Small RNA sequencing of healthy and osteoarthritis diseased anterior cruciate ligament
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB38433 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4171890_1.fastq.gz | Fastqsanger.gz | |||
| ERR4171890_2.fastq.gz | Fastqsanger.gz | |||
| ERR4171891_1.fastq.gz | Fastqsanger.gz | |||
| ERR4171891_2.fastq.gz | Fastqsanger.gz | |||
| ERR4171892_1.fastq.gz | Fastqsanger.gz |
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Project description:Comparison of differential expression of small-noncoding RNAs between healthy and osteoarthritis diseased anterior cruciate ligament
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Project description:To explore the molecular mechanisms of meniscal degeneration after resection of anterior cruciate ligament and lateral collateral ligament, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential role in the development of meniscal degeneration. The anterior cruciate ligament (ACL) and lateral collateral ligament (LCL) of the right rear limbs of Wuzhishan minipig was resected at the same time, and the left rear limbs was sham operated. There were significant differences in gene expression between the two groups. A total of 893 differentially expressed genes were identified, of which 537 were upregulated and 356 were downregulated. This study indicated that several molecular mechanisms were implicated in the development of meniscal degeneration, thus improving our understanding of meniscal degeneration and offering molecular targets for future therapeutic advances.
2020-12-15 | GSE145402 | GEO
Project description:Injury to anterior cruciate ligament (ACL) is common in young individuals and a frequent cause of functional instability and early onset of osteoarthritis. The healing potential of an injured ACL is known to decay over time. The molecular origin of this healing deficiency largely remains elusive but plausibly involves gene transcripts associated with tissue healing. To explore this possibility, we set out to identify transcript expression differences in injured ACL remnants recovered at the time of surgical reconstruction, via microarray (n=24) and RNA-seq (n=8) technologies in transcriptome profiling. We found that time-from-injury was an important determinant of changes in gene expression signatures predominately resulting in repression of several biological processes as identified by gene ontology. The most interesting observation was a time-dependent decline in the gene transcripts as well as the biological processes common to both microarray and RNA-seq analyses. Compared to acute tears, in chronic several important biological processes were namely extracellular matrix organization, angiogenesis, cell adhesion, wound healing, mesenchyme transition, and response to hypoxia. Furthermore, the cross-platform concordance in terms of differentially expressed transcripts or enriched pathways was linearly correlated (r=0.64). Microfluidic digital PCR confirmed the expression of selected differentially expressed transcripts. These intriguing findings suggest an initial attempt of the injured ACL to repair, which drops with time. These findings have implications for efforts to repair the ACL and may be relevant for its reconstruction. These findings also emphasize the utility of differentially expressed transcripts as prognostic biomarkers in patients with ACL injury. Examination of transcript expression differences by time-from-injury in anterior cruciate ligament
2015-01-30 | E-GEOD-65469 | biostudies-arrayexpress
Project description:The anterior cruciate ligament (ACL) is an essential stabilizer of the tibiofemoral articulation. ACL tears often lead to functional instability and are associated with an increased risk for osteoarthritis. The healing potential of the injured ACL is poorly understood and is considered to be limited. Transcriptome-wide expression profiles of 24 human ACL remnants recovered at the time of surgical reconstruction were analyzed utilizing the Agilent human 8x60K microarray platform. Gene ontology was performed on differentially expressed transcripts based on time-from-injury (acute, <3 months; intermediate, 3-12 months; chronic, >12 months). A subset of transcripts was validated via microfluidic digital polymerase-chain-reaction. Expression of periostin, a highly differentially expressed transcript, was tested by immunohistochemistry. Numerous transcripts covering important functional classifications were differentially expressed by time-from-injury. In acute tears, processes representing angiogenesis were repressed while those representing stem-cell differentiation were elevated. In intermediate tears, processes representing stem-cell proliferation concomitant with cellular component organization/cellular localization were elevated. In chronic tears, processes denoting myosin filament organization were elevated while those representing cellular component organization/cell localization and extracellular matrix organization were repressed. Expression levels of periostin were down-regulated in chronic tears compared to acute (42-fold) and intermediate (29-fold) tears. Immunohistochemistry confirmed a decline in periostin expression in tissues from chronic tears. These findings suggest an initial attempt of the injured ACL to repair, which declines with time-from-injury. These findings have implications for efforts to repair the ACL and may be relevant for reconstruction of the ACL. The functional role of periostin in ACL injuries, and the potential implication for surgical treatment, warrants further investigation. Total RNA obtained frominjured anterior cruciate ligament (ACL) tissues from pateints undergoing ACL surgery.
2014-09-13 | E-GEOD-61385 | biostudies-arrayexpress
Project description:Despite ample evidence demonstrating that anterior cruciate ligament (ACL) and meniscus tears are associated with the development of knee osteoarthritis (OA), the contributing factors remain unknown. Synovial inflammation has recently been recognized as a pivotal factor in the pathogenesis of OA. However, there is a lack of data on synovial profiles after ACL or meniscus injuries, which may contribute to posttraumatic OA (PTOA). We performed RNA-seq of 3 inflamed synovial biopsy samples vs 3 normal synovial biopsy samples following ACL and/or meniscus injuries. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein–protein interaction (PPI) analyses were performed to investigate mRNAs with significant differences between the inflamed and normal groups.Next, competing endogenous RNA (ceRNA) networks were constructed based on bioinformatics analyses and quantitative real-time polymerase chain reaction (RT–PCR) results. The association of the identified DEGs with the levels of infiltrating immune cells was explored using Pearson correlation analysis in R software. We aimed to provide greater insights into molecular mechanisms and biologic pathways in synovitis that could regulate post-trauma osteoarthritis progression.
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Project description:The intent of the experiment was to identify genes that were differentially expressed between dogs affected with anterior cruciate ligament (ACL) rupture and breed-matched controls. Anterior cruciate ligament and knee synovial tissue biopsies were collected from 4 ACL rupture affected cases and 4 unaffected control dogs. Cases and controls were matched as closely as possible based on breed, sex, neutered status, age, and weight. Medications that the dogs were taking at the time of sample collection were also considered. We prioritized sample size and quality above all other variables, therefore, two matched pairs of Golden Retrievers were chosen with two matched pairs of Labrador Retrievers for this analysis. Tissues from cases were collected during knee stabilization surgery. Tissues from unaffected control dogs were collected from dogs undergoing pelvic limb amputation or euthanasia for reasons unrelated to this study. Illumina TruSeq RNA libraries were constructed and 150bp paired-end sequencing was performed using the Illumina Hi-Seq 2500 platform. Table 1. Breed, sex, age, and weight of matched case and control pairs chosen for RNA sequencing analysis Cases Matched Controls Breed Sex Age (yr) Weight (kg) Breed Sex Age (yr) Weight (kg) GR1 CM 8.8 30.5 GR2 CM 14.9 N/A GR3 CM 5.6 44.0 GR4 CM 3.9 34.0 LR1 CM 9.7 36.0 LR2 CM 12.7 28.5 LR3 CM 13.3 36.0 LR4 CM 13.5 35.0 GR = Golden Retriever. LR = Labrador Retriever. CM= castrated male. Weight at the time of death was not available for one dog.
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Project description:36 Yucatan minipigs underwent anterior cruciate ligament (ACL) transection and were randomly assigned in equal numbers to no further treatment, reconstruction or ligament repair. Cartilage was harvested at 1 and 4 weeks post-operatively and histology and RNA-sequencing performed. The generated data served to identify the molecular pathophysiology present in early post-traumatic osteoarthritis (PTOA), as well as differences between surgical treatments.
2017-10-22 | E-MTAB-5879 | biostudies-arrayexpress
Project description:36 Yucatan minipigs underwent anterior cruciate ligament (ACL) transection and were randomly assigned in equal numbers to no further treatment, reconstruction or ligament repair. Peri-meniscal synovium was harvested at 1 and 4 weeks post-operatively and histology and RNA-sequencing performed. The generated data served to identify the molecular pathophysiology present in inflamed synovium during the early development of post-traumatic osteoarthritis (PTOA), as well as differences between surgical treatments.
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Project description:Synovium mRNA expression data derived from a pig model of post-traumatic osteoarthritis. Samples were collected from both knees of control pigs (n=6x2=12) and injured knees of pigs that went under unilateral anterior cruciate ligament transection 1, 5, 9 and 14 days after surgery (n=6 per time-point).
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