Shared and unique features distinguishing follicular T helper (TFH) and regulatory (TFR) cells from peripheral lypmh node and Peyer's Patches [Agilent-084107]

Transcriptome analyses were done comparing gene regulation of TFH and TFR cells isolated from Peyer’s Patches (PP) and immunized peripheral lymph nodes (pLN) revealing many regulatory patterns common to all follicular cells. However, in contrast to TFH cells, the kinetic but also the extent of regulation regarding many genes was attenuated in pLN TFR cells when compared to those of PP. Additionally, PP but not pLN TFR cells were largely unresponsive to IL2 and expressed Il4 as well as Il21. Together with fundamental differences in gene expression that were found between cells of both compartments this emphasizes specific adaptations of follicular T cell functions to their micro-milieu. Cells from either pLN or PP were combined from 8-15 mice, the indicated CD4 T cell subtypes sorted by flow cytometry, the purity of the sorts controlled by re-analysis and RNA extracted. The obtained RNA provided the basis for one chip hybridization and subsequent data generation. For PP two independent experiments were done, for immunized pLN (12 days post immunization) three independent were done and for immunized pLN (25 days post immunization) two independent experiment were perforemd.