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Farnesyl diphosphate synthase inhibition remodels the tumor immune microenvironment by activating endogenous retroviruses

ABSTRACT: Farnesyl diphosphate synthase inhibition remodels the tumor immune microenvironment by activating endogenous retroviruses

PROVIDER: PRJEB82516 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	KO-1_DUMC.tsv.gz	Tabular
	KO-2_DUMC.tsv.gz	Tabular
	KO-3_DUMC.tsv.gz	Tabular
	KO-4_DUMC.tsv.gz	Tabular
	KO-5_DUMC.tsv.gz	Tabular

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Similar Datasets

Farnesyl diphosphate synthase inhibition remodels the tumor immune microenvironment by activating endogenous retroviruses

Project description:Farnesyl diphosphate synthase inhibition remodels the tumor immune microenvironment by activating endogenous retroviruses

| PRJEB82515 | ENA

Farnesyl diphosphate synthase inhibition remodels the tumor immune microenvironment by activating endogenous retroviruses

Project description:Farnesyl diphosphate synthase (FDPS) is a crucial enzyme in isoprenoid and cholesterol biosynthesis and the target for nitrogen-containing bisphosphonate (N-BP) drugs widely used for osteoporosis treatment. Here we show that FDPS inhibition overcomes tumor resistance to immune checkpoint blockade (ICB) therapy by activating endogenous retroviruses (ERVs) and promoting a potent type I interferon response. FDPS inhibition, either by genetic knockout or alendronate, enhances the efficacy of ICB therapy substantially in multiple murine tumors by remodeling the immune microenvironment and enhancing lymphocyte infiltration, which is caused by increased type I interferon upregulation. Mechanistically, FDPS inhibition attenuates mitochondrial membrane potential (MtMP), enabling endonuclease G (EndoG) migration from the mitochondria into the nucleus, increasing DNA double-strand breaks and degradation of the heterochromatin maintenance protein TRIM28(KAP1), promoting enhanced ERV transcription and activation of the MDA5/MAVS pathway. The ensuing type I interferon upregulation is responsible for enhanced antigen presentation and sensitization to ICB therapy.

2024-11-14 | GSE281577 | GEO

Project description:Farnesyl diphosphate synthase inhibition remodels the tumor immune microenvironment by activating endogenous retroviruses

| PRJNA1184193 | ENA

Transcriptomic analysis of race L Botryococcus braunii AC768 revealed a race L-specific protein resembling the lycopaoctaene synthase

Project description:The green algal Botryococcus braunii (Chlorophyte) is known for accumulating high levels of hydrocarbons that are a useful alternative to fossil fuels. B. braunii is categorized into three groups based on types of their accumulated hydrocarbons: alkadiene/triene in race A, botryococcenes in race B, and lycopadiene in race L. Transcriptomic studies in race A and race B have discovered tremendous information related to the genes encoding proteins involved in hydrocarbon biosynthesis. However, transcriptome of race L has not been reported. In this study, we report a transcriptome of race L B. braunii AC768 through the de novo assembly using Hiseq platform. Our analyses indicate that photosynthesis and protein biosynthesis are the most abundantly transcribed in actively growing race L B. braunii. We show that the transcriptome of race L shares similar amounts (~20%) of mutual best-hits with that of race A or race B. Sequence homologous analyses indicate that enzymes involved in squalene and phytoene biosynthesis are well separated into geranyl-diphosphate synthase, farnesyl-diphosphate synthase, geranylgeranyl-diphosphate synthase, phytoene synthase, and squalene synthase. Both B. braunii specific enzymes botryococcene synthase SSL3 and lycopaoctaene synthase LOS are found to form distinctive subgroups in the group of squalene synthase. One of the ESTs in AC768 transcriptome that falls into the subgroup with LOS and shares >88% identity with that of LOS. Together, our results show that SSL and LOS are unique to race B and race L B. braunii subspecies, respectively. We propose that phytoene synthase in race L shares higher homolog to squalene synthase than phytoene synthase in other algae.

2019-11-21 | GSE96585 | GEO

Activation of polyisoprenyl diphosphate phosphatase 1 remodels cellular presqualene diphosphate.

Project description:Polyisoprenyl diphosphates play diverse and vital roles in cell function in health and disease. The counter-regulatory lipid signaling molecule, presqualene diphosphate (PSDP), is rapidly converted to its monophosphate form (PSMP) upon cell activation [Levy, B. D., Petasis, N. A., and Serhan, C. N. (1997) Nature 389, 985-990]. The first PSDP phosphatase was recently identified and named polyisoprenyl diphosphate phosphatase 1 (PDP1) [Fukunaga, K., et al. (2006) J. Biol. Chem. 281, 9490-9497]. Here, we present evidence that PDP1 displays properties of a lipid phosphate phosphatase/phosphotransferase with distinct substrate preference for PSDP. Cell activation with PMA increased PSDP phosphatase activity in a concentration-dependent manner, and Western analysis suggested that PDP1 is directly phosphorylated by protein kinase C. Cellular PSDP phosphatase activity was also induced by the receptor-mediated agonists insulin and TNF-alpha. To address PDP1's contribution to cellular PSDP phosphatase activity, HEK293 cells were established that stably expressed PDP1 siRNA, leading to a 60% decrease in the level of PDP1 RNA, and concomitant decreases in PDP1 protein and PMA-initiated PSDP phosphatase activity. HEK293 cells harboring the PDP1 siRNA construct also displayed a marked decrease in the extent of PMA-initiated conversion of cellular PSDP to PSMP. Together, these findings are the first to indicate that PDP1 is activated during cell responses to soluble stimuli to convert PSDP to PSMP. Moreover, they provide evidence that PDP1 can serve as a new checkpoint for polyisoprenyl phosphate remodeling during cell activation.

| S-EPMC2765513 | biostudies-literature

Expression data from lens epithelial cells (LECs) from Shumiya cataract rats (SCR) with or without cataract (Cat+ or Cat-)

Project description:The Shumiya cataract rat (SCR) is a model for hereditary cataract. Two-third of these rats develop lens opacity within 10-11-weeks. Onset of cataract is attributed to the synergetic effect of lanosterol synthase (Lss) and farnesyl-diphosphate farnesyltransferase 1 (Fdft1) mutant alleles that lead to cholesterol deficiency in the lenses, which in turn adversely affects lens biology including the growth and differentiation of lens epithelial cells (LECs). Nevertheless, the molecular events and changes in gene expression associated with the onset of lens opacity in SCR is poorly understood. Our study aimed to identify the gene expression patterns during cataract formation in SCRs, which may be responsible for cataractogenesis in SCR.

2020-07-31 | GSE152616 | GEO

Escherichia coli

Project description:Farnesyl Diphosphate (FPP) Toxicity in E. coli, M9 medium

| PRJNA143665 | ENA

Escherichia coli DH1

Project description:Farnesyl Diphosphate (FPP) Toxicity in E. coli, LB medium

| PRJNA140277 | ENA

FDPS-regulated transcriptome profile revealed its potential functions in osteoporosis as an RNA binding protein

Project description:Farnesyl diphosphate synthase (FDPS), an essencial enzyme involved in mevalonate pathway, is implicated in cancers and osteoporosis by catalyzing head to tail condensation of two molecules of isopentenyl pyrophosphate with dimethylallyl pyrophosphate to form farnesyl pyrophosphate. It has also been identified as an RNA-binding protein (RBP). However, it’s exactly RNA-binding function in diseases, up to now, remain unknown. In the present study, the function of FDPS in HeLa cells was investigated with FDPS overexpression. The results showed that FDPS overexpression promoted proliferation in HeLa cells. FDPS overexpression extensively regulated the expression of genes in cell proliferation, cytokine-mediated signaling pathway, and extracellular matrix organization. In addition, FDPS extensively regulated the alternative splicing of numbers of genes related with osteoporosis, including NAB1, FGFR3, and ALPL, and FDPS-regulated DEGs and ASEs were highly validated by RT-qPCR. This is the first study to investigate the properties of FDPS as an RBP from a genome-wide perspective, our results suggested that FDPS acts as an RBP playing an important role in cancer progression and osteoporosis by altering gene expression and regulating alternative splicing, which contributes to a precise understanding of potentially FDPS-targeted therapies.

2023-02-06 | GSE151605 | GEO

Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BLNCR1 to regulate melanoma cell migration

Project description:This SuperSeries is composed of the following subset Series: GSE33092: Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BLNCR1 to regulate melanoma cell migration [HT-seq] GSE37132: Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BLNCR1 to regulate melanoma cell migration [Affymetrix] Refer to individual Series

2012-04-27 | E-GEOD-37169 | biostudies-arrayexpress

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