bluuebunny/crossref_metadata_2025 huggingface dataset:
PATH-19. DIAGNOSTIC UTILITY OF MOLECULAR PROFILING IN ADULT DIFFUSE GLIOMA
Authors: Ohno Makoto , Nakashima Takuma , Sugino Hirokazu , Yanagisawa Shunsuke , Kawauchi Daisuke , Omura Takaki , Aoki Takuma , Yoshida Akihiko , Suzuki Hiromichi , Narita Yoshitaka
Published: November 2024

INTRODUCTION

With the publication of World Health Organization Classification of the Central Nervous System Tumors (WHO CNS5), molecular profiling has become essential for the diagnosis of CNS tumors. To test for the diagnostic molecular alterations, we developed a targeted DNA sequencing panel (Nakashima et al. 2024) to analyze 113 genes, chromosomal abnormalities, and MGMT promoter methylation. This study aimed to evaluate our diagnostic approach using the targeted sequencing panel.

PATIENTS AND METHODS

We included 72 cases of diffuse adult gliomas diagnosed at our institute between June 2023 and May 2024. We analyzed the tumor diagnoses based on the pathological and immunohistochemical findings as well as the targeted sequencing panel findings.

RESULTS

The tumor diagnoses were as follows: glioblastoma, IDH-wildtype: 32 cases, astrocytoma, IDH-mutant: 17 cases, oligodendroglioma, IDH-mutant and 1p/19q-codeleted: 15 cases, others: 8 cases. Among 32 cases of IDH1/2 mutations, 28 cases (87.5%) with IDH1 R132H mutation were diagnosed by immunohistochemistry using anti-IDH1 R132H antibody, whereas 4 (12.5%) (3 with IDH2 mutation, and 1 with IDH1 R132S) were diagnosed by the targeted sequencing panel. Of the 32 glioblastoma cases, 6 (18.8%) did not show necrosis or microvascular proliferation and were diagnosed based on either TERT promoter mutation, EGFR amplification, or chromosome 7/chromosome 10 abnormalities. Moreover, 24 out of 26 resected cases (92.3%) were diagnosed morphologically, whereas 4 of 6 biopsy cases (66.7%) were diagnosed molecularly (p=0.0056). Among the 17 cases of astrocytoma, IDH-mutant, 2 (11.8%) showed homozygous deletion of CDKN2A/B. There were 4 cases (5.6%) out of 72 that did not satisfy the diagnostic criteria for glioblastoma, astrocytoma, oligodendroglioma.

CONCLUSION

Approximately 95% of cases were diagnosed based on WHO CNS5 criteria with molecular profiling. We also demonstrate molecular profiling is useful in glioblastoma diagnostics, especially in biopsy cases where morphological diagnostic evidence is not recognized.
PATH-22. SINGLE-CELL RNA (SCRNA) SEQUENCING OF PAIRED PRIMARY AND RECURRENT ATYPICAL TERATOID/RHABDOID TUMORS (AT/RT) REVEALED MOLECULAR DIFFERENCES AND THERAPY-RESISTANT PRIMARY TUMOR CELLS
Authors: Altendorf Lea , Roy Rajanya , de Faria Flavia W , Hack Karoline , Koch Arend , Schuhmann Martin U , Hauser Peter , Johann Pascal D , Hasselblatt Martin , Kerl Kornelius , Frühwald Michael C , Schüller Ulrich
Published: November 2024

Atypical teratoid/rhabdoid tumors (AT/RT) are the most common malignant brain tumors during infancy. They split into four molecular types. The major three (AT/RT-SHH, AT/RT-TYR, and AT/RT-MYC) all carry mutations in SMARCB1, the fourth smaller type is characterized by SMARCA4 mutations (AT/RT-SMARCA4). AT/RT are associated with a dismal outcome, and 50% of the patients suffer a progress or recurrence of the tumor. Molecular mechanisms of disease recurrence are currently unclear. Here, we identified molecular characteristics of AT/RT primaries and recurrences, which could help to improve the therapy for relapsed patients. Previously, we investigated tumor tissue from 26 patients revealing signatures of recurrences in comparison to matched primary tumor samples using histology, DNA methylation analysis, and bulk RNA sequencing. To further identify mechanisms regarding tumor progression and recurrence, we performed single-cell RNA (scRNA) sequencing for five of these primary-recurrence pairs so far using formalin-fixed paraffin-embedded (FFPE) tissue. Using Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction, we observed a distinct separation in the gene expression profiles of primary and recurrent tumor cells. In addition, we aimed to identify primary tumor cells which potentially persisted after therapy and developed to recurrences. Therefore, we identified primary tumor cells showing highest similarity to recurrent tumor cells using CIBERSORT and trajectory analysis. Differentially expressed genes of these specific primary tumor cells were investigated. They are involved in cell migration, -adhesion, -proliferation, and -stability, among others. Overall, molecular characteristics that occur in the course of the disease were identified, which may help to define new therapeutic targets for AT/RT recurrences.
PATH-23. SARCOMATOUS TRANSFORMATION OF GLIOBLASTOMA IS ASSOCIATED WITH A DISTINCT MOLECULAR SIGNATURE
Authors: Lucas Calixto-Hope , Al-Adli Nadeem , Young Jacob , Gupta Rohit , Morshed Ramin , Wu Jasper , Ravindranathan Ajay , Shai Anny , Bush Nancy Ann Oberheim , Taylor Jennie , de Groot John , Villanueva-Meyer Javier , Pekmezci Melike , Perry Arie , Bollen Andrew , Theodosopoulos Philip , Aghi Manish , Chang Edward , Hervey-Jumper Shawn , Raleigh David , Diaz Aaron , Costello Joseph , Clarke Jennifer , Butowski Nicholas , Phillips Joanna , Berger Mitchel , Chang Susan , Solomon David
Published: November 2024

A subset of IDH-wildtype glioblastoma (GBM) undergo sarcomatous transformation to gliosarcoma at recurrence which is associated with a propensity for dural and calvarial invasion. However, the underlying biology of sarcomatous transformation and predictive biomarkers for these aggressive tumors are unknown. We performed comprehensive histopathologic, genomic, and epigenomic evaluation of paired initial and recurrent GBM from 106 patients. Eighteen patients (17%) developed sarcomatous transformation at recurrence as defined by fascicular growth, intercellular reticulin deposition, and immunohistochemical evidence of glial to mesenchymal transdifferentiation. Compared to conventional GBM, patients who developed gliosarcoma had shorter interval between initial surgery and first recurrence (8.3 vs. 11.2 months, p=0.002) and reduced overall survival (18.2 vs. 21.9 months, p=0.164). While there were no differences in sex, age, tumor location, or adjuvant therapy, we found differences in the molecular signatures of GBM that transformed to gliosarcoma at recurrence, including a significant enrichment in NF1, TP53, and RB1 alterations and an absence of EGFR amplification. GBM which underwent sarcomatous transformation were enriched for the Mesenchymal epigenetic class at initial surgery (69% vs. 25%) and became enriched for the novel Mesenchymal subclass B at recurrence (43% vs. 2%). Among approximately 850,000 interrogated CpG sites, we identified 1,503 and 2,090 CpG sites within gene regulatory regions that were significantly more hypermethylated or hypomethylated in those initial GBM that transformed to gliosarcoma at recurrence compared to those that did not. Gene Ontology biologic processes enriched in these differentially methylated genes include immune cell signaling, cell-cell adhesion, and TGF-beta signaling. Together, these findings reveal GBM which undergo transformation to gliosarcoma represent a biologically distinct subtype with aggressive clinical course. Enrichment for NF1 and RB1 alterations and differentially methylated immune cell and TGF-beta signaling suggests potential unique therapeutic vulnerabilities for affected patients.
PATH-26. MIDLINE INVOLVEMENT IS ASSOCIATED WITH ABERRANT RB1 SIGNALING IN PATIENTS WITH GRADE 4 IDH-MUTANT ASTROCYTOMA
Authors: Maqbool Muhammad Asad , Jenkins Robert B , Ida Cristiane M , Burns Terence C , Kizilbash Sani H
Published: November 2024

BACKGROUND

The prognostic factors impacting the survival of grade 4 IDH-mutant astrocytoma treated with standard radiation/temozolomide are not well-described.

METHODS

A retrospective cohort was generated of all patients diagnosed at Mayo Clinic with grade 4 IDH-mutant astrocytoma (2021 WHO Classification) on initial diagnosis between 2002-2023, and who received standard radiation/temozolomide. The impact of patient, tumor and molecular variables on overall survival (OS) and progression-free survival (PFS) was evaluated using survival analyses and Cox regression models.

RESULTS

Fifty-eight patients were identified. The median age was 36 years, 64% were male and 93% were white. The median follow up was 3.3 years. The median OS and PFS were 6.9 years and 2.4 years, respectively. CDKN2A/B homozygous deletion significantly reduced both OS (2.5 years vs NR, HR=3.9, p=0.0168) and PFS (1.4 vs 4.5 years, HR=4.2, p=0.0005). Midline involvement (brainstem, basal ganglia, thalamus, cerebellum or corpus callosum) also significantly reduced both OS (2.4 vs 12.8 years, HR=7.0, p=0.0014) and PFS (1.4 vs 4.5 years, HR=4.8, p=0.0002). MGMT promoter hypermethylation showed a trend toward significance for PFS (p=0.082) but did not impact OS. Age, sex, tumor size, ATRX immunohistochemistry and tumor-treating field therapy did not impact survival outcomes. Multivariable analyses revealed that PFS remained significantly impacted by both CDKN2A/B homozygous deletion (HR=3.5, p=0.0051) and midline involvement (HR=3.1, p=0.0125). A significant association between CDKN2A/B homozygous deletion and midline involvement was unexpectedly observed (53% if midline, 24% if non-midline; χ2=4.3, p=0.037). Exploratory analyses revealed that 15/15 (100%) of patients with midline involvement demonstrated aberration in RB1 signaling (CDKN2A/B homozygous deletion, n=8; CDKN2A/B hemizygous deletion or loss of heterozygosity, n=6; CDK4 amplification, n=1).

CONCLUSION

CDKN2A/B homozygous deletion and midline involvement independently impact PFS in patients with grade 4 IDH-mutant astrocytoma treated with standard radiation/temozolomide. Furthermore, midline involvement may be associated with aberrant RB1 signaling.
PATH-29. LONGITUDINAL EPIGENOMIC EVOLUTION OF IDH-WILDTYPE GLIOBLASTOMA
Authors: Al-Adli Nadeem N , Young Jacob S , Lucas Calixto-Hope G , Gupta Rohit , Morshed Ramin A , Wu Jasper , Ravindranathan Ajay , Shai Anny , Bush Nancy Ann Oberheim , Taylor Jennie W , de Groot John , Villanueva-Meyer Javier , Pekmezci Melike , Perry Arie , Bollen Andrew W , Theodosopoulos Philip V , Aghi Manish K , Chang Edward F , Hervey-Jumper Shawn L , Raleigh David R , Diaz Aaron A , Costello Joseph F , Clarke Jennifer L , Butowski Nicholas , Phillips Joanna J , Chang Susan M , Berger Mitchel S , Solomon David A
Published: November 2024

Glioblastoma, IDH-wildtype remains a molecularly heterogeneous disease that is refractory to current therapies. To investigate how longitudinal epigenomic evolution of glioblastoma drives tumor progression and treatment resistance, we performed comprehensive histopathologic assessment, targeted genomic sequencing, and genome-wide DNA methylation profiling of paired initial and recurrent IDH-wildtype glioblastoma samples from 98 patients, as well as a separate longitudinal cohort of IDH-mutant astrocytomas for comparison. Primary treatment-naïve IDH-wildtype glioblastomas had more globally hypomethylated genomes compared to primary IDH-mutant astrocytomas. At time of recurrence, IDH-mutant astrocytomas uniformly became more hypomethylated similar to the global methylation levels in IDH-wildtype glioblastomas. In contrast, recurrent IDH-wildtype glioblastomas were heterogeneous with subsets becoming more globally hypermethylated (27%), hypomethylated (22%), or remaining stable (51%). Accordingly, a substantial proportion (52%) of recurrent glioblastomas underwent methylation class switching compared to their matched primary tumor, with a predominance of the RTK2 epigenetic subtype at initial surgery and the Mesenchymal epigenetic subtype at recurrence. Among approximately 850,000 interrogated CpG sites, we identified only 110 and 153 sites that consistently became more hypermethylated or hypomethylated between initial and recurrent IDH-wildtype glioblastomas, which regulate genes involved in neuronal morphogenesis, oligodendrocyte differentiation, and myelination. In contrast, we identified 260 and 18,527 CpG sites that consistently became more hypermethylated or hypomethylated between initial and recurrent IDH-mutant astrocytomas, which regulate genes involved in neuronal stem-like differentiation, cell cycle control, and other biologic processes. Finally, we developed a DNA methylation evolution signature incorporating change in mean beta-methylation values from initial to recurrent tumor specimens across 347 critical CpG sites that significantly correlated with clinical outcomes for patients with IDH-wildtype glioblastoma. In summary, IDH-wildtype glioblastomas demonstrate heterogeneous epigenomic evolution patterns distinct from IDH-mutant astrocytomas. These changes in epigenetic patterns may identify unique subgroups of glioblastoma with differential treatment response and inform future therapeutic studies targeting differentially methylated gene programs.
PATH-30. CLINICAL OUTCOMES AND PREDICTIVE BIOMARKERS FOR IDH-WILDTYPE GLIOBLASTOMAS DEVELOPING HYPERMUTATION FOLLOWING TEMOZOLOMIDE TREATMENT
Authors: Young Jacob , Lucas Calixto-Hope , Al-Adli Nadeem , Gupta Rohit , Morshed Ramin , Wu Jasper , Ravindranathan Ajay , Shai Anny , Oberheim-Bush Nancy Ann , Taylor Jennie , de Groot John , Villanueva-Meyer Javier , Pekmezci Melike , Perry Arie , Bollen Andy , Theodosopoulos Philip , Aghi Manish , Chang Edward , Hervey-Jumper Shawn , Raleigh David , Diaz Aaron , Costello Joseph , Clarke Jennifer , Butowski Nicholas , Phillips Joanna , Chang Susan , Berger Mitchel , Solomon David
Published: November 2024

Current standard of care for IDH-wildtype glioblastoma (GBM) includes maximal safe resection, adjuvant radiation, and chemotherapy with the alkylating agent temozolomide. A subset of gliomas treated with temozolomide develop somatic hypermutation with a predominance of C>T transitions due to the alkylation effects on DNA. However, the frequency of occurrence, clinical ramifications, and predictive biomarkers for developing temozolomide-induced hypermutation (TMZ-HM) in GBM are unknown. Here we performed comprehensive histopathologic, genomic, and epigenomic evaluation of paired initial and recurrent GBM from 106 patients. Seven patients (7%) developed hypermutation at time of first recurrence, while an additional five patients (5%) developed hypermutation at a subsequent recurrence. Patients who developed TMZ-HM had a significantly longer interval between initial surgery and first recurrence (27.8 vs. 9.9 months, p<0.001). In contrast to IDH-mutant gliomas where TMZ-HM is associated with poor prognosis, those patients with IDH-wildtype GBM who developed TMZ-HM had significantly longer overall survival from both initial surgery (67.9 vs. 20.3 months, p<0.001) and from time of recurrence after development of hypermutation (30.9 vs. 9.5 months, p=0.001). There was no difference in oncogenic alteration frequency in initial GBM that subsequently developed TMZ-HM. However, 4 specific CpG sites out of 12 total interrogated sites in the promoter region of MGMT (a DNA repair enzyme) and 5 specific CpG sites in the promoter region of KCNQ1DN (a negative regulator of c-Myc) were significantly more hypermethylated in those GBM that developed TMZ-HM. We then generated a weighted risk score across these CpG sites that can be used to prospectively identify GBM likely to develop TMZ-HM associated with favorable survival. In summary, patients with GBM that develop TMZ-HM follow a more favorable clinical course, and specific MGMT and KCNQ1DN promoter hypermethylation patterns could serve as a biomarker to identify these patients who may potentially benefit from extended alkylating chemotherapy treatment.
PATH-35. INTEGRATED GENOMIC ANALYSES OF IMMUNODEFICIENCY-ASSOCIATED EPSTEIN-BARR VIRUS- (EBV) POSITIVE PRIMARY CNS LYMPHOMAS
Authors: Kaulen Leon D , Denisova Evgeniya , Hinz Felix , Hai Ling , Friedel Dennis , Henegariu Octavian , Hoffmann Dirk C , Ito Jakob , Kourtesakis Alexandros , Lehnert Pascal , Doubrovinskaia Sofia , Karschnia Philipp , von Baumgarten Louisa , Kessler Tobias , Baehring Joachim M , Brors Benedikt , Sahm Felix , Wick Wolfgang
Published: November 2024

Immunodeficiency-associated primary CNS lymphoma (PCNSL) represents a distinct clinicopathological entity, which is typically Epstein-Barr virus positive (EBV+) and carries an inferior prognosis. Genetic alterations that characterize EBV related CNS lymphomagenesis remain unclear precluding molecular classification and targeted therapies. In this study, a comprehensive genetic analysis of 22 EBV+ PCNSL, integrated clinical and pathological information with exome and RNA sequencing (RNASeq) data. Deconvolution of bulk RNA sequencing data was performed using CIBERSORTx to characterize the tumor microenvironment. EBV+ PCNSL with germline controls carried a median of 55 protein-coding single nucleotide variants (SNVs; range 24-217) and 2 insertions/deletions (range 0-22). Genetic landscape was largely shaped by aberrant somatic hypermutation with a median of 41.01% (range 31.79-53.49%) of SNVs mapping to its target motifs. Tumors lacked established SNVs (MYD88, CD79B, PIM1) and copy number variants (CDKN2A, HLA loss) driving EBV negative PCNSL. Instead, EBV+ PCNSL were characterized by SOCS1 mutations (26%), predicted to disinhibit JAK/STAT signaling, and mutually exclusive gain-of-function NOTCH pathway SNVs (26%). Copy number gains were enriched on 11q23.3, a locus directly targeted for chromosomal aberrations by EBV, that includes SIK3 known to protect from cytotoxic T-cell responses. Losses covered 5q31.2 (STING), critical for sensing viral DNA, and 17q11 (NF1). Unsupervised clustering of RNASeq data revealed two distinct transcriptional groups, that shared strong expression of CD70 and IL1R2, previously linked to tolerogenic tumor microenvironments. Correspondingly, deconvolution of bulk RNASeq data revealed elevated M2-macrophage, T-regulatory cell, mast cell and monocyte fractions in EBV+ PCNSL. In addition to novel insights into the pathobiology of EBV+ PCNSL, the data provide the rationale for the exploration of targeted therapies including JAK-, NOTCH- and CD70-directed approaches.
PATH-50. AI-POWERED AUTOMATED TISSUE SEGMENTATION IMPROVES OUTCOME STRATIFICATION IN GLIOBLASTOMA
Authors: Ayoub Georges , Elharouni Dina , Bossi Connor , Möller Constantin , Malinowski Seth , Japo Julia , Vaidya Anurag Jayant , Zhang Andrew , Shaban Muhammad , Santos Andres , Williamson Drew , Meredith David , Mahmood Faisal , Ligon Keith
Published: November 2024

Glioblastoma displays morphological heterogeneity on routine H&E whole slide images, with conflicting evidence on the reliability of morphological features in predicting tumor behavior and treatment response. However, current standards for assessing morphology and disease status rely on nonquantitative manual evaluation by pathologists, which are prone to inherent variation. We sought to (1) expand the tools available for quantitative assessment and (2) evaluate the utility of this approach in identifying valuable biomarkers. We trained a deep learning-based algorithm using DenseNet on HALO AI platform for automated segmentation of six tissue classes (heavy infiltration, mild infiltration, mesenchymal tissue, geographic necrosis, palisading necrosis, and hemorrhage) on 3232 labeled annotations from 100 whole slide images. Manual pathologists’ estimations from clinical records showed strong correlation with corresponding digital quantifications (p<0.001), and further pixel-wise validation on 828 separate annotations showed high overlap between predicted and ground truth segmentations (precision=0.88, recall= 0.85, F1-score=0.87). We then identified a longitudinal cohort of 115 newly diagnosed glioblastoma tissue paired with the recurrence post-treatment (RT/TMZ), including all 827 H&E whole slide images scanned at 40x. The quantification of longitudinally paired tissue showed a relative increase in geographic necrosis (+62%) and mild infiltration (+110%) and a relative decrease in palisading necrosis (-54%) and heavy infiltration (-35%) between the two timepoints. Patients with rapid clinical progression had more areas of large geographic necrosis (p=0.002), and mesenchymal tissue increase was associated with worse overall survival (p=0.016). Digitally quantified heavy infiltration as a predominant tissue on recurrence outperformed corresponding pathologist estimation of tumor as a predominant tissue on recurrence in stratifying overall-survival (p=0.005 vs p=0.640). Collectively, our AI-powered classifier enables an automated objective quantification of glioblastoma tissue, identifies markers of clinical response, and offers a potential adjunct to enhance routine pathologic reporting of glioblastoma.
PATH-52. DIFFERENCES IN GENE EXPRESSION, GENOME-WIDE METHYLATION AND METABOLITES IN ADULT DIFFUSE GLIOMAS
Authors: Vinocha Anjali , Berdecia Valerie , Wang Daniel , Arjuna Srividya , Shah Mauli , Dono Antonio , Putluri Nagireddy , Esquenazi Yoshua , Ballester Leomar
Published: November 2024

Metabolic reprogramming is a hallmark of cancer, including diffuse gliomas. IDH1 and IDH2 are key enzymes linking cellular metabolism to epigenetic regulation and redox states. IDH1/IDH2 enzymes catalyze the conversion of isocitrate to α-ketoglutarate, while the mutant enzymes increase the production of D-2-hydroxyglutarate, an oncometabolite that induces epigenetic changes, leading to gene expression alterations. Understanding how epigenetic alterations affect metabolic gene expression and metabolite levels in diffuse gliomas could help identify diagnostic biomarkers and therapeutic targets. We studied the expression of metabolism-related genes, metabolites, and genome-wide methylation status, which will facilitate an integral understanding of the metabolic changes in IDH-mutant and IDH-wildtype gliomas. Study design included 47 fresh frozen tissue samples. RNA was extracted and used for gene expression analysis using the NanoString platform (nCounter® Metabolic Pathways Panel), while extracted DNA was used for targeted sequencing with a panel interrogating 600 genes and for genome-wide methylation analysis using the Illumina Epic v2. In addition, unbiased metabolomic analysis by mass spectrometry was performed in 25 tissue and CSF samples out of 47 samples. Methylation status, gene expression and metabolite levels were compared between IDH-mutant and IDH-wildtype gliomas. Results showed significant differences in DNA methylation, gene expression and metabolites between IDH-mutant and IDH-wildtype gliomas. UPP1, an enzyme involved in uracil metabolism, was studied in depth to understand the interplay between DNA methylation, gene expression, and metabolic reprogramming in diffuse glioma. Epigenetic analysis revealed that the CpG sites within the UPP1 gene displayed reduced methylation in IDH wild-type compared to IDH-mutant tumors. IDH wild-type tumors showed higher UPP1 expression compared to their IDH-mutant counterparts. Consequently, we observed higher levels of uracil in tissue and CSF samples from patients with IDH wild-type gliomas. These data provide a framework to study the relationship between mutations, methylation, gene expression and metabolism in diffuse gliomas.
PATH-56. LOSS OF HETEROZYGOSITY OF CDKN2A/B DEFINES AN AGGRESSIVE SUBSET OF RECURRENT, HIGH-GRADE MENINGIOMAS
Authors: Dincer Alper , Ghanekar Shaila , Kocakavuk Emre , Tabor Joanna , Kim Miri , Moliterno Jennifer
Published: November 2024

INTRODUCTION

Loss of heterozygosity (LOH) occurs when one gene allele is lost, leaving the cell with a single functional copy. This genetic alteration drives tumor progression by disabling critical regulatory pathways. Currently, CDKN2A/B homozygous loss is a criterion for WHO Grade 3 meningiomas. However, the impact of CDKN2A/B LOH and other copy-number alterations remains unclear. This study investigates the effects of LOH in the CDKN2A/B tumor suppressor gene on progression-free survival (PFS) and overall survival (OS) in meningiomas.

METHODS

The study included adult patients with sporadic primary or recurrent meningiomas who underwent resection and whole exome sequencing. LOH and copy-number alterations were confirmed on visual inspection of b-allele frequency and mean ratio graphs. Samples of unsuitable quality for evaluation were excluded. CDKN2A/B copy number and LOH were associated with PFS and OS.

RESULTS

The sample included 333 meningiomas (64.6% female [n=215], 18.8% recurrent meningiomas [n=61], and 50 cases of postoperative recurrence [15%]). CDKN2A/B was intact in 88.5% of samples (n=295), while 38 samples (11.4%) exhibited CDKN2A/B LOH. This included homozygous deletions (n=2, 5.2%), heterozygous deletions (n=11, 28.9%), amplifications (n=12, 31.6%), and copy-neutral LOH (n=13, 34.2%). All copy-number alterations were associated with an increased risk of recurrence compared to CDKN2A/B intact samples, so CDKN2A/B LOH was used for subsequent analysis. CDKN2A/B LOH was more frequently associated with prior recurrence (22.9% vs. 8.8%; p=0.004), prior radiation (46% vs. 15.6%; p<0.0001), and WHO Grade 2 and 3 tumors (63.2% vs. 42.7%; p=0.02). CDKN2A/B LOH was associated with worse PFS (HR 3.97 [1.3-11.9]; p=0.01) and worse OS (HR 2.9 [1.03-8.2]; p=0.0429) only in recurrent, high-grade meningiomas, independent of the fraction of the genome altered, mutation count, and Simpson grade. Postoperative radiation therapy did not improve PFS (HR 3.24 [1.06-9.85]; p=0.038).

CONCLUSION

CDKN2A/B LOH is enriched in high-grade, recurrent meningiomas and confers worse PFS and OS despite postoperative radiotherapy. CDKN2A/B LOH is a high-risk biomarker that predicts tumor behavior and patient outcome.
PATH-57. CLINICAL AND MOLECULAR FEATURES OF METHYLATION CLASS DIFFUSE LEPTOMENINGEAL GLIONEURONAL TUMOR
Authors: Dampier Christopher , Singh Omkar , Nasrallah MacLean , Rodriguez Fausto , Eschbacher Jennifer , Morris Meaghan , Abdullaev Zied , Quezado Martha , Pratt Drew , Cimino P J , Aldape Kenneth
Published: November 2024

Genome-wide DNA methylation profiling can help identify rare CNS tumors, including diffuse leptomeningeal glioneuronal tumor (DLGNT). Due to the infrequency of this entity, DLGNT remains poorly understood. To help resolve uncertainty regarding DLGNT, we examined epidemiologic, histologic, and molecular features of 32 (21 newly profiled, 11 publicly available) tumors matching to DLGNT by the DKFZ classifier (v12, score >=0.85). Of these tumors, 25 matched to DLGNT subtype 1 and seven to subtype 2. Subject median age was 12 years in subtype 1 and 22 years in subtype 2 (14.5 overall, range 2-44), with equal numbers of females and males (n=16 each). Spinal cord was the most frequently involved site (n=21), but intracranial lesions were observed (n=6). Leptomeningeal involvement was noted in only four of 11 tumors with available imaging descriptions. In the subset of cases available for histologic review (n=19), oligodendrocyte-like morphology was present in over half (n=11). Microvascular proliferation was uncommon (n=5). Chromosome 1p loss was observed in 29 (91%), and 1p/19q co-deletion was observed in 18 tumors (56%). Gains of 1q and 7q were each observed in 12 (38%), and whole chromosome 7 gain was observed in eight (25%). Loss of 22q was seen in 12 (38%). In the subset of tumors with fusion testing (n=15), KIAA1549::BRAF fusion was present in 12 (80%), and one showed a QKI::RAF1 fusion. Five tumors harbored BRAF mutations, and one harbored a break-point in BRAF without a known fusion partner. In nine subjects with clinical follow-up, there was one death after 3.1 years, and the remaining subjects were alive with a median follow-up of 6.4 years (maximum 19 years). Progression-free survival (PFS) was available for six subjects with a median PFS of 6 years. Presentation of DLGNT without noted leptomeningeal involvement appears common. Further characterization of subject outcomes will help clarify the clinical behavior of DLGNT.
PATH-62. CORRELATES OF NEURAL SIGNALING ELUCIDATE SURVIVAL BENEFIT IN GLIOMAS
Authors: Rampalli Ihika , Katlowitz Kalman , McDonald Malcolm , English Collin , Diab Nabeel , Perry Zachary , Jalali Ali , Rao Ganesh , Deneen Benjamin , Mandel Jacob
Published: November 2024

Recent literature has highlighted neural signaling markers (SM) as drivers for synaptogenesis, invasion, and proliferation in gliomas. Further work on elucidating key mutations can provide improved prognostication and potential treatment targets. Our objective is to identify correlates of neural signaling in relation to glioma histopathology and patient outcomes. We used a combination of bulk RNA sequencing (RNA-seq) and a DNA gene panel (DPG) by Tempus next-generation sequencing. Differential gene expression (DGE) was performed using DESeq2 after subsetting genes for neural SM. Dimensionality reduction was applied through t-SNE projections. Variant calls were analyzed using EnsemblVEP and maftools. Survival analysis was determined through log-rank tests. All analyses were conducted with R. 176 and 184 patient samples were analyzed for RNA-seq and DPG, respectively. t-SNE of DGE highlights two distinct functional clusters with no correlation to WHO classification status (Chi-squared p = 0.39) The median survival for the big cluster was observed at 957 days, while no median survival was reached even after 4,420 days of follow-up in the small cluster (p = 0.01). This contrast remains consistent when examining subsets of gliomas with unmethylated MGMT promoter (p = 0.02) and glioblastomas (p = 0.02), but not others such as IDH mutation status and low-grade gliomas (p > 0.1). Genes upregulated in the small cluster had equal representation of synaptic and paracrine SM (45% and 55%), while the big cluster had a greater representation of paracrine SM (69% and 31%). DPG of low-grade gliomas highlighted 3 somatic signaling mutations (FGFR1, PTPRD, and SLIT2) that are more prevalent in the big cluster. Functional classification based on neural signaling markers can elucidate a novel set of biomarkers that may impact survival in glioma patients. Further studies are required to validate such findings and develop therapeutic targets.
PATH-65. MONITORING MENINGIOMA CELL CYCLE ACTIVITY THROUGH DREAM-MMB ACTIVITY SWITCHING
Authors: Kona Abhinav , Rai Ansh , Rojas Diego , Klisch Tiemo , Patel Akash
Published: November 2024

Meningiomas account for over 40% of all primary intracranial brain tumors, with approximately one-fifth of these tumors recurring. Our lab has previously used molecular techniques to identify three subgroups: MenG A, B, and C, which have been independently validated. Interestingly, only MenG C tumors harbor recurring patients, making it an aggressive subtype of meningioma. One hallmark of MenG C tumors is the overexpression of a distinct set of genes that harbor in their promoter the CDE-CHR DNA-binding element, used by a transcriptional complex that in dormant cells functions as a repressor (DREAM). Before phosphorylation, this complex functions as an activator (MBB) in cycling cells. Upon a phosphorylation-dependent switch, the dual-specificity tyrosine kinase DYRK1A phosphorylates S28 on LIN52, which itself is dimerized with LIN9 of the core complex. Phosphorylation shifts the complex to DREAM, while lack thereof allows the core complex to interact with MYBL2 (now MBB) and activate the same genes repressed in quiescent cells. We seek to quantify this switch activity using an in vivo luciferase sensor using NanoBiT technology. Our biosensor is based on a split nanoluciferase, where one half is fused to the LIN52/LIN9 dimer and the other is fused to MYBL2. When MYBL2 binds to the LIN52/LIN9 dimer, a functional nanoluciferase is formed, and its activity can be measured using a luciferase-specific substrate. As proof of principle, we have increased cell proliferation by increasing FBS concentration in cultured cells as well as by blocking S28 phosphorylation using the DYRK1A-specific inhibitor Harmine. We screened all possible combinations (alternating NanoBiT fragments) for the highest luciferase activity after stimulation. In the future, this biosensor can be used to monitor cell cycle activity in vitro as well as in vivo using low-cost Luciferase reporter assays to better understand the regulation of specific genes in MenG C tumors.
PATH-68. THE CLINICAL AND PROTEOMIC CLASSIFICATION FOR THE PRECISION TREATMENT STRATEGY OF CHORDOMA
Authors: Meng Tong
Published: November 2024

Chordoma is a rare and heterogeneous mesenchymal malignancy, with distinct clinical and biological behaviors. Till now, its comprehensive clinical-molecular characteristics and accurate molecular classification remain obscure, leading to numerous diagnostic and therapeutic challenges. In this research, we enroll a large cohort of chordoma (102 patients) and describe their clinical, imageological and histopathological features. Through tandem mass tag-based proteomic analysis and nonnegative matrix factorization clustering, we classify chordoma into the following three molecular subtypes: bone microenvironment dominant, mesenchymal derived, and mesenchymal to epithelial transition mediated pattern. The three subtypes exhibit discrete clinical prognosis and distinct biological attributes of osteoclastogenesis and immunogenicity, oxidative phosphorylation, and receptor tyrosine kinase activation, suggesting targeted therapeutic strategies of Denosumab, S-Gboxin and Anlotinib, respectively. Notably, these approaches demonstrate positive treatment outcomes for each subtype in vivo and in vitro, as well as in patient-derived xenograft models. Altogether, this work sheds light on the clinical-proteomic characteristics of chordoma that deepens our understanding of this rare disease and provides candidate precision treatment strategy for chordoma according to molecular classification, underscoring their potential for clinical application.
NIMG-05. ARTIFICIAL INTELLIGENCE-BASED RESPONSE ASSESSMENT FOR PATIENTS RECEIVING LASER INTERSTITIAL THERMAL THERAPY
Authors: Haskell-Mendoza Aden , Reason Ellery , Gonzalez Ariel , Jackson Joshua , Sankey Eric , Srinivasan Ethan , Herndon II James , Fecci Peter , Calabrese Evan
Published: November 2024

BACKGROUND

Laser interstitial thermal therapy (LITT) is a minimally invasive option for tissue diagnosis, cytoreduction, and rapid post-operative return to systemic therapies for patients with brain tumors or radiation necrosis. As ablated tissue remains in situ, post-LITT edema may be associated with apparent increased lesion size and transient clinical worsening, complicating assessment of progression.

METHODS

All patients receiving LITT at a single center for tumors or radiation necrosis from 2015 – 2023 with ≥ 9 months of MRI follow-up were retrospectively reviewed. A 3D U-net segmentation model implemented in nnU-Net was developed for automated segmentation of Contrast-enhancing Lesion Volume (CeLV) of LITT-treated lesions on T1-weighted post-contrast MR images. CeLVs were analyzed to establish volumetric post-LITT response assessments.

RESULTS

Across 384 unique MRI exams, 61LITT-treated lesions and 6 control cases of medically-managed radiation necrosis were analyzed. Automated segmentation was qualitatively accurate in 367/384 (95.6%) images. CeLV increased to a median of 68.3% (IQR 35.1 – 109.2%) from baseline at 1 – 3 months from LITT (P = 0.0012) and returned to baseline thereafter. Based on established criteria, volumetric disease progression was defined as lesion expansion 40% from volumetric nadir or baseline. Twenty-one of 56 (37.5%) patients experienced volumetric progression with a progression-free survival of 21.4 (6.0 – 93.4) months. Patients experiencing volumetric progression had lower mOS (17.3 vs 62.1 months, P = 0.0015).

CONCLUSIONS

We observed a stereotyped increase in CeLV at 1 – 3 months post-LITT, which resolved within 6 months of the procedure. Post-LITT disease response can be reliably and feasibly assessed with criteria that account for this transient CeLV expansion. Automated lesion segmentation may speed adoption of volumetric response assessment criteria to clinical practice.
NIMG-07. GLIOBLASTOMA AS A MIMIC OF ACUTE ISCHEMIC STROKE: AN UNDERRECOGNIZED PHENOMENON AND THE IMPACT ON PATIENT OUTCOMES
Authors: Vazquez Sima , Spirollari Eris , Soldozy Sauson , Dominguez Jose , Al-Mufti Fawaz , Aiken Robert , Hanft Simon
Published: November 2024

BACKGROUND

Glioblastoma may present similarly to acute ischemic stroke. This study aims to determine characteristics and outcomes of patients with glioblastoma presenting with stroke-like symptoms. Our objective is to characterize patients with glioblastoma who present as mimics of acute ischemic stroke and identify differences in outcomes when compared to those diagnosed with glioblastoma only.

METHODS

The 2016-2019 National Inpatient Sample (NIS) database was queried for all patients who had a new diagnosis of glioblastoma. Patients with new glioblastoma who carried an admission diagnosis of acute ischemic stroke, but did not undergo thrombectomy, chemical thrombolysis, or hemicraniectomy were categorized as “GBM-Stroke Mimic”. The characteristics and comorbidities between GBM-Stroke Mimic and new glioblastoma patients were compared. Primary outcomes analyzed were discharge disposition and mortality.

RESULTS

Of 61,755 patients newly diagnosed with glioblastoma, 1,000 (1.6%) were GBM-Stroke Mimics. GBM-Stroke Mimic patients more commonly presented with aphasia (P < 0.001) and hemiplegia (P < 0.001). Age greater than 65, atrial fibrillation, diabetes mellitus, hypertension, hyperlipidemia, and long-term anticoagulation/antiplatelet therapy were more commonly associated with GBM-Stroke Mimic patients (all P < 0.001). GBM-Stroke Mimic patients were more likely to be discharged to skilled nursing facility, (p < 0.001), and a diagnosis of GBM-Stroke Mimic was an independent risk factor for inpatient death (P < 0.001).

CONCLUSION

To our knowledge, this is the first study formally investigating the clinical outcomes of glioblastoma when initially diagnosed as stroke. When this misdiagnosis is made, we found an association with increased inpatient mortality, delays of care, and inappropriate resource allocation.
NIMG-13. CHANGES IN CORTICAL ARCHITECTURE ASSOCIATED WITH GLIOBLASTOMA ASSOCIATED EPILEPSY
Authors: Anzak Anam , Pimentel Bernardo Crespo , Caciagli Lorenzo , Marino Silvia , Wandschneider Britta
Published: November 2024

BACKGROUND

Emerging evidence suggests both local hyper-excitability promoting epilepsy, and synaptic and paracrine mediated integration of Glioblastoma into brain-wide neural networks. In this study we sought clinical evidence of disease progression, and concurrent radiological evidence of differences in remote cortical architecture, in Glioblastoma patients with and without epilepsy.

METHODS

55 patients with biopsy-confirmed Glioblastoma, mean-age 59.4yrs±10.9yrs, were studied. 23 patients had a diagnosis of Glioblastoma-related epilepsy on presentation. We compared clinical markers of disease progression in individuals with and without epilepsy. Further, we explored differences in cortical architecture between both groups. Utilising pre-operative T1-weighted, contrast-enhanced MRI scans (n=45), we performed vertex-wise measurements of cortical thickness (CT) and cortical surface area (CSA) using the Virtual Brain Grafting Toolbox and FreeSurfer v.7.0. Radiologically-identifiable tumour and oedema was masked and excluded from analysis. Scans with right-hemispheric tumours were flipped to the left. Linear mixed-effects models were applied to pre-processed imaging-data.

RESULTS

Individuals with epilepsy had shorter progression-free survival (median 4.2 months) than those without seizures (9.3 months, p<0.05) with gold-standard treatment. No significant difference between lesion volumes (tumour and oedema) existed between the two groups (unpaired t-test, p>0.05). Controlling for age and tumour location, significant increases (p<0.01) in CT and CSA were observed in patients with Glioblastoma-related epilepsy in lesion-ipsilateral supramarginal gyrus, superior parietal lobule, precuneus/cuneus and temporal lobe compared to those without epilepsy. Interestingly, significant (p<0.05) increases in CT in lesion-contralateral supramarginal gyrus were additionally observed in those with epilepsy compared to those without.

CONCLUSIONS

Glioblastoma-related epilepsy was associated with poorer survival outcomes and changes in remote cortical architecture. Implicated regions form part of the default mode network, which has previously been identified as a crucial hub for epilepsy. Biological underpinnings of cortical network alterations, and their possible role in promoting not only hyper-excitability but also Glioblastoma progression, require correlation with histopathological characteristics and validation in larger study cohorts.
NIMG-14. HEAD-TO-HEAD COMPARISON OF18F-FET PET AND68GA-PSMA-11 PET IN DISTINGUISHING SMALL VOLUME TUMOR PROGRESSION VS TREATMENT-RELATED CHANGE IN POST-STANDARD OF CARE TREATMENT OF HIGH-GRADE GLIOMA USING DYNAMIC ACQUISITION AND KINETIC MODELING
Authors: Ocana Jesus , Green Mark , Territo Wendy , Hutchins Gary , Veronesi Michael , Nevel Kathryn , Umber Shafique
Published: November 2024

BACKGROUND

The inability to accurately distinguish between tumor progression and treatment-related changes in patients with high-grade glioma on routine imaging can negatively impact patient management and in some cases, outcome. Various imaging methods have been used to address this issue, including 18F-fluoro-ethyl-tyrosine (FET) PET and MR perfusion. However, these methods may not provide reliable results in cases of small lesion size or hemorrhage within the treatment site. The prostate-specific membrane antigen (PSMA) has been observed to be expressed by neovasculature in brain tumors. Since PSMA cannot cross the blood brain barrier, uptake of PSMA in the brain carries high-level of suspicion for residual tumor. Still, further work is needed to better understand PSMA uptake in the tumor bed following standard of care (SOC) treatment and to compare to currently available neuro-oncologic radiotracers, such as FET. We hypothesize that PSMA imaging of glioma neovasculature will provide unique diagnostic information that will aid in the differentiation of small volume tumor progression from treatment-related changes in the post-SOC treatment setting.

METHODS

Patients who underwent clinical Expanded Access PET/MR imaging with 18F-FET were re-imaged in a research protocol that collected a brain 68Ga-PSMA-11 PET/CT scan, as well as a repeat 18F-FET PET/CT. Kinetic modeling of dynamic radiotracer uptake was performed. Scans were assessed for correlation with subsequent imaging and changes in clinical management.

RESULTS

All PSMA scans that were performed were concordant with the initial clinical FET scan, subsequent imaging follow up and appropriate changes in clinical management. The PSMA-detected site was confirmed to be tumor in a single case with subsequent tissue sampling. One patient who was started on bevacizumab after their clinical FET demonstrated a significant decrease in uptake on the research FET scan, but persistent uptake on PSMA.

CONCLUSION

PSMA may effectively show tumor recurrence in post-SOC treatment high-grade glioma patients.
NIMG-22. QUANTITATIVE BRIGHTNESS ANALYSIS OF 5-ALA FLUORESCENCE IN GLIOMA SURGERY
Authors: Kon Takashi , Kobayashi Yusuke , Shimizu Katsuyoshi , Mizutani Tohru , Sato Yosuke
Published: November 2024

OBJECTIVE

The 5 aminolevulinic acid (5-ALA) is used for intraoperative tumor visualization in neurosurgery. We hypothesized that glioma may vary in pathology according to the brightness of 5-ALA fluorescence, which we quantified and compared with the pathological results of glioma.

METHODS

From 2019 to 2023, we investigated 28 glioma patients who underwent surgery with 5-ALA. The pathological diagnosis was based on classification of WHO 2016. The 5-ALA was administered before surgery, and the brightness of 5-ALA fluorescence was quantified.

RESULTS

Seventeen cases of glioblastoma (GBM), four cases of anaplastic astrocytoma (AA), three cases of oligodendroglioma (OL), and four cases of low grade glioma (LGG) were examined. The mean (SD) brightness of 5-ALA fluorescence was 155.9 (56.0) in GBM, 180.5 (64.7) in AA, and 66.3 (18.8) in OL. The brightness in OL was significantly lower than that in GBM and AA (Scheffe’s test, p<0.05). All LGGs showed negative in the brightness.

CONCLUSIONS

The brightness of 5-ALA fluorescence was shown to vary by pathology, which may contribute to intraoperative diagnostic support.
NIMG-30. DEUTERIUM METABOLIC IMAGING (DMI) SHOWS A STRONG RELATION BETWEEN TUMOR GRADE AND GLUCOSE METABOLISM IN PRIMARY BRAIN TUMORS
Authors: Thaw-Poon Serena , Blondin Nicholas A , Liu Yanning , Corbin Zachary A , Baehring Joachim , Omuro Antonio , Moliterno Jennifer , Omay Sacit Bulent , Fulbright Robert K , de Graaf Robin A , De Feyter Henk M
Published: November 2024

BACKGROUND

Metabolic imaging using FDG-PET is a key component of disease management in many cancers outside of the brain, but in brain tumors, it often shows low tumor-to-brain contrast because of high background signal from normal brain. Deuterium metabolic imaging (DMI) is a new 2H magnetic resonance spectroscopic imaging-based technique that when combined with administration of 2H-labeled glucose can provide high tumor-to-brain image contrast because it can detect downstream metabolism instead of only glucose uptake. In this observational study, DMI of glucose metabolism was performed in 22 patients with primary brain tumors of different grades, and at different disease stages.

METHODS

DMI data were acquired using a 4 tesla MRI scanner after oral administration of 0.75g/kg of [6,6’-2H2]-glucose in water. Metabolic maps were generated of 2H-labeled glucose, glutamate+glutamine (Glx), lactate (Lac), and Lac/(Lac+Glx), a proxy for the metabolic shift observed in many cancers known as the Warburg effect. Volumes of interest (VOI) based on contrast-enhancing and non-enhancing tumor regions were created using clinical MRIs and combined with DMI maps to generate tumor-specific values for Lac/(Lac+Glx). Eta-squared was calculated using tumor grade and Lac/(Lac+Glx) as independent and dependent variables; data are reported as mean±SD. Results – Tumor-to-brain image contrast for Lac/(Lac+Glx) was 2.57±0.93 for grade 4 (n=14), 1.74±0.75 for grade 3 (n=6) and 0.94±0.28 for grade 2 lesions (n=3). Lac/(Lac+Glx) was 0.36±0.13 for grade 4; 0.19±0.049 for grade 3; 0.09±0.042 for grade 2 lesions; and 0.14±0.043 for normal brain. Eta-squared between tumor grade and Lac/(Lac+Glx) was 0.52.

CONCLUSIONS

VOI-based analysis showed a high dependence of metabolism-specific image contrast to tumor grade. The apparent relation between lesion grade and Lac/(Lac+Glx) indicates the potential of DMI to complement anatomical MRI and possibly provide a valuable biomarker indicating active tumor tissue and could improve evaluating disease progression.