Abstract LB-249: HDAC11 regulates lysine acetylation of enolase 1

Therapeutic molecules targeting the activity of histone deacetylases (HDACs) are currently under investigation for the treatment of several malignancies. There are currently eighteen human HDACs and while histone deacetylation is associated with transcriptional repression, acetylated lysine targets are functionally diverse and include cytoplasmic, nuclear, and mitochondrial proteins. Here, we used a new class of novel small molecule inhibitors that are highly selective for HDAC11 to identify its role in the regulation of non-histone proteins. Stable isotope labeling with amino acids in cell culture (SILAC) followed by mass spectrometry in the presence of HDAC11 selective inhibitors identified proteins with acetylation and/or expression changes after treatment and were compared to known HDAC substrates to establish a unique set of putative HDAC11 target proteins. Metabolic processes were highly enriched in this data set. Specifically, acetylated enolase 1 (ENO1, 2-phospho-D-glycerate hydrolase) which catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate (PEP) in the glycolytic pathway was highly altered after HDAC11 inhibition. Using acetylated lysine specific immunoprecipitation, we validated the hyperacetylated state of ENO1 upon HDAC11 inhibition. Functional assays confirmed that the HDAC11 inhibition lowered ENO1-mediated PEP production, and reduced proliferation and viability of hematopoietic and solid tumor cells. Similar observations were obtained in HDAC11 knock down cell lines confirming that HDAC11 is a required molecule in the regulation of ENO1-mediated metabolic regulation. The proteomics data also mapped three distinct target lysine residues of HDAC11 in ENO1 and each of these residues were substituted to either an acetylated or an un-acetylated lysine mimic to test their function in ENO1 activity and stability. We confirmed that K335 is the major target site of HDAC11 and its substitution to the acetylated mimic (glutamine) causes loss of enolase activity. Concomitantly, using proton nuclear magnetic resonance spectroscopy we identified some glycolytic intermediates upstream of ENO1 to be increased and downstream intermediates quantitatively reduced after HDAC11 inhibition suggesting that glycolysis is functionally suppressed. Glycolytic pathway disruption was associated with a compensatory increase in oxygen consumption and ATP production through oxidative phosphorylation in these oncogene transformed tumor cells, but not in their non-transformed counterparts. Suppression of fatty acid oxidation by inhibiting carnitine palmitoyltransferase 1 (CPT-1) or blocking glutamine utilization by inhibiting glutaminase (GLS1) in combination with HDAC11 inhibition resulted in a cooperative reduction in cellular ATP levels further supporting a direct role of HDAC11 in regulating glycolysis in tumor cells. For the first time, this study mechanistically and functionally defines a cytoplasmic non-histone protein regulated by HDAC11.

Citation Format: Vasundhara Sharma, Agni Christodoulidou, Lanzhu Yue, Aileen Y. Alontaga, William E. Goodheart, Rebecca Hesterberg, Xiaozhang Zheng, Matthew W. Martin, Jennifer Y. Lee, Pearlie K. Burnette, Kenneth L. Wright. HDAC11 regulates lysine acetylation of enolase 1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-249.

Cereblon tunes c-Myc protein expression and regulates the metabolic function of activated T cells

Immunomodulatory drugs, such as lenalidomide, pomalidomide, and CC122 are glutarimide derivatives that alter T cell effector functions, reverse tolerance, and increase cytokine production. We hypothesized that cereblon (CRBN), the molecular target of these drugs, is a negative regulator of T cell function. Therefore, germline Crbn knockout mice were used to investigate its role in T cell regulation. Similar to human T cells treated with immunomodulatory drugs, stimulated Crbn−/− T cells exhibit increased proliferation and cytokine production and maintain this phenotype in the absence of CD28 co-stimulation. Using Gene Set Enrichment Analysis (GSEA) to identify transcriptional drivers of differentially expressed genes, we found that Myc and its family member Max may drive the observed activated phenotype in Crbn−/− T cell. Crbn−/− T cells have Myc-related phenotypic changes, such as increased cell size, CD98 expression, glucose uptake, glutamine and arginine uptake, increased intracellular polyamine biosynthesis, and oxygen consumption. Similar increases in Myc-related processes were observed in activated human T cells treated with immunomodulatory drugs. While c-myc mRNA is similar, Crbn−/− T cells and drug-treated human T cells have prolonged c-Myc protein expression. CRBN, a substrate receptor for the DDB1/Cul4A/Rbx1 E3 ubiquitin ligase complex, has only one known endogenous substrate which is glutamine synthetase (GS). GS interacts with CRBN through acetylated lysine residues yielding a protein that is succeptable to polyubiquitinlyation. Collectively, this suggests that CRBN tunes c-Myc-regulated pathways in activated T cells and that this process is blocked by immunomodulatory drugs.

Ligand-mediated protein degradation reveals functional conservation among sequence variants of the CUL4-type E3 ligase substrate receptor cereblon

Upon binding to thalidomide and other immunomodulatory drugs, the E3 ligase substrate receptor cereblon (CRBN) promotes proteosomal destruction by engaging the DDB1-CUL4A-Roc1-RBX1 E3 ubiquitin ligase in human cells but not in mouse cells, suggesting that sequence variations in CRBN may cause its inactivation. Therapeutically, CRBN engagers have the potential for broad applications in cancer and immune therapy by specifically reducing protein expression through targeted ubiquitin-mediated degradation. To examine the effects of defined sequence changes on CRBN's activity, we performed a comprehensive study using complementary theoretical, biophysical, and biological assays aimed at understanding CRBN's nonprimate sequence variations. With a series of recombinant thalidomide-binding domain (TBD) proteins, we show that CRBN sequence variants retain their drug-binding properties to both classical immunomodulatory drugs and dBET1, a chemical compound and targeting ligand designed to degrade bromodomain-containing 4 (BRD4) via a CRBN-dependent mechanism. We further show that dBET1 stimulates CRBN's E3 ubiquitin-conjugating function and degrades BRD4 in both mouse and human cells. This insight paves the way for studies of CRBN-dependent proteasome-targeting molecules in nonprimate models and provides a new understanding of CRBN's substrate-recruiting function.

Intracellular protein degradation of BRD4 by dBET1 reveals conserved in vivo cereblon function in human and mouse T-cells

Protein degraders have been developed that can aide in understanding gene function. These chemicals contain complementary bifunctional components that 1) interact with specific proteins, and 2) engage an E3 ligase which leads to polyubiquitination and intracellular degradation by the proteasome. Thalidomide, infamously known for its teratogenic effects, is central to this new technology since it binds cereblon (CRBN) which promiscuously recruits the DDB1/Cul4A/Rbx1 complex to trigger target destruction. Thalidomide, and especially its immunomodulatory derivatives lenalidomide and pomalidomide, induce NK and T-cell activation by degrading IKZF1 which is a transcription factor that suppresses IL-2. Currently, it is debated whether mouse cereblon has conserved function due to a single non-conserved amino acid in mouse CRBN, Ile390 (equivalent to Val388 in human CRBN). First, our work confirms that lenalidomide induces IL-2 and the ubiquitin-dependent degradation of IKZF1 only in human and not mouse T-cells treated with lenalidomide. To further test for species-related effects, a series of theoretical and physical binding assays using mutant CRBN proteins show that the binding of IMiD compounds is not impaired by amino acid differences in mouse CRBN. Using dBET1, a novel thalidomide-JQ1 protein degrader, we show for the first time that mouse CRBN can trigger CRBN-dependent degradation of BRD4 and confirm that the CRBN/DDB1/Cul4A/Rbx1 complex is functional in mouse T-cells. Collectively, our results suggest that IKZF1 has divergent regulation in mouse cells rather than the IMiD complex and provide information relevant to the development of chemical conjugates that induce targeted intracellular protein degradation.