Background
Methods
Menisci and articular cartilage specimens
Preparation and culture of meniscal cells
RNA extraction and microarrays
Real-time RT-PCR
Statistical Analysis
Results
Degeneration of menisci in OA patients
I | Cartilage Grade | # Subjects | Mean Age ± SD |
---|---|---|---|
0 | 1 F | 39 | |
0 | 1 F | 12 | |
0 | 1 M | 43 | |
2 | 3 F, 1 M | 62 ± 13 | |
3 | 6 F, 5 M | 64 ± 9 | |
4 | 15 F, 4 M | 62 ± 11 | |
5 | 12 F, 5 M | 67 ± 9 | |
II
|
Meniscus Grade
|
# Subjects
|
Mean Age ± SD
|
0 | 1 F | 39 | |
0 | 1 F | 12 | |
0 | 1 M | 43 | |
2 | 4 F, 3 M | 57 ± 12 | |
3 | 12 F, 6 M | 64 ± 9 | |
4 | 20 F, 6 M | 66 ± 9 |
Differential gene expression
Patients | Age/Gender/Diagnosis | Grade Meniscus |
---|---|---|
A | 39/F (osteosarcoma) | 0 |
B | 43/M (osteosarcoma) | 0 |
C | 12/F (osteosarcoma) | 0 |
1 | 65/F (OA patient) | 4 |
2 | 56/F (OA patient) | 4 |
3 | 50/F (OA patient) | 4 |
4 | 52/F (OA patient) | 4 |
5 | 61/M (OA patient) | 4 |
Biological process | Gene Name | Gene ID | Differ Exp (fold)* | Description |
---|---|---|---|---|
Immune response | ||||
HLA-DPA1 | M27487 | 5.3 | Major histocompatibility complex, class II, DP alpha 1 | |
IFI6 | NM_022873 | 2.0 | Interferon, alpha-inducible protein 6 | |
CFH | X04697 | 1.7 | Complement factor H | |
CTSS | NM_004079 | 1.6 | Cathepsin S | |
FYN | S74774 | 1.5 | FYN oncogene related to SRC, FGR, YES | |
ILF2 | NM_004515 | -1.3 | Interleukin enhancer binding factor 2, 45 kDa | |
PSMB9 | AI375915 | -1.2 | Proteasome (prosome, macropain) subunit, beta type, 9 | |
Inflammatory Response | ||||
ITGB2 | NM_000211 | 6.6 | Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) | |
CFH | X04697 | 1.7 | Complement factor H | |
BDKRB2 | NM_000623 | 1.3 | Bradykinin receptor B2 | |
Cytokine production | ||||
SRGN | NM_002727 | 2.8 | Serglycin | |
ARNT | AI768497 | 2.3 | Aryl hydrocarbon receptor nuclear translocator | |
INHBA | M13436 | 1.9 | Inhibin, beta A | |
Calcium ion transport | ||||
CACNA1C | F11066 | 1.5 | Calcium channel, voltage-dependent, L type, alpha 1C subunit | |
FYN | S74774 | 1.5 | FYN oncogene related to SRC, FGR, YES | |
CHRNB2 | NM_000748 | 1.4 | Cholinergic receptor, nicotinic, beta 2 (neuronal) | |
Biomineral formation | ||||
ENPP1 | BF057080 | 1.7 | Ectonucleotide pyrophosphatase/phosphodiesterase 1 | |
SRGN | NM_002727 | 2.8 | Serglycin | |
ACVR2A | AI149508 | 1.5 | Activin A receptor, type IIA | |
Cell proliferation | ||||
ITGB2 | NM_000211 | 6.6 | Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) | |
FGF7 | NM_002009 | 4.1 | Fibroblast growth factor 7 (keratinocyte growth factor) | |
ELN | AA479278 | 2.5 | Elastin (supravalvular aortic stenosis, Williams-Beuren syndrome) | |
IGFBP7 | NM_001553 | 2.4 | Insulin-like growth factor binding protein 7 | |
SKAP2 | AB014486 | 2.2 | Src kinase associated phosphoprotein 2 | |
ARNT | AI768497 | 2.3 | Aryl hydrocarbon receptor nuclear translocator | |
FOXO1 | NM_002015 | 1.5 | Forkhead box O1 | |
BCAT1 | AL390172 | 1.5 | Branched chain aminotransferase 1, cytosolic | |
ACVR2A | AI149508 | 1.5 | Activin A receptor, type IIA | |
TCF7L2 | AA664011 | 1.4 | Transcription factor 7-like 2 (T-cell specific, HMG-box) | |
CHRNB2 | NM_000748 | 1.4 | Cholinergic receptor, nicotinic, beta 2 (neuronal) | |
TCFL5 | NM_006602 | 1.2 | Transcription factor-like 5 (basic helix-loop-helix) | |
NRP1 | AA609131 | -1.3 | Neuropilin 1 | |
PHB | AL560017 | -1.3 | Prohibitin | |
TBX5 | NM_000192 | -1.3 | T-box 5 | |
NCK2 | BC000103 | -1.2 | NCK adaptor protein 2 | |
PRPF19 | NM_014502 | -1.2 | PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae) | |
Integrin-mediated signaling pathway | ||||
ITGB2 | NM_000211 | 6.6 | Integrin, beta 2 | |
ITGB8 | BF513121 | 3.6 | Integrin, beta 8 | |
ITGA11 | AF109681 | 1.5 | integrin, alpha 11 | |
GAB2 | NM_012296 | 1.5 | GRB2-associated binding protein 2 | |
Skeletal system/Tissue development | ||||
DSP | NM_004415 | 5.2 | Desmoplakin | |
FGF7 | NM_002009 | 4.2 | Fibroblast growth factor 7 (keratinocyte growth factor) | |
SRGN | NM_002727 | 2.8 | Serglycin | |
INHBA | M13436 | 1.9 | Inhibin, beta A | |
TIMP3 | AW338933 | 1.7 | TIMP metallopeptidase inhibitor 3 | |
ENPP1 | BF057080 | 1.7 | Ectonucleotide pyrophosphatase/phosphodiesterase 1 | |
COL5A1 | N30339 | 1.7 | Collagen, type V, alpha 1 | |
ACVR2A | AI149508 | 1.5 | Activin A receptor, type IIA | |
FBN1 | AW955612 | 1.4 | Fibrillin 1 | |
BARX1 | NM_021570N | -1.9 | BARX homeobox 1 | |
GABBR1 | NM_001470 | -1.9 | Gamma-aminobutyric acid (GABA) B receptor, 1 | |
HOXA11 | H94842 | -1.5 | Homeobox A11 | |
CHST11 | NM_018413 | -1.5 | Carbohydrate (chondroitin 4) sulfotransferase 11 | |
NSDHL | BC000245 | -1.4 | NAD(P) dependent steroid dehydrogenase-like | |
ZNRD1 | AF230337 | -1.3 | Zinc ribbon domain containing 1 | |
SMURF1 | AF199364 | -1.3 | SMAD specific E3 ubiquitin protein ligase 1 | |
DNA repair | ||||
ZSWIM7 | BE645222 | -1.6 | Zinc finger, SWIM-type containing 7 | |
WDR33 | AB044749 | -1.5 | WD repeat domain 33 | |
ASF1A | NM_014034 | -1.5 | ASF1 anti-silencing function 1 homolog A (S. cerevisiae) | |
ATM | U82828 | -1.3 | ataxia telangiectasia mutated | |
PMS2L1 | AI375694 | -1.3 | Postmeiotic segregation increased 2-like 1 | |
ALKBH2 | AI865555 | -1.2 | AlkB, alkylation repair homolog 2 (E. coli) | |
XRCC6 | NM_001469 | -1.2 | X-ray repair complementing defective repair in Chinese hamster cells 6 | |
DCLRE1A | D42045 | -1.2 | DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae) | |
PRPF19 | NM_014502 | -1.2 | PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae) | |
ELN | AA479278 | 2.5 | Elastin (supravalvular aortic stenosis, Williams-Beuren syndrome) | |
Cellular biosynthetic process | ||||
PITX2 | NM_000325 | -6.4 | Paired-like homeodomain 2 | |
NR3C2 | NM_000901 | -5.8 | Nuclear receptor subfamily 3, group C, member 2 | |
GALNT6 | AW014155 | -4.5 | Polypeptide N-acetylgalactosaminyltransferase 6 | |
RGMB | BE855765 | -2.7 | RGM domain family, member B | |
FOXF2 | NM_001452 | -2.2 | Forkhead box F2 | |
ZNF529 | AL109722 | -2.1 | Zinc finger protein 529 | |
BARX1 | NM_021570 | -1.9 | BARX homeobox 1 | |
DHODH | M94065 | -1.9 | Dihydroorotate dehydrogenase | |
LMO4 | BC003600 | -1.8 | LIM domain only 4 | |
BRWD1 | NM_018963 | -1.7 | Bromodomain and WD repeat domain containing 1 | |
TARS2 | NM_025150 | -1.7 | Threonyl-tRNA synthetase 2, mitochondrial (putative) | |
HLX | M60721 | -1.7 | H2.0-like homeobox | |
BNC2 | AI767962 | -1.7 | Basonuclin 2 | |
PGD | NM_002631 | -1.6 | Phosphogluconate dehydrogenase | |
MEIS1 | AL832770 | -1.6 | Meis homeobox 1 | |
ZNF420 | AI339586 | -1.6 | Zinc finger protein 420 | |
ZFP28 | AA831323 | -1.5 | Zinc finger protein 28 homolog (mouse) | |
CARS2 | NM_024537 | -1.5 | Cysteinyl-tRNA synthetase 2, mitochondrial (putative) | |
HOXA11 | H94842 | -1.5 | Homeobox A11 | |
PDLIM1 | BC000915 | 13.2 | PDZ and LIM domain 1 (elfin) | |
ITGB2 | NM_000211 | 6.6 | Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) | |
LMCD1 | NM_014583 | 3.5 | LIM and cysteine-rich domains 1 | |
KRT7 | BC002700 | 3.1 | Keratin 7 | |
ARNT | AI768497 | 2.3 | Aryl hydrocarbon receptor nuclear translocator | |
ZNF415 | NM_018355 | 2.2 | Zinc finger protein 415 | |
ZNF630 | AK000580 | 2.0 | Zinc finger protein 630 | |
INHBA | M13436 | 1.9 | Inhibin, beta A | |
GALNT1 | U41514 | 1.7 | Polypeptide N-acetylgalactosaminyltransferase 1 | |
ENPP1 | BF057080 | 1.7 | Ectonucleotide pyrophosphatase/phosphodiesterase 1 | |
Miscellaneous | ||||
PTGES | AF010316 | 3.2 | Prostaglandin E synthase | |
ADAMTS5 | NM_007038 | 1.7 | ADAM metallopeptidase with thrombospondin type 1 motif, 5 (aggrecanase-2) | |
DSP | NM_004415 | 5.2 | Desmoplakin | |
FMOD | NM_002023 | 2.7 | Fibromodulin | |
sFRP4 | AW089415 | 3.4 | Secreted frizzled-related protein 4 | |
MCAM | M28882 | 2.3 | Melanoma cell adhesion molecule | |
TNXB | NM_004381 | -1.3 | Tenascin XB | |
FUS | NM_004960 | -1.5 | Fusion (involved in t(12;16) in malignant liposarcoma) | |
TBX5 | NM_000192 | -1.3 | T-box 5 |
Gene Name | Gene ID | OA1 | OA1 | OA3 | OA4 | OA5 | Description |
---|---|---|---|---|---|---|---|
BST1 | NM_004334 | 3.9 | 3.4 | 3.3 | 1.6 | 2.2 | bone marrow stromal cell antigen 1 |
FGF9 | NM_002010 | 3.7 | 2.4 | 3.7 | 2.5 | 2.9 | Fibroblast growth factor 9 |
ACAN | NM_013227 | 2.4 | 1.6 | 1.6 | 0.0 | 1.6 | Aggrecan |
COL11A1 | J04177 | 0.0 | 11.5 | 5.8 | 2.2 | 3.6 | Collagen, type XI, alpha 1 |
ANKH | AL833238 | 0.0 | 1.8 | 1.7 | 1.5 | 1.8 | Ankylosis, progressive homolog (mouse) |
MGP | NM_000900 | 11.8 | 4.7 | 21.6 | 0.0 | 17.6 | Matrix Gla protein |
TUFT1 | NM_020127 | 2.8 | 2.7 | 1.9 | 0.0 | 0.0 | Tuftelin 1 |
TFIP11 | NM_012143 | 2.2 | 1.6 | 0.0 | 0.0 | 0.0 | Tuftelin interacting protein 11 |
IL20RB | AL578102 | 2.3 | 2.7 | 0.0 | 2.6 | 7.8 | Interleukin 20 receptor beta |
IL26 | NM_018402 | 1.7 | 1.6 | 1.6 | 0.0 | 3.0 | Interleukin 26 |
COL4A5 | AW052179 | -3.1 | -3.0 | -3.1 | -3.0 | -3.1 | Collagen, type IV, alpha 5 (Alport syndrome) |
MMP9 | NM_004994 | -2.2 | -2.1 | -2.1 | 0.0 | -2.2 | Matrix metallopeptidase 9 |
MMP10 | NM_002425 | -2.7 | -2.6 | -2.7 | -1.5 | -2.6 | Matrix metallopeptidase 10 |
MMP12 | NM_002426 | -2.1 | -2.0 | -2.1 | 0.0 | -2.1 | Matrix metallopeptidase 12 |
FZD10 | NM_007197 | -1.6 | -1.5 | -1.6 | -1.5 | -1.5 | Frizzled homolog 10 (Drosophila) |
CYTL1 | NM_018659 | -2.6 | -2.6 | -2.6 | -2.6 | -2.5 | Cytokine-like 1 |
CHODL | NM_024944 | -2.6 | -2.6 | -2.6 | -2.6 | Chondrolectin |
Validation of differential expression of selected genes
Gene name | Gene ID | Differential Expression* Microarray | Differential Expression* RT-PCR | Description |
---|---|---|---|---|
HLA-DPA1 | M27487 | 5.3 | 10.5 | Major histocompatibility complex, class II, DP alpha |
ITGB2 | NM_000211 | 6.6 | 5.2 | Integrin, beta 2 |
PTGES | AF010316 | 3.2 | 3.4 | Prostaglandin E synthase |
ENPP1 | BF057080 | 1.7 | 2.1 | Ectonucleotide pyrophosphatase/phosphodiesterase 1 |
ADAMTS5 | BI254089 | 1.7 | 1.9 | ADAM metallopeptidase with thrombospondin type 1 motif, 5 |
IL26 | NM_018402 | 1.7 | 4.3 | Interleukin 26 |
TUFT1 | NM_020127 | 2.8 | 3.9 | Matrix metalloproteinase 1 |
MMP10 | NM_002425 | -2.7 | -3.1 | Matrix metalloproteinase 10 |