Reprogramming CBX8-PRC1 function with a positive allosteric modulator

Junghyun L Suh; Daniel Bsteh; Bryce Hart; Yibo Si; Tyler M Weaver; Carina Pribitzer; Roy Lau; Shivani Soni; Heather Ogana; Justin M Rectenwald; Jacqueline L Norris; Stephanie H Cholensky; Cari Sagum; Jessica D Umana; Dongxu Li; Brian Hardy; Mark T Bedford; Shannon M Mumenthaler; Heinz-Josef Lenz; Yong-Mi Kim; Gang Greg Wang; Ken H Pearce; Lindsey I James; Dmitri B Kireev; Catherine A Musselman; Stephen V Frye; Oliver Bell

doi:10.1016/j.chembiol.2021.10.003

Reprogramming CBX8-PRC1 function with a positive allosteric modulator

Cell Chem Biol. 2022 Apr 21;29(4):555-571.e11. doi: 10.1016/j.chembiol.2021.10.003. Epub 2021 Oct 28.

Authors

Junghyun L Suh¹, Daniel Bsteh², Bryce Hart¹, Yibo Si², Tyler M Weaver³, Carina Pribitzer⁴, Roy Lau⁵, Shivani Soni⁶, Heather Ogana⁷, Justin M Rectenwald¹, Jacqueline L Norris¹, Stephanie H Cholensky¹, Cari Sagum⁸, Jessica D Umana¹, Dongxu Li⁹, Brian Hardy¹, Mark T Bedford⁸, Shannon M Mumenthaler¹⁰, Heinz-Josef Lenz⁶, Yong-Mi Kim⁷, Gang Greg Wang⁹, Ken H Pearce¹, Lindsey I James¹¹, Dmitri B Kireev¹, Catherine A Musselman¹², Stephen V Frye¹³, Oliver Bell¹⁴

Affiliations

¹ Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
² Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
³ University of Iowa, Department of Biochemistry, Iowa City, IA 52242, USA.
⁴ Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
⁵ Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA 90033, USA.
⁶ Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
⁷ Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90027, USA.
⁸ Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
⁹ Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
¹⁰ Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA 90033, USA; Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
¹¹ Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
¹² University of Iowa, Department of Biochemistry, Iowa City, IA 52242, USA; University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA.
¹³ Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: svfrye@email.unc.edu.
¹⁴ Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria. Electronic address: oliver.bell@med.usc.edu.

Abstract

Canonical targeting of Polycomb repressive complex 1 (PRC1) to repress developmental genes is mediated by cell-type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7, and 8). Based on their central role in silencing and their dysregulation associated with human disease including cancer, CBX proteins are attractive targets for small-molecule chemical probe development. Here, we have used a quantitative and target-specific cellular assay to discover a potent positive allosteric modulator (PAM) of CBX8. The PAM activity of UNC7040 antagonizes H3K27me3 binding by CBX8 while increasing interactions with nucleic acids. We show that treatment with UNC7040 leads to efficient and selective eviction of CBX8-containing PRC1 from chromatin, loss of silencing, and reduced proliferation across different cancer cell lines. Our discovery and characterization of UNC7040 not only reveals the most cellularly potent CBX8-specific chemical probe to date, but also corroborates a mechanism of Polycomb regulation by non-specific CBX nucleotide binding activity.

Keywords: Polycomb; allosterism; chemical probes; chromatin; chromodomain; epigenetics; methyl-lysine reader; positive allosteric modulator.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cell Cycle Proteins / metabolism
Chromatin
Histones / metabolism
Humans
Neoplasms*
Polycomb Repressive Complex 1* / genetics
Polycomb Repressive Complex 1* / metabolism
Polycomb-Group Proteins / genetics
Polycomb-Group Proteins / metabolism
Protein Binding

Substances

CBX8 protein, human
Cell Cycle Proteins
Chromatin
Histones
PRC1 protein, human
Polycomb-Group Proteins
Polycomb Repressive Complex 1

Abstract

Publication types

MeSH terms

Substances

Grants and funding