Gene Expression
Nebulas
Gene Expression Nebulas概要: 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.
项目整体设计: RNA-seq of mRNA and small non-coding RNA of 10 patients with high and low knee pain
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| 生长方案: | - |
| 处理方案: | 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 |
| 提取方案: | 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) |
| 建库方案: | 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) |
| 分子类型: | rRNA- RNA |
| 库的片段类型: | SINGLE |
| 库的链类型: | Forward |
| 测序平台: | ILLUMINA |
| 测序仪型号: | Illumina HiSeq 2500 |
| 链特异性: | Specific |
| 数据来源 | GEN样本编号 | GEN数据集编号 | 系列编号 | 项目编号 | 样本编号 | 样本名称 | 生物样本编号 | 样本访问号 | 实验访问号 | 释放时间 | 提交时间 | 最后更新时间 | 物种 | 种族 | 族裔 | 年龄 | 年龄单位 | 性别 | 来源名称 | 组织 | 细胞类型 | 细胞亚型 | 细胞系 | 疾病 | 疾病状态 | 发育阶段 | 突变/变异 | 表型 | Condition Detail | 生长方案 | 处理方案 | 提取方案 | 建库方案 | 分子类型 | 库的片段类型 | 链特异性 | 库的链类型 | 加标（Spike-In） | 测序方法 | 测序平台 | 测序仪型号 | 细胞数 | 测序片段数 | 碱基数 | 平均测序片段长度_1 | 平均测序片段长度_2 | 唯一比对率 | 多重比对率 | 覆盖度 |
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