Transcriptome data of Foxp3-Cre, Ube2m&Ube2f-deficient Treg cells from mice

Neddylation is necessary for activation of Cullin-RING Ligases (CRLs) which degrade various immune regulatory proteins. Our recent study showed that while depletion of neddylation E2-E3 pair Ube2f-Sag in regulatory T cells (Treg cells) had no obvious phenotype, the same depletion of either Ube2m or Rbx1 caused inflammation disorders with different severity. Whether these E2s or E3s compensate each other in functional regulations of Treg cells is, however, previously unknown. In this report, we generated Foxp3Cre;Ube2mfl/fl;Ube2ffl/fl or Foxp3Cre;Rbx1fl/fl;Sagfl/fl double null mice by simultaneously deletion of both neddylation E2s or E3s in Treg cells, respectively. Remarkably, Ube2m&Ube2f double null mice developed much severe autoimmune phenotypes than Ube2m-null mice, indicating Ube2m significantly compensates Ube2f in Treg cells. The minor worsen autoimmune phenotypes seen at very early stage in Rbx1&Sag double null than Rbx1-null mice, is likely due to already severe phenotypes of the later, indicating a minor compensation of Rbx1 for Sag. The RNA profiling-based analyses revealed that up- and down-regulations of few signaling pathways in Treg cells are associated with the severity of autoimmune phenotypes. Finally, severer inflammation phenotypes seen in mice with double E3-null than with double E2-null Treg cells indicate a neddylation-independent mechanism of two E3s, also known to serve as the RING component of CRLs in regulation of Treg cell fitness. CD4+YFP+ Treg cells were sorted from the peripheral lymph nodes and spleens of indicated mice (8-12 weeks old). To generate enough materials, 2-3 mice were pooled for one sample. RNA was purified from the sorted cells with the miRNeasy Mini Kit (Qiagen, 21704). The RNAs were reverse transcribed, amplified, labeled (Affymetrix GeneChip pico kit, 703308) to achieve enough cDNAs. Then the cDNA samples were hybridized to Clariom S Arrays, mouse (902931). The Applied Biosystems Expression Console Software 1.4 was employed to analyze the microarray data sets.