Background
Methods
Synovial fluid collection and storage
Stage I | Stage II |
p value (A) R v NR SI; (B) R v NR SI |
p value (A) SI v SII R; (B) SI v SII NR | |||
---|---|---|---|---|---|---|
Responders (n = 8) | Non-responders (n = 7) | Responders (n = 12) | Non-responders (n = 12) | |||
Difference in Lysholm Score | 27 (17–38) | –8 (–4 to –17) | 34 (17–54) | –11 (–4 to –46) | (A) 0.0003; (B) <0.0001 | (A) 0.21; (B) 0.55 |
BMI (kg/m2) | 29 (23–31) | 27 (24–31) | 27 (23–48) | 29 (22–36) | (A) 0.94; (B) 0.54 | (A) 0.73; (B) 0.68 |
Age (years) | 32 (17–49) | 40 (25–50) | 40 (17–90) | 43 (25–52) | (A) 0.28; (B) 0.92 | (A) 0.17; (B) 0.58 |
Male (n) | 8 | 7 | 11 | 10 | (A) >0.99; (B) >0.99 | (A) >0.99; (B) 0.51 |
Smoker (n) | 1 | 2 | 1 | 3 | (A) 0.54; (B) 0.59 | (A) >0.99; (B) >0.99 |
Dilution factor of SF | 5 (3–9) | 4 (2–7) | 4 (1–9) | 3 (2–5) | (A) 0.48; (B) 0.25 | (A) 0.53; (B) 0.50 |
Total defect area (cm2) | 14 (0.4–24) | 6 (0.6–12) | 6 (1–20) | 5 (0.6–12) | (A) 0.74; (B) 0.35 | (A) 0.45; (B) 0.28 |
Patella defect (n) | 1 | 1 | 4 | 2 | (A) >0.99; (B) 0.64 | (A) 0.60; (B) >0.99 |
LFC defect (n) | 2 | 0 | 0 | 0 | (A) 0.47; (B) >0.99 | (A) 0.15; (B) >0.99 |
LTP defect (n) | 1 | 0 | 0 | 0 | (A) >0.99; (B) >0.99 | (A) 0.15; (B) >0.99 |
MFC defect (n) | 2 | 2 | 1 | 6 | (A) >0.99; (B) 0.07 | (A) 0.54; (B) 0.63 |
Trochlea defect (n) | 0 | 3 | 2 | 1 | (A) 0.20; (B) >0.99 | (A) 0.49; (B) 0.12 |
Multiple defects (n) | 1 | 0 | 1 | 1 | (A) >0.99; (B) >0.99 | (A) >0.99; (B) >0.99 |
Unknown defect location (n) | 1 | 1 | 4 | 2 | (A) >0.99; (B) 0.64 | (A) 0.60; (B) >0.99 |
Sample preparation and analysis using label-free proteomics
SF preparation and protein equalisation using ProteoMiner™
Mass spectrometry and label-free quantification
Pathway and network analysis of proteomic datasets
Validation of mass spectrometry using ELISA
Results
Differential abundance of proteins in responders versus non-responders to ACI
Differential abundance of proteins after controlled cartilage injury (Stage I versus Stage II)
Protein | Fold change | |
---|---|---|
Description | Accession | |
Perilipin-4 | Q96Q06 | –4.3 |
Syntaxin-7 | O15400 | –3.9 |
Fermitin family homolog 3 | Q86UX7 | –3.7 |
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | Q9Y3Z3 | –3.7 |
PDZ and LIM domain protein 1 | O00151 | –3.6 |
Sorting nexin-5 | Q9Y5X3 | –3.3 |
Neuroblast differentiation-associated protein AHNAK | Q09666 | –3.2 |
Signal recognition particle 14 kDa protein | P37108 | –3.0 |
Hyaluronan and proteoglycan link protein 3 | Q96S86 | –3.0 |
Heterogeneous nuclear ribonucleoprotein K | P61978 | –2.9 |
ATP-citrate synthase | P53396 | –2.9 |
Fatty acid-binding protein, epidermal | Q01469 | –2.8 |
60S ribosomal protein L12 | P30050 | –2.7 |
Fatty acid-binding protein, adipocyte | P15090 | –2.6 |
Insulin-like growth factor-binding protein 6 | P24592 | –2.6 |
Protein canopy homolog 3 | Q9BT09 | –2.6 |
Tripeptidyl-peptidase 1 | O14773 | –2.5 |
PDZ and LIM domain protein 3 | Q53GG5 | –2.5 |
Cellular nucleic acid-binding protein | P62633 | –2.5 |
Bifunctional glutamate/proline-tRNA ligase | P07814 | –2.5 |
Protein disulfide-isomerase A3 | P30101 | –2.4 |
Peroxiredoxin-6 | P30041 | –2.4 |
Tryptase alpha/beta-1 | Q15661 | –2.4 |
Endoplasmic reticulum resident protein 29 | P30040 | –2.4 |
Peroxiredoxin-1 | Q06830 | –2.4 |
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 | O14745 | –2.4 |
Mitochondrial import inner membrane translocase subunit TIM14 | Q96DA6 | –2.4 |
Mortality factor 4-like protein 1 | Q9UBU8 | –2.4 |
Fructose-bisphosphate aldolase A | P04075 | –2.3 |
Microtubule-associated protein RP/EB family member 1 | Q15691 | –2.3 |
Leucine zipper transcription factor-like protein 1 | Q9NQ48 | –2.3 |
Transcription elongation factor A protein 1 | P23193 | –2.3 |
2',3'-cyclic-nucleotide 3'-phosphodiesterase | P09543 | –2.3 |
Histamine N-methyltransferase | P50135 | –2.3 |
Protein S100-A13
| Q99584 | –2.3 |
Acrosomal protein SP-10 | P26436 | –2.2 |
AP-2 complex subunit beta | P63010 | –2.2 |
S-phase kinase-associated protein 1 | P63208 | –2.2 |
High mobility group protein B3 | O15347 | –2.2 |
Cytokine-like protein 1 | Q9NRR1 | –2.2 |
Mitochondrial fission 1 protein | Q9Y3D6 | –2.2 |
Filamin-A | P21333 | –2.2 |
Nuclear migration protein nudC | Q9Y266 | –2.1 |
Cathepsin K | P43235 | –2.1 |
Prostaglandin E synthase 3 | Q15185 | –2.1 |
Vinculin | P18206 | –2.1 |
Plastin-2 | P13796 | –2.1 |
Coronin-1C | Q9ULV4 | –2.1 |
Ig heavy chain V-I region V35 | P23083 | –2.1 |
Stress-induced-phosphoprotein 1 | P31948 | –2.1 |
Putative phospholipase B-like 2 | Q8NHP8 | –2.1 |
Gelsolin | P06396 | –2.0 |
Spectrin beta chain, erythrocytic | P11277 | –2.0 |
Stathmin | P16949 | –2.0 |
Hsc70-interacting protein | P50502 | –2.0 |
40S Ribosomal protein | P23396 | –2.0 |
Epidermal growth factor receptor substrate 15 | P42566 | 22.5 |
Hemoglobin subunit theta-1 | P09105 | 6.1 |
C-type lectin domain family 11 member A | Q9Y240 | 5.6 |
Periostin | Q15063 | 5.1 |
Collagen alpha-1(I) chain | P02452 | 4.7 |
Spectrin alpha chain, erythrocytic 1 | P02549 | 4.0 |
Collagen alpha-1(V) chain | P20908 | 3.7 |
Fibrinogen gamma chain | P02679 | 3.5 |
Collagen alpha-1(XII) chain | Q99715 | 3.3 |
Complement C1q tumor necrosis factor-related protein 3 | Q9BXJ4 | 3.1 |
Adiponectin | Q15848 | 3.0 |
Adipocyte enhancer-binding protein 1 | Q8IUX7 | 3.0 |
Latent-transforming growth factor beta-binding protein 1 | Q14766 | 3.0 |
Fibrinogen beta chain | P02675 | 3.0 |
Chondroitin sulfate proteoglycan 4 | Q6UVK1 | 2.9 |
Fibrinogen alpha chain | P02671 | 2.8 |
Interstitial collagenase (MMP1) | P03956 | 2.7 |
Secreted phosphoprotein 24 | Q13103 | 2.7 |
Collagen alpha-2(V) chain | P05997 | 2.6 |
Ferritin light chain | P02792 | 2.6 |
C4b-binding protein alpha chain | P04003 | 2.6 |
Nucleobindin-1 | Q02818 | 2.4 |
C4b-binding protein beta chain | P20851 | 2.2 |
Vitamin K-dependent protein S | P07225 | 2.2 |
Fibronectin | P02751 | 2.2 |
Prosaposin | P07602 | 2.1 |
Integrin beta-like protein 1 | O95965 | 2.1 |
Adipocyte plasma membrane-associated protein | Q9HDC9 | 2.1 |
Cytoplasmic dynein 1 heavy chain 1 | Q14204 | 2.0 |
Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D | A1L4H1 | 2.0 |
F-actin-capping protein subunit beta | P47756 | 2.0 |
Mannan-binding lectin serine protease 1 | P48740 | 2.0 |
Thrombospondin-3 | P49746 | 2.0 |
Protein | Fold change | |
---|---|---|
Description | Accession | |
Heat shock protein 75 kDa, mitochondrial | Q12931 | –470.0 |
Microtubule-associated protein 1B | P46821 | –17.2 |
Adenosylhomocysteinase | P23526 | –3.7 |
Complement factor H-related protein 3 | Q02985 | –2.8 |
Mannose-1-phosphate guanyltransferase beta | Q9Y5P6 | –2.7 |
Peroxiredoxin-4 | Q13162 | –2.5 |
Oxysterol-binding protein 1 | P22059 | –2.4 |
Protein canopy homolog 3 | Q9BT09 | –2.1 |
Spermatid perinuclear RNA-binding protein | Q96SI9 | –2.0 |
Ferritin light chain | P02792 | 2.2 |
Secreted phosphoprotein 24 | Q13103 | 2.2 |
Chondroitin sulfate proteoglycan 4 | Q6UVK1 | 2.3 |
Collagen alpha-2(I) chain | P08123 | 2.3 |
Collagen alpha-1(V) chain | P20908 | 2.5 |
26S protease regulatory subunit 6A | P17980 | 2.7 |
Collagen alpha-2(V) chain | P05997 | 2.9 |
Collagen alpha-1(I) chain | P02452 | 3.3 |
Spectrin alpha chain, erythrocytic 1 | P02549 | 4.1 |
Histidine triad nucleotide-binding protein 1 | P49773 | 4.2 |
Platelet factor 4 | P02776 | 4.2 |
Alpha-1-acid glycoprotein 2 | P19652 | 4.3 |
Protein 4.1 | P11171 | 4.3 |
Periostin | Q15063 | 4.5 |
26S proteasome non-ATPase regulatory subunit 13 | Q9UNM6 | 4.6 |
Identification of canonical pathways and protein networks associated with protein changes between Stage I and II
Upstream regulators | Activation z score (SII v SI) |
p value of overlap | Target molecules in dataset | |
---|---|---|---|---|
Non-responders | ||||
TGFB1 | –1.595 | 9.46E–10 | APOB,APOC2,APOE,CD44,COL1A1,COL1A2,COL5A1,COMP,CSPG4,CTSD,ECM1,FETUB,FN1,FTL,GSN,HINT1,HSPG2,HTRA1,IGFBP6,LCAT,MYLK,PCOLCE2,PDXK,POSTN,RAP1A,S100A4,TGFBI | |
DYSF | NP | 2.01E–09 | CFD,FN1,FTL,LCP1,LYZ,PROS1,S100-A13,S100A4 | |
MYC | 3.046 | 2.20E–09 | ALDOA,ANXA5,CCT3,CD44,COL1A1,COL1A2,COL5A1,CSPG4,CTSD,ECM1,FN1,HSPA9,LYZ,NCL,NUCB1,NUDC,PAM,PTN,RPL22,RPL30,TF | |
COL9A1 | 1.308 | 2.79E–09 | COMP,FN1,HSPG2,TGFBI,THBS4 | |
Beta-estradiol | 2.271 | 5.01E–09 | ALDOA,APOE,CD44,COL1A1,COL1A2,COMP,CTSD,F7,FN1,GMFB,HSPA2,HSPA8,HSPA9,HTRA1,IGFBP6,LTF,LYZ,MYLK,PAM,PDIA3,QSOX1,RAP1A,RPS13,S100-A13,SLC9A3R1,TF,THBS4 | |
Lipopolysaccharide | –0.104 | 5.96E–09 | ANXA5,APOB,APOC2,APOE,CD44,CFD,COL1A1,COL1A2,COL5A1,CSPG4,FN1,GSN,HDGFRP3,HMGB2,HSPA8,HTRA1,ITIH2,LBP,LTF,LYZ,PARK7,PCOLCE,PCOLCE2,PDIA3,PLG,TF | |
Dihydrotestosterone | –1.091 | 1.03E–08 | ALDOA,APOE,CCT3,FN1,FTL,GSN,HINT1,LYZ,MYLK,NUCB1,PAM,POSTN,PROS1,RPL30,TF | |
HRAS | 0.623 | 2.52E–08 | CD44,COL1A1,COL1A2,ERP29,FN1,GSN,HSPA8,HTRA1,LYZ,MYH10,PDIA5,PLTP,POSTN,RPL30,S100A4 | |
KRAS | 2.226 | 3.99E–08 | ALDOA,CD44,COL1A1,FN1,GBA,GSN,MYLK,PCOLCE,PDIA3,PSMA7,RNASE4,S100A4 | |
SMARCB1 | –1.195 | 4.82E–08 | APOC4,CD44,COL1A1,COL1A2,GSN,LBP,POSTN,PTN,RAB14 | |
Responders | ||||
CEBPB | –1.067 | 2.03E–07 | APOB,CFD,COL1A1,COL1A2,F7,HSPA8,PLG | |
FLI1 | NP | 3.82E–07 | COL1A1,COL1A2,HSPA8,PF4 | |
S-adenosylhomocysteine | NP | 1.21E–06 | COL1A1,COL1A2 | |
SCX | NP | 1.65E–06 | COL1A1,COMP,POSTN | |
Tgf beta (group) | –1.454 | 5.16E–06 | COL1A1,COL1A2,LCAT,POSTN,TGFBI | |
ENTPD5 | NP | 1.21E–05 | COL1A1,COL1A2 | |
MKX | NP | 1.21E–05 | COL1A1,COL1A2 | |
GATA4 | NP | 2.86E–05 | COL1A1,COL1A2,POSTN,TGFBI | |
Nilotinib | NP | 3.39E–05 | COL1A1,COL1A2 | |
TBX5 | NP | 5.50E–05 | COL1A1,COL1A2,POSTN |