ONTOLOGY SOURCE REFERENCE Term Source Name "mo" "The MGED Ontology" "ArrayExpress" "EFO" "NCBITaxon" "CHEBI" "UBERON" "BTO" "CL" "MO" "DOID" Term Source File "http://mged.sourceforge.net/ontologies/MGEDontology.php" "http://www.ebi.ac.uk/arrayexpress" "http://www.ebi.ac.uk/efo/" "" "http://bioportal.bioontology.org/ontologies/47845" "http://bioportal.bioontology.org/ontologies/50447" "http://bioportal.bioontology.org/ontologies/50306" "http://bioportal.bioontology.org/ontologies/50231" "http://bioportal.bioontology.org/ontologies/50456" "http://bioportal.bioontology.org/ontologies/38801" "http://bioportal.bioontology.org/ontologies/50310" Term Source Version "" "" "" "" "47845" "50447" "50306" "50231" "50456" "38801" "50310" Term Source Description "" "" "" "" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Chemical Entities of Biological Interest Ontology" "Uber Anatomy Ontology" "BRENDA Tissue and Enzyme Source Ontology" "Cell Ontology" "Microarray and Gene Expression Data Ontology" "Human Disease Ontology" INVESTIGATION Investigation Identifier "" Investigation Title "" Investigation Description "" Investigation Submission Date "" Investigation Public Release Date "" Comment [Created with configuration] "" Comment [Last Opened With Configuration] "" INVESTIGATION PUBLICATIONS Investigation PubMed ID "" Investigation Publication DOI "" Investigation Publication Author List "" Investigation Publication Title "" Investigation Publication Status "" Investigation Publication Status Term Accession Number "" Investigation Publication Status Term Source REF "" INVESTIGATION CONTACTS Investigation Person Last Name "" Investigation Person First Name "" Investigation Person Mid Initials "" Investigation Person Email "" Investigation Person Phone "" Investigation Person Fax "" Investigation Person Address "" Investigation Person Affiliation "" Investigation Person Roles "" Investigation Person Roles Term Accession Number "" Investigation Person Roles Term Source REF "" STUDY Study Identifier "E-GEOD-12860" Study Title "Transcriptional profiling of human knee chondrocytes stimulated with supernatant from synovial fibroblasts treated with NSAIDs or other drugs. [original title: Transcription profiling of human chondrocytes antirheumatic drug response: potential molecular targets to stimulate cartilage regeneration]" Study Description "Chondrocytes were isolated from cadaver knees and grown in alginate suspension to mimic cartilage-like conditions. Then, chondrocytes were stimulated with conditioned medium from synovial fibroblasts (SFs) either from rheumatoid arthritis patients (RASFs) or from normal donors (NDSFs). SFs had been pre-treated with a drug from one of three classes: disease-modifying antirheumatic drugs (DMARDs: azathioprine, gold sodium thiomalate, chloroquine phosphate, or methotrexate), nonsteroidal anti-inflammatory drugs (NSAIDs: piroxicam or diclofenac), or steroidal anti-inflammatory drugs (SAIDs: methylprednisolone or prednisolone). [original description: Rheumatoid arthritis (RA) leads to progressive destruction of articular structures. Despite recent progress in controlling inflammation and pain, little cartilage repair has yet been observed. This in vitro study aims to determine the role of chondrocytes in RA-related cartilage destruction and antirheumatic drug-related regenerative processes. Human chondrocytes were three-dimensionally cultured in alginate beads. To determine the RA-induced gene expression pattern, human chondrocytes were stimulated with supernatant of RA synovial fibroblasts (RASF) and normal donor synovial fibroblasts (NDSF), respectively. To examine antirheumatic drug response signatures, human chondrocytes were stimulated with supernatant of RASF that have been treated with disease-modifying antirheumatic drugs (DMARD; azathioprine, sodium aurothiomalate, chloroquine phosphate, methotrexate), non-steroidal anti-inflammatory drugs (NSAID; piroxicam, diclofenac) or steroidal anti-inflammatory drugs (SAID; methylprednisolone, prednisolone). Genome-wide expression profiling with oligonucleotide microarrays was used to determine differentially expressed genes. Real-time RT-PCR and ELISA were performed for validation of microarray data. Following antirheumatic treatment, microarray analysis disclosed a reverted expression of 94 RA-induced chondrocyte genes involved in inflammation/NF-kappaB signaling, cytokine/chemokine activity, immune response, proliferation/differentiation and matrix remodeling. Hierarchical clustering analysis showed that treatment of RASF with the DMARD azathioprine, gold sodium thiomalate and methotrexate resulted in chondrocyte gene expression signatures that were closely related to the healthy€ pattern. Treatment with the SAID methylprednisolone and prednisolone strongly reverted the RA-related chondrocyte gene expression, in particular the expression of genes involved in inflammation/NF-kappaB and cytokine/chemokine activity. The NSAID piroxicam and diclofenac and the DMARD chloroquine phosphate had only moderate to marginal effects. Pathway analysis determined major mechanisms of drug action, for example pathways of cytokine-cytokine receptor interaction, TGF-beta/TLR/Jak-STAT signaling and ECM-receptor interaction were targeted. This in vitro study provides a comprehensive molecular insight into the antirheumatic drug response signatures in human chondrocytes, thereby revealing potential molecular targets, pathways and mechanisms of drug action involved in chondrocyte regeneration. Thus, the present study may contribute to the development of novel therapeutic chondro-protective compounds and strategies. Experiment Overall Design: Drug-related suppression of gene expression in activated chondrocytes was determined by genome-wide microarray analysis. Chondrocytes were stimulated with supernatant of RASF and NDSF. Effect of treatment with DMARDs, NSAIDs and glucocorticoids was tested by treating RASF prior to collection of supernatant. Two RNA pools were analyzed for each group (RASF-stimulated NDSF stimulated and RASF-treated), each pool consisting of equal amounts of RNA from three different donors.]" Comment[Study Grant Number] "" Comment[Study Funding Agency] "" Study Submission Date "" Study Public Release Date "2008-10-25" Study File Name "s_E-GEOD-12860_study_samples.txt" STUDY DESIGN DESCRIPTORS Study Design Type "unknown_experiment_design_type" "transcription profiling by array" Study Design Type Term Accession Number "" "" Study Design Type Term Source REF "" "" STUDY PUBLICATIONS Study PubMed ID "19192274" Study Publication DOI "10.1186/ar2605" Study Publication Author List "Andreas K, Häupl T, Lübke C, Ringe J, Morawietz L, Wachtel A, Sittinger M, Kaps C." Study Publication Title "Antirheumatic drug response signatures in human chondrocytes: potential molecular targets to stimulate cartilage regeneration." Study Publication Status "Published" Study Publication Status Term Accession Number "" Study Publication Status Term Source REF "" STUDY FACTORS Study Factor Name "drug" "drug type" "replicate" "donor pool" "fibroblast disease state" Study Factor Type "treatment" "drug type" "replicate" "donor" "disease state" Study Factor Type Term Accession Number "" "" "" "" "" Study Factor Type Term Source REF "" "" "" "" "" STUDY ASSAYS Study Assay File Name "a_E-GEOD-12860_GeneChip_assay.txt" Study Assay Measurement Type "transcription profiling" Study Assay Measurement Type Term Accession Number "" Study Assay Measurement Type Term Source REF "" Study Assay Technology Type "DNA microarray" Study Assay Technology Type Term Accession Number "" Study Assay Technology Type Term Source REF "" Study Assay Technology Platform "" STUDY PROTOCOLS Study Protocol Name "P-G12860-1" "P-G12860-2" "P-G12860-4" "P-G12860-3" "Affymetrix:Protocol:Hybridization-EukGE-WS2v4_450" "P-AFFY-6" "chondrocyte isolation" Study Protocol Type "grow" "specified_biomaterial_action" "nucleic_acid_extraction" "labeling" "hybridization" "feature_extraction" "sample collection" Study Protocol Type Term Accession Number "" "" "" "" "" "" "" Study Protocol Type Term Source REF "" "" "" "" "mo" "" "" Study Protocol Description "Human chondrocytes obtained from lateral condyle of femur bones of 6 donors post mortem were amplified by cultivation in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100ug/ml streptomycin for 2 passages, subsequently 3D cultured in alginate beads for 14 days in presence of 170uM L-ascorbic acid 2-phosphate and finally stimulated with conditioned medium of RASF, NDSF, or treated RASF." "Human chondrocytes were isolated by enzymatic digestion (1 U collagenase P, 333 U collagenase II and 33 U hyaluronidase), passage 2 chondrocytes were encapsulated in alginate beads (20 Mio cells/ml in 1.5% (w/v) alginate) and stimulated with conditioned medium of NDSF, RASF or treated RASF" "Prior to RNA extraction, alginate beads were solubilized on ice in 55mM sodium citrate, 30mM EDTA and 150mM NaCl and cells were centrifuged at 800g for 5min (4°C). Total RNA isolation was proceeded according to the manufacturer's protocol. Additionally, a proteinase K and DNase I digestion were performed. Isolation of total RNA was done for the different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF." "2.5 ug of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)" "Title: Affymetrix EukGE-WS2v4_450 Hybridization. Description: " "Title: Affymetrix CEL analysis. Description: " "Chondrocytes were isolated post-mortem from donors (n=6; age range 39-74 years, avg. 60) with no known predisposition for joint disorders." Study Protocol URI "" "" "" "" "" "" "" Study Protocol Version "" "" "" "" "" "" "" Study Protocol Parameters Name "" "" "" "" "" "" "" Study Protocol Parameters Name Term Accession Number "" "" "" "" "" "" "" Study Protocol Parameters Name Term Source REF "" "" "" "" "" "" "" Study Protocol Components Name "" "" "" "" "" "MicroArraySuite 5.0" "" Study Protocol Components Type "" "" "" "" "" "" "" Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" STUDY CONTACTS Study Person Last Name "Häupl" Study Person First Name "Thomas" Study Person Mid Initials "" Study Person Email "thomas.haeupl@charite.de" Study Person Phone "" Study Person Fax "" Study Person Address "Rheumatology, Charité, Tucholskystr. 2, Berlin, 10117, Germany" Study Person Affiliation "Charité" Study Person Roles "submitter" Study Person Roles Term Accession Number "" Study Person Roles Term Source REF "" Comment[Study Person REF] ""