Butyrate alters gene expression profiles in gBT-I cells

Purpose: The aim of this study is to dissect if the microbiota-derived metabolite butyrate alters the transcriptome of antigen-activated CD8+ T cells. Methods: mRNA profiles from Ctrl and Butyrate-treated gBT-I were generated by deep sequencing, in triplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: The analysis of RNAseq data of Ctrl and Butyrate-treated gBT-I lead to ~2,000 differentially expressed genes (FDR < 0.05; fold change>2). GSEA enrichment analysis revealed enrichment of memory T cells signatures in gBT-I following butyrate-treatment (Sarkar et al., 2008). Conclusions: Our data shows that butyrate alters the transcriptome of effector CD8+ T cells, in particular their memory signature. in vitro activated gBT-I mRNA profiles on d6 were generated by deep sequencing, in triplicate, using Illumina GAIIx.

研究目的：本研究旨在解析微生物群来源的代谢产物丁酸（butyrate）是否会改变抗原激活的CD8+ T细胞的转录组。
研究方法：采用Illumina GAIIx平台对对照组（Ctrl）与丁酸处理组的gBT-I细胞进行三次生物学重复的深度测序，获取其mRNA表达谱。对通过质量过滤的测序reads，分别采用两种方法在转录本异构体水平开展分析：一是Burrows–Wheeler对齐工具（Burrows–Wheeler Aligner, BWA）结合方差分析（Analysis of Variance, ANOVA），二是TopHat结合Cufflinks。
研究结果：对对照组与丁酸处理组gBT-I细胞的RNA测序数据进行分析，共鉴定得到约2000个差异表达基因（错误发现率FDR < 0.05，倍数变化fold change > 2）。基因集富集分析（Gene Set Enrichment Analysis, GSEA）结果显示，经丁酸处理后的gBT-I细胞富集了记忆性T细胞特征基因集（Sarkar等，2008）。
研究结论：本研究数据表明，丁酸可改变效应性CD8+ T细胞的转录组，尤其是其记忆性细胞特征。本研究同时对体外激活第6天的gBT-I细胞进行了三次生物学重复的Illumina GAIIx深度测序，获取其mRNA表达谱。