Table 1: Methylation analysis of individual loci in osteoarthritis.

Gene Cell Samples Methylation levels Gene expression Strategies for DNA methylation analysis Ref.
ECM
COL2A1 Human chondrocytes AC of the knee with no abnormalities L ↓ Restriction enzyme-based method and DNA bisulfite sequencing [18]
MSC on chondrogenesis L ↑
OA chondrocytes THR vs. #NOF L ↑ Bisulfite pyrosequencing [19]
COL9A1 OA chondrocytes THR vs. #NOF H ↓ Bisulfite pyrosequencing [19]
COL10A1 Human chondrocytes No cartilage abnormalities H ↓ Restriction enzyme-based method and DNA bisulfite sequencing [18]
MSC on chondrogenesis L ↑
ACAN OA chondrocytes Not specified L - [20]
Proteases
MMP3 OA chondrocytes THR vs. #NOF L - Restriction enzyme-based method [21]
MMP9 OA chondrocytes THR vs. #NOF L - Restriction enzyme-based method [21]
MMP13 OA chondrocytes THR vs. #NOF L - Restriction enzyme-based method [21]
OA chondrocytes THR vs. #NOF L ↑ Bisulfite pyrosequencing [22]
OA chondrocytes THR vs. #NOF L ↑ Bisulfite sequencing and pyrosequencing [23]
ADAMTS4 OA chondrocytes THR vs. #NOF L - Restriction enzyme-based method [21]
THR vs. #NOF L ↑ Restriction enzyme-based method [24]
Inflammation
IL1B Human chondrocytesa THR vs. #NOF L ↑ Restriction enzyme-based method [25]
OA chondrocytes THR vs. #NOF L ↑ Bisulfite pyrosequencing [22]
IL8 OA chondrocytes THR vs. #NOF L ↑ Bisulfite pyrosequencing [27]
SOCS2 OA chondrocytes THR vs. #NOF L ↓ Bisulfite pyrosequencing [29]
LEP Min OA and normal chondrocytes THR and TKR vs. Normal chondrocytes H ↓ DNA bisulfite sequencing [31]
Max OA chondrocytes L ↑
ROS-related
SOD2 OA chondrocytes THR vs. #NOF H ↓ DNA bisulfite sequencing [33]
iNOS OA chondrocytes THR vs. #NOF L ↑ Bisulfite sequencing or pyrosequencing. [34]
Chondrogenesis
SOX9 MSC on chondrogenesis Synovium–derived MSC L ↑ DNA bisulfite sequencing [39]
OA chondrocytes THR vs. #NOF H ↓ Methylation-specific PCR and bisulfite sequencing [40]
SOX4 Synovium-derived MSC L ↓ DNA bisulfite sequencing [39]
RUNX2 MSC on chondrogenesis Synovium-derived MSC L ↑ DNA bisulfite sequencing [39]
Growth factors
BMP7 Human aged chondrocytes Knee tissue donors H ↓ Methylation specific PCR [42]
SOST OA chondrocytes TKR vs. Knee fracture L ↑ Methylation-specific PCR and bisulfite sequencing [45]
GDF5 Human chondrocytes CH8 cell line L ↑ Bisulfite pyrosequencing [49]
Other
p21WAF1/CIP1 OA chondrocytes TKR vs. Normal human femoral condyles L ↓ DNA bisulfite sequencing [51]
DIO2 OA chondrocytes THR/TKR vs. Preserved chondrocytes H ↑ MALDI-TOF mass spectrometry [55]

L: Low; H: High; ECM: Extracellular Matrix; AC: Articular Cartilage; MSC: Mesenchymal Stem Cells; THR: Total Hip Replacement; TKR: Total Knee Replacement; #NOF: Fracture of the Neck Of Femur; aExposed to IL-1β and TNF-α; ROS: Reactive Oxygen Species.