The dynamics of Cryptococcus neoformans cell and transcriptional remodeling during infection
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ABSTRACT:
PROVIDER: PRJNA851987 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19793308_1.fastq.gz | Fastqsanger.gz | |||
| SRR19793308_2.fastq.gz | Fastqsanger.gz | |||
| SRR19793309_1.fastq.gz | Fastqsanger.gz | |||
| SRR19793309_2.fastq.gz | Fastqsanger.gz | |||
| SRR19793310_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Investigate the dynamics of cryptococcal cell and transcriptional remodeling during pulmonary infection in a murine model Methods: Dual-RNA sequencing Sample preparation - C57BL/6 mice were infected intratracheally with the H99 strain to analyze the transcriptome. After 6h or 240h of infection, BALF obtained from 6 mice of each condition were pooled together, generating two replicates of 6h and 240h (10d). BALF was centrifuged at 1200 x g and resuspended in 1mL TRIzol Reagent (Invitrogen Life Technologies) for RNA isolation, according to the manufactures' protocol. RNA from H99 yeasts grown in YPD was used as control. Results: Dual RNA-Seq analysis of C. neoformans and mice revealed molecular signatures of early and late events of infection We analyzed the up and downregulated genes after 6h and 10 days of infection, compared to the inoculated yeast (YPD x 6h and YPD x 10d) and the differentially expressed genes (DEGs) between 6h and 10 days of infection (designated BAL6h x BAL10d). These analyses revealed molecular signatures unique to early and late stages of infection. Conclusions: Our findings support a scenario in which the fungus initially deploys mechanisms aimed at survival, proliferation and tissue invasion. Later, the fungus may focus on mechanisms aimed at resistance to the immune response and colonization, that are crucial for disease development. Overall, our study provides new insights into understanding the biology of C. neoformans during infection and generating perspectives for the survey for new therapeutic and diagnostic targets for cryptococcosis.
2022-12-14 | GSE206758 | GEO
Project description:We measured protein translation (by ribosome profiling) and RNA levels (by polyA-enriched RNA-seq) in Cryptococcus neoformans strain H99 and Cryptococcus neoformans strain JEC21. This is the first transcriptome-wide map of translation in this species complex.
2019-06-22 | GSE133125 | GEO
Project description:Cryptococcus neoformans, an environmental opportunistic human fungal pathogen, is a causative agent for acute pulmonary infection and meningoencephalitis. Understanding the host’s response to C. neoformans infection is critical for developing effective treatment. Even though some have elucidated the host response at the transcriptome level, little is known about how it modulates its defense machinery through the proteome mechanism or how protein posttranslational modification responds to the infection. In this work, we employed a Cryptococcus murine infection model and mass spectrometry to systematically determine the proteome and acetylome statuses of two primary organs (lung and brain) in the early stage of infection. To extensively analyze the host response, we compared and integrated the proteome data to the transcriptome results. We demonstrated a significant overlap between two data sets. Critical genes, including genes involved in phagosome, lysosome, or osteoblast differentiation and platelet activation are significantly altered in protein and gene expression during infection. In the acetylome analysis, we demonstrated that lung and brain tissues differentially regulate protein acetylation during infection. The three primary groups of proteins altered in acetylation status are histones, proteins involved in glucose and fatty acid metabolism, and proteins from the immune system. These analyses provide an integrative regulation network of the host responding to C. neoformans and shed new light on understanding the host’s regulation mechanism when responding to C. neoformans.
2020-04-21 | PXD016614 | Pride
Project description:We examined four subsets of alveolar macrophages differentiated by CXCL2 expression and FLT3 fate mapping induced by Cryptococcus neoformans infection. These four subpopulations have distinct mRNA expression pattern indicating the heterogenity within alveolar macrophages.
2020-06-08 | GSE133026 | GEO
Project description:We investigated the effects of the hypoxia-mimetic CoCl2 on the gene expression of pathogenic fungus Cryptococcus neoformans. Keywords: compound treatment design
2009-05-01 | GSE11390 | GEO
Project description:The encapsulated yeast Cryptococcus neoformans can cause a fatal meningoencephalitis in immunocompromised patients. C. neoformans infection is acquired through the respiratory tract, but the cellular and molecular mechanisms of the pulmonary innate immune response are still not well defined. To investigate the response of CCR2+ inflammatory monocytes to C. neoformans, we compared the transcriptomes of CCR2+ inflammatory monocytes from the lungs of naïve versus infected mice.
2019-02-11 | GSE122765 | GEO
Project description:Cryptococcus spp. are environmental fungi that first must adapt to the host environment before they can cause life-threatening meningitis in immunocompromised patients. Host CO2 concentrations are 100-fold higher than the external environment and strains unable to grow at host CO2 concentrations are not pathogenic. Using a genetic screening and transcriptional profiling approach, we found that the TOR pathway is critical for C. neoformans adaptation to host CO2 partly through Ypk1-dependent remodeling of phosphatidylserine asymmetry at the plasma membrane. We also identified a C. neoformans ABC/PDR transporter (PDR9) that is highly expressed in CO2-sensitive environmental strains, suppresses CO2-induced phosphatidylserine remodeling, and increases susceptibility to host concentrations of CO2. Interestingly, regulation of plasma membrane lipid asymmetry by the TOR-Ypk1 axis is distinct in C. neoformans compared to S. cerevisiae. Finally, host CO2 concentrations suppress the C. neoformans pathways that respond to host temperature (Mpk1) and pH (Rim101), indicating that host adaptation requires a stringent balance among distinct stress responses.
2023-10-24 | GSE241788 | GEO
Project description:Cryptococcus neoformans (Cn) is an opportunistic fungal microorganism that causes life-threatening meningoencephalitis. During the infection, the microbial population is heterogeneously composed of cells with varying generational ages, with older cells accumulating during chronic infections. This is attributed to their enhanced resistance to phagocytic killing and tolerance of antifungals like fluconazole (FLC). Using RNA-seq, we investigated how transcriptomic changes in different aspects of metabolism contribute to age-associated FLC tolerance in Cn.
2024-03-06 | GSE260902 | GEO
Project description:Thermotolerance, a key factor essential for the virulence of pathogenic fungi including Cryptococcus neoformans, remains largely unexplored in terms of its underlying mechanism. In this study, our findings demonstrate that Set3C, a widely distributed and conserved histone deacetylase complex, is required for thermotolerance in Cryptococcus neoformans. Specifically, the deletion of the core subunit Set302, responsible for the integrity of the complex, results in a significant reduction in the growth ability under high stress and the viability at extreme temperature. Moreover, the absence of Set302 leads to a decrease in the production of capsule and melanin. Transcriptomics analysis revealed that Set302 regulates a large number of genes compared to normal condition, and their expression is responsive to heat stress. Notably, we observed that Set302 positively influences the expression of genes related to ubiquitin-proteasome system (UPS) at high temperature. Using GFP-α-synuclein overexpression model, we observed a pronounced accumulation of misfolded proteins under heat stress, consequently inhibiting the thermotolerance of Cryptococcus neoformans. Furthermore, the loss of Set302 exacerbates this inhibition of thermotolerance. Interestingly, set302∆ strain exhibits a similar phenotype under proteasome stress as it does under high temperature. We also found that set302∆ strain displayed significantly reduced pathogenicity and colonization ability compared to the wild-type strain in the murine infection model. Collectively, our findings indicate that Set302 modulates the degradation of misfolded proteins through the UPS pathway, thereby affecting the thermotolerance and pathogenicity of Cryptococcus neoformans.
2023-09-05 | GSE242109 | GEO
Project description:Systemic infection with Cryptococcus neoformans, a dangerous and contagious pathogen found throughout the world, frequently results in lethal cryptococcal pneumonia and meningoencephalitis, and no effective treatments of cryptococcosis are available. Here, we describe Prm1, a novel regulator of virulence in C. neoformans. C. neoformans prm1 cells exhibit extreme sensitivity to various environmental stress conditions. Furthermore, prm1 cells show deficiencies in the biosynthesis of chitin, chitosan, and mannoprotein, which in turn result in impairment of cell wall integrity. Treatment of mice with heat-killed prm1 cells was found to facilitate the host immunological defence against infection with wild-type C. neoformans. Further investigation demonstrated that prm1 cells strongly promote pulmonary production of interferon- and Th1 responses, leading to activation of macrophage M1 differentiation and inhibition of M2 polarization. Therefore, our findings suggest that C. neoformans Prm1 may be a viable target for the development of anti-cryptococcosis medications and, cells lacking Prm1 represent a promising candidate for a vaccine.
2023-10-11 | PXD038840 | Pride