Zadeh, Gelareh

The classification and management of central nervous system (CNS) tumours have undergone substantial transformation over the past two decades, with the recognition of an expanding set of molecularly defined disease entities. Genome-wide DNA methylation profiling has emerged as an important complement to histopathology and targeted molecular testing, providing an epigenetic framework that captures tumour lineage, biological state and large-scale genomic alterations within a single assay. Accumulating evidence demonstrates that methylation-based approaches improve diagnostic precision, resolve biologically heterogeneous entities and support clinically meaningful risk stratification across a broad spectrum of CNS tumours. Methylation profiling has also increasingly been applied to outcome prediction, liquid biopsy-based analyses and the resolution of diagnostically challenging or misclassified cases. In addition, advances in multi-omic integration, computational inference from routinely acquired clinical data and evolving implementation frameworks are extending the clinical applicability of epigenetic profiling. This review synthesises the current state of DNA methylation profiling within the diagnostic and clinical framework of CNS tumours and considers how emerging technologies and practice models are shaping its ongoing integration into neuro-oncological care.

Abstract Background Approximately 12 000 adolescents and young adults (ages 15-39, AYAs) are diagnosed with a primary central nervous system (CNS) tumor each year. DNA methylation profiling has transformed CNS tumor classification by refining diagnostic accuracy and identifying biologically distinct subtypes, but its application has not been systematically evaluated in the AYA population. In this study, we examined the spectrum of CNS tumor types across age groups, with a focus on the AYA population. Methods We assembled a large dataset of CNS tumor samples with age annotations and methylation profiles matching with high confidence to a CNS tumor type using the NCI/Bethesda classifier. Prevalence of tumor type, methylation class and DNA copy number aberrations were compared across age strata (pediatric, AYA, and adult). Results The cohort of 21 712 CNS tumors included 5351 tumors from AYAs (25%), which showed a mixed pattern, with tumors typical of childhood (eg, medulloblastoma) as well as those common in older adults (eg, glioblastoma). Several tumor types were specifically enriched in the AYA, including IDH-mutant astrocytoma, pleomorphic xanthoastrocytoma, posterior fossa group B ependymoma, and diffuse hemispheric glioma, H3 G34-mutant, among others. Distinct methylation subclasses of multiple tumor types were observed in the AYA, and patterns of genomic aberrations showed age-specific distributions. Conclusion Large-scale methylation profiling revealed unique classification patterns of CNS tumors in AYAs, with specific tumor types, subclasses, and genomic alterations enriched in this population. These data may serve as a valuable reference resource for better understanding the spectrum of CNS tumors affecting AYA patients.

Abstract Purpose: Glioblastoma (GBM) is the most common and aggressive primary malignant brain tumor, with a median survival of only 15 months. Effective therapeutic advances remain limited, with few clinical trial patients exhibiting robust responses to experimental therapies. This has led to efforts to identify molecular biomarker signatures capable of stratifying patient responses either prognostically (pre-treatment) or diagnostically (post-treatment). This study aims to assess the robustness and reproducibility of published transcriptional GBM biomarker signatures for predicting clinical outcomes in GBM trials. Methods: We analyzed published RNA-seq data from 4 clinical trials involving oncolytic virotherapy and immune checkpoint inhibitors, as well as multiple cohorts of patients treated via the Stupp protocol. The performance of reported immune gene signatures was evaluated across all datasets using both grouped and continuous survival modeling. Intra-patient signature variation between different biopsy sites and timepoints was assessed using longitudinal, multi-site sampling collected by the Break Through Cancer Accelerating GBM Therapies TeamLab. LASSO, multivariate Cox regression, and risk scoring with FDR adjustment were used to identify novel signatures with cross-cohort utility. Key Findings: No single published signature consistently predicted survival across all analyzed trials. A post-treatment ssGSEA antitumor cytokine signature that was associated with survival in the CAN-3110 OV trial (R = 0.74, p < 0.01) was also significantly associated with improved survival in an adjuvant anti-PD1 trial (R = 0.75, p = 0.03) and neoadjuvant anti-PD1 trial (R = 0.30, p = 0.05), but not in standard-of-care controls. PAM clustering of MCP immune signatures, as reported for the DNX-2401 OV+Anti-PD1 trial, also stratified post-treatment survival in the CAN-3110 OV trial (p < 0.01), with the coldest TME subtype consistently predicting worse survival. However, the prognostic value of the most immune enriched TME subtype was inconsistent and did not extend to the Anti-PD1 trials. Furthermore, multi-site, longitudinal biopsy samples revealed marked heterogeneity in biomarker signatures between biopsies from individual patients, even when assessed at the same timepoint. We’ve identified several candidate transcriptomic signatures that show promise for generalizable prognostic value in GBM patient cohorts and are characterizing their spatiotemporal variability. Conclusions: While no individual immune signature is universally predictive in GBM immunotherapy, certain post-treatment cytokine signatures and TME stratifications are significant in multiple immunotherapy contexts, though not in standard-of-care patient cohorts. Marked spatiotemporal heterogeneity in these signatures underscores the need for composite prognostic markers resilient to sampling variance. Citation Format: Christopher M. Jannotta, C Zoe Linke, Charles A. Whittaker, Vikas Patil, Accelerating GBM Therapies TeamLab, Farshad Nassiri, Gelareh Zadeh, E Antonio Chiocca, Alexander L. Ling. Assessing biomarker reproducibility for glioblastoma patient response stratification [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1055.

Abstract Neurosurgical oncology is a rapidly advancing field, driven by interdisciplinary collaboration, technological innovation, and a growing understanding of tumor biology. As we celebrate the 40th anniversary of the AANS/CNS Section on Tumors, this editorial highlights the collaborative spirit that defines the Section and explores the many ways it intersects with other neurosurgical subspecialties and AANS/CNS Sections to optimize patient care. This special edition features a series of articles showcasing these intersections across functional, cerebrovascular, spine, trauma, pain, and pediatric neurosurgery. For example, insights into neuron–glioma interactions—enhanced by tools such as optogenetics and advanced brain mapping—are opening doors to more personalized treatment strategies. Innovations in preoperative embolization for skull base meningiomas are improving surgical precision and outcomes. Similarly, advances in managing vertebral metastatic disease with surgical techniques and stereotactic body radiation therapy (SBRT) are reshaping standards of care. Neuro-intensive care has evolved to support personalized postoperative recovery, with a focus on neurological function and cognitive rehabilitation. In pain management, neuromodulation, including intrathecal drug delivery and spinal cord stimulation, is offering new relief to tumor patients. Adolescents and young adults (AYA) with gliomas remain an underserved population, requiring age-specific treatment frameworks and better integration into clinical trials. This edition celebrates the diverse and collaborative workforce propelling neurosurgical oncology forward.

Abstract Background Current literature suggestsisocitrate dehydrogenase (IDH)-mutant astrocytoma contains several molecular subgroups. In this study, we are interested in determining the connection between different molecular subgroups with grade and/or survival. Methods A cohort of 470 Mayo Clinic adult patients (≥18 years, 56.2% male) with primary IDH-mutant astrocytoma diagnosed by World Health Organization (WHO) 2021 criteria were examined. Results were validated in an independent cohort of 614 Mayo Clinic Neuropathology consult patients and 235 The Cancer Genome Atlas (TCGA) patients. Results The Mayo Clinic Practice cohort confirmed the association of CDKN2A/B deletion with overall survival (OS, homozygous vs hemizygous vs intact, 2.7 vs 9.6 vs 17.2 years, P < .001). Phosphatase and tensin homolog (PTEN) deletion was also associated with poor OS (7.3 vs 17.4 years, P < .001). Increased number of copy number alterations was associated with OS (continuous variable, HR = 1.027, P < .001). Carrying one or more copies of the germline risk allele at rs55705857 was associated with earlier age of onset (median age 33 vs 35 years, P = .01), and a shorter OS after adjusting for age, grade, sex and treatment (HR = 1.81, P = .007). The Mayo Clinic Neuropathology Consult cohort and TCGA were utilized to validate age of onset and survival, respectively. Unsupervised clustering of the copy number alterations identified several clinically significant groups that may define pathways to disease progression. Losses of chromosomes 11p, 13q, 1p, and 10q were all associated with reduced overall survival in the Mayo Clinic cohort. Conclusions Patients with hemizygous loss of CDKN2A/B, loss of PTEN, increased number of copy number alterations, specific chromosomal arm losses or rs55705857 germline risk allele have reduced overall survival.

Abstract Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas arising from Schwann cells and characterized by marked cellular and molecular heterogeneity. Although bulk multi-omic studies have provided valuable insights into MPNST biology, recent advances in single-cell profiling have deepened our understanding of the tumor microenvironment and molecular mechanisms underlying malignant transformation. Single cell analyses have revealed distinct Schwann cell-like, malignant neural crest-like, immune, and stromal cellular subpopulations within MPNSTs and their precursor lesions. Comparative profiling of MPNSTs, neurofibromas, and atypical neurofibromatous neoplasms of uncertain biologic potential, suggest that MPNST progression involves Schwann cell dedifferentiation into a more primitive, stem-like state. In this review, we summarize key discoveries from single-cell characterization studies, and discuss how these findings illuminate MPNST tumorigenesis, cellular plasticity, and potential therapeutic vulnerabilities.

Abstract Background DNA methylation profiling can be used to robustly predict postsurgical outcomes and response to radiotherapy (RT) for meningioma patients. To allow for seamless integration of these complementary models into clinical practice, a practical framework is needed. Methods We leveraged a cohort of nearly 2000 surgically-treated meningiomas with DNA methylation profiling and clinical outcomes data. Existing methylation-based prediction models were dichotomized to yield four risk groups: low and high recurrent risk, each with RT sensitive and resistant subgroups. Risk groups were correlated with progression-free survival in the context of existing biomarkers including extent of resection and WHO grade. Results We first demonstrated that all risk groups benefit from gross total resection. All “high-risk, RT sensitive” tumors (n = 306, 15.7%) also benefited from adjuvant RT: after GTR, median PFS increased from 4.68 (4.13-9.48) years to not reached (P = .003); after subtotal resection (STR), from 2.12 (1.59-3.02) to 4.09 (3.41-not reached) years (P = .004). “Low-risk, RT sensitive cases” (n = 1207, 61.8%) also benefited from RT after STR (median PFS 7.39 (6.66-12.8) vs. 16.53 (10.35-not reached) years, P = .03), suggesting that RT be considered in these patients. Neither “low-risk RT resistant” (n = 84, 4.3%) nor “high-risk RT resistant” (n = 356, 18.2%) cases benefited from RT, and the latter group was associated with universally poor outcomes. Conclusions We identify methylation-defined risk groups of meningioma for which additional benefit is gained from adjuvant RT, leading to a clinical decision-making framework for straightforward integration of molecular models into clinical practice.

Abstract A new mouse model for the classical subtype of human glioblastoma (GBM) has been bred using Cre-mediated EGFRvIII overexpression and homozygous p19-ARF deletion, the mouse homolog of human p14ARF/CDKN2A, in GFAP expressing cells. Transgenic mice develop intraparenchymal and/or leptomeningeal brain lesions with some spinal cord invasion as early as 1 month old and 95% of mice die by 6 months due to hydrocephalus and/or paralysis. Mice with high grade tumors have worse survival and similar features to human classical GBM such as necrosis, high levels of mitosis and infiltration of tumor cells into normal brain. Immunohistochemical analysis confirms EGFRvIII overexpression and p19-ARF loss in Cre-expressing cells, along with patchy positive GFAP and high proliferation by Ki67. Bulk RNA sequencing reveals GEC3 tumors cluster closely with human classical GBM and have significant upregulation of downstream markers in the JAK/STAT and P13K/AKT pathways. Adherent and neurosphere primary culture of dissociated tumors indicate that tumor cells maintain EGFRvIII expression in culture and generate xenograft tumors by 3 weeks after intracranial injections into NODSCID mice. Xenograft tumors are reminiscent of the primary tumor, with similar histopathological features and immunohistochemical staining. Our spontaneous glioma model is a powerful tool for future studies focused on the role of the immune microenvironment on glioma recurrence and resistance.

Abstract Recurrent or refractory IDH-mutant (mt) gliomas represent a population with significant unmet clinical need. The Notch ligand delta-like 3 (DLL3) is a tumor-associated antigen that is highly and homogeneously expressed in IDH-mt gliomas but absent in normal brain tissue, making it an attractive therapeutic target. Tarlatamab is a half-life extended bispecific T-cell engager that targets DLL3 and CD3 to redirect cytotoxic T cells toward DLL3-expressing tumor cells. Given the specific expression of DLL3 in IDH-mt gliomas and promising activity of tarlatamab in other DLL3-positive tumors, this study investigates the safety, efficacy, and intracranial activity of tarlatamab in this patient population. TARGID is an open-label, phase II trial enrolling adult patients with histologically confirmed IDH1 or IDH2-mt astrocytoma or oligodendroglioma following up to two prior lines of systemic therapies. The study comprises two cohorts. Cohort 1 (n=10) includes patients with resectable disease who will receive up to three cycles of tarlatamab prior to surgery; postoperative continuation is permitted. The primary endpoint for this cohort is the change in CD8+ T-cell infiltration in tumor tissue and blood. Cohort 2 (n=34) includes patients with unresectable disease and uses a Simon’s optimal two-stage design (H0: P ≤ 0.1 versus H1: P ≥ 0.25). In the 1st stage, 13 patients will be accrued. If 2 or more responses are observed, 21 additional patients will be enrolled. Tarlatamab is administered intravenously at 10 mg every two weeks, following a 1 mg priming dose on Cycle 1 Day 1. The primary endpoint is objective response rate by RANO 2.0. Exploratory endpoints include DLL3 expression, circulating biomarkers, and immune correlatives. The trial is currently in activation, with first patient enrollment anticipated in Q3 2025. The study is supported by the provision of study drug from Amgen as an investigator-initiated trial.

Abstract Glioblastoma (GBM) progression and recurrence are often driven by therapy-resistant cellular states emerging within hypoxic tumor niches. While hypoxia is a hallmark of GBM, the spatial transcriptomic heterogeneity that underpins resistance in these regions remains poorly characterized. Here, we employ pimonidazole labeling in conjunction with high-resolution spatial and single cell transcriptomics across 29 primary, treatment-naive human GBM samples, syngeneic mouse models, and patient-derived glioma-initiating cells exposed to hypoxia to define the hypoxia-specific tumor microenvironment and its associated cellular programs. We reveal spatially organized sub-niches within hypoxic regions, each supporting diverse cellular programs yet coexisting tumor lineage states with minimal transitions between cell states. Phylogenetic reconstruction based on inferred copy number variations demonstrates consistent evolutionary trajectories from non-hypoxic to hypoxic tumor loci. Specific copy number alterations were enriched in hypoxic regions and associated with immune infiltration and poor prognosis in MGMT-methylated tumors. Cross-species analyses confirmed the conservation of hypoxia-associated gene programs and spatial architectures. Together, our study delineates the cellular, evolutionary, and spatial complexity of hypoxia in GBM, identifies hypoxia-induced genomic alterations that may promote tumor fitness, and offers insights into new therapeutic vulnerabilities within hypoxic niches.