Comment[ArrayExpressAccession] E-GEOD-49872 MAGE-TAB Version 1.1 Public Release Date 2016-08-01 Investigation Title In vivo Gene Expression Profiling of RPE/choroid Post-Intravitreal Injections of Dexamethasone and Triamcinolone at Clinically Relevant Time Points for Patient Care Comment[Submitted Name] In vivo Gene Expression Profiling of RPE/choroid Post-Intravitreal Injections of Dexamethasone and Triamcinolone at Clinically Relevant Time Points for Patient Care Experiment Description PURPOSE To identify retinal pigment epithelial (RPE)/choroid genes and their relevant expression pathways affected by intravitreal injections of dexamethasone and triamcinolone acetonide in mice at clinically relevant time points for patient care. METHODS Differential gene expression of over 34,000 well-characterized mouse genes, in the RPE/choroid of 6 week old C57BL/6J mice were analyzed after intravitreal steroid injections at 1 week and 1 month post injection, using Affymetrix Mouse Genome 430 2.0 microarrays. The data were analyzed using GeneSpringGX12.5 and Ingenuity Pathway Analysis (IPA) microarray analysis software for biologically relevant changes. RESULTS Both triamcinolone and dexamethasone caused differential activation of genes involved in ‘Circadian Rhythm Signaling’ pathway at both time points tested. Triamcinolone (TAA) uniquely induced significant changes in gene expression in ‘Calcium Signaling’ (1 week) and ‘Glutamate Signaling’ pathways (1month). In contrast, Dexamethasone (Dex) affected the ‘GABA Receptor Signaling’ (1 week) and ‘Serotonin Receptor Signaling’ (1month) pathways. CONCLUSIONS Understanding how intraocular steroids affect the gene expression of RPE/choroid is clinically relevant. This in vivo study has elucidated several genes and pathways that are potentially altering the circadian rhythms and several other neurotransmitter pathways in RPE/choroid cells during intravitreal steroid injections, which likely has consequences in the dysregulation of RPE function and neurodegeneration of the retina. Total of 18 RPE/choroid samples were analysed. There were two time points, day7 and day30. Each time point had three groups: BSS control, DEX treatment and TAA treatment. Each group had three biological replicas. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Smit-McBride Smit-McBride Person First Name Zeljka Zeljka Person Email zsmcbride@ucdavis.edu Person Affiliation UC Davis Person Address Ophthalmology, UC Davis, One Shields Ave, Tupper Hall #2403, Davis, CA, USA Person Roles submitter Protocol Name P-GSE49872-1 P-GSE49872-5 P-GSE49872-6 P-GSE49872-2 P-GSE49872-3 P-GSE49872-4 P-GSE49872-7 Protocol Description The data were analyzed with GeneSpring GX 11 using RMA algorhitm as analysis and normalization method. ID_REF = VALUE = RMA normalized signal intensity Biotinylated cRNA were prepared according to the two-cycle Affymetrix protocol from 0.100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Animals were sacrificed within CO2 chamber, eyes were enucleated, disected, retinal tissue was removed and quicky immersed into 300ul RNALater. Samples were stored in RNALater at -20C till the total RNA isolation step. Mice were 2 months old, kept at normal 12/12 light/dark conditions, feed ad libitum Total RNA was isolated using Qiagen RNeasy kit according to the manufacturer's instructions. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name treatment day Experimental Factor Type treatment day Publication Title Comparison of In Vivo Gene Expression Profiling of RPE/Choroid following Intravitreal Injection of Dexamethasone and Triamcinolone Acetonide. Publication Author List Smit-McBride Z, Moisseiev E, Modjtahedi SP, Telander DG, Hjelmeland LM, Morse LS PubMed ID 27429799 Publication DOI 10.1155/2016/9856736 Comment[SecondaryAccession] GSE49872 Comment[GEOReleaseDate] 2016-08-01 Comment[ArrayExpressSubmissionDate] 2013-08-14 Comment[GEOLastUpdateDate] 2016-08-01 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-49872.sdrf.txt