Gene Expression
Nebulas
Gene Expression NebulasSummary: Objectives : Joint pain causes a significant morbidity in osteoarthritis (OA). The synovium as an innervated joint structure might contribute to the peripheral pain in OA. Methods : We used a hypothesis-free next generation RNA sequencing to study protein coding and small non-coding transcriptomes in knee synovial tissues of OA patients (n=10) with high and low knee pain (evaluated by visual analogue scale) followed by Gene Ontology (GO) and pathway analyses and integration of mRNAs and small RNAs data sets. Results : We showed that 33 protein-coding genes and 35 small RNAs were differentially expressed in the knee synovium of patients with high compared to low intensity knee pain, with 30 mRNAs and 14 small RNAs being upregulated and 2 mRNAs and 21 small RNAs being downregulated. Top enriched genes, such as SDIM1 and CPE encode neuronal proteins that share molecular properties with neurotrophic factor BDNF and promote neuronal survival under cellular stress, and OTOF participates in calcium-dependent synaptic exocytosis and modulation of GABAergic activity. TrkB was enriched in several gene networks, suggesting its key role in pain-related transcriptional changes in OA joint. Downregulation of PTX3 in high pain group supports an argument that inflammation and pain are independent processes in symptomatic knee OA. MiR-146a-3p and miR150 appeared as the microRNA candidates in the pathogenesis of OA-related knee pain. Conclusions : Here we uncovered the molecular complexity of pain-related transcriptome changes in the synovium of knee joints in osteoarthritis. We identified new molecular candidates in OA pain setting a firm ground for future mechanistic studies and drug discovery in OA.
Overall Design: RNA-seq of mRNA and small non-coding RNA of 10 patients with high and low knee pain
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| Growth Protocol: | - |
| Treatment Protocol: | Pantozol,Pravastatin,Torasemid,Triatec; Co-Aprovel; -; Lithium; Metoprolol,Sirdalud,Femeston,Pantozol; Fludex; Atenolol,Co-Epril,Madopar,Metformin,Simcora,Tiatral,Zanidip,Tramadol; Tilur,Zolpidem; Aspirin,Surmontil; Aspirin,Calcimagon,Magnesium,Pantozol,Pemzek |
| Extract Protocol: | Synovial tissues were collected from knees of OA patientsat the time of the join-replacement surgery and total RNA was extracted according to the modified Chomczynski and Sacchi protocol,by using TRIzol Reagent (ThermoFisher) |
| Library Construction Protocol: | For mRNA sequencing, the Illumina TruSeq® Stranded total RNA protocol with the TruSeq Stranded total RNA Sample Preparation Kit. For small RNA sequencing, libraries were produced by NEBNext® Small RNA Library Prep Set for Illumina® (NEB #E7330S/L) |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | SINGLE |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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