ONTOLOGY SOURCE REFERENCE
Term Source Name	"ArrayExpress"	"EFO"	"NCBITaxon"	"BTO"	"PATO"	"OBI"	"XCO"	"CHEBI"	""	
Term Source File	"http://www.ebi.ac.uk/arrayexpress/"	"http://www.ebi.ac.uk/efo/efo.owl"	"http://bioportal.bioontology.org/ontologies/47845"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO"	"http://bioportal.bioontology.org/ontologies/50280"	""	"http://bioportal.bioontology.org/ontologies/50737"	"http://bioportal.bioontology.org/ontologies/50716"	""	
Term Source Version	""	""	"47845"	"Jun 2010"	"50280"	""	"50737"	"50716"	""	
Term Source Description	""	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"BRENDA tissue / enzyme source"	"Phenotypic Quality Ontology"	""	"Experimental Conditions Ontology"	"Chemical Entities of Biological Interest Ontology"	""	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-18103"
Study Title	"Adipocytes desensitized and resensitized to insulin through the combined action of TNF-alpha, aspirin, and troglitazone. [original title: A Gene Expression Signature for Insulin Resistance]"
Study Description	"3T3-L1 fibroblasts were cultured and treated in 3 stages. First, they were differentiated into adipocytes with >80% efficiency. Second, they were treated with or without TNF-alpha for 48 hours; treated cells became insulin-resistant. Third, they were treated with or without aspirin and troglitazone for an additional 24 hours; these treated cells became resensitized to insulin. [original description: Insulin resistance is a heterogeneous disorder caused by a range of genetic and environmental factors, and we hypothesise that its aetiology varies considerably between individuals. This heterogeneity provides significant challenges to the development of effective therapeutic regimes for long-term management of type 2 diabetes. We describe a novel strategy, using large-scale gene expression profiling, to develop a gene expression signature (GES) that reflects the overall state of insulin resistance in cells and patients. The GES was developed from 3T3-L1 adipocytes that were made “insulin resistant” by treatment with tumour necrosis factor (TNF-alpha and then reversed with aspirin and troglitazone (“re-sensitized”). The GES consisted of 5 genes whose expression levels best discriminated between the insulin resistant and insulin re-sensitized states. We then used this GES to screen a compound library for agents that affected the GES genes in 3T3-L1 adipocytes in a way that most closely resembled the changes seen when insulin resistance was successfully reversed using aspirin and troglitazone. This screen identified both known and new insulin sensitising compounds including non-steroidal anti-inflammatory agents, beta-adrenergic antagonists, beta-lactams and sodium channel blockers. We tested the biological relevance of this GES in participants in the San Antonio Family Heart Study (n = 1,240) and showed that patients with the lowest GES scores were more insulin resistant (according to HOMA_IR and fasting plasma insulin levels, P < 0.001). These findings show that GES technology can be used for both discovery of insulin sensitising compounds and characterisation of patients into subtypes of insulin resistance according to GES scores, opening the possibility of developing a personalised medicine approach to type 2 diabetes. Three-condition experiment, Vehicle, TNF and TNF+ASA+TGZ with biological replicates: 22 Vehicle, 21 TNF and 21 TNF+ASA+TGZ , independently grown and harvested. One replicate per array.]"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2010-09-10"
Study File Name	"s_E-GEOD-18103_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"21081660"
Study Publication DOI	"10.1152/physiolgenomics.00115.2010"
Study Publication Author List	"Konstantopoulos N, Foletta VC, Segal DH, Shields KA, Sanigorski A, Windmill K, Swinton C, Connor T, Wanyonyi S, Dyer TD, Fahey RP, Watt RA, Curran JE, Molero JC, Krippner G, Collier GR, James DE, Blangero J, Jowett JB, Walder KR"
Study Publication Title	"A gene expression signature for insulin resistance."
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STUDY FACTORS
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-18103_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"differentiation"	"TNF_treatment"	"TNF_treatment_control"	"resensitization"	"resensitization_control"	"P-GSE18103-4"	"P-GSE18103-5"	"P-GSE18103-6"	"P-GSE18103-7"	"P-GSE18103-1"
Study Protocol Type	"differentiation"	"sample treatment protocol"	"sample treatment protocol"	"sample treatment protocol"	"sample treatment protocol"	"nucleic acid extraction protocol"	"labeling protocol"	"hybridization protocol"	"array scanning protocol"	"normalization data transformation protocol"
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Study Protocol Description	"Preconfluent cultures in DMEM + 10% FBS + pen/strep were grown to confluence, maintained for 2 days at postconfluence, and treated with 2 μg/ml insulin, 0.25 μm dexamethasone, and 0.5 mm 3-isobutyl-1-methylxanthine.  After 3 days, the medium was replaced with fresh DMEM + 10% FBS and 2 μg/ml insulin for another 3 days.  Adipocytes were maintained in DMEM + 5% FBS for 2 days thereafter.  Adipocytes were used 8-12 days after initiation of differentiation, after which time more than 80% of fibroblasts had differentiated into mature adipocytes."	"Treated with TNFα (3 ng/ml; Peprotech) for 48 h in DMEM + 10% heat-inactivated FBS (Invitrogen).  Treatments were replenished every 24 h."	"Incubated for 48 h in DMEM + 10% heat-inactivated FBS (Invitrogen).  Media were replenished every 24 h."	"Treated with TNF-alpha (3 ng/ml) + troglitazone (10µM) + aspirin (5mM) for 24 h in DMEM + 0.2% BSA."	"Incubated for 24 h in DMEM + 0.2% BSA."	"Total RNA was extracted from 3T3-L1 adipocytes using TRIzol reagent and purified using RNA clean-up columns as per manufacturer’s instructions."	"Fluorescently labelled cDNA was prepared from 20 µg total RNA using an indirect labeling method. cDNA synthesis was performed in a 30 µl reaction containing 2 µg oligo-dT primer, 200 U Superscript III, 1 x first-strand buffer, 5 mM DTT, 0.5mM dNTP mix and 1.3 µg/µl RNaseOUT (Invitrogen). Synthesis was conducted in a GeneAmp PCR System 9700 (PE Applied Systems) at 46°C for 2 h."	"The hybridization solution (40 µl) was then applied to coverslips and mounted onto the array slide. Hybridization was conducted in humid hybridization chambers in a hybridization oven at 65°C for 16-20 h."	"Microarray slides were scanned using the GenePix 4000B scanner (Molecular Devices)."	"Data were extracted using GenePix Pro 5.1 software (Molecular Devices) with Normalisation (ratio based)  and primary microarray data analysis performed using Acuity 4 software (Molecular Devices). The data used for normalisation had to meet the following filtering criteria ('% > B532+2SD' > 55) AND ('% > B635+2SD' > 55) AND ('F532 % Sat.' < 3) AND ('F635 % Sat.' < 3) AND ('Sum of Medians (635/532)' > 200) AND ('Rgn R² (635/532)' > 0.5) AND ('Flags' >= 0). ID_REF =  VALUE = normalized log2 ratio (Cy5/Cy3) representing test/reference"
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STUDY CONTACTS
Study Person Last Name	"Sanigorski"	"Konstantopoulos"	"Foletta"	"Segal"	"Shields"	"Windmill"	"Sanigorski"	"Swinton"	"Connor"	"Wanyonyi"	"Dyer"	"Curran"	"Molero"	"Krippner"	"Collier"	"James"	"Blangero"	"Jowett"	"Walder"
Study Person First Name	"Andrew"	"Nicky"	"Victoria"	"David"	"Katherine"	"Kelly"	"Andrew"	"Courtney"	"Tim"	"Stephen"	"Thomas"	"Joanne"	"Juan-Carlos"	"Guy"	"Greg"	"David"	"John"	"Jeremy"	"Ken"
Study Person Mid Initials	""	""	"C"	"H"	"A"	""	""	""	""	""	"D"	"E"	""	""	"R"	"E"	""	"B"	"R"
Study Person Email	"geo@ncbi.nlm.nih.gov"	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""
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Study Person Address	"Faculty of Health Medicine Nursing & Behavioural Sciences, Deakin University, Pigdons Rd, Waurn Ponds, Victoria, Australia"	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Person Affiliation	"Deakin University"	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""	""
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