GSE158814
Genome-wide analysis of Chlamydia trachomatis-infected cells
Chlamydia trachomatis is the most common sexually transmitted infection and the bacterial agent of trachoma globally. C. trachomatis undergoes a biphasic developmental cycle involving an infectious elementary body and a replicative reticulate body. Little is currently known about the expression of host cell mRNAs, lncRNAs, and miRNAs at different stages of C. trachomatis development.   Here, we performed RNA-seq and miR-seq on HeLa cells infected with C. trachomatis serovar E at 20 hpi and 44 hpi with or without IFN-? treatment. Our study identified and validated differentially expressed host cell mRNAs, lncRNAs, and miRNAs during infection. Infection at 20 hpi showed the most differential upregulation of both coding and non-coding genes while infection at 44 hpi in the presence of IFN-? resulted in a dramatic downregulation of a large proportion of genes. Using RT-qPCR, we validated the top 5 stage-specific upregulated mRNAs and miRNAs. One of the commonly expressed miRNAs at all three stages, miR-193b-5p, showed significant expression in clinical serum samples of C. trachomatis-infected patients as compared to sera from healthy controls and HIV-1-infected patients. Furthermore, at 20 hpi we observed significant upregulation of antigen processing and presentation, and T helper cell differentiation pathways whereas T cell receptor, mTOR, and Rap1 pathways were modulated at 44 hpi. Treatment with IFN-? at 44 hpi showed the regulation of cytokine-cytokine receptor interaction, FoxO signaling, and Ras signaling pathways.   Our study documents a role for the stage-specific transcriptional manipulation of the host cell genome and important signaling pathways that are necessary for the survival of pathogen and could serve as potential biomarkers in the diagnosis and management of the disease. Overall design: HeLa cells were infected with C. trachomatis and the cells were harvested at 20hr post-infection (hpi) and  44 hpi. Uninfected HeLa cells were used as negative controls (NC). To allow C. trachomatis transformation into the persistent aberrent reticulate body (ARB) stage, cells were treeted with 50 units of interferon-gamma for 44 hpi.  Cells were treated with 50 units of interferon-gamma for 44hr were used as negative control. Cells were harvested at the indicated time followed by RNA extraction. Total RNAs from all samples were used for RNA-seq and miR-sequencing at the Beijing Genome Institute (China).