Transcriptomic remodeling of gastric cells by Helicobacter pylori Outer Membrane Vesicles
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE229512 | GEO | 2024/04/03
REPOSITORIES: GEO
Similar Datasets
Project description:Gram negative bacteria release outer membrane vesicles (OMVs) as part of their natural growth. These OMVs take part in a biological functions including bacterial communication, exchange of genetic material and bacterial pathogenesis. However, the relationship between bacterial growth stage and OMV protein composition has not been explored before nor how their proteome is different to their parent bacterium. In this study, we examined the proteome of Helicobacter pylori and its OMVs from early log, late log or stationary phase of growth and found that globally, the protein content of OMVs over time is vastly different to one another as well as to their parent bacterium. OMVs purified from early log phase of growth contained the greatest number of unique proteins and a significant upregulation of virulence and pathogenic proteins. However, when compared back to their parent bacterium, OMVs from later stages of growth contained more unique proteins than those from earlier stages of growth. We show for the first time the regulation of OMV protein composition by H. pylori that is dependent on bacterial growth stage. Our results have expanded our understanding of the fundamental production of OMVs and the selective packaging of cargo in OMVs that result in specific functions.
2021-03-23 | PXD024918 | Pride
Project description:Outer membrane vesicles (OMVs) are small vesicles constitutively shed by all Gram-negative bacterium, which have been proposed to play a role in Helicobacter pylori persistence and pathogenesis. The methods currently available for the isolation of H. pylori OMVs are diverse and time-consuming, raising the need for a protocol standardization, which was the main aim of this study. Here, we showed that the chemically defined F12 medium, supplemented with cholesterol, nutritionally supports bacterial growth and maintains H. pylori viability for at least 72 h. Additionally, we developed an abridged protocol for isolation of OMVs from these bacterial cultures, which comprises a low-speed centrifugation, supernatant filtration through a 0.45 µm pore, and two ultracentrifugations for OMVs’ recovery and washing. Using this approach, a good yield of highly pure bona fide OMVs was recovered from cultures of different H. pylori strains and in different periods of bacterial growth. Analysis of the proteome of OMVs isolated from H. pylori F12-cholesterol cultures validated the efficacy of our isolation protocol in attaining a higher sample purity with low representation of flagella proteins. The comparison with the proteomes of H. pylori OMVs available in the literature demonstrated that OMVs carry a selective protein cargo, suggesting their importance for H. pylori survival and pathogenesis. In conclusion, this work proposes a time- and cost-efficient protocol for the isolation of H. pylori OMVs from a chemically defined culture medium that is suitable for implementation in research and in the biopharmaceutical field.
2021-05-31 | PXD025393 | Pride
Project description:OMVs were isolated from H. pylori grown during pH 5.3 conditions with the addition of urea to supplement bacterial growth, or during pH 7.2 conditions with or without the addition of urea. Growth of H. pylori during acidic conditions reduced the quantity and size of OMVs produced. Additionally, acidic growth conditions resulted in the production of OMVs with increased packaging of protein, DNA, and RNA compared to OMVs produced during neutral growth conditions. A global data-independent acquisition proteomic analysis comparing the proteomes of OMVs to their parent bacteria demonstrated significant differences in the enrichment of proteins within bacteria and OMVs, supporting that differing conditions of growth impacts OMV composition. We also identified select and marginal differences in the enrichment of proteins within OMVs produced during different pH growth conditions. Overall, our findings reveal that growth of H. pylori during altered pH growth conditions is a factor that determines OMV proteomes, which may affect their subsequent functions in the host.
2023-06-28 | MSV000092295 | MassIVE
Project description:The human gastric epithelium forms highly organized gland structures with different subtypes of cells. The carcinogenic bacterium Helicobacter pylori can attach to gastric cells and subsequently translocate its virulence factor CagA, but the possible host cell tropism of H. pylori is currently unknown. Here, we report that H. pylori preferentially attaches to differentiated cells in the pit region of gastric units. Single-cell RNA-seq shows that organoid-derived monolayers recapitulate the pit region, while organoids capture the gland region of the gastric units. Using these models, we show that H. pylori preferentially attaches to highly differentiated pit cells, marked by high levels of GKN1, GKN2 and PSCA. Directed differentiation of host cells enable enrichment of the target cell population and confirm H. pylori preferential attachment and CagA translocation into these cells. Attachment is independent of MUC5AC or PSCA expression, and instead relies on bacterial TlpB-dependent chemotaxis towards host cell-released urea, which scales with host cell size.
2022-08-20 | GSE167561 | GEO
Project description:H. pylori Outer membrane phospholipase A (OMPLA) has been suggested to play a role in the virulence of this bacterium. The aim of this study was to profile the most significant cellular pathways and biological processes affected in gastric epithelial cells during 24 hours of H. pylori exposure, and to study the inflammatory response to OMPLA+ and OMPLA- H. pylori variants
2012-01-01 | E-MTAB-846 | biostudies-arrayexpress
Project description:Helicobacter pylori clinical isolates can establish themselves in gastric epithelial stem cells and this interaction may have implications for gastric tumorigenesis. Mouse gastric epithelial progenitor cells (mGEPs) were infected for 24hrs with Helicobacter pylori clinical isolates Kx1 and Kx2. Kx1 and Kx2 were also grown in cell media in the absence of cells. Kx1 was isolated from a patient with chronic atrophic gastritis (ChAG) and Kx2 from the same patient 4 years later, when he progressed to gastric adenocarcinoma. Keywords: RNA Expression Array H. pylori strains Kx1 or Kx2 that had been grown to log phase were used to infect mGEP cells.. After 24h, media and non-attached bacteria were washed off and the cells harvested by trypsinization. RNA was prepared from bacteria infecting mGEP cells or bacterial cultures of Kx1 and Kx2 grown in cell media for 24h in the absence of mGEP cells.
2010-05-26 | E-GEOD-10261 | biostudies-arrayexpress
Project description:Casandra W. Philipson, Josep Bassaganya-Riera, Monica Viladomiu, Barbara Kronsteiner, Vida Abedi, Stefan Hoops, Pawel Michalak, Lin Kang, Stephen E. Girardin & Raquel Hontecillas. Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PLOS ONE 10, 9 (2015).
Helicobacter pylori colonizes half of the world's population as the dominant member of the gastric microbiota resulting in a lifelong chronic infection. Host responses toward the bacterium can result in asymptomatic, pathogenic or even favorable health outcomes; however, mechanisms underlying the dual role of H. pylori as a commensal versus pathogenic organism are not well characterized. Recent evidence suggests mononuclear phagocytes are largely involved in shaping dominant immunity during infection mediating the balance between host tolerance and succumbing to overt disease. We combined computational modeling, bioinformatics and experimental validation in order to investigate interactions between macrophages and intracellular H. pylori. Global transcriptomic analysis on bone marrow-derived macrophages (BMDM) in a gentamycin protection assay at six time points unveiled the presence of three sequential host response waves: an early transient regulatory gene module followed by sustained and late effector responses. Kinetic behaviors of pattern recognition receptors (PRRs) are linked to differential expression of spatiotemporal response waves and function to induce effector immunity through extracellular and intracellular detection of H. pylori. We report that bacterial interaction with the host intracellular environment caused significant suppression of regulatory NLRC3 and NLRX1 in a pattern inverse to early regulatory responses. To further delineate complex immune responses and pathway crosstalk between effector and regulatory PRRs, we built a computational model calibrated using time-series RNAseq data. Our validated computational hypotheses are that: 1) NLRX1 expression regulates bacterial burden in macrophages; and 2) early host response cytokines down-regulate NLRX1 expression through a negative feedback circuit. This paper applies modeling approaches to characterize the regulatory role of NLRX1 in mechanisms of host tolerance employed by macrophages to respond to and/or to co-exist with intracellular H. pylori.
2024-09-02 | BIOMD0000000596 | BioModels
Project description:The model is first model of tissue level cellular immune responses to H. pylori in the publication, "Modeling the role of lanthionine synthetase C-like 2 (LANCL2) in the modulation of immune responses to Helicobacter pylori infection" in PlosOne by Leber, Bassaganya-Riera, Tubau-Juni, Zoccoli-Rodriguez, Viladomiu, Abedi, Lu, and Hontecillas.
Abstract:
Immune responses to Helicobacter pylori are orchestrated through complex balances of host-bacterial interactions, including inflammatory and regulatory immune responses across scales that can lead to the development of the gastric disease or the promotion of beneficial systemic effects. While inflammation in response to the bacterium has been reasonably characterized, the regulatory pathways that contribute to preventing inflammatory events during H. pylori infection are incompletely understood. To aid in this effort, we have generated a computational model incorporating recent developments in the understanding of H. pylori-host interactions. Sensitivity analysis of this model reveals that a regulatory macrophage population is critical in maintaining high H. pylori colonization without the generation of an inflammatory response. To address how this myeloid cell subset arises, we developed a second model describing an intracellular signaling network for the differentiation of macrophages. Modeling studies predicted that LANCL2 is a central regulator of inflammatory and effector pathways and its activation promotes regulatory responses characterized by IL-10 production while suppressing effector responses. The predicted impairment of regulatory macrophage differentiation by the loss of LANCL2 was simulated based on multiscale linkages between the tissue-level gastric mucosa and the intracellular models. The simulated deletion of LANCL2 resulted in a greater clearance of H. pylori, but also greater IFNγ responses and damage to the epithelium. The model predictions were validated within a mouse model of H. pylori colonization in wild-type (WT), LANCL2 whole body KO and myeloid-specific LANCL2-/- (LANCL2Myeloid) mice, which displayed similar decreases in H. pylori burden, CX3CR1+ IL-10-producing macrophages, and type 1 regulatory (Tr1) T cells. This study shows the importance of LANCL2 in the induction of regulatory responses in macrophages and T cells during H. pylori infection.
2016-12-01 | MODEL1611160002 | BioModels
Project description:The model is the second model of the publication "Modeling the role of lanthionine synthetase C-like 2 (LANCL2) in the modulation of immune responses to Helicobacter pylori infection" published in PlosOne by Leber, Bassaganya-Riera, Tubau-Juni, Zoccoli-Rodriguez, Viladomiu, Abedi, Lu, and Hontecillas.
Abstract:
Immune responses to Helicobacter pylori are orchestrated through complex balances of host-bacterial interactions, including inflammatory and regulatory immune responses across scales that can lead to the development of the gastric disease or the promotion of beneficial systemic effects. While inflammation in response to the bacterium has been reasonably characterized, the regulatory pathways that contribute to preventing inflammatory events during H. pylori infection are incompletely understood. To aid in this effort, we have generated a computational model incorporating recent developments in the understanding of H. pylori-host interactions. Sensitivity analysis of this model reveals that a regulatory macrophage population is critical in maintaining high H. pylori colonization without the generation of an inflammatory response. To address how this myeloid cell subset arises, we developed a second model describing an intracellular signaling network for the differentiation of macrophages. Modeling studies predicted that LANCL2 is a central regulator of inflammatory and effector pathways and its activation promotes regulatory responses characterized by IL-10 production while suppressing effector responses. The predicted impairment of regulatory macrophage differentiation by the loss of LANCL2 was simulated based on multiscale linkages between the tissue-level gastric mucosa and the intracellular models. The simulated deletion of LANCL2 resulted in a greater clearance of H. pylori, but also greater IFNγ responses and damage to the epithelium. The model predictions were validated within a mouse model of H. pylori colonization in wild-type (WT), LANCL2 whole body KO and myeloid-specific LANCL2-/- (LANCL2Myeloid) mice, which displayed similar decreases in H. pylori burden, CX3CR1+ IL-10-producing macrophages, and type 1 regulatory (Tr1) T cells. This study shows the importance of LANCL2 in the induction of regulatory responses in macrophages and T cells during H. pylori infection.
2016-12-01 | MODEL1611160001 | BioModels
Project description:Helicobacter pylori (H. pylori) is a highly successful pathogen that constitutes a serious threat to human health. However, the dynamic interaction between H. pylori and human gastric epithelium has not been fully documented. Here, by leveraging the advantage of dual RNA sequencing technology, we characterized a cytotoxin-associated genes A (CagA)-modulated bacterial adoption strategy by reinforcing the expression of ATP-binding cassette (ABC) transporter-related genes, metQ and HP_0888 upon co-culturing with human gastric epithelial cells (GES-1), thus, to benefit intracellular H. pylori survival through facilitating the uptake of host-provided nutrients. We further detected a generally repressed impact on electron transportation-associated genes by CagA, leading to the activation of oxidative phosphorylation. Temporal profiling of host mRNA signatures revealed down-regulation of multiple splicing regulators elicited by bacterial infection. Consequently, aberrant pre-mRNA splicing of functional genes that were involved in cell cycle process in response to H. pylori infection were identified. Moreover, we verified a protective effect for gastric H. pylori colonization against chronic dextran sulfate sodium (DSS)-induced colitis. Mechanistically, we profiled a cluster of short chain fatty acids (SCFA)-producing bacteria, Muribaculaceae that was selectively enriched in H. pylori-pre-colonized mice colon, contributing to the restoration of intestinal barrier function damaged by DSS treatment. Taken together, this study represents the first dual-transcriptome analysis of H. pylori during dynamic interaction with gastric epithelium and provide new insights into H. pylori pathogenesis.
2023-09-19 | GSE243405 | GEO