Transcriptomic signatures in cartilage ageing
Arthritis Research & Therapy 2013, 15:R98 doi:10.1186/ar4278Published: 23 August 2013
Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage ageing but do not reveal the full transcriptomic phenotype of chondrocytes such as small non-coding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including non-protein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures.
RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young (4 years old) and four old (greater than 15 years old) donors. RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (p<0.05, expression ratios +/-1.4log2 fold change). Ingenuity Pathway Analysis enabled networks, functional analyses and canonical pathways from differentially expressed genes to be determined.
In total, the expression of 396 transcribed elements including mRNAs, small non-coding RNAs, pseudogenes, and a single microRNA was significantly different in old compared to young cartilage (+/-1.4 log2 fold change, p<0.05). Of these, 93 were at higher levels in the older cartilage and 303 were at lower levels in the older cartilage. There was an over-representation of genes with reduced expression relating to extracellular matrix, degradative proteases, matrix synthetic enzymes, cytokines and growth factors in cartilage derived from older donors compared to young. In addition there was a reduction in Wnt signalling in ageing cartilage.
There was an age-related disregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome.