Inhibition of NAD+-Dependent Metabolic Processes Induces Cellular Necrosis and Tumor Regression in Rhabdomyosarcoma Models

PURPOSE

Deregulated metabolism in cancer cells represents a vulnerability that may be therapeutically exploited to benefit patients. One such target is nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in the NAD+ salvage pathway. NAMPT is necessary for efficient NAD+ production and may be exploited in cells with increased metabolic demands. We have identified NAMPT as a dependency in rhabdomyosarcoma (RMS), a malignancy for which novel therapies are critically needed. Here we describe the effect of NAMPT inhibition on RMS proliferation and metabolism in vitro and in vivo.

EXPERIMENTAL DESIGN

Assays of proliferation and cell death were used to determine the effects of pharmacologic NAMPT inhibition in a panel of ten molecularly diverse RMS cell lines. Mechanism of the clinical NAMPTi OT-82 was determined using measures of NAD+ and downstream NAD+-dependent functions, including energy metabolism. We used orthotopic xenograft models to examine tolerability, efficacy, and drug mechanism in vivo.

RESULTS

Across all ten RMS cell lines, OT-82 depleted NAD+ and inhibited cell growth at concentrations ≤1 nmol/L. Significant impairment of glycolysis was a universal finding, with some cell lines also exhibiting diminished oxidative phosphorylation. Most cell lines experienced profound depletion of ATP with subsequent irreversible necrotic cell death. Importantly, loss of NAD and glycolytic activity were confirmed in orthotopic in vivo models, which exhibited complete tumor regressions with OT-82 treatment delivered on the clinical schedule.

CONCLUSIONS

RMS is highly vulnerable to NAMPT inhibition. These findings underscore the need for further clinical study of this class of agents for this malignancy.

Abstract 6718: Exploiting metabolic vulnerabilities of pediatric rhabdomyosarcoma with novelnicotinamide phosphoribosyltransferase (NAMPT) inhibitor OT-82

Purpose: A hallmark of cancer cells is altered metabolism. Therapeutically, these alterations may be exploited by targeting metabolic vulnerabilities specific to cancer cells. Efficient production of NAD through the NAD salvage pathway is one such potential vulnerability, as some tumor cells demonstrate a high need for rapid NAD turnover. Nicotinamide phosphoribosyltransferase (NAMPT) is the pharmacologically targetable rate-limiting enzyme in this pathway. We report on the effect of targeting NAMPT in models of pediatric rhabdomyosarcoma (RMS), a cancer for which novel therapeutics remain an unmet need.

Experimental Procedures: The relative sensitivity of RMS cell lines to NAMPT inhibitors was first compared to NAMPT inhibitor sensitivity of other cancer cell lines using viability assays. A panel of ten molecularly diverse RMS cell lines was used for the remainder of the evaluations. In vitro activity of NAMPT inhibition was evaluated using assays of proliferation and cell death. Measurements of NAD and functional assessment of NAD-dependent processes, such as glucose metabolism, were used to study the mechanistic activity of NAMPT inhibition in these models. In vivo studies included assessments of toxicity, efficacy, and mechanism of action of a clinical NAMPT inhibitor, OT-82, in four orthotopic RMS models.

Results: RMS cells showed striking sensitivity to NAMPT inhibition with IC-50 values in the low nanomolar range. In vitro, NAMPT inhibition resulted in NAD depletion and impaired cellular proliferation. Effects on glucose metabolism included decreases in glycolytic activity and glycolytic capacity in all cell lines tested, as well as decreased oxidative phosphorylation in a subset of cell lines. The majority of cell lines exhibited ATP depletion and irreversible necrotic cell death. Apoptotic cell death was not observed. In vivo, the effects of OT-82 treatment delivered on the human clinical schedule replicated those seen in vitro, including loss of glycolytic activity as measured using hyperpolarized 13C MRI spectroscopy. In all four xenograft models, complete tumor regressions were observed at multiple doses and with minimal toxicity.

Conclusions: NAMPT inhibition with OT-82 was highly effective in decreasing RMS proliferation and impairing glucose metabolism both in vitro and in vivo. Given these results, there is a critical need for further clinical study of this class of agents for RMS.

Citation Format: Grace McKay-Corkum, Victor J. Collins, Choh Yeung, Takeshi Ito, Sameer H. Issaq, Arnulfo Mendoza, Kazutoshi Yamamoto, Murali Cherukuri, Len Neckers, Christine M. Heske. Exploiting metabolic vulnerabilities of pediatric rhabdomyosarcoma with novelnicotinamide phosphoribosyltransferase (NAMPT) inhibitor OT-82 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6718.

Abstract PR08: Lactate dehydrogenase A is a pharmacologically tractable EWS-FLI1 transcriptional target that regulates the glycolytic dependence of Ewing sarcoma

Altered cellular metabolism, including an increased dependence on aerobic glycolysis, is a hallmark of cancer. Despite the fact that this observation was first made nearly a century ago, effective therapeutic targeting of glycolysis in cancer has remained elusive. One potentially promising approach involves targeting the glycolytic enzyme lactate dehydrogenase (LDH), which is overexpressed and plays a critical role in several cancers. To uncover cell type-specific dependencies to LDH, we screened a diverse panel of 94 cancer cell lines for responsiveness to two novel LDH A/B inhibitors developed through the NCI Experimental Therapeutics Program (NExT). We found that Ewing sarcoma (EWS) cell lines were exquisitely sensitive, with IC50 values approximately ten-fold below the median IC50 of the panel. To understand the mechanism behind this sensitivity, we genetically knocked down LDHA and LDHB using siRNA, and discovered that EWS cell lines were sensitive to loss of LDHA only, which inhibited proliferation and induced apoptosis. Notably, treatment of EWS cells with the LDH inhibitors phenocopied these effects. Additionally, genetic knockdown of EWS-FLI1, the oncogenic driver of EWS, resulted in loss of LDHA, but not LDHB. Analysis of publicly available ChIP-seq data generated using shFLI1-transfected EWS cells revealed that LDHA, but not LDHB, is directly regulated by EWS-FLI1. Functional mechanistic studies of glycolytic intermediates and cellular bioenergetics in EWS cells treated with the LDH inhibitors demonstrated that loss of viability was due to impairment of glycolysis, which occurred both in vitro and in vivo, and perturbation of the NAD+/NADH ratio. The translational potential of these compounds was next evaluated using in vivo analyses of pharmacokinetics, pharmacodynamics, efficacy, and toxicity. Intravenous administration of the LDH inhibitors resulted in diminished LDH activity, reduction of the lactate-to-pyruvate ratio, tumor cell necrosis, and a decrease in tumor growth rate in aggressive xenograft models of EWS. The major dose-limiting toxicity observed was hemolysis, indicating that a narrow therapeutic window exists for these compounds. Taken together, our data suggest that targeting glycolysis through inhibition of LDH should be further investigated as a potential therapeutic approach for cancers such as EWS that exhibit oncogene-dependent expression of LDH and increased glycolytic activity.

This abstract is also being presented as Poster B33.

Citation Format: Choh Yeung, Anna E. Gibson, Sameer H. Issaq, Nobu Oshima, Marielle E. Yohe, Haiyan Lei, Ganesha Rai, Daniel J. Urban, Michelle S. Johnson, Gloria A. Benevides, Giuseppe L. Squadrito, Sandy Eldridge, John Hamre III, Arnulfo Mendoza, Jack F. Shern, Lee J. Helman, Murali C. Krishna, Matthew D. Hall, Victor M. Darley-Usmar, Leonard M. Neckers, Christine M. Heske. Lactate dehydrogenase A is a pharmacologically tractable EWS-FLI1 transcriptional target that regulates the glycolytic dependence of Ewing sarcoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr PR08.

EWS-FLI1-regulated Serine Synthesis and Exogenous Serine are Necessary for Ewing Sarcoma Cellular Proliferation and Tumor Growth

Despite a growing body of knowledge about the genomic landscape of Ewing sarcoma, translation of basic discoveries into targeted therapies and significant clinical gains has remained elusive. Recent insights have revealed that the oncogenic transcription factor EWS-FLI1 can impact Ewing sarcoma cellular metabolism, regulating expression of 3-phosphoglycerate dehydrogenase (PHGDH), the first enzyme in de novo serine synthesis. Here, we have examined the importance of serine metabolism in Ewing sarcoma tumorigenesis and evaluated the therapeutic potential of targeting serine metabolism in preclinical models of Ewing sarcoma. We show that PHGDH knockdown resulted in decreased Ewing sarcoma cell proliferation, especially under serine limitation, and significantly inhibited xenograft tumorigenesis in preclinical orthotopic models of Ewing sarcoma. In addition, the PHGDH inhibitor NCT-503 caused a dose-dependent decrease in cellular proliferation. Moreover, we report a novel drug combination in which nicotinamide phosphoribosyltransferase (NAMPT) inhibition, which blocks production of the PHGDH substrate NAD⁺, synergized with NCT-503 to abolish Ewing sarcoma cell proliferation and tumor growth. Furthermore, we show that serine deprivation inhibited Ewing sarcoma cell proliferation and tumorigenesis, indicating that Ewing sarcoma cells depend on exogenous serine in addition to de novo serine synthesis. Our findings suggest that serine metabolism is critical for Ewing sarcoma tumorigenesis, and that targeting metabolic dependencies should be further investigated as a potential therapeutic strategy for Ewing sarcoma. In addition, the combination strategy presented herein may have broader clinical applications in other PHGDH-overexpressing cancers as well.

Targeting Glycolysis through Inhibition of Lactate Dehydrogenase Impairs Tumor Growth in Preclinical Models of Ewing Sarcoma

Altered cellular metabolism, including an increased dependence on aerobic glycolysis, is a hallmark of cancer. Despite the fact that this observation was first made nearly a century ago, effective therapeutic targeting of glycolysis in cancer has remained elusive. One potentially promising approach involves targeting the glycolytic enzyme lactate dehydrogenase (LDH), which is overexpressed and plays a critical role in several cancers. Here, we used a novel class of LDH inhibitors to demonstrate, for the first time, that Ewing sarcoma cells are exquisitely sensitive to inhibition of LDH. EWS-FLI1, the oncogenic driver of Ewing sarcoma, regulated LDH A (LDHA) expression. Genetic depletion of LDHA inhibited proliferation of Ewing sarcoma cells and induced apoptosis, phenocopying pharmacologic inhibition of LDH. LDH inhibitors affected Ewing sarcoma cell viability both in vitro and in vivo by reducing glycolysis. Intravenous administration of LDH inhibitors resulted in the greatest intratumoral drug accumulation, inducing tumor cell death and reducing tumor growth. The major dose-limiting toxicity observed was hemolysis, indicating that a narrow therapeutic window exists for these compounds. Taken together, these data suggest that targeting glycolysis through inhibition of LDH should be further investigated as a potential therapeutic approach for cancers such as Ewing sarcoma that exhibit oncogene-dependent expression of LDH and increased glycolysis. SIGNIFICANCE: LDHA is a pharmacologically tractable EWS-FLI1 transcriptional target that regulates the glycolytic dependence of Ewing sarcoma.

Abstract B16: Evaluation of LDH inhibition as a treatment strategy in Ewing sarcoma

Long-term outcomes for patients with relapsed, recurrent, or metastatic Ewing sarcoma (ES) remain poor despite advances in multimodal chemotherapy and local tumor control. The discovery of new targets and novel therapies is therefore critical to improving care for these patients. Recent insights into the metabolic landscape of ES have revealed that the EWS/FLI1 fusion oncoprotein regulates metabolic pathways in this disease, including shifting glucose consumption away from oxidative metabolism and towards glycolysis, a pathway that relies on LDH. Targeting this increased dependence on glycolysis presents an opportunity to inhibit the growth of ES cells through a novel therapeutic approach, while potentially limiting the toxicity delivered to normal cells. We therefore sought to evaluate the activity of NCGC-737 and NCGC-006, two novel LDHA/B inhibitors identified and validated as part of the Experimental Therapeutics Program of the National Cancer Institute (NCI-NExT), in ES.

For in vitro studies, proliferation of ES cells lines was assessed after inhibition of LDHA/B by each agent using IncuCyte and MTS assays. Protein expression of phospho- and total LDH was evaluated by Western blot. LDH activity was assessed using the pyruvate-dependent oxidation of NADH. NAD/NADH levels were determined using NAD/NADH-Glo. Analysis of glycolytic profiles was performed using the Agilent Extracellular Flux Analyzer. For in vivo studies, female SCID mice underwent orthotopic injection of ES cells from established cell lines. When tumors reached a desired size, mice were randomized and then treated on a variety of dosing schedules. Toxicity assessments included evaluation of overall appearance, weekly weights, blood sampling, and full necropsies on selected mice. Tumors were measured twice per week for assessment of efficacy. Tumors were harvested at midpoints and at study endpoint for assessments of drug level, target inhibition, and biology.

ES cell lines displayed varying sensitivity to NCGC-737 and NCGC-006, with IC-50 values ranging from 50 nM to 500 nM. While protein expression of phospho-LDH, total LDH-A, and total LDH-B were not correlated with sensitivity to either agent, glycolytic profiles were predictive of sensitivity. Cell lines that underwent a greater reduction in glycolytic capacity (the change in ECAR measured before and after oligomycin treatment) after LDHA/B inhibition experienced a greater antiproliferative effect, while cell lines that were able to maintain glycolytic capacity despite LDHA/B inhibition exhibited less of an effect on growth. In vivo studies to describe the toxicity of these agents demonstrated that hemolysis was the primary dose-limiting toxicity, and was dose dependent. Additional toxicity studies of specific tissues are ongoing and will be reported. Preliminary in vivo studies to optimize dosing regimen established that compared to oral dosing, intravenous dosing resulted in higher and more consistent tumor drug levels and improved target inhibition, with up to 93% of intratumoral LDH activity inhibited. Efficacy studies are ongoing and will be reported.

Preclinical data suggest that inhibition of LDHA/B may represent a potentially novel therapeutic strategy in the treatment of ES.

Citation Format: Christine M. Heske, Anna E. Gibson, Josh T. Baumgart, Choh Yeung, Sameer H. Issaq, A Mendoza, Michelle S. Johnson, Guiseppe L. Squadrito, Lillian Culp, Victor M. Darley-Usmar, Len M. Neckers. Evaluation of LDH inhibition as a treatment strategy in Ewing sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B16.

Bioenergetic properties of human sarcoma cells help define sensitivity to metabolic inhibitors

Sarcomas represent a diverse group of malignancies with distinct molecular and pathological features. A better understanding of the alterations associated with specific sarcoma subtypes is critically important to improve sarcoma treatment. Renewed interest in the metabolic properties of cancer cells has led to an exploration of targeting metabolic dependencies as a therapeutic strategy. In this study, we have characterized key bioenergetic properties of human sarcoma cells in order to identify metabolic vulnerabilities between sarcoma subtypes. We have also investigated the effects of compounds that inhibit glycolysis or mitochondrial respiration, either alone or in combination, and examined relationships between bioenergetic parameters and sensitivity to metabolic inhibitors. Using 2-deoxy-D-glucose (2-DG), a competitive inhibitor of glycolysis, oligomycin, an inhibitor of mitochondrial ATP synthase, and metformin, a widely used anti-diabetes drug and inhibitor of complex I of the mitochondrial respiratory chain, we evaluated the effects of metabolic inhibition on sarcoma cell growth and bioenergetic function. Inhibition of glycolysis by 2-DG effectively reduced the viability of alveolar rhabdomyosarcoma cells vs. embryonal rhabdomyosarcoma, osteosarcoma, and normal cells. Interestingly, inhibitors of mitochondrial respiration did not significantly affect viability, but were able to increase sensitivity of sarcomas to inhibition of glycolysis. Additionally, inhibition of glycolysis significantly reduced intracellular ATP levels, and sensitivity to 2-DG-induced growth inhibition was related to respiratory rates and glycolytic dependency. Our findings demonstrate novel relationships between sarcoma bioenergetics and sensitivity to metabolic inhibitors, and suggest that inhibition of metabolic pathways in sarcomas should be further investigated as a potential therapeutic strategy.

Sec5 and Exo84 foster oncogenic ras-mediated tumorigenesis

The genes encoding the Ras family of small GTPases are mutated to yield constitutively active GTP-bound oncogenic proteins in one third of all human cancers. Oncogenic Ras binds to and activates a number of proteins that promote tumorigenic phenotypes, including the family of Ral guanine nucleotide exchange factors (RalGEF). Activated RalGEFs convert the Ral family of small GTPases, composed of RalA and RalB, from an inactive GDP-bound state to an active GTP-bound state. As both RalA and RalB have been implicated in a variety of tumorigenic phenotypes, we sought to determine which proteins downstream of Rals promote transformation and tumorigenesis. Here, we report that shRNA-mediated knockdown of the Ral effector proteins Sec5 and Exo84, but less so in the case of RalBP1, reduced oncogenic RalGEF-mediated transformation and oncogenic Ras-driven tumorigenic growth of human cells. These results suggest that Rals promote oncogenic Ras-mediated tumorigenesis through, at least in part, Sec5 and Exo84.