Table 4 The proteins included in the reduced datasets identified by RGIFE for the canine proteomics emPAI and ProteinProphet data.
Protein ID | Protein name | Identified from emPAI or ProteinProphet | Protein description | Known link to cartilage inflammation or OA |
|---|---|---|---|---|
MMP-3 | matrix-metalloproteinase 3 | ProteinProphet and emPAI | MMP-3 is a proteolytic enzyme known to degrade components of the ECM, including collagens and cartilage proteoglycans [53]. | Found to be down-regulated in late OA [33]. |
IL-8 | interleukin-8 | ProteinProphet | IL-8 is a chemotactic factor that attracts neutrophils, basophils, and T-cells, but not monocytes. It is also involved in neutrophil activation. It is released from several cell types in response to an inflammatory stimulus [54]. | IL-8 is the major chemotactic factor released in response to proinflammatory cytokines in synovial tissues from RA and OA affected joints [34]. |
TSP1 | thrombospondin-1 | ProteinProphet | Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions [55]. | Levels of TSP1 are increased after the onset of OA [35] |
APOE | apolipoprotein E | ProteinProphet | APOE mediates the binding, internalization, and catabolism of lipoprotein particles [56]. | No known link. |
HPLN1 | hyaluronan and proteoglycan link protein 1 | ProteinProphet | Stabilizes the aggregates of proteoglycan monomers with hyaluronic acid in the extracellular cartilage matrix [57]. | HPLN1 has been associated with OA and osteophyte formation [36]. |
TPIS | triosephosphate isomerase | ProteinProphet | Catalyses the reaction D-glyceraldehyde 3-phosphate = glycerone phosphate [58]. | No known link. |
CLUS | clusterin | emPAI | A glycoprotein that functions as extracellular chaperone that prevents aggregation of non-native proteins, which is involved in many diverse biological functions [59]. | Higher levels of clusterin have been observed in synovial fluid of advanced primary knee and hip OA patients [37]. |
FETUA | alpha-2-HS-glycoprotein/fetuin-A | emPAI | Promotes endocytosis, possesses opsonic properties and influences the mineral phase of bone [60]. | FETUA levels have been found to decrease as the severity of knee OA increases [38]. |
POLG | Genome polyprotein | emPAI | Bacterial protein. | No known link. |
ATPX | ATP synthase subunit b' | emPAI | Bacterial protein. | No known link. |