bluuebunny/crossref_metadata_2025 huggingface dataset:
EPCO-12. MENINGIOMA COPY NUMBER ANALYSIS IDENTIFIES OPTIMIZED SIZE THRESHOLDS AND CO-OCCURRENCE MODELS FOR INDIVIDUALIZED RISK-STRATIFICATION
Authors: Nguyen Minh , Chen William , Choudhury Abrar , Magill Stephen , Nitturi Vijay , Klisch Tiemo , Patel Akash , Raleigh David
Published: November 2024

Arm-level copy number alterations (CNAs) are common in meningiomas and are useful for risk-stratification, but there is no consensus regarding the optimal size threshold to define CNAs for prognostic models. Moreover, the prognostic importance of co-occurring CNA pairs and overall CNA burden in meningiomas remains incompletely understood. To address this, CNAs were analyzed in 691 retrospective meningiomas with clinical data and DNA methylation profiles from 3 international institutions. Arm-level CNAs were defined from DNA methylation profiles using iterative size thresholds ranging from 1-99% of each chromosome arm. The area under the curve (AUC) for 5-year local freedom from recurrence (LFFR) or overall survival (OS) was calculated using CNAs across size thresholds, and AUC standard deviation across thresholds was used as a measure of size-dependence. LASSO and Elastic Net Cox regressions were used to generate multi-CNA models for LFFR or OS and to identify prognostic co-occurring CNA pairs. These analyses identified 13 size-dependent prognostic CNAs in meningiomas, including loss of 1p, 3q, 4p, 4q, 6p, 6q, 9p, 10q, 12q, 14q,18q, and 22q, and gain of 1q. Regression models restricted to size-dependent CNAs improved risk stratification within strata of previously published models (Integrated score, Integrated grade), and identified prognostic CNAs not included in previous models, such as 1q gain, 7p loss, and 12q loss. Ontology analysis of genes in focal prognostic CNAs identified dysregulated STAT signaling and decreased expression of interferon-related genes from matched paired RNA sequencing. Models of size-dependent, prognostic, co-occurring CNA pairs identified 1p/22q codeletion, 1q gain/22q loss, and 9p/18q codeletion as significant predictors of LFFR. Increased CNA burden correlated with higher tumor grade and was significantly associated with worse LFFR and OS. In summary, chromosome-specific size thresholds identify prognostic arm-level CNAs and co-occurring CNA pairs in meningiomas. Thus, granular copy number analysis may improve risk stratification models for meningioma.
EPCO-21. ELUCIDATING THE FUNCTIONAL RELEVANCE OF ATRX-DEFICIENCY IN H3.3-G34-MUTANT DIFFUSE HEMISPHERIC GLIOMA
Authors: Machado Annette Alexandra , Malgulwar Prit Benny , Huse Jason T
Published: November 2024

Diffuse hemispheric gliomas (DHGs) account for 30% of aggressive cerebral tumors in children and young adults, exhibiting abysmal outcomes. Co-existing recurrent mutations in H3.3 histones at residue G34 (H3.3-G34R/V mutation) and concurrent inactivating mutations in TP53 and α-thalassemia/intellectual disability-X-linked gene (ATRX) implicate a coordinated molecular effort to drive oncogenesis. ATRX, a core component of the SWItch/Sucrose Non-Fermentable chromatin remodeling complex, regulates the incorporation of histone H3.3 into chromatin sites across the genome to maintain epigenome integrity. Yet, it is unclear how ATRX loss combines with H3.3-G34R/V mutations to influence cellular phenotype and dysregulate neuro-developmental programs. We propose that ATRX deficiency coordinates with key oncogenic partners by inducing oncogenic transcriptional programs and neuro-developmental pathways in DHGs. To investigate this, we employed CRISPR-editing to model H3.3-G34R followed by ATRX knockdown (ATRX-KD) in a TP53 mutant (TP53-mut) human-induced pluripotent stem cell (h-iPSC) line, developing an isogenic system to map contributions to epigenetic dysfunction made by specific molecular alterations. Upon differentiation of our h-iPSCs to neural stem cells (NSCs), we found unique transcriptional profiles associated with each genetic alteration, with upregulation of forebrain progenitor genes driven by ATRX-loss. Hierarchal clustering of normalized transcript counts revealed gene signatures from each model driving unique functional pathways, with the ATRX-KD and the triple mutant (TP53-mut, ATRX-KD, H3.3-G34R) signatures enriched for neural development pathways. Additionally, both signatures were associated with published transcriptional profiles of G34-mutant DHGs, emphasizing the disease relevance of our models. Further, time-course analysis using cerebral organoids uncovered distinct morphological changes with each alteration, with the triple mutant exhibiting impaired differentiation at later time points. These latter findings suggest that ATRX deficiency transcriptionally influences early neuronal differentiation, effects further refined by H3.3-G34 mutation. To conclude, our innovative models demonstrate the involvement of ATRX in neuro-developmental and differentiation phenotypes, illuminating underlying molecular features of aggressive DHGs.
EPCO-29. PATHOMICS ANALYSIS IDENTIFIES POTENTIAL SUBTYPES OF DIFFUSE GLIOMAS IN H&E-STAINED WHOLE-SLIDE IMAGES
Authors: Becker Aline , Chan Jany , Weible Jason , Machiraju Raghu , Chakravarti Arnab
Published: November 2024

IDH status is the first criteria of diagnostic definition for diffuse gliomas in the 2021 WHO classification. While sufficient number of molecular tools are available to identify IDH1 and/or IDH2 mutations, they impose a time and cost burden on patients. We previously trained deep learning models visually differentiate IDH wild-type (IDHwt) and IDH mutant (IDHmut) gliomas in a small set of H&E-stained whole image slides (WSIs) from TCGA using an Uncertainty-Aware Convolutional Neural Network (CNN) at 10x magnification. In this follow-up study, we aimed to improve our models by expanding our annotations of a more representative subset of the TCGA public data, increasing the sampling magnification to 20x, redesigning the preprocessing filters, adjusting the training pipeline to reduce overfitting, and assessing the confidence in model prediction via uncertainty metrics.

METHODS

By modifying the pre-processing methods from our pilot study, we increased the number of expert-annotated WSIs. Using a 2:1:2 train/validation/test split, we fine-tuned a ResNet18 deep learning model with a pre-trained feature extractor and Monte Carlo dropouts. To identify image features critical for separating by IDH status, we extracted the learned embeddings and performed post-hoc analyses (PCA, t-SNE, and UMAP).

RESULTS

The new set of annotations resulted in ~15-fold increase in the number of WSIs (i.e.,>2.5 million tiles), without any data augmentation. Our prototype model demonstrated clear separation of cases according to IDH status (sensitivity = 0.63, specificity = 0.91, weighted F1 = 0.81).

CONCLUSION

We successfully improved the prediction of IDH status in H&E-stained WSIs and identified potential subtypes of IDHwt and IDHmut diffuse gliomas after significantly increasing the dataset size with appropriate expert annotations. We are currently addressing the data imbalance by annotating additional IDHmut glioma WSIs. Furthermore, we will integrate other biomarkers (1p19q, EGFR etc.) to increase the robustness of histo-pathomics as a surrogate for molecular tests.
EPCO-42. SINGLE-CELL MULTIOMIC ANALYSIS OF BRAIN METASTASES ACROSS MULTIPLE PRIMARY TUMOR TYPES
Authors: Blandford Emily , Delegard Jennifer , Hardigan Andrew , Mohan Aditya , Gregory Simon , Patel Anoop
Published: November 2024

Brain metastases are the most common form of intracranial tumor in adults, however the prognosis remains dismal due to lack of effective treatments and limited understanding of the underlying physiology allowing them to thrive in the foreign cell type environment of the brain. Here we characterized the transcriptomic and epigenomic landscape of 35 human brain metastases obtained from surgical resection using combined scRNA-seq and ATAC-seq spanning the most prevalent primary tumor types including lung adenocarcinoma (n=16), melanoma (n=14), breast (n=10), and renal cell carcinoma (n=6). Varying molecular subtypes across primary tumors were included allowing for a comprehensive analysis between and within primary tumor types. Approximately 200,000 cells total were profiled to a sequencing depth of 50,000 mean reads per cell with 2,500 median genes per cell. ATAC-seq libraries were sequenced to a depth of 25,000 reads per cell with 10-15,000 median fragments per cell. Unbiased clustering and integrated analysis identified various cell types within the tumor, immune microenvironment, and normal brain tissue. Tumor cell identities were confirmed throughout multiple clusters via inferred copy number alteration analyses. Integration with primary tumor atlases highlight differences between cell states of primary and metastatic tumors, revealing shifts of enhancer function in transcriptional regulation of metastatic cells. Overall, our findings describe the genetic and epigenetic states of metastatic cells contributing to the understanding of CNS metastatic colonization.
EPCO-43. DECONVOLUTION OF GLIOBLASTOMA RNA-SEQ REVEALS IMMUNE SUBPOPULATIONS PREDICTING THERAPEUTIC RESPONSE
Authors: Rauf Asad , Ahluwalia Manmeet , Dhawan Andrew
Published: November 2024

Bulk RNA-seq is now among the standard of care for patients with newly diagnosed glioblastoma (GBM), but whether this data can predict therapeutic response is unclear. In silico deconvolution of bulk RNA-seq data allows for quantification of cell types comprising the tumor and its microenvironment. Our study tests whether cell type proportions predict therapeutic response in patients with GBM and high-grade glioma (HGG) enrolled in trials of investigational agents. 127 patients with GBM/HGG underwent post-resection/biopsy whole exome RNA-seq and reads were post-processed using standard computational pipelines. In silico deconvolution was performed using GBMDeconvoluteR, which generates cellular proportions comprising the RNA-seq reads. Multivariate Cox regression models were used to examine each cell proportion as a predictor of progression-free (PFS) and overall (OS) survival. Statistical significance was ascertained using Bonferroni correction for multiple comparisons. Among 54 patients treated with a PD-L1 inhibitor (nivolumab) and VEGF inhibitor (bevacizumab), the proportions of NK cells (p=0.0024), radial glial cells (p=0.0010), and mural cells (p=0.0025), was associated with increased PFS, while proportion of endothelial cells (p=0.0008) was associated with decreased PFS. Astrocyte (p=0.0022), macrophage (p=0.0015), NK cell (p<0.0001), and mural cell (p=0.0004) proportions were associated with longer OS, while endothelial cell proportion (p=0.0001) was associated with shorter OS. Among 21 patients treated with a tyrosine kinase inhibitor (ibrutinib) combined with radiation and temozolomide (RT/TMZ), cell proportions assessed at the time of diagnosis did not predict PFS or OS. In 52 patients with HGG treated with a JAK inhibitor (ruxolitinib) with RT/TMZ, only mural cell proportion was associated with a longer OS (p=0.0017). Our results highlight how bulk RNA-seq data can be used to predict therapeutic response. In GBM patients treated with immunotherapies, the proportion of NK cells may predict response. Further work will examine which gene programs are predictive of therapeutic response.
EPCO-48. RESOLVING INTRATUMORAL TRANSCRIPTIONAL HETEROGENEITY ACROSS THE CORE-EDGE SPATIAL AXIS IN GLIOBLASTOMA
Authors: Luo Adam , Casella Kelly , Baraban Ezra , Lucas Calixto-Hope , Shenderov Eugene
Published: November 2024

Intratumoral heterogeneity promotes tumor progression, treatment resistance, and recurrence in glioblastoma (GBM), and the cellular tumor core and infiltrating edge represent transcriptionally distinct cellular ecosystems. In this study, we characterize and validate the molecular differences across the core-edge spatial axis in GBM by applying whole-transcriptome GeoMx Digital Spatial Profiling (DSP) to 5 IDH-wildtype tumors. Three 3-micron tissue cores were extracted from each tumor and arranged into a tissue microarray (TMA). Core and edge regions of interest (ROIs) were chosen through coregistration of H&E and immunofluorescent TMA scans. Following DSP, data for 44 ROIs (30 core and 14 edge) and 8530 RNA targets were bioinformatically analyzed. Single-sample gene set enrichment analysis aligned the DSP core and edge regional signatures to those of publicly annotated datasets, substantiating our profiling methodology. Unsupervised analyses revealed ROI clusters unique to each tumor specimen for both pre- and post-normalized data. To mitigate a potential patient-level effect in subsequent differential gene expression and pathway analyses, we leveraged a linear mixed-effect model using core versus edge as a fixed effect and tumor specimen as a random effect. Our analyses showed upregulation of epigenomic markers in core ROIs and neuronal markers in edge ROIs. Further, core and edge signatures were incongruent with the canonical GBM subtypes (Mesenchymal, Classical, Proneural) and malignant cell states (OPC-like, NPC-like, AC-like, MES-like). Cellular deconvolution analysis highlighted differential enrichment of neoplastic cells in core ROIs and neuroglia (astrocytes and oligodendrocytes) in edge ROIs. In summary, we leverage spatial profiling to further validate the geographic molecular heterogeneity of GBM, which is characterized by divergent neuronal programs within the infiltrating edge.
EPCO-53. CHARACTERIZING THE FUNCTIONAL IMPACT OF GERMLINE-INHERITED RISK ALLELES IN GLIOMA EVOLUTION
Authors: Barathi Bhargavi Brahmendra , Malgulwar Prit , Liu Yang , Kannan Kasthuri , Huse Jason
Published: November 2024

Efforts to understand etiology of glioma led researchers to investigate associated genetic factors. Genome Wide Association Studies (GWAS) conducted to that end, uncovered an association of various single nucleotide polymorphisms (SNP) among hallmark oncogenes and tumor suppressors as risk variants in glioma incidence. Here, we perform in vitro modeling of four risk alleles/SNPs((rs723527 (EGFR), rs55705857 (MYC), rs7572263 (IDH1), rs78378222 (TP53)) mapped to non-coding regulatory regions of the genome, to assess their causal contribution to glioma evolution. To model the aforementioned risk alleles in an in-vitro system, we used a CRISPR-knock in strategy in human induced pluripotent stem cells (hiPSCs) and verified by Sanger sequencing. To study the effects of the risk alleles on brain cell types, we generated a cerebral organoid model from the edited and control lines and subjected them to downstream morphological and transcriptomic analyses. While we did not see morphological changes in the histological sections relative to controls at the early 14-day timepoint, we observed increased differentiation in both control and risk cohorts, along with an absence of neural rosettes, at the late 90-day timepoint. Bulk RNA-seq of the organoids at 14-days resulted in positive enrichment of oncogenic signaling pathways and negative enrichment of DNA repair pathways in the risk allele cohorts. Furthermore, single cell RNA seq of 14 and 90-day samples revealed a sharp decrease in neural stem cell clusters in both IDH and TP53 cohorts, while control organoids demonstrated robust production of immature neurons at 90 days. Overall, we observed a significant increase in differentiation into mature cell clusters in the control, relative to the risk allele organoids. Ongoing efforts are aimed at understanding this apparent differentiation block in the IDH and TP53 compartments, relative to control. Further analysis will lead to addressing key understudied areas of glioma etiology and associated mechanisms of risk incidence.
EPCO-55. SPATIAL HETEROGENEITY IN THE TUMOR CORE AND INFILTRATING MARGIN OFIDHWT GLIOBLASTOMA
Authors: Khan Saad , Wang Anthony , Desai Rupen , Foltz Jennifer , Leuthardt Eric , Patel Bhuvic , Dahiya Sonika , Kim Albert , Dunn Gavin , Petti Allegra
Published: November 2024

We integrated single-cell RNA-sequencing, Visium spatial transcriptomic, and Xenium in situ transcriptomic data to identify differences in cell composition between the tumor core and infiltrating edge in IDHWT glioblastoma (GBM). Using CellTrek, an algorithm that maps single cells to their most-likely locations in spatial transcriptomic data, we identified extensive spatial organization in GBM. Cell mapping revealed distinct regions enriched for tumor, immune, endothelial, neuronal, and glial cells. These were associated with the location of the tissue sample – edge regions were enriched for neurons and glia (as expected), while core regions were enriched for tumor cells and infiltrating immune cells, particularly macrophages. Within the core samples, the tumor and immune cells tended to occupy distinct spatial niches. Spatial clustering of mapped tumor cells across all samples revealed five spatially segregated tumor cell states, each associated with specific biological processes, including (1) histone methylation, (2) proliferation, (3) wound-healing, EMT, and antigen presentation, (4) hypoxia response, and (5) stem cell differentiation. These tumor cell states exhibited preferential colocalization with specific non-malignant cell types. For instance, antigen-presenting/wound-healing tumor cells tended to colocalize with diverse immune cells, while stem-like tumor cells tended to reside in neuron-rich regions at the tumor edge. Next, to identify ligand-receptor interactions governing this spatial organization, we analyzed known ligand-receptor pairs within all three data types. This revealed known and novel mediators of tumor cell interactions with vasculature, lymphoid cells, myeloid cells, neurons, and glia. While some interactions were shared across all tumor cell states (e.g. all tumor cell states interacted with myeloid cells via APP/CD74 interactions), others were specific to particular tumor cell states (e.g. wound-healing/antigen-presenting tumor cells interacted with macrophages via CSF1/CSF1R, while proliferating and stem-like tumor cells interacted with neurons through multiple known NRXN/NLGN interactions). These interactions suggest potential targets for clinical disruption of the tumor ecosystem.
EPCO-58. INTEGRATIVE PROTEOGENOMIC ANALYSES REVEAL INSIGHTS INTO SUBTYPE-SPECIFIC GLIOMA RISK
Authors: Nakase Taishi , Smith-Byrne Karl , Cario Clinton L , Ostrom Quinn T , Guerra Geno A , Melin Beatrice S , Rentoft Matilda , Wrensch Margaret , Wiencke John K , Jenkins Robert B , Eckel-Passow Jeanette E , Bondy Melissa L , Francis Stephen S , Kachuri Linda
Published: November 2024

Gliomas are heterogeneous brain tumors with prognostically-significant subtypes and few risk factors. IDH-wildtype glioblastoma, the most common subtype, carries a dismal prognosis. Using the largest GWAS dataset with histological (11,304 cases, 304,523 controls) and molecular (3,418 cases, 8,156 controls) subtypes, we analyzed the plasma and brain proteome to uncover proteins associated with glioma susceptibility. Using protein quantitative trait loci (pQTL) for 1,776 proteins in brain tissue, we identified 21 candidate proteins, including 9 associations with high probability (>70%) of colocalization (shared causal genetic variants for glioma risk and protein abundance). We confirmed known risk genes such as EGFR (p=1.9×10-35) and D2HGDH (p=1.1×10-5). We also identified novel risk proteins, including ENPP6, a choline phosphodiesterase overexpressed in glioma, for IDH-wildtype glioblastoma (OR=0.62, p=7.6×10-5), and galectin-3, a lectin encoded by a tumor fitness gene in CRISPR screens of glioma proliferation and a clinical drug target, for glioma overall (OR=1.37, p=1.3×10-5). Analyses of the plasma proteome using pQTLs for 1,362 proteins from 3 cohorts (N=88,838) identified 9 colocalized associations in whole blood. Most risk signals were subtype-specific, such as CRELD1 (p=2.5×10-5) for triple-negative glioblastoma. We found three candidate risk proteins for IDH-mutant 1p19q-intact glioma: immunoglobulin glycoprotein BCAM (p=9.6×10-8), neurotrophin receptor SorCS2 (p=3.6×10-5) and immune checkpoint PD-1 (p=1.1×10-5). Interestingly, genetically-predicted PD-1 levels had a larger effect on IDH-mutant 1p19q-intact (OR=2.75, 95% CI=1.61-4.69) than IDH-wildtype (OR=0.73, 95% CI=0.51-1.05) tumors, suggesting germline differences in immune checkpoint mechanisms among subtypes. For all colocalized candidates, genetically-predicted protein abundance was correlated with cis-regulated transcriptional activity in brain tissue. For example, genetically-predicted SORCS2 gene expression in brain tissue was associated with plasma SorCS2 levels (Z=16.1, p=1.1×10-68). Our analysis identified candidate proteins involved in immune response and neuronal proliferation, which may enable prioritization of drug targets and provide insight into disease mechanisms for glioma.
EPCO-59. FIRST CASE REPORT OF COMBINED GERMLINE NF1 AND BRCA2 MUTATIONS PRESENTED WITH NEUROFIBROMAS AND LIPOMATOSIS
Authors: Choi Yoon
Published: November 2024

Both Neurofibromatosis type 1(NF1) and BRCA2 are common tumor suppressor genes, with mutations in each associated with genetic tumor syndromes. However, it is extremely rare to observe two different germline mutations in one patient. To the author’s knowledge, this is the first case report of a patient with germline mutations in both pathological NF1 and BRCA2 genes. We report a 41-year-old male patient with neurofibromas and lipomatosis. The patient with known family history of NF1, was diagnosed with NF1 after skin biopsy at 28 years old. At 40 years old, he underwent resection of a large intrathoracic neurofibroma. For genetic confirmation, next generation sequencing test was performed on both the intrathoracic neurofibroma tumor sample and saliva sample, revealing unexpected pathological germline mutation in both NF1 and BRCA2 genes. Consequently, the patient underwent resection of multiple lesions in the chest, abdomen, and upper extremities due to concern for potential breast cancers, and pathology of these lesions predominantly showed lipomas and one angiolipoma. Patient has family members with NF1 including a maternal aunt, a maternal cousin, and one son. However, there is no family history of lipomatosis or cancers commonly associated with BRCA2 mutation such as breast, ovarian, pancreatic, or prostate cancer. While lipomas are reported in patients with NF1, it is unusual that patient does not have typical café-au-lait spots or multiple neurofibromas but instead has multiple lipomas. This unusual presentation may be related to his unique genetic condition involving germline mutations in two tumor suppressor genes. Long term follow-up with screening tests for known tumors associated with each genetic mutation will be essential.
ANGI-05. UNSUPERVISED DECONVOLUTION OF SPATIOTEMPORAL HETEROGENEITY REVEALS HIGH-RESOLUTION INVASION STATES IN GLIOBLASTOMA
Authors: Manoharan Varsha Thoppey , Abdelkareem Aly , Brown Samuel , Gillmor Aaron , Hall Courtney , Seo Heewon , Narta Kiran , Grewal Sean , Dang Ngoc Ha , Ahn Bo Young , Osz Kata , Lun Xueqing , Mahoney Douglas , Senger Donna , Chan Jennifer , Morrissy Sorana
Published: November 2024

Diffuse invasion of glioblastoma cells through normal brain tissue is a key contributor to tumor aggressiveness, resistance to conventional therapies, and dismal prognosis in patients. A deeper understanding of how components of the tumor microenvironment (TME) contribute to overall tumor organization and to programs of invasion may reveal opportunities for improved therapeutic strategies. Towards this goal, we applied a novel computational workflow to a spatiotemporally profiled GBM xenograft cohort, leveraging the ability to distinguish human tumor from mouse TME to overcome previous limitations in analysis of diffuse invasion. Our analytic approach, based on unsupervised deconvolution, performs reference-free discovery of cell types and cell activities within the complete GBM ecosystem. We present a comprehensive catalogue of 15 tumor cell programs set within the spatiotemporal context of 90 mouse brain and TME cell types, cell activities, and anatomic structures. Distinct tumor programs related to invasion were aligned with routes of perivascular, white matter, and parenchymal invasion. Furthermore, sub-modules of genes serving as program network hubs were highly prognostic in GBM patients. The compendium of programs presented here provides a basis for rational targeting of tumor and/or TME components. We anticipate that our approach will facilitate an ecosystem-level understanding of immediate and long-term consequences of such perturbations, including identification of compensatory programs that will inform improved combinatorial therapies.
ANGI-09. GRAPH NETWORK ANALYSIS IDENTIFIES GENETIC COMMUNITIES OF CSF2RA AND RBFOX1 AS REGULATORS OF INVASIVE HIGH-GRADE GLIOMA BIOLOGY
Authors: Flick Matthew , Stevens Victoria , Sereduk Christopher , Plaisier Christopher , Barajas Ramon , Hu Leland , Kannan Kasthuri , Tran Nhan
Published: November 2024

BACKGROUND

High-grade glioma (HGG) is the most common and aggressive form of primary brain cancer. Standard of care surgery employs Magnetic Resonance Imaging to identify the contrast enhancing (CE) core for resection, leaving a non-enhancing (NE) invasive rim of tumor which contributes to recurrence. Recent multi-omics analyses identified predominant neuronal and immune signatures within NE tumor. Here, we apply a graph network to integrate regionally heterogeneous data from a unique dataset of spatially-localized CE and NE biopsies from a large cohort of patients with HGG.

METHODS

RNA-sequencing of 1159 differentially expressed genes across 159 IDH-wt biopsies (74 patients) from NE/CE regions were represented as nodes in a Neo4j network. Candidate genes for network random walks occurred exclusively within NE communities detected by modularity optimization and localized by cell-type using single-cell RNA-sequencing (scRNAseq). CSF2RA and RBFOX1 were selected as sources (walk length = 5; 10,000 walks/source node). Frequently occurring genes (one-tailed test) in walks were ranked by correlation with CSF2RA/RBFOX1 expression in NE samples and analyzed by gene set enrichment analysis for biological processes (clusterProfiler). Random walk genes were visualized (DoHeatmap) against composite NE/CE scRNAseq profiles.

RESULTS

CSF2RA and RBFOX1 were upregulated in NE samples (logFC = 0.789, 1.85). Upregulation of CSF2RA, an immune receptor, in the Glycolytic/Plurimetabolic and RBFOX1, a neurodevelopmental regulator, in the Neuronal glioma subtypes were observed in NE samples (ANOVA p < 0.05). CSF2RA walk genes (n=46) enriched metabolic/proliferative signatures, while RBFOX1 walk genes (n=201) showed neurodevelopmental upregulation. scRNAseq localized CSF2RA to monocytes/macrophages while RBFOX1 was expressed in distinct astrocyte/neuroepithelial populations.

CONCLUSION

CSF2RA and RBFOX1’s gene networks modulate immune and neurodevelopmental processes influencing glioma progression in NE tumor. Understanding the region-specific roles of these networks may offer strategies for targeting cells in the invasive glioma rim.
BIOM-01. CDKN2A HOMOZYGOUS DELETION HAS STRONGER PROGNOSTIC POWER THANIDH MUTATION IN CNS WHO GRADE 4 GLIOMAS
Authors: Kim Young Zoon , Da Park Hyun
Published: November 2024

We conducted retrospective analysis of glioma cohorts in our institute. Medical records were reviewed for 142 glioblastoma patients for 15 years, and pathological slides were examined again for the updated diagnosis according to 2021 WHO classification of CNS tumors. The IDH mutation and CDKN2A deletion were examined by NGS analysis using ONCOaccuPanel®. Traditional prognostic factors were also examined. Mean follow-up duration was 27.5 months (ranged from 4.1 to 43.5 months) and mean overall survival (OS) was 19.4 months (95% CI 16.3 – 20.9 months). After the exclusion of 4 patients with poor status of pathologic samples, total 109 glioblastoma which were diagnosed by previous WHO criteria were changed into 26 (23.9%) astrocytoma, IDH-mutant, CNS WHO grade 4 and 83 (76.1%) glioblastoma, IDH-wildtype, CNS WHO grade 4. Among them, 61 patients (56.0%) had CDKN2A deletion. Group A was classified for 59 patients with IDH-wildtype and present CDKN2A deletion, group B was classified for 16 patients with IDH-mutant and present CDKN2A deletion, group C was classified for 48 patients with IDH-wildtype and absent CDKN2A deletion, and group D was classified for 13 patients with IDH-mutant and absent CDKN2A deletion. Group A had a mean OS of 15.70 months (95% CI 13.86 – 17.54 months), group B had a mean OS of 19.37 months (95% CI 13.43 – 25.30 months), group C had a mean OS of 22.63 months (95% CI 20.10 – 25.17 months), and group D had a mean OS of 33.38 months (95% CI 29.35 – 37.40 months). Multivariate analysis showed IDH mutation (mutant vs. wildtype; HR 6.358), and CDKN2A deletion (absence vs. presence; HR 13.452). The presenting study suggest that CDKN2A deletion should play a powerful prognostic role in CNS WHO grade 4 gliomas as well as low grade glioma. Even if CNS WHO grade 4 gliomas had mutant IDH, they can have poor clinical outcome due to CDKN2A deletion.
BIOM-02. A HIGH-GRADE GLIOMA, NOT ELSEWHERE CLASSIFIED IN AN OLDER ADULT WITH DISCORDANT GENETIC AND EPIGENETIC ANALYSES
Authors: Yuen Carlen , Bao Silin , Kong Xiao-Tang , Terry Merryl , Pekmezci Melike
Published: November 2024

World Health Organization (WHO) Classification of Tumors of the Central Nervous System (CNS) uses integrated diagnoses, which incorporates both histologic and molecular features of the neoplasms. With each new iteration, there is refinement and expansion of the diagnostic categories. DNA methylation profiling is a powerful technique to diagnose existing CNS tumors and define new tumor types. However, challenging diagnostic cases that do not conform to the updated WHO classification remain. We present a case of a 72-year-old male with a high grade glioma (HGG) suggestive of high grade astrocytoma with piloid features (HGAP), but it did not “match” to HGAP on DNA methylation profiling, which is essential diagnostic criterion for HGAP. This resulted in an HGG, not elsewhere classified (NEC) diagnosis. This lack of classification posed additional challenges for treatment decision-making.
BIOM-09. CLINICAL EFFECT OF CD25 ON THE MTX-BASED CHEMOSENSITIVITY OF PRIMARY CENTRAL NERVUS SYSTEM LYMPHOMA
Authors: Yamanishi Shunsuke , Nagashima Hiroaki , Tanaka Kazuhiro , Sasayama Takashi
Published: November 2024

INTRODUCTION

Primary central nervous system diffuse large B-cell lymphoma (PCNSL) is treated with chemotherapy, mainly with high-dose methotrexate (HD-MTX), but some cases are resistant to treatment and relapse in a short period. However, a biomarker that predicts the chemosensitivity and recurrence has not yet been identified. In this study, we used surface marker analysis of tumor tissue using flow cytometry to search for biomarkers related to chemosensitivity and early recurrence.

METHODS

From 2017 to 2023, 25 patients were diagnosed with PCNSL by biopsy in Kobe University Hospital, and flow cytometry of the biopsy tissues were performed. Cerebrospinal fluid (CSF) examination including sIL2R, β2MG, and IL-10 was performed in all cases before surgery, and treatment based on methotrexate was administered postoperatively. We retrospectively analyzed patient characteristics, flow cytometry data, treatment details, response rate, time to recurrence, and overall survival.

RESULTS

The mean age of the patients was 71 (range, 37-80) years. In univariate analysis, high expression level of CD25 (interleukin-2 receptor, IL-2R) in the tissue was associated with a lower response rate to MTX-based chemotherapy (Fisher’s exact test, p=0.0072) and had a tendency of shorter time to recurrence. However, there were no significant differences in progression-free survival and overall survival. There was no correlation between expression level of CD25 in tissue and sIL-2R in CSF. Expression level of sIL-2R in CSF was independent of CD25 expression in tissue.

CONCLUSION

There are some reports that CD25 can be a prognostic factor in follicular lymphoma, but no reports in PCNSL. Here, we suggested that high expression level of CD25 in PCNSL tissue was associated to chemoresistance and early recurrence. In cases of PCNSL with high CD25 expression level, additional whole-brain irradiation and transition to tirabrutinib be considered because there are possibilities of chemoresistance and early recurrence.
BIOM-10. CLINICAL PERFORMANCE EVALUATION OF A BRAIN CANCER LIQUID BIOPSY
Authors: Cameron James , Baker Matthew , Antoniou Georgios , Brennan Paul , Butler Holly , Eustace David , Gray Ewan , Jakola Asgeir , Jenkinson Michael , Koljenovic Senada , Lazarus Alan , Mathew Ryan , Palmer David , Phang Isaac , Sala Alexandra , Weiss Tobias
Published: November 2024

Diagnostic delays impact the quality of life and survival of patients with brain cancer. Currently, with no blood test to assist them, clinicians must make their referral decision based on symptoms. Existing symptom-based referral guidelines inadequately stratify patients for brain imaging based on suspicion of cancer. A simple, rapid liquid biopsy placed in a primary care setting would enable more efficient triage of patients with non-specific symptoms related to brain cancer. The Dxcover® Liquid Biopsy is a rapid multi-omic liquid biopsy that interrogates a blood sample with infrared radiation and produces a distinctive signature that represents the whole biomolecular profile of the sample, and is sensitive to the hallmarks of brain cancer. The nature of the technology also allows for the diagnostic models to be tailored towards higher sensitivity (or specificity) depending on clinical priorities and international healthcare markets. In initial feasibility studies, we recruited 988 patients prospectively with non-specific symptoms associated with a brain tumor, and the algorithm detected 96% of the patients with brain tumors and 100% of glioblastomas (GBM), when tuned for greater sensitivity. EMBRACE is a prospective, observational, multicenter study, currently recruiting patients across seven sites in the United Kingdom, Belgium, Sweden and Switzerland. The study duration is 24 months and will recruit a minimum of 2200 participants. The target population is comprised of patients presenting to primary care with non-specific symptoms that are associated with brain cancer, such as headache and new onset neurological defect. The primary objective is to determine the clinical performance of the liquid biopsy for patients with brain cancer, in terms of diagnostic sensitivity and specificity. The test performance will be determined by comparing the liquid biopsy result to diagnostic imaging. Earlier and expeditious diagnoses in these patients are crucial to reduce the morbidities and mortalities associated with brain cancer. This simple, non-invasive liquid biopsy would facilitate the triage of brain tumor patients for rapid imaging.
BIOM-14. TRANSMEMBRANE WATER EFFLUX RATE (KIO) IS AN MRI-DETECTABLE BIOMARKER TO EVALUATE THE EFFICIENCY OF TTFIELDS TREATMENT ON GLIOBLASTOMA
Authors: Hu Songtao , Jia Yinhang , He Qingping , Chu Jiaqi , Wang Yongjie , Bai Ruiliang
Published: November 2024

BACKGROUND

Tumor Treating Fields (TTFields) has emerged as an effective treatment modality for Glioblastoma, shown to improve both OS and PFS. Yet how to monitor response to TTFields remains unclear. In this study, we proposed using transmembrane water efflux rate (kio), a non-invasive biomarker detectable in conventional MRI and reflecting cell membrane permeability, to assess the treatment efficiency of TTFields.

METHODS

U-87 MG human glioblastoma cell line were treated with TTFields at frequency of 200 kHz and varying field strengths of 0 V/cm, 0.8 V/cm, 1.2 V/cm and 1.6 V/cm using the inovitro system from Novocure. The measurement of kio was performed on a 0.5 T benchtop MRI system (Pure Devices GmbH) using a home-developed filter-exchange imaging (FEXI) sequence. Cell membrane morphology were quantitatively analysed using scanning electron microscopy. Patients with newly diagnosed glioblastoma (ndGBM) who underwent DCE-MRI before and after TTFields treatment were identified and the change of FEXI-kio value were analysed.

RESULTS

In the same frequency, the effect of TTFields on cancer cell proliferation is dependent on intensity, manifested a decrease in cell growth rate under high electric field intensity. As the TTFields electric field intensity increased, the cell membrane permeability (kio) also increased, exhibits a significant negative correlation with glioblastoma cell growth rate (p=0.031). Scanning electron microscopy reveals that TTFields can induce significant cell membrane pores, and the total surface area of membrane pores correlates significantly positively with FEXSY-kio index. DCE-MRI data obtained from 4 ndGBM before and after TTFields therapy showed that the FEXI-kio value is increased after TTFields treatment.

CONCLUSION

This study demonstrated that TTFields increases membrane permeability by inducing cell membrane holes, and kio is a promising non-invasive MRI biomarker to evaluate the efficiency of TTFields treatment.
BIOM-15. METASTATIC BIFOCAL GERMINOMA: A CASE HIGHLIGHTING DRAMATIC EARLY RADIOLOGICAL RESPONSE TO STEROIDS AND REBOUND FOLLOWING DISCONTINUATION, AND THE UTILITY OF CIRCULATING MIR-371A-3P QUANTIFICATION AND VINBLASTINE MONOTHERAPY PRIOR TO DEFINITIVE CRANIOSPINAL IRRADIATION
Authors: Scarpini Cinzia , Ward Dawn , Phyu Poe , Jalloh Ibrahim , Thorp Nicky , Fisher Benjamin , Hendriks Emile , Salisbury Lyndsay , Nicholson James , Ajithkumar Thankamma , Horan Gail , Burke Amos , Coleman Nicholas , Allinson Kieren , Murray Matthew
Published: November 2024

BACKGROUND

In Europe, bifocal germinoma is diagnosed based on typical age (>8-10y), symptoms (diabetes insipidus), radiological appearances, and serum/CSF AFP/HCG markers below thresholds. A 12yo male presented with 4-month headaches, 3-month polyuria/polydipsia, visual and somnolence/memory issues. Weight=71.1kg; height=166cm. MRI head/spine revealed hydrocephalus and 19×14×15mm (volume=2.09cm3) enhancing pineal lesion with nodular suprasellar and septum-pellucidum soft tissue. CSF positive for malignant cells. Serum/CSF AFP/HCG markers below thresholds. Metastatic bifocal germinoma diagnosed. Dexamethasone (8mg/day=4.4mg/m2/day) commenced for raised pressure. Proton referral (craniospinal-irradiation) made, but 8 weeks to expected start; hence, external-ventricular-drain (EVD) placed and weekly vinblastine commenced (PMIDs:32642701/34520101).

METHODS

Serum/CSF placental-alkaline-phosphatase (PLAP) and miR-371a-3p measured at diagnosis and CSF longitudinally. MRI performed at d9+d19 post-vinblastine. RESULTS. At diagnosis, CSF miR-371a-3p PCR positive (raw-Cq=18.64) (PMID:37386046); serum miR-371a-3p and serum/CSF PLAP all negative. In follow-up, CSF miR-371a-3p levels fell with weekly vinblastine, consistent with treatment response; PLAP remained non-informative. Repeat CSF cytology after two vinblastine doses was negative. D9 MRI showed reduction in tumour size/enhancement [pineal lesion 13×7×12mm (0.57cm3) from 19×14×15mm] and reduced ventricular size. Dexamethasone switched to maintenance-dose hydrocortisone (10mg+5mg+2.5mg=9.7mg/m2/day). D19 MRI, however, showed increased tumour volume again (pineal=17×10×14mm; 1.25cm3), albeit less than at diagnosis, with CSF miR-371a-3p down to raw-Cq=26.92 (>300-fold reduction from diagnosis). EVD removed and septostomy performed; biopsy confirmed germinoma only (<5% cells) with >95% inflammatory cells (lymphocytes/macrophages). Vinblastine continued until protons without further tumour-associated comorbidity; MRI pre-protons showed pineal 10×10×12mm (0.63cm3; partial-remission) and post-protons complete-remission. Conclusion. Early radiological response to dexamethasone, with rebound on maintenance hydrocortisone, presumably secondary to lymphocytic re-infiltration of tumour (PMID:18000859). Reassuringly, circulating miR-371a-3p was informative for germinoma diagnosis (confirmed by biopsy) and treatment response. Weekly vinblastine useful bridge to definitive radiotherapy, explored in upcoming MonoGerm trial.
BIOM-17. EVALUATION OF CARBONIC ANHYDRASE TYPE IX (CA IX) EXPRESSION AS TARGET FOR RADIOLIGAND THERAPY IN GLIOBLASTOMA
Authors: Mair Maximilian J , Tomasich Erwin , Polten David , Greutter Lisa , Widhalm Georg , Eckert Franziska , Wöhrer Adelheid , Berghoff Anna S , Preusser Matthias , Albert Nathalie L
Published: November 2024

BACKGROUND

Glioblastoma represents an unmet need in neuro-oncology. Radioligand therapies are effective and approved in extracranial malignancies such as prostate cancer and neuroendocrine tumors, but data on their use is limited in brain tumors. In addition, rational target selection in gliomas is complicated by tumor heterogeneity. In extracranial tumors, clinical trials of radionuclide treatments targeting carbonic anhydrase IX (CA IX) are ongoing.

METHODS

Tumor samples of glioblastoma (isocitrate dehydrogenase [IDH]-wildtype) were retrieved from the Neuro-Biobank of the Medical University of Vienna. Formalin-fixed, paraffin-embedded tissue specimen were stained using rabbit anti-CA IX antibody (clone EP161, Cell Marque) on a Ventana Benchmark Ultra platform (Roche Diagnostics). CA IX expression was assessed semiquantitatively.

RESULTS

Overall, 29 patient samples were included in this study. Median age at surgery was 65 years (range: 55 – 74), and 22/29 (75.9%) were male. Median overall survival (OS) reached 11.6 months (95% confidence interval: 7.3 – 16.3). In total, 24/29 (82.8%) of specimen were positive for CA IX, of whom 20/29 (69.0%) exhibited moderate to high membranous CA IX expression and 4/29 (13.8%) showed weak immunoreactivity. CA IX staining displayed pronounced spatial heterogeneity, as positive areas were primarily seen in pseudo-palisading tumor cells around necrotic foci. Patients with stronger CA IX staining tended to have longer OS (median: 14.2 months) compared to those with absent or weak CA IX expression (median OS: 6.2 months; p = 0.075). Inclusion of further samples of different glioma subtypes is ongoing.

CONCLUSIONS

CA IX could represent a promising target for radioligand therapy in glioblastoma given the strong CA IX immunoreactivity in most samples. Intratumoral heterogeneity in CA IX expression should be considered in the design of appropriate compounds and the choice of optimal radionuclides to maximize efficacy.
BIOM-23. DEUTERIUM METABOLIC IMAGING OF RESPONSE TO PRECISION THERAPY IN BRAF-V600E MUTANT GLIOMAS
Authors: Batsios Georgios , Udutha Suresh , Gillespie Anne Marie , Petritsch Claudia , Mueller Sabine , Viswanath Pavithra
Published: November 2024

Oncogenic BRAF-V600E mutations are frequently observed in low- and high-grade gliomas in adults and children. BRAF transduces signals from receptor tyrosine kinases to downstream effectors such as MEK1/2 and ERK, which regulate both metabolism and proliferation. The combination of the BRAF-V600E inhibitor dabrafenib and the MEK1/2 inhibitor trametinib (Dab/Tra) improves patient survival. However, there is considerable variation in the durability of response, underscoring the need for early biomarkers of treatment response. Magnetic resonance imaging (MRI), which is the gold standard for patient management, does not reliably assess response to therapy. Since the BRAF/MEK pathway regulates metabolism, the goal of this study was to determine whether Dab/Tra induces alterations in glucose metabolism that can be leveraged for non-invasive imaging. Using gene expression profiling, in vivo metabolomics, and stable isotope tracing, we show that Dab/Tra downregulates glucose metabolism to lactate in human and murine BRAF-V600E mutant models (AM38, 2341). In vivo infusion with [U-13C]-glucose in mice bearing intracranial AM38 tumors confirmed that Dab/Tra downregulates glucose metabolism to lactate in the tumor in vivo. Mechanistically, Dab/Tra destabilizes hypoxia inducible factor-1a and downregulates glycolytic genes, including SLC2A1, HK2, PFKFB3, and LDHA. Deuterium metabolic imaging (DMI) is a novel, clinical stage method of tracing glucose metabolism in vivo. Our studies show that lactate production from [6,6-2H]-glucose is reduced in AM38 and 2341 cells treated with Dab/Tra. Importantly, lactate production is reduced within 48 h of treatment with Dab/Tra in mice bearing intracranial AM38 tumors at the clinical magnetic field strength of 3T. Furthermore, this drop in 2H-lactate production is observed in the absence of MRI-detectable volumetric alterations and is predictive of extended survival. Collectively, our studies mechanistically link BRAF/MEK inhibition with downregulation of glycolysis and identify [6,6’-2H]-glucose as a novel contrast agent for imaging early response to therapy. Clinical translation of our studies will enable precision imaging of response to therapy for patients with BRAF-mutant gliomas.
BIOM-34. INTRACRANIAL MANAGEMENT OF HER-2 OVEREXPRESSION BREAST CANCER WITH EXTENSIVE VOLUME OR SYMPTOMATIC BRAIN METASTASES
Authors: Li Juan , Zhen Junjie , Ai Ruyu , Lai Mingyao , Wang Hui , Cai Linbo
Published: November 2024

BACKGROUND

HER-2 overexpression in breast cancer often leads to brain metastases, necessitating effective intracranial control strategies. This study aimed to evaluate the correlation between intracranial disease volume, symptomatic presentation, and treatment outcomes in HER-2 overexpressing breast cancer patients with brain metastases.

METHODS

A retrospective analysis was conducted on cases of HER-2 overexpressing breast cancer patients with brain metastases. Clinical records were reviewed to extract patient demographics, treatment modalities, and intracranial disease characteristics. Intracranial tumor burden was quantified at diagnosis and post-initial treatment. High intracranial tumor burden was defined as either total metastatic volume >15 cc, or the largest lesion >3 cm. Responses were assessed using established criteria. The correlation between intracranial disease parameters and intracranial progression-free survival (PFS) and overall survival (OS) was determined.

RESULTS

The study comprised 65 patients with HER-2 overexpression breast cancer and brain metastases. Symptomatic presentation was observed in 69.2% of patients at the diagnosis of brain metastases. Treatment with HER-2 target therapy alone or in combination with other modalities resulted in substantial intracranial responses, with 81.5% achieving at least a partial response at 3 months from therapy initiation. Median intracranial PFS and OS for patients with high intracranial burden were 9 and 22 months, respectively. Patients with high intracranial burden and symptomatic presentation at diagnosis demonstrated worse PFS and OS to those with lower burden and absence of symptoms (p < 0.05 for each).

CONCLUSION

Intracranial control in HER-2 overexpressing breast cancer patients with large volume or symptomatic brain metastases appears promising with combination with HER-2 targeted therapy and radiotherapy. Despite the varying intracranial disease burdens and symptomatic presentations, the use of HER-2 targeted therapy combined with radiotherapy demonstrates favorable intracranial responses, highlighting their potential in managing such cases.