Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type APC and OX40L-TG APC induced T helper 17 cell Transcriptomes [RNA-seq]

Purpose:The goals of this study are to evaluate the effect of OX40 ligation on transcriptome profiling of in vitro polarized T helper 17 cell (RNA-seq). Methods: mRNA profiles of CD4+ T cells cultured in vitro under Th17-polarizing conditions for 48hrs (both Ctrl and OX40L treated groups) were generated by deep sequencing, using Illumina RapidRun. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays Results: Among the 398 genes that were significantly affected by OX40, only about 11% were previously identified as ROR?t target genes in Th17 cells. Conclusions: Our study suggests that OX40 unlikely affects Th17 commitment, but most likely impairs their effector differentiation. As IL-17A and IL-17F are Th17-defining cytokines, their suppression suggests that OX40 may inhibits effector functions of Th17 cells. Overall design: mRNA profiles of CD4+ T cells cultured in vitro under Th17 differentiation conditions for 48 hours in the presence of WT-APCs or OX40L-TG APCs were generated by deep sequencing using Illumina RapidRun.

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Xiao X, Shi X, Fan Y, Wu C, Zhang X, Minze L, Liu W, Ghobrial RM, Lan P, Li XC