Tbet dysregulation compensates for Ets-deficiency in iNKT1 cells

The goal of this study was to compare the gene expression program of liver iNKT1 cells from Control mice to those with a postselection deletion of the transcription factor Ets1 and heterozybous deletion of Tbx21. Ets1-floxed and Tbx21-floxed alleles were deleted in iNKT1 cells using Tbx21Cre bacterial artifical chromosome transgenic mice that also carry a Rosa26-floxed-stop-YFP reporter. Control iNKT1 cells were Tbx21Cre+ Rosa26-floxed-stop-YFP reporter+ and cKOHet iNKT cells were Tbx21Cre+ Ets1F/F Tbx21F/+ Rosa26-floxed-stop-YFP reporter+. The differentially expressed genes were compared to those in liver iNKT1 cells with postselection deletion of Ets1 only. We examined gene expression by RNA-sequencing of sorted iNKT1 cells (CD1d-Tet-PBS57+ YFP+) from the liver. Reads were aligned to the mm10 reference genome using Tophat v 2.1.0. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 3 independent replicates by EdgeR. We found that iNKT1 cells lacking Ets1 upregulated Tbx21 and its protein Tbet, many Tbet target genes, and CD8 effector T cell associated genes. Overall design: Expression profiling analysis of RNA from thymic and liver iNKT1 cells isolated from Ctrl (Tbx21Cre; Rosa26-YFP+) and cKO (Tbx21Cre; Rosa26-YFP+; Ets1F/F) mice by RNA-sequencing. 3 independent replicates for each sample.