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Sample GSM1116970 Query DataSets for GSM1116970
Status Public on Dec 30, 2013
Title Synovial tissue after to Methotrexate therapy, repl 7
Sample type RNA
 
Source name Knee synovial biopsies, obtained by needle arthroscopy, 12 weeks after initiation of Methotrexate therapy (15 mg, q1w)
Organism Homo sapiens
Characteristics gender: M
age: 64
disease activity score (das)-28crp: 4.01
Treatment protocol All patients included in the protocol met the American College of Rheumatology 1987 revised classification criteria for RA. They were all methotrexate (MTX) naive at inclusion and 3 of them were treated with low-dose glucocorticoids (prednisone ≤ 7.5 mg/day). All patients presented knee synovitis at inclusion. Patients were randomized into 2 groups: 12 received intravenous 8 mg/kg/month tociliuzumab (TCZ) therapy during 6 months, and 8 were treated with MTX that was administered orally at a 15 mg/week dose. Disease activity at baseline and at 3 months was evaluated using Disease Activity Score (DAS)-28CRP.
Synovial biopsy samples from 20 patients (12 in TCZ-treated group, 8 in MTX-treated group) were obtained by needle mini-arthroscopy of the affected knee at baseline (T0) and 12 weeks (T12) after initiation of therapy. For each procedure, 4–8 synovial samples were kept overnight at 4°C in an RNA stabilizing solution (RNALater; Ambion) and then stored at –80°C for later RNA extraction.The same amount of tissue was snap-frozen in liquid nitrogen and kept at –80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formaldehyde and embedded in paraffin for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsy samples harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation. The study was approved by the ethics committee of the Université catholique de Louvain, and informed consent was obtained from all patients.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the synovial biopsy samples using the Nucleospin® RNA II extraction kit (Macherey-Nagel, Düren, Germany), including DNase treatment of the samples. At least 2 µg total RNA could be extracted for further processing from 12 and 8 paired samples at T0 and T12 in TCZ- and MTX-treated groups, respectively. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). All samples had a RNA integrity number (RIN) > 6.5
Label Biotin
Label protocol Complementary RNA (cRNA) was synthetized and biotin-labeled according to a standard Affymetrix procedure (GeneChip® 3’ IVT express kit, Affymetrix, High Wycombe, UK), as previously described. Briefly, total RNA was first reverse transcribed into single-stranded complementary DNA (cDNA) using T7 oligo(dT) primer. The second-strand cDNA is then synthetized using DNA polymerase and Rnase H to simultaneously degrade RNA. The double-stranded cDNA served as template for the in vitro transcription reaction, which was performed for 16 hours in the presence of a biotinylated ribonucleotide analog mix. At the end of the procedure, biotinylated cRNA was purified and fragmented to prepare the target for hybridization to GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix, UK)
 
Hybridization protocol GeneChip® HGU133 Plus 2.0 arrays were hybridized overnight at 45°C with 10 µg fragmented biotinylated cRNA. The slides were then washed and stained using EukGE-WS2v5 fluidics protocol on the GeneChip® Fluidics station 450.
Scan protocol The slides were scanned on the GeneChip® Scanner 3000 (Affymetrix, UK).
Description MTX7 T12
Data processing Statistical analyses of microarray data were performed using GeneSpring software (Agilent Technologies). Fluorescence intensity data were normalized by robust multiarray analysis.
 
Submission date Apr 08, 2013
Last update date Dec 30, 2013
Contact name Bernard Robert Lauwerys
E-mail(s) Bernard.Lauwerys@uclouvain.be
Phone +3227645391
Organization name Université catholique de Louvain
Department Institut de Recherches Expérimentales et Cliniques
Lab Pôle de pathologies rhumatismales et systémiques
Street address Avenue Hippocrate 10
City Brussels
ZIP/Postal code 1200
Country Belgium
 
Platform ID GPL570
Series (1)
GSE45867 Effects of tocilizumab versus methotrexate therapy on gene expression profiles in the early rheumatoid arthrtis synovium

Data table header descriptions
ID_REF
VALUE log2 RMA (GeneSpring) normalized value intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at -0.064352036
AFFX-BioB-M_at -0.18737507
AFFX-BioB-3_at -0.23827219
AFFX-BioC-5_at -0.08621311
AFFX-BioC-3_at -0.06798267
AFFX-BioDn-5_at -0.07788181
AFFX-BioDn-3_at -0.13048744
AFFX-CreX-5_at -0.09661484
AFFX-CreX-3_at -0.10702419
AFFX-DapX-5_at 0.34058
AFFX-DapX-M_at 0.29191017
AFFX-DapX-3_at 0.2036581
AFFX-LysX-5_at 0.017223358
AFFX-LysX-M_at 0.07688141
AFFX-LysX-3_at 0.17801237
AFFX-PheX-5_at -0.003195763
AFFX-PheX-M_at 0.12749815
AFFX-PheX-3_at 0.14154434
AFFX-ThrX-5_at 0.003380776
AFFX-ThrX-M_at 0.17432165

Total number of rows: 54675

Table truncated, full table size 1195 Kbytes.




Supplementary file Size Download File type/resource
GSM1116970_MTX_7_T12.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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