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RNA-sequencing from inflamed and normal synovial membrane after anterior cruciate ligament and/or meniscus injuries

ABSTRACT: RNA-sequencing from inflamed and normal synovial membrane after anterior cruciate ligament and/or meniscus injuries

PROVIDER: PRJNA879078 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21521661.fastq.gz	Fastqsanger.gz
	SRR21521662.fastq.gz	Fastqsanger.gz
	SRR21521663.fastq.gz	Fastqsanger.gz
	SRR21521664.fastq.gz	Fastqsanger.gz
	SRR21521665.fastq.gz	Fastqsanger.gz

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RNA-sequencing from inflamed and normal synovial membrane after anterior cruciate ligament and/or meniscus injuries

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

Presence of meniscus tear alters gene expression profile of anterior cruciate ligament tears

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

Gene signature of the embryonic meniscus

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

Experimental study on gene expression profile of medial meniscus after resection of anterior cruciate ligament and lateral collateral ligament

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

Gene signature of the embryonic meniscus

2013-10-01 | GSE47799 | GEO

Presence of meniscus tear alters gene expression profile of anterior cruciate ligament tears

Project description:Presence of meniscus tear alters gene expression profile of anterior cruciate ligament tears

| PRJNA430860 | ENA

Small RNA sequencing of healthy and osteoarthritis diseased anterior cruciate ligament

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

Experimental study on gene expression profile of medial meniscus after resection of anterior cruciate ligament and lateral collateral ligament

Project description:Experimental study on gene expression profile of medial meniscus after resection of anterior cruciate ligament and lateral collateral ligament

| PRJNA607087 | ENA

Mesenchymal stem cells from an inflammed area and normal tissue post anterior cruciate ligament injury

Project description:Mesenchymal stem cells from an inflammed area and a uninflammed tissue post anterior cruciate ligament injury

2021-10-04 | PXD026787 | Pride

Bioinformatics Analysis of Degenerative Meniscus Tissue in Knee Osteoarthritis of Wuzhishan Pig

Project description:Meniscus degeneration is one of the manifestations of knee osteoarthritis, but its specific molecular mechanism is still not very clear. We used Wuzhishan pig's anterior cruciate ligament resection to prepare meniscus degeneration models, and applied gene chip technology to detect the expression of differential genes in the degenerated meniscus tissue. The study detected a total of 893 differentially expressed genes, mainly related to hormones, apoptosis, inflammation and other mechanisms, and analyzed that TRP channels may play a key role. All in all, we have established a reliable animal model of meniscus degeneration and found that meniscus degeneration involves several possible molecular mechanisms, which provide molecular targets for future treatment of the disease.

2020-08-13 | GSE156132 | GEO

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