Detection of phenotype-specific therapeutic vulnerabilities in breast cells using a CRISPR loss-of-function screen

Cellular phenotype plasticity between the epithelial and mesenchymal states has been linked to metastasis and heterogeneous responses to cancer therapy, and remains a challenge for the treatment of triple-negative breast cancer (TNBC). Here, we used isogenic human breast epithelial cell lines, D492 and D492M, representing the epithelial and mesenchymal phenotypes, respectively. We employed a CRISPR-Cas9 loss-of-function screen targeting a 2240-gene 'druggable genome' to identify phenotype-specific vulnerabilities. Cells with the epithelial phenotype were more vulnerable to the loss of genes related to EGFR-RAS-MAPK signaling, while the mesenchymal-like cells had increased sensitivity to knockout of G₂ -M cell cycle regulators. Furthermore, we discovered knockouts that sensitize to the mTOR inhibitor everolimus and the chemotherapeutic drug fluorouracil in a phenotype-specific manner. Specifically, loss of EGFR and fatty acid synthase (FASN) increased the effectiveness of the drugs in the epithelial and mesenchymal phenotypes, respectively. These phenotype-associated genetic vulnerabilities were confirmed using targeted inhibitors of EGFR (gefitinib), G₂ -M transition (STLC), and FASN (Fasnall). In conclusion, a CRISPR-Cas9 loss-of-function screen enables the identification of phenotype-specific genetic vulnerabilities that can pinpoint actionable targets and promising therapeutic combinations.

Characterization of the interactions of potent allosteric inhibitors with glutaminase C, a key enzyme in cancer cell glutamine metabolism

Altered glycolytic flux in cancer cells (the "Warburg effect") causes their proliferation to rely upon elevated glutamine metabolism ("glutamine addiction"). This requirement is met by the overexpression of glutaminase C (GAC), which catalyzes the first step in glutamine metabolism and therefore represents a potential therapeutic target. The small molecule CB-839 was reported to be more potent than other allosteric GAC inhibitors, including the parent compound bis-2-(5-phenylacetamido-1,2,4-thiadiazol-2-yl)ethyl (BPTES), and is in clinical trials. Recently, we described the synthesis of BPTES analogs having distinct saturated heterocyclic cores as a replacement for the flexible chain moiety, with improved microsomal stability relative to CB-839 and BPTES. Here, we show that one of these new compounds, UPGL00004, like CB-839, more potently inhibits the enzymatic activity of GAC, compared with BPTES. We also compare the abilities of UPGL00004, CB-839, and BPTES to directly bind to recombinant GAC and demonstrate that UPGL00004 has a similar binding affinity as CB-839 for GAC. We also show that UPGL00004 potently inhibits the growth of triple-negative breast cancer cells, as well as tumor growth when combined with the anti-vascular endothelial growth factor antibody bevacizumab. Finally, we compare the X-ray crystal structures for UPGL00004 and CB-839 bound to GAC, verifying that UPGL00004 occupies the same binding site as CB-839 or BPTES and that all three inhibitors regulate the enzymatic activity of GAC via a similar allosteric mechanism. These results provide insights regarding the potency of these inhibitors that will be useful in designing novel small-molecules that target a key enzyme in cancer cell metabolism.

Fluorination at the 4 position alters the substrate behavior of L-glutamine and L-glutamate: Implications for positron emission tomography of neoplasias

Two 4-fluoro-L-glutamine diastereoisomers [(2S,4R)-4-FGln, (2S,4S)-4-FGln] were previously developed for positron emission tomography. Label uptake into two tumor cell types was greater with [¹⁸F](2S,4R)-4-FGln than with [¹⁸F](2S,4S)-4-FGln. In the present work we investigated the enzymology of two diastereoisomers of 4-FGln, two diastereoisomers of 4-fluoroglutamate (4-FGlu) (potential metabolites of the 4-FGln diastereoisomers) and another fluoro-derivative of L-glutamine [(2S,4S)-4-(3-fluoropropyl)glutamine (FP-Gln)]. The two 4-FGlu diastereoisomers were found to be moderate-to-good substrates relative to L-glutamate of glutamate dehydrogenase, aspartate aminotransferase and alanine aminotransferase. Additionally, alanine aminotransferase was shown to catalyze an unusual γ-elimination reaction with both 4-FGlu diastereoisomers. Both 4-FGlu diastereoisomers were shown to be poor substrates, but strong inhibitors of glutamine synthetase. Both 4-FGln diastereoisomers were shown to be poor substrates compared to L-glutamine of glutamine transaminase L and α-aminoadipate aminotransferase. However, (2S,4R)-4-FGln was found to be a poor substrate of glutamine transaminase K, whereas (2S,4S)-4-FGln was shown to be an excellent substrate. By contrast, FP-Gln was found to be a poor substrate of all enzymes examined. Evidently, substitution of H in position 4 by F in L-glutamine/L-glutamate has moderate-to-profound effects on enzyme-catalyzed reactions. The present results: 1) show that 4-FGln and 4-FGlu diastereoisomers may be useful for studying active site topology of glutamate- and glutamine-utilizing enzymes; 2) provide a framework for understanding possible metabolic transformations in tumors of ¹⁸F-labeled (2S,4R)-4-FGln, (2S,4S)-4-FGln, (2S,4R)-4-FGlu or (2S,4S)-4-FGlu; and 3) show that [¹⁸F]FP-Gln is likely to be much less metabolically active in vivo than are the [¹⁸F]4-FGln diastereoisomers.

Abstract C42: Mitochondrial glutaminase regulation and small molecule inhibition of glutamine metabolism

The mitochondrial enzyme glutaminase isoform C (GAC) has recently gained significant attention for its critical role in supporting glutamine dependent proliferation in a variety of cancer cells and has been a significant focus for therapeutic intervention (1,2). To this end, we have combined biophysical techniques with cellular metabolic assays to gain insight as to the mechanism of action of the novel GAC inhibitor, compound 968, shown previously to inhibit Dbl (for Diffuse B-cell Lymphoma) oncogene dependent transformation (2). We have developed a fluorescence resonance energy transfer (FRET) approach, along with X-ray crystallography and multi-angle light scattering (MALS), to study the oligomer dynamics of GAC in relation to its activation in vitro. To compliment in vitro biophysical studies of GAC activation and inhibition, we employed stable 13C-isotope tracing assays in a model Dbl-inducible cell system to monitor 13C incorporation in TCA cycle intermediates derived from 13C-glutamine.

Using dynamic FRET assays, as well as novel GAC mutants that are trapped as constitutive dimer or monomer species, we show that the dimer-to-tetramer transition is indeed directly linked to activation of the enzyme. Subsequently we go on to show that the two previously described allosteric GAC inhibitors, 968 and BPTES, elicit their inhibitory effects through distinctly different mechanisms. Both, however, target specific oligomeric states of GAC: compound 968 preferentially binds to the monomeric form of GAC to disrupt critical oligomer contacts, in stark contrast to BPTES, which binds to and induces tetramer formation by interacting with a loop located near the glutamine binding site. The binding of compound 968 to the monomeric form of GAC was found to induce a conformational change that renders the enzyme inactive, however still able to participate in oligomer formation and dissociation. The consequence of this 968-bound GAC species in vivo was investigated by first showing that 968 treatment of a Dbl-inducible MEF cell line with 968 was capable of reversing Dbl-induced transformation as evidenced by the inhibition of focus formation and proliferation. In this same model cell system, we show that induction of the Dbl-oncogene leads to an increase in glutaminolysis and glutamine fueled anaplerosis by monitoring 13C-enrichment in TCA cycle intermediates derived from 13C-glutamine, and that this increased glutaminolysis is potently inhibited by 968 treatment. These results highlight advances in understanding the mechanism of glutaminase regulation as well as the potential future of small molecules targeting glutamine metabolism as therapeutics.

(1) Wang, J.B. et al., (2010) Cancer Cell 18, 207-219

(2) Le, A. et al., (2012) Cell Metabolism 15, 110-121

This project was supported by the Chemical Biology Training Grant (Award Number T32GM008500) from the National Institute of General Medical Sciences and the NIH

Citation Format: Clint Stalnecker, Jon Erickson, Sekar Ramachandran, Ralph DeBerardinis, Rick Cerione. Mitochondrial glutaminase regulation and small molecule inhibition of glutamine metabolism. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr C42.