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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-Seq analysis of ada2M-NM-^T, nrg1M-NM-^T and cir1M-NM-^T and KN99M-NM-1 wildtype cells in capsule inducing and non-inducing conditions

ABSTRACT: To contextualize the cryptococcal Spt-Ada-Gcn5 Acetyltransferase (SAGA) member Ada2 in the capsule regulatory network, RNA-Seq was performed on wildtype, ada2M-NM-^T and two other transcription factors, nrg1M-NM-^T and cir1M-NM-^T, which like ada2M-NM-^T are also defective for capsule formation, virulence and filamentation. Mutant and wildtype cells were grown in capsule inducing and non-inducing conditions for 90 minutes and transcriptional profiling was performed by RNA-Seq analysis.

ORGANISM(S): Cryptococcus neoformans

SUBMITTER: Brian Haynes

PROVIDER: E-GEOD-32049 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Toward an integrated model of capsule regulation in Cryptococcus neoformans

Project description:This SuperSeries is composed of the following subset Series: GSE31911: Cryptococcal H99 cells grown in 8 conditions for capsule induction GSE32049: RNA-Seq analysis of ada2?, nrg1? and cir1? and KN99? wildtype cells in capsule inducing and non-inducing conditions GSE32075: ChIP-Seq of H3K9 acetylation for wildtype and ada2? cells in Cryptococcus neoformans Refer to individual Series

2011-12-10 | E-GEOD-32228 | biostudies-arrayexpress

Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation

Project description:Purpose: Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying TFs involved in a specific process and used it to map regulation of the key virulence factor of Cryptococcus neoformans, its capsule. Results: The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. It also reveals a hierarchy comprising executive, mid-level, and “foreman” TFs. When grouped by temporal expression pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of 41 TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. Conclusions: These data resources and analyses provide the first integrated, systems level view of capsule regulation and biosynthesis. Our methods dramatically improve the efficiency with which transcriptional networks can be analyzed, making genomic approaches accessible to labs focused on specific physiological processes. A total of 288 expression profiles were generated by RNA-Seq analysis of Mutant and wildtype cells grown in capsule inducing conditions for 90 minutes. In addition, 3 replicate expression profiles were generated for wildtype cells grown in : a capsule non-inducing condition, a capsule inducing condition for 180 minutes, a capsule inducing condition for 480 minutes, and a capsule inducing condition for 1440 minutes. In addition, ChIP-seq of NRG1(CNAG_05222) in capsule inducing conditions, and USV101(CNAG_05420) in both capsule inducing and non-inducing conditions were generated.

2015-01-14 | E-GEOD-60398 | biostudies-arrayexpress

Usv101 is a key regulator of cryptococcal virulence and determinant of host response

Project description:Cryptococcus neoformans is a fungal pathogen responsible for hundreds of thousands of deaths per year. Its critical virulence factor is a polysacharride capsule which grows large upon entry into a mammalian host. We previously identified USV101 as a transcription factor whose deletion results in enlarged capsules. Here, we characterize strains lacking or overexpressing USV101 in terms of their virulence-related phenotypes, the altered course of infection by them and immune response to them in a mouse model, the relationship of Usv101 to other transcription factors involved in capsule regulation, and the changes in Usv101 activity during capsule induction. To study the function of Usv101, a key C. neoformans regulator of virulence, and its interactions with downstream capsule-regulating TFs GAT201 and SP1, expression profiles were generated by RNA-seq of a usv101 deletion mutant, a USV101 overexpression mutant, strains expressing GAT201 under various promoters, various double mutants, and wildtype cells grown in a capsule non-inducing condition, a capsule inducing condition for 90 minutes, or a capsule inducing condition for 24 hours.

2016-03-31 | E-GEOD-69532 | biostudies-arrayexpress

ChIP-Seq of H3K9 acetylation for wildtype and ada2Δ cells in Cryptococcus neoformans

Project description:SAGA member Ada2 is required for the majority of H3K9 acetylation in C. neoformans. To identify specific genomic loci that exhibit Ada2-dependent H3K9 acetylation, we performed ChIP-Seq against H3K9ac in wildtype and ada2Δ cells. ChIP-Seq was performed using antibodies for H3K9ac in KN99 wildtype cells and ada2Δ cells. Input and IPed DNA was collected in triplicate from each strain and sequenced on an Illumnina HiSeq 2000 flow cell producing 84 million reads. Due to the lack of quality scores, raw reads are omitted from the submission.

2012-01-01 | E-GEOD-32075 | biostudies-arrayexpress

Streptococcus sp. NM strain:NM

Project description:Streptococcus sp. NM strain:NM Genome sequencing and assembly

| PRJNA484102 | ENA

Basement Membranes from Human Retinal Blood Vessels, Inner Limiting Membranes, and Lens Capsules

Project description:Three types of BMs from adult human eyes, the inner limiting membrane, the retinal vascular BMs and the lens capsule, were isolated for analysis by 1D-SDS-PAGE and LC-MS/MS.

2014-07-16 | PXD001025 | Pride

Cross talk between the cell wall integrity and cAMP/protein kinase A pathways in Cryptococcus neoformans

Project description:Cryptococcus neoformans is a fungal pathogen of immunocompromised people that causes fatal meningitis. The fungal cell wall is essential to viability and pathogenesis of C. neoformans, and biosynthesis and repair of the wall is primarily controlled by the cell wall integrity (CWI) signaling pathway. Previous work by us and others have shown that deletion of genes encoding the four major kinases in the CWI signaling pathway, namely PKC1, BCK1, MKK2 and MPK1 results in severe cell wall phenotypes, sensitivity to a variety of cell wall stressors and, for Mpk1, reduced virulence in a mouse model. Here, we examined the global transcriptional response of gene deletions of BCK1, MKK2 and MPK1 compared to wild-type cells. We found over 1000 genes were differentially expressed in one or more of the deletion strains, with 115 genes differentially expressed in all three strains, many of which have been identified as genes regulated by the cAMP/protein kinase A (PKA) pathway. Biochemical measurements of cAMP levels in the kinase deletion stains revealed significantly less cAMP in all of the deletion strains compared to wild-type cells. The deletion strains also produced significantly smaller capsules than wild type KN99 under capsule inducing conditions, although they shed similar levels of capsule as wild type. Finally, addition of exogenous cAMP led to reduced sensitivity to cell wall stress and restored surface capsule to near wild-type levels. Thus, we have direct evidence of cross talk between the CWI and cAMP/PKA pathways that may have important implications for regulation of cell wall and capsule homeostasis. Comparison of three gene deletion strains to wild-type, with 3 biological replicates for each sample.

2014-07-01 | E-GEOD-57217 | biostudies-arrayexpress

Butyrophilin 3A1 binds phosphorylated antigens and stimulates human TCR M-NM-3M-NM-4 cells.

Project description:We used genetic approaches to identify butyrophilin 3A1 (BTN3A1) as the molecule that binds and presents phosphorylated antigens to VM-NM-39VM-NM-42 TCRM-bM-^@M-^Sexpressing cells. BTN3A1 represents a novel antigenM-bM-^@M-^Spresenting molecule for the activation of VM-NM-39VM-NM-42 TCRM-bM-^@M-^Sexpressing cells which play important roles in human tumor immunity and host defense. 3 replicates of 4 cell lines (12 samples total) were analysed. Data was RMA normalized, and genes that expressed above the negative control in all 4 cell lines from chromosome 6 considered for further analysis

2012-10-01 | E-GEOD-37634 | biostudies-arrayexpress

Compositional analysis of extracellular aggregates in the eyes of patients with exfoliation syndrome and exfoliation glaucoma.

Project description:Exfoliation syndrome (XFS) is a condition characterized by the production of insoluble fibrillar aggregates (exfoliation material; XFM) in the eye and elsewhere. Many patients with XFS progress to exfoliation glaucoma (XFG), a significant cause of global blindness. We used quantitative mass spectrometry to analyze the composition of XFM in lens capsule specimens and aqueous humor samples from XFS and XFG patients and individuals without XFS. Pieces of lens capsule and samples of aqueous humor were obtained with consent from patients undergoing cataract surgery. Tryptic digests of capsule or aqueous samples were analyzed by HPLC-mass spectrometry and relative differences between samples were quantified using the tandem mass tag technique. The distribution of XFM on the capsular surface was visualized by scanning electron microscopy and super-resolution light microscopy. A small set of proteins was consistently upregulated in XFS samples, including microfibril components fibrillin-1 (FBN1), latent TGFBeta-binding protein-2 (LTBP-2), and LTBP-3. Lysyl oxidase-like 1 (LOXL1), a protein linked strongly to XFS in genetic studies, was an abundant XFM protein. Ligands of the TGFBeta superfamily were prominent, including LEFTY2, a protein known for its role in establishing the embryonic body axis. Elevated levels of LEFTY2 were also detected in aqueous humor from XFG patients and confirmed by ELISA. This analysis verified the presence of several suspected XFM proteins and identified novel components. Quantitative comparisons between patient samples revealed a consistent XFM proteome. The expression of FBN1, LOXL1, and LEFTY2 was particularly strong in XFG patients in comparison to XFS patients.

2022-02-17 | PXD026764 | Pride

The ER protein translocation channel subunit Sbh1 controls virulence of Cryptococcus neoformans

Project description:C. neoformans is an opportunistic human pathogen whose polysaccharide capsule anchored to the cell wall is critical for virulence. Biogenesis of both cell wall and capsule relies on the secretory pathway. Protein secretion begins with protein translocation across the endoplasmic reticulum (ER) membrane through a highly conserved channel formed by three proteins, Sec61, Sbh1, and Sss1. Sbh1 is most divergent and contains multiple phosphorylation sites which may allow it to control entry into the secretory pathway in a regulated, species- and protein-specific manner. We show here that in contrast to S. cerevisiae, C. neoformans lacking SBH1 are barely temperature-sensitive, but that absence of SBH1 causes a cell-wall defect in both species. Comparison of the proteomes of wildtype and Δsbh1 C. neoformans revealed a small set of secretory and transmembrane proteins whose expression under infection-like conditions was upregulated in wildtype, but not in the Δsbh1 mutant. These proteins are mostly involved in cell-wall biogenesis. We found that adhesion to macrophages was compromised in the Δsbh1 strain and in mice, the C. neoformans Δsbh1 mutant was virtually avirulent. We conclude that upon contact with the host Sbh1 controls entry of virulencefactors into the secretory pathway of Cryptococcus neoformans.

2023-01-27 | PXD013894 | Pride

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