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
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
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 BeadChip array, which allows for the analysis of >480,000 CpG sites.
Project description:Large scale RNA-Seq analysis was performed to investigate the transcriptomic response to osteoarthritis in cartilage and investigate potential subgroups of patients. Data were collected from intact knee cartilage (posterior lateral condyle) from at total of 60 patients with osteoarthritis (OA) following total knee replacement and 10 control non-OA patients following amputation.
Project description:In total, 70 samples on macroscopically preserved and lesioned OA cartilage from the same patient was taken for RNA-seq. Subsequently, paired-end 2×100 bp RNA library sequencing (Illumina TruSeq RNA Library Prep Kit, Illumina HiSeq 2000 and TruSeq Stranded Total RNA LT Sample Prep Kit, Illumina HiSeq 4000) was performed.
Project description:Age as the primary rise factor could be play an important role in incidence and development of osteoarthritis. Several studies have confirmed some tissue specific microRNA were associated with development of osteoarthritis. But if age related microRNA or miRNA cluster would be involved in pivotal post-transcriptional gene regulation in osteoarthritis is unclear. In view of this, we have an idea that several age-related miRNAs would be screened from the rat knee cartilage at different development ages by miRNAs Microarray analysis. We used microarrays to detail the global programme of gene expression underlying the rat knee cartilage and identified distinct classes of age-related miRNAs during this process. The rat knee articular cartilage were selected at successive stages of the rat developmental for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of cartilage at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected cartilage according to the rat developmental stages, i.e. seven time-points: newborn (T0), childhood (T1), youth(T2), adult (T3), middle-aged (T4) early-stage elderly(T5) and latter-stage elderly(T6). The objective of the study is to identify miRNA profile of knee articular cartilage at different developmental ages in rats. Total RNA were extracted from the knee articular cartilage of Sprague-Dawley rats at postnatal day 0(T0), week1(T1), week 4(T2), mon3(T3), mon 6(T4), mon 12(T5), and mon 18(T6). The microRNA profile in the specimens was detected with the Affymetrix GeneChip® miRNA 3.0 Array.
Project description:This experiment captures the expression of genes between two sites of human cartilage within the same patients to allow investigation of genomic responses to damage during osteoarthritis. Eight patients with symptomatic OA undergoing total knee replacement (n=8, age range 65-79 years, mean age 70.3) were used in this study. Cartilage from paired osteochondral samples were isolated from the intact PLC (posterior lateral condyle) and the damaged DMC (distal medial condyle) for RNA-seq analysis.
Project description:Developmental dysplasia of the hip (DDH) is one of the significant risk factors for hip osteoarthritis. In order to investigate the factors that induce early articular cartilage degeneration of the hip joints that are exposed to reduced dynamic loads arising from hip dislocation , we created rodent models of hip dislocation by swaddling. Notably, expression of periostin (Postn) was increased in the acetabular articular cartilage of the DDH models; Postn was a candidate gene associated with early articular cartilage degeneration. We showed that early articular cartilage degeneration was suppressed in Postn-/- DDH mice. Furthermore, a microgravity environment induced the expression of Postn in chondrocytes through STAT3 signaling. Postn induced catabolic factors, interleukin-6 and matrix metalloproteinase 3, in articular chondrocytes through integrin-nuclear factor κB signaling. Additionally, interleukin-6 stimulated Postn expression through STAT3 signaling. Thus, Postn plays a critical role in early articular cartilage degeneration associated with hip dislocation.
Project description:Osteoarthritis (OA) is the most prevalent joint disease with the typifying feature being the progressive degradation of articular cartilage during disease progression. In this study we used whole transcriptome RNA-seq as a tool to compare gene expression changes between age-matched osteoarthritic human hip OA cartilage (n=10) compared to control (neck of femur fracture) cartilage (n=6) [GSE107308]. All cartilage was from patients undergoing acetabulofemoral joint replacement. Cartilage RNA was isolated from cartilage within 2 hr of joint replacement surgery, mRNA was polyA purified and transcript expression was analysed using 78-base paired-end sequencing generating on average 28 million reads/sample sequencing. The data shows excellent correlation with our previous microarray data but identifies significantly more differentially expressed transcripts plus novel transcript variants, several of which have been validated by real-time qPCR. Our work sheds further light on chondrocyte transcriptome expression and highlights gene expression changes and novel transcripts potentially important in osteoarthritis progression