PROJECT SUMMARY/ABSTRACT
Histone deacetylases (HAT) are zinc-dependent enzymes that catalyze the removal of acetyl groups from the
epsilon amine of lysine side chains. These proteins have been widely pursued as anti-cancer drug targets, but
therapeutic development has been largely unsuccessful given the essential nature of many HDAC proteins.
Recently, we discovered a synthetic lethal relationship between HDAC1 and HDAC2, which is caused by
recurrent chromosomal deletions that result in hemizygous deletion of HDAC1 in neuroblastoma and HDAC2 in
multiple myeloma. As a result of HDAC1 deletion, neuroblastoma cells are hypersensitive to disruption of
HDAC2, and vice versa in multiple myeloma. Using dTAG-mediated degradation or CRISPR/Cas9-based gene
disruption, we discovered that targeting HDAC1/2 synthetic lethality (e.g. degrading HDAC2 in neuroblastoma
cells with a hemizygous HDAC1 deletion) results in dissociation of the NuRD chromatin remodeler complex, of
which HDAC1/2 are members. Dissociation of the complex results in degradation of NuRD subunits that are
selectively required for neuroblastoma and multiple myeloma survival, suggesting that HDAC1/2 synthetic
lethality can be leveraged to target subunit-specific NuRD vulnerabilities in cancer. We hypothesize that HDAC1
deletions cause the NuRD subunits, HDAC2 / MBD3 / MTA3, to be essential for neuroblastoma, whereas HDAC2
deletions cause vulnerabilities to loss of their paralogs, HDAC1 / MBD2 / MTA2, in multiple myeloma. Here, we
will address this hypothesis and explore the translational potential of these vulnerabilities by developing small-
molecule modulators that target NuRD structure and/or function. In Aim 1, we will (i) Determine whether MBD
and MTA vulnerabilities are caused by HDAC1/2 deletions using CRISPR/Cas9, inducible RNAi, and dTAG-
based approaches in vitro and in vivo, (ii) Reveal whether the loss of NuRD subunits required for cancer cell
survival leads to dissociation and/or degradation of the NuRD complex using unbiased proteomics approaches,
and (iii) Establish if HDAC1/MBD2/MTA2 and HDAC2/MBD3/MTA3 form distinct NuRD sub-complexes as a
result of HDAC2 and HDAC1 deletions, respectively. These experiments will determine if subunit-specific NuRD
vulnerabilities are caused by HDAC1/2 deletions or simply exploited by HDAC1/2 synthetic lethality. In Aim 2,
we will develop small molecules targeting the NuRD complex to exploit NuRD vulnerabilities in genetically
defined cancer sub-types. Specifically, we will: (i) develop paralog-selective PROTACs that distinguish between
HDAC1 and HDAC2, (ii) determine the potential for covalent ligands of MTA3-Cys532 to disrupt NuRD structure
and/or function in MTA3-dependent cancers, and (iii) develop MTA3-targeted PROTACs based on ligands that
covalently engage MTA3-C532. Altogether, successful completion of these aims will determine the mechanisms
underlying NuRD vulnerabilities in cancer and advance novel chemical tools to drug and study them.