Table I. Chondrogenesis-regulated proteins in OA hBMSCs, identified in this work by SILAC and nano-LC-MS/MS analysis.
| Acc Noa | Protein name | Gene symbol | Pept (95%)b | Ratioc | p value | EFd |
|---|---|---|---|---|---|---|
| Proteins increased at day 14 of chondrogenic differentiation | ||||||
| Q04446 | 1,4-alpha-glucan-branching enzyme | GBE1 | 6 | 2411 | 0.005 | 1,612 |
| P21589 | 5′-nucleotidase | 5NTD | 4 | 1559 | 0.030 | 1438 |
| P15121 | Aldose reductase | AKR1B1 | 3 | 2779 | 0.046 | EF > 2 |
| P15144 | Aminopeptidase N | ANPEP | 20 | 1637 | 0.000 | 1086 |
| P07355 | Annexin A2 | ANXA2 | 88 | 1458 | 0.000 | 1085 |
| P08758 | Annexin A5 | ANXA5 | 50 | 1583 | 0.000 | 1096 |
| P25705 | ATP synthase subunit alpha, mitochondrial | ATPA | 5 | 1271 | 0.042 | 1255 |
| P06576 | ATP synthase subunit beta, mitochondrial | ATPB | 16 | 1231 | 0.024 | 1194 |
| P98160 | Basement membrane-specific heparan sulfate proteoglycan core protein or Perlecan | HSPG2 | 2 | 1940 | 0.030 | 1652 |
| P12109 | Collagen alpha-1(VI) chain | COL6A1 | 8 | 1512 | 0.040 | 1480 |
| P12110 | Collagen alpha-2(VI) chain | COL6A2 | 19 | 1921 | 0.000 | 1179 |
| P12111 | Collagen alpha-3(VI) chain | COL6A3 | 87 | 1866 | 0.000 | 1112 |
| P14625 | Endoplasmin | HSP90B1 | 30 | 1514 | 0.002 | 1272 |
| P04406 | Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | 62 | 1362 | 0.012 | 1263 |
| P62826 | GTP-binding nuclear protein Ran | RAN | 4 | 2027 | 0.011 | 1492 |
| Q9BTM1 | Histone H2A type 1-J | H2AFJ | 11 | 2135 | 0.005 | 1572 |
| P62807 | Histone H2B type 1-C/E/F/G/I | HIST1H2BC | 23 | 2516 | 0.000 | 1471 |
| P62805 | Histone H4 | HIST1H4A | 19 | 2518 | 0.003 | 1688 |
| P00338 | l-lactate dehydrogenase A chain | LDHA | 30 | 1545 | 0.001 | 1247 |
| P07195 | l-lactate dehydrogenase B chain | LDHB | 7 | 2099 | 0.025 | 1757 |
| P43490 | Nicotinamide phosphoribosyltransferase | NAMPT | 4 | 1501 | 0.033 | 1507 |
| P30041 | Peroxiredoxin-6 | PRDX6 | 5 | 1380 | 0.032 | 1323 |
| P00558 | Phosphoglycerate kinase 1 | PGK1 | 38 | 1437 | 0.048 | 1433 |
| P18669 | Phosphoglycerate mutase 1 | PGAM1 | 14 | 1402 | 0.000 | 1164 |
| P02545 | Prelamin-A/C | LMNA | 45 | 1420 | 0.021 | 1343 |
| Q6DRA6 | Putative histone H2B type 2-D | HIST2H2BD | 5 | 3595 | 0.006 | 1539 |
| P46940 | Ras GTPase-activating-like protein | IQGA1 | 3 | 1938 | 0.045 | 1885 |
| P04179 | Superoxide dismutase [Mn], mitochondrial | SOD2 | 16 | 2040 | 0.002 | 1434 |
| P24821 | Tenascin | TNC | 18 | 1756 | 0.034 | 1674 |
| P29401 | Transketolase | TKT | 4 | 1706 | 0.043 | 1631 |
| P60174 | Triosephosphate isomerase | TPI1 | 26 | 1530 | 0.001 | 1264 |
| O14773 | Tripeptidyl-peptidase 1 | TPP1 | 4 | 1658 | 0.006 | 1257 |
| Q16851 | UTP-glucose-1-phosphate uridylyltransferase | UGP2 | 2 | 1449 | 0.049 | 1443 |
| Proteins decreased at day 14 of chondrogenic differentiation | ||||||
| P61981 | 14–3-3 protein gamma | 1433G | 10 | 0.791 | 0.046 | 1254 |
| P62277 | 40S ribosomal protein S13 | RS13 | 2 | 0.601 | 0.038 | 1580 |
| P13639 | Elongation factor 2 | EEF2 | 9 | 0.682 | 0.024 | 1374 |
| P21333 | Filamin-A | FLNA | 56 | 0.509 | 0.001 | 1475 |
| P13489 | Ribonuclease inhibitor | RNH1 | 13 | 0.239 | 0.034 | EF > 2 |
| P50454 | Serpin H1 | SERPINH1 | 21 | 0.577 | 0.002 | 1351 |
| Q9Y490 | Talin-1 | TLN1 | 17 | 0.425 | 0.017 | 1974 |
| Q01995 | Transgelin | TAGLN | 15 | 0.171 | 0.000 | EF > 2 |
| P67936 | Tropomyosin alpha-4 chain | TPM4 | 11 | 0.297 | 0.001 | 1480 |
| O60701 | UDP-glucose 6-dehydrogenase | UGDH | 11 | 0.759 | 0.026 | 1255 |
aProtein accession number according to SwissProt and TrEMBL databases.
bNumber of unique peptides (Pept) used for protein identification at 95% confidence.
cAverage SILAC ratios (n = 3) that represent the relative protein abundance in hBMSCs at day 14 versus day 2 of chondrogenic differentiation.
dError factor (a measure of the error in the average ratio), calculated by Protein Pilot 4.0 software for quantification accuracy.
MS = mass spectrometry; LC = liquid-chromatography; SILAC = stable isotope labelling by amino acids in cell culture; OA hBMSCs = osteoarthritic human bone marrow mesenchymal stem cells.