Cryptococcus neoformans is a pathogenic yeasts that infect mostly immunocompromised people. The strain H99 belongs to the C. neoformans variety grubii group. This is the reference strain that have already been sequenced. A project initiated by the Broad Institute aims at analysing the genome of about 300 clinical isolates including 28 of our French isolates. Part of our French isolates have been screened in terms of interaction with macrophages (774). Huge variations in terms of phagocytosis and intracellular proliferation of the yeasts were observed between clinical isolates (Alanio et al. mBio 2011). Thirteen of these clinical isolates together with H99 were studied in terms of transcriptome (using RNASeq). This work was performed by MA Dillies at the PF2. We correlated the expression of about 150 genes with the phenotype of the 13 clinical isolates and H99.

The recent analysis of the Cryptococcus neoformans transcriptomes revealed the presence of thousands of lncRNAs. In these yeasts, different types of lncRNAs seem to exist. The ones that are antisense of coding genes (the NATs), the ones that are located between coding genes (the lincRNAs) and some others that seem to result from alternative transcription start site selection. We  identified growth conditions under which the expression of some of them is regulated. We have also identified some genes implicated in the regulation of some of these lncRNAs. This project deals with the characterisation of these lncRNAs, the analysis of their regulation and the study of their function in the biology and virulence of this pathogenic yeast.

Le génome de Cryptococcus neoformans a été réannoté grâce à des données RNA-seq. Ces nouvelles annotations doivent être soumises dans les banques publiques.

Cryptococcus neoformans is a sugar-coated yeast that is able to interact closely with numerous organisms in the environment including amebae, paramecium of nematodes. The interaction with these organisms probably shaped its virulence. The ability to survive nutrient starvation, oxidative stress, desiccation, both in the environment and in humans, indicates a high level of physiological and metabolic plasticity of the yeast. In humans, after primary infection during childhood, the yeast is able to survive within the host for years before reactivation, leading to a deadly disseminated fungal infection. This phenomenon, called dormancy / quiescence is one of the main biological features of this fungus in relation with disease pathogenesis. It is known in bacteria, parasites and other fungi. There is no consensus on the definition of dormancy. Most often, dormant cells are characterized by a low metabolic activity sometimes undetectable under normal laboratory conditions and the ability to be resuscitated by adequate stimuli. In C. neoformans, dormancy has only been demonstrated epidemiologically in our laboratory but not experimentally so far. We developed an assay where yeasts cells exhibiting characteristics of potentially dormant cells were generated. Our current project aims at exploring the conditions leading to, the biology of the entry in and the mechanisms sustaining dormancy.

Cryptococcus neoformans is a ubiquitous yeast present in the environment that is able to interact closely with numerous organisms including amoeba, paramecium or nematodes. The interaction with these organisms shaped its virulence with acquisition of infectious properties as a consequence especially in mammals . The ability to survive nutrient starvation, oxidative stress, desiccation, both in the environment and during infection, indicates a high level of physiological and metabolic plasticity of the yeast. In humans, after primary infection during childhood, the yeast is able to survive within the host for years before reactivation upon immunosuppression, leading to a life threatening  disseminated fungal infection. This phenomenon, called dormancy / quiescence is one of the main biological features of this fungus in relation with disease's pathogenesis. It is well known in bacteria (tuberculosis), parasites (Plasmodium, Toxoplasma). In C. neoformans, dormancy has only been demonstrated epidemiologically in our laboratory but not experimentally so far. We developed an assay where yeasts cells exhibiting characteristics of potentially dormant cells were generated. Indeed, dormant cells are characterized by a low metabolic activity sometimes undetectable under normal laboratory conditions, altered growth capacity, and the ability to resuscitate upon adequate stimulus. Dormant cells are known to have increased mitochondrial masse and activity justifying a screening strategy of a collection of KO mutants for mitochondrial proteins. In parallel the whole proteome, transcriptome and secretome will be obtain with the ambition to correlate these parameters. Our current project aims at exploring the metabolism of the dormant yeast to have a comprehensive picture of the pathways that are required for the maintenance of dormancy and fo exit from dormancy.