Enhancing standard of care chemotherapy efficacy using DNA-dependent protein kinase (DNA-PK) inhibition in preclinical models of Ewing sarcoma

Disruption of DNA damage repair via impaired homologous recombination is characteristic of Ewing sarcoma (EWS) cells. We hypothesize that this disruption results in increased reliance on non-homologous end joining (NHEJ) to repair DNA damage. In this study, we investigated if pharmacological inhibition of the enzyme responsible for NHEJ, the DNA-PK holoenzyme, alters the response of EWS cells to genotoxic standard of care chemotherapy. We used analyses of cell viability and proliferation to investigate the effects of clinical DNA-PK inhibitors (DNA-PKi) in combination with six therapeutic or experimental agents for EWS. We performed calculations of synergy using the Loewe Additivity Model. Immunoblotting evaluated treatment effects on DNA-PK, DNA damage, and apoptosis. Flow cytometric analyses evaluated effects on cell cycle and fate. We used orthotopic xenograft models to interrogate tolerability, drug mechanism, and efficacy in vivo. DNA-PKi demonstrated on-target activity, reducing phosphorylated DNA-PK levels in EWS cells. DNA-PKi sensitized EWS cell lines to agents that function as topoisomerase 2 (TOP2) poisons and enhanced the DNA damage induced by TOP2 poisons. Nanomolar concentrations of single agent TOP2 poisons induced G2M arrest and little apoptotic response, while adding DNA-PKi mediated apoptosis. In vivo, the combination of AZD-7648 and etoposide had limited tolerability but resulted in enhanced DNA damage, apoptosis, and EWS tumor shrinkage. The combination of DNA-PKi with standard of care TOP2 poisons in EWS models is synergistic, enhances DNA damage and cell death, and may form the basis of a promising future therapeutic strategy for EWS.

Stress biology: Complexity and multifariousness in health and disease

Preserving and regulating cellular homeostasis in the light of changing environmental conditions or developmental processes is of pivotal importance for single cellular and multicellular organisms alike. To counteract an imbalance in cellular homeostasis transcriptional programs evolved, called the heat shock response, unfolded protein response, and integrated stress response, that act cell-autonomously in most cells but in multicellular organisms are subjected to cell-nonautonomous regulation. These transcriptional programs downregulate the expression of most genes but increase the expression of heat shock genes, including genes encoding molecular chaperones and proteases, proteins involved in the repair of stress-induced damage to macromolecules and cellular structures. Sixty-one years after the discovery of the heat shock response by Ferruccio Ritossa, many aspects of stress biology are still enigmatic. Recent progress in the understanding of stress responses and molecular chaperones was reported at the 12th International Symposium on Heat Shock Proteins in Biology, Medicine and the Environment in the Old Town Alexandria, VA, USA from 28th to 31st of October 2023.

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.

Phase I trial of Ganitumab plus Dasatinib to Cotarget the Insulin-Like Growth Factor 1 Receptor and Src Family Kinase YES in Rhabdomyosarcoma

PURPOSE

Antibodies against insulin-like growth factor (IGF) type 1 receptor have shown meaningful but transient tumor responses in patients with rhabdomyosarcoma (RMS). The SRC family member YES has been shown to mediate IGF type 1 receptor (IGF-1R) antibody acquired resistance, and cotargeting IGF-1R and YES resulted in sustained responses in murine RMS models. We conducted a phase I trial of the anti-IGF-1R antibody ganitumab combined with dasatinib, a multi-kinase inhibitor targeting YES, in patients with RMS (NCT03041701).

PATIENTS AND METHODS

Patients with relapsed/refractory alveolar or embryonal RMS and measurable disease were eligible. All patients received ganitumab 18 mg/kg intravenously every 2 weeks. Dasatinib dose was 60 mg/m2/dose (max 100 mg) oral once daily [dose level (DL)1] or 60 mg/m2/dose (max 70 mg) twice daily (DL2). A 3+3 dose escalation design was used, and maximum tolerated dose (MTD) was determined on the basis of cycle 1 dose-limiting toxicities (DLT).

RESULTS

Thirteen eligible patients, median age 18 years (range 8-29) enrolled. Median number of prior systemic therapies was 3; all had received prior radiation. Of 11 toxicity-evaluable patients, 1/6 had a DLT at DL1 (diarrhea) and 2/5 had a DLT at DL2 (pneumonitis, hematuria) confirming DL1 as MTD. Of nine response-evaluable patients, one had a confirmed partial response for four cycles, and one had stable disease for six cycles. Genomic studies from cell-free DNA correlated with disease response.

CONCLUSIONS

The combination of dasatinib 60 mg/m2/dose daily and ganitumab 18 mg/kg every 2 weeks was safe and tolerable. This combination had a disease control rate of 22% at 5 months.

Impact of race and ethnicity on presentation and outcomes of patients treated on rhabdomyosarcoma clinical trials: A report from the Children's Oncology Group

BACKGROUND

Racial and ethnic disparities have been demonstrated in pediatric and adult cancers. However, there is no consensus on whether such disparities exist in the presentation, treatment, and outcome of patients with rhabdomyosarcoma (RMS).

METHODS

Patient information from the seven most recent RMS clinical trials was obtained from the Children's Oncology Group (COG). Chi-squared analyses were used to compare patient, tumor, and treatment characteristics across racial and ethnic groups. Pairwise analyses comparing Non-Hispanic Black (NHB) versus Non-Hispanic White (NHW) racial groups and Hispanic versus NHW ethnic groups were conducted for significant characteristics. Kaplan-Meier method and Wilcoxon signed-rank tests were performed to analyze outcomes.

RESULTS

In the overall cohort (n = 2157), patients' self-identified race/ethnicity was: 0.4% American Indian/Alaska Native, 2.6% Asian, 12.6% Hispanic, 0.2% Native American/other Pacific Islander, 12.8% NHB, 61.9% NHW, and 9.6% unknown. Six characteristics differed by race/ethnicity: age, histology, IRS group, invasiveness, metastatic disease, and FOXO1 fusion partner. Five were significant in pairwise comparisons: NHB patients were more likely to present at age ≥ 10 years and with invasive tumors than NHW patients; Hispanic patients were more likely to present with alveolar histology, metastatic disease, and IRS group IV disease than NHW patients. No differences were found in event free or overall survival of the entire cohort, in risk group-based subset analyses, or among patients with high-risk characteristics significant on pairwise analysis.

CONCLUSIONS

While NHB and Hispanic patients enrolled in COG trials presented with higher risk features than NHW patients, there were no outcome differences by racial or ethnic group.

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.

Results of a phase I trial of ganitumab plus dasatinib in patients with rhabdomyosarcoma (RMS)

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Background: Antibodies against the insulin-like growth factor type 1 receptor (IGF1-R) have shown transient objective partial responses (PR) in patients with RMS followed by rapid development of resistance. Preclinical data demonstrate that activation of the SRC family kinase YES acts as a bypass resistance mechanism to IGF-1R targeting. Co-targeting IGF-1R and YES results in sustained responses in murine RMS models. We developed a phase I/II trial of the anti-IGF-1R antibody ganitumab combined with the multi-kinase inhibitor dasatinib in patients with RMS (NCT03041701). During the phase II part of the study, ganitumab became unavailable, and the trial was terminated early. We report here the results of the completed phase I study. Methods: Patients with relapsed/refractory alveolar or embryonal RMS and measurable disease were eligible. A 3+3 dose escalation design was used to determine the maximum tolerated dose (MTD), and evaluable patients were assessed for response using RECISTv1.1 criteria. All patients received ganitumab 18 mg/kg intravenously every 2 weeks. Dasatinib was administered orally on a continuous schedule. Dose level (DL)1 was 60 mg/m2/dose (max 100 mg) once daily; DL2 was 60 mg/m2/dose (max 70 mg) twice daily. MTD was determined based on cycle 1 dose-limiting toxicities (DLTs) and responses were assessed every 2 cycles. Results: Thirteen eligible patients (5M, 8F), median age 18 years (range 8-29 years) with embryonal (n = 6) and alveolar (n = 7) RMS were enrolled at DL1 (n = 7) and DL2 (n = 6). Median number of prior systemic therapies was 3 (range 1-6), all had received prior radiation, 5 prior surgery, and 2 prior high dose chemotherapy with stem cell rescue. Of 11 patients evaluable for toxicity, 1/6 had a DLT at DL1 (grade 3 diarrhea) and 2/5 had DLTs at DL2 (grade 3 pneumonitis and grade 3 hematuria) confirming DL1 as MTD. Common non-DLTs at least possibly attributed to dasatinib, ganitumab, or both included thrombocytopenia (n = 12), anemia (n = 10), lymphopenia (n = 8), hypophosphatemia (n = 7), hypocalcemia (n = 6), elevated transaminases (n = 5), fatigue (n = 5), nausea (n = 5), and vomiting (n = 5). The most common grade 3-4 adverse events were cytopenias and electrolyte abnormalities. Of 9 patients evaluable for response, 1 had a confirmed PR at DL2 sustained for 5 cycles, and 1 had prolonged stable disease (SD) for 6 cycles at DL1. Patients received a median of 1.5 cycles (range 0-6). Analysis of correlative biology studies of ctDNA and target expression are ongoing. Conclusions: The combination of dasatinib and ganitumab was safe and tolerable at DL1 in patients with relapsed and refractory RMS. Once daily dasatinib at 60 mg/m2/dose (max 100 mg) combined with 18 mg/kg ganitumab every 2 weeks was determined to be the MTD. PR and SD for > 4 months were observed in this phase I trial suggesting that the addition of a YES-targeting agent may delay the development of acquired resistance to IGF-1R antibody therapy in RMS. Clinical trial information: NCT03041701.

Evaluating the effects of critical metabolite depletion in pediatric rhabdomyosarcoma (RMS) using a novel inhibitor of nicotinamide phosphoribosyltransferase (NAMPT)

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Background: RMS is the most common pediatric cancer of the soft tissues. Patients who present with metastatic disease or experience recurrence have a poor prognosis; survivors often suffer from long-term systemic effects resulting from cytotoxic chemotherapy. Thus, novel therapies are needed. NAMPT inhibitors are a class of drugs targeting a key metabolic enzyme in the production of NAD+, a coenzyme critical to energy generation in some cancer cells. In this study, we evaluated the mechanism and functional outcomes of treatment with the clinical NAMPT inhibitor, OT-82, in preclinical models of RMS. Methods: Live cell analysis via IncuCyte was used to determine the temporal effects of OT-82 on cell growth in a diverse panel of ten fusion positive and negative RMS cell lines. Analysis of the proposed mechanism of action was performed using NAD/NADH detection assays and rescue experiments with nicotinamide mononucleotide (NMN), the product of NAMPT. Markers of cellular apoptosis and necrosis were quantified with flow cytometric assays. Specific metabolic effects of OT-82 were determined with ATP quantification and real-time extracellular flux analysis of oxidative phosphorylation and glycolysis. In vivo studies were performed in orthotopic RMS models. Tumor dimensions were measured with calipers, and toxicity was assessed by observation and body weight measurement. Results: Treatment of RMS cell lines with OT-82 dosed in the low nanomolar range resulted in time- and dose-dependent decreases in NAD+ levels and proliferation in all cell lines tested. Addition of NMN rescued cell growth, confirming the on-target activity and functional effect of OT-82. Flow cytometric assays revealed cell-line dependent differences in cell fates, with a subset of cell lines staining positive for markers of necrosis, and the other subset staining negative for markers of necrosis and apoptosis. Functional investigation verified that necrotic cell lines did not regrow after withdrawal of OT-82 in culture (durable responders), whereas non-necrotic cell lines recovered growth (transient responders). Additionally, ATP levels in durable responders decreased with OT-82 treatment but remained stable in transient responders. Extracellular flux analysis revealed that both durable and transient responders experienced inhibition of glycolysis, but that oxidative phosphorylation was only reduced in the durable responders. In vivo studies using OT-82 on a clinically-relevant schedule demonstrated that all RMS xenografts underwent complete tumor regression, with durable responder models experiencing a longer tumor-free period following discontinuation of treatment. Conclusions: In vitro and in vivo efficacy of OT-82 suggest that targeting NAD+ metabolism through NAMPT inhibition may be a promising approach for the treatment of RMS.

Racial and ethnic differences in presentation and clinical outcomes for pediatric rhabdomyosarcoma (RMS)

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Background: Race and ethnicity are recognized risk factors for many cancer types, including several pediatric cancers. Though racial and ethnic disparities in the presentation, treatment, and survival of certain cancers have been widely demonstrated, there is conflicting evidence about whether such disparities exist in RMS, the most common pediatric soft tissue sarcoma. Understanding the role of race and ethnicity in the presentation, treatment, and prognosis of RMS is important to promote improved survival in patients of all racial and ethnic groups. Methods: Patient, tumor, and treatment characteristics of patients enrolled on Children’s Oncology Group studies D9602, D9802, D9803, ARST0331, ARST0431, ARST0531, and ARST08P1 were compared across racial and ethnic groups using a chi-square test. Significant characteristics underwent pairwise analysis, comparing the Non-Hispanic Black (NHB) and Non-Hispanic White (NHW) groups. Outcome analyses were performed using the Kaplan-Meier method and Wilcoxon signed-rank test. Results: Race and ethnicity incidence among the 2157 study patients were as follows: 8 (0.4%) American Indian or Alaska Native, 56 (2.6%) Asian, 271 (12.6%) Hispanic, 4 (0.2%) Native American or other Pacific Islander, 275 (12.8%) Non-Hispanic Black, 1335 (61.9%) Non-Hispanic White, and 208 (9.6%) unknown. Thirteen patient and tumor factors relating to presentation and treatment were evaluated for differences by race and ethnicity; the following five were significant: age, IRS group, tumor invasiveness, metastatic disease, and FOXO1 fusion partner. Pairwise comparison of NHB and NHW patients for these factors demonstrated that NHBs are more likely than NHWs to present at age 10 years or greater (p = 0.002) and that NHB patients are more likely to present with invasive tumors (p = 0.012). Incidence of metastatic disease at diagnosis was not significantly different between the groups (p = 0.202). No differences in treatment, including extent of surgical resection (p = 0.259) or use of radiation therapy (p = 0.920), were found. Neither event free survival nor overall survival were significantly different across the entire cohort (EFS p = 0.457, OS p = 0.159) or in subset analysis by risk group (low risk: EFS p = 0.856, OS p = 0.558; intermediate risk: EFS p = 0.907, OS p = 0.493; high risk: EFS p = 0.218, OS p = 0.397), by age (< 1y: EFS p = 0.489, OS p = 0.546; 1-9y: EFS p = 0.417, OS p = 0.112; ≥10y: EFS p = 0.556, OS p = 0.609), in invasive tumors (EFS p = 0.704, OS p = 0.872), or in metastatic disease (EFS p = 0.270, OS p = 0.373). Conclusions: These data indicate that while differences in the presenting features of RMS exist between racial groups, with NHB patients exhibiting higher risk features, patients treated on these clinical trials did not experience differences in outcomes by racial group. This suggests NHB patients may experience a survival benefit from clinical trial enrollment.

An update on rhabdomyosarcoma risk stratification and the rationale for current and future Children's Oncology Group clinical trials

Children and adolescents with rhabdomyosarcoma (RMS) comprise a heterogeneous population with variable overall survival rates ranging between approximately 6% and 100% depending on defined risk factors. Although the risk stratification of patients has been refined across five decades of collaborative group studies, molecular prognostic biomarkers beyond FOXO1 fusion status have yet to be incorporated prospectively in upfront risk-based therapy assignments. This review describes the evolution of risk-based therapy and the current risk stratification, defines a new risk stratification incorporating novel biomarkers, and provides the rationale for the current and upcoming Children's Oncology Group RMS studies.

Relapsed Rhabdomyosarcoma

Relapsed rhabdomyosarcoma (RMS) represents a significant therapeutic challenge. Nearly one-third of patients diagnosed with localized RMS and over two-thirds of patients with metastatic RMS will experience disease recurrence following primary treatment, generally within three years. Clinical features at diagnosis, including primary site, tumor invasiveness, size, stage, and histology impact likelihood of relapse and prognosis post-relapse. Aspects of initial treatment, including extent of surgical resection, use of radiotherapy, and chemotherapy regimen, are also associated with post-relapse outcomes, as are features of the relapse itself, including time to relapse and extent of disease involvement. Although there is no standard treatment for patients with relapsed RMS, several general principles, including tissue biopsy confirmation of diagnosis, assessment of post-relapse prognosis, determination of the feasibility of additional local control measures, and discussion of patient goals, should all be part of the approach to care. Patients with features suggestive of a favorable prognosis, which include those with botryoid RMS or stage 1 or group I embryonal RMS (ERMS) who have had no prior treatment with cyclophosphamide, have the highest chance of achieving long-term cure when treated with a multiagent chemotherapy regimen at relapse. Unfortunately, patients who do not meet these criteria represent the majority and have poor outcomes when treated with such regimens. For this group, strong consideration should be given for enrollment on a clinical trial.

Survival outcomes of patients with localized FOXO1 fusion-positive rhabdomyosarcoma treated on recent clinical trials: A report from the Soft Tissue Sarcoma Committee of the Children's Oncology Group

BACKGROUND

The objective of this analysis was to evaluate the clinical factors influencing survival outcomes in patients with localized (clinical group I-III), FOXO1 fusion-positive rhabdomyosarcoma (RMS).

METHODS

Patients with confirmed FOXO1 fusion-positive RMS who were enrolled on 3 completed clinical trials for localized RMS were included in the analytic cohort. Outcomes were analyzed using the Kaplan-Meier method to estimate event-free survival (EFS) and overall survival (OS), and the curves were compared using the log-rank test. A Cox proportional hazards regression model was used to perform multivariate analysis of prognostic factors that were significant in the univariate analysis.

RESULTS

The estimated 4-year EFS and OS of 269 patients with localized, FOXO1 fusion-positive RMS was 53% (95% CI, 47%-59%) and 69% (95% CI, 63%-74%), respectively. Univariate analysis revealed that several known favorable clinical characteristics, including age at diagnosis between 1 and 9 years, complete surgical resection, tumor size ≤5 cm, favorable tumor site, absence of lymph node involvement, confinement to the anatomic site of origin, and PAX7-FOXO1 fusion, were associated with improved outcomes. Multivariate analysis identified older age (≥10 years) and large tumor size (>5 cm) as independent, adverse prognostic factors for EFS within this population, and patients who had both adverse features experienced substantially inferior outcomes.

CONCLUSIONS

Patients with localized, FOXO1 fusion-positive RMS can be further risk stratified based on clinical features at diagnosis, and older patients with large primary tumors have the poorest prognosis.

Rigosertib Induces Mitotic Arrest and Apoptosis in RAS-Mutated Rhabdomyosarcoma and Neuroblastoma

Relapsed pediatric rhabdomyosarcomas (RMS) and neuroblastomas (NBs) have a poor prognosis despite multimodality therapy. In addition, the current standard of care for these cancers includes vinca alkaloids that have severe toxicity profiles, further underscoring the need for novel therapies for these malignancies. Here, we show that the small-molecule rigosertib inhibits the growth of RMS and NB cell lines by arresting cells in mitosis, which leads to cell death. Our data indicate that rigosertib, like the vinca alkaloids, exerts its effects mainly by interfering with mitotic spindle assembly. Although rigosertib has the ability to inhibit oncogenic RAS signaling, we provide evidence that rigosertib does not induce cell death through inhibition of the RAS pathway in RAS-mutated RMS and NB cells. However, the combination of rigosertib and the MEK inhibitor trametinib, which has efficacy in RAS-mutated tumors, synergistically inhibits the growth of an RMS cell line, suggesting a new avenue for combination therapy. Importantly, rigosertib treatment delays tumor growth and prolongs survival in a xenograft model of RMS. In conclusion, rigosertib, through its impact on the mitotic spindle, represents a potential therapeutic for RMS.

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.

Beyond Energy Metabolism: Exploiting the Additional Roles of NAMPT for Cancer Therapy

Tumor cells have increased requirements for NAD⁺. Thus, many cancers exhibit an increased reliance on NAD⁺ production pathways. This dependence may be exploited therapeutically through pharmacological targeting of NAMPT, the rate-limiting enzyme in the NAD⁺ salvage pathway. Despite promising preclinical data using NAMPT inhibitors in cancer models, early NAMPT inhibitors showed limited efficacy in several early phase clinical trials, necessitating the identification of strategies, such as drug combinations, to enhance their efficacy. While the effect of NAMPT inhibitors on impairment of energy metabolism in cancer cells has been well-described, more recent insights have uncovered a number of additional targetable cellular processes that are impacted by inhibition of NAMPT. These include sirtuin function, DNA repair machinery, redox homeostasis, molecular signaling, cellular stemness, and immune processes. This review highlights the recent findings describing the effects of NAMPT inhibitors on the non-metabolic functions of malignant cells, with a focus on how this information can be leveraged clinically. Combining NAMPT inhibitors with other therapies that target NAD⁺-dependent processes or selecting tumors with specific vulnerabilities that can be co-targeted with NAMPT inhibitors may represent opportunities to exploit the multiple functions of this enzyme for greater therapeutic benefit.

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.

Insights into pediatric rhabdomyosarcoma research: Challenges and goals

Overall survival rates for pediatric patients with high-risk or relapsed rhabdomyosarcoma (RMS) have not improved significantly since the 1980s. Recent studies have identified a number of targetable vulnerabilities in RMS, but these discoveries have infrequently translated into clinical trials. We propose streamlining the process by which agents are selected for clinical evaluation in RMS. We believe that strong consideration should be given to the development of combination therapies that add biologically targeted agents to conventional cytotoxic drugs. One example of this type of combination is the addition of the WEE1 inhibitor AZD1775 to the conventional cytotoxic chemotherapeutics, vincristine and irinotecan.

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.

STA-8666, a novel HSP90 inhibitor/SN-38 drug conjugate, causes complete tumor regression in preclinical mouse models of pediatric sarcoma

Long-term survival in patients with metastatic, relapsed, or recurrent Ewing sarcoma and rhabdomyosarcoma is dismal. Irinotecan, a topoisomerase 1 inhibitor, has activity in these sarcomas, but due to poor bioavailability of its active metabolite (SN-38) has had limited clinical efficacy. In this study we have evaluated the efficacy and toxicity of STA-8666, a novel drug conjugate which uses an HSP90 inhibitor to facilitate intracellular, tumor-targeted delivery of the topoisomerase 1 inhibitor SN-38, thus preferentially delivering and concentrating SN-38 within tumor tissue. We present in vivo evidence from mouse xenograft models that STA-8666 results in more persistent inhibition of topoisomerase 1 and prolonged DNA damage compared to irinotecan. This translates into superior antitumor efficacy and survival in multiple aggressive models of both diseases in mouse xenografts, as well as in an irinotecan-resistant model of pediatric osteosarcoma, demonstrated by dramatic tumor shrinkage, durable remission and prolonged complete regressions following short-term treatment, compared to conventional irinotecan. Gene expression analysis performed on xenograft tumors treated with either irinotecan or STA-8666 showed that STA-8666 affected expression of DNA damage and repair genes more robustly than irinotecan. These results suggest that STA-8666 may be a promising new agent for patients with pediatric-type sarcoma.

Matrix Screen Identifies Synergistic Combination of PARP Inhibitors and Nicotinamide Phosphoribosyltransferase (NAMPT) Inhibitors in Ewing Sarcoma

Purpose: Although many cancers are showing remarkable responses to targeted therapies, pediatric sarcomas, including Ewing sarcoma, remain recalcitrant. To broaden the therapeutic landscape, we explored the in vitro response of Ewing sarcoma cell lines against a large collection of investigational and approved drugs to identify candidate combinations.Experimental Design: Drugs displaying activity as single agents were evaluated in combinatorial (matrix) format to identify highly active, synergistic drug combinations, and combinations were subsequently validated in multiple cell lines using various agents from each class. Comprehensive metabolomic and proteomic profiling was performed to better understand the mechanism underlying the synergy. Xenograft experiments were performed to determine efficacy and in vivo mechanism.Results: Several promising candidates emerged, including the combination of small-molecule PARP and nicotinamide phosphoribosyltransferase (NAMPT) inhibitors, a rational combination as NAMPTis block the rate-limiting enzyme in the production of nicotinamide adenine dinucleotide (NAD⁺), a necessary substrate of PARP. Mechanistic drivers of the synergistic cell killing phenotype of these combined drugs included depletion of NMN and NAD⁺, diminished PAR activity, increased DNA damage, and apoptosis. Combination PARPis and NAMPTis in vivo resulted in tumor regression, delayed disease progression, and increased survival.Conclusions: These studies highlight the potential of these drugs as a possible therapeutic option in treating patients with Ewing sarcoma. Clin Cancer Res; 23(23); 7301-11. ©2017 AACR.

Abstract B14: Hsp90-inhibitor drug conjugate STA-12-8666 demonstrates complete tumor regression in preclinical models of pediatric sarcoma

Long-term survival in patients with metastatic relapsed or recurrent Ewing sarcoma (ES) and rhabdomyosarcoma (RMS) is dismal. Encouraging responses to irinotecan, a topoisomerase 1 (Top1) inhibitor, have been seen in these patients; however, limitations in irinotecan bioavailability, including low conversion rate to the active metabolite (SN-38) and high excretion rate of the inactive form, hinder efficacy. HSP90 is widely expressed in cancer cells, and HSP90 inhibitors (HSP90i) have favorable pharmacokinetics for anticancer use, as they remain in tumors for longer periods of time and at higher steady-state levels compared to normal tissue. This property makes them ideal intracellular delivery vehicles for chemotherapeutic drugs, allowing for high tumor exposure and low systemic toxicity. STA-12-8666 (Synta Pharmaceuticals) is an HSP90i drug conjugate (HDC) consisting of a weak HSP90i attached to SN-38 through a cleavable chemical linker. The purpose of this study was to test this HDC in xenograft models of pediatric sarcoma and to investigate its mechanism of action.

To test therapeutic efficacy of this HDC, female SCID mice underwent orthotopic injection of ES or RMS cells from established cell lines or PDX tissue. When tumors reached a desired size, mice were randomized and then treated weekly with HDC, vehicle, ganetespib (a highly potent HSP90i), high dose irinotecan, protracted dose irinotecan, or irinotecan plus ganetespib. Tumors were measured twice per week, and mice were weighed weekly to determine drug tolerability. Tumors were harvested at midpoints and at study endpoint for biology studies. Activity of pharmacodynamic (PD) markers was investigated in tumor tissue.

In xenograft models of ES and RMS, treatment with HDC produced superior antitumor efficacy compared to the other arms. When initial treatment began in mice with palpable tumors (between 100 and 500 mm3 (ES) or 50 and 90 mm3 (RMS)), all tumors underwent complete regression after 2 doses of HDC, with total tumor eradication in all ES mice and several RMS mice. In the RMS group, 6/8 mice relapsed by 23 weeks, and all 6 of those responded to retreatment with HDC. When initial treatment was delayed until tumors reached between 800 mm3 and 1000 mm3, complete regressions were again achieved in ES after 2 doses and RMS after 4 doses. Compared with high dose weekly irinotecan, which also induced tumor regression, mice treated with HDC had longer and more persistent remissions. A dose response effect was seen in HDC with cures noted in mice with ES at the 100- and 150-mg/kg doses and longest remissions noted in RMS in the 150-mg/kg group. Tolerability of the HDC was excellent with no toxicity-related deaths or weight loss in any treated mice. Studies using PDX models are ongoing and will be reported.

Activity of γH2AX in tumor samples was explored as a PD marker of Top1 inhibitor activity. Mice bearing ES were treated with a single dose of vehicle, irinotecan, or HDC and one mouse per group was sacrificed at serial intervals between 6 hours and 10 days post-treatment. Expression of γH2AX in irinotecan mice began to wane between days 1 and 3, whereas in HDC mice, it was still detectable at day 7, suggesting that HDC results in more persistent inhibition of topoisomerase 1 compared to irinotecan. To look at the potential role of HSP90 inhibition in this HDC, HSP70 activity was investigated as a marker of HSP90 inhibition in samples from the dose finding experiment. In ES, no HSP70 was detected in samples from mice treated with irinotecan or HDC, suggesting the primary mechanism of action is via SN-38. In RMS, HSP70 was slightly induced in mice treated with higher doses of the HDC, perhaps contributing to the higher relapse rate in this model.

Preclinical data suggest that this HDC may be a promising anticancer agent for ES and RMS patients.

Citation Format: Christine M. Heske, Arnulfo Mendoza, Choh Yeung, David A. Proia, Len Neckers, Lee J. Helman. Hsp90-inhibitor drug conjugate STA-12-8666 demonstrates complete tumor regression in preclinical models of pediatric sarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B14.