Transcriptome analysis of ageing in uninjured human Achilles tendon

Abstract

IntroductionThe risk of tendon injury and disease increases significantly with increasing age. The aim of the study was to characterise transcriptional changes in human Achilles tendon during the ageing process in order to identify molecular signatures that might contribute to age-related degeneration.MethodsRNA for gene expression analysis using RNA-Seq and quantitative real-time polymerase chain reaction analysis was isolated from young and old macroscopically normal human Achilles tendon. RNA sequence libraries were prepared following ribosomal RNA depletion, and sequencing was undertaken by using the Illumina HiSeq 2000 platform. Expression levels among genes were compared by using fragments per kilobase of exon per million fragments mapped. Differentially expressed genes were defined by using Benjamini-Hochberg false discovery rate approach (P <0.05, expression ratios 1.4 log2 fold change). Alternative splicing of exon variants were also examined by using Cufflinks. The functional significance of genes that showed differential expression between young and old tendon was determined by using ingenuity pathway analysis.ResultsIn total, the expression of 325 transcribed elements, including protein-coding transcripts and non-coding transcripts (small non-coding RNAs, pseudogenes, long non-coding RNAs and a single microRNA), was significantly different in old compared with young tendon (±1.4 log2 fold change, P <0.05). Of these, 191 were at higher levels in older tendon and 134 were at lower levels in older tendon. The top networks for genes differentially expressed with tendon age were from cellular function, cellular growth, and cellular cycling pathways. Notable differential transcriptome changes were also observed in alternative splicing patterns. Several of the top gene ontology terms identified in downregulated isoforms in old tendon related to collagen and post-translational modification of collagen.ConclusionsThis study demonstrates dynamic alterations in RNA with age at numerous genomic levels, indicating changes in the regulation of transcriptional networks. The results suggest that ageing is not primarily associated with loss of ability to synthesise matrix proteins and matrix-degrading enzymes. In addition, we have identified non-coding RNA genes and differentially expressed transcript isoforms of known matrix components with ageing which require further investigation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13075-015-0544-2) contains supplementary material, which is available to authorized users.

Pleiotropic roles of the matricellular protein Sparc in tendon maturation and ageing

“…An age-related decrease in the expression of several of the identified genes, including collagen type I (Col1a1) and type III (Col3a1), fibromodulin (Fmod), and matrix metalloproteinases 2/9, has been previously reported132223. However, our screen also revealed a reduction in secreted protein acidic and rich in cysteine (SPARC; BM-40; osteonectin) in healthy-aged tendon, which to our knowledge, has not been reported thus far (Fig.…”

Identification of Novel Equine (Equus caballus) Tendon Markers Using RNA Sequencing

“…The expression of both EYA2 and GPRIN3 has already been confirmed in human tendon tissue using RNA-seq [26]. Microarray analysis performed by Jelinsky et al [23] has also confirmed EYA2 expression in human and rat tendon.…”

“…This technique has been used in equine musculoskeletal tissue to determine transcriptomic signatures associated with ageing in cartilage [25]. More recently, Peffers et al described the use of RNA-seq in tendon for the purpose of studying differentially expressed genes in young versus old macroscopically normal human Achilles tendons [26]. We hypothesize that it is possible to identify specific genetic markers of horse tendon tissue using deep-sequencing technology.…”

Long intergenic non-coding RNA expression signature in human breast cancer

“…integrated SAGE-seq findings22, we confirmed that this lincRNA also showed an increased expression in breast cancers. Another study about transcriptome analysis of aging identified the down-regulation of this lincRNA35. Further functional investigation of the lincRNA RP5-1198O20 in either carcinogenesis or aging would be interesting.…”