Microevolution of pathogenic yeasts during interactions with the host immune system

Candida albicans and C. glabrata are the two most important causes of candidemia - a life-threatening, systemic fungal infection. As commensals and opportunistic pathogens, these yeasts have to be able to adapt to the many different niches inside their human host. We aim to use in vitro and in vivo forced microevolution experiments, both to determine the ability of these fungi to adapt to host-induced stresses, and to identify novel potential pathogenicity factors. To this end, we will first expose C. glabrata to macrophages in a serial passage setup and follow the genetic, phenotypic, and transcriptional changes induced by constant host-fungus interaction. In a second approach, we will use a mutant of C. albicans, which is unable to form hyphae, a property which is essential for virulence and escape from phagocytes. Again, the mutant will be exposed to macrophages in serial passages and its ability to survive and regain hyphal formation by transcriptional rewiring will be followed. Finally, we will investigate the ability of C. albicans to adapt to different host niches. In a murine infection model, we will follow the genetic and transcriptional (transcriptional rewiring) changes as well as changes of organotropism of the fungus after serial re-isolation and infection, and we will compare this to data from a collection of clinical isolates obtained from different host niches. We expect to find adaptations and mechanisms in both fungi, which may constitute novel, `hidden` pathogenicity factors.

Candida albicans and C. glabrata are the two most important causes of candidemia a life-threatening, systemic fungal infection. As commensals and opportunistic pathogens, these yeasts have to be able to adapt to the many different niches inside their human host. This project aimed to use in vitro and in vivo forced microevolution experiments, as well as whole-genome dual species transcriptomics analysis to determine the ability of these fungi to adapt to host-induced stresses during immune cell invasion. A major goal was to identify novel potential pathogenicity factors that could contribute to immune evasion and or persistence of fungal pathogens in the host. We demonstrated that host immune cell phagocytosis can trigger severe transcriptional changes in the fungal pathogens. We discover for the first time interspecies regulatory networks in both host and in fungal pathogens, whose interplay determine the magnitude and duration and specificity of the host immune response, and thus the outcome of fungal infections. Remarkably, considerable differences exist between Candida albicans and Candida glabrata, since the latter tends to resist host immune defense much better and thus can persist in the host for prolonged periods without getting cleared. This may also be due to the low level of host inflammation triggered by Candida glabrata. Moreover, using dual species RNA-Seq, which was accomplished for the first time to study the dynamics of fungal pathogen host interactions in primary immune cells such as dendritic cells, we demonstrate that the host immune surveillance triggers a stage-specific splicing of potential virulence genes in Candida albicans. Since most spliced genes affect fungal ribosome biogenesis, a new hypothesis emerged from this work, suggesting that splicing of certain genes may contribute to the evasion of host immune surveillance by the generation of functionally distinct ribosomes. This sets the stage for our future work to decipher the molecular mechanisms and signals that trigger the splicing events in fungal pathogens exposed to host immune defense. Finally, the project lead to several collaborative publications with the group of Bernhard Hube from the KHI in in Jena. In particular, we demonstrate that the complexity of the host immune response may also represent a key driver of microevolution within fungal genome. The underlying processes could aid the pathogen in surviving or escaping from the host immune surveillance. The key collaborative publications papers resulting from this project are listed in the publication list this report.