Indoximod-based chemo-immunotherapy for pediatric brain tumors: A first-in-children phase I trial

BACKGROUND

Recurrent brain tumors are the leading cause of cancer death in children. Indoleamine 2,3-dioxygenase (IDO) is a targetable metabolic checkpoint that, in preclinical models, inhibits anti-tumor immunity following chemotherapy.

METHODS

We conducted a phase I trial (NCT02502708) of the oral IDO-pathway inhibitor indoximod in children with recurrent brain tumors or newly diagnosed diffuse intrinsic pontine glioma (DIPG). Separate dose-finding arms were performed for indoximod in combination with oral temozolomide (200 mg/m2/day x 5 days in 28-day cycles), or with palliative conformal radiation. Blood samples were collected at baseline and monthly for single-cell RNA-sequencing with paired single-cell T cell receptor sequencing.

RESULTS

Eighty-one patients were treated with indoximod-based combination therapy. Median follow-up was 52 months (range 39-77 months). Maximum tolerated dose was not reached, and the pediatric dose of indoximod was determined as 19.2 mg/kg/dose, twice daily. Median overall survival was 13.3 months (n = 68, range 0.2-62.7) for all patients with recurrent disease and 14.4 months (n = 13, range 4.7-29.7) for DIPG. The subset of n = 26 patients who showed evidence of objective response (even a partial or mixed response) had over 3-fold longer median OS (25.2 months, range 5.4-61.9, p = 0.006) compared to n = 37 nonresponders (7.3 months, range 0.2-62.7). Four patients remain free of active disease longer than 36 months. Single-cell sequencing confirmed emergence of new circulating CD8 T cell clonotypes with late effector phenotype.

CONCLUSIONS

Indoximod was well tolerated and could be safely combined with chemotherapy and radiation. Encouraging preliminary evidence of efficacy supports advancing to Phase II/III trials for pediatric brain tumors.

IMMU-04. SINGLE-CELL RNA-SEQUENCING IDENTIFIES FUNCTIONAL MACROPHAGE SUBSETS THAT ARE ENRICHED IN RESPONSE TO DIFFERENTIAL PHAGOCYTOSIS INDUCTION AGAINST GLIOMA

Pediatric diffuse midline gliomas (DMGs), are fatal brain tumors of childhood arising in the ventral pons. Currently, radiation therapy (RT) is the mainstay treatment for DIPG. However, RT is not a curative treatment and provides only temporary relief for most patients. Recent advances in immunotherapy have yielded some fantastic opportunities to effectively treat patients with high-grade pediatric brain tumors. In this study, we demonstrate that fractionated RT (4Gy X 3) induces immunogenic cell death and activates multiple damage-associated molecular patterns (DAMPs) on DMG/DIPG cells. Furthermore, combining 4Gy X 3 with anti-CD47 therapy enhances the in vitro phagocytosis of DIPG/DMG cells by peripheral blood mononuclear cell-derived macrophages. Next, using single-cell RNA sequencing (scRNA-seq), we investigated the transcriptomic profile of macrophages that were co-cultured with irradiated or non-irradiated DMG cells in the presence of either phosphate-buffered solution (PBS) or anti-CD47 monoclonal antibody for 24 hours. Our findings identified eleven distinct macrophage clusters displaying different gene expression patterns in all the treatment conditions. However, PBS treatment led to a marked increase in macrophages expressing antigen-presentation genes (HLA-DR and HLA-DQB1). 4Gy X 3 treatment led to the enrichment of macrophages expressing genes related to the oxidative phosphorylation pathway, whereas anti-CD47 treatment led to the enrichment of macrophages expressing genes related to interferon-gamma response and ERK-signaling pathway. Lastly, mice intracranially transplanted with DMG/DIPG that received 4Gy X 3 and anti-CD47 therapy showed a significant decrease in tumor growth and an increase in survival rate than those receiving either monotherapy alone. We are currently performing scRNA-seq validation studies on tumors obtained from orthotopic and syngeneic models of DMG. In summary, our results highlight the functional heterogeneity of macrophages and suggest that combining fractionated RT with anti-CD47 therapy has potent anti-tumor effects and may be used as a novel therapeutic approach for treating Glioma patients.

CTIM-32. FIRST-IN-CHILDREN PHASE 1 TRIAL OF INDOXIMOD-BASED CHEMO-IMMUNOTHERAPY FOR PATIENTS WITH PEDIATRIC BRAIN TUMORS: ANALYSIS OF SAFETY, TOLERABILITY, AND 5-YEAR OUTCOME

BACKGROUND

Recurrent brain tumors are the leading cause of cancer death in children. We conducted a first-in-children, two-institution, Phase 1 open-label dose-confirmation study using a 3 + 3 design, with expansion cohorts, to determine the recommended pediatric dose of the IDO pathway-inhibitor indoximod (NCT02502708). DESIGN/

METHODS

Eligible patients were 3-22 years old with either recurrent malignant brain tumor or newly-diagnosed diffuse intrinsic pontine glioma (DIPG). Palliative radiation, surgery or dexamethasone were allowed as needed for patient management. Separate dose-finding arms were performed for indoximod plus temozolomide (200 mg/m2/day orally for 5 days of each 28-day cycle) and for indoximod plus conformal radiation (in patients for whom re-irradiation was planned as standard-of-care). At progression, patients who were otherwise clinically stable were offered crossover to indoximod plus a second-line chemotherapy regimen (cyclophosphamide 2.5 mg/kg/day orally and etoposide 50 mg/m2/day orally for 21 days of each 28-day cycle).

RESULTS

Between December 2015 and January 2019, the study enrolled 81 brain tumor patients, including newly-diagnosed DIPG (n = 13) or recurrent ependymoma (n = 27), glioblastoma/high-grade glioma (n = 19), medulloblastoma (n = 13), or other CNS tumors ( n= 9). Median follow-up was 52 months (range 39-77 months). No dose-limiting toxicities were observed, and the pediatric indoximod dose was determined (19.2 mg/kg/dose, given twice daily). Indoximod was well tolerated and did not affect the ability to deliver chemotherapy or radiation as planned. Median overall survival was 13.6 months (n = 81). Median overall survival was 34.7 months for the subset of patients who continued indoximod with second-line chemotherapy after progression on indoximod plus temozolomide (n = 18).

CONCLUSIONS

Indoximod was well tolerated and could be combined with a variety of standard treatments for pediatric brain tumors. Preliminary anti-tumor activity and overall survival suggest that indoximod with standard therapy should be further evaluated in pediatric brain tumors, and potentially other pediatric solid tumors.

EPEN-01. Response assessment in pediatric intracranial ependymoma: recommendations from the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group

INTRODUCTION: Ependymomas remain a major cause of cancer-related death in childhood and adolescence, with recurrence occurring in up to 50% of patients. Despite exciting molecular advances in understanding ependymoma tumorigenesis and recurrence, MRI remains the mainstay for assessing objective response to therapy and duration of disease stability. Standardized response assessment criteria for clinical trials studying pediatric intracranial ependymoma are critically needed in order to accurately compare results between studies. METHODS: To generate these standardized response criteria in pediatric intracranial ependymoma, a multidisciplinary team of pediatric neuro-oncologists, neuroradiologists, neurosurgeons, radiation oncologists, and molecular biologists formed the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group. The expert members reviewed relevant published literature, assessed current clinical practices, and engaged in iterative discussions to provide consensus recommendations for objective response assessment in pediatric intracranial ependymoma for use in prospective clinical trials. RECOMMENDATIONS AND CONCLUSIONS: The primary sequences for detecting and measuring disease and assessing radiologic response to therapy should be the contrast-enhanced T1-weighted sequence or T2-weighted sequence (T2 or T2-FLAIR) depending on which sequence the tumor is best visualized. When metastatic disease is present, only the three largest lesions will be followed in addition to any residual disease at the primary tumor focus. Importantly, the RAPNO working group notes that radiologic response to therapy is of limited value in clinical trials of patients with ependymoma, since most patients enroll on clinical trials with either no evidence of disease or only minimal disease. In recurrent or progressive disease that cannot be resected, true radiologic disease response to therapy is less clinically meaningful as a study endpoint than event-free and/or overall survival (representing prolonged stable disease) but may provide a signal of efficacy worthy of future exploration in patients with complete to near complete resections.

ATRT-23. SIRT2 cooperates with SMARCB1 to induce a differentiation block in ATRT

Atypical Teratoid Rhabdoid Tumor is a highly aggressive pediatric brain tumor with poor prognosis driven by loss of the chromatin remodeling factor SMARCB1 that is responsible for determining cellular pluripotency and lineage commitment. The mechanisms by which SMARCB1 deletion results in tumorigenesis remain unclear. We investigated the effect of SIRT2 inhibition in ATRT which was identified as a primary dependency in ATRT. SIRT2 inhibition with shRNA or Thiomyristoyl (TM) decreased ATRT cell growth, inhibited clonogenic potential and leaded to the cell cycle arrest. SIRT2 inhibition effectively suppresses pluripotency-associated genomic programs, significantly changed stem cell frequency, decreased tumor-sphere formation of ATRT cells and attenuated tumor cell self-renewal. In vivo SIRT2 inhibition decreased oncogenic markers and increased accumulation neuronal differentiation markers. Furthermore, SIRT2 induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. Single-cell RNA transcriptome analysis of xenoftaft tumors reveals elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes following TM treatment in ATRT. We demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted ATRT.

NFB-22. Neurofibromatosis Therapeutics Program: Development of a Program

Neurofibromatosis (NF) therapeutics is a vital field in the care of children with NF. Recent developments in the treatment of plexiform neurofibromas (PN) have increased the numbers of patients seen for therapy. The Neurofibromatosis Therapeutics Program (NTP) provides high quality care to patients receiving therapy for brain tumors and PNs, as well as tumors related to NF2. The program at Children’s Hospital Colorado (CHCO) includes a physician, nurse practitioner, and nurse care coordinator. The team collaborates with other disciplines in the care of the NF patient with plexiform neurofibromas and/or CNS tumors. As the program grew, key players were identified in each subspecialty and educated about the NTP. We have ongoing regular communication with a large number of subspecialists regarding protocols, clinical care pathways, and mutual patients. In addition, an extensive tissue collection study of plexiform neurofibromas and brain tumors enhances NTPs devotion to both clinical and lab research. Weekly clinical care meetings ensure continuity in the care of the nearly 140 patients with NF1 and NF2 under our program. Monthly strategy and vision meetings focus on grant applications, education of primary care providers and subspecialists in our large catchment area, development of new clinical pathways, treatment roadmaps, and growth of our program. Over the last two years of being a formalized program, we have increased research on the epigenetics of plexiform neurofibromas, opened a Phase 2 clinical trial for a Mek inhibitor, and increased our patient volume. The Covid pandemic has increased our ability to manage treatment side effects virtually through telehealth and online patient portals. Future goals of the NTP include completion of a program website, quarterly patient and provider newsletters, educational offerings, collaboration with other centers on Mek inhibitor side effects, adolescent and young adult education on tumor risk, and transition to adult care.

HGG-12. Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy

BACKGROUND: Dynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. PTEFb-mediated promoter proximal pause-release of Pol II is a conserved regulatory mechanism for synchronous transcriptional induction best described in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy. DESIGN/METHOD: In order to examine the dynamics of chromatin reorganization following radiotherapy, we performed a combination of ChIP-, ATAC-, and RNA-seq in model systems of diffuse intrinsic pontine glioma (DIPG) and other pediatric high-grade gliomas (pHGG) following IR exposure. We interrogated IR-induced gene expression in the presence or absence of PTEFb blockade, including both mechanistic and functional consequences of concurrent inhibition or genetic depletion. We utilized culture models with live cell imaging to assess the therapeutic synergy of PTEFb inhibition with IR, as well as the therapeutic index of this intervention relative to normal controls. Finally, we employed orthotopic models of pHGG treated with conformal radiotherapy and CNS-penetrant PTEFb inhibitors in order to assess tolerability and anti-tumor effect in vivo. RESULTS: Rapid genome-wide redistribution of active chromatin features and PTEFb facilitates Pol II pause-release to drive nascent transcriptional induction within hours of exposure to therapeutic ionizing radiation. Concurrent inhibition of PTEFb imparts a transcription elongation defect, abrogating canonical adaptive programs such as DNA damage repair and cell cycle regulation. This combination demonstrates a potent, synergistic therapeutic potential agnostic of glioma subtype, leading to a marked induction of tumor cell apoptosis and prolongation of xenograft survival. CONCLUSION: These studies reveal a central role for PTEFb underpinning the early adaptive response to radiotherapy, opening new avenues for combinatorial treatment in these lethal malignancies.

EPEN-30. 5FU with Radiation Followed by Maintenance of 5FU and ATRA Significantly Improves Survival of 1q+/6q- PFA Ependymoma Xenograft Models

In a screen of over 100 FDA approved drugs on PFA 1q+ EPN cells, 5-fluorouracil (5FU) and All-Trans-Retinoic Acid (ATRA) were identified as inhibitors of EPN cell line growth. We performed in-vitro cell growth assays combining increasing doses of radiation and 5FU and found a significant synergistic effect on cell growth and apoptosis in 1q+ PFA EPN cell lines. Further growth attenuation was seen when ATRA was added 48 hours following radiation and 5FU treatment. This led us to development of preclinical studies in the 1q+ PFA orthotopic xenograft models MAF-811_XF and MAF-928_XF. In the initial cohort, tumors were allowed to establish prior to treatment start confirmed by MRI. In both MAF-811 and MAF-928, chemotherapy improved survival compared to no treatment. As consistent with standard of care, radiation significantly improved survival (p=0.0016) but there was no added benefit to combining 5FU or 5FU+ATRA with radiation. A second cohort was treated using the same treatment approach, however radiation and 5FU were started with minimal to no visible tumors by MRI. Interestingly, we found a significant increase in survival between vehicle control and combination 5FU+ATRA (HR 5.121, 95% CI: 0.2506, 2.409, p=0.048) in MAF-811 mice. However, again with radiation, there was no significant change in survival with only a single cycle of 5FU+ATRA. This led to continued maintenance of 5FU+ATRA cycles of 6 weeks with 2 weeks off for 4 cycles post radiation in mice with minimal tumor. When 5FU with radiation is followed by 5FU+ATRA and is continued in mice with minimal disease, survival significantly improved when compared to radiation alone (HR 9.020, 95% CI: 1.933 to 42.09, p=0.007). These studies highlight the importance of chemotherapy in minimal disease and is the rationale for a Phase I/II study in relapsed PFA EPN and in upfront 1q+ PFA EPN.

HGG-17. Novel Fusion in Congenital Brainstem Diffuse High-Grade Glioma

BACKGROUND: Infant-type hemispheric glioma, previously termed infantile glioblastoma multiforme, is a rare infantile neoplasm with improved survival and distinct molecular features when compared to other pediatric and adult-type high-grade glioma. Infant-type high-grade gliomas are typically located in the cerebral hemispheres and are characterized by ALK, ROS1, MET, and NTRK fusions. Typical brainstem gliomas (diffuse midline glioma, H3 K27-altered or diffuse intrinsic pontine glioma) are comparatively rare in this age group. As a result, the biology of brainstem congenital high-grade gliomas is poorly described. RESULTS: A 3 month old female who initially presented with failure to thrive had an apneic event and was found to have an infiltrative mass in the medulla with expansion into the pons and cervical spine on magnetic resonance imaging. She underwent surgical biopsy with pathology revealing diffuse high-grade glioma, WHO grade 4. Next generation sequencing showed no alterations to H3F3A, IDH, or fusions involving BRAF, ALK, ROS1, MET, or NTRK. Whole-transcriptome sequencing revealed a novel fusion of PDGFRB:APOBEC3C. She received chemotherapy with 2 cycles of carboplatin/etoposide and 2 cycles of carboplatin/etoposide/imatinib before having disease progression. She then underwent palliative radiation (35 Gy in 10 fractions) with near complete regression of her disease. Surprisingly, our patient has not had any progression of disease or new lesions now two years from her last therapy. CONCLUSION: Congenital high-grade glioma is a rare, unique entity that greatly differs from its adult and childhood counterparts. Here, we discuss a previously-unreported fusion of PDGFB:APOBEC3C in a patient with congenital brainstem diffuse high-grade glioma with a favorable clinical course. This highlights the importance of routine molecular characterization, both to better understand the complex biology of this rare disease and to guide prognosis and clinical decision making for individual patients and families.

MEDB-44. Transcriptomic resolution of subgroup-specific medulloblastoma architecture

Despite a growing understanding and stratification of medulloblastoma, it remains an aggressive childhood brain tumor with high morbidity and mortality. Multimodal genomic and epigenomic analysis has permitted the classification of medulloblastoma into four subgroups with varying biology and clinical behavior: WNT, Sonic-Hedgehog (SHH), Group 3, and Group 4. In our previously published work, Single-cell RNA sequencing (scRNAseq) identified distinct tumor cell subpopulations in specific medulloblastoma groups. However, this technology is limited by its lack of architectural information. Spatial transcriptomics is a relatively new technology that permits the analysis of gene expression as it occurs within organized tissue. In our ongoing study, we utilized Visium spatial transcriptomics, integrated with scRNAseq data and immunohistochemistry, to analyze frozen samples of medulloblastomas (SHH, Group 4, and Group 3 with and without MYC amplification). In SHH in particular, we were able to identify scRNAseq populations within the geographically constricted Visium data, including SHH-C2, a population located in histologic nodules, the predominant neuronal-differentiated population SHH-C1, and progenitor populations (SHH-B1 and B2). In addition, we were able to visualize clusters not detectable by scRNAseq – a cluster lining nodules with expression of vascular endothelium marker, reticulin and M2-macrophage genes, and a novel DNA-repair cluster. In addition, Visium data permits the spatial constraint of proliferating cells, which is frequently problematic in scRNAseq, as dividing cells cluster independently. The proliferation is highest in the SHH-B2 minor progenitor population, absent in the SHH-C1 major differentiated population, and is moderate in other population including the SHH-C2 nodules. Group 3 and 4 medulloblastoma are more complex but show preliminary corroboration with scRNAseq data. In summary, Visium allows us to map subpopulations identified by scRNAseq to tumor architecture more definitively and rapidly than IHC. These novel insights advance our understanding of medulloblastoma, a critical step in improving treatment options for children with this disease.

EPEN-29. Spatial transcriptomic analysis of ependymoma implicates unresolved wound healing as a driver of tumor progression

Ependymoma is a childhood brain tumor that remains incurable in approximately 50 percent of cases, most commonly in posterior fossa subgroup A (PFA). Uncovering how heterogeneous cell types within the tumor microenvironment (TME) interact is crucial to a complete understanding of PFA disease progression. The underlying cellular components of the PFA TME have been revealed by single-cell RNAseq (scRNAseq), identifying divergent epithelial differentiation and epithelial-mesenchymal transition (EMT) lineages. Here, we utilize spatial transcriptomics (Visium) of 14 PFA samples, integrated with scRNAseq, to chart neoplastic and immune cell architecture, with a higher resolution of cellular heterogeneity than scRNAseq alone. At a gross level, all PFA were primarily comprised of neoplastic epithelial and mesenchymal transcriptomic spatial zones, each containing a diversity of hierarchical cellular stages. In all samples we revealed spatially and transcriptomically-distinct mesenchymal zone-associated subclusters, including a quiescent undifferentiated progenitor-like subpopulation and clusters with characteristics of early and late stage EMT. Two early stage EMT clusters were distinguished by signatures of either myeloid cell interaction or hypoxia, and both were demonstrated to be EMT-initiating processes in in-vitro PFA experimental models. Myeloid cell interaction is the predominant initiating stage of EMT in PFA, occurring in zones that are spatially distinct from hypoxia induced EMT. Other mesenchymal clusters represent later EMT stages characterized by wound repair and tissue remodeling. Increased proliferation was a general characteristic of epithelial zone clusters, which included a second undifferentiated progenitor-like population that showed a particularly high mitotic rate and was associated with histologically hypercellular areas. Given the biological parallels with normal wound healing, we propose that mesenchymal and epithelial zones interact to create a cycle of persistent tissue damage response and mitogenic re-epithelialization signals. Unresolved wound repair is therefore a potential driver of PFA progression, a new concept that could provide novel targets for effective therapeutic intervention.

IMG-17. Advanced MRI On The Cellular and Vascular Phenotype of Mouse Ependymoma Models and Chemo-Radiation Treatment Response

Ependymoma (EPN) is an aggressive pediatric brain tumor, for which the benefits of chemotherapy in pediatric patients have not been defined. EPN treated with surgery and radiation recur in 23-66% of patients. Our group has previously established aggressive behaviors of EPN, including high tumor cellularity, cytological anaplasia, high mitotic index, tumor necrosis, and the presence of inflammatory cells such as M2-type myeloid cells. Here we report on an advanced 9.4 Tesla MRI protocol for characterizing the cellular and vascular phenotype and treatment response to chemo-radiation therapy (CRT) in an orthotopic mouse model of patient derived xenografts (PDX) of pediatric EPN . Female severely immune deficient (SCID) mice were used for intracranial inoculation of disaggregated tumors from pediatric EPN patients (n=22). High-resolution T2w-MRI was able to detect cerebellar microlesions as small as 0.2 mm diameter; the median tumor volumes at the baseline were 21±12 mm3. Using diffusion-weighted based cell-size imaging, iron-oxide based vessel-size imaging and quantitative T2-maps, the EPN-specific phenotype was characterized by an increased cell size (S=14 microns), increased vessel density index (Q=0.54), and low ADC values (0.63x10-3). Once the intracranial tumors reached at least 5 mm3, animals were treated with CRT (10 Gy radiation plus 30 mg/kg 5-fluorouracil, n=6). CRT resulted in a tumor shrinkage, tumor necrosis with decreased cell sizes and increased ADC values, and a dramatic vascular-inflammatory response (decreased Q and DT2 values with the injection of iron oxide nanoparticles as macrophage-specific contrast). In summary, orthotopically implanted PDX EPN in mice closely mimic histological features, anatomical location and radiological features of the primary tumors. A significant decrease in vessel size density and an increase in inflammatory cells were seen as soon as 2 days after CRT. The late response (2 weeks post CRT) is characterized by decreased cellularity, cell size, and tumor volumes.

LGG-42. Thromboembolic toxicity observed with concurrent trametinib and lenalidomide therapy

INTRODUCTION: Event-free survival of pediatric low-grade glioma (pLGG) is poor, and patients often require multiple treatment strategies. The hallmark of pLGGs are genetic aberrations of the mitogen-activated protein kinase pathway, which lead to constitutive pathway activation. MEK and RAF inhibitors target this pathway and are efficacious in early phase trials in recurrent pLGGs. However, not all patients respond to monotherapy, and many experience progression after completion of therapy. Evaluating combination therapies that may enhance efficacy or prolong disease stabilization is warranted. Lenalidomide is an immunomodulatory agent with an anti-tumor effect demonstrated in phase 1 trials in recurrent pediatric central nervous system (CNS) tumors. OBJECTIVE: To describe our institutional experience using concurrent trametinib and lenalidomide in the treatment of primary pediatric central and peripheral nervous system (PNS) tumors. METHODS: Retrospective review of patients’ medical records. RESULTS: Four patients with locally recurrent primary CNS or PNS tumors, three with WHO grade II pilomyxoid astrocytomas and one with a plexiform neurofibroma, were treated with trametinib and lenalidomide concurrently. Two patients developed severe thromboembolic events. One patient was treated with combination therapy for seven months until trametinib and lenalidomide were held after urgent ventriculoperitoneal shunt revision. Shortly following shunt revision, he experienced near-complete vision loss. MRI of the brain demonstrated a left posterior watershed territory hypoxic-ischemic injury. In a second patient, after four months of combination therapy, surveillance echocardiogram showed an incidental finding of severe biventricular dysfunction with a left ventricular ejection fraction (LVEF) of 17.7% and two mural thrombi in the left ventricular apex. She started losartan and enoxaparin and discontinued trametinib and lenalidomide. Her LVEF normalized four months later, and the mural thrombi resolved. CONCLUSIONS: Given the severe thromboembolic events experienced by these patients treated with concomitant trametinib and lenalidomide, this combination requires further investigation, and we urge caution if used concurrently.

NFB-18. Integration of single-nuclei RNA-sequencing and spatial transcriptomics to define the complex tumor microenvironment of NF1-associated plexiform neurofibroma and highly-aggressive malignant peripheral nerve sheath tumors

During formation of plexiform neurofibroma (PN), a complex tumor microenvironment (TME) develops, with recruitment of other cell types being critical for growth and progression. Approximately 10% of PN can undergo transformation into malignant peripheral nerve sheath tumors (MPNST) which is a substantial cause of mortality in older teenagers and young adults. We sought to apply single cell transcriptomic analysis to PN and MPNST to provide a clearer understanding of the complex TME and how this contributes to transformation and disease progression. Due to the cohesive cellularity of PN, single-cell RNA-sequencing is difficult and may result in a loss of detection of critical cellular subpopulations. Single-nuclei RNA-sequencing (snRNA-seq) is an alternative approach that can be applied to fibrous and bulk frozen tissues, such as NF1-associated PN. Our initial snRNA-seq analysis of PN indicates that PN have a TME comprised of a variety of cellular subpopulations, with the predominant fraction being fibroblast-like cells. snRNA-seq analysis of MPNST also shows high cellular heterogeneity, including distinct fibroblast-like subpopulations distinct from PN fibroblast clusters, increased proliferating populations and antigen presenting cells. MPNST cluster separately from PN, suggesting an evolutionary shift in tumor biology. We are currently validating our findings using Visium spatial transcriptomic profiling, allowing us to apply TME architectural context to the PN and MPNST subpopulations identified by snRNA-seq. These techniques provide a deeper understanding of the complex cellular heterogeneity of human PN and MPNST that has not previously been used to describe the TME of these tumors. The mechanisms of tumorigenesis and malignancy described can provide targets for novel therapies ultimately benefitting patients with these devastating tumors of childhood and early adulthood.

RONC-05. Peri-transplant Radiation Therapy for Young Children Treated with High-Dose Chemotherapy for Primary Brain Tumors

PURPOSE: The role of peri-transplant radiation therapy (RT) in young children with primary brain tumors is unclear. We characterized our institutional practice patterns and patient outcomes. MATERIALS AND METHODS: The cohort included all patients treated with high-dose chemotherapy for primary brain tumors at our institution from 2011-2017. Rates of local control (LC), progression-free survival (PFS), overall survival (OS), and radiation-associated injury were assessed. RESULTS: Of 37 eligible patients, 29 (78%) received peri-transplant RT at a median age of 4 years. Patients treated with RT were more likely to have metastatic (p=0.0121) and incompletely resected (p=0.056) disease, and to have high-risk histologies including atypical teratoid rhabdoid tumor, nongerminomatous germ cell tumor, pineoblastoma, primitive neuro-ectodermal tumor, glioneuronal tumor and group 3 medulloblastoma. Of those treated with RT, 13 (45%) received craniospinal irradiation (CSI) and 16 (55%) received focal RT. The median CSI dose was 23.4 Gy (IQR: 18-36; boost median 54 Gy [IQR: 53.7-55.8]) and focal RT dose was 50.4 Gy (IQR: 50.4-54.5). Compared to the focal RT group, patients treated with CSI were older (p=0.0499) and more likely to have metastatic disease (p=0.0004). For the complete cohort, at a median follow-up of 3.8 years, the 2-year rate of LC was 82% (95% CI: 70-96%), PFS was 63% (95% CI: 49-81%), and OS was 65% (95% CI: 51-82%). These rates did not differ significantly between patients treated with and without peri-transplant RT. Two cases of fatal myelopathy were observed after spinal cord doses within the highest tertile (41.4 CGE and 36 Gy); both cases occurred in patients who received RT before high-dose chemotherapy. CONCLUSION: Peri-transplant RT was used for high-risk disease. Oncologic outcomes after RT were encouraging. However, 2 cases of grade 5 myelopathy were observed. If used cautiously, RT may contribute to durable remission in patients at high risk of relapse.

NFB-14. Post-operative use of MEK inhibitors to prevent rebound growth following partial resection of plexiform neurofibromas

BACKGROUND: Plexiform neurofibromas (PNs) can cause significant morbidity leading to functional impairment, pain, and disfigurement. Management of PNs is challenging. Complete surgical resection is often not possible due to tumor growth along vital structures, and rebound growth is frequently experienced with partially resected PNs. The mitogen-activated protein kinase pathway has been implicated in the growth of PNs, and MEK1/2 inhibitors have been shown to be an effective treatment of PNs. OBJECTIVE: To describe our institutional experience using post-operative MEK1/2 inhibitors in the treatment of pediatric patients with PNs following subtotal resection (STR). METHODS: A single-institution retrospective record review. RESULTS: A total of 35 patients had STR of their PN. Fourteen patients underwent resection alone, ten patients received adjuvant mechanistic target of rapamycin (mTOR) inhibitors and eleven patients received adjuvant MEK1/2 inhibitors. The mean follow-up time was 5.1 years, but relatively shorter for patients receiving adjuvant MEK1/2 inhibitors. Mean time from resection to start of adjuvant therapy and mean duration of adjuvant therapy for patients in the mTOR inhibitor group was 3.3 weeks and 3.9 months, respectively, and for patients in the MEK1/2 inhibitor group was 3.1 weeks and 8.5 months, respectively. The number of patients in each group requiring additional treatment with surgical resection or medical therapy, was 11 of 14 patients (78.6%) in the resection only group, 7 of 10 patients (70%) in the adjuvant mTOR inhibitor group and 3 of 11 patients (27.3%) in the adjuvant MEK1/2 inhibitor group. CONCLUSIONS: A short course of MEK1/2 inhibitors following subtotal resection of PNs is effective in the short term in preventing rebound growth when compared to STR alone or adjuvant mTOR inhibitors. Treatment is well tolerated and should be considered as adjuvant therapy in pediatric patients. Long-term follow-up is necessary to judge the effectiveness of this approach.

EPEN-11. Phase 0/I Study of GM-CSF and Intrathecal Trastuzumab In Children With Recurrent Posterior Fossa Ependymoma

BACKGROUND: Posterior fossa ependymoma (PF EPN) is a pediatric central nervous system malignancy that has a poor outcome to standard therapeutic approaches. The majority of PF EPN have been shown to harbor increased HER2 expression, making it a logical therapeutic target. Trastuzumab is a monoclonal antibody that targets HER2, and sargramostim (GM-CSF) stimulates hematopoietic progenitor cell proliferation. The combination of trastuzumab and GM-CSF has been shown to trigger antibody-dependent cell cytotoxicity in-vitro in patient-derived PF EPN cell lines. METHODS: Children aged 1–21 years with relapsed PF EPN, no ventriculoperitoneal shunt, and no CSF obstruction are eligible for the Phase 0/I single-institution clinical trial at Children’s Hospital Colorado. Stratum 1 involves intrathecal (IT) trastuzumab and subcutaneous (subQ) GM-CSF prior to standard-of-care surgical resection. Stratum 2 involves a 3 + 3 phase I design with serial IT trastuzumab doses, each preceded by three days of GM-CSF, to establish the maximum tolerated dose for IT trastuzumab. RESULTS: Trastuzumab was detected in a sufficient number of tumors after presurgical IT delivery in Stratum 1 to open Stratum 2. Seven patients (3 female) have been enrolled in Stratum 2. Median age at enrollment is 8.1 years (range, 3–20 years). CSF pharmacokinetic analysis demonstrate detectable trastuzumab up to 14 days after IT doses. No dose-limiting toxicities or grade 3 or 4 adverse events have occurred. Four patients completed all planned study therapy and remain progression-free post-therapy (median, 23 months, range, 6-42 months). Three patients progressed on therapy (median, 4 cycles). Biologic correlative studies are in process. CONCLUSIONS: IT trastuzumab penetrates PF EPN tumor tissue and demonstrates an excellent safety profile. Stratum 2 remains open to accrual at Dose Level 2. IT trastuzumab+GM-CSF warrants consideration for a multi-institutional Phase II trial.

MODL-26. Development of humanized immune system, posterior fossa A ependymoma patient-derived xenograft model

Cellular interactions between tumor and immune cells are critical in ependymoma biology. We have shown distinct immunobiology phenotypes by ependymoma molecular subgroups, with PFA2 developing an anti-tumor immune phenotype and in contrast PFA1 tumor immune cells being pro-tumor. We recently established two fully characterized pediatric PFA1 intracranial xenograft models in NSG mice. These models, while critical for advancing PFA studies, lack the ability to make lymphocytes. To address this we have established a humanized orthotopic model of PFA1 ependymoma that are grafted to produce functional human lymphocytes. To do this, CD34+ human umbilical cord blood was injected into the cranial facial vein of newborn, irradiation immunodepleted, BRGS mice. Human immune chimerism was determined at 10 weeks by flow cytometry of peripheral blood. Next, we injected existing PDX model MAF-928_XF cells into the 4th ventricle at 12 weeks age and tumors were monitored by MRI. Initial scanning found the tumors were delayed in developing, consistent with other humanized solid tumor mouse models. Mice were euthanized between 32-34 weeks age and necropsies were performed to isolate brain, lymph nodes, blood and spleen. Human chimerism was detectable, by flow cytometry, in spleen, lymph nodes and blood, and most cells were T-cells. Human T-cells were detectable in all tumors, in proportions consistent with human disease (0.05-0.5% of CD45+). Tumors also had 35-50% mouse myeloid infiltration. Tumors were MHC I negative and MHC II positive, and PD-L1 low. Histology was consistent with human ependymoma. We are using spatial proteomics to determine cellular location and phenotype of infiltrating immune cells. Initial studies indicate this model will be usable for modeling the critical tumor-immune interactions and pre-clinically testing the next therapies in PFA ependymoma and can be easily adapted to other pediatric brain tumors in which immune factors have a critical role.

EPEN-12. Sunitinib induces apoptosis-mediated cytotoxicity in PFA ependymoma

Ependymoma (EPN) has been previously shown to be selectively targeted by three classes of FDA-approved chemotherapy drugs: fluorinated pyrimidines, retinoids, and a subset of small molecule receptor tyrosine kinase inhibitors (RTKIs). We have identified sunitinib malate as an RTKI with ependymoma selectivity, in addition to previously identified ependymoma-selective RTKIs axitinib, imatinib, and pazopanib. Sunitinib—which targets VEGFR, PDGFR and c-kit—elicited unexpectedly high levels of cytotoxic apoptosis (caspase 3/7 cleavage) in EPN PFA cell lines harboring high-risk chromosome 1q gain and 6q loss. In this in-vitro screen of 100+ FDA-approved chemotherapy drugs, sunitinib was the only RTKI in the top five most cytotoxic drugs, a group that included idarubicin HCl, topotecan HCl, daunorubicin HCl, and doxorubicin. Additionally, sunitinib exhibited comparable caspase 3/7 cleavage levels in normoxia and hypoxia, suggesting that this therapy would be as effective in treatment of tumors with potentially resistant hypoxic necrotic cores. The effect of sunitinib on EPN cellular proliferation was tracked visually using Incucyte cell imaging technology, demonstrating consistent dose-dependent inhibition of proliferation. Sunitinib achieved more acute upregulation of apoptosis than axitinib, an EPN-selective RTKI currently being studied in preclinical models. A prior phase II trial of sunitinib in pediatric EPN and high-grade glioma showed that treatment was well tolerated but with no clinical benefit as a monotherapy. However, given encouraging clinical results of combining sunitinib with radiation, our ongoing preclinical studies of sunitinib in EPN are being conducted in the context of radiation which is standard treatment for EPN. Sunitinib presents a promising treatment to an intractable pediatric brain tumor that exhibits high rates of relapse and morbidity in affected individuals.

EPEN-16. Epithelial Progenitor Cell Abundance and Copy Number Variant Gains and Losses Impact the Biology of Recurrent Ependymoma

Ependymoma (EPN) is a common pediatric brain tumor that is fatal in approximately 50% of cases. Posterior fossa A (PFA) EPN has the highest rate of recurrence and the worst prognosis of all EPN subtypes. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent ependymoma remains largely unknown, which hinders clinical advances. In this study, we use paired samples of primary and recurrent disease from the same patient to investigate the drivers of recurrence. DNA methylation studies reveal frequent copy number variants at recurrence that were not present at primary presentation. We report a frequent gain of chromosome 1q and loss of 6p at recurrence, which has not been previously reported and may be a driver of recurrent disease. We have previously shown that PFA EPN is comprised of 4 main neoplastic cell populations, two well-differentiated populations termed ciliated and transportive ependymal cells, a mesenchymal cell population, and an undifferentiated population. Using spatial transcriptomics (Visium) integrated with single-nuclei RNA-seq (Chromium), we discovered that a highly proliferative EPN progenitor population of epithelial lineage is significantly upregulated at recurrence which we hypothesize drives refractory disease. Accordingly, we found higher expression of EPN progenitor gene signatures in bulk RNA transcriptomes of primary tumors that later recurred compared to tumors that never recurred. Together, these findings highlight the biologic differences between primary and recurrent disease and add to our understanding of treatment resistance in childhood ependymoma.

SWK-10. Survivorship: Education, Clinical Guidelines, and Transition to Adult Care

As the cure rates of patients with pediatric brain tumors increases, the long term care needs of the survivors increase as well. Survivorship includes several facets of multidisciplinary care including education, clinical care guidelines, and transition to adult medical care. The neuro-oncology program at a large tertiary care hospital has developed a team to address survivorship needs. The Children’s Oncology Group (COG) Long-Term Follow-Up Guidelines for Survivors of Childhood, Adolescent, and Young Adult Cancers was utilized as a backbone that was then customized for neuro-oncology patient education including disease type and treatment. The education was compiled into patient handouts as well as electronic medical record (EMR) statements that can easily be added to a clinic note or letter to referring providers. In addition, a diagnosis and treatment summary was placed both in the EMR as well as given to patients at various time points to ensure long term knowledge. Next, follow-up guidelines and roadmaps were developed and customized to tumor type and treatment received (surgery, radiation, chemotherapy). The roadmaps ensure patients are receiving high-quality comprehensive follow-up and screening from a large multidisciplinary team. Finally, patients will transition to adult care. With a large seven state catchment area, the adult care providers vary on local provider availability, knowledge, and medical complexity of the survivor. Each patient is evaluated based on their needs, availability of care locally, and ability to travel. The team developed relationships with the clinical team at the academic center adjacent to the pediatric hospital to support a smooth transition to adult care. The adult neuro-oncology care team can also serve as a consulting service for local adult providers. The survivorship team will continue to address the complex needs of brain tumor survivors and provide education for a smooth transition to adult care.

MEDB-28. CDK9 is a druggable mediator sustaining Myc-driven circuitry in medulloblastoma

BACKGROUND: Though long recognized as a master regulator of cell proliferation across a wide range of cancers, Myc has proven elusive to direct therapeutic targeting. The CDK9-containing PTEFb, complexed with either BRD4 or SEC, facilitates Myc-driven transcriptional programs and is necessary for sustaining expression of Myc itself. Advances in development of clinical-grade CDK9 inhibitors creates an opportunity to examine this as a rational therapy for Myc-driven medulloblastoma. METHODS: We used both RNAi depletion and a panel of pharmacologic agents to characterize the mechanistic and functional consequences of CDK9 inhibition in Myc-driven medulloblastoma. We used a combination of clonogenic assays and live cell imaging to assess the cytotoxic effects of CDK9 activity loss. We then performed a combination of CUT&RUN and RNA-seq to evaluate alterations to Myc binding and downstream Myc-driven transcriptional programs. Finally, we employed orthotopic xenograft models of medulloblastoma to assess CNS penetration, tolerability, and anti-tumor efficacy of lead CDK9i candidate compounds. RESULTS: Genetic or pharmacologic inhibition of CDK9 leads to a loss of Myc expression and downregulation of hallmark Myc-driven transcriptional programs. This corresponds to a loss of cell fitness, as measured by decreased proliferation and clonogenic potential. Clinically relevant CDK9 inhibitors show variable efficacy in vivo, but the CNS-penetrant zotiraciclib achieved a significant prolongation in xenograft survival. CONCLUSION: CDK9 catalytic activity represents a druggable vulnerability underpinning Myc-driven transcriptional programs. The development of CNS-penetrant CDK9 inhibitors may open new avenues for rational therapy in these high-risk medulloblastomas.

IMMU-10. TUMOR ASSOCIATED MYELOID CELLS DRIVE THE IMMUNOBIOLOGY OF HIGH RISK PEDIATRIC EPENDYMOMA

Molecular profiling of pediatric ependymoma (EPN) has previously identified discrete neoplastic subpopulations, of which Mesenchymal EPN Cells (MEC) characterize Posterior Fossa A tumors (PFA). MECs are associated with tumor immunosuppression. Here we further characterize the EPN immune environment using single-cell sequencing, spatial phenotyping and cytokine analyses to better define infiltrating myeloid subpopulations. We hypothesize that neoplastic and myeloid cells interact to propagate an immune suppressive environment conferring resistance to traditional therapies. We delineated myeloid cell subpopulations from single-cell RNA-seq of 26 pediatric EPNs and validated them through deconvolution of bulk gene expression profiling (n=299). To define subpopulation spatial distribution, we interrogated a range of tumor and myeloid markers using multiplex immunofluorescence (mIF). Finally, using single-cell cytokine analyses, we gained further insight into myeloid subpopulation function. Eight distinct myeloid subpopulations were identified, relating to macrophages, microglia and monocytes. A subpopulation of cells with wound healing ontologies and characterized by TREM1 expression, demonstrated features of myeloid derived suppressor cells, including IL6/STAT3 pathway activation. We called these hypoxia-M. Like MEC neoplastic cells, hypoxia-M was associated specifically with PFA1 subgroup EPN in both single-cell and bulk tumor gene expression profiling (p<0.001). Additionally, the presence of MEC and hypoxia-M correlated strongly in gene expression (r2=0.92, p<0.001) and IHC analyses, where they co-located to borders between necrosis, blood vessels and viable tumor. Analysis using mIF (n=54) confirmed MEC/hypoxia-M co-location and highlighted that all types of immune cell corralled in significant numbers around areas of vasculature and necrosis. Single cell cytokine analyses demonstrated that hypoxia-M secrete IL-8 which, we hypothesize, amplify the pro-tumor phenotype in PFA1 tumor microenvironment. EPN is characterized by discrete myeloid cell subpopulations which contribute to the tumor microenvironment. Treatment strategies must focus on modifying this pro-tumor, immunosuppressive microenvironment to deliver more effective treatment for childhood ependymoma.

ATRT-10. Single-cell transcriptional profiling of ATRTs reveals heterogeneous signatures of tumor and non-malignant cell populations

Atypical Teratoid/Rhabdoid Tumors (ATRTs) are known for exhibiting high inter-tumor heterogeneity, even though they are almost all characterized by a common loss of SMARCB1 (or rarely SMARCA4). Three subgroups have been identified at bulk methylome and transcriptome level: ATRT-TYR, ATRT-SHH, and ATRT-MYC. To better understand the biology underlying each subgroup and potentially unveil their (different) cell(s) of origin, we performed single-cell transcriptomic analyses in 22 ATRTs using fresh frozen samples and both 10X and Smartseq technology. All data, grouped by technology, underwent quality control and normalization, regressing out the biases introduced by each sample. Tumor microenvironment (TME) and tumor bulk (TB) clusters were characterized by a combination of copy number variant analyses, enrichment in literature lists of marker genes for specific cell populations, and in-depth analysis of differentially enriched (DE) genes. Non-negative Matrix Factorization (NMF) was applied to TB to reveal major transcriptional profiles, which were grouped into meta-signatures. A total of 71 gene lists were retrieved from NMF (TB) and DE analyses (TME + TB), that gathered into 11 signature groups by Jaccard similarity, with one extra group accounting for unique signatures. Three groups targeted TME, accounting for either microglia, fibroblasts and endothelial cells, or OPCs, oligodendrocytes, astrocytes and neurons. These signatures are enriched in specific clusters across technologies. The remaining eight groups divide into two types, either enriched in clusters predominantly formed by cells of one or two ATRT subgroups or signatures enriched for a particular phenotype, such as cilial, cycling, axonogenesis or EM transition. While the first type is enriched across clusters in a gradient fashion, the second shows enrichment for selected clusters across technologies. Further analyses on the integrated dataset and additional samples are ongoing to validate and refine these 11 signature groups in ATRTs to see how this may lead to new treatment approaches.