Molecular subgroups of medulloblastoma: the current consensus

EphA2 and phosphoantigen-mediated selective killing of medulloblastoma by γδT cells preserves neuronal and stem cell integrity

Medulloblastoma (MB) is a pediatric brain tumor that develops in the cerebellum, representing one of the most common malignant brain cancers in children. Standard treatments include surgery, chemotherapy, and radiation, but despite a 5-y survival rate of approximately 70%, these therapies often lead to significant neurological damage in the developing brain. This underscores the urgent need for less toxic, more effective therapeutic alternatives. Recent advancements in cancer immunotherapy, including immune checkpoint inhibitors and CAR-T cell therapy, have revolutionized cancer treatment. One promising avenue is the use of Gamma Delta (γδ)T cells, a unique T cell population with potential advantages, such as non-alloreactivity, potent tumor cell lysis, and broad antigen recognition. However, their capacity to recognize and target MB cells remains underexplored. To investigate the therapeutic potential of γδT cells against MB, we analyzed the proportion and status of MB-infiltrated γδT cells within patient datasets. We next investigated the expression of γδT cell ligands on MB cells and identified the EphA2 receptor and the phosphoantigen/Butyrophilin complex as key ligands, activating Vγ9 Vδ1 and Vγ9 Vδ2 T cells, respectively, leading to significant MB cell lysis in both monolayer and spheroid models. Importantly, preliminary safety data showed that γδT cells did not target differentiated neurons or neuroepithelial stem cells derived from induced pluripotent stem cells, underscoring the selectivity and safety of this approach. In conclusion, γδT cells trigger an efficient and specific killing of MB and would offer a promising novel therapeutic strategy.

Molecular classification of medulloblastoma using immunohistochemistry: A single centre study

Medulloblastoma (MB) is the second most common malignant paediatric central nervous system (CNS) tumour. The World Health Organisation (WHO) advocates an integrated pathological and molecular approach to diagnosis. Immunohistochemistry (IHC) has been proven to be a valid surrogate for molecular subtyping in low resource settings. This study aimed to use IHC to classify MB into different molecular subtypes. Patients diagnosed with medulloblastoma between 2011 and 2021 were included in the study. Clinicopathological characteristics, treatment patterns and outcomes were reviewed. Molecular subgrouping into wingless signalling activated (WNT), sonic hedgehog (SHH), and non-WNT/non-SHH was performed by immunohistochemical staining, using β-catenin, Yes-associated protein 1 (YAP1) and GRB2-Associated Binding Protein 1 (GAB1) antibodies. Of the 32 children evaluated, the mean age at diagnosis was 9.9 years with M: F ratio of 1.5:1. Classic (75.8 %) and desmoplastic/nodular (24.2 %) were the only two histopathological variants reported. Non-WNT/non-SHH constituted the majority of cases (54.5 %), followed by SHH (36.4 %) and WNT subgroups (9.1 %). The 5-year overall survival and 5-year progression-free survival was 41 % and 38 % respectively. The 30-day operative mortality rate was 28.1 %. Molecular subgroups determined by immunohistochemistry, can be easily incorporated into routine practice in low resource settings. The overall survival rate in our cohort is lower than thate reported in the literature due to high post-operative mortality and low uptake of adjuvant oncotherapy.

Computational and biological modeling of IGF1R inhibition for multifocal medulloblastoma

BACKGROUND

Leptomeningeal metastasis in medulloblastoma poses challenges for effective treatments due to the blood-brain barrier (BBB), which may be addressed through intrathecal or intraventricular drug delivery. However, the lack of pharmacokinetic modeling for pathological cerebrospinal fluid (CSF) geometries has limited the ability to predict effective intrathecal and intraventricular drug exposure.

METHODS

A patient-specific computational fluid dynamics "in silico" trial was conducted to simulate CSF movement to examine the tumor microenvironment in terms of drug-target exposure over time following intraventricular delivery via Omaya Reservoir. Simultaneously, we conducted cellular adhesion experiments to test the therapeutic potential of IGF1R inhibition on metastasis under patient-specific flow conditions generated by computational analysis.

RESULTS

A 3-dimensional computational fluid dynamics (CFD) model based on patient-specific conditions was obtained to predict an efficacious drug concentration, providing guidance for therapeutic drug exposure at targeted sites. Microfluidic experiments for IGF1R inhibition of cellular adhesion showed the potential for reduced attachment of medulloblastoma to leptomeningeal cells to prevent metastasis.

CONCLUSIONS

This study offers insights from patient-specific in silico trials for the precision delivery of small-molecule drugs for the treatment of central nervous system (CNS) malignancies.

Chromatin modification abnormalities by CHD7 and KMT2C loss promote medulloblastoma progression

Medulloblastoma (MB), a common malignant pediatric brain tumor arising in the cerebellum, is characterized by mutations in chromatin modifiers, highlighting the significance of chromatin modification abnormalities in its progression. While animal models have effectively demonstrated this, a comprehensive evaluation of the oncogenic potential of these mutations remains incomplete. In this study, we use CRISPR-mediated gene editing to knock out chromatin modifier genes mutated in human SHH MB, along with the Ptch1 gene, in cerebellar granule neuron progenitors of neonatal mice. This reveals that depletion of Chd7 and Kmt2c accelerates tumor growth. Multi-layered omics analysis uncovers that inhibition of the neuronal differentiation program by chromatin dysregulation is a key signaling pathway in tumor progression. Additionally, forced expression of Neurod1, a common target of these chromatin modifiers, inhibits proliferation and promotes differentiation. These findings highlight converging chromatin modification abnormalities from distinct mutations in Sonic Hedgehog MB and suggest that epigenetic drugs activating neuronal genes have significant potential as novel treatments.

Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosis

MYC-driven group-3 medulloblastomas (MBs) are malignant pediatric brain cancers without cures. To define actionable metabolic dependencies, we identify upregulation of dihydrolipoyl transacetylase (DLAT), the E2-subunit of pyruvate dehydrogenase complex (PDC) in a subset of group-3 MB with poor prognosis. DLAT is induced by c-MYC and targeting DLAT lowers TCA cycle metabolism and glutathione synthesis. We also note upregulation of isocitrate dehydrogenase 1 (IDH1) gene expression in group-3 MB patient tumors and suppression of IDH1 epigenetically reduces c-MYC and downstream DLAT levels in multiple c-MYC amplified cancers. DLAT is a central regulator of cuproptosis (copper-dependent cell death) induced by the copper ionophore elesclomol. DLAT expression in group-3 MB cells correlates with increased sensitivity to cuproptosis. Elesclomol is brain-penetrant and suppresses tumor growth in vivo in multiple group-3 MB animal models. Our data uncover an IDH1/c-MYC dependent vulnerability that regulates DLAT levels and can be targeted to kill group-3 MB by cuproptosis.

Medulloblastoma's master regulators and their association with patients' risk

Medulloblastoma (MB) is the most common malignant pediatric brain tumor, accounting for approximately 20% of all childhood brain tumors. Despite recent advances, current treatments like surgery, radiation, and chemotherapy still lead to severe side effects and high morbidity. Limited knowledge exists regarding the regulatory mechanisms behind the MB transcriptional alterations in high-aggressive subgroups like Group 3 and Group 4, hindering the development of targeted therapies. Identifying key transcriptional regulators, known as master regulators (MRs), can elucidate the dysregulated pathways underlying MB progression and uncover potential treatment targets. In this study, we utilize primary MB gene expression samples to infer its regulatory network. Subsequently, we applied the Master Regulator Analysis identifying the transcription factors BHLHE41, RFX4, and NPAS3 as its main transcriptional regulators, showing tumor suppressor features. We also identified eight risk MRs highly associated with patient outcome: four regulators (MYC, REL, ZSCAN5 A, and ZFAT) with activities associated with poor prognosis, and four (PAX6, ARNT2, ZNF157, and HIVEP3) acting antagonistically, being associated with good outcome. Our results offer key insights into the molecular mechanisms driving these tumors and identify novel potential therapeutic targets, addressing the urgent need for more effective and less toxic treatments.

Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects by RaMBat

As the most common pediatric brain malignancy, medulloblastoma (MB) includes multiple distinct molecular subtypes characterized by clinical heterogeneity and genetic alterations. Accurate identification of MB subtypes is essential for downstream risk stratification and tailored therapeutic design. Existing MB subtyping approaches perform poorly due to limited cohorts and severe batch effects when integrating various MB data sources. To address these concerns, we propose a novel approach called RaMBat for accurate MB subtyping from diverse data sources with severe batch effects. Benchmarking tests based on 13 datasets with severe batch effects suggested that RaMBat achieved a median accuracy of 99%, significantly outperforming state-of-the-art MB subtyping approaches and conventional machine learning classifiers. RaMBat could efficiently deal with the batch effects and clearly separate subtypes of MB samples from diverse data sources. We believe RaMBat will bring direct positive impacts on downstream MB risk stratification and tailored treatment design.

Immunohistochemical detection of 5-hydroxymethylcytosine as a prognostic biomarker in non-WNT/Non-SHH medulloblastomas

Although reduced levels of global 5-hydroxymethylcytosine (5hmC) have been observed in medulloblastomas (MBs), it remains unclear whether immunohistochemical (IHC) evaluation of 5hmC can serve as a prognostic biomarker for patients with MB. We performed IHC staining using a 5hmC antibody on a cohort of 114 pediatric MBs, including 69 non-WNT/non-SHH MBs. The 5hmC staining score was evaluated using a 9-point scale based on both the staining intensity and the percentage positive cells. We found that a low 5hmC staining score (< 5 points) was associated with poor outcomes in patients with non-WNT/non-SHH MB (both P < 0.001). Multivariate Cox regression analyses demonstrated the 5hmC staining score was an independent prognostic predictor for progression-free survival (P < 0.001) and overall survival (P = 0.004) in patients with non-WNT/non-SHH MB. Both the receiver operating characteristic curves and calibration curves demonstrated the excellent performance of the nomogram models established based on the Cox regression models. The high predictive accuracy of the nomogram models was confirmed in a validation cohort comprising 32 patients with non-WNT/non-SHH MB. In conclusion, IHC evaluation of 5hmC may serve as a cost-effective and readily accessible approach for the prognostic stratification of patients with non-WNT/non-SHH MB.

T-type calcium channels regulate medulloblastoma and can be targeted for therapy

PURPOSE

The goal of this study was to investigate the role and therapeutic targeting of T-type calcium channels in medulloblastoma, a common and deadly pediatric brain tumor that arises in the cerebellum.

METHODS

T-type calcium channel expression was assessed in publicly available bulk and single cell RNA-seq datasets. The effects of T-type calcium channel blocker mibefradil on cell growth, death and invasion were assessed with cell counting, alamar blue, trypan blue and transwell assays. Proteomic-based drug target and signaling pathway mapping was performed with Reverse Phase Protein Arrays (RPPA). Co-expression modules of single cell RNA-seq data were generated using high dimensional weighted gene co-expression network analysis (hdWGCNA). Orthotopic xenografts were used for therapeutic studies with the T-Type calcium channel blocker mibefradil.

RESULTS

T-type calcium channels were upregulated in more than 30% of medulloblastoma tumors and patients with high expression associated with a worse prognosis. T-type calcium channels had variable expression across all the subgroups of medulloblastoma at the bulk RNA-seq and single-cell RNA-seq level. Mibefradil treatment or siRNA mediated silencing of T-type calcium channels inhibited tumor cell growth, viability and invasion. RPPA-based protein/phosphoprotein signal pathway activation mapping of T-type calcium channel inhibition and single cell hdWGCNA identified altered cancer signaling pathways. Oral administration of mibefradil inhibited medulloblastoma xenograft growth and prolonged animal survival.

CONCLUSION

Our results represent a first comprehensive multi-omic characterization of T-type calcium channels in medulloblastoma and provide preclinical data for repurposing mibefradil as a treatment strategy for these relatively common pediatric brain tumors.

Adult Medulloblastoma: Clinicomolecular Spectrum, An Institutional Experience

Medulloblastoma is uncommon and molecularly lesser known in adults than their pediatric counterparts. This study aims to describe the clinicopathological and molecular characteristics of medulloblastoma in adults. Methods. The clinical, histopathological, and molecular features of 113 medulloblastoma patients of >18 years of age were reviewed. Molecular grouping (wingless pathway activated [WNT]-activated, sonic hedgehog activated [SHH]-activated, non-WNT/non-SHH, Group 3 and non-WNT/non-SHH, Group 4) was done by gene expression profiling. Results. The age-range was 19 to 59 years. The most common histoarchitecture was classic (64%), followed by desmoplastic/nodular (31%) and large cell/anaplastic (5%). The most common molecular group was SHH-activated (65%), followed by WNT-activated (14%), non-WNT/non-SHH, Group 4 (10%), and non-WNT/non-SHH, Group 3 (3%). All desmoplastic/nodular tumors were SHH-activated; while large cell/anaplastic had SHH-activated, WNT-activated and non-WNT/non-SHH, Group 3. TP53-mutant pattern of immunophenotype was observed in 7% (3 SHH-activated; 1 WNT-activated; 1 non-WNT/non-SHH, Group 3; 2 indeterminate). Within the SHH-activated group, TP53-mutant pattern immunophenotype was noted in 3 tumors and 1 was MYCN-amplified. In the WNT-activated group, both monosomy 6 and CTNNB1 mutation were seen in 3 tumors and 3 each had an isolated alteration. Conclusion. SHH-activated medulloblastoma is the most common group and WNT-activated is not rare in adults. Non-WNT/non-SHH, Group 3 though rare is not nonexistent in adults.

Alternative spliceosomal protein Eftud2 mediated Kif3a exon skipping promotes SHH-subgroup medulloblastoma progression

Alternative splicing plays a pivotal role in various facets of organogenesis, immune response, and tumorigenesis. Medulloblastoma represents a prevalent childhood brain tumor, with approximately one-third classified as the Sonic Hedgehog (SHH) subgroup. Nevertheless, the contribution of alternative splicing to medulloblastoma oncogenesis remains elusive. This investigation delineated an upregulation of the spliceosomal protein Eftud2 in the SHH-subgroup medulloblastoma mouse model and human medulloblastoma patients. Targeted ablation of Eftud2 in granule precursor cells (GNPs) within the cerebellum prolonged the survival of SHH-subgroup medulloblastoma mice, indicating a putative association between Eftud2 expression and medulloblastoma prognosis. Functional assays unveiled that EFTUD2 depletion in human medulloblastoma cells significantly curtailed cellular proliferation by impeding the activation of the SHH signaling pathway. Through multi-omics sequencing analysis, it was discerned that Eftud2 influences exons 10-11 skipping of Kif3a, a kinesin motor critical for primary cilia formation. Notably, exons 10-11 skipping in Kif3a augmented human medulloblastoma cell proliferation by potentiating the transcriptional activity of Gli2. These findings underscore a robust correlation between Eftud2 and SHH-subgroup medulloblastoma, emphasizing its regulatory role in modulating downstream transcription factors through the alternative splicing of pivotal genes within the SHH signaling pathway, thereby propelling the aggressive proliferation of SHH-subgroup medulloblastoma.

Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of LSD1 and OXPHOS

The histone H3 lysine 4 (H3K4) methyltransferase KMT2D (also called MLL4) is one of the most frequently mutated epigenetic modifiers in many cancers, including medulloblastoma (MB). Notably, heterozygous KMT2D loss frequently occurs in MB and other cancers. However, its oncogenic role remains largely uncharacterized. Here, we show that heterozygous Kmt2d loss in murine cerebellar regions promotes MB genesis driven by heterozygous loss of the MB-suppressor gene Ptch via the upregulation of tumor-promoting programs (e.g., oxidative phosphorylation [OXPHOS]). Downregulation of the transcription-repressive tumor suppressor NCOR2 by heterozygous Kmt2d loss, along with Ptch+/--increased MYCN, upregulated tumor-promoting genes. Heterozygous Kmt2d loss substantially diminished enhancer marks (H3K4me1 and H3K27ac) and the H3K4me3 signature, including those for Ncor2. Combinatory pharmacological inhibition of the enhancer-decommissioning H3K4 demethylase LSD1 and OXPHOS significantly reduced the tumorigenicity of MB cells bearing heterozygous Kmt2d loss. Our findings suggest the molecular and epigenetic pathogenesis underlying the MB-promoting effect of heterozygous KMT2D loss.

Therapeutic approaches for targeting the pediatric brain tumor microenvironment

Central nervous system (CNS) tumors are the most frequent solid malignant tumors in pediatric patients and are the leading cause of tumor-related death in children. Treatment for this heterogeneous group of tumors consists of various combinations of safe maximal surgical resection, chemotherapy, and radiation therapy which offer a cure for some children but often cause debilitating adverse late effects in others. While therapies targeting the tumor microenvironment (TME) like immune checkpoint inhibition (ICI) have been successful in treating some cancers, these therapies failed to exhibit treatment efficacy in the majority of pediatric brain tumors in the clinic. Importantly, the pediatric TME is unique and distinct from adult brain tumors and designing therapies to effectively target these tumors requires understanding the unique biology of pediatric brain tumors and the use of translational models that recapitulate the TME. Here we describe the TME of medulloblastoma (MB) and diffuse midline glioma (DMG), specifically diffuse intrinsic pontine glioma (DIPG), and further present the current drug delivery approaches and clinical administration routes targeting the TME in these tumors, including preclinical and clinical studies.

Adult tentorial medulloblastoma mimicking meningioma: A case report and systematic review

Background

Tentorial medulloblastomas in adults are exceedingly rare and may clinically and radiologically mimic meningiomas. This case report, with a systematic review, aims to outline the clinical, radiological, pathological, and management strategies for adult tentorial medulloblastoma.

Case Description

A 37-year-old male patient presented with headaches, vertigo, and vomiting. Imaging investigations revealed a tentorial extra-axial mass, initially considered a meningioma. The patient subsequently underwent surgical resection followed by chemoradiation. Histopathological examination ultimately identified the mass as an eccentrically located adult medulloblastoma. We conducted a systematic review of the literature, analyzing four studies that reported similar cases. This analysis included clinical and demographic information, diagnosis through imaging and histopathology, treatment methods, and outcomes for seven cases, including our own.

Conclusion

Adult tentorial medulloblastomas are extremely rare tumors that may mimic meningiomas, posing significant clinical challenges. Accurate diagnosis necessitates advanced imaging techniques and histopathological confirmation. The primary treatment strategy involves maximal surgical resection, supplemented by chemoradiotherapy.

The dual HDAC/PI3K inhibitor CUDC-907 inhibits the growth and proliferation of MYC-driven Group 3 medulloblastoma

Metastatic Group 3 medulloblastoma (G3 MB) have been shown in several studies to be very high risk, particularly those harboring MYC amplification. More effective therapies are especially important for these patients. CUDC-907, a novel dual inhibitor targeting the MYC upstream pathway (HDAC/PI3K), shows significant antitumor efficacy across multiple cancer types. However, the antitumor effects and underlying mechanisms of CUDC-907 in MB, particularly in very high-risk MB, remain unexplored. In this study, we showed that MYC amplified G3 MB cells, patient-derived organoids and xenograft models were sensitive to CUDC-907. CUDC-907 inhibited MYC expression through the HDAC and PI3K pathways, and then induced G0/G1 phase arrest through the MYC-P21/P27-CDKs/cyclins axis. Furthermore, when CUDC-907 was combined with chemotherapeutic drug cisplatin, G0/G1 phase blocking effect was further enhanced. CUDC-907 in combination with radiotherapy (RT) inhibited DNA damage repair and increased DNA damage. These findings indicate that CUDC-907, either as a monotherapy or in combination with chemoradiotherapy, represents a promising therapeutic strategy for MYC amplified G3 MB, potentially influencing future clinical trials targeting this patient population.

Pediatric CNS tumors: Overview and treatment paradigms

Central nervous system (CNS) tumors represent the most common solid tumors occurring in children, with gliomas, medulloblastomas and ependymomas being the most frequently diagnosed. The most recent 2021 World Health Organization (WHO) Classification of Tumors of the CNS (CNS5) has integrated molecular genetics with traditional histopathology leading to more accurate diagnosis and risk stratification/prognostication with subsequent development of personalized treatment paradigms. Pediatric gliomas are traditionally subdivided into low-grade (pLGG) or high-grade gliomas (pHGG). pLGG tend to have excellent overall survival, however, the disease course maybe characterized by multiple recurrences resulting in significant morbidity. Surgical resection is standard with medical therapy (chemotherapy or oral molecular targeted therapy) reserved in the event of radiographic/symptomatic progression. pHGG have poor overall survival despite intensive multimodality therapy. Ependymomas occur in the infratentorial and supratentorial brain as well as in the spine, with the standard treatment including maximal safe resection with involved field radiation therapy that is curative in two-thirds of patients overall. Medulloblastomas are the most common malignant embryonal CNS tumor arising in the cerebellum and are biologically heterogeneous. Given the risk of CSF dissemination, medulloblastomas require surgery, craniospinal radiation as well as multi agent chemotherapy, an approach that is curative in the majority of patients with non-metastatic disease. The field of pediatric neuro-oncology has made robust strides in the past few decades and the role of molecular diagnostics has continued to improve our understanding of pediatric tumor biology and offer more personalized treatment paradigms.

Advancements and challenges in CAR T cell therapy for pediatric brain tumors: A review

Chimeric Antigen Receptor (CAR) T cell therapy represents a groundbreaking advancement in immunotherapy, initially gaining FDA approval for treating hematological malignancies. This therapy has shown promising results in solid tumors, particularly in pediatric brain tumors, which are the leading cause of cancer-related death in children. CAR T cells are engineered to target specific antigens on tumor cells, thereby reducing off-target effects and increasing the cytotoxic impact on cancer cells. Over the years, CAR T cell technology has evolved through five generations, each enhancing the structure, functionality, and safety of these cells. Despite these advancements, the application of CAR T cells in solid tumors, especially within the central nervous system (CNS), faces significant challenges. These include the physical barrier posed by the blood-brain barrier (BBB), the immunosuppressive tumor microenvironment (TME), and the heterogeneity of tumor antigens. The review discusses several promising antigenic targets for CAR T cells in pediatric brain tumors, such as HER2, EphA2, IL-13Rα2, and Survivin, which have been explored in recent clinical trials. These trials have shown early promise in improving patient outcomes, though the risks of cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) remain concerns. The future of CAR T cell therapy lies in overcoming these barriers through innovative approaches like "Armored CARs" or TRUCKs, designed to modulate the TME and improve CAR T cell efficacy in solid tumors. Additionally, combination therapies and safety switches in next-generation CAR T cells are being explored to enhance therapeutic potential while minimizing adverse effects.

miR-512-3p as a Potential Biomarker of Poor Outcome in Pediatric Medulloblastoma

The tumorigenesis of medulloblastoma (MB), the most frequent malignant brain tumor in children, is not completely known. MicroRNA (miRNA) expression profiles have been associated with human cancers; however, the role played by miRNAs in pediatric MB has been poorly explored. Global miRNA expression in MB and non-neoplastic cerebellum samples was evaluated by microarray assay. Nine miRNAs (miR-31-5p, -329, -383, -433, -485-3p, -485-5p, -491, -512-3p, and 539-5p) in 51 pediatric MB and 7 pediatric non-neoplastic cerebellum samples were chosen for validation by qRT-PCR. The validated miRNAs were less expressed in the MB samples than in the non-neoplastic controls. In our cohort of patients, higher miR-512-3p expression was associated with incomplete degree of resection, classification as high risk, classification as group 4, and poor overall survival. In silico analysis in an independent cohort of MB patients identified that some of the miR-512-3p target genes were also correlated with prognostic features. Our results have shown that miR-512-3p could be associated with poor clinical outcomes in pediatric MB, suggesting that miR-512-3p is a potential biomarker of prognosis.

The T cell receptor landscape of childhood brain tumors

The diverse T cell receptor (TCR) repertoire confers the ability to recognize an almost unlimited array of antigens. Characterization of antigen specificity of tumor-infiltrating lymphocytes (TILs) is key for understanding antitumor immunity and for guiding the development of effective immunotherapies. Here, we report a large-scale comprehensive examination of the TCR landscape of TILs across the spectrum of pediatric brain tumors, the leading cause of cancer-related mortality in children. We show that a T cell clonality index can inform patient prognosis, where more clonality is associated with more favorable outcomes. Moreover, TCR similarity groups' assessment revealed patient clusters with defined human leukocyte antigen associations. Computational analysis of these clusters identified putative tumor antigens and peptides as targets for antitumor T cell immunity, which were functionally validated by T cell stimulation assays in vitro. Together, this study presents a framework for tumor antigen prediction based on in situ and in silico TIL TCR analyses. We propose that TCR-based investigations should inform tumor classification and precision immunotherapy development.

Targeting processive transcription for Myc-driven circuitry in medulloblastoma

Background

Medulloblastoma is the most common malignant brain tumor of childhood. The highest-risk tumors are driven by recurrent Myc amplifications (Myc-MB) and experience poorer outcomes despite intensive multimodal therapy. The Myc transcription factor defines core regulatory circuitry for these tumors and acts to broadly amplify downstream pro-survival transcriptional programs. Therapeutic targeting of Myc directly has proven elusive, but inhibiting transcriptional cofactors may present an indirect means of drugging the oncogenic transcriptional circuitry sustaining Myc-MB.

Methods

Independent CRISPR-Cas9 screens were pooled to identify conserved dependencies in Myc-MB. We performed chromatin conformation capture (Hi-C) from primary patient Myc-MB samples to map enhancer-promoter interactions. We then treated in vitro and xenograft models with CDK9/7 inhibitors to evaluate effect on Myc-driven programs and tumor growth.

Results

Eight CRISPR-Cas9 screens performed across three independent labs identify CDK9 as a conserved dependency in Myc-MB. Myc-MB cells are susceptible to CDK9 inhibition, which is synergistic with concurrent inhibition of CDK7. Inhibition of transcriptional CDKs disrupts enhancer-promoter activity in Myc-MB and downregulates Myc-driven transcriptional programs, exerting potent anti-tumor effect.

Conclusions

Our findings identify CDK9 inhibition as a translationally promising strategy for the treatment of Myc-MB.

K ey P oints

CDK9 is an intrinsic dependency in Myc-driven medulloblastomaDual CDK9/7 inhibition disrupts Myc-driven transcriptional circuitryCDK9 inhibitors should be developed as pharmaceutical agents for Myc-MB.

I mportance of the S tudy

Medulloblastoma is the most common malignant brain tumor of childhood, and outcomes for high-risk subgroups remain unsatisfactory despite intensive multimodal therapy. In this study, we pool multiple independent CRISPR-Cas9 screens to identify transcriptional cofactors such as CDK9 as conserved dependencies in Myc-MB. Using Hi-C from primary patient samples, we map Myc enhancer-promoter interactions and show that they can be disrupted using inhibition of transcriptional CDKs. CDK9 inhibitor treatment depletes Myc-driven transcriptional programs, leading to potent anti-tumor effect in vitro and prolongation of xenograft survival in vivo . With a large number of CDK9 inhibitory compounds now in clinical development, this study highlights the opportunity for clinical translation of these for children diagnosed with Myc-MB.

Multi-omics approach reveals the impact of prognosis model-related genes on the tumor microenvironment in medulloblastoma

Background

The tumor microenvironment (TME) significantly impacts the progression and prognosis of medulloblastoma (MB). This study aimed to develop a TME-associated risk score(TMErisk) model using RNA sequencing data to predict patient outcomes and elucidate biological mechanisms.

Methods

RNA sequencing data from 322 Tiantan and 763 GSE85217 MB samples were analyzed. Key gene modules related to immune and stromal components were identified using Weighted Gene Co-expression Network Analysis (WGCNA). Significant genes were screened using LASSO-COX and COX regression models. Single-cell RNA sequencing (scRNA-seq), single-cell ATAC sequencing (scATAC-seq), and spatial RNA analyses validated the findings.

Results

Differential expression analysis identified 731 upregulated and 15 downregulated genes in high vs. low immune score MB patients, and 686 upregulated and 43 downregulated genes in high vs. low stromal score patients. Eight key genes (CEBPB, OLFML2B, GGTA1, GZMA, TCIM, OLFML3, NAT1, and CD1C) were included in the TMErisk model, which demonstrated strong prognostic power. High TMErisk scores correlated with poorer survival, distinct immune cell infiltration patterns, and lower tumor cell stemness. Single-cell analyses revealed the expression dynamics of TMErisk genes across cell types, including macrophages, T cells, and NK cells, and identified key regulatory transcription factors. Spatial transcriptomics showed significant clustering of TMErisk genes in tumor regions, highlighting spatial heterogeneity and the formation of immune hubs.

Conclusions

The TMErisk model enhances our understanding of the MB tumor microenvironment, serving as a robust prognostic tool and suggesting new avenues for targeted therapy.

The Principle of Cortical Development and Evolution

Human's robust cognitive abilities, including creativity and language, are made possible, at least in large part, by evolutionary changes made to the cerebral cortex. This paper reviews the biology and evolution of mammalian cortical radial glial cells (primary neural stem cells) and introduces the concept that a genetically step wise process, based on a core molecular pathway already in use, is the evolutionary process that has molded cortical neurogenesis. The core mechanism, which has been identified in our recent studies, is the extracellular signal-regulated kinase (ERK)-bone morphogenic protein 7 (BMP7)-GLI3 repressor form (GLI3R)-sonic hedgehog (SHH) positive feedback loop. Additionally, I propose that the molecular basis for cortical evolutionary dwarfism, exemplified by the lissencephalic mouse which originated from a larger gyrencephalic ancestor, is an increase in SHH signaling in radial glia, that antagonizes ERK-BMP7 signaling. Finally, I propose that: (1) SHH signaling is not a key regulator of primate cortical expansion and folding; (2) human cortical radial glial cells do not generate neocortical interneurons; (3) human-specific genes may not be essential for most cortical expansion. I hope this review assists colleagues in the field, guiding research to address gaps in our understanding of cortical development and evolution.

Single-cell transcriptomic sequencing identifies subcutaneous patient-derived xenograft recapitulated medulloblastoma

BACKGROUND

Medulloblastoma (MB) is one of the most common malignant brain tumors that mainly affect children. Various approaches have been used to model MB to facilitate investigating tumorigenesis. This study aims to compare the recapitulation of MB between subcutaneous patient-derived xenograft (sPDX), intracranial patient-derived xenograft (iPDX), and genetically engineered mouse models (GEMM) at the single-cell level.

METHODS

We obtained primary human sonic hedgehog (SHH) and group 3 (G3) MB samples from six patients. For each patient specimen, we developed two sPDX and iPDX models, respectively. Three Patch+/- GEMM models were also included for sequencing. Single-cell RNA sequencing was performed to compare gene expression profiles, cellular composition, and functional pathway enrichment. Bulk RNA-seq deconvolution was performed to compare cellular composition across models and human samples.

RESULTS

Our results showed that the sPDX tumor model demonstrated the highest correlation to the overall transcriptomic profiles of primary human tumors at the single-cell level within the SHH and G3 subgroups, followed by the GEMM model and iPDX. The GEMM tumor model was able to recapitulate all subpopulations of tumor microenvironment (TME) cells that can be clustered in human SHH tumors, including a higher proportion of tumor-associated astrocytes and immune cells, and an additional cluster of vascular endothelia when compared to human SHH tumors.

CONCLUSIONS

This study was the first to compare experimental models for MB at the single-cell level, providing value insights into model selection for different research purposes. sPDX and iPDX are suitable for drug testing and personalized therapy screenings, whereas GEMM models are valuable for investigating the interaction between tumor and TME cells.

Transcription of Clock Genes in Medulloblastoma

We investigated the transcription of circadian clock genes in publicly available datasets of gene expression in medulloblastoma (MB) tissues using the R2 Genomics Analysis and Visualization Platform. Differential expression of the core clock genes among the four consensus subgroups of MB (defined in 2012 as Group 3, Group 4, the SHH group, and the WNT group) included the core clock genes (CLOCK, NPAS2, PER1, PER2, CRY1, CRY2, BMAL1, BMAL2, NR1D1, and TIMELESS) and genes which encode proteins that regulate the transcription of clock genes (CIPC, FBXL21, and USP2). The over-expression of several clock genes, including CIPC, was found in individuals with the isochromosome 17q chromosomal aberration in MB Group 3 and Group 4. The most significant biological pathways associated with clock gene expression were ribosome subunits, phototransduction, GABAergic synapse, WNT signaling pathway, and the Fanconi anemia pathway. Survival analysis of clock genes was examined using the Kaplan-Meier method and the Cox proportional hazards regression model through the R2 Genomics Platform. Two clock genes most significantly related to survival were CRY1 and USP2. The data suggest that several clock proteins, including CRY1 and USP2, be investigated as potential therapeutic targets in MB.

A forward genetic screen identifies potassium channel essentiality in SHH medulloblastoma maintenance

Distinguishing tumor maintenance genes from initiation, progression, and passenger genes is critical for developing effective therapies. We employed a functional genomic approach using the Lazy Piggy transposon to identify tumor maintenance genes in vivo and applied this to sonic hedgehog (SHH) medulloblastoma (MB). Combining Lazy Piggy screening in mice and transcriptomic profiling of human MB, we identified the voltage-gated potassium channel KCNB2 as a candidate maintenance driver. KCNB2 governs cell volume of MB-propagating cells (MPCs), with KCNB2 depletion causing osmotic swelling, decreased plasma membrane tension, and elevated endocytic internalization of epidermal growth factor receptor (EGFR), thereby mitigating proliferation of MPCs to ultimately impair MB growth. KCNB2 is largely dispensable for mouse development and KCNB2 knockout synergizes with anti-SHH therapy in treating MB. These results demonstrate the utility of the Lazy Piggy functional genomic approach in identifying cancer maintenance drivers and elucidate a mechanism by which potassium homeostasis integrates biomechanical and biochemical signaling to promote MB aggression.

Ferroptosis Transcriptional Regulation and Prognostic Impact in Medulloblastoma Subtypes Revealed by RNA-Seq

Medulloblastoma (MB) is the most common malignant brain tumor in children, typically arising during infancy and childhood. Despite multimodal therapies achieving a response rate of 70% in children older than 3 years, treatment remains challenging. Ferroptosis, a form of regulated cell death, can be induced in medulloblastoma cells in vitro using erastin or RSL3. Using two independent medulloblastoma RNA-sequencing cohorts (MB-PBTA and MTAB-10767), we investigated the expression of ferroptosis-related molecules through multiple approaches, including Weighted Gene Co-Expression Network Analysis (WGCNA), molecular subtype stratification, protein-protein interaction (PPI) networks, and univariable and multivariable overall survival analyses. A prognostic expression score was computed based on a cross-validated ferroptosis signature. In training and validation cohorts, the regulation of the ferroptosis transcriptional program distinguished the four molecular subtypes of medulloblastoma. WGCNA identified nine gene modules in the MB tumor transcriptome; five correlated with molecular subtypes, implicating pathways related to oxidative stress, hypoxia, and trans-synaptic signaling. One module, associated with disease recurrence, included epigenetic regulators and nucleosome organizers. Univariable survival analyses identified a 45-gene ferroptosis prognostic signature associated with nutrient sensing, cysteine and methionine metabolism, and trans-sulfuration within a one-carbon metabolism. The top ten unfavorable ferroptosis genes included CCT3, SNX5, SQOR, G3BP1, CARS1, SLC39A14, FAM98A, FXR1, TFAP2C, and ATF4. Patients with a high ferroptosis score showed a worse prognosis, particularly in the G3 and SHH subtypes. The PPI network highlighted IL6 and CBS as unfavorable hub genes. In a multivariable overall survival model, which included gender, age, and the molecular subtype classification, the ferroptosis expression score was validated as an independent adverse prognostic marker (hazard ratio: 5.8; p-value = 1.04 × 10-9). This study demonstrates that the regulation of the ferroptosis transcriptional program is linked to medulloblastoma molecular subtypes and patient prognosis. A cross-validated ferroptosis signature was identified in two independent RNA-sequencing cohorts, and the ferroptosis score was confirmed as an independent and adverse prognostic factor in medulloblastoma.

MYC-dependent upregulation of the de novo serine and glycine synthesis pathway is a targetable metabolic vulnerability in group 3 medulloblastoma

BACKGROUND

Group 3 medulloblastoma (MBGRP3) represents around 25% of medulloblastomas and is strongly associated with c-MYC (MYC) amplification, which confers significantly worse patient survival. Although elevated MYC expression is a significant molecular feature in MBGRP3, direct targeting of MYC remains elusive, and alternative strategies are needed. The metabolic landscape of MYC-driven MBGRP3 is largely unexplored and may offer novel opportunities for therapies.

METHODS

To study MYC-induced metabolic alterations in MBGRP3, we depleted MYC in isogenic cell-based model systems, followed by 1H high-resolution magic-angle spectroscopy (HRMAS) and stable isotope-resolved metabolomics, to assess changes in intracellular metabolites and pathway dynamics.

RESULTS

Steady-state metabolic profiling revealed consistent MYC-dependent alterations in metabolites involved in one-carbon metabolism such as glycine. 13C-glucose tracing further revealed a reduction in glucose-derived serine and glycine (de novo synthesis) following MYC knockdown, which coincided with lower expression and activity of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in this pathway. Furthermore, MYC-overexpressing MBGRP3 cells were more vulnerable to pharmacological inhibition of PHGDH compared to those with low expression. Using in vivo tumor-bearing genetically engineered and xenograft mouse models, pharmacological inhibition of PHGDH increased survival, implicating the de novo serine/glycine synthesis pathway as a pro-survival mechanism sustaining tumor progression. Critically, in primary human medulloblastomas, increased PHGDH expression correlated strongly with both MYC amplification and poorer clinical outcomes.

CONCLUSIONS

Our findings support a MYC-induced dependency on the serine/glycine pathway in MBGRP3 that represents a novel therapeutic treatment strategy for this poor prognosis disease group.

Central nervous system tumors in adolescents and young adults: A Society for Neuro-Oncology Consensus Review on diagnosis, management, and future directions

Adolescents and young adults (AYAs; ages 15-39 years) are a vulnerable population facing challenges in oncological care, including access to specialized care, transition of care, unique tumor biology, and poor representation in clinical trials. Brain tumors are the second most common tumor type in AYA, with malignant brain tumors being the most common cause of cancer-related death. The 2021 WHO Classification for central nervous system (CNS) Tumors highlights the importance of integrated molecular characterization with histologic diagnosis in several tumors relevant to the AYA population. In this position paper from the Society for Neuro-Oncology (SNO), the diagnosis and management of CNS tumors in AYA is reviewed, focusing on the most common tumor types in this population, namely glioma, medulloblastoma, ependymoma, and CNS germ cell tumor. Current challenges and future directions specific to AYA are also highlighted. Finally, possible solutions to address barriers in the care of AYA patients are discussed, emphasizing the need for multidisciplinary and collaborative approaches that span the pediatric and adult paradigms of care, and incorporating advanced molecular testing, targeted therapy, and AYA-centered care.

Molecular and clinical heterogeneity within MYC-family amplified medulloblastoma is associated with survival outcomes: A multicenter cohort study

BACKGROUND

MYC/MYCN are the most frequent oncogene amplifications in medulloblastoma (MB) and its primary biomarkers of high-risk (HR) disease. However, while many patients' MYC(N)-amplified tumors are treatment-refractory, some achieve long-term survival. We therefore investigated clinicobiological heterogeneity within MYC(N)-amplified MB and determined its relevance for improved disease management.

METHODS

We characterized the clinical and molecular correlates of MYC- (MYC-MB; n = 64) and MYCN-amplified MBs (MYCN-MB; n = 95), drawn from >1600 diagnostic cases.

RESULTS

Most MYC-MBs were molecular group 3 (46/58; 79% assessable) and aged ≥3 years at diagnosis (44/64 [69%]). We identified a "canonical" very high-risk (VHR) MYC-amplified group (n = 51/62; 82%) with dismal survival irrespective of treatment (11% 5-year progression-free survival [PFS]), defined by co-occurrence with ≥1 additional established risk factor(s) (subtotal surgical-resection [STR], metastatic disease, LCA pathology), and commonly group 3/4 subgroup 2 with a high proportion of amplified cells. The majority of remaining noncanonical MYC-MBs survived (i.e. non-group 3/group 3 without other risk features; 11/62 (18%); 61% 5-year PFS). MYCN survival was primarily related to molecular group; MYCN-amplified SHH MB, and group 3/4 MB with additional risk factors, respectively defined VHR and HR groups (VHR, 39% [35/89]; 20% 5-year PFS/HR, 33% [29/89]; 46% 5-year PFS). Twenty-two out of 35 assessable MYCN-amplified SHH tumors harbored TP53 mutations; 9/12 (75%) with data were germline. MYCN-amplified group 3/4 MB with no other risk factors (28%; 25/89) had 70% 5-year PFS.

CONCLUSIONS

MYC(N)-amplified MB displays significant clinicobiological heterogeneity. Diagnostics incorporating molecular groups, subgroups, and clinical factors enable their risk assessment. VHR "canonical" MYC tumors are essentially incurable and SHH-MYCN-amplified MBs fare extremely poorly (20% survival at 5 years); both require urgent development of alternative treatment strategies. Conventional risk-adapted therapies are appropriate for more responsive groups, such as noncanonical MYC and non-SHH-MYCN MB.

Long-term outcome of the Milano-hyperfractionated accelerated radiotherapy strategy for high-risk medulloblastoma, including the impact of molecular subtype

BACKGROUND

We applied the strategy for M+ medulloblastoma across all high-risk subgroups, including LC/A histology, TP53 mutations, and MYC/MYCN amplification.

METHODS

Patients over 3 years old received, after surgery, staging and histo-biological analysis, sequential high-dose-methotrexate(HD-MTX), high-dose-etoposide(HD-VP16), high-dose-cyclophosphamide(HD-Cyclo), and high-dose-carboplatin(HD-Carbo). Hyperfractionated-accelerated-radiotherapy-craniospinal(HART-CSI), administered twice daily 1.3 Gy-fractions reached a total dose tailored to the patients' age and pre-radiation response to chemotherapy(CT): 31.2 Gy if under 10-years-old and complete response(CR) or partial response(PR) obtained or absence of metastatic disease, 39 Gy in other/older patients. Boosts to posterior fossa/residual metastatic(M+) deposits were given up to a total dose of 60 Gy/9 Gy, respectively, but avoided if metastatic nodules were very big or patients were very young. Two courses of high-dose-thiotepa were delivered in case of not CR/PR after the pre-radiotherapy (RT) phase and in all M0 patients either-pre/post-HART. Subgrouping was performed where the tissue was available.

RESULTS

Eighty-nine patients were enrolled, with a median age of 8.8 years, and a median follow-up of 136 months. Overall survival (OS) and event-free survival (EFS) at 5/15 years were 75.9/66.5% and 68.2/65.3%, respectively; 5/28 fatal events were not related to relapse(3 developed secondary malignancies). Sex, age less than 10 years, histological subtype, presence of MYC/MYCN amplification, reduction in CSI dose, omission of RT-boosts, implementation of myeloablative therapy, presence-absence of metastases did not impact prognosis.Patients progressing after pre-HART CT(14/89) and stable-disease(SD)+PD after HART(10/89) negatively affected outcome(P < .001).Subgrouping in 66/89 patients' samples demonstrated a significantly worse EFS for patients with Sonic Hedgehog(SHH)-tumors(#15, 2 with constitutional TP53-mutations) versus groups 3 and 4(15 and 29 patients, respectively, group3/4 in 7).Patients younger than 10 received lower CSI doses if stratified according to CT response.

CONCLUSIONS

This strategy, partly adopted in the ongoing SIOPE protocol, confirmed improved EFS and OS over previously reported outcomes in all high-risk categories; SHH tumors appeared the most aggressive.

Targeting protein synthesis pathways in MYC-amplified medulloblastoma

MYC is one of the most deregulated oncogenic transcription factors in human cancers. MYC amplification/or overexpression is most common in Group 3 medulloblastoma and is positively associated with poor prognosis. MYC is known to regulate the transcription of major components of protein synthesis (translation) machinery, leading to promoted rates of protein synthesis and tumorigenesis. MTOR signaling-driven deregulated protein synthesis is widespread in various cancers, including medulloblastoma, which can promote the stabilization of MYC. Indeed, our previous studies demonstrate that the key components of protein synthesis machinery, including mTOR signaling and MYC targets, are overexpressed and activated in MYC-amplified medulloblastoma, confirming MYC-dependent addiction of enhanced protein synthesis in medulloblastoma. Further, targeting this enhanced protein synthesis pathway with combined inhibition of MYC transcription and mTOR translation by small-molecule inhibitors, demonstrates preclinical synergistic anti-tumor potential against MYC-driven medulloblastoma in vitro and in vivo. Thus, inhibiting enhanced protein synthesis by targeting the MYC indirectly and mTOR pathways together may present a highly appropriate strategy for treating MYC-driven medulloblastoma and other MYC-addicted cancers. Evidence strongly proposes that MYC/mTOR-driven tumorigenic signaling can predominantly control the translational machinery to elicit cooperative effects on increased cell proliferation, cell cycle progression, and genome dysregulation as a mechanism of cancer initiation. Several small molecule inhibitors of targeting MYC indirectly and mTOR signaling have been developed and used clinically with immunosuppressants and chemotherapy in multiple cancers. Only a few of them have been investigated as treatments for medulloblastoma and other pediatric tumors. This review explores concurrent targeting of MYC and mTOR signaling against MYC-driven medulloblastoma. Based on existing evidence, targeting of MYC and mTOR pathways together produces functional synergy that could be the basis for effective therapies against medulloblastoma.

Modulation of Stemness and Differentiation Regulators by Valproic Acid in Medulloblastoma Neurospheres

Changes in epigenetic processes such as histone acetylation are proposed as key events influencing cancer cell function and the initiation and progression of pediatric brain tumors. Valproic acid (VPA) is an antiepileptic drug that acts partially by inhibiting histone deacetylases (HDACs) and could be repurposed as an epigenetic anticancer therapy. Here, we show that VPA reduced medulloblastoma (MB) cell viability and led to cell cycle arrest. These effects were accompanied by enhanced H3K9 histone acetylation (H3K9ac) and decreased expression of the MYC oncogene. VPA impaired the expansion of MB neurospheres enriched in stemness markers and reduced MYC while increasing TP53 expression in these neurospheres. In addition, VPA induced morphological changes consistent with neuronal differentiation and the increased expression of differentiation marker genes TUBB3 and ENO2. The expression of stemness genes SOX2, NES, and PRTG was differentially affected by VPA in MB cells with different TP53 status. VPA increased H3K9 occupancy of the promoter region of TP53. Among the genes regulated by VPA, the stemness regulators MYC and NES showed an association with patient survival in specific MB subgroups. Our results indicate that VPA may exert antitumor effects in MB by influencing histone acetylation, which may result in the modulation of stemness, neuronal differentiation, and the expression of genes associated with patient prognosis in specific molecular subgroups. Importantly, the actions of VPA in MB cells and neurospheres include a reduction in the expression of MYC and an increase in TP53.

Arrested development: the dysfunctional life history of medulloblastoma

Medulloblastoma is a heterogeneous embryonal tumor of the cerebellum comprised of four distinct molecular subgroups that differ in their developmental origins, genomic landscapes, clinical presentation, and survival. Recent characterization of the human fetal cerebellum at single-cell resolution has propelled unprecedented insights into the cellular origins of medulloblastoma subgroups, including those underlying previously elusive groups 3 and 4. In this review, the molecular pathogenesis of medulloblastoma is examined through the lens of cerebellar development. In addition, we discuss how enhanced understanding of medulloblastoma origins has the potential to refine disease modeling for the advancement of treatment and outcomes.

Modulation of Stemness and Differentiation Regulators by Valproic Acid in Medulloblastoma Neurospheres

Changes in epigenetic processes such as histone acetylation are proposed as key events influencing cancer cell function and the initiation and progression of pediatric brain tumors. Valproic acid (VPA) is an antiepileptic drug that acts partially by inhibiting histone deacetylases (HDACs) and could be repurposed as an epigenetic anticancer therapy. Here, we show that VPA reduced medulloblastoma (MB) cell viability and led to cell cycle arrest. These effects were accompanied by enhanced H3K9 histone acetylation (H3K9ac) and decreased expression of the MYC oncogene. VPA impaired the expansion of MB neurospheres enriched in stemness markers and reduced MYC while increasing TP53 expression in these neurospheres. In addition, VPA induced morphological changes consistent with neuronal differentiation and the increased expression of differentiation marker genes TUBB3 and ENO2. The expression of stemness genes SOX2, NES, and PRTG was differentially affected by VPA in MB cells with different TP53 status. VPA increased H3K9 occupancy of the promoter region of TP53. Among the genes regulated by VPA, the stemness regulators MYC and NES showed an association with patient survival in specific MB subgroups. Our results indicate that VPA may exert antitumor effects in MB by influencing histone acetylation, which may result in the modulation of stemness, neuronal differentiation, and the expression of genes associated with patient prognosis in specific molecular subgroups. Importantly, the actions of VPA in MB cells and neurospheres include a reduction in the expression of MYC and an increase in TP53.

Trends in childhood cancer: Incidence and survival analysis over 45 years of SEER data

BACKGROUND

The SEER Registry contains U.S. cancer statistics. To assess trends in incidence and survival and the impact of demographic factors among pediatric patients with cancer, we assessed nearly 5 decades (1975-2019) of data.

METHODS

All patients below the age of 20 with histology-confirmed malignancy were studied. Kaplan-Meier survival curves were generated to evaluate survival trends across treatment periods and ICCC classes. JoinPoint analysis was conducted to identify changes in incidence and survival.

RESULTS

The incidence of childhood cancer increased from 14.23 cases per 100,000 children in 1975-1979 to 18.89 in 2010-2019, with an average annual percent change of 0.73. This rise was more pronounced in several cancers, including leukemias, lymphomas, brain tumors, hepatic tumors, and gonadal germ cell tumors. Age-adjusted cancer mortality decreased from 4.9 to 2.3 per 100,000. Cancer-related mortality was consistently higher in boys than in girls, and in Black children than in White children. Survival significantly improved, with 5- and 10-year survival rates rising from 63.1% to 85.2% and from 58.8% to 82.7%, respectively. Leukemias showed a substantial increase in 5-year survival from 48.2% ± 1.7% to 85.1% ± 0.4% in 2010-2019. Lymphomas also showed significant improvement, with survival increasing from 72.9% ± 1.7% to 94.2% ± 0.3%. Despite these improvements, the survival of CNS tumors, bone tumors, and sarcomas remained suboptimal, with 5-year survival estimates of approximately 60%. Our joinpoint analysis confirmed our findings but revealed an interesting increase in the incidence of lymphomas limited to the years between 2005 and 2014.

CONCLUSION

This research elucidates advancements in survival among pediatric patients with cancer. The results offer critical perspectives on pediatric oncology, highlighting the imperative for ongoing innovation in therapeutics. Although the increase in incidence may partially stem from enhanced diagnostic capabilities and more comprehensive registration processes, the underlying causes remain unclear.

Pediatric neuro-oncology: Highlights of the last quarter-century

The last quarter century has heralded dramatic changes in the field of pediatric neuro-oncology, with the era defined by profound developments in the understanding of the biological underpinnings of childhood central nervous system (CNS) tumors and translational therapeutics. Although there have been momentous strides forward in biologic, diagnostic, therapeutic, and experimental domains, considerable challenges remain and CNS tumors remain the leading cause of pediatric cancer-related mortality. Here, we review the significant advances in the field of pediatric neuro-oncology over the last 25 years and highlight ongoing hurdles facing future progress.

ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip

Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma). Overexpression of ZIC1 suppresses the growth of group 3 medulloblastoma models, whereas it promotes the proliferation of SHH medulloblastoma precursor cells. SHH medulloblastoma ZIC1 mutants show increased activity versus wild-type ZIC1, whereas G4 medulloblastoma ZIC1 mutants exhibit LOF phenotypes. Distinct ZIC1 mutations affect cells of the rhombic lip in diametrically opposed ways, suggesting that ZIC1 is a critical developmental transcriptional regulator in both the normal and transformed rhombic lip and identifying ZIC1 as an exquisitely context-dependent driver gene in medulloblastoma.

Genomic landscape of medulloblastoma subtypes in an Asian cohort

Background

Medulloblastoma (MB) is a highly malignant childhood brain tumor. Previous research on the genetic underpinnings of MB subtypes has predominantly focused on European and American cohorts. Given the notable genetic differences between Asian and other populations, a subtype-specific study on an Asian cohort is essential to provide comprehensive insights into MB within this demographic. The aim of this study is to investigate the genomic landscape of MB subtypes in an Asian cohort to better understand the genetic variations and potential implications for clinical practice.

Methods

We conducted a study on an Asian cohort comprising 113 MB patients. Genomic sequencing was performed using MGISEQ-2000 platform. We analyzed the participants' characteristics and compared them with previous studies. All germline variants of the ten susceptibility genes of interest (APC, BRCA2, PTCH1, PTCH2, ELP1, SUFU, CTNNB1, SMARCA4, GPR161, and TP53) were annotated and validated.

Results

Our study identified 14 valid germline variants that met our criteria, with these variants being detected in the genes APC, BRCA2, PTCH1, PTCH2, ELP1, and SUFU. Of these, six variants were classified as pathogenic in ClinVar: two in PTCH2 (c.C1573T), one in ELP1 (c.C583T), and three in PTCH1 (c.G1370T, c.C2066T, c.C529T). The remaining eight variants were of uncertain significance, including those in SUFU (c.T833C), ELP1 (c.T2A), BRCA2 (c.G7488C), and APC (c.C3247A, c.A1G, c.A8042G, c.A3056G, c.G822C). Our findings highlight a subtype-based germline variant landscape specific to the Asian cohort and reinforce the connection between SUFU, PTCH1, and the SHH subtype of MB. Additionally, the identification of ELP1-related cases supports the newest findings in this area and provides typical copy number variation (CNV) results for future investigation.

Conclusions

This study provides valuable insights into the genetic landscape of MB in an Asian cohort, emphasizing the importance of population-specific research. The subtype-specific germline variant landscape identified in this study contributes to the understanding of MB and its genetic underpinnings in Asian populations, potentially guiding future research and therapeutic strategies.

Pediatric Central Nervous System Embryonal Tumors: Presentation, Diagnosis, Therapeutic Strategies, and Survivorship-A Review

Central nervous system (CNS) embryonal tumors represent a diverse group of neoplasms and have a peak incidence in early childhood. These tumors can be located anywhere within the CNS, and presenting symptoms typically represent tumor location. These tumors display distinctive findings on neuroimaging and are staged using magnetic resonance imaging of the brain and spine as well as evaluation of cerebrospinal fluid. Diagnosis is made based on an integrated analysis of histologic and molecular features via tissue sampling. Risk stratification is based on integration of clinical staging and extent of resection with histologic and molecular risk factors. The therapeutic approach for these tumors is multimodal and includes surgery, chemotherapy, and radiation, tailored to the individual patient factors (including age) and specific tumor type. Comprehensive supportive care including management of nausea, nutrition support, pain, fertility preservation, and mitigation of therapy-related morbidity (including hearing protection) is imperative through treatment of CNS embryonal tumors. Despite advances in therapy and supportive care, the long-term consequences of current treatment strategies are substantial. Integration of less toxic, molecularly targeted therapies and a comprehensive, multidisciplinary approach to survivorship care are essential to improving survival and the overall quality of life for survivors.

Association of imaging biomarkers with molecular subtypes of medulloblastoma

Background and purpose: The World Health Organization (WHO) subdivided medulloblastoma into genetic and histopathological groups, each with a specific therapeutic intervention and different clinical outcomes. These subtypes may present with distinct imaging features. Therefore, the current study aimed to identify magnetic resonance imaging (MRI) biomarkers to predict the precise pathological characteristics of medulloblastoma. Methods: This study included 28 patients with a first diagnosis of medulloblastoma who underwent preoperative brain MRI with subsequent surgical resection and histopathological confirmation at our hospital between 2010 and 2022. Conventional MRI parameters, including apparent diffusion coefficient (ADC) mean values, were correlated with molecular subtypes to identify distinct MRI biomarkers. Results: Out of 28 tumors, two (7.1%) tumors exhibited wingless (WNT) activation, thirteen (46.4%) exhibited sonic hedgehog (SHH) activation, and thirteen (46.4%) exhibited non-WNT/non-SHH activation (Group 3 or 4). Statistical analysis revealed a significant association of SHH-activated tumors with paramidline/cerebellar location and the presence of peritumoral edema (p value = <0.0001). No significant correlations were found between the genetic subtypes and the other MRI parameters. A distinctive distribution of the ADC-mean values among the various genetic subtypes with recognizable tendencies was identified. However, it was statistically insignificant. Conclusion: Conventional MRI features of the paramidline/hemispheric location and the presence of peritumoral edema were significantly correlated with the SHH activated pathway and hence can be used to facilitate the preoperative implementation of SHH-targeted therapeutic intervention. Although the ADC-mean measurements were not statistically significant, a recognizable distribution of values among the various genetic subtypes was identified.

High Expression of GABAA Receptor β Subunit Genes Is Associated with Longer Overall Survival in Medulloblastoma

Background/Objectives: Most of the rapid inhibitory neurotransmission in the brain is mediated through activation of the γ-aminobutyric acid (GABA) type A (GABAA) receptor, which is a ligand-gated ion channel. GABAA receptor activation via GABA binding allows for an intracellular influx of Cl- ions, thus inducing cellular hyperpolarization. Each GABAA receptor consists of a combination of five subunits, and several subunits have been proposed as biomarkers and therapeutic targets in cancer. Here, we show the expression of genes encoding β subunits of the GABAA receptor, namely GABRB1, GABRB2, and GABRB3, across the four different molecular subgroups of medulloblastoma (MB), which is the most common malignant pediatric brain tumor. We also show the associations of GABAA receptor β subunits with MB patients' overall survival (OS). Methods: The expression of genes encoding GABAA receptor β subunits was analyzed using a previously described dataset comprising 763 MB tumor samples. Patients were classified into high- and low-gene-expression groups, and the Kaplan-Meier estimate was used to examine the relationship between gene expression levels and patient OS. Results: High GABRB1 expression was associated with better OS within each of the four molecular subgroups. The GABRB2 gene showed higher transcript levels in Group 3 MB compared to all other subgroups, and high expression was associated with better prognosis in Group 3 tumors. GABRB3 expression was significantly higher in Group 3 and Group 4 MB, and high expression of GABRB3 genes was associated with longer OS in the sonic hedgehog (SHH) subgroup. The high expression of GABRB1, GABRB2, and GABRB3 is associated with longer patient OS in a subgroup-specific manner. Conclusions: These results indicate a role for GABAA receptors containing β subunits in influencing MB progression.

Advances in CAR-T therapy for central nervous system tumors

The application of chimeric antigen receptor T-cell therapy in central nervous system tumors has significantly advanced; however, challenges pertaining to the blood-brain barrier, immunosuppressive microenvironment, and antigenic heterogeneity continue to be encountered, unlike its success in hematological malignancies such as acute lymphoblastic leukemia and diffuse large B-cell lymphomas. This review examined the research progress of chimeric antigen receptor T-cell therapy in gliomas, medulloblastomas, and lymphohematopoietic tumors of the central nervous system, focusing on chimeric antigen receptor T-cells targeting antigens such as EGFRvIII, HER2, B7H3, GD2, and CD19 in preclinical and clinical studies. It synthesized current research findings to offer valuable insights for future chimeric antigen receptor T-cell therapeutic strategies for central nervous system tumors and advance the development and application of this therapeutic modality in this domain.

Copy number variation heterogeneity reveals biological inconsistency in hierarchical cancer classifications

Cancers are heterogeneous diseases with unifying features of abnormal and consuming cell growth, where the deregulation of normal cellular functions is initiated by the accumulation of genomic mutations in cells of - potentially - any organ. At diagnosis malignancies typically present with patterns of somatic genome variants on diverse levels of heterogeneity. Among the different types of genomic alterations, copy number variants (CNV) represent a distinct, near-ubiquitous class of structural variants. Cancer classifications are foundational for patient care and oncology research. Terminologies such as the National Cancer Institute Thesaurus provide large sets of hierarchical cancer classification vocabularies and promote data interoperability and ontology-driven computational analysis. To find out how categorical classifications correspond to genomic observations, we conducted a meta-analysis of inter-sample genomic heterogeneity for classification hierarchies on CNV profiles from 97,142 individual samples across 512 cancer entities, and evaluated recurring CNV signatures across diagnostic subsets. Our results highlight specific biological mechanisms across cancer entities with the potential for improvement of patient stratification and future enhancement of cancer classification systems and provide some indications for cooperative genomic events across distinct clinical entities.

Medulloblastomas Initiated by Homologous Recombination Defects in Mice

Germline mutations of homologous-recombination (HR) genes are among the top contributors to medulloblastomas. A significant portion of human medulloblastomas exhibit genomic signatures of HR defects. Whether ablation of Brca2 and Palb2, and their related Brca1 and Bccip genes, in the mouse brain can differentially initiate medulloblastomas was explored here. Conditional knockout mouse models of these HR genes and a conditional knockdown of Bccip (shBccip-KD) were established. Deletion of any of these genes led to microcephaly and neurologic defects, with Brca1- and Bccip- producing the worst defects. Trp53 co-deletion significantly rescued the microcephaly with Brca1, Palb2, and Brca2 deficiency but exhibited limited impact on Bccip- mice. For the first time, inactivation of either Brca1 or Palb2 with Trp53 was found to induce medulloblastomas. Despite shBccip-CKD being highly penetrative, Bccip/Trp53 deletions failed to induce medulloblastomas. The tumors displayed diverse immunohistochemical features and chromosome copy number variation. Although there were widespread up-regulations of cell proliferative pathways, most of the tumors expressed biomarkers of the sonic hedgehog subgroup. The medulloblastomas developed from Brca1-, Palb2-, and Brca2- mice were highly sensitive to a poly (ADP-ribose) polymerase inhibitor but not the ones from shBccip-CKD mice. These models recapitulate the spontaneous medulloblastoma development with high penetrance and a narrow time window, providing ideal platforms to test therapeutic agents with the ability to differentiate HR-defective and HR-proficient tumors.

Case report: A case study of variant calling pipeline selection effect on the molecular diagnostics outcome

Next-generation sequencing technologies have not only defined a breakthrough in medical genetics, but also been able to enter routine clinical practice to determine individual genetic susceptibilities. Modern technological developments are routinely introduced to genetic analysis overtaking the established approaches, potentially raising a number of challenges. To what extent is the advantage of new methodologies in synthetic metrics, such as precision and recall, more important than stability and reproducibility? Could differences in the technical protocol for calling variants be crucial to the diagnosis and, by extension, the patient's treatment strategy? A regulatory review process may delay the incorporation of potentially beneficial technologies, resulting in missed opportunities to make the right medical decisions. On the other hand, a blind adoption of new technologies based solely on synthetic metrics of precision and recall can lead to incorrect conclusions and adverse outcomes for the specific patient. Here, we use the example of a patient with a WHO-diagnosed desmoplastic/nodular SHH-medulloblastoma to explore how the choice of DNA variant search protocol affects the genetic diagnostics outcome.

Transcriptomic landscape identifies two unrecognized ependymoma subtypes and novel pathways in medulloblastoma

Medulloblastoma and ependymoma are prevalent pediatric central nervous system tumors with significant molecular and clinical heterogeneity. We collected bulk RNA sequencing data from 888 medulloblastoma and 370 ependymoma tumors to establish a comprehensive reference landscape. Following rigorous batch effect correction, normalization, and dimensionality reduction, we constructed a unified landscape to explore gene expression, signaling pathways, gene fusions, and copy number variations. Our analysis revealed distinct clustering patterns, including two primary ependymoma compartments, EPN-E1 and EPN-E2, each with specific gene fusions and molecular signatures. In medulloblastoma, we achieved precise stratification of Group 3/4 tumors by subtype and in SHH tumors by patient age. Our landscape serves as a vital resource for identifying biomarkers, refining diagnoses, and enables the mapping of new patients' bulk RNA-seq data onto the reference framework to facilitate accurate disease subtype identification. The landscape is accessible via Oncoscape, an interactive platform, empowering global exploration and application.

Risk-Stratified Radiotherapy in Pediatric Cancer

While the cure rate of cancer in children has markedly improved in the last few decades, late effects continue to be a problem in survivors. Radiotherapy, which is a major component of treatment in many cancers, is one of the major agents responsible for late toxicity. In the past decade, radiotherapy has been omitted in patients achieving excellent response to chemotherapy, such as in Hodgkin lymphoma and some Wilms tumors with lung metastases. Likewise, response to chemotherapy has been used to determine whether lower doses of radiation can be delivered in intracranial germinoma and pediatric nasopharyngeal carcinoma. Molecular subtyping in medulloblastoma is currently being employed, and in WNT-pathway M0 tumors, the reduction in radiotherapy dose to the craniospinal axis and tumor bed is currently being investigated. Finally, dose escalation was recently evaluated in patients with rhabdomyosarcoma > 5 cm who do not achieve a complete response to initial 9 weeks of chemotherapy as well as for unresectable Ewing sarcoma patients to improve local control.

Epidemiology and survival of primary intracranial malignant tumor patients with drop metastasis: a population-based analysis

BACKGROUND

Drop metastasis significantly impacts the survival of patients with primary intracranial malignant tumors. Using the information of collaborative stage from the SEER database, we aim to analyze the epidemiology and prognosis of primary intracranial malignant tumor patients with drop metastasis.

METHODS

We analyzed the distribution of patients and the frequency according to the demography and clinical characteristics of patients with drop metastasis. We also analyzed the survival of these patients with drop metastasis. Multivariate Cox proportional hazards models were used to analyze possible prognostic indicators.

RESULTS

A total of 56,839 cases with primary intracranial malignant tumors were ultimately included in this cohort study. A total of 792 cases were confirmed to have drop metastasis. The average rate of drop metastasis was 1.4%. Most of the patients with drop metastases were diagnosed before ten years old. The three most common primary intracranial malignant tumors with drop metastasis were glioblastoma, embryonal/primitive/medulloblastoma, and anaplastic astrocytoma. Embryonal/primitive/medulloblastoma had the highest drop metastasis rate, at 11.6%. Tumors located in the infratentorial space and ventricles had a higher rate of drop metastasis than tumors in other locations. The prognosis for patients with drop metastasis is poor. Routine complete treatment (surgery of the primary tumor plus chemoradiotherapy) can significantly improve overall survival.

CONCLUSION

We conducted a population-based analysis of primary intracranial malignant tumor patients with drop metastasis. Our study can help clinicians acquire general information on the epidemiology and survival of primary intracranial malignant tumor patients with drop metastasis.

PP2A activation overcomes leptomeningeal dissemination in group 3 medulloblastoma

Leptomeningeal dissemination (LMD) is the primary cause of treatment failure in children with group 3 medulloblastoma (MB). Building on our previous work on protein phosphatase 2A (PP2A) activation in MB, here we present preclinical and molecular data on the effects of two novel classes of PP2A activators on disease processes of LMD in group 3 MB. The PP2A activators used in this study are ATUX-6156 and ATUX-6954 (diarylmethylcycloamine sulfonylureas), and ATUX-1215 and ATUX-5800 (diarylmethyl-4-aminotetrahydropyran-sulfonamides). Treatment with these compounds led to suppression of the endogenous PP2A inhibitor, cancerous inhibitor of PP2A (CIP2A), enhanced phosphatase activity (10-60%), and reduced MB viability, migration, and invasion, prerequisites for MB cells to access the cerebrospinal fluid, affecting the initiation stage of LMD. PP2A activator treatment of MB cells led to apoptosis mediated via caspase 9/PARP signaling due to decreased phosphorylation of Bad, impeding the dispersal stage of LMD. Cell proliferation and LMD-driving cellular traits and molecules pertinent to the third stage, colonization, were also affected. Treatment with ATUX-1215 or ATUX-5800 prevented LMD in an intraventricular murine model of MB, possibly mediated by disruption of the CCL2-CCR2 axis by altered NF-kB phosphorylation via disrupted AKT signaling. The present investigation offers proof-of-principle data for PP2A-based reactivation therapy for Group 3 MB and provides the first indications that PP2A reactivation may challenge the current paradigm in targeting the 3-stage process of MB LMD. Further investigations of PP2A activators are warranted as these compounds may prove beneficial as therapeutics for MB.

Upregulation of apoptotic genes and downregulation of target genes of Sonic Hedgehog signaling pathway in DAOY medulloblastoma cell line treated with arsenic trioxide

Sonic hedgehog (SHH) medulloblastoma etiology is associated with the SHH molecular pathway activation at different levels. We investigated the effect of arsenic trioxide as a downstream-level inhibitor of the SHH signaling pathway on morphology, cytotoxicity, migration, and SHH-related and apoptotic gene expression of DAOY cells. Cells were treated at various arsenic trioxide (ATO)concentrations (1, 2, 3, 5, and 10 μM) for different times (24 and 48 hr). Following treatments, the morphology of the cells was investigated at ×20 and ×40 magnification by an inverted microscope. Then, cytotoxicity was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and trypan blue assays. Cell migration was analyzed through the wound-healing assay. Furthermore, the expression of SHH-related (GLI1, GLI2, SMO, and MYCN) and apoptotic genes (BAX, BCL2, and TP53) was assessed by real-time quantitative polymerase chain reaction (qPCR). Finally, GLI1, SMO, and MYCN markers were analyzed through immunocytochemistry. Data were analyzed by SPSS (version 16) and P≤0.05 was considered significant. Morphological changes were seen at 3 and 2 μM in 24 and 48 hr of treatment, respectively. The MTT assay showed a dose-dependent cytotoxicity indicating an IC50 value of 3.39±0.35 and 2.05±0.64 μM in 24 and 48hr treatment, respectively. In addition, the trypan blue assay showed higher IC50 values of 4.29±0.25 and 3.92±0.22 μM in 24 and 48 hr treatment, respectively. The wound-healing assay indicated a dose-dependent reduction of cell migration speed showing a 50% reduction at 2.89±0.26 μM. Significant downregulation of GLI1 and GLI2, as well as the upregulation of BAX, BAX/BCL2 ratio, and TP53 were evident. Significant increases in GLI1 and MYCN markers were also evident in immunocytochemistry. ATO, as a downstream effective inhibitor of the SHH pathway, substantially leads to cell death, cell migration inhibition, apoptosis upregulation, and downregulation of SHH target genes in DAOY medulloblastoma. Since ATO is a toxic chemotherapeutic agent, it must be used at low concentrations (2 μM) in order not to damage healthy cells.