Cindy Boer

40 | Chapter 1.2 Table 1: Summary of Epigenomewide Studies of DNA Methylation in Osteoporosis and Osteoarthritis Joint trait # and type of samples Tissue/Cell type Adjustments Technique Results Pathway enrichment Ref. Knee/hip OA 24 intact vs damaged Cartilage No 450K array 550 DMS SMAD3, angiogenesis, inflammation [46] Knee/hip OA 31 intact vs damaged Cartilage Sex, age, BMI, disease status 450K array 6272 DMS, 357 DMR Skeletal development [45] Knee/hip OA Intact vs damaged 12 discovery, 26 repli- cation Cartilage No 450K array 9896 DMS, 271 DMR Skeletal system develop- ment [43] Knee and hip OA and neo- cartilage 12 cartilage vs 8 neo- cartilage from MSCs Cartilage No 450K array 5706 DMS Developmental and transcription regulation processes [51] Knee OA 5 intact vs damaged Cartilage No Agilent Promoter array 1214 promo- ters Development, TGFbeta‐, MAPK, hedgehog [47] Knee OA 10 intact vs damaged Cartilage No RRBS >1000 DMRs Embryogenesis and skele- tal development [44] Knee OA pro- gression 12 early vs interm; early vs late Cartilage Sub- chondral bone No 450K array 0;519 DMS 72;397 DMS Skeletal system devel- opment Morphogenesis, skeletal development, HOX [142] Knee OA and controls 18 controls vs 23 OA Cartilage No 27K array 91 DMS Inflammation, transcrip- tion activity, phosphoryla- tion, MAPK [50] Knee OA and controls 11 controls vs 12 OA Cartilage Sex, BMI (age) 450K array 929 DMS (0 after age adjustment) Integrin, Wnt, FGF [143] Knee OA and controls 4 TKR vs 4 controls Chondrocytes No MeDIP seq 70,591 DhMR Many, including Wnt, bone remodeling, inflammation [144]