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The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma

Min Pan, William C. Wright, Rich Chapple, Asif Zubair, Manbir Sandhu, Jake Batchelder, Jonathan Low, Kaley B Blankenship, Yingzhe Wang, Brittney Gordon, Payton Archer, Samuel W. Brady, Sivaraman Natarajan, Matthew J. Posgai, John Schuetz, Darcie Miller, Ravi Kalathur, Siquan Chen, Jon Patrick Connelly, M. Madan Babu, Michael A. Dyer, Shondra M. Pruett-Miller, Burgess B. Freeman III, Taosheng Chen, Lucy A. Godley, View ORCID ProfileScott Blanchard, Elizabeth Stewart, John Easton, Paul Geeleher
doi: https://doi.org/10.1101/2021.02.25.432934
Min Pan
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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William C. Wright
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Rich Chapple
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Asif Zubair
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Manbir Sandhu
2Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Jake Batchelder
2Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
3Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Jonathan Low
3Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Kaley B Blankenship
4Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
5Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Yingzhe Wang
6Preclinical Pharmacokinetic Shared Resource, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Brittney Gordon
5Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Payton Archer
4Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
5Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Samuel W. Brady
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Sivaraman Natarajan
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Matthew J. Posgai
7Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
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John Schuetz
8Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Darcie Miller
2Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Ravi Kalathur
2Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Siquan Chen
9Cellular Screening Center, The University of Chicago, Chicago, IL 60637, USA
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Jon Patrick Connelly
10Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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M. Madan Babu
2Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Michael A. Dyer
5Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
11Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Shondra M. Pruett-Miller
10Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Burgess B. Freeman III
6Preclinical Pharmacokinetic Shared Resource, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Taosheng Chen
3Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Lucy A. Godley
7Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
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Scott Blanchard
2Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
3Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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  • ORCID record for Scott Blanchard
Elizabeth Stewart
4Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
5Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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John Easton
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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  • For correspondence: paul.geeleher@stjude.org john.easton@stjude.org
Paul Geeleher
1Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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  • For correspondence: paul.geeleher@stjude.org john.easton@stjude.org
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ABSTRACT

Survival in high-risk pediatric neuroblastoma has remained around 50% for the last 20 years, with immunotherapies and targeted therapies having had minimal impact. Here, we identify the small molecule CX-5461 as selectively cytotoxic to high-risk neuroblastoma and synergistic with low picomolar concentrations of topoisomerase I inhibitors improving survival in vivo in orthotopic patient-derived xenograft neuroblastoma mouse models. CX-5461 recently progressed through phase I clinical trial as a first-in-human inhibitor of RNA-POL I. However, we also use a comprehensive panel of in vitro and in vivo assays to demonstrate that CX-5461 has been mischaracterized and that its primary target at pharmacologically relevant concentrations, is in fact topoisomerase II beta (TOP2B), not RNA-POL I. These findings are important because existing clinically approved chemotherapeutics have well-documented off-target interactions with TOP2B, which have previously been shown to cause both therapy-induced leukemia and cardiotoxicity—often-fatal adverse events, which can emerge several years after treatment. Thus, while we show that combination therapies involving CX-5461 have promising anti-tumor activity in vivo in neuroblastoma, our identification of TOP2B as the primary target of CX-5461 indicates unexpected safety concerns that should be examined in ongoing phase II clinical trials in adult patients before pursuing clinical studies in children.

Competing Interest Statement

The authors have declared no competing interest.

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The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma
Min Pan, William C. Wright, Rich Chapple, Asif Zubair, Manbir Sandhu, Jake Batchelder, Jonathan Low, Kaley B Blankenship, Yingzhe Wang, Brittney Gordon, Payton Archer, Samuel W. Brady, Sivaraman Natarajan, Matthew J. Posgai, John Schuetz, Darcie Miller, Ravi Kalathur, Siquan Chen, Jon Patrick Connelly, M. Madan Babu, Michael A. Dyer, Shondra M. Pruett-Miller, Burgess B. Freeman III, Taosheng Chen, Lucy A. Godley, Scott Blanchard, Elizabeth Stewart, John Easton, Paul Geeleher
bioRxiv 2021.02.25.432934; doi: https://doi.org/10.1101/2021.02.25.432934
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The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma
Min Pan, William C. Wright, Rich Chapple, Asif Zubair, Manbir Sandhu, Jake Batchelder, Jonathan Low, Kaley B Blankenship, Yingzhe Wang, Brittney Gordon, Payton Archer, Samuel W. Brady, Sivaraman Natarajan, Matthew J. Posgai, John Schuetz, Darcie Miller, Ravi Kalathur, Siquan Chen, Jon Patrick Connelly, M. Madan Babu, Michael A. Dyer, Shondra M. Pruett-Miller, Burgess B. Freeman III, Taosheng Chen, Lucy A. Godley, Scott Blanchard, Elizabeth Stewart, John Easton, Paul Geeleher
bioRxiv 2021.02.25.432934; doi: https://doi.org/10.1101/2021.02.25.432934

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