Gene expression profile of differentially recognized Mtb-epitopes as a function of disease history

Purpose: The goals of this study are to compare two types of Mtb epitope-specific transcriptome profiling (RNA-seq) in individuals with latent TB infection. Methods: Epitope-specific T cells were isolated by IFNg capture assay or activation induced marker assay (CD25, OX40). Total RNA was purified using miRNAeasy micro kit from Qiagen and amplified using Smart-seq2 protocol. Nextera CT sequencing libraries were prepared and samples were sequenced using HiSeq2500 from Illumina. The sequence reads that passed quality filters were mapped against the hg19 reference using TopHat. Differentially expressed genes between the two epitope sets were identified by Bioconductor package DESeq2, pairwise comparisons and Benjamimi-Hochberg-adjusted p values. Results: Quantile normalized gene expression values and pairwise comparisons between the epitope-specific memory T cells revealed 9 differentially expressed genes (adjusted p<0.05) for IFNg capture and 1 differentially expressed gene for activation induced marker assay. Comparison of T cells specific for 2 types of differentially recognized Mtb epitope sets using RNA-seq