Characterization of the Cartilage DNA Methylome in Knee and Hip Osteoarthritis

Abstract

ObjectiveThe aim of this study was to characterize the genome-wide DNA methylation profile of chondrocytes from knee and hip cartilage obtained from patients with osteoarthritis (OA) and hip cartilage obtained from patients with femoral neck fracture, providing the first comparison of DNA methylation between OA and non-OA hip cartilage, and between OA hip and OA knee cartilage.MethodsThe study was performed using the Illumina Infinium HumanMethylation450 BeadChip array, which allows the annotation of ∼480,000 CpG sites. Genome-wide methylation was assessed in chondrocyte DNA extracted from 23 hip OA patients, 73 knee OA patients, and 21 healthy hip control patients with femoral neck fracture.ResultsAnalysis revealed that chondrocytes from the hip cartilage of OA patients and healthy controls have unique methylation profiles, with 5,322 differentially methylated loci (DMLs) identified between the 2 groups. In addition, a comparison between hip and knee OA chondrocytes revealed 5,547 DMLs between the 2 groups, including DMLs in several genes known to be involved in the pathogenesis of OA. Hip OA samples were found to cluster into 2 groups. A total of 15,239 DMLs were identified between the 2 clusters, with an enrichment of genes involved in inflammation and immunity. Similarly, we confirmed a previous report of knee OA samples that also clustered into 2 groups.ConclusionWe demonstrated that global DNA methylation using a high-density array can be a powerful tool in the characterization of OA at the molecular level. Identification of pathways enriched in DMLs between OA and OA-free cartilage highlight potential etiologic mechanisms that are involved in the initiation and/or progression of the disease and that could be therapeutically targeted.

Cartilage damage in osteoarthritis and rheumatoid arthritis—two unequal siblings

“…In a comparison of hip cartilage from patients with OA and unaffected controls, 5,322 dif ferentially methylated loci were identified. 83 Interestingly, the hipOA samples clustered into two groups, with a total of 15,239 differentially methylated loci between them, including genes involved in inflammation and immu nity. 83 In another study, 1,214 differentially methylated genetic targets were identified in a comparison of paired samples of knee cartilage showing mild or severe OA.…”

“…83 Interestingly, the hipOA samples clustered into two groups, with a total of 15,239 differentially methylated loci between them, including genes involved in inflammation and immu nity. 83 In another study, 1,214 differentially methylated genetic targets were identified in a comparison of paired samples of knee cartilage showing mild or severe OA. 84 A number of the identified genes were related to devel opmental and celldifferentiation pathways, supporting the proposed involvement of these mechanisms in OA.…”

DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism

“…DNMT1, however, is largely responsible for maintaining the DNA methylation signatures created by these de novo enzymes during cell division. Recent genome-wide methylation profiling studies have identified differentially methylated loci in the genome of human OA chondrocytes, thereby suggesting the involvement of DNMT-driven mechanisms in the development and/or progression of OA (18,(22)(23)(24)(25)(26). This study was designed to address the potential role of the de novo Dnmt3 enzymes in regulating murine articular cartilage homeostasis.…”

Impact of human platelet lysate on the expansion and chondrogenic capacity of cultured human chondrocytes for cartilage cell therapy

“…mRNA was reverse-transcribed in a Progene thermocycler (Techne, Staffordshire, UK) using a high-capacity cDNA reverse transcription kit (4368814; Applied Biosystems) following the manufacturer's instructions. qRT-PCR was performed on three pellet replicates (from each patient) to determine gene expression relative to two reference genes, according to published guidelines (Bustin et al, 2009): hypoxanthine-guanine phosphoribosyltransferase-1 (HPRT1 human; RT00059066) (Foldager et al, 2009;Rushton et al, 2014) and TATA box-binding protein (TBP; QT00000721) (Foldager et al, 2009;PomboSuarez et al, 2008) were selected based on low coefficiencies of variance across both supplement types (data not shown). Several genes (Table 1) were chosen to determine the chondrogenic phenotype after redifferentiation.…”