Transcriptome analysis of IFNγ producing and non-producing CD4 T cells during chronic intestinal inflammation.

Purpose: The goal of this study is to compare transcriptome profiles of IFNγ producing (Thy1.1+) and IFNγ non-producing (Thy1.1-) CD4 T cells during chronic intestinal inflammation using RNA sequencing. Methods: Total mRNA was isolated from FACS sorted CD44+Thy1.1+ and CD44+Thy1.1-CD4 T cells and sequenced in duplicate using Illumina HiSeq 2500 (2x100 base pair, paired-end reads). The sequence reads were aligned using mouse GRCm38.75 reference genome. DESeq2 software was used for differential expression analysis. Results: Differential expression analysis with DESeq2 algorithm revealed that a total of 942 and 1091 genes were significantly increased in the IFNγ+ and IFNγ- effector CD4 T cells, respectively (adjusted p value <0.05). We also performed gene set enrichment analysis (GSEA) by pre-ranking RNA sequencing data according to an adjusted p-value and the sign of differential expression. GSEA regults suggested that IFNγ+ CD4 T cells had terminally differentiated phenotype, while IFNγ- CD4 T cells had transcriptional profile associated with self-renewal and stemness. Conclusions: Our study suggests that effector CD4 T cells exist in a spectrum of differentiation status during chronic intestinal inflammation, which impacts pathogenicity of CD4 T cells. mRNA profiles of IFNγ producing and non-producing CD4 T cells during chronic intestinal inflammation.