Transcriptomic analysis of injured and uninjured knee joints from Trem2 KO mice [bulk RNA-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA826900 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18762761.fastq.gz | Fastqsanger.gz | |||
| SRR18762762.fastq.gz | Fastqsanger.gz | |||
| SRR18762763.fastq.gz | Fastqsanger.gz | |||
| SRR18762764.fastq.gz | Fastqsanger.gz | |||
| SRR18762765.fastq.gz | Fastqsanger.gz |
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Project description:Trem2 is a single-pass transmembrane receptor of the immunoglobulin superfamily and is primarily expressed in myeloid cells. Cells from injured and uninjured knee joints of wildtype C57BL/6 mice and Trem2 KO mice were sequenced to determine if Trem2 plays a role in macrophage differentiation or function after joint injury.
2022-07-18 | GSE200842 | GEO
Project description:Post traumatic osteoarthritis (PTOA) is a painful joint disease characterized by the degradation of bone, cartilage, and connective tissues. PTOA is initiated by trauma to joint-stabilizing tissues, such as the anterior cruciate ligament, medial meniscus or by intra-articular fractures. In humans, ~50% of joint injuries progress to chronic PTOA, while the rest spontaneously resolve. To understand molecular programs contributing to PTOA development, we examined injury-induced fluctuations in immune cell populations and transcriptional shifts by single-cell sequencing of synovial joints in PTOA -susceptible C57BL6/J (B6) and -resistant MRL/MpJ (MRL) mice. A potent myeloid driven anti-inflammatory response was discovered in MRL injured joints that significantly contrasted the pro-inflammatory signaling seen in B6 joints. We found Trem2+ macrophages classically described as M2 (CD206+Trem2+) to be enriched in the uninjured joints of MRL mice, and these populations were consistently elevated in this strain, post injury. To evaluate whether Trem2 is essential to macrophage-mediated homeostasis in the joint, we examined Trem2 deficient mice and determined that these mice develop spontaneous OA. Overall, these data suggest that the PTOA resistant MRL mouse strain displays enhanced capacity of clearing debris and apoptotic cells induced by inflammation after injury due to an increase in activated macrophages within the synovial tissue and joint space. Furthermore, we showed that Trem2 is essential for preserving cartilage homeostasis in B6, and we postulate that the elevated levels of Trem2+ joint-resident macrophages in MRL are in part responsible for the PTOA-resistant phenotype in this strain.
2024-12-31 | GSE220167 | GEO
Project description:Osteoarthritis (OA) of the hand is a common disease resulting in pain and impaired function. The pathogenesis of hand OA (HOA) is elusive and models to study it have not been described so far. Culture of chondrocytes is a model to study the development of cartilage degeneration, which is a hallmark of OA and well established in OA of the knee and hip. In the current study we investigated the feasibility human chondrocyte culture derived from proximal interphalangeal (PIP) finger joints of dissecting room cadavers. Index and middle fingers without signs of osteoarthritis were obtained from 30 cadavers using two different protocols. Hyaline cartilage from both articulating surfaces of the proximal interphalangeal (PIP) joint was harvested and digested in collagenase. Cultured chondrocytes were monitored for contamination, viability, and expression of chondrocyte specific genes. Chondrocytes derived from knee joints of the cadavers were cultured under identical conditions. Gene expression comparing chondrocytes from PIP and knee joints was carried out using Affymetrix GeneChip Human 2.0 ST arrays. The resulting differentially expressed genes were validated by real-time PCR and immunohistochemistry.Chondrocytes harvested up to 101 hours after death of the donors were viable. mRNA expression of collagen 2A1, aggrecan and Sox9 was significantly higher in chondrocytes as compared to cultured fibroblasts. Comparison of gene expression by chondrocytes from PIP and knee joints yielded 528 differentially expressed genes. Chondrocytes from the same joint region had a higher grade of similarity than chondrocytes of the same individual. These results were validated using real-time PCR and immunohistochemistry.We demonstrate for the first time a reliable method for culture of chondrocytes derived from PIP joints. PIP chondrocytes show a specific gene expression pattern and could be used as tool to study cartilage degeneration in HOA. Three samples of cultured chondrocytes from knee and proximal interphalangeal finger joints were compared. Gene expression of the four most differentially regulated genes was confirmed by real-time PCR in 10 independent samples.
2016-07-03 | E-GEOD-68038 | biostudies-arrayexpress
Project description:Osteoarthritis (OA) of the hand is a common disease resulting in pain and impaired function. The pathogenesis of hand OA (HOA) is elusive and models to study it have not been described so far. Culture of chondrocytes is a model to study the development of cartilage degeneration, which is a hallmark of OA and well established in OA of the knee and hip. In the current study we investigated the feasibility human chondrocyte culture derived from proximal interphalangeal (PIP) finger joints of dissecting room cadavers. Index and middle fingers without signs of osteoarthritis were obtained from 30 cadavers using two different protocols. Hyaline cartilage from both articulating surfaces of the proximal interphalangeal (PIP) joint was harvested and digested in collagenase. Cultured chondrocytes were monitored for contamination, viability, and expression of chondrocyte specific genes. Chondrocytes derived from knee joints of the cadavers were cultured under identical conditions. Gene expression comparing chondrocytes from PIP and knee joints was carried out using Affymetrix GeneChip Human 2.0 ST arrays. The resulting differentially expressed genes were validated by real-time PCR and immunohistochemistry.Chondrocytes harvested up to 101 hours after death of the donors were viable. mRNA expression of collagen 2A1, aggrecan and Sox9 was significantly higher in chondrocytes as compared to cultured fibroblasts. Comparison of gene expression by chondrocytes from PIP and knee joints yielded 528 differentially expressed genes. Chondrocytes from the same joint region had a higher grade of similarity than chondrocytes of the same individual. These results were validated using real-time PCR and immunohistochemistry.We demonstrate for the first time a reliable method for culture of chondrocytes derived from PIP joints. PIP chondrocytes show a specific gene expression pattern and could be used as tool to study cartilage degeneration in HOA.
2016-01-01 | GSE68038 | GEO
Project description:We report differences in gene expression between wildtype and Slc7a5 knockout CD4+ T cells obtained from mouse knee joints with antigen induced arthritis
2022-12-21 | GSE168750 | GEO
Project description:Synovial joints are structures where two bones meet and essential for mobility. For example, knee joints allow flexion and extension in a single plan for stable walking motions, whereas phalangeal joints together with skeletal muscles facilitate fine motor movements in hands. Joint is enclosed in a capsule and lined by a synovial membrane inside. Articular cartilage covering bone surfaces provide a wear-resistant structure that reduces friction during movement. Meniscus acts like a shock absorber to avoid direct grinding between bone surfaces. Cruciate ligaments reinforce the integrity of a joint by mounting two bones in place and limit the degree of joint movement. All these complex structures with different shapes are fit within the joint capsule for purpose. We established lineage maps of individual joint lineages for human and mouse to understand the progenitors, transcriptional regulators, signaling cues and extracellular matrix (ECM) involved in each differentiation trajectory. We asked whether LGR5+ joint progenitor cells are presence in early stage and decline with maturation as in our findings of mouse, and whether LGR5 and COL22A1 demarcate the chondrogenic and ligamentogenic lineages in human.
2025-06-10 | GSE206303 | GEO
Project description:Profiling the knee joints of mice with Type 1 diabetes mellitus
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Project description:Purpose: To analyze gene expression in calcific (C3H) and non-calcific (B6) hearts Methods: B6 and C3H mice were induced cardiac injury by rapid freeze thaw of cardiac tissue (cryo-injury). A left thoracotomy was performed at the level of 2nd intercostal space and the exposed beating heart was frozen for 10 seconds by gently pressing a pre-cooled steel rod of 1mm diameter in dry ice. Freezing of cardiac tissue was confirmed by the rapid discoloration of the tissue. Seven days after injury, injured and uninjured regions from same heart were used for RNA sequence. Results: In contrast to only 70 odd genes that were differentially upregulated following injury in non-calcified mouse hearts (B6) about 960 genes were upregulated in C3H hearts following injury induced calcification. Out of the 960 differentially upregulated genes, only 35 were found to be common or upregulated in both C3H and B6 hearts after injury illustrating of the overlapping but dramatically different magnitude of the injury response. Families of genes regulating diverse aspects of an injury response including inflammation, extracellular matrix proteins, cell proliferation and collagen production were differentially expressed between the calcific and non-calcific hearts after injury. The mean expression of osteogenic genes (osteogenic signature) was significantly higher in injured C3H hearts compared to uninjured C3H hearts. The osteogenic signature was not higher in injured B6 hearts compared to control uninjured B6 hearts. Conclusions: Calcific hearts compared to non-calcific hearts responded to injury with a dramatically different transcriptional program.
2016-11-07 | GSE87837 | GEO
Project description:Injuries to the anterior cruciate ligament (ACL) often result in post-traumatic osteoarthritis (PTOA). PTOA accounts for ~12% of all osteoarthritis (OA) cases, yet the mechanisms contributing to OA after joint injury are not well understood. To better understand the molecular mechanisms behind PTOA development following ACL injury, we profiled ACL injury-induced gene expression changes in knee joints of three mouse strains with varying susceptibility to PTOA: STR/ort (highly susceptible), C57BL/6 (moderately susceptible) and super-healer MRL/MpJ (not susceptible) and identified genes differentially expressed between these strains at 0-day [before injury], 1-day, 1-week, and 2-weeks post-injury. This study highlights many new potential therapeutic targets and OA biomarkers.
2018-11-28 | GSE112641 | GEO
Project description:Comparative Transcriptomics of STR/ort, C57BL/6 and MRL/MpJ Knee Joints
| PRJNA448594 | ENA