Dual RNA-seq analysis of Mycobacterium tuberculosis-infected lung macrophages reveals cell-lineage specific host-pathogen dynamics

Background: Dissecting the in-vivo host-pathogen interplay is crucial in understanding the molecular mechanisms governing control or progression of the infection. While Dual RNA-seq offers significant advantages over traditional approaches in the analysis of intracellular infections, to date technical challenges have restricted the application of this technology predominantly to tissue culture infection models. We addressed this problem by developing new protocols which allowed us to perform, for the first time, Dual RNA-seq on Mycobacterium tuberculosis-infected and ontogenetically distinct macrophages isolated directly from murine lungs. Results: Through analysis of the Mtb transcripts specifically induced during infection of alveolar and interstitial macrophages, we first identified an in-vivo signature, a set of 180 genes uniquely upregulated by Mtb in mouse lung macrophages. Furthermore, comparative analysis of transcripts from both Mtb and the two macrophage lineages uncovers that alveolar macrophages exhibit an M2-like polarization profile and promote bacterial growth through increased access to iron and fatty acids, while the interstitial macrophages exhibit a pro-inflammatory profile and restrict bacterial growth through iron sequestration and higher levels of nitric oxide. Conclusions: Our study reports a new bacterial transcripts enrichment protocol which enabled us to perform dual-RNA seq at the infected cell level, providing a comprehensive look at the divergent transcriptional signatures that characterizes survival of Mtb in the two major myeloid cells. The data re-emphasizes the significance of nutritional immunity for in vivo control of infection via an unbiased interrogation of both host and pathogen transcriptomes. Our approach provides a new tool to probe bacterial physiology at the host cell level in an in-vivo environment and therefore has a broad impact in understanding infections of intracellular pathogens. Examination of the transcriptional profile of both Mtb and the host cell in 2 different myeloid lineages isolated directly from the mouse lungs.