Introduction
Materials and methods
Materials
Isolation and culture of chondrocytes
Phosphorothioate ODNs
Treatment groups
RNA Isolation
Microarray and pathway analysis
Pathway analysis and classification by gene ontology
Validation experiments -quantitative real time PCR
Primer | Orientation | Sequence | Annealing temp and time | Accession no. |
---|---|---|---|---|
18SrRNA
| Qiagen QuantiTect Primer Assay | 62°C, 40 sec | [GenBank:X03205] | |
β-actin
| Forward | 5'-TCCATCATGAAGTGTGACGTGGAC-3' | 62°C, 40 sec | [GenBank:NM_001101] |
Reverse | 5'-TTGATCTTCATTGTGCTGGGTGCC-3' | |||
BMP-2
| Qiagen QuantiTect Primer Assay | 60°C, 40 sec | [GenBank::NM_001200] | |
GAPDH
| Forward | 5'-TGGACTCCACGACGTACTCAG-3' | 62°C, 40 sec | [GenBank:NM_002046] |
Reverse | 5'-CGGGAAGCTTGTCATCAATGGAA-3' | |||
Gremlin-1
| Forward | 5'-ATACCTGAAGCGAGACTGGTGCAA-3' | 64°C, 40 sec | [GenBank:NM_013372] |
Reverse | 5'-AACAGAAGCGGTTGATGATGGTGC-3' | |||
IL-6
| Forward | 5'-GTCAATTCGTTCTGAAGAGGTGAGT-3' | 64°C, 40 sec | [GenBank:NM_000600] |
Reverse | 5'-CCCCAGGAGAAGATTCCAAAGATG-3' | |||
IL-8
| Forward | 5'-AGACATACTCCAAACCTTTCCACCC-3' | 58°C, 30 sec | [GenBank:NM_000584] |
Reverse | 5'-ATTTCTGTGTTGGCGCAGTGTGGT-3' | |||
LIF-1
| Forward | 5'-TAAGGAGGCCTCGCAGGATGTC-3' | 64°C, 30 sec | [GenBank:NM_002309] |
Reverse | 5'-TAGTCGTGTACCTTGGCACCTC-3' |
Statistical analysis for real-time
Results
Microarray analysis: overview of data
Analysis of catabolic genes: cytokines and their regulators
Gene | rhOP-1 vs Cntr | OP-1AS vs Cntr | |
---|---|---|---|
fold change | fold change | Accession no. | |
LIF
| 15.86↓ | 2.26↑ | [GenBank:NM_002309] |
IL-11
| 8.69↓ | 1.82↑ | [GenBank:NM_000641] |
IL-8
| 4.01↓ | 1.80↑ | [GenBank:NM_000584] |
IL-6
| 2.09↓ | 1.60↑ | [GenBank:NM_000600] |
IL-5Rα
| 2.47↑ | 2.40↑ | [GenBank:NM_000564] |
TNF-α induced protein 6
| 2.14↓ | [GenBank:NM_007115] | |
TNF-α induced protein-3
| 2.02↓ | 1.60↑ | [GenBank:NM_006290] |
TNF-R12
| 1.79↓ | [GenBank:NM_016639] | |
TNF-R9
| 1.73↓ | 1.57↓ | [GenBank:NM_001561] |
TNF-R5
| 1.88↑ | [GenBank:NM_001250] | |
TNF-13
| 1.69↓ | [GenBank:NM_003808] | |
IL1-R1
| 1.59↓ | [GenBank:NM_000877] | |
TNF-R11B (osteoprotegerin)
| 1.58↓ | [GenBank:NM_002546] | |
IL-13Rα1
| 1.55↓ | [GenBank:NM_001560] | |
IL-12β
| 1.74↓ | [GenBank:NM_002187] | |
IL-1R accessory protein-like 1
| 1.64↓ | [GenBank:NM_014271] | |
TNF-R6
| 2.08↓ | [GenBank:NM_000043] |
rhOP-1 vs Cntr | OP-1AS vs Cntr | ||
---|---|---|---|
fold change | fold change | Accession no. | |
Genes from IL-6 signaling pathway
| |||
ELK-1
| 1.89↓ | [GenBank:NM_005229] | |
IL-6
| 2.09↓ | 1.60↑ | [GenBank:NM_000600] |
IL-6R
| 1.81↓ | [GenBank:NM_000565] | |
IL-6 signal transducer (oncostatin M receptor) | 1.63↓ | [GenBank:NM_002184] | |
STAT1
| 2.42↓ | [GenBank:NM_007315] | |
NFκBIα
| 1.86↓ | 1.58↑ | [GenBank:NM_020529] |
Protein inhibitor of activated STAT3
| 1.84↓ | [GenBank:NM_006099] | |
STAT6
| 1.53↓ | [GenBank:NM_003153] | |
MAP 3 kinase 7
| 1.67↓ | [GenBank:NM_003188] | |
MAPK 14
| 1.52↓ | [GenBank:L35253] | |
MAPK1
| 1.55↓ |
Analysis of catabolic genes. Neuromediators
rhOP-1 vs Cntr | OP-1AS vs Cntr | ||
---|---|---|---|
fold change | fold change | Accession no. | |
Bradykinin Rβ1 | 1.85↓ | 1.59↑ | [GenBank:NM_000710] |
Bradykinin Rβ2 | 1.68↓ | [GenBank:NM_000623] | |
Tachykinin R1 | 1.64↓ | [GenBank:NM_001058] | |
Nerve growth factor-β | 1.93↓ | [GenBank:NM_002506] | |
Tachykinin1 precursor (Substance K, Substance P) | 2.26↓ |
Analysis of catabolic genes: Transcription factors
rhOP-1 vs Cntr | rhOP-1AS vs Cntr | ||
---|---|---|---|
fold change | fold change | Accession no. | |
Transcription factor 8 (represses IL-2 expression) | 3.28↓ | 2.97↓ | [GenBank:NM_030751] |
NF-κB2
| 2.77↓ | [GenBank:NM_002502] | |
STAT1
| 2.42↓ | [GenBank:NM_007315] | |
Transcription factor AP-2α | 2.07↓ | 1.52↓ | [GenBank:NM_003220] |
Suppression of tumorigenicity | 2.04↓ | 2.20↓ | [GenBank:NM_013437] |
Runx1
| 1.89↓ | 1.64↓ | [GenBank:NM_001754] |
NFκBIα
| 1.86↓ | 1.58↑ | [GenBank:NM_020529] |
NFYβ
| 1.68↓ | 1.75↓ | [GenBank:NM_006166] |
Activating transcription factor 7 | 1.66↓ | [GenBank:NM_006856] | |
MADS box transcription enhancer factor 2-d | 1.65↓ | [GenBank:NM_005920] | |
Upstream transcription factor 2, c-fos interacting | 1.58↓ | [GenBank:NM_003367] | |
Transcription factor (p38 interacting protein) | 1.57↓ | [GenBank:NM_017569] | |
MADS box transcription enhancer factor 2-C | 1.60↑ | 1.94↓ | [GenBank:NM_002397] |
Protein inhibitor of activated STAT3 | 1.84↓ | [GenBank:NM_006099] | |
Ubiquitin-like 1 (sentrin) | 1.60↓ | [GenBank:NM_003352] | |
STAT6
| 1.53↓ | [GenBank:NM_003153] |
Analysis of catabolic genes: Matrix degrading proteases, cathepsins, and apoptosis-related genes
rhOP-1 vs Cntr | rhOP-1AS vs Cntr | ||
---|---|---|---|
fold change | fold change | Accession no. | |
Bcl-2
| 2.45↓ | [GenBank:NM_001191] | |
Caspase 4, apoptosis-related cysteine protease | 2.11↓ | 1.59↓ | [GenBank:NM_001225] |
Programmed cell death 8 (apoptosis-inducing factor) | 1.70↓ | [GenBank:NM_004208] | |
Calpain 9 | 1.55↓ | [GenBank:NM_006615] | |
Caspase 6 | 2.18↓ | [GenBank:NM_001226] | |
Caspase 8 | 1.82↓ | [GenBank:NM_001228] | |
Caspase 2 | 1.50↑ | [GenBank:NM_001224] | |
MMPs and inhibitors
| |||
TIMP-3
| 2.06↓ | [GenBank:NM_000362] | |
MMP-14
| 1.55↓ | [GenBank:NM_004995] | |
MMP-2
| 2.31↓ | [GenBank:NM_004530] | |
TIMP-4
| 1.69↓ | [GenBank:NM_003256] | |
MMP-9
| 1.50↓ | [GenBank:NM_004994] | |
ADAM and ADAMTS
| |||
ADAM-19
| 1.83↓ | [GenBank:NM_023038] | |
ADAM-15
| 1.51↓ | [GenBank:NM_003815] | |
ADAMTS-12
| 1.88↑ | 2.03↑ | [GenBank:NM_030955] |
ADAMTS-7
| 1.58↑ | [GenBank:NM_014272] | |
ADAM-10
| 2.34↓ | [GenBank:NM_001110] | |
ADAM-28
| 1.63↓ | [GenBank:NM_014265] | |
ADAM-9
| 1.61↓ | [GenBank:NM_003816] | |
ADAM-7
| 1.56↑ | [GenBank:NM_003817] | |
Cathepsins
| |||
Cathepsin B | 2.14↓ | [GenBank:NM_001908] | |
Cathepsin C | 1.75↓ | [GenBank:NM_001814] | |
Cathepsin S | 1.75↓ | [GenBank:NM_004079] | |
Other proteases
| |||
Transglutaminase 2 | 2.10↓ | [GenBank:NM_004613] | |
Plasminogen activator-urokinase | 1.57↓ | [GenBank:NM_002658] | |
Tissue Plasminogen Activator | 1.56↑ | [GenBank:NM_000930] |
Analysis of anabolic genes: transforming growth factor-beta (TGF-β)/BMP family, their receptors and regulators of signaling
rhOP-1 vs Cntr | rhOP-1AS vs Cntr | ||
---|---|---|---|
fold change | fold change | Accession no. | |
GDF-15
| 3.04↓ | 2.03↑ | [GenBank:NM_004864] |
BMP-2
| 2.67↓ | [GenBank:NM_001200] | |
Inhibin-βa (activin A) | 2.32↓ | 2.15↑ | [GenBank:NM_002192] |
BMP-2 inducible kinase | 1.61↓ | [GenBank:NM_017593] | |
Parathyroid hormone-like hormone | 1.60↓ | 2.17↑ | [GenBank:NM_002820] |
ID2
| 2.32↓ | [GenBank:NM_002166] | |
Notch 4
| 2.32↓ | [GenBank:NM_004557] | |
MAD-6
| 2.05↓ | [GenBank:NM_005585] | |
Gremlin
| 1.88↑ | 1.94↓ | [GenBank:NM_013372] |
GDF-10
| 1.86↓ | [GenBank:NM_004962] | |
ID4
| 1.82↑ | 1.84↓ | [GenBank:NM_001546] |
ID3
| 1.73↓ | [GenBank:NM_002167] | |
MAD interacting protein | 1.69↓ | [GenBank:NM_004799] | |
MAD-4
| 1.67↓ | [GenBank:NM_005359] | |
Notch 1
| 1.65↓ | [GenBank:NM_017617] | |
MAD-7
| 1.62↓ | [GenBank:NM_005904] | |
TGF-α
| 1.54↓ | ||
Receptors
| |||
Frizzled homolog 10 (Drosophila) | 1.57↓ | [GenBank:NM_007197] | |
Activin-α RI
| 1.53↓ | [GenBank:NM_001105] | |
Activin A-RIIB
| 2.42↓ | [GenBank:NM_001106] | |
BMPR1A
| 1.83↓ | [GenBank:NM_004329] | |
TGF-βRI
| 1.51↓ | [GenBank:NM_004612] | |
TGF-βRIII
| 1.50↓ | [GenBank:NM_003243] | |
TGF-β R2
| 1.58↑ | [GenBank:NM_003242] | |
Activin A-RIB
| 1.53↑ | [GenBank:NM_004302] | |
Bone formation
| |||
Osteomodulin | 1.78↑ | 2.56↓ | [GenBank:NM_005014] |
Analysis of anabolic genes: other growth factors
rhOP-1 vs Cntr | OP-1AS vs Cntr | |
---|---|---|
fold change | fold change | |
IGF-BP1
| 2.17↓ | |
Nerve growth factor-β | 1.93↓ | |
VEGF-β
| 1.62↓ | 1.50↓ |
Endothelial cell growth factor 1 (platelet-derived) | 1.56↓ | |
VEGF
| 1.52↓ | |
Capillary morphogenesis protein 1 | 1.52↓ | |
FGF-7
| 2.87↓ | |
FGF-R2
| 1.69↑ | 2.83↓ |
IGF-BP5
| 1.90↓ | |
FGF-R3
| 1.87↑ | 1.80↓ |
IGF-1R
| 1.73↓ | |
PDGF-Rα
| 1.62↑ | 1.70↓ |
PDGF-Rβ
| 1.68↓ | |
IGF-BP7
| 1.58↓ | |
IRS2 (insulin receptor substrate 2) | 2.10↓ | 1.70↑ |
DPYSL2 (dihydropyrimidinase-like 2) | 1.60↑ | 1.60↓ |
MET (hepatocyte growth factor receptor) | 1.70↓ | 1.60↑ |
SPRY2: sprouty homolog 2 (Drosophila) | 1.60↓ | 1.60↑ |
SORBS1: sorbin and SH3 domain containing 1 | 1.70↑ | 1.50↓ |
PIK3R1 (Phosphoinositide-3-kinase, regulatory subunit 1) | 1.72↑ | |
MAP2K2 (mitogen-activated protein kinase kinase 2) | 1.61↑ | |
PDE3B (phosphodiesterase 3B, cGMP-inhibited) | 2.00↑ | |
SOCS3 (suppressor of cytokine signaling 3) | 1.79↑ |
Matrix proteins and their receptors
rhOP-1 vs Cntr | OP-1AS vs Cntr | ||
---|---|---|---|
fold change | fold change | Accession no. | |
Matrix proteins
| |||
Collagen IV-α3 | 1.82↓ | 1.54↓ | [GenBank:NM_000091] |
Laminin-β1 | 1.65↓ | 3.38↓ | [GenBank:NM_002291] |
Chondroitin sulfate PG6 (bamacan) | 1.60↓ | 1.52↑ | [GenBank:NM_005445] |
Versican (chondroitin sulfate PG2) | 2.98↓ | [GenBank:NM_004385] | |
Collagen I-α1 | 2.63↓ | [GenBank:NM_000088] | |
Collagen XIV-α1 | 2.59↓ | [GenBank:NM_021110] | |
Collagen I-α2 | 2.57↓ | [GenBank:NM_000089] | |
Cartilage associated protein | 2.13↓ | [GenBank:NM_006371] | |
Cadherin 11 (OB-cadherin (osteoblast)) | 2.03↓ | [GenBank:NM_001797] | |
Collagen XVI-α1 | 2.00↓ | [GenBank:NM_001856] | |
Dermatan Sulfate PG3 | 1.57↑ | 1.95↓ | [GenBank:NM_004950] |
Collagen V-α1 | 1.89↓ | [GenBank:NM_000093] | |
Bone sialoprotein | 1.83↓ | [GenBank:NM_004967] | |
Collagen VIII-α2 | 1.73↓ | [GenBank:NM_005202] | |
Collagen VI-α1 | 1.70↓ | [GenBank:NM_001848] | |
Collagen IV-α1 | 1.70↓ | [GenBank:NM_001845] | |
Collagen IV-α2 | 1.69↓ | [GenBank:NM_001846] | |
Syndecan | 1.58↑ | 1.67↓ | [GenBank:NM_002997] |
Collagen V-α2 | 1.65↓ | [GenBank:NM_000393] | |
Osteonectin | 1.51↓ | [GenBank:NM_003118] | |
Cadherin 19 | 1.50↓ | [GenBank:NM_021153] | |
Collagen IX-α3 | 1.59↑ | [GenBank:NM_001853] | |
Cadherin | 1.54↑ | [GenBank:NM_001408] | |
COMP | 1.52↑ | [GenBank:NM_000095] | |
Collagen IV-α5 | 1.89↑ | [GenBank:NM_000495] | |
Chondroitin sulfate PG4 | 1.64↑ | [GenBank:NM_001897] | |
Matrix protein receptors
| |||
HAS2
| 1.78↓ | [GenBank:NM_005328] | |
CD44
| 2.34↓ | [GenBank:NM_000610] | |
Integrins
| |||
Integrin-α5 | 1.77↓ | [GenBank:NM_002205] | |
Integrin-β4 | 1.64↓ | [GenBank:AF011375] | |
Integrin-α6 | 2.34↓ | [GenBank:NM_000210] | |
Integrin-β-like 1 | 2.07↓ | [GenBank:NM_004791] | |
Integrin-β3 | 1.72↓ | [GenBank:NM_000212] | |
Integrin-αE | 1.70↓ | [GenBank:NM_002208] |