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RNAseq analysis of the effects of inorganic long-chain polyphosphates on murine macrophages

ABSTRACT: RNAseq analysis of the effects of inorganic long-chain polyphosphates on murine macrophages

PROVIDER: PRJNA544063 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9099720.fastq.gz	Fastqsanger.gz
	SRR9099730.fastq.gz	Fastqsanger.gz
	SRR9099721.fastq.gz	Fastqsanger.gz
	SRR9099731.fastq.gz	Fastqsanger.gz
	SRR9099722.fastq.gz	Fastqsanger.gz

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RNA-seq of human primary epithelial nasal cells infected with SARS-CoV-2 (20A clade) and treated with long chain inorganic polyphosphates (polyP120) against vehicle-(saline solution)- treated controls

Project description:Primary human nasal epithelial cells collected by nasal brushing of healthy donors (data deposited at: EVA- EMBL-EBI; project ID: PRJEB42411; analyses: ERZ1700617) were plated (3x105 cells) and infected with SARS-CoV-2 viral particles 20A (EPI_ISL_514432-S66; MOI, 0.03). After 24 hours, the infected cells were treated with 18.5 microMolar long chain inorganic polyphosphates (polyP120) or vehicle (saline solution) as the negative control for the treatment. After 36 hours, the cells were lysed, and their RNA were extracted for RNAseq.

2024-05-31 | E-MTAB-13363 | biostudies-arrayexpress

RNAseq analysis of the effects of inorganic long-chain polyphosphates on murine macrophages

Project description:We used unbiased RNAseq analysis from bone marrow-derived macrophages of five individually treated sets of cells from C57BL/6J mice. Cells were treated for 12h with LPS, LPS+L-polyP, L-polyP, or remained untreated. We found several hundred genes to be regulated by the addition of L-polyP. In the combinated treatment with LPS as compared to LPS alone, we found especially interferon-regulated genes to be differentially expressed.

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A broad response to intracellular long-chain polyphosphate in human cells

Project description:Polyphosphates (polyP) are ancient molecules comprised of inorganic phosphates joined by high energy phosphoanhydride bonds in chains of 3-1000 units in length. In this study, we describe a system to produce polyP in mammalian cells by ectopic expression of the E. coli ppk1+ gene. Production of the EcPpk1 protein results in polyP accumulation throughout the cell, including the nucleus. Using transcriptomic and proteomic analyses, we demonstrate a broad impact of polyP on diverse pathways, including activation of the ERK1/2-EGR1 signaling axis. PolyP accumulation also results in redistribution of several chromatin bound proteins and a translation initiation factor from the nucleus to the cytoplasm. Our work will serve as a novel resource to interrogate polyP biology in higher eukaryotes.

2020-04-22 | GSE149011 | GEO

Effect of polyphosphates on osteoblast mineralization

Project description:Rat osteoblasts ROB17/2.8 cells were cultured in the presence of high (1mg/ml) or low (0.01mg/ml) concentration of polyphosphates.

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Project description:RNA-seq of human primary epithelial nasal cells infected with SARS-CoV-2 (20A clade) and treated with long chain inorganic polyphosphates (polyP120) against vehicle-(saline solution)- treated controls

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Effect of polyphosphates on osteoblast mineralization

Project description:Rat osteoblasts ROB17/2.8 cells were cultured in the presence of high (1mg/ml) or low (0.01mg/ml) concentration of polyphosphates. Poly(P) induced gene expression in rat osteoblast ROS17/2.8 cells was measured after the treatment with high (1mg/ml) or low (0.01mg/ml) for 24 h.

2016-03-15 | E-GEOD-79176 | biostudies-arrayexpress

Long-chain polyphosphates impair SARS-CoV-2 infection and replication.

Project description:Inorganic polyphosphates (polyPs) are linear polymers composed of repeated phosphate (PO4 3-) units linked together by multiple high-energy phosphoanhydride bonds. In addition to being a source of energy, polyPs have cytoprotective and antiviral activities. Here, we investigated the antiviral activities of long-chain polyPs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In molecular docking analyses, polyPs interacted with several conserved amino acid residues in angiotensin-converting enzyme 2 (ACE2), the host receptor that facilitates virus entry, and in viral RNA-dependent RNA polymerase (RdRp). ELISA and limited proteolysis assays using nano- LC-MS/MS mapped polyP120 binding to ACE2, and site-directed mutagenesis confirmed interactions between ACE2 and SARS-CoV-2 RdRp and identified the specific amino acid residues involved. PolyP120 enhanced the proteasomal degradation of both ACE2 and RdRp, thus impairing replication of the British B.1.1.7 SARS-CoV-2 variant. We thus tested polyPs for functional interactions with the virus in SARS-CoV-2-infected Vero E6 and Caco2 cells and in primary human nasal epithelial cells. Delivery of a nebulized form of polyP120 reduced the amounts of viral positive-sense genomic and subgenomic RNAs, of RNA transcripts encoding proinflammatory cytokines, and of viral structural proteins, thereby presenting SARS-CoV-2 infection in cells in vitro.

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A broad response to intracellular long-chain polyphosphate in human cells

Project description:Polyphosphates (PolyP) are highly anionic, linear polymers composed of long chains of inorganic phosphates linked together by phosphoanhydride bonds. PolyP chains are found in all kingdoms of life, and play roles in phosphate homeostasis, cell growth, infection, and blood coagulation. Unlike in bacteria and yeast, the mammalian enzymes responsible for the synthesis and degradation of polyP are unknown, which presents a challenge for the study of polyP in higher eukaryotes. To overcome this, we use a system to produce polyP inside of human cells through the ectopic expression of the E. coli Ppk1 synthetic enzyme. Here, we present the results from large-scale transcriptomic and proteomic analyses of polyP producing HEK293T cells. We uncovered >350 RNAs and 14 proteins that show changes following in vivo polyP accumulation. Follow up on specific hits revealed that the internal accumulation of polyP resulted in a significant decrease in the dehydrogenase/reductase DHRS2 without a corresponding increase in p53 phosphorylation, and activation of the ERK1/2-ERG1 signaling axis. Finally, following upregulation of internal polyP we observed the relocalization and redistribution of several nuclear proteins, including chromatin bound proteins DEK, TAF10, GTF2I and the translation initiation factor eIF5b. Altogether, our work serves as a novel resource to understand the impact of increased intracellular polyP in mammalian cells.

2020-09-24 | PXD018896 | Pride

Analysis of inorganic polyphosphates by capillary gel electrophoresis.

Project description:This paper describes the development of a method that uses capillary gel electrophoresis (CGE) to analyze mixtures of inorganic polyphosphate ((P(i))(n)). Resolution of (P(i))(n) on the basis of n, the number of residues of dehydrated phosphate, is accomplished by CGE using capillaries filled with solutions of poly(N,N-dimethylacrylamide) (PDMA) and indirect detection by the UV absorbance of a chromophore, terephthalate, added to the running buffer. The method is capable of resolving peaks representing (P(i))(n) with n up to approximately 70; preparation and use of authentic standards enables the identification of peaks for (P(i))(n) with n = 1-10. The main advantages of this method over previously reported methods for analyzing mixtures of (P(i))(n) (e.g., gel electrophoresis, CGE using polyacrylamide-filled capillaries) are its resolution, convenience, and reproducibility; gel-filled capillaries are easily regenerated by pumping in fresh, low-viscosity solutions of PDMA. The resolution is comparable to that of ion-exchange chromatography and detection of (P(i))(n) by suppressed conductivity. The method is useful for analyzing (P(i))(n) generated by the dehydration of P(i) at low temperature (125-140 degrees C) with urea, in a reaction that may have been important in prebiotic chemistry. The method should also be useful for characterizing mixtures of other anionic, oligomeric, or polymeric species without an intrinsic chromophore (e.g., sulfated polysaccharides, oligomeric phospho-diesters).

| S-EPMC2926810 | biostudies-literature

Inorganic polyphosphates stimulates matrix production in human annulus fibrosus cells.

Project description:IntroductionUbiquitously found in all life forms, inorganic polyphosphates (polyP) are linear polymers of repeated orthophosphate units. Present in intervertebral disc tissue, polyP was previously shown to increase extracellular matrix production in nucleus pulposus (NP) cells. However, the effects of polyP on human annulus fibrosus (hAF) cell metabolism is not known.Methods and resultsHere, hAF cells cultured in the presence of 0.5 to 1 mM polyP, chain length 22 (polyP-22), showed an increase in glycosaminoglycan content, proteoglycan and collagen synthesis, and aggrecan and collagen type 1 gene expression. Gene expression level of matrix metalloproteinases 1 was reduced while matrix metalloproteinases 3 level was increased in hAF cells treated with 1 mM polyP. Adenosine triphosphate (ATP) synthesis was also significantly increased in hAF cell culture 72 hours after the exposure to 1 mM polyP-22.ConclusionsPolyP thus has both anabolic and bioenergetic effects in AF cells, similar to that observed in NP cells. Together, these results suggest polyP as a potential energy source and a metabolic regulator of disc cells.

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