Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single,Candida albicansinfected macrophages

Abstract

13The control of fungal infections depends on interactions with innate immune cells including 14 macrophages, which are among the first host cell types to respond to pathogens such as Candida 15albicans. This fungus is a member of the healthy human microbiome, although also a devastating 16 pathogen in immunocompromised individuals. Consistent with recent findings from studies of other 17 pathogens, we observed that within a population of interacting macrophages and C. albicans, there are 18 distinct host-pathogen subpopulations reflecting cell specific trajectories and infection outcomes. Little 19 is known about the molecular mechanisms that control these different fates. To address this, we 20 developed an experimental system to isolate the major host-fungal pathogen subpopulations observed 21 during ex vivo infection using fluorescent markers. We separated subpopulations of macrophages 22 infected with live C. albicans from uninfected cells and assessed the variability of gene expression in 23 both host and fungal pathogen for each subpopulation across time using RNA-Seq. In infected cells, we 24 observed a coordinated, time-dependent shift in gene expression for both host and fungus. The early 25 response in macrophages was established upon exposure to C. albicans prior to engulfment and 26 involved up-regulation of pathways and regulatory genes required for cell migration, pathogen 27 recognition, activation of engulfment, and phagocytosis; this pro-inflammatory response declined during 28 later time points in parallel with expression changes in C. albicans. After phagocytosis, the initial 29 response of C. albicans was to up-regulate genes related to survival in the nutrient-limited and stressful 30 environment within macrophages; at later time points, gene expression shifted to initiate hyphal growth 31 and escape. To further probe the heterogeneity seen observed in host-pathogen interactions, we 32 performed RNA-Seq of single macrophages infected with C. albicans. We observed that some genes 33 show higher levels of heterogeneity in both host and fungal pathogen cells that we could not detect in 34 subpopulation samples; we observed that the time shift in expression is asynchronous and that 35 expression changes in both the host and pathogen are tightly coupled. This work highlights how 36 . CC-BY 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. BY 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint . http://dx.doi.org/10.1101/350322 doi: bioRxiv preprint first posted online Jun. 19, 2018; 3To overcome these challenges, we developed an experimental system to isolate subpopulations of 70 distinct infection outcomes and examined host and pathogen gene expression in parallel, in sorted 71 subpopulations a...

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