GSE125395
Global transcriptional changes in the JJN3 myeloma cell line that occur as a result of treatment with 2 pyrrolobenzodiazepine (PBD) monomers
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-?B 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. Overall design: JJN3 cells were treated with 30nM of DC-1-170 and DC-1-192 for 4 hours alongside untreated controls in triplicate.