Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment II

ABSTRACT: We used single-cell RNA sequencing to interrogate granulomas from Mycobacterium marinum infected zebrafish (Danio rerio) of a genetic mutant and matched WT siblings. Granulomas are comprised of several cell types and we sought to understand the consequences of genetic disruption of the gene apolipoprotein db (apodb) on granuloma cells types and cell-specific transcription.

ORGANISM(S): Danio rerio

PROVIDER: GSE324157 | GEO | 2026/07/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment

Project description:We used single-cell RNA sequencing to interrogate granulomas from Mycobacterium marinum infected zebrafish (Danio rerio) of a genetic mutant. This sample was compared to a previously published granuloma scRNAseq dataset from wildtype zebrafish. Granulomas are comprised of several cell types and we sought to understand the consequences of genetic disruption of the gene leukotriene A4 hydrolase (lta4h) on granuloma cells types and cell-specific transcription. This is the first comparison of mycobacterial granuloma scRNAseq from a genetic mutant to wildtype.

2026-07-31 | GSE299987 | GEO

Macrophage Epithelial Reprogramming Underlies Mycobacterial Granuloma Formation and Promotes Infection

Project description:Mycobacterium tuberculosis infection in humans triggers formation of granulomas, tightly organized immune cell aggregates that are the central structure of tuberculosis. Infected and uninfected macrophages interdigitate, assuming an altered, flattened appearance. Although pathologists have described these changes for over a century, the molecular and cellular programs underlying this transition are unclear. We find that mycobacterial granuloma formation is accompanied by macrophage induction of canonical epithelial molecules and structures. Using the zebrafish-Mycobacterium marinum model, we identify fundamental macrophage reprogramming events that parallel E-cadherin-dependent mesenchymal-epithelial transitions. Macrophage-specific disruption of E-cadherin function results in disordered granuloma formation, enhanced immune cell access, decreased bacterial burden and increased host survival, suggesting that the granuloma can also serve a bacteria-protective role. In humans, we find that granuloma macrophages are similarly transformed. Long considered largely through the prism of immune signaling pathways, granuloma macrophages are reprogrammed by epithelial modules that alter the trajectory of mycobacterial infection.

2016-10-18 | GSE81913 | GEO

Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment

Project description:Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment

| PRJNA1277811 | ENA

Wildtype granuloma cells from M. marinum-infected zebrafish

Project description:We use our previously published single-cell RNA sequencing protocol to interrogate the transcriptional nature of granuloma structures extracted from Mycobacterium marinum-infected zebrafish (Danio rerio).

2025-12-17 | GSE314022 | GEO

Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment II

Project description:Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment II

| PRJNA1433541 | ENA

A Non-Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization

Project description:Using the zebrafish-M. marinum model, we identify the basis of granuloma macrophage transformation. Single-cell RNA-seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis-infected macaques reveal that, even in the presence of robust type 1 immune responses, countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling, mediated via stat6, is absolutely required for epithelialization and granuloma formation.

2021-03-23 | GSE161712 | GEO

Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation

Project description:Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection, but the identities, arrangement, cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum-zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA-seq on flow-sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.

2025-06-13 | GSE296119 | GEO

Proteomic analysis of Mycobacterial Biofilm Matrix and Development of Biofilm-binding Synthetic Nanobodies

Project description:Tissue-penetrating nanobodies as drug-delivery vehicles have shown efficacy in treating hard-to-reach and -treat diseases. The present study reports nanobodies with application potential in the treatment of tuberculosis (TB), especially the antibiotic tolerant biofilms that form in TB granulomas. Using Mycobacterium marinum (Mmr) as a model pathogen, we identified the most abundant matrix proteins in cultured biofilms and granuloma biofilms from infected zebrafish, and used them as targets to produce synthetic nanobodies (sybodies). Surface-exposed proteins on Mmr biofilms were identified using a combination of in vitro cell surface biotinylation proteomics andex vivo proteomics on granulomas extracted from Mmr-infected adult zebrafish. We identified a total of 3080 and 41 mycobacterial biofilm matrix-associated proteins by in vitro and ex vivo proteomics, respectively. The molecular chaperones GroEL1 and GroEL2 were identified in both datasets, and fulfilled the criteria of ideal nanobody targets. We created sybodies against GroEL1 and GroEL2, and showed that they bind the intact in vitro and ex vivo Mmr-biofilms. Taken together, the present study reports a proof-of-concept showing that biotinylation proteomics of biofilms complemented with ex vivo proteomics of granuloma biofilms is a valuable strategy to uncover optimal nanobody targets within the biofilm matrix. Nanobody-based strategies have great potential to provide new and much-needed solutions for more effective treatment of tuberculosis, as well asother chronic biofilm infections with increased antibiotic tolerance and high risk for emerging antibiotic resistance

2023-03-30 | PXD033425 | Pride

Bulk RNA-seq of laser-microdissected granuloma and adjacent non-granuloma regions from FFPE lung tissues of pulmonary sarcoidosis

Project description:Sarcoidosis is a systemic granulomatous disease with heterogeneous organ involvement and clinical outcomes. To characterize transcriptional features associated with pulmonary sarcoid granulomas, we performed bulk RNA sequencing of laser-microdissected granuloma regions and adjacent non-granuloma regions from formalin-fixed paraffin-embedded (FFPE) lung tissue specimens obtained from patients with pulmonary sarcoidosis. The dataset includes paired regional samples derived from clinically obtained lung specimens. These data provide a resource for investigating localized gene expression differences associated with granuloma formation in pulmonary sarcoidosis.

2026-04-23 | GSE328831 | GEO

Lymphoid function of the tuberculous granuloma

Project description:Induced lymphoid structures associated with pulmonary granulomas have been observed during TB in both humans and mice and could orchestrate host defense. In order to determine whether granulomas perform lymphoid functions, mice lacking secondary lymphoid organs (SLOs) were infected with Mycobacterium tuberculosis (MTB). As in wild type mice (WT), granulomas developed, MTB was controlled, and antigen-specific T cell responses including T central memory (TCM) cells were generated in the complete absence of SLOs. Moreover, T cell activation correlated with granuloma formation in these mice and TCM cells accumulated in lungs and participated in protection against secondary MTB infection. Lung granulomas may therefore represent tertiary lymphoid organs (TLOs) capable of priming robust T cell responses and mediating host defense during chronic MTB at the site of infection.

2010-12-22 | GSE15335 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data