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Selective targeting of MYC mRNA by stabilized antisense oligonucleotides

Abstract

MYC is a prolific proto-oncogene driving the malignant behaviors of numerous common cancers, yet potent and selective cell-permeable inhibitors of MYC remain elusive. In order to ultimately realize the goal of therapeutic MYC inhibition in cancer, we have initiated discovery chemistry efforts aimed at inhibiting MYC translation. Here we describe a series of conformationally stabilized synthetic antisense oligonucleotides designed to target MYC mRNA (MYCASOs). To support bioactivity, we designed and synthesized this focused library of MYCASOs incorporating locked nucleic acid (LNA) bases at the 5ʹ- and 3ʹ-ends, a phosphorothioate backbone, and internal DNA bases. Treatment of MYC-expressing cancer cells with MYCASOs leads to a potent decrease in MYC mRNA and protein levels. Cleaved MYC mRNA in MYCASO-treated cells is detected with a sensitive 5ʹ Rapid Amplification of cDNA Ends (RACE) assay. MYCASO treatment of cancer cell lines leads to significant inhibition of cellular proliferation while specifically perturbing MYC-driven gene expression signatures. In a MYC-induced model of hepatocellular carcinoma, MYCASO treatment decreases MYC protein levels within tumors, decreases tumor burden, and improves overall survival. MYCASOs represent a new chemical tool for in vitro and in vivo modulation of MYC activity, and promising therapeutic agents for MYC-addicted tumors.

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Fig. 1: Design and characterization of a library of MYC-targeting antisense oligonucleotides.
Fig. 2: MYCASOs decrease MYC protein expression in cancer cell lines.
Fig. 3: MYCASOs downregulate MYC expression through RNase H1-mediated cleavage of MYC mRNA.
Fig. 4: Phenotypic response to MYCASO treatment.
Fig. 5: Transcriptomic analysis of MYCASO-3 treated cells.
Fig. 6: In vivo effects of MYASO-3 in a MYC-induced model of hepatocellular carcinoma.

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Acknowledgements

We thank M. Gabay and D. Felsher (Stanford University), S. He, T. Look, E. Dhimolea, C. Mitsiades, and members of the Lurie Family Imaging Center (Dana-Farber Cancer Institute) for assistance with animal studies. This work was supported by a US National Cancer Institute (NCI) Pathway to Independence Award (K99/R00CA190861) (C.J.O), and institutional funding from DFCI, MGH, and the Broad Institute (J.E.B, C.J.O, T.G.), and the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute (D.G.A.).

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TG designed and performed experiments, analyzed data; HW, JT performed animal experiments; RB synthesized reagents; ML performed bioinformatics analysis; CL, LTN performed immunohistochemistry analysis; YZ, DGA, DTT, XC supervised and planned research; YZ, JEB, CJO conceptualized study, supervised and planned research. TG, JEB, CJO wrote the paper.

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Correspondence to James E. Bradner or Christopher J. Ott.

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CJO, RB, YZ, and JEB are listed as inventors in an issued patent related to the compounds described in this manuscript (WO2013123451A1). D.T.T. has received consulting fees from ROME Therapeutics, Foundation Medicine, Inc., NanoString Technologies, EMD Millipore Sigma, Pfizer, and Third Rock Ventures that are not related to this work. DTT is a founder and has equity in ROME Therapeutics, PanTher Therapeutics and TellBio, Inc., which is not related to this work. DTT receives research support from ACD-Biotechne, PureTech Health LLC, and Ribon Therapeutics, which was not used in this work. Dr. Ting’s interests were reviewed and are managed by Massachusetts General Hospital and Mass General Brigham in accordance with their conflict of interest policies. JEB is now an executive and shareholder of Novartis and has been a founder and shareholder of SHAPE (acquired by Medivir), Acetylon (acquired by Celgene), Tensha (acquired by Roche), Syros, Regenacy and C4 Therapeutics.

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Gill, T., Wang, H., Bandaru, R. et al. Selective targeting of MYC mRNA by stabilized antisense oligonucleotides. Oncogene 40, 6527–6539 (2021). https://doi.org/10.1038/s41388-021-02053-4

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