Epigenetic re-wiring of breast cancer by pharmacological targeting of C-terminal binding protein

Jung S Byun,Anna María Nápoles,Kevin Gardner,Alana Jones,Dae Ik Yi,Sara Gil Hernandez,Jee‐Hye Shin ,Mohamed Kabbout,Stephen M Hewitt,Samson Park,Ambar Caban,Megan L Peach,Sandeep K Singhal ,Ryan Yancey,Adriana De Siervi,Laura Guasch,Lalage M Wakefield,Binwu Tang,Nasreen A Vohra ,Marc C Nicklaus,Tingfen Yan

doi:10.1038/s41419-019-1892-7

Abstract

The C-terminal binding protein (CtBP) is an NADH-dependent dimeric family of nuclear proteins that scaffold interactions between transcriptional regulators and chromatin-modifying complexes. Its association with poor survival in several cancers implicates CtBP as a promising target for pharmacological intervention. We employed computer-assisted drug design to search for CtBP inhibitors, using quantitative structure-activity relationship (QSAR) modeling and docking. Functional screening of these drugs identified 4 compounds with low toxicity and high water solubility. Micro molar concentrations of these CtBP inhibitors produces significant de-repression of epigenetically silenced pro-epithelial genes, preferentially in the triple-negative breast cancer cell line MDA-MB-231. This epigenetic reprogramming occurs through eviction of CtBP from gene promoters; disrupted recruitment of chromatin-modifying protein complexes containing LSD1, and HDAC1; and re-wiring of activating histone marks at targeted genes. In functional assays, CtBP inhibition disrupts CtBP dimerization, decreases cell migration, abolishes cellular invasion, and improves DNA repair. Combinatorial use of CtBP inhibitors with the LSD1 inhibitor pargyline has synergistic influence. Finally, integrated correlation of gene expression in breast cancer patients with nuclear levels of CtBP1 and LSD1, reveals new potential therapeutic vulnerabilities. These findings implicate a broad role for this class of compounds in strategies for epigenetically targeted therapeutic intervention.

Highlights

Introduction TheC-terminal binding protein (CtBP) was first described as a phosphoprotein that binds to the C-terminal end of the E1a adenovirus oncogene[1,2,3]
Over-expression of CtBP is associated with downregulation of a variety of pro-epithelial genes in ER+ tumors but has little effect on the expression of these genes in breast cancer cell types with more mesenchymal or stromal features[14]
We applied a functional screen for the loss of CtBP transcriptional repressive activity by screening the 24 compounds for the ability to upregulate FOXA1 and OVOL2, two genes that are intimately involved in maintaining the epithelial phenotype[25,26,27,28]

Summary

Introduction

C-terminal binding protein (CtBP) was first described as a phosphoprotein that binds to the C-terminal end of the E1a adenovirus oncogene[1,2,3]. These proteins were later found to represent a dimeric family of proteins, composed of CtBP1 and CtBP2, that can homodimerize or heterodimerize in the nucleus to influence multiple different epigenetic nuclear events by. Byun et al Cell Death and Disease (2019)10:689 regulated by NADH/NAD+7,11. The ability of CtBP to bind and undergo redox cycles with NADH/NAD+ and substrate implicates a substantial role for CtBP in the regulation of genomic responses to changes in cellular metabolism[9,12]

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Results

Conclusion