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Global transcriptional changes in the JJN3 myeloma cell line that occur as a result of treatment with 2 pyrrolobenzodiazepine (PBD) monomers

ABSTRACT: Global transcriptional changes in the JJN3 myeloma cell line that occur as a result of treatment with 2 pyrrolobenzodiazepine (PBD) monomers

PROVIDER: PRJNA516213 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8467600_1.fastq.gz	Fastqsanger.gz
	SRR8467600_2.fastq.gz	Fastqsanger.gz
	SRR8467610_1.fastq.gz	Fastqsanger.gz
	SRR8467610_2.fastq.gz	Fastqsanger.gz
	SRR8467601_1.fastq.gz	Fastqsanger.gz

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Global transcriptional changes in the JJN3 myeloma cell line that occur as a result of treatment with 2 pyrrolobenzodiazepine (PBD) monomers

Project description:Background: This study characterises a group of Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) monomeric hybrids to investigate the global transcriptional changes that occur as a result of treatment in these cells. It was also of interest to determine whether compounds show a selective inhibitory effect on the NF-kB consenus sequence and hence NF-kB signalling. Methods: NF-kB is often overexpressed and over-active in multiple myeloma. Therefore, JJN3 myeloma cells were selected for this investigation. These cells were treated with 2 PBD monomers - DC-1-170 and DC-1-192 - at a concentration of 30nM, in triplicate alongside untreated controls. They were lysed in Trizol reagent (Thermo Fisher) and RNA was extracted using an RNeasy mini-prep kit (Qiagen). Isolated RNA was then taken forward for RNA-seq. Downstream analysis was performed using GenView2 software (in-house analysis tool developed by Peter Giles) and Ingenuity Pathway Analysis (Qiagen). Results: RNA-seq analysis revealed an overall inhibitory effect on gene transcription as a result of treatment with both PBD monomers, with a small proportion of genes experiencing increased transcription. Approximately 80% of genes that were altered were common to both PBD compounds tested. Both PBD compounds also showed significant inhibition of NF-kB signalling. Conclusions: RNA-sequencing confirmed gene set enrichment for NF-κB pathway genes although as expected, other canonical pathways were also affected. This could be linked with the toxicity that these cells experience as a result of treatment with PBD monomer hybrids.

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Affymetrix U133Plus2.0 data sets of Human Myeloma Cellline JJN3 with non-specific, scrambled shRNA or CKS1B shRNA

Project description:This series represents Affymetrix U133Plus2.0 data sets of JJN3 transduced with levivirus expressing non-specific scrambled shRNA or CKS1B shRNA Keywords: JJN3 CKS1B shRNA

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Project description:This series represents Affymetrix U133Plus2.0 data sets of JJN3 transduced with levivirus expressing non-specific scrambled shRNA or CKS1B shRNA Experiment Overall Design: This series represents Affymetrix U133Plus2.0 data sets of JJN3 transduced with levivirus expressing non-specific scrambled shRNA or CKS1B shRNA

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