RNA-seq of achilles tendon from young and old donors to study age-related changes in tendon
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Homo sapiens
SUBMITTER: Mandy Peffers
PROVIDER: E-MTAB-2449 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Transcriptome analysis of ageing in uninjured human Achilles tendon.
Peffers Mandy Jayne MJ Fang Yongxiang Y Cheung Kathleen K Wei Tim Koh Jia TK Clegg Peter David PD Birch Helen Lucy HL
Arthritis research & therapy 20150218
<h4>Introduction</h4>The 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.<h4>Methods</h4>RNA for gene expression analysis using RNA-Seq and quantitative real-time polymerase chain reaction analysis was isolated from young and old macroscopically normal human Ac ...[more]
Similar Datasets
Project description:Amniotic derived cells are ideal seed cells for regenerative medicine protocols since they conjugate a remarkable plasticity to safety properties. This study investigated the role exerted by human amniotic cells during the process of tendon healing. In particular, in the present research it has been evaluated, by microarray technique, the presence of transcriptome variations in human amniotic epithelial (hAECs) and mesenchymal (hAMCs) stem cells when xenotransplanted into the preclinical ovine model of tendon defect, compared to freshly isolated ones. This analysis allowed to understand in which way, after 28 days transplantation, hAECs and hAMCs transcripts have been affected. Total of 4 experiments.Two-condition experiment, Human amniotic stem cells xenotransplantated in a sheep achilles tendon vs.HAEC/HAMC Biological replicates: 2 Xenotrasplatations. One replicate per array.
2014-06-30 | E-GEOD-53594 | biostudies-arrayexpress
Project description:Healing process after connective tissues (CT) injury is complex but important as CT are critical for human moving, and patient outcome of CT injured patients is protracted with high individual variation. Specific markers which could be used for healing prognosis will be great help to monitor patient outcome, and furtherly improve target treatment and patient recovery. Although several common factors like age, gender and body mass index (BMI) were reported to predict ATR healing outcome [references], more specific markers which can be used as predictors of patient outcome after ATR are still lacking. Several biomarkers have been reported to associate with tendon healing, and indicated their relationship with patient outcome(1-4). These results highlight the potential of protein expression detection and analysis for tendon study in general and healing outcome prognosis in particular. Collagen type I (Col1a1) is the main component of Achilles tendon and plays vital role in tendon healing via involving in collagen fibrils production among tendon fibroblasts(5). Higher production of Col1a1 is associated with faster tendon repair(6), previous study on animal model reported the increased Col1a1 synthesis can exert a positive effect on tendon healing[?]. Thus, functional proteins with high impact on Col1a1 can be used not only to improve tendon healing, also can be as targets for healing improvement and outcome prediction. The proteome file of Achilles tendon which is important to increase understanding of tendon healing and help to identify accurate outcome-related biomarkers is however lagged behind. The identification of proteomic profile of Achilles tendon is very much limited in number of proteins and sample size(7-9), and is even few on human. Recent improvement in proteomic assay based on mass spectrometry (MS) made it possible to assemble the proteomic landscape of human tissues(10, 11) with high quality and sensitivity. To characterize the proteomic components in human Achilles tendon, we utilized biopsies from ATR patients with both good and poor 1-year healing outcome. A validated platform including quantitative MS and clinical database was used to identify proteomic landscape and potential bio-predictors of clinical outcome. Our study may provide a more comprehensive landscape of proteins for human Achilles tendon, as well as specific biomarkers which can be used for long term outcome prognosis after ATR.
2023-05-10 | PXD033163 | Pride
Project description:Tendon is a highly aligned connective tissue, in which the macro-structure consists of collagen-rich fascicles surrounded by interfascicular matrix (IFM). In a series of recent studies in equine tissue, we have demonstrated specialisation of tendon composition, structure and mechanics to achieve the tendon’s functional requirements, specifically reporting extensive specialisation of the IFM region in the energy storing superficial digital flexor tendon. We have also demonstrated loss of functional specialisms with ageing, leading to a hypothesised new paradigm for tendinopathy, focused on the importance of the IFM. However, to date, there have been no studies focused on structure-function specialisation or the IFM in functionally distinct human tendons. Here, we compare the positional anterior tibialis tendon and energy storing Achilles tendon, performing a detailed analysis of the composition and mechanical properties of both fascicle and IFM regions, to test the hypothesis that the IFM in the energy storing Achilles tendon has specialised composition and mechanical properties, and that these specialisations are lost with ageing. We demonstrate that the IFM is specialised in the energy storing Achilles tendon, with greater elasticity and fatigue resistance than in the positional anterior tibialis tendon. While there were few age-related alterations in mechanics, we did identify age-related alterations in the IFM proteome of the Achilles tendon specifically, which is predicted to be regulated by TGF-beta signalling and may be responsible for the trend towards decreased fatigue resistance observed in the Achilles IFM with ageing.
2020-11-11 | PXD018212 | Pride
Project description:Tendons play fundamental role in the musculoskeletal system and locomotion by transferring forces generated by muscles to the skeleton. Chronic tendon injuries and diseases are among the leading causes of musculoskeletal disability. For many types of tendinopathies, women have worse clinical outcomes than men. It is possible that tendon sex-based differences in protein composition are related to an altered injury response. The aim of this study was to compare the proteome of male and female tendon using label-free protein quantification. These data could provide new insight into pathways which may beinvolved in tendinopathies, and potentially in the differential injury response of female tendon.
2017-01-16 | PXD004612 | Pride
Project description:To identify if genes is regulated by time of day in human tendinopathic tendon, RNAseq analysis was performed on biopsies taken from tendinopathic and contralateral patella tendon 12 hours apart in young tendinopathic subjects (9 AM and 9 PM).
2023-02-09 | E-MTAB-11938 | biostudies-arrayexpress
Project description:We used the coupled isobaric tag for relative and absolute quantitation-liquid chromatography-electrospray ionization-tandem mass spectrometry approach to examine protein expression in acute Achilles tendon rupture patients.
2024-01-26 | PXD046451 | Pride
Project description:Healing after Achilles tendon rupture (ATR) is protracted with high individual variation and unsatisfactory outcome. Biomarkers prognostic of healing are unknown while physical and mechanical factors are used for predicting long-term healing outcomes in clinics today. The present study was designed to investigate the proteomic profile of healing, identify potential biomarkers, and asess the association with the patient's long term outcomes after ATR. Using quantitative Mass Spectrometry (MS) analysis, 1423 proteins in healing and contralateral healthy Achilles tendon from 28 ATR patients were quantified. Comparing healing and healthy protein profiles, we identified 821 overlapping proteins. Further analysis revealed 390 up-regulated and 17 down-regulated proteins in healing compared to the healthy contralateral side,mainly related to extracellular matrix organization, inflammation, and reduced exocytosis and metabolic pathways. Our analysis based on clinical parameters, identified complement factor D (CFD) as the most reliable predictive biomarker of successful tendon healing.Our findings identidied identified prognostic biomarkers and potential therapeutic target for improving tendon or ligament injuries.
2022-05-25 | PXD029202 | Pride
Project description:To identify if genes is regulated by time of day in human tendon, RNAseq analysis was performed on biopsies taken from patella tendon 12 hours apart in young healthy subjects (9 AM and 9 PM).
2023-02-09 | E-MTAB-11937 | biostudies-arrayexpress
Project description:We have compared the gene expression profile of rat Achilles tendon-derived stem cells in post-natal tendon development. Rat tendon stem/progenitor cells (TSPCs) were isolated at different stages of post-natal development: TSPCs-1d, TSPCs-7d and TSPCs-56d. TSPCs at different post-natal development stages (1d, 7d and 56d) were isolated, cultured and used for microarray analyses at passage 2. All TSPCs in this study were of isolated from more than one individual. Total RNA was extracted and fragmented biotin-tagged cRNA was hybridized to Rat Genome 230 2.0 Array.
2015-07-10 | E-GEOD-68485 | biostudies-arrayexpress
Project description:Tendons play a critical role in the transmission of forces between muscles and bones, and chronic tendon injuries and diseases are among the leading causes of musculoskeletal disability. For many types of tendinopathies, women have worse clinical outcomes than men. It is possible that sex-based differences in tendon morphology, composition and mechanical properties may explain the greater susceptibility of women to develop tendinopathies. Our objective was to evaluate the mechanical properties, biochemical composition, transcriptome, and cellular activity of plantarflexor tendons from four month old male and female C57Bl/6 mice using in vitro biomechanics, mass spectrometry-based proteomics, genome-wide expression profiling, and cell culture techniques. Differences between groups were tested using t-tests (α=0.05). While the Achilles tendons of male mice were approximately 6% larger than female mice (P<0.05), the cell density of female mice was around 19% larger than males (P<0.05). No significant differences in the length (P=0.34), peak force (P=0.86), peak stress (P=0.52) or energy loss during stretch (P=0.94) of plantaris tendons were observed. Mass spectrometry proteomics analysis revealed no significant difference between sexes in the abundance of major extracellular matrix (ECM) proteins like collagen types I (P=0.30) and III (P=0.68), but female mice had approximately two-fold elevations (P<0.05) in different minor ECM proteins such as fibronectin, periostin, and tenascin. Using microarray analysis, there was no significant differences (P>0.05) in the expression of most major and minor ECM genes, and in the expression of genes involved in tendon fibroblast specification or proliferation. Whole tendon qPCR analysis showed significant expression differences in elastin, scleraxis, and tenomodulin. Cell culture techniques to test the effects of sex-specific extracellular environment on cellular activity show significant differences in gene expression of type I and III collagen, Ki67, scleraxis, and tenomodulin. Histologic analysis demonstrated that males have larger tendon cross-sectional area and lower cell density when compared to females. However, there were no differences between the sexes in the mechanical properties of tendons or in the majority of primary structural extracellular matrix proteins, although elevations were observed in some minor ECM proteins. Microarray analysis also showed no significant sex-based differences in the expression of major genes associated with collagen composition, extracellular components and turnover, and fibroblast proliferation. Cell culture tests of non-autonomous cellular activity show no major signals for ECM synthesis nor fibroblast proliferation. Our results indicate that while male mice expectedly had larger tendons, male and female mice have very similar mechanical properties and biochemical composition, with small increases in minor ECM proteins and proteoglycans in female tendons. The role that these minor ECM proteins and proteoglycans play in tendon repair should be evaluated in future studies. No treatment administered, study done to evaluate normal expression profiles of male and female tenocytes. This analysis is based on a Mouse Gene ST 2.1 strip that was processed in the microarray facility in May 2015 using the wt-pico kit.
2016-08-11 | E-GEOD-85415 | biostudies-arrayexpress