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RNAseq of Plasmodium falciparum 3D7 parasites treated with the Jumonji pan inhibitor JIB-04

ABSTRACT: RNAseq of Plasmodium falciparum 3D7 parasites treated with the Jumonji pan inhibitor JIB-04

PROVIDER: PRJNA481730 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7536760.fastq.gz	Fastqsanger.gz
	SRR7536761.fastq.gz	Fastqsanger.gz
	SRR7536752.fastq.gz	Fastqsanger.gz
	SRR7536762.fastq.gz	Fastqsanger.gz
	SRR7536753.fastq.gz	Fastqsanger.gz

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RNAseq of Plasmodium falciparum 3D7 parasites treated with the Jumonji pan inhibitor JIB-04

Project description:Little is known about the role of the three Jumonji C (JmjC) enzymes in Plasmodium falciparum (Pf). Here, we show that JIB-04 and other established inhibitors of mammalian JmjC histone demethylases kill asexual blood stage parasites and are even more potent at blocking gametocyte development and gamete formation. In late stage parasites, JIB-04 increased levels of trimethylated lysine residues on histones, suggesting the inhibition of P. falciparum Jumonji demethylase activity. These epigenetic defects coincide with deregulation of invasion, cell motor, and sexual development gene programs, including gene targets coregulated by the PfAP2-I transcription factor and chromatin-binding factor, PfBDP1. Mechanistically, we demonstrate that PfJmj3 converts 2-oxoglutarate to succinate in an iron-dependent manner consistent with mammalian Jumonji enzymes, and this catalytic activity is inhibited by JIB-04 and other Jumonji inhibitors. Our pharmacological studies of Jumonji activity in the malaria parasite provide evidence that inhibition of these enzymatic activities is detrimental to the parasite.

2020-07-12 | GSE117307 | GEO

Global transcriptional response of P. falciparum NF54 early gametocytes treated with the Jumonji histone demethylase inhibitor JIB-04

Project description:Global transcriptomic profiling of JIB-04 treated and untreated control early gametocytes to determine the downstream effects of Jumonji histone demethylase inhibition on development

2021-04-20 | GSE163189 | GEO

Identification of genes modulated by JIB-04 in lung cancer cells

Project description:JIB-04 is an inhibitor of Jumonji histone demethylases identified through a cell based screen that measures the reactivation of an epigenetically silenced transgene. The active JIB-04 E-isomer shows selectivity for cancer vs. normal cells affecting both transcriptional patterns and cell viability in a cancer specific manner. H358 lung cancer cells or the patient matched HCC4017 (cancer) vs. HBEC30KT (immortalized normal) lung cell pair were treated with DMSO vehicle or 500nM E-isomer or 500 nM Z-isomer of JIB-04 for 4 h or 24 h and RNA extracted.

2013-07-08 | E-GEOD-46632 | biostudies-arrayexpress

Identification of genes modulated by JIB-04 in lung cancer cells

2013-07-08 | GSE46632 | GEO

The Jumonji-domain histone demethylase inhibitor JIB-04 deregulates oncogenic programs and increases DNA damage in Ewing Sarcoma, resulting in impaired cell proliferation and survival, and reduced tumor growth

Project description:The overall goal of this study was to characterize the activity and mechanism(s) of action of the pan-Jumonji domain histone demethylase small molecule inhibitor JIB-04 in the pediatric bone and soft tissue cancer Ewing Sarcoma.

2019-01-03 | GSE119832 | GEO

Transcriptional alterations of P. falciparum 3D7-A heat shock-adapted vs control parasites.

Project description:Periodic fever is the most characteristic clinical feature of human malaria. However, how parasites survive malarial febrile episodes, which often involve temperatures of >40ºC, is not known. To understand the molecular basis of heat shock (HS) resistance in Plasmodium falciparum, we took advantage of previously developed P. falciparum lines adapted to periodic HS (3D7-A-HS) and their non-selected controls maintained in parallel (3D7-A). Their ability to adapt in only a few cycles suggested that the parental parasite population contained a selectable subset of parasites resistant to HS. Transcriptomic analysis of both 3D7-A-HS and 3D7-A was used to study the differences at a transcriptional level that could be related with the HS-resistant phenotype.

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P.falciparum strain 3D7, SIR2 knockout

Project description:This experiment studies the effect of knocking out the transcriptional regulator SIR2 in 3D7 parasites. RNA was harvested from ring-stage parasites at 8 hours post-infection. Keywords = SIR2 Keywords = epigenetic regulation Keywords = antigenic variation Keywords = var Keywords = Plasmodium falciparum Keywords: other

2005-03-08 | GSE2369 | GEO

Transcriptome analysis by RNA sequencing after treatment with JIB-04 in hepatocellular carcinoma

Project description:Our RNA sequencing analysis revealed that the JIB-04 treatment altered the expression of genes that are involved in the cell cycle, p53 signaling pathway, and apoptosis, and are also related to several cancers including hepatocellular carcinoma. JIB-04 also altered the expression of genes involved in various signaling pathways such as the FoxO signaling pathway, the PI3K-Akt signaling pathway, which is crucial for the proliferation and maintenance of hepatocellular carcinoma cells.

2022-08-03 | GSE179345 | GEO

Transgenic Plasmodium falciparum parasites line 3D7/DDGFP-PfAP2-HC: transcriptional differences between 3D7/DDGFP-PfAP2-HC control parasites (cultured in presence of Shield-1; ON) vs PfAP2-HC-depleted parasites (cultured in absence of Shield-1; OFF)

Project description:Transcriptional profiling of transgenic P. falciparum asexual blood stage parasites of the transgenic strain 3D7/DDGFP-PfAP2-HC at five time points during intra-erythrocytic parasite development. The DD (FKBP destabilisation domain) allows for the conditional expression of fusion proteins: DD fusion proteins are rapidly degraded or stably expressed in absence or presence of the stabilising ligand Shield-1, respectively (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in DDGFP-PfAP2-HC-expressing compared to DDGFP-PfAP2-HC-depleted parasites during the intra-erythtrocytic cell cycle.

2020-10-06 | GSE159061 | GEO

Transcriptome analysis by RNA sequencing after treatment with JIB-04 in colorectal cancer

Project description:We investigate RNA sequencing analysis revealed that the JIB-04 treatment altered the expression of genes that are involved in the cell cycle, apoptosis, and DNA replication and are also related to several cancers including colorectal cancer. JIB-04 also altered the expression of genes involved in various signaling pathways such as the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the Wnt signaling pathway, which is crucial for the proliferation and maintenance of colorectal cancer cells.

2018-11-01 | GSE106407 | GEO

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