Immunohistochemical and Histopathological Characterization of Spina Bifida Defect Tissues Removed After Prenatal and Postnatal Surgical Repair

Background: Myelomeningocele or spina bifida is an open neural tube defect that is characterized by protrusion of the meninges and the spinal cord through a deformity in the vertebral arch and spinous process. Myelomeningocele of post-natal tissue is well described; however, pre-natal tissue of this defect has no known previous histologic characterization. We compared the histology of different forms of pre-natal myelomeningocele and post-natal myelomeningocele tissue obtained via prenatal intrauterine and postnatal surgical repairs. Methods: Pre-and post-natal tissues from spina bifida repair surgeries were obtained from lipomyelomeningocele, myeloschisis, and myelomeningocele spina bifida defects. Tissue samples were processed for H&E and immunohistochemical staining (KRT14 and p63) to assess epidermal and dermal development. Results: Prenatal skin near the defect site develops with normal epidermal, dermal, and adnexal structures. Within the grossly cystic specimens, histology shows highly dense fibrous connective tissue with complete absence of a normal epidermal development with a lack of p63 and KRT14 expression. Conclusion: Tissues harvested from prenatal and postnatal spina bifida repair surgeries appear as normal skin near the defect site. However, cystic tissues consist of highly dense fibrous connective tissue with complete absence of normal epidermal development.

Accelarated immune ageing is associated with COVID-19 disease severity

BACKGROUND

The striking increase in COVID-19 severity in older adults provides a clear example of immunesenescence, the age-related remodelling of the immune system. To better characterise the association between convalescent immunesenescence and acute disease severity, we determined the immune phenotype of COVID-19 survivors and non-infected controls.

RESULTS

We performed detailed immune phenotyping of peripheral blood mononuclear cells isolated from 103 COVID-19 survivors 3-5 months post recovery who were classified as having had severe (n = 56; age 53.12 ± 11.30 years), moderate (n = 32; age 52.28 ± 11.43 years) or mild (n = 15; age 49.67 ± 7.30 years) disease and compared with age and sex-matched healthy adults (n = 59; age 50.49 ± 10.68 years). We assessed a broad range of immune cell phenotypes to generate a composite score, IMM-AGE, to determine the degree of immune senescence. We found increased immunesenescence features in severe COVID-19 survivors compared to controls including: a reduced frequency and number of naïve CD4 and CD8 T cells (p < 0.0001); increased frequency of EMRA CD4 (p < 0.003) and CD8 T cells (p < 0.001); a higher frequency (p < 0.0001) and absolute numbers (p < 0.001) of CD28-ve CD57+ve senescent CD4 and CD8 T cells; higher frequency (p < 0.003) and absolute numbers (p < 0.02) of PD-1 expressing exhausted CD8 T cells; a two-fold increase in Th17 polarisation (p < 0.0001); higher frequency of memory B cells (p < 0.001) and increased frequency (p < 0.0001) and numbers (p < 0.001) of CD57+ve senescent NK cells. As a result, the IMM-AGE score was significantly higher in severe COVID-19 survivors than in controls (p < 0.001). Few differences were seen for those with moderate disease and none for mild disease. Regression analysis revealed the only pre-existing variable influencing the IMM-AGE score was South Asian ethnicity ([Formula: see text] = 0.174, p = 0.043), with a major influence being disease severity ([Formula: see text] = 0.188, p = 0.01).

CONCLUSIONS

Our analyses reveal a state of enhanced immune ageing in survivors of severe COVID-19 and suggest this could be related to SARS-Cov-2 infection. Our data support the rationale for trials of anti-immune ageing interventions for improving clinical outcomes in these patients with severe disease.

Histological and neuroimaging comparison of SMART syndrome versus focal neuronal gigantism

Two of the rarest radiation-induced adverse effects are focal neuronal gigantism (FNG) and SMART syndrome (stroke-like migraine attacks after radiation therapy). Both conditions develop years, and sometimes decades, after receipt of therapeutic radiation to the brain. To date, there are only 3 previously reported cases of FNG, all of which describe cortical thickening, enlarged "hypertrophic" neurons, and neuronal cytological changes. No detailed studies exist of histological features of SMART or the comparison between FNG and SMART. In this study, we contrast histological and neuroimaging features of 3 FNG vs. 4 SMART cases, the latter diagnosed by a neuroradiologist, neurooncologist, and/or neurosurgeon. We confirm the cortical thickening, dyslamination, neuronal cytomegaly, and gliosis in FNG vs. cortical architectural preservation and normal neuronal cytology in SMART, although both showed gliosis, scattered neurons with cytoplasmic accumulation of tau and neurofibrillary protein and variable co-existence of other radiation-induced lesions. Both conditions lacked significant inflammation or consistent small vessel hyalinization throughout the entire resection specimen. The absence of pathognomonic histologic alterations in SMART cases suggests underlying vascular dysregulation. Despite differing histology, some overlap may exist in neuroimaging features. Molecular assessment conducted in 2 cases of FNG was negative for significant alterations including in the MAPK pathway.

Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas

Plexiform neurofibroma (PN) is a leading cause of morbidity in children with the genetic condition Neurofibromatosis Type 1 (NF1), often disfiguring or threatening vital structures. During formation of PN, a complex tumor microenvironment (TME) develops, with recruitment of neoplastic and non-neoplastic cell types being critical for growth and 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. To bypass this barrier, we performed single-nuclei RNA-sequencing (snRNA-seq) on 8 frozen PN samples, and integrated this with spatial transcriptomics (ST) in 4 PN samples and immunohistochemistry to provide morphological context to transcriptomic data. SnRNA-seq analysis definitively charted the heterogeneous cellular subpopulations in the PN TME, with the predominant fraction being fibroblast subtypes. PN showed a remarkable amount of inter-sample homogeneity regarding cellular subpopulation proportions despite being resected from a variety of anatomical locations. ST analysis identified distinct cellular subpopulations which were annotated using snRNA-seq data and correlated with histological features. Schwann cell/fibroblast interactions were identified by receptor/ligand interaction analysis demonstrating a high probability of Neurexin 1/Neuroligin 1 (NRXN1/NLGN1) receptor-ligand cross-talk predicted between fibroblasts and non-myelinated Schwann cells (NM-SC) and subtypes, respectively. We observed aberrant expression of NRXN1 and NLGN1 in our PN snRNA-seq data compared to a normal mouse sciatic nerve single-cell RNA-seq dataset. This pathway has never been described in PN and may indicate a clear and direct communication pathway between putative NM-SC cells of origin and surrounding fibroblasts, potentially driving disease progression. SnRNA-seq integrated with spatial transcriptomics advances our understanding of the complex cellular heterogeneity of PN TME and identify potential novel communication pathways that may drive disease progression, a finding that could provide translational therapy options for patients with these devastating tumors of childhood and early adulthood.

Unveiling the potential application of intraoperative brain smear for brain tumor diagnosis in low-middle-income countries: A comprehensive systematic review

Background

Immediate intraoperative histopathological examination of tumor tissue is indispensable for a neurosurgeon to track surgical resection. A brain smear is a simple, rapid, and cost-effective technique, particularly important in the diagnosis of brain tumors. The study aims to determine the effectiveness of intraoperative brain smear in the diagnosis of brain tumors in low- and middle-income countries (LMICs), while also evaluating its sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and overall accuracy.

Methods

A comprehensive search of the literature was conducted using PubMed, Scopus, and Google Scholar. The retrieved articles were independently screened by two reviewers. The data was extracted, processed, and organized using Microsoft Excel.

Results

A total of 59 out of 553 articles screened were included in the final analysis. The sensitivity and specificity of the intraoperative smear of brain tumors were found to be over 90% in most studies. The PPV was consistently above 90% in 11 studies, reaching 100% in one study and the NPV varied, ranging from 63% to 100%, and the accuracy was found to be >80% in most studies. One recurrent theme in the majority of the included studies was that an intraoperative brain smear is a cost-effective, quick, accessible, and accurate method of diagnosing brain tumors, requiring minimal training and infrastructure.

Conclusion

Intraoperative brain smear is a simple, rapid, cost-effective, and highly sensitive diagnostic modality for brain tumors. It can be a viable and accessible alternative to more traditional methods such as frozen sections and can be incorporated into neurosurgical practice in LMICs as a reliable and efficient diagnostic tool.

Reliability of Optical Coherence Tomography Angiography Retinal Blood Flow Analyses

Purpose

Investigate the association between the optical coherence tomography angiography (OCTA) metrics derived from different analysis programs to understand the comparability of studies using these different approaches.

Methods

Secondary analysis of a prospective observational study (March 2018-September 2021). Forty-four right eyes and 42 left eyes from 44 patients were included. Patients were either undergoing upper gastrointestinal surgery with a critical care stay planned or were already in the critical care unit with sepsis. OCTA scans were obtained in an ophthalmology department or critical care setting. Fourteen OCTA metrics were compared within and between the programs, and agreement was measured by Pearson's R coefficient and intraclass correlation coefficient.

Results

Correlation was highest between all Heidelberg metrics and Fractalyse (all >0.84), and lowest between Matlab skeletonized or foveal avascular zone metrics and all other measures (e.g., skeletal fractal dimension and vessel density at -0.02). Agreement between eyes was moderate to excellent in all metrics (0.60-0.90).

Conclusions

The significant variability between metrics and programs used for OCTA analysis demonstrates that they are not interchangeable and supports a recommendation for perfusion density metrics to be reported as standard.

Translational Relevance

Agreement between different OCTA analyses is variable and not interchangeable. The high agreement between non-skeletonized vessel density metrics suggests that these should be routinely reported.

Genomic and epigenomic re-categorization of congenital glioblastoma and desmoplastic infantile ganglioglioma

INTRODUCTION

The recently updated World Health Organization classification of central nervous system (CNS) tumors, 5th edition, (CNS5) reclassifies pediatric tumors according to their distinct molecular drivers, recognizing a new entity-infant-type hemispheric glioma (IHG). Defined by its unique epigenetic signature, and/or genomic fusions in ALK, ROS1, NTRK, or MET gene, IHG subsumes many cases previously classified as congenital glioblastoma (cGBM). Histologic features of IHG are still poorly defined with known overlap with a clinic radiologically similar entity-desmoplastic infantile ganglioglioma/astrocytoma (DIG).

METHODS

We revisited our cohort of cGBMs and DIGs, now reclassifying them according to CNS5 and compared the clinical, radiologic, molecular and histologic features between the two.

RESULTS

3/6 cases of cGBM that underwent targeted NGS fusion mutation panel were positive for ALK fusions (involving MAP4, MZT2Bex2, and EML4 genes as fusion partners), and 1/6 showed GOPC:ROS1 fusion. Interestingly, GOPC:ROS1 fusion was also shared by 1/5 cases of histologically defined DIG. DNA methylation profiling using the Heidelberg classifier (v12.3) recategorized 2/5 DIG cases as IHG (including the case with ROS1 alteration).

CONCLUSION

In conclusion, histology alone is insufficient to distinguish IHG from DIG, necessitating epigenomic and genomic testing for the diagnosis of early-life gliomas.

Some CNS sarcomas seen: A 22-year series

AIMS

Central nervous system (CNS) and spine are seldom impacted by primary or metastatic sarcomas. We reviewed our 22-year experience with metastatic versus primary mesenchymal sarcomas in adults versus pediatric patients, additionally asking how many might today undergo nomenclature changes using CNS World Health Organization, 5^th edition criteria.

MATERIALS AND METHODS

Case identification via text word search of pathology databases from our adult and pediatric referral hospitals, 2000 to August 2022, with exclusion of peripheral nervous system and primary chondro-osseous and notochordal tumors. Demographic, immunohistochemical, fluorescence in situ hybridization (FISH), and fusion results performed at the time of original diagnosis were acquired from reports.

RESULTS

57 cases were identified, with a 16 : 15 primary and 19 : 7 metastatic ratio in adult versus pediatric patients. Ewing sarcoma was the most frequent type (n = 18, 7 adult, 11 pediatric), with a rare primary PEComa, 2 alveolar soft part sarcomas, and metastatic angiosarcoma in the cohort. Only 3 cases, an intracranial sarcoma, DICER-1 mutant formerly diagnosed as rhabdomyosarcoma, an intracranial mesenchymal tumor, FET::CREB fusion-positive formerly diagnosed as angiomatoid fibrous histiocytoma, and a CIC-rearranged sarcoma required nomenclature updating by CNS WHO5 criteria.

CONCLUSIONS

Few primary or metastatic, adult or pediatric, CNS/spinal sarcomas required nomenclature updates; almost all had been satisfactorily classified at the time of diagnosis, using immunohistochemistry, FISH, or fusion results.

A novel preclinical model of craniospinal irradiation in pediatric diffuse midline glioma demonstrates decreased metastatic disease

Background

Diffuse midline glioma (DMG) is an aggressive pediatric central nervous system tumor with strong metastatic potential. As localized treatment of the primary tumor improves, metastatic disease is becoming a more important factor in treatment. We hypothesized that we could model craniospinal irradiation (CSI) through a DMG patient-derived xenograft (PDX) model and that CSI would limit metastatic tumor.

Methods

We used a BT245 murine orthotopic DMG PDX model for this work. We developed a protocol and specialized platform to deliver craniospinal irradiation (CSI) (4 Gy x2 days) with a pontine boost (4 Gy x2 days) and compared metastatic disease by pathology, bioluminescence, and MRI to mice treated with focal radiation only (4 Gy x4 days) or no radiation.

Results

Mice receiving CSI plus boost showed minimal spinal and brain leptomeningeal metastatic disease by bioluminescence, MRI, and pathology compared to mice receiving radiation to the pons only or no radiation.

Conclusion

In a DMG PDX model, CSI+boost minimizes tumor dissemination compared to focal radiation. By expanding effective DMG treatment to the entire neuraxis, CSI has potential as a key component to combination, multimodality treatment for DMG designed to achieve long-term survival once novel therapies definitively demonstrate improved local control.

Childhood Small-Vessel Primary Angiitis of the Central Nervous System: Overlap With MOG-Associated Disease

BACKGROUND

Childhood (c) primary angiitis of the central nervous system (PACNS) is a rare condition that most often affects small vessels (SV), is nearly exclusively lymphocytic, and devoid of vessel necrosis. Diagnosis of cSV-PACNS is challenging. We noted possible histological overlap of cSV-PACNS with myelin oligodendrocyte glycoprotein disease (MOGAD) on biopsy, prompting a 10-year retrospective review of our experience.

MATERIALS AND METHODS

Database-search for brain biopsy cases, age <18 years, performed for an acquired neurological deficit with suspicion of vasculitis, with histological evidence of lymphocytic small-vessel inflammation.

RESULTS

We identified 7 patients; 2/7 were serum-positive for anti-MOG antibodies and 1/7 for anti-NMDA antibodies. The remaining 4/7 proved to be idiopathic lymphocytic vasculitis/cSV-PACNS. All 7 showed overlapping features of lymphocytes permeating parenchymal SV walls, vessel wall distortion without fibrinoid necrosis, and absence of microglial clusters or intravascular thrombi. Tissue infarction was confined to a single case of idiopathic lymphocytic vasculitis. Although demyelination was diligently sought, only subtle demyelination was identified in the 2 MOGAD cases and absent in the remainder.

CONCLUSION

There is considerable histological overlap between cSV-PACNS and at least some cases of MOGAD or anti-NMDA-encephalitis; at diagnosis, the differential should include cSV-PACNS but correct classification requires post-biopsy serological testing.

Optical coherence tomography angiography as a surrogate marker for end-organ resuscitation in sepsis: A review

Sepsis is a severe illness which results in alterations in the end organ microvascular haemodynamics and is associated with a high risk of mortality. There is currently no real-time method of monitoring microcirculatory perfusion during sepsis. Retinal microcirculation is closely linked to cerebral perfusion and may reflect systemic vascular alterations. Retinal perfusion can be assessed using the non-invasive imaging technique of optical coherence tomography angiography (OCTA). This narrative review aims to discuss the utility of using retinal imaging and OCTA in systemic illness and sepsis. OCTA can be used as a functional, non-invasive and real-time biomarker along with other haemodynamic parameters for assessing and managing patients with sepsis.

Extra-CNS and dural metastases in FGFR3::TACC3 fusion+ adult glioblastoma, IDH-wildtype

BACKGROUND

Adult glioblastomas (GBMs), IDH-wildtype, WHO grade 4 with FGFR3::TACC3 fusion have a better prognosis than standard GBMs. Whether this extended survival leads to late biological consequences is unknown. Although constituting only 4% of all GBMs, FGFR3::TACC3 fusion-positive GBMs manifest recurrent morphological features that allow prediction of this subtype, possibly affecting trial eligibility and/or targeted therapies. However, we have previously shown that an identical histological pattern can be present in wildtype examples, and conversely, occasional FGFR3::TACC3 fusion-positive tumors lack this stereotypic morphology; thus, ultimately molecular characterization is required. We now report for the first time an adult with FGFR3::TACC3 fusion-positive GBM showing archetypal histological features who developed extracranial metastases to provide further insight into potential behavior of the GBM type.

METHODS

Report of a 70-year-old man with left parietal GBM who developed 2 subsequent metastases, all 3 of which were assessed by next-generation sequencing (NGS) and DNA methylation.

RESULTS

Biopsy-proven dural metastases occurred at 8 months and cervical lymph node metastasis at 12-month post-diagnosis before the patient succumbed at 23 months. By NGS, all 3 tumors showed FGFR3::TACC3 fusion as well as an additional PDZD2::TERT fusion of uncertain significance. DNA methylation profiling demonstrated mesenchymal subtype in the initial biopsy and RTKII subtype in subsequent dural and lymph node metastases, indicating intratumor spatial heterogeneity or temporal evolution.

CONCLUSION

Rarely, FGFR3::TACC3 fusion-positive GBM patients may develop dural and extracranial metastatic spread, the latter with subclass switching on epigenomic analysis.

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.

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.

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.

An intraocular solitary fibrous tumor/hemangiopericytoma with extrascleral extension: Case report and review of literature

Purpose

To report a case of intraocular solitary fibrous tumor/hemangiopericytoma (SFT/HPC) complicated by extrascleral extension and to review the current literature regarding intraocular SFT/HPC.

Observations

A twenty-two year old male presented with decreased vision in his left eye and was found to have a subretinal mass with extrascleral extension. He underwent enucleation of his left eye and histopathology confirmed a diagnosis of SFT/HPC.

Conclusions and importance

To our knowledge, this is the seventh case of intraocular SFT/HPC ever reported and the first to report extrascleral extension. At the time of publication, there was no evidence of metastases. Extensive clinical, ophthalmic and radiographic imaging, and histopathologic data are presented to contribute to the current understanding of intraocular SFT/HPC.

Population-based analysis of CNS tumor diagnoses, treatment, and survival in congenital and infant age groups

BACKGROUND

Congenital (< 3 months) and infant (3 to 11 months) brain tumors are biologically different from tumors in older children, but their epidemiology has not been studied comprehensively. Insight into epidemiological differences could help tailor treatment recommendations by age and increase overall survival (OS).

METHODS

Population-based data from SEER were obtained for 14,493 0-19-year-olds diagnosed with CNS tumors 1990-2015. Congenital and infant age groups were compared to patients aged 1-19 years based on incidence, treatment, and survival using Chi-square and Kaplan-Meier analyses. Hazard ratios were estimated from univariate and multivariable Cox proportional hazards survival analyses.

RESULTS

Between the < 3-month, 3-5-month, 6-11 month, and 1-19-year age groups, tumor type distribution differed significantly (p < 0.001). 5-year OS for all tumors was 36.7% (< 3 months), 56.0% (< 3-5 months), 63.8% (6-11 months), and 74.7% (1-19 years) (p < 0.001). Comparing between age groups by tumor type, OS was worst for < 3-month-olds with low-grade glioma, medulloblastoma, and other embryonal tumors; OS was worst for 3-5-month-olds with ependymoma, < 1-year-olds collectively with atypical teratoid-rhabdoid tumor, and 1-19-year-olds with high-grade glioma (HGG) (log rank p < 0.02 for all tumor types). Under 3-month-olds were least likely to receive any treatment for each tumor type and least likely to undergo surgery for all except HGG. Under 1-year-olds were far less likely than 1-19-year-olds to undergo both radiation and chemotherapy for embryonal tumors.

CONCLUSIONS

Subtype distribution, treatment patterns, and prognosis of congenital/infant CNS tumors differ from those in older children. Better, more standardized treatment guidelines may improve poorer outcomes seen in these youngest patients.

Histopathologic features of nasal glial heterotopia (nasal glioma)

PURPOSE

Nasal glioneuronal heterotopia (NGH) is an uncommon developmental abnormality of the nasal cavity or paranasal soft tissue. Few detailed histologic studies of NGH exist, and molecular analyses have not been performed to date.

METHODS

We describe six cases of pediatric NGH and two representative encephaloceles encountered in our practice over the past 20 years.

RESULTS

Two clinically distinct patient groups were noted, those with 1) intranasal nasal cavity mass (n = 3), or 2) extranasal cutaneous mass on the nose (n = 3, 1 on nasal apex, 2 on nasal bridge). Intranasal cases presented within the first week of life, whereas the extranasal NGH presented at ages of 4, 7, and 8 months. Resection was curative in 5/6 cases, with a single case showing local recurrence. Histologic examination showed a predominantly glial cell composition, with nests of GFAP-immunoreactive neuropil containing large, often multinucleated astrocytes. Neurons, although difficult to identify on H&E-stains, were readily observed in all cases by NeuN-immunostain. At least focal leptomeninges were noted in 2/3 intranasal and 1/3 extranasal NGHs on routine histology, SSTR2A immunohistochemistry further confirmed leptomeninges/ arachnoid cells in 4/6 cases. 1 of 4 NGH (extranasal) cases showed copy number variations in chromosome 16, 17 and 19, which were also present in 1/2 encephalocele cases. The full significance of these alterations remains unknown.

CONCLUSION

We find evidence of histologic overlap between NGH and encephalocele, and, for the first time, report molecular alterations shared between the two entities, suggesting that these conditions may represent spectrum of the same histopathologic entity.

Novel RAF Fusions in Pediatric Low-Grade Gliomas Demonstrate MAPK Pathway Activation

Brain tumors are the most common solid tumor in children, and low-grade gliomas (LGGs) are the most common childhood brain tumor. Here, we report on 3 patients with LGG harboring previously unreported or rarely reported RAF fusions: FYCO1-RAF1, CTTNBP2-BRAF, and SLC44A1-BRAF. We hypothesized that these tumors would show molecular similarity to the canonical KIAA1549-BRAF fusion that is the most widely seen alteration in pilocytic astrocytoma (PA), the most common pediatric LGG variant, and that this similarity would include mitogen-activated protein kinase (MAPK) pathway activation. To test our hypothesis, we utilized immunofluorescent imaging and RNA-sequencing in normal brain, KIAA1549-BRAF-harboring tumors, and our 3 tumors with novel fusions. We performed immunofluorescent staining of ERK and phosphorylated ERK (p-ERK), identifying increased p-ERK expression in KIAA1549-BRAF fused PA and the novel fusion samples, indicative of MAPK pathway activation. Geneset enrichment analysis further confirmed upregulated downstream MAPK activation. These results suggest that MAPK activation is the oncogenic mechanism in noncanonical RAF fusion-driven LGG. Similarity in the oncogenic mechanism suggests that LGGs with noncanonical RAF fusions are likely to respond to MEK inhibitors.

Intracranial mesenchymal tumors with FET-CREB fusion are composed of at least two epigenetic subgroups distinct from meningioma and extracranial sarcomas

‘Intracranial mesenchymal tumor, FET‐CREB fusion‐positive’ occurs primarily in children and young adults and has previously been termed intracranial angiomatoid fibrous histiocytoma (AFH) or intracranial myxoid mesenchymal tumor (IMMT). Here we performed genome‐wide DNA methylation array profiling of 20 primary intracranial mesenchymal tumors with FET‐CREB fusion to further study their ontology. These tumors resolved into two distinct epigenetic subgroups that were both divergent from all other analyzed intracranial neoplasms and soft tissue sarcomas, including meningioma, clear cell sarcoma of soft tissue (CCS), and AFH of extracranial soft tissue. The first subgroup (Group A, 16 tumors) clustered nearest to but independent of solitary fibrous tumor and AFH of extracranial soft tissue, whereas the second epigenetic subgroup (Group B, 4 tumors) clustered nearest to but independent of CCS and also lacked expression of melanocytic markers (HMB45, Melan A, or MITF) characteristic of CCS. Group A tumors most often occurred in adolescence or early adulthood, arose throughout the neuroaxis, and contained mostly EWSR1‐ATF1 and EWSR1‐CREB1 fusions. Group B tumors arose most often in early childhood, were located along the cerebral convexities or spinal cord, and demonstrated an enrichment for tumors with CREM as the fusion partner (either EWSR1‐CREM or FUS‐CREM). Group A tumors more often demonstrated stellate/spindle cell morphology and hemangioma‐like vasculature, whereas Group B tumors more often demonstrated round cell or epithelioid/rhabdoid morphology without hemangioma‐like vasculature, although robust comparison of these clinical and histologic features requires future study. Patients with Group B tumors had inferior progression‐free survival relative to Group A tumors (median 4.5 vs. 49 months, p = 0.001). Together, these findings confirm that intracranial AFH‐like neoplasms and IMMT represent histologic variants of a single tumor type (‘intracranial mesenchymal tumor, FET‐CREB fusion‐positive’) that is distinct from meningioma and extracranial sarcomas. Additionally, epigenomic evaluation may provide important prognostic subtyping for this unique tumor entity.

Innumerable Meningiomas Arising in a Patient With Tuberous Sclerosis Complex Decades After Radiation Therapy

Meningioma is the most common radiation-induced brain neoplasm, usually occurring after a latency of 20 - 35 years, with multiplicity in 10% of cases. Radiation-induced meningiomas (RIMs) have not previously been reported in patients with tuberous sclerosis complex (TSC), unlike their well-known occurrence in other familial tumor predisposition syndrome patients. We report a TSC patient who developed numerous intracranial meningiomas twenty five year after radiation therapy for subependymal giant cell astrocytoma (SEGA). Autopsy examination showed innumerable, coalescent, benign, meningothelial meningiomas, WHO grade 1, ranging in size from 0.2 cm to 3.3 cm. Autopsy also showed small residual SEGA, radiation-induced cerebral vasculopathy, and classic TSC features including several small subependymal nodules ("candle gutterings"), white matter radial heterotopia, facial angiofibromas, dental enamel pitting, one ash leaf spot, and multiple hepatic and renal angiomyolipomas. Next-generation sequencing analysis utilizing a 500+ gene cancer panel demonstrated chromosomal loss involving the majority of chromosome 22, including the NF2 gene locus, as well as a truncating nonsense mutation in TSC1 p. R509*. While TSC patients rarely require radiation therapy, this striking case suggests that patients with TSC should be monitored closely if cranial therapeutic radiation is administered.

Secondary parenchymal CNS involvement by lymphoma including rare types: Follicular and EBV-positive NK/T cell lymphoma, nasal type

BACKGROUND

Secondary CNS involvement by systemic lymphomas (SCNSL) is uncommon, but when it occurs, is usually due to diffuse large B cell lymphoma (DLBCL). Three recent unusual cases serve to highlight diagnostic challenges.

OBJECTIVE

To report SCNSL from DLBCL and two unusual lymphoma types: follicular lymphoma with high-grade transformation to DLBCL and NK/T cell lymphoma, nasal type (ENKL), nasal type.

RESULTS

SCNSL in the DLBCL case occurred at 7-year interval from primary in a 54-year-old woman who presented with stroke-like symptoms and a right postcentral gyrus 2.6 × 2.9 × 2.6 cm. mass. The follicular lymphoma occurred at 6-month interval in a 69-year-old woman with 1 month of diplopia and 2 weeks of cognitive decline; multifocal lesions involved temporal lobe, subependymal periventricular areas, brainstem, cerebellum, hypothalamus, corpus callosum and gyrus rectus. The ENKL occurred at 25-month interval from nasal biopsy in a 45-year-old man with 1 week of altered mental status; multifocal cerebral and brainstem lesions were identified. Histological features in cases 1 and 3 were identical to the primary lymphoma, with high-grade transformation to DLBCL in the follicular lymphoma.

CONCLUSION

Unusual features in our series include longer interval from primary to relapse in case 1 with DLBCL (usually <2 years of diagnosis), and SCNSL occurring from either follicular lymphoma or EKNL, nasal type (<6% of cases). Pathologists play an important role in excluding infectious, especially in cases with parenchymal lesions and characterizing the lymphoma type in SCNSL.

LGG-13. PILOCYTIC ASTROCYTOMAS WITH NOVEL BRAF FUSIONS DEMONSTRATE MAPK PATHWAY ACTIVATION

Background

Pilocytic astrocytomas (PAs) are the most common pediatric low-grade glioma subtype. Oftentimes, PAs demonstrate somatic genetic alterations, the most common being the BRAF-KIAA1549 fusion, which results in constitutive activation of the MAPK pathway. Better understanding of the effects of other RAF fusions is necessary to determine the potential utility of MAPK-targeting therapies.

Methods

Three patients presented to Children’s Hospital Colorado and were ultimately diagnosed with PAs harboring previously unreported gene fusions identified as FYCO-RAF1, CCTTNNBP2-BRAF, and SLC44A1-BRAF. Utilizing immunohistochemistry, we stained novel samples and controls for ERK and pERK (phosphorylated ERK) to assess the activation of the MAPK pathway. PAs with known BRAF-KIAA1549 fusions (4 samples) and normal brain tissue (5 samples) were used as positive and negative controls, respectively. We additionally performed RNA sequencing to better understand expression changes associated with these fusions, utilizing Metascape and GSEA (Gene Set Enrichment Analysis) for analysis.

Results

Immunohistochemistry of negative control samples demonstrated less p-ERK than ERK (ratios of 0.6–0.9, mean 0.8). All samples with novel fusions demonstrated statistically significantly higher p-ERK expression compared to negative controls (ratios of 1.3–1.7, mean 1.4). These experimental samples also all fell within the p-ERK to ERK expression range of the positive control samples, which demonstrated the widest range of expression (ratios of 1.1–4.5, mean 2.2). Our molecular analysis further confirmed these results, with GSEA demonstrating positively upregulated MAPK and ERK pathways in 2 positive controls and 1 novel fusion sample. Metascape analysis emphasized overall similar gene expression between these samples, demonstrating many shared genes and functional pathways.

Conclusions

We identified 3 previously unreported RAF fusions in PA that demonstrate activation of the MAPK pathway, although not as extensively as seen in some positive control samples with BRAF-KIAA1549 fusions. MEK inhibition may be a useful therapeutic strategy in these tumors if targeted therapy is indicated.

Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology

Ependymoma (EPN) is a brain tumor commonly presenting in childhood that remains fatal in most children. Intra-tumoral cellular heterogeneity in bulk-tumor samples significantly confounds our understanding of EPN biology, impeding development of effective therapy. We, therefore, use single-cell RNA sequencing, histology, and deconvolution to catalog cellular heterogeneity of the major childhood EPN subgroups. Analysis of PFA subgroup EPN reveals evidence of an undifferentiated progenitor subpopulation that either differentiates into subpopulations with ependymal cell characteristics or transitions into a mesenchymal subpopulation. Histological analysis reveals that progenitor and mesenchymal subpopulations co-localize in peri-necrotic zones. In conflict with current classification paradigms, relative PFA subpopulation proportions are shown to determine bulk-tumor-assigned subgroups. We provide an interactive online resource that facilitates exploration of the EPN single-cell dataset. This atlas of EPN cellular heterogeneity increases understanding of EPN biology.

NTRK Fusions Can Co-Occur With H3K27M Mutations and May Define Druggable Subclones Within Diffuse Midline Gliomas

Diffuse midline gliomas (DMGs) are incurable pediatric tumors with extraordinarily limited treatment options. Decades of clinical trials combining conventional chemotherapies with radiation therapy have failed to improve these outcomes, demonstrating the need to identify and validate druggable biologic targets within this disease. NTRK1/2/3 fusions are found in a broad range of pediatric cancers, including high-grade gliomas and a subset of DMGs. Phase 1/2 studies of TRK inhibitors have demonstrated good tolerability, effective CNS penetration, and promising objective responses across all patients with TRK fusion-positive cancers, but their use has not been explored in TRK fusion-positive DMG. Here, we report 3 cases of NTRK fusions co-occurring within H3K27M-positive pontine diffuse midline gliomas. We employ a combination of single-cell and bulk transcriptome sequencing from TRK fusion-positive DMG to describe the phenotypic consequences of this co-occurring alteration. We then use ex vivo short-culture assays to evaluate the potential response to TRK inhibition in this disease. Together, these data highlight the importance of routine molecular characterization of these highly aggressive tumors and identify a small subset of patients that may benefit from currently available targeted therapies.

ddPCR Analysis Reveals BRAF V600E Mutations Are Infrequent in Isolated Pituitary Langerhans Cell Histiocytosis Patients

Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia with a highly variable clinical presentation affecting people of all ages. Mutations in BRAF V600E are the most identifiable molecular alteration in LCH although its incidence in pediatric patients with isolated pituitary stalk involvement is not well described. Pediatric patients with LCH and isolated pituitary stalk involvement typically present with central diabetes insipidus. Diagnosis requires a transcranial biopsy which often yields scant tissue. We sought to determine the prevalence of BRAF V600E mutations in patients with isolated pituitary stalk LCH using digital droplet polymerase chain reaction because this method requires minimal tumor DNA. We identified 8 patients with isolated pituitary stalk thickening who underwent a biopsy at Children's Hospital Colorado from January 2001 to December 2019, as well as 6 patients with systemic LCH diagnosed by biopsy in the same period as a comparison. Only one out of the 8 patients with isolated thickened pituitary stalk was found to have a detectable BRAF V600E mutation. Five out of the 6 patients with systemic LCH had a detectable BRAF V600E mutation. In our series, BRAF V600E mutations are rare in pediatric patients with LCH and isolated pituitary stalk involvement.

Intracranial mesenchymal tumor with FET-CREB fusion-A unifying diagnosis for the spectrum of intracranial myxoid mesenchymal tumors and angiomatoid fibrous histiocytoma-like neoplasms

Intracranial mesenchymal tumors with FET‐CREB fusions are a recently described group of neoplasms in children and young adults characterized by fusion of a FET family gene (usually EWSR1, but rarely FUS) to a CREB family transcription factor (ATF1, CREB1, or CREM), and have been variously termed intracranial angiomatoid fibrous histiocytoma or intracranial myxoid mesenchymal tumor. The clinical outcomes, histologic features, and genomic landscape are not well defined. Here, we studied 20 patients with intracranial mesenchymal tumors proven to harbor FET‐CREB fusion by next‐generation sequencing (NGS). The 16 female and four male patients had a median age of 14 years (range 4–70). Tumors were uniformly extra‐axial or intraventricular and located at the cerebral convexities (n = 7), falx (2), lateral ventricles (4), tentorium (2), cerebellopontine angle (4), and spinal cord (1). NGS demonstrated that eight tumors harbored EWSR1‐ATF1 fusion, seven had EWSR1‐CREB1, four had EWSR1‐CREM, and one had FUS‐CREM. Tumors were uniformly well circumscribed and typically contrast enhancing with solid and cystic growth. Tumors with EWSR1‐CREB1 fusions more often featured stellate/spindle cell morphology, mucin‐rich stroma, and hemangioma‐like vasculature compared to tumors with EWSR1‐ATF1 fusions that most often featured sheets of epithelioid cells with mucin‐poor collagenous stroma. These tumors demonstrated polyphenotypic immunoprofiles with frequent positivity for desmin, EMA, CD99, MUC4, and synaptophysin, but absence of SSTR2A, myogenin, and HMB45 expression. There was a propensity for local recurrence with a median progression‐free survival of 12 months and a median overall survival of greater than 60 months, with three patients succumbing to disease (all with EWSR1‐ATF1 fusions). In combination with prior case series, this study provides further insight into intracranial mesenchymal tumors with FET‐CREB fusion, which represent a distinct group of CNS tumors encompassing both intracranial myxoid mesenchymal tumor and angiomatoid fibrous histiocytoma‐like neoplasms.

EPID-13. A POPULATION-BASED ANALYSIS OF CNS TUMOR DIAGNOSES, TREATMENT, AND SURVIVAL IN CONGENITAL AND INFANT AGE GROUPS

BACKGROUND

Congenital (<3 months) and infant (3 to 11 months) brain tumors are biologically different from tumors in older children, but epidemiology of these tumors has not been studied comprehensively. Insight into epidemiological differences could help tailor treatment recommendations by age and increase overall survival (OS).

METHODS

Population-based data from the SEER 18 registries was obtained for 14,493 0-19-year-olds diagnosed with CNS tumors between 1990 and 2015. Incidence, treatment, and survival were analyzed using Chi-square and Kaplan-Meier analyses.

RESULTS

Between the <3 month, 3–5 month, 6–11 month, and 1–19 year age groups, tumor type distribution differed significantly (p<0.001); high-grade glioma (HGG) was most common in the <3-month-olds, while low-grade glioma (LGG) was most common in the other groups. 5-year OS for all tumors was 36.7% (<3 months), 56.0% (<3–5 months), 63.8% (6–11 months), and 74.7% (1–19 years) (log rank p<0.001). OS by tumor type was worst for <3-month-olds with LGG, medulloblastoma, and other embryonal tumors; OS was worst for 3-5-month-olds with ependymoma, <1-year-olds collectively with atypical teratoid-rhabdoid tumor, and 1-19-year-olds with HGG (log rank p<0.02 for all tumor types). <3-month-olds were least likely to receive any treatment for each tumor type and least likely to undergo surgery for all except HGG. <1-year-olds were far less likely than 1-19-year-olds to undergo radiation for embryonal tumors, as expected, but were also less likely to undergo chemotherapy.

CONCLUSIONS

Congenital/infant CNS tumors differ pathologically, therapeutically, and prognostically from those in older children. Treatment changes could help address poorer outcomes for these young patients.

DIPG-42. TOWARD MULTIMODALITY THERAPY FOR DIPG/DMG: DEVELOPMENT AND INVESTIGATION OF CRANIOSPINAL IRRADIATION AND CONVECTION-ENHANCED DELIVERY PDX MODELS

BACKGROUND

Diffuse intrinsic pontine glioma (DIPG) and diffuse midline glioma (DMG) are metastatic diseases, as demonstrated by early convection-enhanced delivery (CED) clinical trials in which prolonged local tumor control can sometimes be achieved, but fatal disseminated disease then develops. We hypothesize that improvements in treatment of both focal disease and the entire neuraxis are necessary for long-term survival, and patient-derived xenograft (PDX) models can help advance these efforts.

METHODS

We used a BT245 murine orthotopic DIPG PDX model for this work. We developed a protocol and specialized platform to deliver craniospinal irradiation (CSI) with a pontine boost. We separately compared intratumoral drug concentration by CED and intraperitoneal delivery. In our CED model, mice receive gemcitabine 60 ug x1 in 15 ul at 0.5 ul/minute through a stepped catheter design with silica tubing extending 2mm beyond a 27G needle.

RESULTS

Mice receiving CSI (4 Gy x2d) plus boost (4 Gy x2d) showed minimal spinal and brain leptomeningeal metastatic disease by bioluminescence, MRI, and pathology compared to mice receiving radiation to the pons only (4 Gy x4d) or no radiation. CED achieved an intratumoral gemcitabine concentration 50-fold greater than intraperitoneal dosing when controlled for dose.

CONCLUSIONS

In a DIPG PDX model, CSI+boost minimizes tumor dissemination compared to focal radiation, and CED achieves clinically significant improvements in intratumoral chemotherapy concentration compared to systemic delivery. Adding these modalities to current treatment could improve both focal and metastatic tumor control, leading to meaningful improvements in survival.

MODL-24. AN ORGANOTYPIC CHUNK CULTURE TECHNIQUE TO STUDY DISEASE MECHANISM AND DEVELOP TARGETED THERAPEUTICS FOR PEDIATRIC ADAMANTINOMATOUS CRANIOPHARYNGIOMA

BACKGROUND

Advances in the treatment of Adamantinomatous Craniopharyngioma (ACP) face challenges with translation to clinical study due to the absence of robust culture models of the disease. We developed a technique for culturing human ACP tissue in an organotypic chunk culture format that retains the tumor microenvironment for a duration sufficient to evaluate potential targeted therapeutics.

METHODS

Intraoperatively collected tumor tissue from pediatric ACP was cut into volumes of approximately 3 mm3 and rested over a semi-permeable insert placed in the wells of a 6-well plate. Specimens were cultured in (1) Control media, media containing (2) Tocilizumab, (3) Trametinib, and (4) combination of Tocilizumab and Trametinib, for 24 and 96 hours. Specimens were harvested for paraffin embedding, protein and gene expression assays. Supernatants were collected to assay secreted components. Paraffin embedded specimens were sectioned and stained for H&E, Pan-CK, Beta-Catenin, cleaved Caspase-3, Ki-67, and Phospho-ERK.

RESULTS

H&E staining revealed characteristic histologic features of ACP with epithelial cells with palisading nuclei, wet keratin and ghost cells. Tumor sections were markedly positive for epithelial cell markers, Pan-CK and Beta-Catenin. Ki-67 and cleaved Caspase-3 were restricted to a small fraction of cells, indicating low index of proliferation and apoptosis under the culture conditions. The response to drug treatments shall be determined using gene expression assays and evaluation of the secreted components.

CONCLUSION

The organotypic chunk culture technique appears to maintain the viability and integrity of ACP tumors for several days and may serve as an appropriate model for pre-clinical studies to develop targeted therapeutics for pediatric ACP.

DIPG-34. SUPER ELONGATION COMPLEX AS A TARGETABLE DEPENDENCY IN H3K27M+ DIFFUSE MIDLINE GLIOMA

Mutations in the histone 3 gene (H3K27M) are the eponymous driver in diffuse intrinsic pontine gliomas (DIPGs) and other diffuse midline gliomas (DMGs), aggressive pediatric brain tumors for which no curative therapy currently exists. To identify specific epigenetic dependencies within the context of the H3K27M mutation, we performed an shRNA screen targeting 408 genes classified as epigenetic/chromatin-associated molecules in patient-derived DMG cultures. This identified AFF4, a component of the super elongation complex (SEC), as necessary for DMG cells to maintain growth and self-renewal. We hypothesized that aberrant SEC expression occurs as a consequence of the H3K27M mutation and that this dysregulated SEC signaling overcomes repressive transcriptional regulation in order to suppresses differentiation and promote self-renewal of DMG tumor stem cells. We interrogated the role of AFF4 in DMG using an shRNA lentiviral approach. We demonstrate a significant decrease in in vitro clonogenicity and stem cell maintenance following AFF4 depletion. We employed RNA-seq-based gene set enrichment analysis to delineate differentiation programs under SEC regulatory control. Finally, we sought to determine whether CDK9, the catalytic subunit of the SEC, represents a therapeutic vulnerability in DMG. Using RNA polymerase II ChIP-seq, we demonstrate that CDK9 pharmacologic inhibition restores regulatory Pol II pausing, promotes cellular differentiation, and leads to potent anti-tumor effect both in vitro and in patient-derived xenograft models. These studies present a biologic rationale for the translational exploration of CDK9 inhibition as a promising therapeutic approach.

MBRS-46. CHARTING NEOPLASTIC AND IMMUNE CELL HETEROGENEITY IN HUMAN AND GEM MODELS OF MEDULLOBLASTOMA USING scRNAseq

We explored cellular heterogeneity in medulloblastoma using single-cell RNA sequencing (scRNAseq), immunohistochemistry and deconvolution of bulk transcriptomic data. Over 45,000 cells from 31 patients from all main subgroups of medulloblastoma (2 WNT, 10 SHH, 9 GP3, 11 GP4 and 1 GP3/4) were clustered using Harmony alignment to identify conserved subpopulations. Each subgroup contained subpopulations exhibiting mitotic, undifferentiated and neuronal differentiated transcript profiles, corroborating other recent medulloblastoma scRNAseq studies. The magnitude of our present study builds on the findings of existing studies, providing further characterization of conserved neoplastic subpopulations, including identification of a photoreceptor-differentiated subpopulation that was predominantly, but not exclusively, found in GP3 medulloblastoma. Deconvolution of MAGIC transcriptomic cohort data showed that neoplastic subpopulations are associated with major and minor subgroup subdivisions, for example, photoreceptor subpopulation cells are more abundant in GP3-alpha. In both GP3 and GP4, higher proportions of undifferentiated subpopulations is associated with shorter survival and conversely, differentiated subpopulation is associated with longer survival. This scRNAseq dataset also afforded unique insights into the immune landscape of medulloblastoma, and revealed an M2-polarized myeloid subpopulation that was restricted to SHH medulloblastoma. Additionally, we performed scRNAseq on 16,000 cells from genetically engineered mouse (GEM) models of GP3 and SHH medulloblastoma. These models showed a level of fidelity with corresponding human subgroup-specific neoplastic and immune subpopulations. Collectively, our findings advance our understanding of the neoplastic and immune landscape of the main medulloblastoma subgroups in both humans and GEM models.

EPEN-31. SINGLE-CELL RNAseq OF CHILDHOOD EPENDYMOMA REVEALS DISTINCT NEOPLASTIC CELL SUBPOPULATIONS THAT IMPACT ETIOLOGY, MOLECULAR CLASSIFICATION AND OUTCOME

Ependymoma (EPN) is a brain tumor commonly presenting in childhood that remains fatal in the majority of children. Intra-tumoral cellular heterogeneity in bulk-tumor samples significantly confounds our understanding of EPN biology, impeding development of effective therapy. We therefore used single-cell RNA sequencing to catalog cellular heterogeneity of 26 childhood EPN, predominantly from ST-RELA, PFA1 and PFA2 subgroups. ST-RELA and PFA subgroups clustered separately, with ST-RELA clustering largely according to individual sample-of-origin. PFA1 and PFA2 subgroup EPNs cells were intermixed and revealed 4 major subpopulations – 2 with characteristics of ependymal differentiation (transporter and ciliated phenotype subpopulations), an undifferentiated subpopulation and a mesenchymal phenotype. Pseudotime analysis showed the undifferentiated progenitor subpopulation either differentiating into ependymal differentiation subpopulations or transitioning into the mesenchymal subpopulation. Histological analysis revealed that undifferentiated and mesenchymal subpopulations cells colocalized to perinecrotic/perivascular zones, the putative ependymoma stem cell niche. Deconvolution of PFA bulk transcriptome data showed that undifferentiated and mesenchymal subpopulations were associated with a poor prognosis; whereas the ciliated ependymal cell-differentiated subpopulation was associated with a good prognosis. In conflict with current distinct classification paradigms, the ratio of mesenchymal and ciliated subpopulations determined bulk-tumor subgroups assignment to PFA1 and PFA2 respectively. This atlas of EPN cellular heterogeneity provides an important advance in our understanding of EPN biology, identifying high-risk associated subpopulations for therapeutic targeting.

Senescence Induced by BMI1 Inhibition Is a Therapeutic Vulnerability in H3K27M-Mutant DIPG

Diffuse intrinsic pontine glioma (DIPG) is an incurable brain tumor of childhood characterized by histone mutations at lysine 27, which results in epigenomic dysregulation. There has been a failure to develop effective treatment for this tumor. Using a combined RNAi and chemical screen targeting epigenomic regulators, we identify the polycomb repressive complex 1 (PRC1) component BMI1 as a critical factor for DIPG tumor maintenance in vivo. BMI1 chromatin occupancy is enriched at genes associated with differentiation and tumor suppressors in DIPG cells. Inhibition of BMI1 decreases cell self-renewal and attenuates tumor growth due to induction of senescence. Prolonged BMI1 inhibition induces a senescence-associated secretory phenotype, which promotes tumor recurrence. Clearance of senescent cells using BH3 protein mimetics co-operates with BMI1 inhibition to enhance tumor cell killing in vivo.

The effects of ephrinB2 signaling on proliferation and invasion in glioblastoma multiforme

The aggressive nature of glioblastoma multiforme (GBM) may be attributed to the dysregulation of pathways driving both proliferation and invasion. EphrinB2, a membrane-bound ligand for some of the Eph receptors, has emerged as a critical target regulating these pathways. In this study, we investigated the role of ephrinB2 in regulating proliferation and invasion in GBM using intracranial and subcutaneous xenograft models. The Cancer Genome Atlas analysis suggested high transcript and low methylation levels of ephrinB2 as poor prognostic indicators in GBM, consistent with its role as an oncogene. EphrinB2 knockdown, however, increased tumor growth, an effect that was reversed by ephrinB2 Fc protein. This was associated with EphB4 receptor activation, consistent with the data showing a significant decrease in tumor growth with ephrinB2 overexpression. Mechanistic analyses showed that ephrinB2 knockdown has anti-invasive but pro-proliferative effects in GBM. EphB4 stimulation following ephrinB2 Fc treatment in ephrinB2 knockdown tumors was shown to impart strong anti-proliferative and anti-invasive effects, which correlated with decrease in PCNA, p-ERK, vimentin, Snail, Fak, and increase in the E-cadherin levels. Overall, our study suggests that ephrinB2 cannot be used as a sole therapeutic target. Concomitant inhibition of ephrinB2 signaling with EphB4 activation is required to achieve maximal therapeutic benefit in GBM.

Distinguishing Encephaloclastic Lesions Resulting From Primary or Secondary Pyruvate Dehydrogenase Deficiency From Other Neonatal or Infantile Cavitary Brain Lesions

The central nervous system (CNS) is a highly complex and energy-dependent organ that is subject to a wide variety of metabolic, hypoxic-ischemic, and infectious insults that result in cystic changes. Diagnosis of metabolic defects causing extensive cystic changes is particularly challenging for the pediatric pathologist, due to the rarity of these conditions. Pyruvate dehydrogenase (PDH) deficiency is one of the most common etiologies of congenital lactic acidosis, caused by mutations in subunits of the large mitochondrial matrix complex, and characterized by periventricular cysts, although few detailed reports focusing on neuropathologic findings exist. In addition, rare defects in other mitochondrial enzymes such as short-chain enoyl-CoA hydratase (SCEH, encoded by ECHS1 gene) can cause secondary PDH deficiency and present with neonatal lactic acidosis, but neuropathological findings have never been reported. Nonmetabolic conditions can also produce CNS cystic lesions, primarily in newborns. The pathologist must therefore distinguish between these etiologically disparate conditions which can produce CNS cavitary lesions. Here, we compare and contrast the gross and microscopic findings of cysts associated with cases of PDH and SCEH deficiencies with other neonatal cystic brain diseases including periventricular leukomalacia, neonatal Alexander disease, Canavan disease, and a case of cysts associated with a vascular abnormality. Our studies show that PDH and SCEH deficiencies are not grossly or histologically distinguishable from each other and both are associated with smooth-walled cysts largely limited to the telencephalic germinal matrix. Both show an absence of prominent hemosiderin deposits, Rosenthal fibers, vacuolization of the white matter, and gliosis or axonal damage in the surrounding parenchyma. These features can help distinguish PDH/SCEH deficiency from other pediatric/neonatal cystic CNS disorders, especially those produced by hypoxic ischemic conditions. Cysts, usually bilateral, confined to the telencephalic germinal matrix should elicit metabolic and genetic testing to appropriately diagnose PDH and SCEH and distinguish them from each other.

Super Elongation Complex as a Targetable Dependency in Diffuse Midline Glioma

Histone 3 gene mutations are the eponymous drivers in diffuse midline gliomas (DMGs), aggressive pediatric brain cancers for which no curative therapy currently exists. These recurrent oncohistones induce a global loss of repressive H3K27me3 residues and broad epigenetic dysregulation. In order to identify therapeutically targetable dependencies within this disease context, we performed an RNAi screen targeting epigenetic/chromatin-associated genes in patient-derived DMG cultures. This identified AFF4, the scaffold protein of the super elongation complex (SEC), as a molecular dependency in DMG. Interrogation of SEC function demonstrates a key role for maintaining clonogenic potential while promoting self-renewal of tumor stem cells. Small-molecule inhibition of SEC using clinically relevant CDK9 inhibitors restores regulatory RNA polymerase II pausing, promotes cellular differentiation, and leads to potent anti-tumor effect both in vitro and in patient-derived xenograft models. These studies present a rationale for further exploration of SEC inhibition as a promising therapeutic approach to this intractable disease.

BPTF regulates growth of adult and pediatric high-grade glioma through the MYC pathway

High-grade gliomas (HGG) afflict both children and adults and respond poorly to current therapies. Epigenetic regulators have a role in gliomagenesis, but a broad, functional investigation of the impact and role of specific epigenetic targets has not been undertaken. Using a two-step, in vitro/in vivo epigenomic shRNA inhibition screen, we determine the chromatin remodeler BPTF to be a key regulator of adult HGG growth. We then demonstrate that BPTF knockdown decreases HGG growth in multiple pediatric HGG models as well. BPTF appears to regulate tumor growth through cell self-renewal maintenance, and BPTF knockdown leads these glial tumors toward more neuronal characteristics. BPTF's impact on growth is mediated through positive effects on expression of MYC and MYC pathway targets. HDAC inhibitors synergize with BPTF knockdown against HGG growth. BPTF inhibition is a promising strategy to combat HGG through epigenetic regulation of the MYC oncogenic pathway.

Preclinical and clinical investigation of intratumoral chemotherapy pharmacokinetics in DIPG using gemcitabine

Background

Hundreds of systemic chemotherapy trials in diffuse intrinsic pontine glioma (DIPG) have not improved survival, potentially due to lack of intratumoral penetration, which has not previously been assessed in humans.

Methods

We used gemcitabine as a model agent to assess DIPG intratumoral pharmacokinetics (PK) using mass spectrometry.

Results

In a phase 0 clinical trial of i.v. gemcitabine prior to biopsy in children newly diagnosed with DIPG by MRI, mean concentration in 4 biopsy cores in patient 1 (H3K27M diffuse midline glioma) was 7.65 µM. These compare favorably to levels for patient 2 (mean 3.85 µM, found to have an H3K27-wildtype low-grade glioma on histology), and from a similar study in adult glioblastoma (adjusted mean 3.48 µM). In orthotopic patient-derived xenograft (PDX) models of DIPG and H3K27M-wildtype pediatric glioblastoma, gemcitabine levels and clearance were similar in tumor, pons, and cortex and did not depend on H3K27 mutation status or tumor location. Normalized gemcitabine levels were similar in patient 1 and the DIPG PDX.

Conclusions

These findings, while limited to one agent, provide preliminary evidence for the hypotheses that lack of intratumoral penetration is not why systemic chemotherapy has failed in DIPG, and orthotopic PDX models can adequately model intratumoral PK in human DIPG.

The Inflammatory Milieu of Adamantinomatous Craniopharyngioma and Its Implications for Treatment

Pediatric Adamantinomatous Craniopharyngiomas (ACPs) are histologically benign brain tumors that often follow an aggressive clinical course. Their suprasellar location leaves them in close proximity to critical neurological and vascular structures and often results in significant neuroendocrine morbidity. Current treatment paradigms, involving surgical resection and radiotherapy, confer significant morbidity to patients and there is an obvious need to discover effective and safe alternative treatments. Recent years have witnessed significant efforts to fully detail the genomic, transcriptomic and proteomic make-up of these tumors, in an attempt to identify potential therapeutic targets. These studies have resulted in ever mounting evidence that inflammatory processes and the immune response play a critical role in the pathogenesis of both the solid and cystic portion of ACPs. Several inflammatory and immune markers have been identified in both the cyst fluid and solid tumor tissue of ACP. Due to the existence of effective agents that target them, IL-6 and immune checkpoint inhibitors seem to present the most likely immediate candidates for clinical trials of targeted immune-related therapy in ACP. If effective, such agents may result in a paradigm shift in treatment that ultimately reduces morbidity and results in better outcomes for our patients.

Targeted fusion analysis can aid in the classification and treatment of pediatric glioma, ependymoma, and glioneuronal tumors

BACKGROUND

The use of next-generation sequencing for fusion identification is being increasingly applied and aids our understanding of tumor biology. Some fusions are responsive to approved targeted agents, while others have future potential for therapeutic targeting. Although some pediatric central nervous system tumors may be cured with surgery alone, many require adjuvant therapy associated with acute and long-term toxicities. Identification of targetable fusions can shift the treatment paradigm toward earlier integration of molecularly targeted agents.

METHODS

Patients diagnosed with glial, glioneuronal, and ependymal tumors between 2002 and 2019 were retrospectively reviewed for fusion testing. Testing was done primarily using the ArcherDx FusionPlex Solid Tumor panel, which assesses fusions in 53 genes. In contrast to many previously published series chronicling fusions in pediatric patients, we compared histological features and the tumor classification subtype with the specific fusion identified.

RESULTS

We report 24 cases of glial, glioneuronal, or ependymal tumors from pediatric patients with identified fusions. With the exception of BRAF:KIAA1549 and pilocytic/pilomyxoid astrocytoma morphology, and possibly QKI-MYB and angiocentric glioma, there was not a strong correlation between histological features/tumor subtype and the specific fusion. We report the unusual fusions of PPP1CB-ALK, CIC-LEUTX, FGFR2-KIAA159, and MN1-CXXC5 and detail their morphological features.

CONCLUSIONS

Fusion testing proved to be informative in a high percentage of cases. A large majority of fusion events in pediatric glial, glioneuronal, and ependymal tumors can be identified by relatively small gene panels.

Clinicopathologic and molecular features of intracranial desmoplastic small round cell tumors

Desmoplastic small round cell tumors (DSRCTs) are highly aggressive sarcomas that most commonly occur intra-abdominally, and are defined by EWSR1-WT1 gene fusion. Intracranial DSRCTs are exceptionally rare with only seven previously reported fusion-positive cases. Herein, we evaluate the clinical, morphologic, immunohistochemical and molecular features of five additional examples. All patients were male (age range 6-25 years; median 11 years), with four tumors located supratentorially and one within the posterior fossa. The histologic features were highly variable including small cell, embryonal, clear cell, rhabdoid, anaplastic and glioma-like appearances. A prominent desmoplastic stroma was seen in only two cases. The mitotic index ranged from <1 to 12/10 HPF (median 5). While all tumors showed strong desmin positivity, epithelial markers such as EMA, CAM 5.2 and other keratins were strongly positive in only one, focally positive in two and negative in two cases. EWSR1-WT1 gene fusion was present in all cases, with accompanying mutations in the TERT promoter or STAG2 gene in individual cases. Given the significant histologic diversity, in the absence of genetic evaluation these cases could easily be misinterpreted as other entities. Desmin immunostaining is a useful initial screening method for consideration of a DSRCT diagnosis, prompting confirmatory molecular testing. Demonstrating the presence of an EWSR1-WT1 fusion provides a definitive diagnosis of DSRCT. Genome-wide methylation profiles of intracranial DSRCTs matched those of extracranial DSRCTs. Thus, despite the occasionally unusual histologic features and immunoprofile, intracranial DSRCTs likely represent a similar, if not the same, entity as their soft tissue counterpart based on the shared fusion and methylation profiles.

Targetable molecular alterations in congenital glioblastoma

INTRODUCTION

Congenital glioblastomas (cGBMs) are uncommon tumors presenting in early infancy, variably defined as diagnosed at birth or at age less than 3 months by strict criteria, or more loosely, as occurring in very young children less than 12 months of age. Previous studies have shown that cGBMs are histologically indistinguishable from GBMs in older children or adults, but may have a more favorable clinical outcome, suggesting biological differences between congenital versus other GBMs. Due to the infrequency of cGBMs, especially when employing strict inclusion criteria, molecular features have not been sufficiently explored.

METHODS

Archer FusionPlex Solid Tumor Kit, Archer VariantPlex Solid Tumor Kit, Illumina RNAseq were utilized to study cGBMs seen at our institution since 2002. A strict definition for cGBM was utilized, with only infants less than age 3 months at clinical presentation sought for this study.

RESULTS

Of the 8 cGBM cases identified in our files, 7 had sufficient materials for molecular analyses, and 3 of 7 cases analyzed showed fusions of the ALK gene (involving MAP4, MZT2Bex2 and EML4 genes as fusion partners). One case showed ROS1 fusion. Somatic mutations in TSC22D1, BMG1 and DGCR6 were identified in 1 case. None of the cases showed alterations in IDH1/2, histone genes, or the TERT gene, alterations which can be associated with GBMs in older children or adults.

CONCLUSIONS

Our results show that cGBMs are genetically heterogeneous and biologically different from pediatric and adult GBMs. Identification of ALK and ROS1 raise the possibility of targeted therapy with FDA-approved targeted inhibitors.

Establishment of patient-derived orthotopic xenograft model of 1q+ posterior fossa group A ependymoma

BACKGROUND

Treatment for pediatric posterior fossa group A (PFA) ependymoma with gain of chromosome 1q (1q+) has not improved over the past decade owing partially to lack of clinically relevant models. We described the first 2 1q+ PFA cell lines, which have significantly enhanced our understanding of PFA tumor biology and provided a tool to identify specific 1q+ PFA therapies. However, cell lines do not accurately replicate the tumor microenvironment. Our present goal is to establish patient-derived xenograft (PDX) mouse models.

METHODS

Disaggregated tumors from 2 1q+ PFA patients were injected into the flanks of NSG mice. Flank tumors were then transplanted into the fourth ventricle or lateral ventricle of NSG mice. Characterization of intracranial tumors was performed using imaging, histology, and bioinformatics.

RESULTS

MAF-811_XC and MAF-928_XC established intracranially within the fourth ventricle and retained histological, methylomic, and transcriptomic features of primary patient tumors. We tested the feasibility of treating PDX mice with fractionated radiation or chemotherapy. Mice tolerated radiation despite significant tumor burden, and follow-up imaging confirmed radiation can reduce tumor size. Treatment with fluorouracil reduced tumor size but did not appear to prolong survival.

CONCLUSIONS

MAF-811_XC and MAF-928_XC are novel, authentic, and reliable models for studying 1q+ PFA in vivo. Given the successful response to radiation, these models will be advantageous for testing clinically relevant combination therapies to develop future clinical trials for this high-risk subgroup of pediatric ependymoma.

Denosumab Therapy Obscures Histological Features of Giant Cell Tumor of Bone

Giant cell tumor (GCT) of bone is a locally aggressive tumor with low metastatic potential, usually originating in long bones. Numerous spinal examples have been reported and thus GCTs can be encountered by neuropathologists. We describe a 69-year-old man with more than a 10-year history of GCT primary to the femur that had recently metastasized to the occipital skull bone. The patient had been receiving denosumab, an adjuvant therapy for GCT, prior to the metastasis. Review of the histological features of the original primary tumor in the femur showed archetypal features of GCT, but the posttreatment occipital skull metastasis showed a predominantly low-to-medium cell density spindle cell tumor with complete depletion of osteoclastic giant cells. Although this effect of the drug is increasingly being recognized by soft tissue pathologists, the current case illustrates the potentially confusing histology of postdenosumab-treated GCT for neuropathologists. The absence of giant cells leads the posttherapy primary or metastatic lesion to show histologic similarity to a multitude of benign and malignant fibro-osseous lesions or spindle cell sarcoma and highlights the importance of eliciting appropriate clinical history.