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Genome-wide promoter methylation analysis of human osteoarthritis

ABSTRACT: Osteoarthritis (OA) is a chronic disease of the joint characterized by a progressive degradation of articular cartilage and subchondral bone. In healthy tissue, specialized cells called chondrocytes are regulating a balanced cartilage catabolism and anabolism. By contrast osteoarthritic joints are characterized by a dramatic increase of cartilage catabolism, due to changes of gene expression patterns within chondrocytes. To identify potential epigenetic differences regulating this process a genome-wide methylation screening of paired unaffected and osteoarthritic knee cartilage samples was performed. Therefore samples of macroscopic arthritic and non-arthritic cartilage areas of the femoral condyle of five female patients were collected and DNA isolation was performed. For being able to investigate methylation changes on a genome-wide scale using only limited amounts of DNA a specific amplification protocol for mainly methylated DNA has been established, based on combinations of different methylation-sensitive and –independent restriction digestions. The amplified DNA was then labeled and hybridized onto Agilent “Human Promoter Whole Genome” microarrays. A random variance t-test for paired (per patient) samples was performed, identifying 1214 differentially methylated genetic targets between arthritic and non-arthritic samples. The biological relevance of these genes was then further investigated via Gene Ontology (GO) and KEGG pathway analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE48422 | GEO | 2014/07/01

SECONDARY ACCESSION(S): PRJNA209998

REPOSITORIES: GEO

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Genome-wide promoter methylation analysis of human osteoarthritis

Project description:Osteoarthritis (OA) is a chronic disease of the joint characterized by a progressive degradation of articular cartilage and subchondral bone. In healthy tissue, specialized cells called chondrocytes are regulating a balanced cartilage catabolism and anabolism. By contrast osteoarthritic joints are characterized by a dramatic increase of cartilage catabolism, due to changes of gene expression patterns within chondrocytes. To identify potential epigenetic differences regulating this process a genome-wide methylation screening of paired unaffected and osteoarthritic knee cartilage samples was performed. Therefore samples of macroscopic arthritic and non-arthritic cartilage areas of the femoral condyle of five female patients were collected and DNA isolation was performed. For being able to investigate methylation changes on a genome-wide scale using only limited amounts of DNA a specific amplification protocol for mainly methylated DNA has been established, based on combinations of different methylation-sensitive and M-bM-^@M-^Sindependent restriction digestions. The amplified DNA was then labeled and hybridized onto Agilent M-bM-^@M-^\Human Promoter Whole GenomeM-bM-^@M-^] microarrays. A random variance t-test for paired (per patient) samples was performed, identifying 1214 differentially methylated genetic targets between arthritic and non-arthritic samples. The biological relevance of these genes was then further investigated via Gene Ontology (GO) and KEGG pathway analysis. DNA isolated of paired arthritic and non-arthritic knee cartilage samples of five different female osteoarthritis patients (10 samples) was methylation-specifically amplified using combinations of methylation-sensitive and -insensitive restriction enzymes. Amplicons were dye labeled (Cy3) and hybridized onto 2x244k Agilent Human Promoter microarrays.

2014-07-01 | E-GEOD-48422 | biostudies-arrayexpress

Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (methylation)

Project description:The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. Genome wide DNA methylation profiling of normal and osteoarthritic samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in cartilage knee samples. Samples included 18 healthy controls and 23 OA patients.

2013-04-01 | GSE43269 | GEO

Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (methylation)

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Genome-wide DNA methylation study of hip and knee osteoarthritic and healthy cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis

Project description:Cartilage samples were collected from hip or knee joint replacement patients either due to primary OA or hip fractures as controls. DNA was extracted from the collected cartilage and assayed by Illumina Infinium HumanMethylation450 âBeadChip array, which allows for the analysis of >480,000 CpG sites. Bisulphite converted DNA from 5 hip osteoarthritic, 6 knee osteoarthritic and 7 hip healhty cartilage samples were hybridised to the Illumina Infinium HumanMethylation450 âBeadChip array

2016-07-01 | E-GEOD-73626 | biostudies-arrayexpress

Characterization of the cartilage DNA methylome in knee and hip osteoarthritis.

Project description:The aim of this study was to characterise the genome-wide DNA methylation profile of osteoathritis (OA) chondrocytes from both knee and hip cartilage, providing the first comparison of DNA methylation between OA and non-OA hip cartilage, and between OA hip and OA knee cartilage. The study was performed using the Illumina Infinium HumanMethylation450 BeadChip array. Genome-wide methylation was assesed in chondrocyte DNA extracted from 23 OA hip, 73 OA knee and 21 healthy hip controls (NOF - neck of femure samples). Keywords: Methylation profiling by array

2015-09-02 | GSE63695 | GEO

The transient chondrocyte phenotype in osteophytic cartilage - a role of PEDF?

2013-01-31 | GSE43923 | GEO

The transient chondrocyte phenotype in osteophytic cartilage - a role of PEDF?

Project description:Pigment Epithelium-Derived Factor (PEDF) has recently been identified as a factor that is significantly upregulated in late-stage osteoarthritic cartilage in which chondrocytes are confronted with terminal differentiation and cell death. Since PEDF is known to induce cell death of endothelial cells, it may also be responsible for terminal differentiation and cell death in cartilage. Using cDNA microarray analysis, we found PEDF among the factors with the strongest differential expression and significant higher levels (118.5-fold) in osteophytic cartilage compared with articular cartilage. This study explored if PEDF interferes with the stable chondrocyte phenotype by promoting terminal differentiation or cell death.

2013-01-31 | E-GEOD-43923 | biostudies-arrayexpress

Real-time quantitative PCR analysis of UPR genes in human osteoarthritic chondrocytes specimens treated with thapsigargin compared to the untreated (control) chondrocytes

Project description:Human osteoarthritic (OA) chondrocytes were obtained from the cartilage of femoral condyles and tibial plateaus from three patients undergoing total knee arthroplasty. The chondrocytes were released from the cartilage, seeded at high density, and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum and an antibiotic mixture (100 units/ml penicillin base and 100 μg/ml streptomycin base) at 37°C in a humidified atmosphere of 5% CO2/95% air. The chondrocytes from each of the three donors were left untreated (control) and treated with thapsigargin (50nM for 20hours).Total RNA was extracted from the chondrocytes and processed for qPCR according to the manufacturer's instructions (SA Biosciences RT2 Profiler PCR Array PAHS-089Z).

2015-10-06 | GSE73746 | GEO

Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (gene expression)

Project description:The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. A subsequent validation of methylation profiles were performed in an idependent cohort of OA samples with Affymetrix Hugene 1.1 st array This represents the gene expression component of the study only

2013-04-01 | GSE43191 | GEO

Real-time quantitative PCR analysis of UPR genes in human normal and osteoarthritic chondrocytes

Project description:Human chondrocytes were obtained from the cartilage of femoral condyles and tibial plateaus from individuals within 12 hours of death (normal) and from patients undergoing total knee arthroplasty (osteoarthritic, OA). The chondrocytes were released from the cartilage, seeded at high density, and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum and an antibiotic mixture (100 units/ml penicillin base and 100 μg/ml streptomycin base) at 37°C in a humidified atmosphere of 5% CO2/95% air. Total RNA was extracted from the primary chondrocytes and processed for qPCR according to the manufacturer's instructions (SA Biosciences RT2 Profiler PCR Array PAHS-089Z).

2015-10-06 | GSE73749 | GEO

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