Comparative transcriptomics of host-pathogen interactions and hybridization in Candida pathogens

Opportunistic human fungal pathogens pose a serious threat for global healthcare. In part due to an increasing number of immunocompromised people worldwide, the incidence of fungal infections has been growing in the last two decades (Pfaller and Diekema, 2007; Oren and Paul, 2014). These infections range from superficial rushes, affecting a quarter of the human population, to life-threatening invasive mycoses, which kill 1.5 million people annually (Havlickova, Czaika and Friedrich, 2008; Brown et al., 2012). Yeasts from the Candida clade are among the major opportunistic human fungal pathogens (Guinea, 2014). These fungi normally constitute part of the healthy human microbiome, but in immunocompromised states they can originate severe infections, with mortality rates reaching 60-70% (Flevari et al., 2013; Klingspor et al., 2015). Candida pathogens have several peculiarities which make them difficult to deal with. They are phylogenetically diverse, novel pathogenic species are constantly appearing - sometimes through interspecies hybridization - and they often develop resistance to antimycotic drugs (Gabaldon, Naranjo-Ortiz and Marcet-Houben, 2016; Ksiezopolska and Gabaldon, 2018; Mixao and Gabaldon, 2018). Due to these properties, we still lack fast and accurate diagnostics tools and effective approaches for treating candidiasis. Despite the great importance of Candida infections for our health, the research on host-pathogen interactions of these yeasts, and fungi in general, has been traditionally somewhat neglected compared to other microorganisms (‘Stop neglecting fungi’, 2017). Advances in next-generation sequencing in the previous decade have opened unprecedented possibilities for studying the biology of these fungi. For example, genome sequencing serves as an important tool, which has already allowed to disentangle complex phylogenetic relationships among Candida and uncovered hybridization as one of the driving forces underlying the emergence of novel Candida pathogens (Pryszcz et al., 2015; Gabaldon, Naranjo-Ortiz and Marcet-Houben, 2016; Mixao et al., 2019). Transcriptome sequencing by means of RNA-Seq is a powerful technique which dissects the dynamic interactions between host and pathogen at the level of gene expression (Westermann, Barquist and Vogel, 2017). Despite the proven power of this methodology to disentangle the direct and immediate mechanisms of host-pathogen interplay during infection, so far there are only a handful of studies using this technique on Candida pathogens. Thus, there are still numerous fundamental and technical issues in the context of human-Candida interactions that can be effectively addressed using transcriptomics. In this thesis, we applied large scale comparative transcriptomics and bioinformatics to investigate central basic and methodological aspects of host-pathogen interactions and emergence of virulence in Candida pathogens. In particular, we investigated the transcriptomic basis of host-pathogen interactions in vitro between human epithelium and four major Candida species, revealing generalized and specific mechanisms. Apart from the protein coding portion of fungal transcriptomes, we assessed, for the first time, the potential role of long non-coding transcripts in the virulence of these fungi. We additionally made the first steps towards clarifying how hybridization shapes the transcriptomes of yeast hybrids, and whether this shaping has links to the emergence of pathogenesis. From a methodological perspective, we developed novel experimental approaches and bioinformatics tools that greatly facilitate the study of host-fungus interactions, and which usage can be extended beyond the research topics of this thesis. Collectively, in the frame of this thesis we exploited the power of large scale comparative transcriptomics for addressing several key aspects of host-microbe interactions and emergence of pathogenicity in Candida species. The results of our work significantly extend our understanding of these important questions, and also open new exciting perspectives for future research in the field. Moreover, the tools and the extensive transcriptome sequencing data generated in this project will certainly serve as a rich and powerful resource for the research community. References Pfaller, M. A. and Diekema, D. J. (2007) ‘Epidemiology of invasive candidiasis: a persistent public health problem’, Clinical microbiology reviews, 20(1), pp. 133–163. 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