RT Journal Article SR Electronic T1 Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single, Candida albicans infected macrophages JF bioRxiv FD Cold Spring Harbor Laboratory SP 350322 DO 10.1101/350322 A1 José F. Muñoz A1 Toni Delorey A1 Christopher B. Ford A1 Bi Yu Li A1 Dawn A. Thompson A1 Reeta P. Rao A1 Christina A. Cuomo YR 2018 UL http://biorxiv.org/content/early/2018/06/19/350322.abstract AB The control of fungal infections depends on interactions with innate immune cells including macrophages, which are among the first host cell types to respond to pathogens such as Candida albicans. This fungus is a member of the healthy human microbiome, although also a devastating pathogen in immunocompromised individuals. Consistent with recent findings from studies of other pathogens, we observed that within a population of interacting macrophages and C. albicans, there are distinct host-pathogen subpopulations reflecting cell specific trajectories and infection outcomes. Little is known about the molecular mechanisms that control these different fates. To address this, we developed an experimental system to isolate the major host-fungal pathogen subpopulations observed during ex vivo infection using fluorescent markers. We separated subpopulations of macrophages infected with live C. albicans from uninfected cells and assessed the variability of gene expression in both host and fungal pathogen for each subpopulation across time using RNA-Seq. In infected cells, we observed a coordinated, time-dependent shift in gene expression for both host and fungus. The early response in macrophages was established upon exposure to C. albicans prior to engulfment and involved up-regulation of pathways and regulatory genes required for cell migration, pathogen recognition, activation of engulfment, and phagocytosis; this pro-inflammatory response declined during later time points in parallel with expression changes in C. albicans. After phagocytosis, the initial response of C. albicans was to up-regulate genes related to survival in the nutrient-limited and stressful environment within macrophages; at later time points, gene expression shifted to initiate hyphal growth and escape. To further probe the heterogeneity seen observed in host-pathogen interactions, we performed RNA-Seq of single macrophages infected with C. albicans. We observed that some genes show higher levels of heterogeneity in both host and fungal pathogen cells that we could not detect in subpopulation samples; we observed that the time shift in expression is asynchronous and that expression changes in both the host and pathogen are tightly coupled. This work highlights how analysis of subpopulations and single host-pathogen pairs can resolve population heterogeneity and trace distinct trajectories during host interactions with fungal pathogens.