Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profile of peripheral blood reveals potential genetic biomarkers for diagnosis of Osteoarthritis in German shepherd dogs

ABSTRACT: Canine forms of osteoarthritis (OA) are very similar to those in humans and represent a welfare problem in the dog world population. In this study, we investigated the transcriptomic profile of peripheral blood in German Shepherd dogs with OA in order to identify diagnosis biomarkers. The bulk RNA-seq experiment was performed in a cohort of 12 adult dogs, 5 affected and 7 unaffected. Radiographs of the affected dogs revealed severe osteoarthritis in hip and elbow joints. The expression analysis showed 171 differentially expressed genes (DEGs), 113 were upregulated and 58 were downregulated compared to control dogs P (< 0.01). This pool of genes was functional annotated for signaling pathways using PANTHER tools. No overrepresented pathways were found. To gain further insights of the functional role of the DEGs in OA, we set a threshold of log2FoldChange value between -1.5 and 1.5. We ended up with 24 top up- and downregulated transcripts. Prioritization of these DEGs according to their known functional knowledge, revealed 5 possible candidates for OA biomarkers. The downregulated OSCAR gene encodes the osteoclast associated Ig-like receptor, which is involved in osteoclastogenesis regulation and bone homeostasis. In addition, the upregulated microRNA MIR339-1 and ncRNAs: LOC106559235 (downregulated), LOC102156762 (downregulated) and LOC111096460 (upregulated) are regulatory sequences, stable for gene profiling assessment in blood and related to OA pathogenesis regulation. We suggest OSCAR as the more likely candidate biomarker for OA diagnosis in dogs and, provide evidence of new circulating regulatory sequences differentially expressed in canine OA.

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE191273 | GEO | 2021/12/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Synovial biopsies of osteoarthritis patients

2016-06-02 | GSE82107 | GEO

Synovial biopsies of osteoarthritis patients

Project description:Synovial biopsies were obtained from osteoarthritis (OA) synovium to find genes upregulated during OA. The genes upregulated during OA can be used to identify disease characteristic genes. 10 microarrays of end-stage OA synovial biopsies were compared to 7 microarrays of synovial biopsies from individuals without a joint disease. Genes with >1.2-fold upregulation and P<0.05 in OA VS HC were selected from the analysis.

2016-06-02 | E-GEOD-82107 | biostudies-arrayexpress

Proteomic Analysis of Canine Hepatobiliary Neuroendocrine Neoplasms

Project description:Neuroendocrine neoplasms of the gallbladder and liver occur rarely in dogs and humans. A recent reclassification of human neuroendocrine neoplasms by the World Health Organization has refined categorization of these tumors by morphology, replicative indices, and molecular signatures. In humans, these factors correlate with survival outcomes. Improved characterization of these tumors is needed in dogs to identify diagnostic biomarkers and determine therapeutic strategies. To achieve this objective, the proteome of 3 canine hepatobiliary neoplasms was compared to normal canine adrenal and liver tissue from formalin-fixed paraffin-embedded samples. Thirty-two upregulated and 121 downregulated differentially expressed proteins were identified in the hepatobiliary neuroendocrine neoplasm samples. Among the upregulated proteins is galectin-1, a multivalent carbohydrate binding protein known to play a role in lung and pancreatic neuroendocrine neoplasia development and progression in humans. Drugs targeting the galectin family have shown promise as anticancer therapeutics in cervical cancer, prostate cancer, lung and pancreatic neuroendocrine neoplasia in human medicine. Galectin-1 may represent a novel treatment target in hepatobiliary neuroendocrine neoplasia in both humans and dogs.

2023-03-11 | PXD028822 | Pride

Identification of exosomal mRNA, lncRNA and circRNA signatures in an osteoarthritis synovial fluid-exosomal study

Project description:Aims Osteoarthritis (OA) is a common degenerative disease that is pathologically characterized by destruction of the joint matrix and reduction of articular chondrocytes, resulting in joint deformity and motor dysfunction. However, the molecular mechanisms governing this pathology have not been fully elucidated to date. Methods In this study, we determined the expression levels of lncRNAs, circRNAs, and mRNAs extracted from synovial exosomes of OA and control patients. A network of circRNA/lncRNA–miRNA–mRNA interactions was established using MiRanda and TargetScan software to explore OA pathogenesis. The exosomal lncRNA, circRNA and mRNA expression profiles of the OA and control groups were analysed using LC human competing endogenous RNA (ceRNA) microarrays. The differentially expressed genes were identified to determine their potential roles in the pathogenesis of OA by bioinformatic analysis. Results Compared with the control group, 11 mRNAs, 52 lncRNAs, and 30 circRNAs were upregulated, while 41 mRNAs, 144 lncRNAs, and 68 circRNAs were downregulated in osteoarthritis synovial exosomes. The final ceRNA network of lncRNAs and circRNAs exhibited a complex interaction between ncRNA and mRNA related to OA pathological mechanisms. An intersection analysis of the ceRNA network showed that 22 miRNAs, 45 lncRNAs, and 34 circRNAs in the PI3K/Akt and autophagy pathways correlated with 7 enriched mRNAs and may play important roles in OA pathological mechanisms. Conclusion Our work analysed mRNA/lncRNA/circRNA expression and displayed the ceRNA network of lncRNAs and circRNAs to profile the pathogenesis of OA in synovial exosomes. The results of this study may help to elucidate the pathogenesis of OA and may provide important references for further research attempting to identify more effective targets for the diagnosis and therapy of OA.

2021-10-02 | GSE185059 | GEO

Expression data from glucosamine-treated human synovial MH7A cells

Project description:Osteoarthritis (OA) is one of the major joint diseases. Glucosamine (GlcN) is widely used as a dietary supplement for OA. However, its precise mechanisms are not well understood. GlcN is utilized for the O-linked-N-acetylglucosamine (O-GlcNAc) modification of proteins, which participates in the regulation of cellular functions. In this study, we comprehensively analyzed the effect of GlcN and alloxan (O-GlcNAc transferase inhibitor, which prevented O-GlcNAc modification) on the gene expression using DNA microarray. GlcN downregulated or upregulated genes. Furthermore, among the GlcN-downregulated or upregulated genes, the expression of 62.7% of the genes was restored by alloxan.. Thus, it is suggested that GlcN regulates the gene expression by an O-GlcNAc modification-dependent or -independent mechanism.

2016-11-07 | GSE72575 | GEO

Direct Comparison of Canine and Immune Responses Using Transcriptomic and Functional Analyses

Project description:The canine spontaneous cancer model is increasingly utilized to evaluate new combined cancer immunotherapy approaches. While the major leukocyte subsets and phenotypes are closely related in dogs and humans, the functionality of T cells and antigen presenting cells in the two species has not been previously compared in detail. Such information would be important in interpreting immune response data and evaluating the potential toxicities of new cancer immunotherapies in dogs. To address this question, we used in vitro assays to compare the transcriptomic, cytokine, and proliferative responses of activated canine and human T cells, and also compared responses in activated macrophages. Transcriptomic analysis following T cell activation revealed shared expression of 515 significantly upregulated genes and 360 significantly downregulated immune genes. Pathway analysis identified 33 immune pathways shared between canine and human activated T cells, along with 34 immune pathways that were unique to each species. Activated human T cells exhibited a marked Th1 bias, whereas canine T cells were transcriptionally less active overall. Despite similar proliferative responses to activation, canine T cells produced significantly less IFN-g than human T cells. Moreover, canine macrophages were significantly more responsive to activation by IFN-g than human macrophages, as reflected by co-stimulatory molecule expression and TNF-a production. Thus, these studies revealed overall broad similarity in responses to immune activation between dogs and humans, but also uncovered important key quantitative and qualitative differences, particularly with respect to T cell responses, that should be considered in designing and evaluating cancer immunotherapy studies in dogs.

2023-12-15 | GSE226767 | GEO

miRNA sequencing of synovial fluid derived extracellular vesicles between normal and osteoarthritis (OA) patients

Project description:To determine whether extracellular vesicles were also present in human disease, we isolated and evaluated extracellular vesicles from synovial fluid from normal and OA patients at relatively advanced ages (70 - 80 years). Here we report the altered expression of synovial fluid extracellular vesicles-derived miRNAs in osteoarthritis compared to normal patients with age-relate degeneration to investigate potential biomarkers for OA diagnosis. The OA donors had clinical evidence of OA based on pain that led to total joint arthroplasty.

2019-02-18 | GSE126677 | GEO

Microarray profiling analysis of long non-coding RNAs expression in osteoarthritis

Project description:Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or <-2.0-fold change; p<0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, QPCR was used to validate chip results. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA. OA cartilage were collected from 19 patients undergoing total knee joint replacement due to severe OA, and normal cartilage were collected from 11 patients (trauma, thromboangiities obliterans, or osteosarcoma, or limb amputation) without history of rheumatoid arthritis or OA

2018-05-11 | GSE113825 | GEO

Longitudinal quantification of the GCF proteome during progression from gingivitis to periodontitis in a canine model

Project description:Inflammatory periodontal disease (periodontitis) is widespread in dogs. This study aimed to evaluate site-specific changes in the canine gingival crevicular fluid (GCF) proteome during the longitudinal progression from very mild gingivitis to mild periodontitis. Periodontitis diagnosis in dogs requires anaesthesia, our ultimate aim was to develop a periodontitis diagnostic that could be applied to samples taken from conscious dogs. The objective of this work was to identify potential biomarkers of periodontal disease progression in the GCF of dogs.

2016-03-21 | PXD003337 | Pride

Osteoarthritis-related changes in gene expression in knee articular chondrocytes in a rat model of osteoarthritis.

Project description:Cartilage destruction in osteoarthritis (OA) results from disturbed chondrocyte metabolism. Here, we used microarrays to show that TGF alpha and CCL2 are simultaneously upregulated in a rat model of OA and cooperate to drive cartilage degradation. The goals of the experiments included here were to a) characterize gene expression in knee joint articular chondrocytes at various stages of development of OA (2 and 8 weeks after surgical induction of OA), and b) to establish trends in gene expression among groups of genes related to the TGF alpha-EGFR axis, over time, in OA. The model chosen to study these results has been previously validated (Appleton, CT et al, 2007, Arthritis Rheum) and used to describe similar gene expression results at a different time point (4 weeks) after induction of OA. The rat model of OA involves surgical destabilization of the knee joint, followed by forced low-intensity mobilization over several weeks; a sham surgery is used as the control (representing a healthy non-OA knee joint) wherein a surgical incision is made but not structural (i.e. ligamentous) modification is made to the joint. Altogether, our data indicate that TGF and CCL2 cooperate to drive cartilage degradation in osteoarthritis. A total of 12 samples were analyzed. 3 replicates were used per condition: OA surgery at 2 weeks, OA surgery at 8 weeks, Sham (control) surgery at 2 weeks and Sham surgery at 8 weeks. Expression of OA samples was assessed relaitve to Sham (control) expression levels.

2012-11-15 | E-GEOD-42295 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data