Simultaneous transcriptional profiling of Chlamydia and their host cells by heterogenous RNA-Seq (hRNA-Seq)

Bacterial pathogens subvert host cells by using their gene products to manipulate cellular pathways for survival and replication; in turn, host cells respond to invading pathogens through cascading changes in gene expression. Deciphering this complex temporal and spatial interplay is crucial for improved diagnostics and therapeutics. However, the technical limitations of existing methods of expression profiling, such as microarray analysis, significantly reduce their utility for obtaining both bacterial and host expression profiles from infected cells. We developed the heterogeneous RNA-Seq (hRNA-Seq) method to simultaneously capture prokaryotic and eukaryotic expression profiles of bacteria-infected cells. As proof of principle, hRNA-Seq was applied to <em>Chlamydia</em>-infected cells, successfully obtaining the transcriptomes of both <em>Chlamydia</em> and their host cells at 1 and 24 hours post-infection. Substantial transcription was found in the immediate-early period of infection for both <em>Chlamydia</em> and the host cell. Numerous novel host responses were found; in particular we discovered putative positive feedback mechanisms for <em>Chlamydia</em>-induced fibrotic scarring.