Phase 2 trial of palbociclib and ganitumab in patients with relapsed Ewing sarcoma

BACKGROUND

Ewing sarcoma (EWS) is an aggressive sarcoma with few treatment options for patients with relapsed disease. Cyclin-dependent kinase 4 (CDK4) is a genomic vulnerability in EWS that is synergistic with IGF-1R inhibition in preclinical studies. We present the results of a phase 2 study combining palbociclib (CDK4/6 inhibitor) with ganitumab (IGF-1R monoclonal antibody) for patients with relapsed EWS.

PATIENTS AND METHODS

This open-label, non-randomized, phase 2 trial enrolled patients ≥12 years with relapsed EWS. All patients had molecular confirmation of EWS and RECIST measurable disease. Patients initially received palbociclib 125 mg orally on Days 1-21 and ganitumab 18 mg/kg intravenously on Days 1 and 15 of a 28-day cycle. The primary endpoints were objective response (complete or partial) per RECIST and toxicity by CTCAE. An exact one-stage design required ≥4 responders out of 15 to evaluate an alternative hypothesis of 40% response rate against a null of 10%. The study was closed following enrollment of the 10th patient due to discontinuation of ganitumab supply.

RESULTS

Ten evaluable patients enrolled [median age 25.7 years (range 12.3-40.1)]. The median duration of therapy was 2.5 months (range 0.9-10.8). There were no complete or partial responders. Three of 10 patients had stable disease for >4 cycles and 2 had stable disease at completion of planned therapy or study closure. Six-month progression-free survival was 30% (95% CI 1.6%-58.4%). Two patients had cycle 1 hematologic dose-limiting toxicities (DLTs) triggering palbociclib dose reduction to 100 mg daily for 21 days. Two subsequent patients had cycle 1 hematologic DLTs at the reduced dose. Eighty percent of patients had grade 3/4 AEs, including neutropenia (n = 8), white blood cell decreased (n = 7), and thrombocytopenia (n = 5). Serum total IGF-1 significantly increased (p = 0.013) and ctDNA decreased during the first cycle.

CONCLUSIONS

This combination lacks adequate therapeutic activity for further study, though a subset of patients had prolonged stable disease.

Mitochondrial Dysfunction Is a Driver of SP-2509 Drug Resistance in Ewing Sarcoma

Expression of the fusion oncoprotein EWS/FLI causes Ewing sarcoma, an aggressive pediatric tumor characterized by widespread epigenetic deregulation. These epigenetic changes are targeted by novel lysine-specific demethylase-1 (LSD1) inhibitors, which are currently in early-phase clinical trials. Single-agent-targeted therapy often induces resistance, and successful clinical development requires knowledge of resistance mechanisms, enabling the design of effective combination strategies. Here, we used a genome-scale CRISPR-Cas9 loss-of-function screen to identify genes whose knockout (KO) conferred resistance to the LSD1 inhibitor SP-2509 in Ewing sarcoma cell lines. Multiple genes required for mitochondrial electron transport chain (ETC) complexes III and IV function were hits in our screen. We validated this finding using genetic and chemical approaches, including CRISPR KO, ETC inhibitors, and mitochondrial depletion. Further global transcriptional profiling revealed that altered complex III/IV function disrupted the oncogenic program mediated by EWS/FLI and LSD1 and blunted the transcriptomic response to SP-2509.

IMPLICATIONS

These findings demonstrate that mitochondrial dysfunction modulates SP-2509 efficacy and suggest that new therapeutic strategies combining LSD1 with agents that prevent mitochondrial dysfunction may benefit patients with this aggressive malignancy.

Phase 2 trial of palbociclib and ganitumab in patients with relapsed Ewing sarcoma

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Background: Ewing sarcoma (EwS) is an aggressive sarcoma with few treatment options for patients with relapsed disease. CDK4 is a known genomic vulnerability in EwS, but an unappealing monotherapy target given propensity for innate resistance. In laboratory studies to identify targets synergistic with CDK4 inhibition, IGF-1R scored highly. We present the results of a phase 2 study combining palbociclib (CDK4/6 inhibitor) with ganitumab (IGF-1R monoclonal antibody) for patients with relapsed or refractory EwS. Methods: This was a prospective open-label, non-randomized, single-center, phase 2 study (NCT04129151) for patients with relapsed EwS and RECIST measurable disease. Patients with relapsed EwS ≥12 years and a documented fusion consistent with EwS were eligible. Patients initially received Palbociclib 125 mg on days 1-21 and ganitumab 18 mg/kg on days 1 and 15 of a 28-day cycle. The primary endpoints were objective response (complete or partial) per RECIST and toxicity by CTCAE. Secondary endpoints included progression-free survival (PFS) and overall survival (OS). A one-stage design required ≥4 responders out of 15 to evaluate an alternative hypothesis of 40% response rate against a null of 10%. Results: Ten evaluable patients enrolled between 5/2019-8/2021. The study closed 12/2021 due to lack of ganitumab drug supply. The median age at enrollment was 25.7 years (range 12.3-40.1; Table). The median duration of therapy was 2.5 months (range = 0.9-10.8). There were no complete or partial responders. Three of 10 patients had stable disease for > 4 cycles and 2 had stable disease at completion of planned therapy or study closure. 6-month PFS was 30±14.5%. Two patients had cycle 1 hematologic DLTs triggering the pre-defined toxicity rule; the palbociclib dose was subsequently reduced to 100 mg daily for 21 days. Among the remaining 8 patients, two had cycle 1 hematologic DLTs at the 100 mg dose. 80% of patients had grade 3/4 AEs; the most commons AEs were neutropenia (n = 8), white blood cell decreased (n = 7), and thrombocytopenia (n = 5). Total IGF-1 testing demonstrated intrapatient elevations in serum levels after a single cycle of therapy. Analysis of serial ctDNA samples is ongoing. Conclusions: Four responders out of 15 were required to reject the null hypothesis of a 10% response rate. With 0/10 responders, we concluded that this combination lacked adequate therapeutic activity for further study. The combination was tolerable at a palbociclib dose of 100 mg, with primarily hematologic toxicity in patients with relapsed EwS. Clinical trial information: NCT04129151. [Table: see text]

A first-generation pediatric cancer dependency map

Exciting therapeutic targets are emerging from CRISPR-based screens of high mutational-burden adult cancers. A key question, however, is whether functional genomic approaches will yield new targets in pediatric cancers, known for remarkably few mutations, which often encode proteins considered challenging drug targets. To address this, we created a first-generation pediatric cancer dependency map representing 13 pediatric solid and brain tumor types. Eighty-two pediatric cancer cell lines were subjected to genome-scale CRISPR-Cas9 loss-of-function screening to identify genes required for cell survival. In contrast to the finding that pediatric cancers harbor fewer somatic mutations, we found a similar complexity of genetic dependencies in pediatric cancer cell lines compared to that in adult models. Findings from the pediatric cancer dependency map provide preclinical support for ongoing precision medicine clinical trials. The vulnerabilities observed in pediatric cancers were often distinct from those in adult cancer, indicating that repurposing adult oncology drugs will be insufficient to address childhood cancers.

Abstract PD7-08: Igf1r mediates cdk4/6 inhibitor (cdk4/6i) resistance in tumor samples and in cellular models

Background: Deciphering the molecular landscape of resistance to the CDK4/6 inhibitors represents a critically important question for patients with hormone-receptor positive (HR+) metastatic breast cancer (MBC). Emerging insights from sequencing efforts suggest that inactivating alterations in the RB1 tumor suppressor occur in a small minority of patients and that a variety of heterogeneous mediators provoke resistance in patient samples. Proteins implicated in CDK4/6i resistance include cell cycle regulators such as cyclin E1/2, CDK6, and aurora kinase as well as known oncogenic signal transduction mediators involved in activation of the RAS-MEK and AKT-mTOR pathways. The insulin-like growth factor 1 receptor (IGF1R) has been implicated in modulating anti-estrogen resistance, and IGF1R inhibitors are currently in various stages of pre-clinical and clinical development.

Methods: We identified patients with amplification events in IGF1R from a database containing targeted sequencing of solid tumor samples obtained from patients with HR+ MBC enrolled on a research biopsy protocol. Tumor biopsies may have been obtained at various points during each patient’s clinical treatment course. HR+ T47D cells were modified to over-express IGF1R via lentiviral infection and selection. Derivative cell lines were treated with IGF-1 ligand and downstream activation of the PI3K/AKT and RAS/MEK pathways were assessed via western blotting. Control cells (expressing GFP) were mixed with IGF1R-expressing cells 1:1 and cultured in the presence of IGF-1 ligand and palbociclib or other drugs, for 1-3 weeks. At the timepoint of interest, cells were harvested and the relative proportion of GFP or IGF1R-expressing cells were interrogated via flow cytometry.

Results: We identified seven patients with HR+ MBC and IGF1R amplifications via targeted sequencing of tumor biopsies. Five of these patients had exposure to CDK4/6i-based therapy in the metastatic setting. Three patients demonstrated intrinsic resistance to CDK4/6i treatment (with duration <6 months) and biopsies were obtained prior to CDK4/6i exposure or, in one case, while on treatment. In an additional patient, after nine months of CDK4/6i-based therapy, an IGF1R amplification was present at the time of progression. In one counter-example, a baseline biopsy revealed IGF1R amplification and subsequent clinical benefit with CDK4/6i, exceeding 10 months, was noted. T47D cells over-expressing IGF1R demonstrated increased pERK and pAKT activation following introduction of IGF-1 ligand. Control GFP and IGF1R-expressing cells were plated 1:1 and cultured in the presence of IGF-1 ligand and palbociclib. In a flow cytometry-based competition assay, an IGF-1 dose-dependent increase in the relative proportion of IGF1R-expressing cells was noted after one, two, and three weeks of palbociclib treatment. The extent of IGF1R-expressing cell enrichment was attenuated in the presence of either a MEK inhibitor or an IGF1R inhibitor.

Conclusions: IGF1R amplification events were identified in tumor biopsy samples that reflect either intrinsic or acquired resistance to CDK4/6i-based therapy. HR+ breast cancer cells which over-express IGF1R demonstrate enrichment under palbociclib drug selection in a flow cytometry-based competition assay, which was abrogated by concurrent use of a MEK or IGF1R inhibitor. These results suggest that IGF1R may join the increasingly heterogeneous landscape of CDK4/6i resistance mediators. Further exploration of this possibility is warranted. A subset of patients with IGF1R-mediated CDK4/6i resistance could benefit from therapeutic strategies designed to downregulate MEK or IGF1R activity.

Citation Format: Seth A. Wander, Pingping Mao, Maxwell R. Lloyd, Gabriela N. Johnson, Kailey Kowalski, Utthara Nayar, Lillian M. Guenther, Kimberly Stegmaier, Eric P. Winer, Nancy U. Lin, Nikhil Wagle. Igf1r mediates cdk4/6 inhibitor (cdk4/6i) resistance in tumor samples and in cellular models [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD7-08.

Abstract CT195: A phase 2 clinical trial of palbociclib and ganitumab for relapsed/refractory Ewing sarcoma

Background: Ewing sarcoma is a classic translocation-associated malignancy, with nearly all cases carrying an identifiable EWSR1 or FUS translocation. The translocation leads to an aberrant fusion oncoprotein that is thought to function as a pathogenic transcription factor. Despite our understanding of the fundamental biology of this disease, targeting this transcription factor has been elusive. The insulin-like growth factor receptor (IGF-1R) pathway has been long implicated in the pathogenesis of Ewing sarcoma based on early findings that IGF-1 and IGF-1R are overexpressed in Ewing sarcoma. A range of preclinical studies have demonstrated the activity of IGF-1R targeting antibodies in multiple Ewing sarcoma cell lines. Multiple early phase studies of IGF-1R inhibitors have demonstrated that approximately 10% of patients with relapsed disease respond to these agents as monotherapy. Recent work has identified CDK4 as a genomic vulnerability in Ewing sarcoma. Given that CDK4/6 inhibitor monotherapy is prone to resistance, a series of investigations were undertaken to identify potential combination approaches. In an open reading frame experiment designed to determine whether over expression of specific genes would confer resistance, IGF-1R scored highly. Subsequent in vitro and in vivo experiments demonstrated synergy between CDK4/6 inhibition and IGF-1R inhibition. We have translated these findings into an open phase 2 clinical trial of ganitumab, a monoclonal antibody inhibitor of IGF-1R, and palbociclib, a small molecule inhibitor of CDK4/6. Methods: This is a Phase 2, single-arm, single-stage, investigator-initiated clinical trial of palbociclib and ganitumab in patients 12-50 years of age with relapsed/refractory Ewing sarcoma (NCT04129151). The primary objectives are to estimate the objective radiographic response rate to the combination of palbociclib and ganitumab and to describe the toxicity of this drug combination in patients with relapsed/refractory Ewing sarcoma. Palbociclib is given at a dose of 100 mg PO on days 1-21 of a 28-day cycle. Ganitumab is given via IV at a dose of 18 mg/kg on days 1 and 15. The primary endpoint is objective response by RECIST, with disease evaluated after every 2 cycles. Up to 18 patients will be enrolled to yield 15 response evaluable patients. With 15 evaluable patients the study will have 91% power and a type-1 error rate of 0.056 to determine whether the response rate in this population is greater than 40% and significantly different from the 10% response rate seen with IGF-1R monotherapy.

Pharmacodynamic testing for confirmation of IGF-1R inhibition (serum IGF-related proteins) is required for all patients. Circulating tumor DNA (ctDNA) is measured at study entry, on cycle 1 day 15, at start of cycle 2 and at each disease evaluation. ctDNA levels will be measured using next generation sequencing for quantification of ctDNA and association with response, and for identification of genomic and epigenetic markers of resistance. Enrollment began in December 2019.

Citation Format: David S. Shulman, Katherine Thornton, Edwin Choy, Lillian M. Guenther, Kerri Cavanaugh, Megan Forsyth, Kylene DeSmith, Catherine Clinton, Kimberly Stegmaier, Brian Crompton, Wendy B. London, Steven G. DuBois. A phase 2 clinical trial of palbociclib and ganitumab for relapsed/refractory Ewing sarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT195.

A Combination CDK4/6 and IGF1R Inhibitor Strategy for Ewing Sarcoma

PURPOSE

Novel targeted therapeutics have transformed the care of subsets of patients with cancer. In pediatric malignancies, however, with simple tumor genomes and infrequent targetable mutations, there have been few new FDA-approved targeted drugs. The cyclin-dependent kinase (CDK)4/6 pathway recently emerged as a dependency in Ewing sarcoma. Given the heightened efficacy of this class with targeted drug combinations in other cancers, as well as the propensity of resistance to emerge with single agents, we aimed to identify genes mediating resistance to CDK4/6 inhibitors and biologically relevant combinations for use with CDK4/6 inhibitors in Ewing.

EXPERIMENTAL DESIGN

We performed a genome-scale open reading frame (ORF) screen in 2 Ewing cell lines sensitive to CDK4/6 inhibitors to identify genes conferring resistance. Concurrently, we established resistance to a CDK4/6 inhibitor in a Ewing cell line.

RESULTS

The ORF screen revealed IGF1R as a gene whose overexpression promoted drug escape. We also found elevated levels of phospho-IGF1R in our resistant Ewing cell line, supporting the relevance of IGF1R signaling to acquired resistance. In a small-molecule screen, an IGF1R inhibitor scored as synergistic with CDK4/6 inhibitor treatment. The combination of CDK4/6 inhibitors and IGF1R inhibitors was synergistic in vitro and active in mouse models. Mechanistically, this combination more profoundly repressed cell cycle and PI3K/mTOR signaling than either single drug perturbation.

CONCLUSIONS

Taken together, these results suggest that IGF1R inhibitors activation is an escape mechanism to CDK4/6 inhibitors in Ewing sarcoma and that dual targeting of CDK4/6 inhibitors and IGF1R inhibitors provides a candidate synergistic combination for clinical application in this disease.

Response Evaluation Criteria in Solid Tumors (RECIST) following neoadjuvant chemotherapy in osteosarcoma

BACKGROUND

In osteosarcoma, patient survival has not changed in over 30 years. Multiple phase II trials have been conducted in osteosarcoma using the Response Evaluation Criteria in Solid Tumors (RECIST) as a primary endpoint; however, none of these have revealed new treatment strategies. We investigated RECIST in newly diagnosed patients who received neoadjuvant chemotherapy proven to be beneficial.

METHODS

Patients treated from 1986 to 2011 for newly diagnosed osteosarcoma with paired tumor imaging before and after adequate neoadjuvant chemotherapy were included in this retrospective study. Two radiologists performed independent, blinded (to image timing) RECIST measurements of primary tumor and lung metastases at diagnosis and post-neoadjuvant chemotherapy. Association between RECIST and histological necrosis and outcome were assessed.

RESULTS

Seventy-four patients met inclusion criteria. Five-year overall survival and progression-free survival (PFS) were 77 ± 7% and 61 ± 8%, respectively. No patients had RECIST partial or complete response in the primary tumor. Sixty-four patients (86%) had stable disease, and 10 (14%) had progressive disease (PD). PD in the primary tumor was associated with significantly worse PFS in localized disease patients (P = 0.02). There was no association between RECIST in the primary tumor and necrosis. There were an insufficient number of patients with lung nodules ≥1 cm at diagnosis to evaluate RECIST in pulmonary metastases.

CONCLUSIONS

PD by RECIST predicts poor outcome in localized disease patients. In bone lesions, chemotherapy proven to improve overall survival does not result in radiographic responses as measured by RECIST. Further investigation of RECIST in pulmonary metastatic disease in osteosarcoma is needed.

Abstract 3401: Genetic down-regulation of MET alters the metastatic phenotype of osteosarcoma cells

The MET tyrosine kinase receptor is important during human development for normal cell growth and migration. Activating alterations of MET have also been identified in several carcinomas. Previous immunohistochemistry studies in our laboratory found high levels of MET in 85% of osteosarcoma tumor samples. In addition, pharmacologic modulation of MET resulted in a migratory decrease in some osteosarcoma cell lines. This led us to hypothesize that MET is necessary for osteosarcoma metastasis, and genetic down-regulation of MET expression would reduce the metastatic phenotype of osteosarcoma cells.

We used lentiviral shRNA constructs to knockdown MET expression in several osteosarcoma cell lines. These included MNNG-HOS, a metastatic chemically transformed line that expresses constitutively activated MET, MG63.2, a highly metastatic variant of poorly metastatic MG63, AI and LR, which are two newly derived cell lines that have extremely high MET levels. We quantified levels of MET expression using a sensitive and quantitative electrochemiluminescence (ECL) assay and assessed in vitro parameters of metastasis including motility, migration, and invasion.

MET expression was assessed by ECL in protein lysates from frozen osteosarcoma tumor samples and cell lines, and 15-20% of samples showed extremely high levels of total MET. AI, LR and MG63.2 had the highest levels of MET expression. MNNG-HOS has activation of MET due to translocation of the 3′end of MET with the 5′end of TPR. We utilized these lines for shRNA knock down of MET. ECL quantification of total MET levels revealed greater than 70% decrease in MET expression with shRNA knockdown in all four cell lines, compared with cells infected with scramble shRNA controls. As predicted for MNNG-HOS, shRNA constructs targeting the 3’ tyrosine kinase domain of MET resulted in marked decreased motility, compared to intermediate decreases using shRNA constructs targeting the 5’ region. Knock down of MET in MG63.2 resulted in inhibition of both motility and migration. AI and LR assays are in progress.

Taken together, these data are the first evidence that genetic down-regulation of MET results in a decreased metastatic phenotype in osteosarcoma. This is a promising finding, as several small molecule tyrosine kinase inhibitors targeting MET are in development. We are currently testing our hypothesis in a mouse model to determine the ability of the above genetically knocked-down MET cell lines to decrease metastasis in vivo. Concurrently, in preparation for translational studies, we are also assessing MET specific tyrosine kinase inhibitors utilizing the parental cell lines described above.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3401.