Phase 1 trial of seclidemstat (SP-2577) in patients with relapsed/refractory Ewing sarcoma

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Background: Ewing sarcoma (ES), a rare bone and soft tissue sarcoma mainly of adolescents and young adults, is characterized by a chromosomal translocation resulting in a fusion oncoprotein. Lysine specific demethylase 1 (LSD1) has been shown to associate with the fusion oncoprotein and promote oncogenic transcriptional activity making LSD1 an attractive target for ES treatment. Seclidemstat is a novel, selective, reversible oral LSD1 inhibitor capable of inhibiting both LSD1’s catalytic and scaffolding functions. This is the first report of an LSD1 inhibitor in a Phase 1 trial focused exclusively on ES. Methods: SALA-002-EW16 is a Phase 1 trial of single agent seclidemstat in patients (pts) with relapsed or refractory (R/R) ES. This report describes the completed monotherapy dose escalation. Pts > 12 years received oral SP-2577 twice daily in 28-day cycles under fasting conditions at the assigned dose level. The primary objective was safety and tolerability. Secondary objectives include to determine maximum-tolerated dose (MTD), recommended Phase 2 dose (RP2D), preliminary efficacy, pharmacokinetics, and pharmacodynamics. Results: As of December 30, 2020, 27 pts with R/R ES were enrolled. Pts received escalating doses of SP-2577 at 75 (n = 1), 150 (n = 2), 300 (n = 4), 600 (n = 6), 900 (n = 8), or 1200 mg PO BID (n = 6). The median age was 25 years (range 15–68), 63% were male, and pts had received a median of 3 (range 2–12) prior systemic therapies. There were no treatment-related deaths. The most common ( > 5%) grade 3 treatment-related adverse events (TRAEs) were vomiting (15%), abdominal pain (11%), and hypokalemia (11%). One pt (4%) with grade 3 pancreatitis reported a grade 4 AE of elevated lipase. All remaining grade 3 TRAEs, including hematological TRAEs, were reported in only one pt each. Four pts discontinued study for an AE (weight loss, pancreatitis, vomiting, abdominal pain). Three pts had a dose reduction. The first cycle dose-limiting toxicities were gastrointestinal-related AEs observed in 2 pts at 1200 mg BID. Thus, the MTD/RP2D was established as 900 mg BID. Peak plasma concentrations occurred at a median of 4 hours (h) post-dose and median terminal half-life was 6 h; exposure was dose proportional through 900 mg BID. One pt at 600 mg BID achieved a reduction in target lesions starting at end of C2 with further target lesion tumor shrinkage through end of C4 and C6 (maximum 76% tumor shrinkage) with coincident new non-target lesion appearance at end of C2. Of pts evaluable for response at the end of C2 (12 pts), two additional pts (16.7%) at 600 mg BID and 900 mg BID had overall stable disease. Conclusions: Seclidemstat has a manageable safety profile with proof-of-concept preliminary activity in heavily pretreated pts with relapsed/refractory ES. These data support the planned Phase 2 expansion of seclidemstat as single agent and in combination with chemotherapy in ES and other sarcomas that share similar translocations. Clinical trial information: NCT03600649.

Patterns of Translocation Testing in Patients Enrolling to a Cooperative Group Trial for Newly Diagnosed Metastatic Ewing Sarcoma: A Report From the Children's Oncology Group

CONTEXT.—

Molecular diagnostics play an increasing role in the diagnosis of Ewing sarcoma. The type of molecular testing used in clinical practice has been poorly described.

OBJECTIVE.—

To describe patterns of translocation testing for newly diagnosed Ewing sarcoma.

DESIGN.—

Children's Oncology Group (COG) trial AEWS1221 was a phase III randomized trial enrolling patients with newly diagnosed metastatic Ewing sarcoma from 2014 to 2019. Patients were required to have a histologic diagnosis of Ewing sarcoma, but translocation testing was not required. Sites provided types and results of any molecular diagnostics performed.

RESULTS.—

Data from 305 enrolled patients were available. The most common type of molecular testing was fluorescence in situ hybridization (FISH) performed on the primary tumor (236 of 305 patients; 77.4%), with positive testing for an EWSR1 or FUS translocation in 211 (89.4%). Reverse transcription-polymerase chain reaction (RT-PCR) on the primary tumor was performed in 61 of 305 (20%), with positive results in 48 of 61 patients (78.7%). Next-generation sequencing was reported in 7 patients on primary tumor and in 3 patients on metastatic sites. Evaluating all types of testing on either primary or metastatic tumor, 16 of 305 patients (5.2%) had no reported translocation testing. Evaluating all results from all testing, 44 of 305 patients (14.4%) lacked documentation of an abnormality consistent with a molecular diagnosis of Ewing sarcoma.

CONCLUSIONS.—

COG sites enrolling in a Ewing sarcoma trial have high rates of testing by FISH or PCR. A small proportion of patients have no translocation testing on either primary or metastatic sites. Next-generation sequencing techniques are not yet commonly used in this context.

Making the most of small samples: Optimization of tissue allocation of pediatric solid tumors for clinical and research use

INTRODUCTION

Tissue from pediatric solid tumors is in high demand for use in high-impact research studies, making the allocation of tissue from an anatomic pathology laboratory challenging. We designed, implemented, and assessed an interdepartmental process to optimize tissue allocation of pediatric solid tumors for both clinical care and research.

METHODS

Oncologists, pathologists, surgeons, interventional radiologists, pathology technical staff, and clinical research coordinators participated in the workflow design. Procedures were created to address patient identification and consent, prioritization of protocols, electronic communication of requests, tissue preparation, and distribution. Pathologists were surveyed about the value of the new workflow.

RESULTS

Over a 5-year period, 644 pediatric solid tumor patients consented to one or more studies requesting archival or fresh tissue. Patients had a variety of tumor types, with many rare and singular diagnoses. Sixty-seven percent of 1768 research requests were fulfilled. Requests for archival tissue were fulfilled at a significantly higher rate than those for fresh tissue (P > .001), and requests from resection specimens were fulfilled at a significantly higher rate than those from biopsies (P > .0001). In an anonymous survey, seven of seven pathologists reported that the process had improved since the introduction of the electronic communication model.

CONCLUSIONS

A collaborative and informed model for tissue allocation is successful in distributing archival and fresh tissue for clinical research studies. Our workflows and policies have gained pathologists' approval and streamlined our processes. As clinical and research programs evolve, a thoughtful tissue allocation process will facilitate ongoing research.

Abstract A67: Improving tissue allocation for research in pediatric solid tumors

Introduction: In pediatric cancer, there is an urgent need for research that can identify and validate new therapeutic modalities for pediatric cancers. Diagnostic biopsy samples remain the ideal tissue samples for research and must be collected from surplus biopsy material, which is often extremely limited. Here we describe our efforts to optimize tissue allocation for clinical care and research as a joint effort between Department of Pathology at Boston Children’s Hospital and the Pediatric Solid Tumor Program at the Dana-Farber/Boston Children’s Cancer and Blood Disorders Center.

Methods: Oncologists, pathologists, surgeons, interventional radiologists, pathology technical staff, and clinical research coordinators participated in the workflow design. The group agreed to develop a formalized procedure to address these five steps: 1) patient identification and consent, 2) prioritization of research objectives, 3) advance communication of tissue requests to the pathology staff, 4) tissue preparation, and 5) tissue distribution. It was unanimously agreed that all tissue must flow through the pathology department. On or before the day of surgery, clinical research teams sent the pathologist a patient-specific electronic communication indicating research consent and detailing the prioritized disease-specific research requests, including the procedure planned, all tissue types and tissue volumes requested, and details of any special preparation needed, such as avoiding decalcification in bone tumors. The communication was optimized to be clear but brief, with the goal of minimizing the impact to the pathologist’s work load. Pathologists were surveyed about the change in process.

Results: Over a five-year period (2013-2018), 662 pediatric DFCI/BCH solid tumor patients have consented to one or more trials that request FFPE, frozen, or fresh tissue. Tumor types represent a spectrum of cases, with many rare and singular diagnoses. Of 1,768 research tissue requests, 1,121 (63%) were fulfilled. Clinical study requests from resection specimens were the most likely to be fulfilled (95% of 390 requests fulfilled), while basic research requests from core biopsies were the least likely to be fulfilled (26% of 255 requests fulfilled). In an anonymous survey, 7 of 7 pathologists report that the process had improved since the introduction of the electronic communication.

Conclusions: A collaborative and informed model for tissue allocation is successful in distributing tissue for clinical studies and basic research projects. Our workflows and policies have gained pathologist approval and streamlined our processes. As clinical and research programs evolve, a thoughtful tissue allocation process will facilitate ongoing research.

Citation Format: R. Seth Pinches, Catherine Clinton, Abigail Ward, Stephanie C Meyer, Alyaa Al-Ibraheemi, Suzanne Forrest, Gianna R. Strand, Hillary Detert, Anne Piche-Schulman, Kristen Gil, Tamara Restrepo, Rosemarie Tavares-Proulx, Jeffrey Goldsmith, Raja Shaikh, Christopher Weldon, Sanda Alexandrescu, Allison F. O’Neill, Monica Hollowell, Marian H. Harris, Katherine A. Janeway, Brian D. Crompton, Alanna Church. Improving tissue allocation for research in pediatric solid tumors [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 A67.

Abstract A06: The added value of examining germline variants in a precision cancer therapy study

Introduction: Tumor profiling is becoming a more routine part of clinical care. Many academic centers and commercial entities offer tumor sequencing of cancer-related genes without matched germline profiling. We hypothesize that tumor-only sequencing may limit full clinical interpretation and have decreased sensitivity to identify significant germline variants.

Methods: The Genomic Assessment Improves Novel Therapy (GAIN) Consortium is a clinical cancer genomics study for patients with high-risk solid malignancies. Patients in this study were selected for subanalysis if panel sequencing of 447 genes was performed on a tumor and interpreted by an expert panel prior to the availability of matched germline sequencing. Interpretation of tumor sequencing included both therapeutic recommendations and a curation of cancer-related variants of potential clinical significance if present in the germline. Germline sequencing was separately performed targeting 147 genes (a subset of the somatic panel) and analyzed with a germline-specific pipeline to identify and filter variants. We examined clinical recommendations in the somatic reports that were based on single-nucleotide variants identified from the 147 overlapping genes. We compared these interpretations with results from the matched germline data.

Results: We identified 159 participants with somatic and germline sequencing reports meeting the eligibility criteria. Germline sequencing identified 38 pathogenic or likely pathogenic (P/LP) germline variants in 35 of 159 patients (22%). Of those 35 patients, 17 (49%) had a P/LP variant in an autosomal dominant cancer predisposition gene, 19 (54%) in an autosomal recessive gene, and 1 (2.9%) in a noncancer gene. Of the 38 total variants, 21 (55%) were identified by the analytic pipeline used for somatic sequencing and noted as potential germline variants in the somatic reports. Forty treatment recommendations were made from the somatic data within the overlapping genes. Ten (25%) treatment recommendations were based on variants that were later determined to be germline. These included variants in TP53, SDHA, SMARCA4, TSC2, FAM175A, CHEK2, and AKT1, many of which were noted in the somatic reports to be variants of uncertain significance or possibly germline.

Conclusions: In this study, we found that clinically actionable germline variants were under-reported when relying on analytical pipelines and clinical interpretations developed for the analysis of tumor samples. In the absence of germline sequencing, we also found that cancer treatment recommendations can be made based on mutations identified from tumor sequencing that are germline variants. In many cases, these recommendations remain appropriate (e.g., PARP inhibitors for BRCA1/2) while in other cases germline data facilitated a more nuanced interpretation of actionability. These findings support the use of germline genetic testing and paired tumor-germline analysis in precision cancer medicine studies.

Citation Format: Jaclyn Schienda, Catherine M. Clinton, Laura B. Corson, Alma Imamovic-Tuco, Navin Pinto, Luke Maese, Theodore W. Laetsch, AeRang Kim, Susan I. Vear, Margaret E. Macy, Mark A. Applebaum, Rochelle Bagatell, Amit J. Sabnis, Daniel A. Weiser, Julia L. Glade-Bender, Samuel L. Volchenboum, Wenjun Kang, Danielle Manning, Jonathan Nowak, Joshua Schiffman, Neal I. Lindeman, Alanna J. Church, Katherine A. Janeway, Brian D. Crompton, Junne Kamihara. The added value of examining germline variants in a precision cancer therapy study [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 A06.

Abstract B13: Leveraging cloud-based computational resources for gene fusion discovery with potential clinical implications for pediatric solid tumor patients

Introduction: Gene fusions are important oncogenic drivers with significant clinical impact in some cancer types. This is particularly true in pediatric cancers that often have low mutational burden and lack other diagnostic markers and therapeutic targets. Many gene fusions are rare or private to the individual patient and can be difficult to detect with methods optimized for common fusions. Unbiased sequencing methods and expansive computational resources are needed for expanding our ability to characterize fusions. Building a comprehensive catalog of oncogenic gene fusions will improve our understanding of their diversity and fully harness their potential for clinical impact.

Methods: Patients are eligible for the GAIN/iCat2 study if they have been diagnosed with high-risk or recurrent/refractory extracranial solid tumor at age 30 or less and have a sample available for sequencing. Enrolled patients with an unclear diagnosis after standard clinical testing are nominated for transcriptome sequencing by the study investigators. We developed a computational pipeline in Google Cloud for gene fusion discovery utilizing paired end Illumina RNA-Seq data, multiple fusion callers, and a custom algorithm for integrative data analysis. The multicaller fusion detection approach enables us to address the high false-positive rate typical for gene fusion calling in transcriptomic data while improving the sensitivity to detect the more challenging fusions. After filtering, the fusions are annotated using the databases of known fusions and cancer genes. The predicted fusion transcripts are inspected visually, and the fusions are selected based on relevance to diagnostic classification or therapy to be validated by an orthogonal method.

Results: 41 tumor samples were sequenced and analyzed for gene fusions. A total of 203 candidate fusions were detected by two or more fusion callers. Based on functional annotations and potential impact on diagnosis or therapeutic approaches, 12 fusion transcripts of interest were identified, 10 of which were validated by either pre-enrollment testing or an orthogonal method. Of 16 mesenchymal cases, 6 validated fusions had diagnostic relevance and 3 validated fusions had therapeutic implications (ERC1-BRAF, RBPMS-NTRK2, and VCAN-IL23R). Two patients responded to matched targeted therapy. In one case, diagnostic classification was revised.

Conclusions: Whole-transcriptome sequencing in this selected patient population identified some fusion transcripts with clinical relevance. Determining the biologic significance of previously unreported fusions will require orthogonal sequencing such as whole genome, functional studies, and analysis of larger patient populations. Improved accuracy and scalability of methods for large-scale gene fusion analysis in the growing public datasets are likely to expand the landscape of gene fusions in cancer.

Citation Format: Alma Imamovic, Alanna J. Church, Laura B. Corson, Deirdre Reidy, Navin Pinto, Luke Maese, Theodore W. Laetsch, AeRang Kim, Susan I. Vear, Margaret E. Macy, Mark A. Applebaum, Rochelle Bagatell, Amit J. Sabnis, Daniel A. Weiser, Julia L. Glade-Bender, Gianna R. Strand, Lobin A. Lee, R. Seth Pinches, Catherine M. Clinton, Brian D. Crompton, Neal I. Lindeman, Steven G. DuBois, Katherine A. Janeway, Eliezer M. Van Allen. Leveraging cloud-based computational resources for gene fusion discovery with potential clinical implications for pediatric solid tumor patients [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 B13.

Abstract A59: Sequencing identifies diagnostically relevant alterations in pediatric solid tumor patients

Introduction: Molecular techniques have been incorporated into the diagnostic algorithms for many specific tumors, but the diagnostic role of next-generation sequencing has not been described at a population level. We report diagnostically relevant alterations identified by large-scale sequencing in a prospective cohort of pediatric solid tumors.

Methods and Objectives: Patients are eligible for the GAIN / iCat2 study if they have a high-risk, recurrent, or refractory extracranial solid tumor diagnosed at age 30 or less and have an adequate sample for sequencing available. After informed consent, tumor was sequenced using a next-generation sequencing assay that evaluates 447 genes and includes data about sequence variants, copy number alterations, and, in selected genes, translocations. Some cases received additional sequencing via RNASeq or targeted RNA sequencing for further evaluation of fusions. Diagnostic relevance was determined according to AMP/ASCO/CAP standards and guidelines for the reporting of sequence variants in cancer.

Results: 349 patients were enrolled as of December 31, 2018, and had tumor tissue successfully sequenced. These patients represent 60 unique diagnoses according to the WHO ICD-O classification. The most common single diagnoses were osteosarcoma (n=64), Ewing sarcoma (n=44), and alveolar rhabdomyosarcoma (n=32). For 349 patients, 184 (53%) had one or more genetic alterations that were diagnostically relevant, of which 159 (86%) were structural variants, 16 (8%) were sequence variants, and 9 (5%) were copy number variations. Alterations of high diagnostic relevance include CIC-DUX4 fusions in sarcoma (n=8), TP53 intron 1 rearrangements in osteosarcoma (n=26), DICER1 sequence variants in various tumors (n=7), and BCOR internal tandem duplications in clear-cell sarcoma of kidney and primitive myxoid mesenchymal tumor of infancy (n=3).

Conclusions: Diagnostically relevant alterations were identified in over half of pediatric solid tumor patients evaluated. Gene fusions are particularly prevalent. These results support a role for sequencing that includes robust fusion assessment to inform diagnosis in patients with pediatric solid tumors.

Citation Format: Alanna J. Church, Laura B. Corson, Alma Imamovic-Tuco, Gianna R. Strand, Dierdre Reidy, Duong Doan, Robert S. Pinches, Mark A. Applebaum, Rochelle Bagatell, Brian D. Crompton, Steven G. DuBois, Julia L. Glade Bender, Theodore W. Laetsch, Lobin A. Lee, Neal I. Lindeman, Marian H. Harris, Margaret E. Macy, Luke Maese, Navin Pinto, Amit J. Sabnis, Eliezer M. Van Allen, Susan I. Vear, Daniel A. Weiser, Catherine M. Clinton, Katherine A. Janeway. Sequencing identifies diagnostically relevant alterations in pediatric solid tumor patients [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 A59.

Abstract A28: Targeted sequencing in 388 patients with high-risk or recurrent/refractory pediatric extracranial solid malignancies: An interim report from the GAIN Consortium/iCat2 Study

Background: Gene variants with potential therapeutic significance have been reported in 30-60% of childhood malignancies. The 12-institution Genomic Assessment Informs Novel therapy (GAIN) consortium is conducting the individualized cancer therapy 2 (iCat2) study (NCT02520713) with the objective of evaluating the impact of tumor profiling on outcome. We provide an interim report on patients enrolled on the ongoing GAIN/iCat2 study.

Methods and Objectives: Patients are eligible if they have a high-risk, recurrent/refractory (RR), or difficult-to-diagnose extracranial solid tumor diagnosed at ≤30 years and adequate sample available for sequencing. A next-generation targeted panel assay is performed. Results are returned with a GAIN report containing clinical interpretation, including an individualized cancer therapy (iCat) recommendation if there is evidence supporting a link between an identified variant and response to molecularly targeted therapy. iCat recommendations are tiered from 1 to 5 based on the level of clinical and preclinical support, with tier 1 being the highest and tier 5 the lowest. Potential extraordinary responders are selected for further review based on having treatment duration of ≥1 year for chemotherapy or ≥4 months or a partial response for targeted therapy.

Results: 388 eligible patients were enrolled by 1/1/2019 with the most common diagnoses being osteosarcoma, Ewing sarcoma, and rhabdomyosarcoma. 366 patients (94%) have had at least one successful sequencing result, with 349 having molecular and GAIN reports suitable for inclusion in this analysis. 68% of patients (237/349) have received iCat recommendations, with 41% (143/349) having the highest tier of 1-2 and 27% (94/349) having a highest tier of 3-5. Common genes for which tier 1-2 iCat recommendations were made include TP53 (15%), SMARCB1 (4%), PIK3CA (3%), CDK4 (2%), and KRAS (2%). Common alterations for which tier 3-5 recommendations were made include EWSR1 fusions (12%), MYC/MYCN amplifications (8%), and CDKN2A deletions (7%). Of 170 RR patients with treatment follow-up data entered as of June 2019, 15% (25/170) have received matched targeted therapy. Six of these (24%) are considered extraordinary responders. Of note, extraordinary responses were also seen with some second-line chemotherapy and multitargeted kinase inhibitors.

Conclusions: The proportion of patients with clinically significant gene variants is higher in this study than in some previous reports. Providing an iCat recommendation for alterations in genes such as TP53 where evidence is mixed, increased availability of molecularly targeted therapy trials, and more evidence may all be responsible for this increased rate. Reassessment of iCat recommendation tiers based on current evidence is ongoing. Extraordinary responses occur in a subset of children with extracranial solid malignancies who receive matched targeted therapy. Study enrollment is ongoing with further assessments of the impact of tumor profiling on outcome planned.

Citation Format: Laura B. Corson, Alanna J. Church, Deirdre Reidy, Pei-Chi Kao, Wenjun Kang, Navin Pinto, Luke Maese, Theodore W. Laetsch, AeRang Kim, Susan I. Vear, Margaret E. Macy, Mark A. Applebaum, Lobin A. Lee, Duong Doan, R. Seth Pinches, Seong Choi, Suzanne J. Forrest, Catherine M. Clinton, Brian D. Crompton, Laura E. MacConaill, Samuel L. Volchenboum, Neal I. Lindeman, Steven G. DuBois, Wendy B. London, Katherine A. Janeway. Targeted sequencing in 388 patients with high-risk or recurrent/refractory pediatric extracranial solid malignancies: An interim report from the GAIN Consortium/iCat2 Study [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 A28.

Chasing ctDNA in Patients With Sarcoma

Liquid biopsies are new technologies that allow cancer profiling of tumor fragments found in body fluids, such as peripheral blood, collected noninvasively from patients with malignancies. These assays are increasingly valuable in clinical oncology practice as prognostic biomarkers, as guides for therapy selection, for treatment monitoring, and for early detection of disease progression and relapse. However, application of these assays to rare cancers, such as pediatric and adult sarcomas, have lagged. In this article, we review the technical challenges of applying liquid biopsy technologies to sarcomas, provide an update on progress in the field, describe common pitfalls in interpreting liquid biopsy data, and discuss the intersection of sarcoma clinical care and commercial assays emerging on the horizon.

Abstract A55: Circulating tumor DNA in newly diagnosed intermediate-risk rhabdomyosarcoma

Background: Patients with intermediate-risk rhabdomyosarcoma (IR RMS) have approximately 60-70% chance of survival with current therapies. However, biomarkers of outcome and response to therapy are lacking for these patients. Circulating tumor DNA (ctDNA) has been shown to be prognostic in a wide range of cancer types, but it is unknown whether patients with IR RMS have detectable levels of ctDNA.

Objective: To study ctDNA prevalence and prognostic impact in newly diagnosed IR RMS, we utilized two next-generation sequencing (NGS) approaches that detect the presence of somatic copy-number changes and oncogenic translocations.

Methods: Cell-free DNA was extracted from serum samples obtained from patients with newly diagnosed IR RMS who enrolled on the COG studies ARST0531 and D9803, including patients with embryonal (ERMS) and alveolar (ARMS) histology subtypes. While both subtypes are characterized by frequent somatic copy-number variants (CNVs), ARMS is also defined by recurrent translocations. To detect CNVs, we performed ultra-low passage whole-genome sequencing (ULP-WGS). Translocations were detected with a validated custom hybrid capture assay (TranSS-Seq).

Results: Serum samples were analyzed from 132 patients with IR RMS, including 75 with ERMS and 57 with ARMS. ctDNA was detected by CNVs in 70% (92/132) of IR RMS patients with similar detection rates in each histology: 65% (49/75) in ERMS and 75% (43/57) in ARMS. Among the ARMS samples sequenced, only 37% (18/49) were positive by TranSS-Seq. Furthermore, copy-number events resulting in amplifications of the somatic translocation frequently resulted in miscalculation of ctDNA content by the TranSS-Seq method. Estimates of event-free and overall survival were lower in patients with detectable ctDNA, though the differences were not statistically significant.

Conclusion: Patients with IR RMS frequently have detectable levels of ctDNA that can be measured by NGS assays designed to detect somatic structural events. This study relied on previously banked serum samples and a relatively small retrospective analysis. These findings provide justification for our current efforts to utilize a large prospective study, COG ARST1431, to collect pretreatment and serial blood samples using procedures optimized for ctDNA assays. Sequencing of matched tumor samples is ongoing to understand the differences in sensitivity between ULP-WGS and TranSS-Seq for ctDNA detection in patients with ARMS.

Citation Format: Samuel Abbou, David Hall, Donald A. Barkauskas, Kelly Klega, Anwesha Nag, Aaron R. Thorner, Mark Krailo, Steven Dubois, Douglas S. Hawkins, Brian D. Crompton. Circulating tumor DNA in newly diagnosed intermediate-risk rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A55.

Abstract A61: Evaluation of ctDNA in children with relapsed or refractory neuroblastoma treated with 131I-MIBG

Objectives: Circulating tumor DNA (ctDNA) has been shown to be detectible in children with neuroblastoma, yet little is known about the dynamics of how ctDNA levels change during treatment. 131I-MIBG is a targeted radiopharmaceutical selectively taken up by 90% of neuroblastomas. We evaluated changes in ctDNA levels and identified somatic events from ctDNA in a cohort of patients treated with 131I-MIBG.

Methods: NANT 11-01 is a randomized phase 2 study for patients with relapsed or refractory neuroblastoma designed to evaluate the benefit of radiosensitizing agents in combination with 131I-MIBG (MIBG vs. MIBG + vincristine/irinotecan vs. MIBG + vorinostat). Patients had samples collected beginning prior to therapy (c1d1), 72 hours after 131I-MIBG (c1h72), cycle 1 day 15 (c1d15) and for patients who met criteria for a second cycle, cycle 2 day 1 (c2d1). Ultra-low-pass whole-genome sequencing (ULP-WGS) was used to quantify ctDNA in each plasma sample by identifying somatic segmental copy number changes. The correlation between baseline %ctDNA and disease burden using Curie score from the patient’s pretreatment MIBG scan was assessed with linear regression. ctDNA levels and copy number changes were analyzed descriptively.

Results: 112 samples from 49 patients were evaluated. The number of patients with detectable ctDNA changed throughout therapy as follows: c1d1 40.4% (19/47); c1h72 42.5% (17/40); c1d15 18% (2/11); and c2d1 0% (0/14) detectable. Among patients with detectable ctDNA, median ctDNA levels at these timepoints were as follows: 17% (range 3.9-91%) at c1d1; 22% (range 2.9-86%) at c1hr72; and 18% (range 3.5-33%) at c1d15. There was a nonsignificant positive correlation between baseline ctDNA levels and baseline Curie score (n=47; R2 = 0.07; p=0.081). MYCN amplification was detected in ctDNA in 4 out of 5 patients with detectable ctDNA known to have MYCN amplified tumors, but never in patients without known MYCN amplification.

Conclusions: ctDNA is detectable using ULP-WGS at multiple time points for patients with neuroblastoma treated with 131I-MIBG. ctDNA levels declined during therapy and were rarely detectable at cycle 1 day 15 or by the start of cycle 2. MYCN amplification was identified in the plasma from the majority of patients with MYCN amplified disease if ctDNA levels were detectable. After enrollment is completed for this study, we plan to determine whether baseline ctDNA and changes in ctDNA levels are associated with treatment response.

Citation Format: David S. Shulman, Kelly Klega, Araz Marachelian, Katherine K. Matthay, Julie R. Park, M. Meaghan Granger, Steven G. DuBois, Brian D. Crompton. Evaluation of ctDNA in children with relapsed or refractory neuroblastoma treated with 131I-MIBG [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A61.

A phase II study of larotrectinib for children with newly diagnosed solid tumors and relapsed acute leukemias harboring TRK fusions: Children’s Oncology Group study ADVL1823

TPS10560

Background: In children, fusions of the NTRK1/2/3 genes (TRK fusions) occur in soft tissue sarcomas, including infantile fibrosarcoma (IFS), congenital mesoblastic nephroma, high- and low-grade gliomas, secretory breast carcinoma, and papillary thyroid cancer. Rarely, TRK fusions also occur in Ph-like acute lymphoblastic leukemia and acute myeloid leukemia. Larotrectinib is a selective TRK inhibitor FDA-approved for the treatment of TRK fusion solid tumors in patients with no satisfactory alternative treatments or whose cancer has progressed following initial treatment. In children, larotrectinib demonstrated a 94% overall response rate (ORR) with a 12-month progression free survival rate of 75% (1). Methods: Patients <30 years with any newly diagnosed unresectable solid tumor or relapsed/refractory acute leukemia with TRK fusions are eligible. TRK fusions must be locally identified in a CLIA/CAP laboratory and are confirmed centrally using a targeted RNA sequencing panel. Patients with high-grade gliomas are excluded. Patients receive larotrectinib 100 mg/m2/dose BID (max of 100 mg/dose) continuously in 28-day cycles. Patients with solid tumors who achieve CR will discontinue larotrectinib at the completion of at least 12 total cycles of therapy and 6 cycles after achieving CR. Those whose tumors become surgically resectable may undergo on study resection and discontinue therapy if an R0/R1 (IFS) or R0 (other tumors) resection is obtained. All other patients will receive 26 cycles in the absence of unacceptable toxicity or progressive disease. The primary endpoint is the ORR to larotrectinib according to RECIST 1.1 in children with IFS. The study uses a Simon 2-stage minimax design, and the regimen will be considered of sufficient interest if 16 of 21 (76%) patients with IFS demonstrate response. Patients with other solid tumors and leukemias will be analyzed in separate cohorts as secondary objectives. Correlative studies include serial sampling of circulating tumor DNA and neurocognitive assessments. This is the first Children’s Oncology Group study to assign frontline therapy based on the presence of a molecular marker independent of histology, and the first clinical trial to evaluate larotrectinib for the treatment of leukemia. Enrollment began in October 2019 (NCT03834961). 1. Tilburg CMv, DuBois SG, Albert CM, et al: Larotrectinib efficacy and safety in pediatric TRK fusion cancer patients. Journal of Clinical Oncology 37:10010-10010, 2019 Clinical trial information: NCT03834961.

Provocative questions in osteosarcoma basic and translational biology: A report from the Children's Oncology Group

Patients who are diagnosed with osteosarcoma (OS) today receive the same therapy that patients have received over the last 4 decades. Extensive efforts to identify more effective or less toxic regimens have proved disappointing. As we enter a postgenomic era in which we now recognize OS not as a cancer of mutations but as one defined by p53 loss, chromosomal complexity, copy number alteration, and profound heterogeneity, emerging threads of discovery leave many hopeful that an improving understanding of biology will drive discoveries that improve clinical care. Under the organization of the Bone Tumor Biology Committee of the Children's Oncology Group, a team of clinicians and scientists sought to define the state of the science and to identify questions that, if answered, have the greatest potential to drive fundamental clinical advances. Having discussed these questions in a series of meetings, each led by invited experts, we distilled these conversations into a series of seven Provocative Questions. These include questions about the molecular events that trigger oncogenesis, the genomic and epigenomic drivers of disease, the biology of lung metastasis, research models that best predict clinical outcomes, and processes for translating findings into clinical trials. Here, we briefly present each Provocative Question, review the current scientific evidence, note the immediate opportunities, and speculate on the impact that answered questions might have on the field. We do so with an intent to provide a framework around which investigators can build programs and collaborations to tackle the hardest problems and to establish research priorities for those developing policies and providing funding.

Abstract 3104: A high prevalence of chromosomal translocations as drivers in high-risk pediatric solid cancers

The GAIN iCat2 Project is a collaboration between Dana-Farber/Boston Children's Cancer and Blood Disorder Center and eleven pediatric oncology centers across the United States to sequence relapsed, metastatic, difficult-to-diagnose, and high-risk extracranial solid tumors from 825 patients. The goals are to gain a better understanding of the genomic events in pediatric cancers and determine the clinical impact of matched targeted therapy. Tumor samples are sequenced on one of four gene panels performed in CLIA certified, CAP accredited laboratories, most often utilizing OncoPanel at the Center for Advanced Molecular Diagnostics, Brigham Women’s Hospital. This panel assesses SNVs and CNVs in 447 cancer-associated genes and interrogates intronic regions of 60 genes frequently involved in oncogenic translocation. For undifferentiated sarcomas and tumors in which oncogenic drivers are not identified by the gene panel, whole exome sequencing or RNA sequencing for fusion detection may be done. Interpretation of genomic results, including potential implications for diagnosis and hereditary risks, as well as assessment of possible matched targeted therapies and suitable trials are summarized in a report to the primary oncology provider.

An interim analysis of tumors from the first 275 patients enrolled who have OncoPanel results was performed to assess genomic alterations most prevalent in this group of pediatric cancers. 50% (137/275) have structural alterations in their tumors with over half of these (74/137) harboring an oncogenic fusion that is the main, or only identified, driver of the cancer. These include fusions pathognomonic for diseases such as Ewing sarcoma, alveolar rhabdomyosarcoma, synovial sarcoma, desmoplastic small round cell tumors, mesenchymal chondrosarcoma, low grade fibromyxoid sarcoma, and NUT midline carcinoma. Other cases showed recurrent disruption of key tumor suppressors, such as TP53 intron 1 translocations in osteosarcoma. Lastly, more generalized, key, cancer-driving fusions were seen with rearrangements involving BRAF, NOTCH, and NTRK. In addition to aiding in diagnosis, identification of fusions has led to targeted therapy recommendations for many patients. SNVs and CNVs also helped clarify diagnoses, especially in the case of DICER1 and SMARCB1 alterations, and identified potential targeted therapies to consider for relapsed patients. Although patient recruitment is ongoing, this study shows promise for advancing our understanding and treatment of pediatric cancers and highlights the critical importance of incorporating techniques for fusion detection in tumor profiling.

Citation Format: Laura B. Corson, Alma Imamovic-Tuco, Gianna R. Strand, Deirdre Reidy, Duong Doan, Mark A. Applebaum, Rochelle Bagatell, Brian D. Crompton, Steven G. DuBois, Julia L. Glade Bender, AeRang Kim, Theodore W. Laetsch, Lobin A. Lee, Neal I. Lindeman, Laura E. MacConaill, Margaret E. Macy, Luke Maese, Seth Pinches, Navin Pinto, Amit J. Sabnis, Eliezer M. Van Allen, Susan I. Vear, Daniel A. Weiser, Catherine M. Clinton, Katherine A. Janeway, Alanna J. Church. A high prevalence of chromosomal translocations as drivers in high-risk pediatric solid cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3104.

Abstract CT109: A Phase I dose escalation and expansion study of seclidemstat (SP-2577) a first-in class reversible LSD1 inhibitor for patients with relapsed or refractory Ewing sarcoma

Introduction: Ewing sarcoma is an aggressive pediatric and young adult bone tumor dependent almost exclusively on the EWS/ETS fusion protein family for transcriptional activity. EWS/FLI is the most common fusion resulting in the repression of vital tumor suppressor genes by the activity of lysine-specific histone demethylase 1 (LSD1). Seclidemstat (SP-2577) is a first in class, orally bioavailable, small molecule with reversible and noncompetitive selective inhibition of LSD1 at low nanomolar concentrations (IC50: 25-50 nM). Seclidemstat has demonstrated disruption of global transcriptional function of EWS/ETS fusions and impairs multiple EWS/ETS-associated oncogenic phenotypes in xenograft models of Ewing sarcoma. This Phase I study aims primarily to assess the safety and tolerability of seclidemstat and to secondarily characterize the pharmacokinetics (PK), food effects, and preliminary anti-tumor activity via RECIST 1.1. Exploratory objectives include using circulating tumor cells, cell-free DNA, and hemoglobin F as pharmacodynamic markers of response.

Methods: This multi-center phase I study (NCT03600649) is open-label and non-randomized and utilizes an accelerated dose escalation phase followed by a conventional 3+3 design to determine the maximum tolerated dose (MTD). Initially, one subject per dose cohort will be recruited in the accelerated dose escalation phase until the first instance of grade 2 or greater drug related toxicity or dose limiting toxicity (DLT). Further cohorts will be recruited in cohorts of three subjects in the 3+3 dose escalation phase. Once a declared suitable dose and schedule for further investigation has been identified, 14 additional patients will be enrolled in the dose expansion part of the study for a total of 20 patients treated at the MTD. The starting dose of seclidemstat is 75 mg PO BID with seven dose levels planned by modified Fibonacci schema. Food effects on PK are planned on day 1 and 2 of cycles 1 and 2. Patients at least 12 years of age will be included with histologically confirmed relapsed or refractory Ewing sarcoma with adequate performance status and organ function. Archival tumor tissue is required during screening. Tumor biopsies and measurable disease are required in dose expansion only. This trial is currently open for requirement at five locations in the United States. Dose level 2 (150 mg PO BID) began enrollment in November 2018 with no drug related grade 2 or greater adverse events or DLTs observed in dose level 1.

Citation Format: Damon Reed, Steven G. DuBois, Richard Gorlick, Leo Mascarenhas, Douglas Harrison, Jonathan Metts, Stephen L. Lessnick, Brian D. Crompton, David M. Loeb, Rose Hernandez, Jeff Larson, David D. Stenehjem. A Phase I dose escalation and expansion study of seclidemstat (SP-2577) a first-in class reversible LSD1 inhibitor for patients with relapsed or refractory Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT109.

Abstract CT112: A Phase I multicenter trial of the dual MDM2/MDMX inhibitor ALRN-6924 in children and young adults with relapsed/refractory pediatric cancers

BACKGROUND: TP53 mutations are rare across pediatric cancers. Recent work using CRISPR-Cas9 screens has demonstrated that MDM2 and MDMX are strong dependencies in a range of TP53-wildtype pediatric malignancies. Increased expression of MDM2 and MDMX is a common mechanism for suppressing p53 in pediatric malignancies and can occur by copy number gain or amplification, as has been reported in retinoblastoma and hepatoblastoma. In pediatric high-grade gliomas, activating PPM1D mutations drive p53 suppression, likely through MDM2 stabilization.

ALRN-6924 is a novel, first-in-class, cell-permeating stapled peptide that disrupts the inhibitory interactions between MDM2/MDMX(MDM4) and p53. ALRN-6924 has been evaluated in two adult Phase I trials, with good tolerability and evidence of clinical activity across a range of cancer subtypes. Given the oncogenic roles of MDM2 and MDMX in pediatric malignancies, we developed a Phase I clinical trial designed to evaluate the tolerability, pharmacokinetics, and pharmacodynamic and antitumor activity of ALRN-6924.

METHODS: This is a Phase I, open-label, investigator-initiated multicenter study of ALRN-6924 in children 1-21 years of age with relapsed/refractory cancer (NCT03654716). The primary objectives are to determine the recommended phase 2 dose, and to describe toxicities and pharmacokinetic parameters of ALRN-6924 in this population. The monotherapy arm consists of two cohorts: Cohort A for patients with TP53-wildtype solid tumors and lymphomas; and Cohort B for patients with retinoblastoma, or TP53-wildtype tumors that meet any of the following criteria: hepatoblastoma, malignant rhabdoid tumor, MDM2 or MDMX amplification, TET2 loss, or PPM1D activating mutations. Patients with CNS primary tumors are only eligible for Cohort B. In Cohorts A and B, patients receive ALRN-6924 intravenously on Days 1, 4, 8 and 11 of a 21-day cycle starting at a dose of 2.2 mg/kg. An expansion cohort for patients eligible for Cohort B will open following completion of monotherapy dose escalation. Patients with relapsed/refractory leukemias enroll to Cohort C and receive ALRN-6924 in combination with low-dose cytarabine on days 1, 8 and 15 of a 28-day cycle starting at a dose of 2.7 mg/kg. Pharmacokinetic sampling and pharmacodynamic testing (serum MIC-1 modulation) is required for all patients. Correlative biology studies will include evaluation of circulating tumor DNA for TP53 mutations in patients with solid tumors and serial assessment of leukemic blasts in patients with relapsed leukemia. Enrollment began in October 2018. Up to 69 patients will be enrolled.

Citation Format: David S. Shulman, Kieuhoa T. Vo, Elizabeth Fox, Jodi A. Muscal, Loren D. Walensky, Yana Pikman, Kimberly Stegmaier, Alanna Church, Brian D. Crompton, Andrew E. Place, Susan N. Chi, Allison F. O'Neill, Junne Kamihara, Suzanne Ezrre, Cecilia Carlowicz, Dawn Pinchasik, Hasan Al-Sayegh, Clement Ma, Wendy B. London, Steven G. DuBois. A Phase I multicenter trial of the dual MDM2/MDMX inhibitor ALRN-6924 in children and young adults with relapsed/refractory pediatric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT112.

Assessment of circulating tumor DNA in pediatric solid tumors: The promise of liquid biopsies

Circulating tumor DNA can be detected in the blood and body fluids of patients using ultrasensitive technologies, which have the potential to improve cancer diagnosis, risk stratification, noninvasive tumor profiling, and tracking of treatment response and disease recurrence. As we begin to apply "liquid biopsy" strategies in children with cancer, it is important to tailor our efforts to the unique genomic features of these tumors and address the technical and logistical challenges of integrating biomarker testing. This article reviews the literature demonstrating the feasibility of applying liquid biopsy to pediatric solid malignancies and suggests new directions for future studies.

High-throughput Chemical Screening Identifies Focal Adhesion Kinase and Aurora Kinase B Inhibition as a Synergistic Treatment Combination in Ewing Sarcoma

PURPOSE

Ewing sarcoma is an aggressive solid tumor malignancy of childhood. Although current treatment regimens cure approximately 70% of patients with localized disease, they are ineffective for most patients with metastases or relapse. New treatment combinations are necessary for these patients.

EXPERIMENTAL DESIGN

Ewing sarcoma cells are dependent on focal adhesion kinase (FAK) for growth. To identify candidate treatment combinations for Ewing sarcoma, we performed a small-molecule library screen to identify compounds synergistic with FAK inhibitors in impairing Ewing cell growth. The activity of a top-scoring class of compounds was then validated across multiple Ewing cell lines in vitro and in multiple xenograft models of Ewing sarcoma.

RESULTS

Numerous Aurora kinase inhibitors scored as synergistic with FAK inhibition in this screen. We found that Aurora kinase B inhibitors were synergistic across a larger range of concentrations than Aurora kinase A inhibitors when combined with FAK inhibitors in multiple Ewing cell lines. The combination of AZD-1152, an Aurora kinase B-selective inhibitor, and PF-562271 or VS-4718, FAK-selective inhibitors, induced apoptosis in Ewing sarcoma cells at concentrations that had minimal effects on survival when cells were treated with either drug alone. We also found that the combination significantly impaired tumor progression in multiple xenograft models of Ewing sarcoma.

CONCLUSIONS

FAK and Aurora kinase B inhibitors synergistically impair Ewing sarcoma cell viability and significantly inhibit tumor progression. This study provides preclinical support for the consideration of a clinical trial testing the safety and efficacy of this combination for patients with Ewing sarcoma.

Correction: Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group

The authors have noticed that the final paragraph of the Results section contains errors in the number of patients involved. The correct number of patients is included in the text below. These errors do not affect the Figure referenced.In osteosarcoma, we focused on 8q gain as a specific biological feature of interest. Among the 41 patients with detectable ctDNA in the osteosarcoma cohort, 8q gain was detected in 73.2% (30/41). The 3-year EFS for patients with 8q gain (n = 30) in ctDNA was 60.0% (95% CI 40.5-75.0) compared to 80.8 (95% CI 42.4-94.9) in patients without 8q gain (n = 11) in ctDNA (p = 0.18; Fig. 3).

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition

Renal medullary carcinoma (RMC) is a rare and deadly kidney cancer in patients of African descent with sickle cell trait. We have developed faithful patient-derived RMC models and using whole-genome sequencing, we identified loss-of-function intronic fusion events in one SMARCB1 allele with concurrent loss of the other allele. Biochemical and functional characterization of these models revealed that RMC requires the loss of SMARCB1 for survival. Through integration of RNAi and CRISPR-Cas9 loss-of-function genetic screens and a small-molecule screen, we found that the ubiquitin-proteasome system (UPS) was essential in RMC. Inhibition of the UPS caused a G2/M arrest due to constitutive accumulation of cyclin B1. These observations extend across cancers that harbor SMARCB1 loss, which also require expression of the E2 ubiquitin-conjugating enzyme, UBE2C. Our studies identify a synthetic lethal relationship between SMARCB1-deficient cancers and reliance on the UPS which provides the foundation for a mechanism-informed clinical trial with proteasome inhibitors.

Renal medullary carcinoma (RMC for short) is a rare type of kidney cancer that affects teenagers and young adults. These patients are usually of African descent and carry one of the two genetic changes that cause sickle cell anemia. RMC is an aggressive disease without effective treatments and patients survive, on average, for only six to eight months after their diagnosis.

Recent genetic studies found that most RMC cells have mutations that prevent them from producing a protein called SMARCB1. SMARCB1 normally acts as a so-called tumor suppressor, preventing cells from becoming cancerous. However, it was not clear whether RMCs always have to lose SMARCB1 if they are to survive and grow.

Often, diseases are studied using laboratory-grown cells and tissues that have certain features of the disease. No such models had been created for RMC, which has slowed efforts to understand how the disease develops and find new treatments for it. Hong et al. therefore worked with patients to develop new lines of cells that can be used to study RMC in the laboratory. These RMC cells started dying when they were given copies of the SMARCB1 gene, which supports the theory that RMCs have to lose SMARCB1 in order to grow.

Hong et al. then used a set of genetic reagents that can suppress or delete genes that are targeted by drugs, and followed this by testing a range of drugs on the RMC cells. Drugs and genetic reagents that reduced the activity of the proteasome – the structure inside cells that gets rid of old or unwanted proteins – caused the RMC cells to die. These proteasome inhibitor drugs also killed other kinds of cancer cells with SMARCB1 mutations.

Proteasome inhibitors are already used to treat different types of cancer. Potentially, a clinical trial could be run to see if they will treat patients whose cancers lack SMARCB1. Further work is also needed to determine the exact link between SMARCB1 and the proteasome.

Detection of Circulating Tumor DNA in Patients With Leiomyosarcoma With Progressive Disease

Purpose

Leiomyosarcoma (LMS) is a soft tissue sarcoma characterized by multiple copy number alterations (CNAs) and without common recurrent single nucleotide variants. We evaluated the feasibility of detecting circulating tumor DNA (ctDNA) with next-generation sequencing in a cohort of patients with LMS whose tumor burden ranged from no evidence of disease to metastatic progressive disease.

Patients and Methods

Cell-free DNA in plasma samples and paired genomic DNA from resected tumors were evaluated from patients with LMS by ultra-low passage whole genome sequencing (ULP-WGS). Sequencing reads were aligned to the human genome and CNAs identified in cell-free DNA and tumor DNA by ichorCNA software to determine the presence of ctDNA. Clinical data were reviewed to assess disease burden and clinicopathologic features.

Results

We identified LMS ctDNA in eleven of sixteen patients (69%) with disease progression and total tumor burden over 5 cm. Sixteen patients with stable disease or low disease burden at the time of blood draw were found to have no detectable ctDNA. Higher ctDNA fraction of total cell-free DNA was associated with increasing tumor size and disease progression. Conserved CNAs were found between primary tumors and ctDNA in each case, and recurrent CNAs were found across LMS samples. ctDNA levels declined following resection of progressive disease in one case and became detectable upon disease relapse in another individual patient.

Conclusion

These results suggest that ctDNA, assayed by a widely available sequencing approach, may be useful as a biomarker for a subset of uterine and extrauterine LMS. Higher levels of ctDNA correlate with tumor size and disease progression. Liquid biopsies may assist in guiding treatment decisions, monitoring response to systemic therapy, surveying for disease recurrence and differentiating benign and malignant smooth muscle tumors.

Duality of purpose: Participant and parent understanding of the purpose of genomic tumor profiling research among children and young adults with solid tumors

PURPOSE

Increasing use of genomic tumor profiling may blur the line between research and clinical care. We aimed to describe research participants' perspectives on the purpose of genomic tumor profiling research in pediatric oncology.

METHODS

We surveyed 45 participants (response rate 85%) in a pilot study of genomic profiling in pediatric solid tumors at four academic cancer centers following return of sequencing results. We defined understanding according to a one-item ("basic") definition (recognizing that the primary purpose was not to improve the patient's treatment) and a four-item ("comprehensive") definition (primary purpose was not to improve patient's treatment; primary purpose was to improve treatment of future patients; there may not be direct medical benefit; most likely result of participation was not increased likelihood of cure).

RESULTS

Sixty-eight percent of respondents (30/44) demonstrated basic understanding of the study purpose; 55% (24/44) demonstrated comprehensive understanding. Understanding was more frequently seen in those with higher education and greater genetic knowledge according to basic (81% vs 50%, p=0.05; and 82% vs 46%, p=0.03, respectively) and comprehensive definitions (73% vs 28%, p=0.01; 71% vs 23%, p=0.01). Ninety-three percent of respondents who believed the primary purpose was to improve the patient's care simultaneously stated that the research also aimed to benefit future patients.

CONCLUSIONS

Most participants in pediatric tumor profiling research understand that the primary goal of this research is to improve care for future patients, but many express dual goals when participating in sequencing research. Some populations demonstrate increased rates of misunderstanding. Nuanced participant views suggest further work is needed to assess and improve participant understanding, particularly as tumor sequencing moves beyond research into clinical practice.

Therapeutic Targeting of KDM1A/LSD1 in Ewing Sarcoma with SP-2509 Engages the Endoplasmic Reticulum Stress Response

Multi-agent chemotherapeutic regimes remain the cornerstone treatment for Ewing sarcoma, the second most common bone malignancy diagnosed in pediatric and young adolescent populations. We have reached a therapeutic ceiling with conventional cytotoxic agents, highlighting the need to adopt novel approaches that specifically target the drivers of Ewing sarcoma oncogenesis. As KDM1A/lysine-specific demethylase 1 (LSD1) is highly expressed in Ewing sarcoma cell lines and tumors, with elevated expression levels associated with worse overall survival (P = 0.033), this study has examined biomarkers of sensitivity and mechanisms of cytotoxicity to targeted KDM1A inhibition using SP-2509 (reversible KDM1A inhibitor). We report, that innate resistance to SP-2509 was not observed in our Ewing sarcoma cell line cohort (n = 17; IC₅₀ range, 81 -1,593 nmol/L), in contrast resistance to the next-generation KDM1A irreversible inhibitor GSK-LSD1 was observed across multiple cell lines (IC₅₀ > 300 μmol/L). Although TP53/STAG2/CDKN2A status and basal KDM1A mRNA and protein levels did not correlate with SP-2509 response, induction of KDM1B following SP-2509 treatment was strongly associated with SP-2509 hypersensitivity. We show that the transcriptional profile driven by SP-2509 strongly mirrors KDM1A genetic depletion. Mechanistically, RNA-seq analysis revealed that SP-2509 imparts robust apoptosis through engagement of the endoplasmic reticulum stress pathway. In addition, ETS1/HIST1H2BM were specifically induced/repressed, respectively following SP-2509 treatment only in our hypersensitive cell lines. Together, our findings provide key insights into the mechanisms of SP-2509 cytotoxicity as well as biomarkers that can be used to predict KDM1A inhibitor sensitivity in Ewing sarcoma. Mol Cancer Ther; 17(9); 1902-16. ©2018 AACR.

Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors

Objective

Liquid biopsies are being rapidly used in adult cancers as new biomarkers of disease. Circulating tumor DNA (ctDNA) levels have been reported to be proportional to disease burden, correlate with treatment response, and predict relapse. However, little is known about how frequently ctDNA is detectable in pediatric patients with solid tumors. Therefore, we developed a next-generation sequencing approach to detect and quantify ctDNA in the blood of patients with the most common pediatric solid tumors.

Methods

Detection of ctDNA requires assays sensitive to somatic events typically observed in the cancer type being studied. In pediatric solid tumors, structural variants are more common than recurrent point mutations. We adapted an ultralow passage whole-genome sequencing approach to capture copy number variants and a hybrid capture sequencing assay to detect translocations in liquid biopsy samples from pediatric patients.

Results

Copy number changes seen by ultralow passage whole-genome sequencing enabled detection of ctDNA in patients with osteosarcoma, neuroblastoma, alveolar rhabdomyosarcoma, and Wilms tumor. In Ewing sarcoma, detection of the EWSR1 translocation was a more sensitive approach. For patients with samples collected at multiple time points, changes in ctDNA levels corresponded to treatment response. We also found that disease-specific genomic biomarkers of prognosis were detectable in ctDNA.

Conclusion

This study demonstrates that liquid biopsy approaches that detect somatic structural variants are well suited to pediatric solid tumors. We show that children with the most common solid tumor malignancies have detectable levels of ctDNA, which may be used to track disease response and identify genomic subclassifiers of disease. Efforts to profile larger collections of clinically annotated specimens are under way to validate the clinical use of these assays.