Issue No. 40, September 2021
VCU Institute of Molecular Medicine (VIMM) NEWS & VIEWS
The VIMM, established in 2008 by Paul B. Fisher, MPh, PhD, FNAI, the Founding Director, is comprised of outstanding scientists/clinicians from VCU School of Medicine, VCU and external experts focusing on important medically-related research in cancer, neurodegeneration and infectious diseases. The purpose of this NEWS & VIEWS is to highlight the exciting research being performed by VIMM members.     
Pharmacological Inhibition of the Nucleosome Remodeling Factor (NURF) with Bromodomain Inhibitors Controls TNBC Cancer Growth.
 
Recent work from the Landry Lab (Human and Molecular Genetics and the VIMM) has shown that inhibiting the NURF subunit Bromodomain PHD-Finger Containing Transcript Factor (BPTF) using a first in class bromodomain inhibitor controls the growth of triple negative breast cancer (TNBC) using several mouse and human models. A second project led by the Pomerantz group (University of Minnesota) in close collaboration with the Landry Lab is developing the next generation of BPTF bromodomain inhibitors with improved selectivity, solubility, and in vivo activity, setting the stage for additional studies focused on this novel and relevant therapeutic target.
 
Highlights of the studies:

  • Epigenetic regulators have been targeted for small molecule design, but until recently, development of chromatin remodeling factors has lagged.
  • Genetic silencing of BPTF or treatment with an inhibitor of the BPTF bromodomain sensitizes mouse and human TNBC cells in culture to the cytotoxic effects of topoisomerase 2 poisons such as doxorubicin and etoposide.
  • Sensitization occurs, in large part, through the inability to resolve crosslinked topoisomerase 2 on chromatin.
  • The sensitization of BPTF inhibited TNBC cells proceeds through autophagy – a regulated process where the cell undergoes self-cannibalization to generate metabolic intermediates and energy for cell survival.
  • First time in vivo administration of a NURF inhibitor showed sensitization of TNBC, and this sensitization appeared to require autophagy.
  • Several novel small molecule inhibitors to the BPTF bromodomain have now been developed with improved selectivity, solubility, and in vivo activity.

Breast cancer is a leading cause of death among women in the United States. Triple negative breast cancer (TNBC) is a difficult disease to treat because there are no effective targeted therapies. Standard of care therapies are cytotoxic in nature and have significant toxic side effects to patients. Developing novel approaches for treating TNBC, which reduce the amount of toxic therapy required for treatment, but yet maintain the antitumor effects, could greatly improve the quality of life for patients.
 
NURF is a chromatin remodeling complex with prototypical ATP-dependent nucleosome sliding activities. It functions primarily to regulate cell-type specific gene expression. It is composed of three main subunits including BPTF – a unique and essential subunit to NURF, the ATPase SNF2L and pRbAp46/48. Several labs have shown, in a variety of cancer types, that BPTF is overexpressed in cancer compared to normal tissue and that its overexpression is correlated with a more aggressive cancer with poorer survival. Several groups have shown that BPTF regulates pro cancer pathways such as MITF and Myc, and can sensitize cancers to chemotherapies. We have previously shown that BPTF expression in mouse models of TNBC suppresses the antitumor immune response, and when BPTF is inhibited genetically, both the adaptive and innate immune response have improved tumor growth control. These results using preclinical mouse models suggested that targeting BPTF, and therefore the NURF complex, could have therapeutic benefits for the treatment of TNBC. Key to this initiative are effective small molecular inhibitors to NURF. In 2015, work from the Pomerantz lab at the University of Minnesota, a key collaborator of the Landry Lab, discovered that the inhibitor AU1, can selectively inhibit the BPTF bromodomain establishing the first-in-class NURF inhibitor.

New research from the Landry and Gewirtz (Pharmacology and Toxicology) Labs published in Molecular Cancer Research explored a potential role of inhibiting the NURF complex to improve the antitumor effects of standard of care chemotherapies and radiation used to treat TNBC. This work showed that BPTF promotes resistance to the topoisomerase II (Top2) poisons doxorubicin and etoposide. Inhibiting BPTF genetically sensitizes TNBC to doxorubicin and etoposide induced increased DNA damage, Top2 crosslinking and autophagy. Sensitization to doxorubicin was confirmed in vivo with the syngeneic 4T1 breast tumor model using both genetic and pharmacological inhibition of BPTF. Pharmacologic inhibition of BPTF was accomplished using the Pomerantz Lab’s AU1 inhibitor. The effects of BPTF inhibition in vivo are autophagy dependent, based on genetic autophagy inhibition. Finally, treatment of 4T1, 66cl4, 4T07, MDA-MB-231 but not ER positive 67NR and MCF7 breast cancer cells with the selective BPTF bromodomain inhibitor, AU1, recapitulates genetic BPTF inhibition, including in vitro sensitization to doxorubicin, increased Top2-DNA crosslinks and DNA damage. Additional tumor studies using the MDA-MB-231 cells and genetic inhibition of BPTF show sensitization to doxorubicin in vivo. Taken together, these studies demonstrate that BPTF inhibition leads to improved antitumor activity of Top2 poisons, enhanced of Top2 crosslinking and enhanced therapy induced autophagy (Figure 1). These studies also suggest that BPTF can be targeted with small molecule inhibitors to enhance the effectiveness of Top2-targeted cancer chemotherapeutic drugs.
Figure1 – Model for how NURF Inhibition Leads to Sensitization to TOP2 Poisons. NURF inhibition promotes the persistence of TOP2 poison induced DNA damage and autophagy. In vivo the autophagy is important for an enhanced tumor growth control when NURF inhibition is combined with TOP2 poisons. Possible mechanisms of the enhancement includes immune mediated or tumor microenvironment mediated tumor cell growth control.
In an effort to further develop NURF as a viable therapeutic target, the Pomerantz lab recently published in the Journal of Medical Chemistry, with the Landry lab as a key collaborator, several new classes of BPTF bromodomain inhibitors. In their publication, the Pomerantz lab shows the development of pyridazinone-based BPTF inhibitors through a structure-based design approach. The lead compound, BZ1 possesses high potency (Kd = 6.3 nM) and >350-fold selectivity over BET bromodomains. With the Landry lab, they showed that this new class of inhibitors sensitizes 4T1 breast cancer cells to doxorubicin, but not BPTF knockdown cells, suggesting specificity to BPTF. Given the high potency and good physicochemical properties of these inhibitors, these inhibitors are anticipated to be useful starting points for chemical tool development to explore the biological roles of BPTF.
 
Ongoing studies from the Landry, Gewirtz and Pomeranz labs will investigate the effectiveness of these new BPTF bromodomain inhibitors in promoting sensitization to FDA approved chemotherapies using medium throughput screening, their ability to sensitize to Top2 inhibitors through enhanced mitophagy, and their ability to stimulate the antitumor immune response. It is hoped that NURF inhibitors will eventually enter the clinic in early phase trials as a means to treat TNBC in combination with standard of care therapy regimens.
 
Publications:
Zahid H, Buchholz C, Singh M, Ciccone M, Chan A, Nithianantham S, Shi K, Aihara H, Fischer M, Schonbrunn E, dos Santos C, Landry JW and Pomerantz W. (2021) New design rules for developing potent, cell-active inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF bromodomain inhibition. J Med Chem. doi: 10.1021/acs.jmedchem.1c01294. Online ahead of print.
 
Tyutyunyk-Massey L, Sun Y, Dao N, Ngo H, Dammalapati M, Vaidyanathan A, Singh M, Haqqani S, Haueis J, Finnegan R, Deng X, Kirberger SE, Bos PD, Bandyopadhyay D, Pomerantz WCK, Pommier Y, Gewirtz DA, Landry JW. (2021) Autophagy-Dependent Sensitization of Triple-Negative Breast Cancer Models to Topoisomerase II Poisons by Inhibition of The Nucleosome Remodeling Factor. Mol Cancer Res. 19(8):1338-1349.
 
Tyutyunyk-Massey, L., Haqqani, S., Mandava, R., Kentiba, K., Dammalapati, M., Dao, N., Haueis, J., Gewirtz, D. and Landry, J.W. (2018) Leveraging Epigenetics to Enhance the Cellular Response to Chemotherapies and Improve Tumor Immunogenicity. Adv Cancer Res. 138:1-39.
 
About the Investigators: Joseph W. Landry is an Associate Professor in the Department of Human and Molecular Genetics and a Member of the VIMM, Virginia Commonwealth University School of Medicine, Richmond, Virginia. Work on this project is funded by the DoD grant W81XWH1910489. David Gewirtz is a Professor in the Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, Virginia. Work on this project is funded by the DoD grant W81XWH1910489. Yves Pommier is a senior investigator in the Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland. Work on this project is funded by NIH intramural program of the National Cancer Institute Z01-BC-006161. William Pomerantz is an associate professor in the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota. Work on this project is funded by the NIH GMS grant R01GM121414. Dipankar Bandyopadhyay is a professor in the Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, Virginia. Paula Bos is an assistant professor in the Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, Virginia. Work from VCU faculty on this project was supported by the NIH-NCI Cancer Center Support Grant P30 CA016059.