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Series GSE99662 Query DataSets for GSE99662
Status Public on Nov 05, 2018
Title Pain-driven transcriptome changes in synovium of knee osteoarthritis patients
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary 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
 
Contributor(s) Bratus-Neuenschwander A
Citation(s) 29973527
Submission date Jun 05, 2017
Last update date Jul 25, 2021
Contact name Francesc Castro-Giner
Organization name ETH Zurich
Street address Otto-​Stern-Weg 7
City Zurich
ZIP/Postal code CH-8093
Country Switzerland
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (20)
GSM2649432 patient_12_High_Pain_sRNA
GSM2649433 patient_13_Low_Pain_sRNA
GSM2649434 patient_14_Low_Pain_sRNA
Relations
BioProject PRJNA389258
SRA SRP108597

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE99662_RAW.tar 73.8 Mb (http)(custom) TAR (of DATA, TXT)
GSE99662_gene_counts_matrix.txt.gz 2.0 Mb (ftp)(http) TXT
GSE99662_gene_rpkm_matrix.txt.gz 3.8 Mb (ftp)(http) TXT
GSE99662_gene_tpm_matrix.txt.gz 3.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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