Presence of meniscus tear alters gene expression profile of anterior cruciate ligament tears
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA430860 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6503060.fastq.gz | Fastqsanger.gz | |||
| SRR6503070.fastq.gz | Fastqsanger.gz | |||
| SRR6503080.fastq.gz | Fastqsanger.gz | |||
| SRR6503090.fastq.gz | Fastqsanger.gz | |||
| SRR6503100.fastq.gz | Fastqsanger.gz |
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Project description:Anterior cruciate ligament (ACL) tears occur in isolation or in combination with other intra-articular injuries such as meniscus tears. The impact of injury pattern on the molecular biology of the injured ACL is unknown. Here, we tested the hypothesis that the biological response of the ACL to injury varies based on the presence or absence of concomitant meniscus tear. RNA-seq analysis was performed on 28 ACL tears remnants (12 isolated, 16 combined). 16,654 transcripts were differentially-expressed between isolated and combined injury groups at false-discovery-rate of 0.05. Due to the large number of differentially expressed transcripts, we undertook an Ensembl approach to discover features that acted as hub-genes that did not necessarily have large fold-changes or high statistical significance, but instead had high biological significance. Our data revealed a negatively-correlated turquoise-module containing 5960 transcripts (down-regulated in combined injury) and a positively-correlated blue-module containing 2260 transcripts (up-regulated in combined injury). TNS1, MEF2D, NOTCH3, SOGA1, and MLXIP were highly-connected hub-genes in the turquoise-module and SCN2A, CSMD3, LRC44, USH2A, and LRP1B were critical hub-genes in the blue-module. Transcripts in the turquoise-module were associated with biological-adhesion, actin-filament organization, cell-junction assembly, and cell-matrix adhesion. The blue-module transcripts were enriched for neuron-migration and exocytosis-regulation. These findings indicate a loss of healing and gain of neurogenic signaling in combined ACL and meniscus tears, suggesting they have diminished potential for repair. The biological response of the ACL to injury could have implications for the healing potential of the ligament and the long-term health of the knee.
2018-01-23 | GSE109419 | GEO
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.
2022-11-18 | GSE213070 | GEO
Project description:Analysis of gene expression in E16 mouse meniscus, articular cartilage, and cruciate ligaments Limbs were dissected from E16 CD-1 mice. Samples were frozen in OCT and cryosectioned. Meniscus, articular carilage, and cruciate ligament were isolated using laser capture microdissection. Total RNA was isolated from these tissues, amplified, and gene expression was analyzed using microarrays. Three biological replicates were analyzed for each tissue type. Total RNA extracted from E16 mouse meniscus, articular cartilage, and cruciate ligaments
2013-10-01 | E-GEOD-47799 | biostudies-arrayexpress
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.
2014-09-13 | GSE61385 | GEO
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:Analysis of gene expression in E16 mouse meniscus, articular cartilage, and cruciate ligaments Limbs were dissected from E16 CD-1 mice. Samples were frozen in OCT and cryosectioned. Meniscus, articular carilage, and cruciate ligament were isolated using laser capture microdissection. Total RNA was isolated from these tissues, amplified, and gene expression was analyzed using microarrays. Three biological replicates were analyzed for each tissue type.
2013-10-01 | GSE47799 | GEO
Project description:Background: Meniscus tears are the most common injury in the knee and are associated with an increased risk of osteoarthritis (OA). The molecular profile of knees with meniscus tears is not well-studied. Therefore, to advance our understanding of the early response of the knee to injury, we compared the gene expression profile of meniscus and articular cartilage within the same knees following meniscus injury. Hypothesis/Purpose: To identify differences between the molecular signatures of meniscus and articular cartilage from knees with intact articular cartilage undergoing arthroscopic partial meniscectomy. Study Design: Descriptive laboratory study Methods: Patients (n=12) with a known isolated medial meniscus tear without any knee chondrosis or radiographic OA were consented prior to surgery. During arthroscopic partial meniscectomy, a sample of their injured meniscus and a sample of their articular cartilage off the medial femoral condyle were procured. The transcriptome signatures, as measured through Affymetrix microarray, were compared between the two tissues and underlying biological processes were explored computationally. Results: 3566 gene transcripts were differentially expressed between meniscus and articular cartilage. Gene transcripts down-regulated in articular cartilage were associated with extracellular matrix organization, wound healing, cell adhesion, and chemotaxis. Gene transcripts up-regulated in articular cartilage were associated with blood vessels morphogenesis and angiogenesis. Examples of individual genes with significant differences in expression between the two tissues include IBSP (23.76 fold; P < 0.001), upregulated in meniscus, and TREM1 (3.23 fold; P = 0.006), upregulated in meniscus. Conclusion: The meniscus and articular cartilage have distinct gene expression profiles in knees with meniscus tears and intact articular cartilage. Total RNA obtained from injured meniscus and normal articular cartilage from patients undergoing partial meniscectomy.
2015-03-06 | E-GEOD-66635 | biostudies-arrayexpress
Project description:Comparison of differential expression of small-noncoding RNAs between healthy and osteoarthritis diseased anterior cruciate ligament
2020-10-31 | E-MTAB-9106 | biostudies-arrayexpress