells compared to MCF10A cells without zinc exposure (T0), MCF-7 T120/MCF10A T120 is the expression fold change of the proteins in MCF-7 cells compared to MCF10A cells following the zinc exposure for 120 min (T120), MCF-7 T120/MCF-7 T0 is the expression fold change of the proteins in MCF-7 cells following zinc exposure for T120 compared to T0, and MCF10A T120/MFC10A T0 is the fold change of the proteins in MCF10A cells following zinc exposure for T120 compared to T0. Molecular functions: I, apoptosis; II, signalling; III, catalytic activity; IV, RNA binding; V, protein synthesis; VI, protein binding; VII, structural; VIII, metal ion binding; IX, molecular chaperone; X, DNA binding; XI, DNA synthesis; XII, metabolism; XIII, lipid binding.