Gene expression profiles of in vitro induced Foxp3+ regulatory T cells in mice. Mus musculus

Platelets are a rich source of many cytokines and chemokines including transforming growth factor β-1 (TGFβ1). TGFβ1 is required to convert conventional CD4+ T (Tconv) cells into induced regulatory T (iTreg) cells that express the transcription factor Foxp3. To explore whether other platelet contents will affect the properties of TGFβ induced Treg cell, we used platelet lysate that contain many other cytokines and chemokines besides TGFβ1 (pltTGFβ) to induce Foxp3 expression (pltTGFb-iTreg) from conventional CD4+ T (Tconv) cells. We used purified TGFβ1 to induce Treg (purTGFβ-iTreg) cells as a control. Gene expression profiles in iTreg cells were analyzed by microarray asay. Overall design: RNA was purified from pltTGFβ-iTreg, purTGFβ-iTreg, and Tconv cells. cDNA was labeled and hybridized to the Mouse Genome 430 2.0 GeneChip. Three biological replicates were performed and the results were averaged. Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. Probe sets that exhibited a 1.4-fold difference (|log2 ratio| > 0.5) relative to Tconv cells were identified and those that possessed a false discovery rate of <10% were used in subsequent analyses. The statistical significance of differential gene expression was determined through ANalysis Of VAriation (ANOVA) and false discovery rates (FDR) using Partek Genomics Suite 6.6. Hierarchical clustering was conducted with Genesis6. Pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery.