Citations

Abstract Glioblastoma (GBM) is a highly aggressive brain tumor with poor survival outcomes and limited tools for accurate prediction of individual patient prognosis. While many prognostic models rely on advanced molecular testing, such methods are not routinely accessible across most clinical settings. In this study, we identify a practical and clinically applicable approach to estimate prognosis for GBM patients using three objective and readily accessible features: the patient’s age, tumor surface irregularity determined from MRI scans, and the expression of ICAM1 measured by standard immunohistochemistry. We show that higher ICAM1 levels are linked to worse survival and a more inflamed but immunosuppressive tumor microenvironment. These findings are functionally validated in ICAM1-wildtype and knockout mouse models using single-cell proteomics via cytometry by time-of-flight, and an immune-comprehensive panel of antibodies. By combining age, ICAM1, and MRI-derived shape features into a single Clinical-Imaging-Molecular (CIM) score, we developed a model that can reliably separate patients with a GBM into higher- and lower-risk groups. This score was validated across multiple international institutions and patient populations and does not require genomic sequencing or specialized technologies. The CIM model could serve as a supplement for care providers to better tailor treatment plans and follow-up strategies for individual patients, making personalized care more achievable even in resource-limited settings.

Abstract Molecular testing has become critical components in the diagnostic classification of the central nervous system (CNS) tumors. However, these methods require substantial resources, limiting accessibility for many patients. Recent advances in artificial intelligence (AI) and computer vision empower deep learning models to infer molecular features from histopathology images, which may often be more readily available than molecular testing, to classify CNS tumors. We trained pan-CNS tumor models to predict DNA methylation and gene expression from whole-slide images (WSIs). These molecular predictions were then used in a hierarchical machine learning framework, termed Neuropath-AI, to predict nine broad tumor families and 52 tumor types using a large diverse cohort of 5,715 histopathology samples, of which 2,988 had paired DNA methylation profiling and 848 had paired RNA-sequencing. We evaluated Neuropath-AI on another large independent multi-institutional cohort of 5,516 CNS tumors, for which Neuropath-AI predicted tumor class with an associated confidence score. Neuropath-AI designated 46% of test samples as predictable with high-confidence, which it then accuracy classified in 97% of samples. It made moderate-confidence (and above) predictions for 87% of test samples, for which it achieved a diagnostic accuracy of 80% for the top-1 prediction and 86% accuracy for a top-2 predictions. A comparison with human neuropathologists showed that Neuropath-AI is comparable at classifying tumors. A second test showed that human neuropathologists were more accurate when the Neuropath-AI classifier results were provided to them, testifying to the potential translational benefit of integrating AI classification tools into the pathologist’s workflow. Our model provides the basis for a clinically applicable deep learning assistant to improve human efficiency and accuracy of CNS tumor diagnosis. The model will be made publicly available and can be readily implemented to assist human pathologists in clinical workflows, in further expanded prospective studies.

Abstract We describe a 46-year-old male with Neurofibromatosis type 1 (NF1) and a previously known parenchymal medullary mass identified in 2022, initially managed with surveillance. In late 2023, he developed a progressive brainstem syndrome prompting presentation to our center. MRI showed a T2/FLAIR hyperintense, heterogeneously enhancing ventral medullary mass with leptomeningeal involvement, a non-enhancing right pontine lesion, right optic nerve glioma, and nodular leptomeningeal foci at T4 and L4–L5. He received IMRT to the brainstem prior to tissue diagnosis with good local response. Due to progression at T4, biopsy revealed a hypercellular, mitotically active glioma without necrosis or microvascular proliferation. Molecular profiling demonstrated IDH1/2-wildtype, H3K27M-negative, retained ATRX, intact 1p/19q, and CDKN2A/B homozygous deletion. DNA methylation profiling classified the tumor as high-grade astrocytoma with piloid features (HGAP). Spinal lesions responded to proton therapy, but new metastatic foci emerged in the subependymal lateral ventricles, leptomeninges, and cervical spinal cord. He underwent whole-brain radiation, oral temozolomide, and intrathecal cytarabine/etoposide. In June 2024, cell-free DNA analysis showed a similar molecular profile with newly identified 1p/19q codeletion, diverging from tissue findings. The patient remains alive >3 years from initial presentation. HGAP is a novel molecular class of IDH-wildtype gliomas defined by DNA methylation profiling and MAPK pathway alterations (commonly NF1, BRAF, FGFR1), CDKN2A/B codeletion, and ATRX alterations. These tumors often resemble glioblastoma or diffuse midline gliomas on imaging and are typically infratentorial or spinal, complicating biopsy. Prognostic data are limited, with <50% 5-year overall survival and no clear prognostic value of MGMT promoter methylation. This case illustrates multifocal HGAP in a patient with NF1 with favorable survival. The acquired 1p/19q codeletion raises questions about tumor mosaicism, subclonal evolution, and prognostic implications.

Abstract Pediatric, adolescent and young adult patients (Ped/AYA; 0–39 years) with meningiomas are underrepresented in neuro-oncology research, despite meningiomas being the second most common primary brain tumor in this age group. While DNA methylation-based models have advanced classification and prognostication in adults, their utility in younger populations remains uncertain. To address this gap, we aimed to evaluate the performance of current DNA methylation-based classification and recurrence prediction models in Ped/AYA patients with meningiomas and identify age-associated molecular differences. As part of this study, we analyzed 1,568 meningioma samples with DNA methylation and clinical data, including subsets with whole-exome and RNA sequencing. Patients were grouped into Ped/AYA (≤39 years, n = 213) and adult (>39 years, n = 1,355) cohorts. We assessed classifier performance, performed subgroup-specific model retraining, and compared molecular profiles across age groups. Our results showed that molecular classification differed significantly between age groups, with Ped/AYA tumors less frequently belonging to the most aggressive Proliferative Molecular Group. The DNA methylation-based recurrence model performed well in adults (AUC = 0.83) but poorly in the Ped/AYA cohort (AUC = 0.57). However, retraining the model on only younger patients improved performance (AUC = 0.75). In addition, Ped/AYA tumors exhibited significantly fewer chromosomal alterations, including lower frequencies of 1p, 6q, and 14q loss (p<0.05). Taken together, these findings indicate that predominantly adult-trained methylation models underperform in younger meningioma patients due to both biological divergence and exclusion from training datasets. Our findings underscore the need for age-specific molecular tools to improve prognostication and support personalized care across the lifespan in neuro-oncology.

Abstract There are no approved treatments for relapsed/refractory (R/R) PCNSL. We show promising efficacy in the salvage setting using emavusertib in combination with ibrutinib, which targets the BCR and TLR pathways. These 2 major pathways are associated with activation of NF-κB. Updated safety and efficacy data of this combination in R/R PCNSL from the ongoing Phase 1/2 TakeAim Lymphoma trial (NCT03328078) will be presented. As of 01 May 2025, 33 patients with R/R PCNSL were treated with emavusertib in combination with ibrutinib. Eligible patients receive emavusertib in combination with ibrutinib until tumor progression or unacceptable toxicity. Median age was 63 years (range 43-81); 16 patients were male. Median prior anti-cancer therapy was 2 (range 1-5); 26 (78.8%) patients had prior BTKi exposure. Median duration of emavusertib/ibrutinib treatment was 51 days (range 5-798). Grade ≥ 3 treatment-related adverse events (TRAEs) were reported in 11 (33.3%) patients; neutropenia in 5 (15.2%) patients, amylase increased, lipase increased, and leukopenia in 2 (6.1%) patients each. The majority of Grade ≥ 3 TRAEs were reversible and manageable. Among the 19 BTKi-experienced patients treated for ≥ 28 days, there were 5 CRs and 2 PRs, with an ORR of 36.8%. Three patients with CR were on treatment for 10+ mos, with 1 CR patient ongoing with DOT of 26.2+ mos. Among the 5 BTKi-naïve patients treated for ≥ 28 days, 1 achieved CR and 3 had PR, with ORR of 80%; the CR patient is ongoing with DOT of 18.1+ mos. The ORR in the combined population was 45.8% (6 CRs; 5 PRs). The combination of emavusertib and ibrutinib demonstrates promising clinical activity and an acceptable safety profile in patients with R/R PCNSL. This regimen appears capable of overcoming resistance to prior BTKi therapy. Patient enrollment in this trial continues.

Abstract PCNSL is a rare and aggressive NHL with no approved treatments for R/R patients, representing a critical unmet need. MyD88 mutations in ~70% of PCNSL patients drive IRAK4 activation, promoting NF-κB signaling, inflammation, and tumor progression. Emavusertib, a potent oral IRAK4 inhibitor, crosses the blood-brain barrier and shows preclinical synergy with BTKis, and has the ability to re-sensitize BTKi-resistant cell lines. This study evaluates the molecular and PK data associated with responses to emavusertib + ibrutinib combination therapy in R/R PCNSL patients. The safety, clinical activity, and potential biomarkers of emavusertib in R/R PCNSL are being investigated in the ongoing TakeAim Lymphoma trial (NCT03328078). Pre-dose and 1.5-hour post-dose plasma samples were collected on Day 1 of Cycles 3, 5, and 7. CSF samples were obtained via a lumbar puncture within 1.5 hrs of collection of the post-dose plasma PK sample on Cycle 3 Day 1. As of 06 December 2024, CSF concentration was available for 7 patients. The mean emavusertib concentration in CSF was 81.3 ng/ml (54.7-104.0) in patients receiving 100 mg emavusertib BID (n=4). In patients receiving 200 mg emavusertib BID (n=3), the mean emavusertib concentration in CSF was higher at 175.7 ng/ml (114.8-209.4), which is 2.2 × the mean value in patients who received 100 mg emavusertib BID (p-value = 0.02). MyD88 mutation status was available for 7 patients of which all had prior BTKi exposure. Among these patients, 6 had MyD88 mutations of which 4 had responded (3 CRs and 1 PR) to the combination with DOR up to 18.9 mos with data collection ongoing. Preliminary CNS PK data demonstrate that emavusertib concentration in CSF increases with increasing emavusertib dose. Patients with MyD88 mutations showed expected promising preliminary efficacy to emavusertib + ibrutinib combination and may overcome BTKi resistance. Enrollment is ongoing.

Abstract BACKGROUND Most meningiomas are considered benign tumors, however, a subset of meningiomas are characterized by a more aggressive clinical course and require multimodal treatment. Beyond surgery and radiation, there are no effective medical treatments available. Somatostatin receptor 2 (SSTR2) is expressed by the majority of meningiomas. [177Lu]Lu-DOTA-TATE (177Lu-Dotatate) is a SSTR2-targeting radioligand therapeutic agent that has been successful in other oncological entities, including neuroendocrine tumors. Here we report the results of a phase 2 clinical trial (NCT03971461) evaluating 177Lu-Dotatate in patients with advanced and treatment-refractory intracranial meningiomas. METHODS In this multicenter, open-label, phase 2 study, adults with advanced intracranial meningiomas received 177Lu-Dotatate at 7.4 GBq (200 mCi) every eight weeks for four doses. [68Ga]Ga-DOTA-TATE (68Ga-Dotatate) PET was performed before and at the end of treatment. The primary endpoint was progression-free survival at 6 months (PFS-6). Correlative studies evaluated the association of PFS-6, objective response rate, progression-free survival, overall survival with radiographic tumor measurements, and 68Ga-Dotatate uptake on PET. RESULTS Thirty-two patients (F=21, M=11) with progressive meningiomas (WHO 1=7, WHO 2=24, WHO 3=1) were enrolled. Median age was 65.5 (range 41-78) years. All patients previously underwent tumor resection and at least one course of radiation. Three patients (9%) had received medical therapy. Treatment with 177Lu-Dotatate was well tolerated, no treatment-limiting toxicities were observed. Of 29 evaluable patients at the data cutoff, 19 patients (66%) had achieved PFS-6 (WHO 1=4, WHO 2=15). Radiographically, the best response was partial response (PR) in 2 patients (6%) and stable disease (SD) in 20 patients (63%). CONCLUSIONS Treatment with SSTR2-targeting 177Lu-Dotatate is well tolerated and 66% of patients achieved PFS-6, comparing favorably to historical benchmarks, 177Lu-Dotatate therefore may be a useful new therapeutic modality for patients with advanced meningiomas and will be further explored in MOMENTUM-1 (NCT#06955169), an open-label, randomized, phase 2 trial.

Abstract BACKGROUND CNS germinoma is typically treated with combination of chemotherapy and radiotherapy, with steroids used temporarily for symptom management. METHODS We report a case of CNS germinoma initially treated with steroid monotherapy with reduction in radiographic enhancement. RESULTS A 25 year old male initially presented with polydipsia and polyurea that improved with desmopressin, consistent with central diabetes insipidus. Brain imaging was unremarkable and he was lost to follow up. 3 years later, he developed progressively worsening bitemporal scotomas, intermittent binocular horizontal diplopia, reduced visual acuity, headaches, weight gain, and sexual dysfunction. MRI brain revealed enhancement of the pituitary stalk, optic chiasm and optic nerves, floor of the third ventricle, lateral ventricles, periventricular white matter, and anterior corpus callosum and fornix with associated T2 hyperintensity within the optic chiasm and adjacent brain parenchyma. Biopsy was consistent with germinoma. He was started on a dexamethasone taper beginning at 4 mg every 6 hours and plateauing at 4 mg twice daily. 3 weeks after steroid initiation, the areas of enhancement surrounding the frontal horns of the lateral ventricles showed reduction in size. DISCUSSION Reduced tumoral enhancement with steroid monotherapy is a well-known phenomenon in CNS lymphoma and has been reported in gliomas, attributed to direct induction of apoptosis in CNS lymphoma and alterations in the blood brain barrier via suppression of vascular permeability factors in both. This case adds to the scant literature regarding change in enhancement patterns with steroid monotherapy in CNS germinomas, which is likely related to a reduction in tumoral diffuse lymphocyte infiltration with steroid administration. The reduction in enhancement seen in multiple CNS mass-like pathologies emphasizes the importance of a tissue diagnosis for germinomas, as this steroid response is transient and not indicative of true tumor regression. Definitive treatment of germinomas is combination chemotherapy and radiation.

Abstract A major barrier in understanding adult diffuse gliomas lies in the inability to track tumor evolution in real time. To address this, we employed a novel method known as continuous lineage tracing, which integrates CRISPR/Cas9-based expressed DNA barcoding with single-cell RNA sequencing, enabling a phylogenetic approach to studying tumor development. Patient-derived glioma-initiating cell lines were engineered with expressed barcodes targeted by CRISPR/Cas9 and implanted into mice to create intracranial xenografts. Tumors underwent single-cell RNA sequencing; expressed barcodes were used to infer clonal relationships, and transcriptomic profiles enabled cell state classification. Phylogenetic lineage trees were reconstructed using lineage inference algorithms to characterize cell fitness, expansion, and plasticity. Our analysis uncovered extensive intra-clonal cell state heterogeneity, indicating active phenotype switching prior to therapy. We identified consistent transcriptional programs associated with tumor engraftment and in vivo clonal advantage. Lineage tracing revealed gene expression signatures linked to key phenotypes: fitness, enriched for neural-mesenchymal and injury-response pathways; expansion, associated with RNA splicing; and plasticity, correlated with cell cycle and DNA repair programs. Glioma stem cells appeared to span a transcriptional continuum from undifferentiated, high-fitness states to more differentiated, low-fitness states, with high-fitness cells potentially representing transitional phenotypes. We then validated these findings in a cohort of 185 surgically resected gliomas with matched bulk RNA and proteomic data. Phylogenetic gene signatures differed markedly between IDH-mutant and IDH-wildtype tumors. When stratified by tumor type, both fitness and expansion signatures were significantly associated with overall survival in GBM (median 12.6 months, p=0.041) and oligodendrogliomas (median 66 months, p=0.027). This study demonstrates the utility of continuous lineage tracing to reconstruct tumor evolution and identify transcriptional programs linked to tumor growth and prognosis. Our approach provides a powerful framework for dissecting glioma biology and identifying potential therapeutic vulnerabilities.

Abstract BACKGROUND Chromosomal instability is a well-recognized hallmark of tumorigenesis. However, it is not known how markers for chromosomal instability, such as total distance of DNA altered or total copy number variations (CNV), affect survival, particularly in IDH wild type glioblastoma. Additionally, whether alterations in pathways that impact cellular responses to chromosomal instability, such as the TP53 or RB1 axis, influence survival, similarly remain poorly understood. METHODS To better characterize potential prognostic impact of markers of chromosomal instability on patient outcomes, we assessed the Mayo Clinic cohort of IDH wild type glioblastomas (n=449) for whom chromosomal microarray data was available. RESULTS We found that while total distance of DNA altered on microarray analysis was not associated with overall survival (OS) (p=0.4030, univariate analysis), the least altered tumors (stratified by quartiles) when assessed by numbers of CNVs demonstrated improved OS (p=0.0057, univariate analysis). We next evaluated alterations in the MDM2/4-TP53 signaling axis, as well as the CDKN2A/B-CDK4/6-RB1 axis, as both amplifications and losses impacting these pathways have been well characterized in adult diffuse gliomas. While TP53 status was not predictive of OS (p=0.1504, univariate analysis), amplification of MDM2 or MDM4 was predictive of decreased OS (p=0.0071, univariate analysis). We also found that tumors without alterations in the CDKN2A/B-CDK4/6-RB1 axis had improved OS when compared to altered tumors (p<0.0001, univariate analysis). Multivariate Cox regression analysis, adjusting for age and sex, confirmed prognostic impact of MDM2/4 amplification status (HR 1.4090, p=0.0370) and CNV status (HR 0.6798, p=0.00312) on OS. CONCLUSIONS CNV status and MDM2/4 amplification represent previously unappreciated molecular markers for prognostication in IDH wild type glioblastoma. Further work is underway to confirm our findings through multi-institutional collaborations and to account for additional potential prognostic factors.