Citations

Abstract Diffuse midline and diffuse hemispheric glioma contain the driver mutations H3.3 K27M and G34R/V, respectively. These mutations alter histone methylations, suggesting that dysregulation of gene expression may contribute to tumor formation. We recently reported that these mutations also inhibit the phosphorylation of H3.3 at Serine 31. Importantly, H3.3 S31A mice developed high-grade gliomas – similar to those from G34R and K27M mice – indicating that loss of phosphoS31 promotes gliomagenesis. Chk1, a key kinase in DNA damage response and mitotic fidelity, phosphorylates H3.3 S31. H3.3 S31 is phosphorylated at the pericentromere in metaphase and is typically absent during interphase. Reduction of S31 phosphorylation by H3.3 K27M, G34R, G34V, or S31A was sufficient to induce mitotic errors leading to aneuploidy. Using CRISPR/Cas9, we generated novel H3.3 WT/WT and WT/S31A lines from glioma patient-derived SF-8628 (H3.3 WT/K27M) and KNS-42 (H3.3 WT/G34V) cells. Immunofluorescence of metaphase spreads revealed H3.3 phosphoS31 at the pericentromeres as expected. Interestingly, total Chk1 and active Chk1 (pS296) were significantly enriched at the pericentromeres of H3.3 K27M and G34V cells, as compared to H3.3 WT cells. While total ATR and active ATR (pT1989) were present at the pericentromere, their levels were unaltered by the H3.3 mutations. Surface plasmon resonance of purified proteins revealed that Chk1 has two binding affinities for H3.3 - likely corresponding to the previously identified Chk1 phosphorylation sites (T11 and S31) on H3.3. Chk1 binding at one site was unaffected by H3.3 K27M, while the second site showed an altered dissociation from H3.3 K27M. In summary, our data suggest that the low pericentromeric pS31 levels associated with H3.3 glioma mutations result from Chk1 recognizing the mutant histone, but without completing a phosphorylation cycle, becoming trapped at the pericentromere. This result suggests that H3.3 mutations, by trapping Chk1, may impede Chk1 activities beyond just reducing H3.3 phosphorylation.

Abstract INTRODUCTION Brain metastases (BM) are the most common intracranial tumor, with a poor prognosis of 10-16 months, and lung adenocarcinoma (LUAD) is the most common source. Currently, we cannot reliably predict which patients will develop BMs clinically, so most are detected after they develop and growing to cause deficits. Here, we use tumor DNA methylomes to predict which patients are likely to develop BM through the course of disease and we use both cerebrospinal fluid (CSF) and plasma methylomes for BM liquid biopsy, enabling their early detection and treatment. METHODS DNA methylomes were acquired from 419 tumor and plasma samples from 363 LUAD and BM patients. We built DNA methylation-based models that predict BM development and that also identify BMs non-invasively from CSF and plasma in discovery data subsets. A nomogram was built that predicts BM risk using methylation scores and clinical stage together. Models were evaluated in independent validation sets. RESULTS Our model predicting BM development was accurate (Univariable Cox: HR=5.7, 95% CI=1.9-17.2), p=0.0023), independent of clinical factors (Multivariable Cox: HR=8.9, 95% CI=2.0-40.5, p=0.0046), and more predictive than cancer staging used currently clinically (AUC=0.81 versus 0.65). Our combinatorial nomogram using methylation and staging data together showed enhanced BM prediction (Univariable Cox: HR=17.2, 95% CI=4.1-71.3, p<0.0001; AUROC=0.82). Our models identifying BM through biofluid methylomes accurately distinguished BM from differential diagnoses of gliomas and lymphomas in plasma (AUROC=0.80, 95% CI=0.68-0.93) and with greater accuracy in CSF (AUROC=0.93, 95% CI=0.71-1.0). CONCLUSION Overall, we show the first approaches for robust molecular prediction of BM development and for reliable liquid biopsy of BM. This work is expected to transform cancer management by identifying high-risk lung cancer patients after initial treatment for inclusion in screening protocols using neuroimaging and liquid biopsy, to identify BM development early with less advanced disease and more optimal therapeutic outcomes.

Abstract Cerebrospinal fluid (CSF) cell-free DNA (cfDNA) is under evaluation as a liquid biopsy tool across multiple neuro-oncologic indications, including diagnosing lesions of uncertain etiology, delineating progression from pseudoprogression, and confirming suspected leptomeningeal disease (LMD). We evaluated the real-world performance of CSF cfDNA sequencing for identification of variant alleles (VA) using targeted panel sequencing (PredicineCARE) and/or copy number alterations (CNA) using low-pass whole-genome sequencing (LPWGS; PredicineSCORE) in a diverse cohort across three aforementioned indications. From 82 adult patients, 93 samples (92.4% from lumbar puncture and 7.6% from ventriculoperitoneal shunt taps) were analyzed. For CNS progression, gliomas were most frequently evaluated (60%); for LMD, metastatic disease was most common (86.7%). Median CSF volume utilized for analysis was 4.60 mL (range: 0.40-7.50 mL). Median cfDNA yield was 0.29 ng/mL (range: 0.00–1037.74 ng/mL). For lesions of uncertain etiology (n=40 patients, 1 sample/patient), VAs were identified in 10 samples (25%); an additional 10 samples had sufficient cfDNA for LPWGS (25%). 50% of samples in this indication had insufficient cfDNA for testing. For suspected progression (n=26 patients, 35 samples), VAs were identified in 6 samples (17.1%); an additional 14 samples underwent LPWGS (40%); 15 had insufficient cfDNA for further testing (42.9%). For suspected LMD (n=16 patients, 18 samples), VAs were quantifiable in 4 samples (22.2%); LPWGS could be performed in an additional 9 (50%); 5 had insufficient cfDNA (27.8%). Across indications, identification of known tumor-associated alterations in CSF, including those confirmed previously by tissue, served as a non-surgical diagnostic adjunct. In some patients, targetable mutations could be identified via CSF. Conversely, absence of such alterations and/or low cfDNA yields may lower suspicion for active neuro-oncologic disease, when evaluated alongside clinical history. Despite modest cell-free DNA yield, CSF cfDNA evaluation provides valuable information to aid clinical decision-making across neuro-oncologic indications.

Abstract NF2-related schwannomatosis is a genetic condition characterized by mutation in the NF2 gene resulting in tumor formation throughout the nervous system. The most common tumors in these patients include bilateral vestibular schwannomas and multiple meningiomas which, despite their benign classification, lead to significant neurologic deficits including hearing loss, ataxia, hydrocephalus, and brainstem compression. Loss of NF2, which encodes the protein Merlin, is also the most common mutation in spontaneous meningiomas and schwannomas. Current treatment consists of resection followed by radiation for more aggressive tumors. Unfortunately, these treatments are not curative and are associated with significant risk due to tumor location, involvement of neurovasculature, cognitive impairment, and radiation-induced tumor induction. Therefore, identifying additional therapeutics for these patients is critical. Molecular profiling across large cohorts of sporadic meningiomas have identified molecular signatures associated with NF2 mutation, indicating upregulation of Wnt5a/b and the alternative Wnt5a/b-YAP/TAZ signaling pathway. In NF2 knock-out human arachnoid and Schwann cells, we find a significant upregulation of YAP in NF2-null lines compared to controls. Additionally, when stimulated with Wnt5a/b, controls upregulate both beta catenin (canonical Wnt) and YAP (alternative Wnt). However, in NF2-null lines only YAP is increased, indicating a preference for the alternative pathway in the absence of canonical Wnt signaling. In primary NF2-mutant meningioma lines, targeting this pathway via blocking Wnt secretion with the inhibitor LGK974 or YAP signaling with verteporfin, which is FDA approved, results in decreased cell viability and proliferation in vitro. These results indicate activation of the Wnt5a/b-YAP/TAZ alternative signaling pathway in NF2-mutant meningeal and Schwann cells, and a potential therapeutic effect of blocking this pathway in NF2-mutant meningiomas with a previously-FDA approved inhibitor. Additional research is needed on the receptors and molecular mediators playing a role in this pathway and how these drugs may have therapeutic benefits in vivo

Abstract IDH-wildtype glioblastoma (GBM) is the most malignant primary adult brain tumor, with a five-year survival rate below 5%. Despite maximal treatment, including surgical resection, radiotherapy, and temozolomide (TMZ), recurrence is universal, driven by profound intratumoral heterogeneity, diffuse invasion, and therapy resistance. A hallmark of IDH-wildtype GBM is frequent alteration of epidermal growth factor receptor (EGFR), including amplification (50%), the EGFRvIII deletion variant (25%), and extracellular missense mutations such as G598V and A289V (10–15%). These missense mutations increase ligand affinity and receptor activity, yet their downstream signaling consequences and role in shaping the tumor phenotypes remain poorly defined. Recent pathway-based subclassifications identified four subtypes in IDH-wildtype GBM. Notably, neuronal (NEU) and glycolytic/plurimetabolic (GPM) subtypes predominate the invasive tumor margins. NEU programs are enriched in synaptic and neurodifferentiation signals, while GPM programs are associated with metabolic adaptation, angiogenesis, and immune evasion. Here, we show EGFR-G598V and EGFR-A289V mutations differentially regulate these invasive subtypes identities. Transcriptional analysis reveals EGFR G598V upregulates metabolic and inflammatory pathways consistent with the GPM phenotype, while EGFR A289V activates genes involved in neuronal differentiation and synaptic function, aligning with the NEU subtype. Phosphoproteomics and kinase-substrate analysis further uncovered distinct kinases to be functionally activated/inhibited in EGFR A289V-expressing cells and G598V cells. Mechanistic studies revealed EGFR A289V induces sustained EGFR phosphorylation at Y992, activating PLCγ2 via the SRC-family kinase LCK. This cascade drives calcium release, CAMK1 activation, and STAT5 phosphorylation, defining a novel EGFR A289V–LCK/PLCγ2/CAMK1/STAT5 axis. In addition, Y1068 phosphorylation is also constitutively active in EGFR A289V, resulting in increased BRAF activation. In contrast, EGFR G598V activates MAPK6 and CAMK2 inducing AKT2 activation, reinforcing GPM-associated signaling. These findings uncover mutation-specific signaling networks that drive subtype fate in invasive GBM and highlight unique pathway(s) as tractable targets for subtype-directed therapy in EGFR-mutant GBM.

Abstract While immunotherapy has transformed treatment in multiple solid tumors, its efficacy in high-grade glioma (HGG) remains limited. Understanding the molecular and clinical factors that influence HGG’s response to immunotherapy is essential to improving outcomes. We identified patients with grade 4 gliomas who had been treated with checkpoint inhibitor (CPI), virus therapy, or CMV-specific T- cell therapy and determined the association between their molecular, clinical, and demographic characteristics and survival outcomes. We identified 66 patients, 57 glioblastoma and 9 astrocytoma, IDH-mutant grade 4; 38 were treated with CPI, 22 with virus therapy, and 6 with CMV-specific T- cell therapy. PIK3CA mutation was associated with shorter PFS and OS (p=0.022, 0.073, respectively) among all patients and a shorter OS among CPI-treated patients (p=0.004). PIK3CA wild-type tumors had less PD-1 expression in CD3+/CD8+ T cells. In CPI-treated patients, IDH1/2 mutation was associated with a shorter OS (p=0.002), and mutations in RB1 and TERT promoter were associated with a shorter PFS (p-value=0.00056, 0.022, respectively). Length of CPI therapy of more than 6 months was associated with increased PFS and OS (p=0.048, 0.062, respectively), while steroid use at baseline was associated with a shorter OS (p=0.00023). Multifocal disease was associated with shorter PFS and OS durations (p=0.0017, 0.0013, respectively) among all patients. In HGG, PIK3CA, IDH1/2, RB1, and TERT promoter mutations may be associated with a poor response to immunotherapy. These results need to be validated in larger studies. Our results may provide the rationale for clinical trials combining PI3K and IDH inhibitors with CPI in HGG.

Abstract PURPOSE Age over 40 years is commonly regarded as a “high risk” feature and potential indication for adjuvant chemoradiotherapy for patients with lower grade glioma in most clinical practice guidelines. However, these recommendations are based on retrospective observations and their subsequent incorporation into legacy clinical trials. It is unclear whether age remains a relevant prognostic factor in the molecular era. METHODS The Prospective Gliomas Research [PROGRES] Database contains individual patient-level data from 11 prospective clinical trials or observational registries, including seven international trials from the RTOG, EORTC, or Alliance cooperative groups. We determined the association of age with progression-free survival (PFS) in low grade or anaplastic glioma, stratified by isocitrate dehydrogenase (IDH1/2) status. We validated our findings in a separate multi-institutional retrospective cohort (Retrospective Glioma Research [REGRES] Database). RESULTS We identified 1,619 and 1,271 eligible patients in the PROGRES and REGRES cohorts, respectively. IDH-wildtype tumors were more common in patients >40 years (38% vs, 5%, odds ratio: 11.3 [95%CI 6.5 – 19.7]). Age was associated with PFS in IDH-wildtype (5-year PFS: 6% vs, 24%, P =.003) but not in IDH-mutant glioma (60% vs, 59%, P = 0.22, P value of interaction <.001). In IDH-wildtype tumors, older age predicted aggressive molecular features, including TERT promoter mutation (65% vs, 28%), EGFR amplification (41% vs, 15%), and chromosome +7/-10 alteration (57% vs, 25%). Age was not predictive of a benefit from chemoradiotherapy versus radiotherapy alone in IDH-mutant glioma. CONCLUSION Older age is a putative surrogate for IDH-wildtype status, but was not an independent predictor of progression in IDH-mutant lower grade glioma and did not predict benefit from chemoradiotherapy. In the absence of additional clinical or molecular risk factors, age alone should not be considered an indication for administration or deferral adjuvant treatment. Practice guidelines should be revised to reflect contemporary prognostic factors in the molecular era.

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.

Abstract Medulloblastoma (MB) is one of the most prevalent malignant brain tumors in children, with tremendous cognitive and neuroendocrine disability among survivors. Group 3 (G3) MBs have poor overall survival at <50%, higher frequency of metastasis, and no targeted therapies. Amplification of MYC and activation of TGFβ signaling are frequent in G3MB. Remarkably, some tumors have no reported mutations, suggesting roles for chromatin-driven mechanisms in this disease. We have generated novel humanized models for G3MB by transducing neuroepithelial stem cells (NESC) derived from human induced pluripotent stem cells with TGFβ effectors alone and/or in combination with MYC, prioritizing combinations observed in patients. We determined that both MYC and TGFβ effectors drove tumor formation in vivo with the combination driving more aggressive tumors and higher frequency of metastasis. Importantly, NESC-derived tumors clustered with human G3MB, indicating our models recapitulated human disease. To decipher mechanisms of resistance, we integrated CUT&RUN for MYC genomic localization and histone PTMs with RNA-sequencing and discovered MYC-bound neural developmental genes repressed in MYC and TGFβR1-driven lines. These gene signatures were associated with the Polycomb Repressive Complex (PRC) and demarcated with H3K27me3; the histone mark directly regulated by PRC. Further interrogation identified JARID1B, a MYC binding partner and H3K4me3 demethylase, as a regulator of these repressed neural genes. This is further reinforced by the observation of higher H3K27me3 levels concurrent with increased JARID1B expression in human G3MB patient samples, compared to other subtypes. We postulate that deregulation of MYC and context-specific targeting to the chromatin template culminates in transcriptional alterations that promote aggressive G3MB. These studies support a critical role of MYC in repressing target genes to drive tumor formation and JARID1B as a new target for therapy. Collectively, we present a critical framework for understanding mechanisms of resistance and the chromatin landscape of MYC- and TGFβ-driven G3MB.

Abstract Telomere length variation is a hallmark of genomic instability, however, its role in shaping the structural variant (SV) landscape of diffuse astrocytoma remains poorly understood. In this study, we employed Oxford Nanopore long-read sequencing to investigate the association between SVs and chromosome arm-specific telomere length in a clinical patient cohort consisting of n = 20 individuals diagnosed with an IDH mutant astrocytoma. Oxford Nanopore long-read sequencing was performed to a depth of ~20-40× coverage. SVs were identified using Sniffles, copy number alterations were assessed using DNAcopy and chromosome arm-specific telomere length was estimated with Telogator. Statistical analyses were conducted to assess associations between telomere dynamics, structural variation, and copy number changes. Astrocytoma genomes exhibited a broad spectrum of structural variants, including deletions and insertions, with significant enrichment in the short arms of acrocentric chromosomes. A subset of samples demonstrated markedly shorter telomeres relative to the overall cohort, accompanied by an increased burden of structural variants, particularly duplications and inversions, suggesting enhanced genomic instability. Notably, a prominent accumulation of deletion and insertion SVs was observed near chromosome ends and centromeres, highlighting the (sub)telomeric and peri(centromeric) regions as SV hotspots. Statistical modeling revealed a significant association between telomere length and arm-specific variation, including telomeric deletions, inversions, and copy number losses. In summary, our findings reveal a previously underappreciated link between SVs and telomere length in astrocytomas. Genomic rearrangements caused by telomere shortening may represent critical drivers of genome instability and could serve as novel biomarkers for disease progression.