Brain tumors are the most common solid tumor in children and the leading cause of cancer-related deaths. Over the last few years, improvements have been made in the diagnosis and treatment of children with Central Nervous System tumors. Unfortunately, for many patients with high-grade tumors, the overall prognosis remains poor. Lower survival rates are partly attributed to the lack of efficacious therapies. The advent and success of immune checkpoint inhibitors (ICIs) in adults have sparked interest in investigating the utility of these therapies alone or in combination with other drug treatments in pediatric patients. However, to achieve improved clinical outcomes, the establishment and selection of relevant and robust preclinical pediatric high-grade brain tumor models is imperative. Here, we review the information that influenced our model selection as we embarked on an international collaborative study to test ICIs in combination with epigenetic modifying agents to enhance adaptive immunity to treat pediatric brain tumors. We also share challenges that we faced and potential solutions.

A, Representative IHC images of BMI-1 staining in DIPG patient tumors and their matched normal tissue. Images are different areas of the same section.

A, Soft agar assay of an additional cell line, CCHMC-DIPG-1, to assess sensitization to IR when treated with PTC596 and its respective quantification. Error bars represent the SD from two independent experiments run in triplicate. B, Relative cell growth calculated by WST-1 assay at Day 7 used to calculate the CI values in figure 4C. Three independent experiments were performed and data from one experiment is shown as a representative result. Error bars represent the SD from triplicates.

B, tSNE plot of scRNAseq data from the Filbin-Cohort representing correlations between different samples and C, relative BMI-1 expression. D, Correlation of Bmi-1 expression and stemness score in murine DIPG tumor and control brain stem.

Immunoblot analysis of BMI-1 and H2AK119Ub after treatment of DIPG cells with PTC596 and EPZ011989 at Days 6 and 8 as represented in figure 5D.

A, Scheme representing the experiment design of PTC596 treatment, drug wash-off and time points to evaluate PTC596 activity by immunoblot analysis of BMI-1, H2AK119Ub (Day 4) and cell growth by WST-1 assay (Days 8 and 11) in HFF, CCHMC-DIPG-1 and CCHMC-DIPG-2 cells. β-actin and total H2A served as loading control. Error bars represent the SD from triplicates.

Abstract Immunotherapy has emerged as groundbreaking in cancer treatment showing improved overall survival of patients with advanced cancers. However, its application for diffuse midline glioma (DMG) is still challenging due to the non-inflammatory immune environment with lack of T lymphocyte infiltration, low mutation burden associated with low or absence of neo-antigen expression and suppressive immune microenvironment in DMG. Therefore, determination of novel factors that not only trigger the immune response but also evading the tumor immunosuppression is imperative. The cGAS-STING pathway was shown to elicit the maturation and activation of dendritic cells (DCs) in response to the release of double stranded DNA (dsDNA) from tumor cells leading to effective cytotoxic T-cell infiltration and activity. Here, we aimed to determine the effects of a small molecule PTC596 (BMI-1 modulator and tubulin biding molecule) in cGAS-STING pathway activation and induction of antitumor immunity. We have previously reported the single agent efficacy for PTC596 in controlling tumor growth and improving survival compared to vehicle-treated mice. Our preliminary results using PTC596, indicate the presence of multinucleated cells and the formation of micronuclei, colocalizing with cGAS and induction of STAT1 activation (marker of inflammation through type 1 IFN). We are currently evaluating purified DCs post-PTC596 treatment for the activation of the cGAS-STING pathway and interferon-stimulated genes (ISGs) and determining their cross-priming capacity. In vivo, using our established syngeneic orthotopic DIPG models, we are evaluating the T cell infiltration (CD3, CD4 and CD8), and characterizing the tumor microenvironment in response to PTC596. Data collected from the above experiments will be presented and discussed.

E, Representative IF-FISH images of metaphase spreads with centromere probe (red) and γH2AX (green) in CCHMC-DIPG-1 and SU-DIPG-IV cells treated with PTC596 (60 nM and 30 nM respectively) for 48 hrs. DAPI (blue) indicates chromosomes. White arrowheads indicate chromosomes with PSCS.

Abstract Diffuse intrinsic pontine glioma (DIPG) is one of the most aggressive tumors of the central nervous system in children. Radiotherapy remains the only standard treatment but is rarely curative. In recent years, several immunotherapy strategies have emerged as an option to treat DIPG. However, the low mutational burden and rare infiltration of T lymphocytes, render these tumors immunologically “cold” and therefore pose challenges for general immunotherapy. We have previously reported in pediatric brain tumors the preclinical validation of THIO (6-thio-2’-deoxyguanosine), a telomerase substrate precursor analog. Treatment of cancer cells with THIO caused both telomeric and genomic DNA damage and rapid cell death. In vivo treatment delayed tumor growth in mouse models of high-risk medulloblastoma and DIPG. Importantly, THIO crosses the blood-brain barrier and specifically targets tumor cells in an orthotopic mouse model of DIPG. The cGAS-STING pathway is a cellular mechanism that senses cytosolic double stranded DNA, stimulating type I interferons (IFNs) and IFN-stimulated genes, thereby activating the innate and adaptive anti-tumor immune responses. Micronuclei resulting from cell division in the presence of unresolved DNA damage, has been shown to be recognized by the cGAS-STING pathway. THIO was shown to induce anti-tumor immunity through micronuclei formation in colon and lung tumor models. We hypothesized that THIO treatment will activate anti-tumor immunity in DIPG. Our results indicate that THIO treatment sensitized DIPG cells to ionizing radiation (IR) leading to a significant decrease in DIPG cell proliferation. We are currently testing this combination in vivo in an orthotopic mouse model of DIPG. We will present results on the potential of THIO to activate anti-tumor immunity through the activation of Sting pathway in a syngeneic mouse model of DIPG. These preclinical studies will support potential use of THIO in combination with IR to treat children with high-risk pediatric brain tumors.

Survival probability of mice post-drug withdrawal starting from drug holiday. P values are indicated, *p<0.05.

Abstract Despite recent therapeutic advancements in the treatment of pediatric brain tumors, high-risk brain tumors (pHRBT) remain the leading cause of cancer-related deaths in children. In recent years, immunotherapy has become a viable treatment option for several cancers including brain tumors. However, several factors have limited the use of immunotherapy in the treatment of pHRBT. For example, an "immunologically cold" tumor environment has been predominantly implicated in the failure of checkpoint inhibitors (ICIs) as monotherapy in pHRBT. Nevertheless, priming the effects of ICIs with epigenetic modulators through a process called “viral mimicry” that induces the expression of human endogenous retroviruses has the potential to enhance immunotherapy by sparking a T-cell mediated immune response. However, the inadequate understanding of the limitations of the preclinical models has prevented the development of efficient immunotherapy strategies for pHRBT. Although several studies and reviews have compiled some limitations of the available models, a hands-on experience using preclinical models for ICIs testing has not been fully communicated. Here, we share our bedside to bench experience with syngeneic and humanized mouse models of DIPG, ATRT, and medulloblastoma using ICIs therapy in conjunction with an epigenetic alteration. We will present and discuss the limitations of mouse models for the development of immunotherapies for pHRBT. For instance, our results indicated that the baseline levels of MHC-I expression in patients’ DIPG tumors were comparable to matched normal tissue. However, these levels were significantly lower in mouse DIPG tumors. To compensate for this difference, we treated mice with IFN-γ in combination with an epigenetic modulator. Surprisingly, the addition of INF-γ had a negative effect on animal overall survival compared to the treatment with the epigenetic modulator alone. Together, our experience demonstrated the importance of suitability assessment of current models for developing and translating successful immunotherapy strategies to treat pHRBT.

Diffuse intrinsic pontine glioma (DIPG) remains an incurable disease with median overall survival <12 months despite decades of clinical trials investigating multimodal therapies. Immunotherapy represents a promising treatment paradigm which has been successfully used in other cancers. An adequate understanding of the tumor microenvironment and immunologic profile is essential to identify potential immunotherapeutic targets to inform immunotherapy design. Previous studies have shown that most DIPG tumors harbor low mutational burden compared to adult cancers and are characterized by a non-inflammatory microenvironment, limiting the development of immunotherapies in this disease. Our team’s prior work similarly demonstrated that most DIPG tumors have an immunologically “cold” microenvironment, but a subset of tumors harbors a more inflammatory gene expression profile and/or higher mutational burden, with trends toward improved survival and favorable radiographic response to radiation. Here, we applied a deconvolution analysis using CIBERSORTx on bulk RNA-seq data from 28 DIPG patients’ tumors paired with matched normal tissue specimens, to profile the immune microenvironment of DIPG and evaluate immune-related gene expression to determine percentages of different types of immune cells. Our results indicate that DIPGs have very limited lymphocyte infiltration. However, the infiltration of macrophages “M2-like” type cells and CD4 memory resting T cells were significantly higher in tumors compared to normal tissue samples. Similar results were found using single-cell RNA sequencing performed on biopsy and autopsy tissue, with less than 5% of total cells identified as immune cells. MHC I components were widely expressed in DIPGs with no significant difference between tumor and normal tissue. Expression of CD11B and CD68 were higher in tumor compared to normal tissue, suggesting enrichment of myeloid cells. Overall, deconvolution analysis of bulk RNA-seq can be used to profile DIPG tumors’ immune microenvironment to aid in the thoughtful design of effective immunotherapeutic strategies for this disease.

Abstract Diffuse intrinsic pontine glioma (DIPG) is an aggressive and incurable disease of the central nervous system in children with median overall survival of less than one year. In recent years, several immunotherapy strategies have emerged as an option to treat DIPG. However, the low mutational burden and rare infiltration of T lymphocytes, render these tumors immunologically “cold” and therefore pose challenges for general immunotherapy. The myeloid component was implicated in the immunosuppression in other solid tumors. Previous data have shown that DIPG tumors are enriched in macrophages, but their role in tumor growth and progression have not been elucidated. Specifically, it remains unclear whether the myeloid cells are recruited to the tumor microenvironment from the peripheral circulation. Here, we examined the recruitment of myeloid cell populations to the tumor microenvironment and further delineated their role in tumor progression in a syngeneic mouse model of DIPG. We showed that this DIPG mouse model displays an immune microenvironment similar to that of patients’ DIPGs. DIPG tumors harbored rare tumor infiltrating lymphocytes and are enriched in myeloid cells. To further characterize the phenotype and functions of these myeloid populations, we evaluated the changes in proportions of myeloid cell subsets using flow cytometry (CD11b, Ly6c, Ly6G, MHCII, F4/80, CD206, Arg1) in the bone marrow, peripheral blood, and in the tumor microenvironment during tumor progression. Also, we investigated the role of these myeloid cells in angiogenesis and immune suppression by performing histological and expression analyses of endothelial markers and chemokines (CD31, CD34, KDR, IL-10, IL-13, IL-4, CCL2, CCL5). Furthermore, decitabine (DNA methyltransferase inhibitor) treated tumors showed a decrease in myeloid population associated with a reduction in tumor growth, suggesting an important role of myeloid populations in tumor growth and progression.

Abstract Diffuse intrinsic pontine gliomas (DIPGs) are the most aggressive tumors of the central nervous system in children. Median survival of patients is less than one year post-diagnosis. Radiotherapy remains the only standard treatment but is rarely curative. Immunotherapy is an emerging and promising treatment strategy for children with DIPG. However, general immunotherapy has not lived up to its promise to treat many cancers, including DIPGs, in part due to incomplete understanding of the barriers posed by the tumor microenvironment. We therefore evaluated the immune cell infiltration in a syngeneic mouse model of DIPG and in DIPG tumors collected from patients. We evaluated the expression profiles of T lymphocytes and myeloid cell markers in a cohort of 28 DIPG tumors compared to matched normal tissue specimens. Our data indicate that the expression of MHC I components in DIPG tumors is similar to that of matched normal tissue. Moreover, the well-known immune checkpoint, PD-L1, was not overexpressed in DIPG tumors. Using immunohistochemistry, we demonstrated only rare infiltration of lymphocytes but high enrichment of myeloid cells in tumor tissue. We found similar results in a syngeneic mouse model of DIPG. Collectively, our results indicate that DIPG tumors harbor rare lymphocytes and are enriched in myeloid cells. Recent studies have demonstrated that DNA methyltransferase inhibitors prime some tumors for more effective checkpoint blockade by activating expression of human endogenous retroviruses and sparking a T-cell mediated immune response through a process called “viral mimicry.” We tested the effect of decitabine in a syngeneic mouse model of DIPG. Decitabine reduced the tumor growth kinetics compared to vehicle but was unable to induce the recruitment of lymphoid cells in DIPG tumors. Importantly, we observed a noticeable reduction in the myeloid component of the DIPG microenvironment suggesting a possible role of myeloid cells in tumor growth and progression.

Diffuse intrinsic pontine glioma (DIPG) remains an incurable childhood brain cancer with a median overall survival of less than 12 months, affecting 200-300 children annually in the United States. Hence, there is an unmet need for the development of novel and effective targeted therapies. BMI-1 is a subunit of the multimeric protein complex Polycomb repressor complex 1 (PRC1) implicated in self-renewal of normal and cancer cells, and in DNA damage signaling. We have previously identified BMI-1 as a potential therapeutic target in DIPG and have shown that BMI-1 is highly expressed in DIPG tumors regardless of H3K27 mutational status. Treatment of DIPG cells with PTC596, a small molecule initially identified as a BMI-1 modulator, and ionizing radiation (IR) impairs the kinetics of DNA damage response. in vivo, treatment with PTC596 alone delayed tumor growth kinetics and induced in-tumor apoptosis. However, we observed tumor regrowth once PTC596 treatment is completed or discontinued. In the present study, we evaluated the use of PTC596 in combination with IR. Our in vivo results indicate that PTC596 sensitizes DIPG cells to IR inducing a prolonged cell growth arrest 14 days post-treatment compared to IR or PTC596 alone. The effectiveness of this combination is currently evaluated in murine orthotopic DIPG models and the results will be presented. PTC596 is being tested in newly diagnosed children with DIPG and high-grade gliomas (NCT03605550). Data collected from this study will support the development of a novel therapy including PTC596 in combination with radiotherapy to treat children with DIPG.

An adequate understanding of the relationships between radiographic and genomic features in diffuse intrinsic pontine glioma (DIPG) is essential, especially in the absence of universal biopsy, to further characterize the molecular heterogeneity of this disease and determine which patients are most likely to respond to biologically-driven therapies. Here, a radiogenomics analytic approach was applied to a cohort of 28 patients with DIPG. Tumor size and imaging characteristics from all available serial MRIs were evaluated by a neuro-radiologist, and patients were divided into three radiographic response groups (partial response [PR], stable disease [SD], progressive disease [PD]) based on MRI within 2 months of radiotherapy (RT) completion. Whole genome and RNA sequencing were performed on autopsy tumor specimens. We report several key, therapeutically-relevant findings: (1) Certain radiologic features on first and subsequent post-RT MRIs are associated with worse overall survival, including PD following irradiation as well as present, new, and/or increasing peripheral ring enhancement, necrosis, and diffusion restriction. (2) Upregulation of EMT-related genes and distant tumor spread at autopsy are observed in a subset of DIPG patients who exhibit poorer radiographic response to irradiation and/or higher likelihood of harboring H3F3A mutations, suggesting possible benefit of upfront craniospinal irradiation. (3) Additional genetic aberrations were identified, including DYNC1LI1 mutations in a subgroup of patients with PR on post-RT MRI; further investigation into potential roles in DIPG tumorigenesis and/or treatment sensitivity is necessary. (4) Whereas most DIPG tumors have an immunologically "cold" microenvironment, there appears to be a subset which harbor a more inflammatory genomic profile and/or higher mutational burden, with a trend toward improved overall survival and more favorable radiographic response to irradiation, in whom immunotherapy should be considered. This study has begun elucidating relationships between post-RT radiographic response with DIPG molecular profiles, revealing radiogenomically distinct subgroups with unique clinical trajectories and therapeutic targets.

Abstract Diffuse intrinsic pontine glioma (DIPG) is a poor-prognosis pediatric brain tumor with a median survival of less than one year. No effective therapy is currently available, and no therapeutic advances have been made in several decades. BMI-1 is a member of the multimeric protein complex Polycomb repressor complex 1 (PRC1). It has been implicated in self-renewal of normal and cancer cells, and in DNA damage signaling. We have previously identified BMI-1 as a potential therapeutic target in DIPG and have shown that BMI-1 is highly expressed in DIPG tumors regardless of histone 3 subtype. In the present study, we show that the modulation of BMI-1 leads to DNA damage, M phase cell cycle arrest, chromosome abnormalities and cell death. Furthermore, modulation of BMI-1 sensitizes DIPG patient-derived stem-like cells to ionizing radiation (IR). Treatment of DIPG stem-like cells with PTC596, a BMI-1 modulator, and IR, impairs the kinetics of DNA damage response (DDR). Both DDR foci formation and resolution were delayed, resulting in further reduction in cell viability compared with either treatment alone. In vivo, treatment of mice bearing DIPG xenografts with PTC596 leads to decreased tumor volume and growth kinetics, increased in-tumor apoptosis and sustained animal survival benefit. Gene expression analysis indicates that BMI-1 expression correlates positively with DIPG stemness and BMI-1 signature. Together our findings indicate that BMI-1 modulation is associated with mitotic abnormalities, impaired DDR and cell death, supporting the combination of BMI-1 modulation and radiation as a promising novel therapy to treat children with DIPG.

AbstractDiffuse intrinsic pontine glioma (DIPG) is a poor-prognosis pediatric brain tumor with a median survival of less than 1 year. No effective therapy is currently available, and no therapeutic advances have been made in several decades. We have previously identified BMI-1 as a potential therapeutic target in DIPG and have shown that BMI-1 is highly expressed in DIPG tumors regardless of histone 3 subtype. In the present study, we show that the modulation of BMI-1 leads to DNA damage, M phase cell-cycle arrest, chromosome scattering, and cell death. Interestingly, EZH2 inhibition did not alter these effects. Furthermore, modulation of BMI-1 sensitizes DIPG patient-derived stem-like cells to ionizing radiation (IR). Treatment of DIPG stem-like cells with PTC596, a BMI-1 modulator, and IR impairs the kinetics of DNA damage response (DDR). Both DDR foci formation and resolution were delayed, resulting in further reduction in cell viability compared with either treatment alone. In vivo, treatment of mice bearing DIPG xenografts with PTC596 leads to decreased tumor volume and growth kinetics, increased intratumoral apoptosis, and sustained animal survival benefit. Gene expression analysis indicates that BMI-1 expression correlates positively with DIPG stemness and BMI-1 signature. At the single-cell level, the analysis reveals that BMI-1 pathway is upregulated in undifferentiated cells and positively correlates with stemness in DIPG tumors.Implications:Together, our findings indicate that BMI-1 modulation is associated with mitotic abnormalities, impaired DDR, and cell death, supporting the combination of BMI-1 modulation and radiation as a promising novel therapy for children with DIPG.