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Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC).

ABSTRACT: Peroxisomes are essential but often underappreciated metabolic organelles. In this study, we demonstrate that exuberant interferon signaling reshapes the macrophage peroxisome compartment following severe COVID-19. To uncover the molecular characteristics underlying the protective role of macrophage peroxisomes after viral infection, we isolated RNA from wild-type (WT) and Pex5-deficient alveolar macrophages (AMs) with or without Poly(I:C) treatment in vitro, followed by bulk RNA sequencing. Our analysis revealed enhanced expression of inflammation-associated pathways and innate immune responses in Pex5-deficient AMs. However, these cells also exhibited attenuated activation of tissue development-related pathways and impaired mitochondrial functions, regardless of Poly(I:C) treatment.

ORGANISM(S): Mus musculus

PROVIDER: GSE281262 | GEO | 2025/03/10

REPOSITORIES: GEO

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Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC)

Project description:Peroxisomes are essential but often overlooked metabolic organelles. To explore how macrophage peroxisomes protect the lung, we conducted single-cell RNA sequencing (scRNA-seq) on lungs from both naïve and SARS-CoV-2-infected Pex5^flox/flox (WT) and Cd11c-cre Pex5^flox/flox (KO) mice at 7 days post-infection (d.p.i). scRNA-seq revealed an increased proportion of inflammatory monocytes, neutrophils, and monocyte-derived macrophages (MDMs) in the lungs of infected KO mice, alongside a marked reduction in alveolar type 2 (AT2) cells and alveolar macrophages (AMs) compared to infected WT mice. AMs from KO mice showed elevated expression of genes involved in inflammatory responses, innate immunity, and cellular stress signaling, while genes related to wound healing, cell differentiation, and lipid metabolism were downregulated, compared to AMs from WT mice at 7 d.p.i.

2025-03-10 | GSE280545 | GEO

Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC).

Project description:Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC).

| PRJNA1182823 | ENA

Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC)

Project description:Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC)

| PRJNA1179376 | ENA

Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol

Project description:E. histolytica is believed to be devoid of peroxisomes, like most anaerobic protists. In this work, we provided the first evidence that peroxisomes are present in E. histolytica, although the set of proteins (peroxins) responsible for peroxisome biogenesis was reduced to only seven members (Pex1, Pex6, Pex5, Pex11, Pex14, Pex16, and Pex19). Targeting matrix proteins to peroxisomes is reduced to the PTS1-dependent pathway mediated via the soluble Pex5 receptor, while the PTS2 receptor Pex7 is absent. Immunofluorescence microscopy showed that peroxisomal markers (Pex5, Pex14, Pex16, Pex19) are present in vesicles distinct from mitosomes, the endoplasmic reticulum and the endosome/phagosome system, except Pex11, which has dual localization in peroxisomes and mitosomes. Immunoelectron microscopy revealed that Pex14 localized to vesicles of approximately 90-100 nm in diameter. Proteomic analyses of affinity-purified peroxisomes and in silico PTS1 predictions provided datasets of 655 and 56 peroxisomal candidates, respectively; however, only six proteins were shared by both datasets, including myo-inositol dehydrogenase (myo-IDH). Peroxisomal NAD-dependent myo-IDH appeared to be a dimeric enzyme with high affinity to myo-inositol (Km 0,044 mM) and can utilize also scyllo-inositol, D-glucose and D-xylose as substrates. Phylogenetic analyses revealed that orthologs of myo-IDH with PTS1 are present in E. dispar, E. nutalli and E. moshkovskii but not in E. invadens, and form a monophyletic clade of mostly peroxisomal orthologs with free-living M. balamuthi and P. schiedti. The presence of peroxisomes in E. histolytica and other archamoebae breaks the paradigm of peroxisome absence in anaerobes and provides a new potential target for the development of antiparasitic drugs.

2021-10-29 | PXD026653 | Pride

Integrative Omics reveals changes in the cellular landscape of yeast without peroxisomes

Project description:Peroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namely Saccharomyces cerevisiae wild-type and pex3 cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. Cells were grown on acetate, a carbon source that involves peroxisomal enzymes of the glyoxylate cycle and does not repress peroxisomal proteins. Transcripts of peroxisomal β-oxidation genes and the corresponding proteins were enhanced in pex3 cells. Peroxisome-deficiency also caused reduced levels of membrane bound peroxins, while the soluble receptors Pex5 and Pex7 were enhanced at the protein level. In addition, we observed alterations in non-peroxisomal transcripts and proteins, especially mitochondrial proteins involved in respiration or import processes. Our results not only reveal the impact of the absence of peroxisomes in yeast, but also represent a rich resource of candidate genes/proteins that are relevant in peroxisome biology.

2024-05-01 | GSE261289 | GEO

White adipose tissue from aP2-Pex5 knockout and control mice

Project description:These arrays contain data from gonodal adipose tissue of aP2-Pex5 -/- male mice 4 arrays from gonadal adipose tissue from control mice (Swiss background) are compared with 4 arrays from gonadal adipose tissue of aP2-Pex5 knockout mice. The latter lack functional peroxisomes in adipose tissue.

2012-03-01 | E-GEOD-31940 | biostudies-arrayexpress

A genome-wide screen for peroxisome regulators connects peroxisomes with Wnt signaling through RNF146 and tankyrase

Project description:Peroxisomes are membrane-bound organelles that help cells specialize their metabolism. In humans, peroxisomes are required for normal development, yet the genes regulating peroxisome function remain unclear. Thus, we performed a genome-wide CRISPRi screen to identify novel factors involved in peroxisomal homeostasis. We found that transcriptional inhibition of RNF146, an E3 ligase activated by poly(ADP-ribose), dramatically reduced the import of proteins into peroxisomes. The observed RNF146-mediated loss of peroxisome import depended on the stabilization and activity of the poly(ADP-ribose) polymerase tankyrase, which binds the peroxisomal membrane protein PEX14. We propose a model in which RNF146 and tankyrase regulate peroxisome import efficiency by tuning PARsylation of proteins at the peroxisome membrane. Interestingly, we found that perturbations to peroxisomes altered tankyrase’s selection of substrates, including the beta-catenin destruction complex component AXIN1. The loss of peroxisomes caused tankyrase and RNF146-dependent degradation of AXIN1 and a concomitant increase of beta-catenin transcription. Together, these observations not only suggest previously undescribed roles for RNF146 in peroxisomal regulation, but also a novel role in bridging peroxisome function with Wnt/beta-catenin signaling during development.

2024-06-01 | GSE266892 | GEO

A genome-wide screen for peroxisome regulators connects peroxisomes with Wnt signaling through RNF146 and tankyrase [Amplicon-sequencing]

2024-06-01 | GSE266855 | GEO

Hepatitis C virus alters the morphology and function of peroxisomes.

Project description:Despite the introduction of effective treatments for hepatitis C in clinics, issues remain regarding the liver diseases induced by chronic hepatitis C virus (HCV) infection. HCV is known to disturb the metabolism of infected cells, especially lipid metabolism and redox balance, but the mechanisms leading to HCV-induced pathogenesis are still poorly understood. In an APEX2-based proximity biotinylation screen, we identified ACBD5, a peroxisome membrane protein, as located in the vicinity of HCV replication complexes. Confocal microscopy confirmed the relocation of peroxisomes near HCV replication complexes and indicated that their morphology and number are altered in approximately 30% of infected Huh-7 cells. Peroxisomes are small versatile organelles involved among other functions in lipid metabolism and ROS regulation. To determine their importance in the HCV life cycle, we generated Huh-7 cells devoid of peroxisomes by inactivating the PEX5 and PEX3 genes using CRISPR/Cas9 and found that the absence of peroxisomes had no impact on replication kinetics or infectious titers of HCV strains JFH1 and DBN3a. The impact of HCV on peroxisomal functions was assessed using sub-genomic replicons. An increase of ROS was measured in peroxisomes of replicon-containing cells, and this increase was more pronounced than in mitochondria or the cytosol, suggesting that the redox balance of peroxisomes is specifically impaired in cells replicating HCV. Our study provides evidence that peroxisome function and morphology are altered in HCV-infected cells.

2023-10-24 | PXD044994 | Pride

Hypothalamus

Project description:These arrays contain data from hypthalamus tissue of nestin-Pex5 -/- male mice Gene expression in biological replicates from hypothalamus of 4 wild type mice was compared with 4 NestinPex5-/- mice. In the latter, functional peroxisomes were deleted from all neural cells.

2012-03-01 | E-GEOD-31938 | biostudies-arrayexpress

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