A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors
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Andrew J. Annalora1, Shawn O’Neil2, Jeremy D. Bushman3, James E. Summerton3, Craig B. Marcus1 and Patrick L. Iversen1,4
1Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
2Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
3Onco-Tools, LLC, Philomath, OR 97370, USA
4LS Pharma, LLC, Grand Junction, CO 81507, USA
Andrew J. Annalora, email: email@example.com
Keywords: antisense oligonucleotides; phosphorodiamidate morpholino oligomers; transcriptomics; Ewing’s family of tumors; RNA-based therapeutics
Received: May 10, 2018 Accepted: June 19, 2018 Published: July 17, 2018
Ewing’s sarcoma treatment failures are associated with high mortality indicating a need for new therapeutic approaches. We used a k-mer counting approach to identify cancer-specific mRNA transcripts in 3 Ewing’s Family Tumor (EFT) cell lines not found in the normal human transcriptome. Phosphorodiamidate morpholino oligomers targeting six EFT-specific transcripts were evaluated for cytotoxicity in TC-32 and CHLA-10 EFT lines and in HEK293 renal epithelial control cells. Average morpholino efficacy (EC50) was 0.66 ± 0.13 in TC-32, 0.25 ± 0.14 in CHLA-10 and 3.07 ± 5.02 μM in HEK293 control cells (ANOVA p < 0.01). Synergy was observed for a cocktail of 12 morpholinos at low dose (0.3 μM) in TC-32 cells, but not in CHLA-10 cells. Paired synergy was also observed in both EFT cell lines when the PHGDH pre-mRNA transcript was targeted in combination with XAGE1B or CYP4F22 transcripts. Antagonism was observed when CCND1 was targeted with XAGE1B or CYP4F22, or when IGFBP-2 was targeted with CCND1 or RBM11. This transcriptome profiling approach is highly effective for cancer drug discovery, as it identified new EWS-specific target genes (e.g. CYP4F22, RBM11 and IGBP-2), and predicted effective antisense agents (EC50 < 1 μM) that demonstrate both synergy and antagonism in combination therapy.
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