bluuebunny/crossref_metadata_2025 huggingface dataset:
ANGI-04. DISTINCT EXPRESSION OF TARGET MOLECULES BETWEEN TUMOR CELLS IN CEREBROSPINAL FLUID AND LEPTOMENINGES FOR LEPTOMENINGEAL METASTASIS
Authors: Kijima Noriyuki , Achiha Takamune , Kuroda Hideki , Tachi Tetsuro , Murakami Koki , Kishima Haruhiko
Published: November 2024

PURPOSE

Metastatic brain tumor frequently present with leptomeningeal metastasis. The leptomeningeal metastasis is usually diagnosed by cerebrospinal fluid (CSF) cytology and/or contrast enhanced magnetic resonance imaging. However, it remains to be known whether tumor cells from CSF faithfully represent the tumor cells of leptomeniges. Therefore, this study aimed to clarify the transcriptome differences between tumor cells from cerebrospinal fluid, and spinal cords

METHODS

MDA-MB-231 cells labeled with GFP and luciferase were injected into the right ventricle of immunodeficient mice. Tumor cells from cerebrospinal fluid, and spinal cords were sorted and analyzed the transcriptome differences by RNA sequencing,

RESULTS

RNA sequencing analysis showed distinct transcriptome profiles between tumor cells from cerebrospinal fluid and spinal cord. Genes related to ECM receptor interaction and PI3K-Akt signaling pathway such as COL1A1, COL1A2, THBS1 were significantly highly upregulated in tumor cells from spinal cord compared to those from CSF

CONCLUSIONS

Tumor cells from spinal cord had different characteristics in transcriptome from those from CSF. Different therapeutic strategies might be needed to regulate tumor cells from spinal cord and those from CSF.
ANGI-06. CEREBROSPINAL FLUID MAY BE THE MOST IMPORTANT PATHWAY FOR BRAIN METASTASES: A DATA-DRIVEN HYPOTHESIS AND CLINICAL IMPLICATIONS
Authors: Tuohy Kyle , Dowd Richard , Ouyang Tao , Thamburaj Krishnamoorthy , Aregawi Dawit , Olmez Inan , Mansouri Alireza , Glantz MIchael
Published: November 2024

INTRODUCTION

Hematogenous spread of brain metastases represents conventional wisdom. However, compelling physiologic evidence suggests that brain metastases may reach the CNS by way of the CSF either via the choroid plexus or directly from the bone marrow. We provide clinical evidence that invasion of brain parenchyma occurs through the CSF, and we model the therapeutic implications of this novel hypothesis.

METHODS

First, we assessed whether brain metastases were contiguous with a CSF space in 204 consecutive patients using pre-treatment MRI. Then, CSF was examined for malignant cells in 66 consecutive brain metastasis patients. Next, we contoured normal brain MRIs of 3 patients to calculate the percentage of brain within 5 mm of a CSF space. Finally, we queried an international neoplastic meningitis registry for patients with brain metastases to evaluate response to intra-CSF chemotherapy alone.

RESULTS

In 204 consecutive patients with brain metastases, the mean number of metastases was 4.63 (SD 6.26), and 85% of metastases touched a CSF space. In 67% of patients, all metastases touched a CSF space. In our consecutive cohort of 66 patients with CSF analysis, 44% with one, 46% with two, 63% with three, and 71% with >3 metastases had malignant cells in the CSF (R2=0.93, p=0.04). Brain contouring revealed that up to 75% of the brain parenchyma lies within 5 mm of a CSF space. Seven of 10 patients with both brain and CSF metastases receiving only intrathecal chemotherapy experienced disappearance or substantial reduction in the size of their metastases.

CONCLUSIONS

This data suggest that brain metastases may access the CNS through the CSF. Intrathecal chemotherapy can reach most brain metastases and can produce objective responses. We suggest that the CSF should be monitored in all patients with, or at risk for, brain metastases, and true cures may require treatment of the CSF space.
ANGI-11. SEX DIFFERENCES IN SOX2 GLIOBLASTOMA EXPRESSION OUTSIDE MRI-DEFINED CONTRAST ENHANCEMENT AT AUTOPSY
Authors: Bobholz Samuel , Lowman Allison , Aaronsen Daniel , Winiarz Aleksandra , Duenweg Savannah , Flatley Michael , Nath Biprojit , Kyereme Fitzgerald , Connelly Jennifer , Mrachek Kelly , Krucoff Max , Banerjee Anjishnu , LaViolette Peter
Published: November 2024

INTRODUCTION

Sex-determining region Y-box 2 (SOX2) has recently been used as a marker for pluripotency to identify cellular glioblastoma invasion pathologically. This can be used to identify areas of tumor invasion consisting of sparse individual cells, likely highlighting the furthest margin of tumor invasion. This study aligned large format SOX2 stained tissue samples to conventional MRI to determine demographic factors that impact the presence of SOX2 positive invasion outside the T1 contrast-enhanced tumor margin.

METHODS

The cohort for this study consisted of 36 IDH-wildtype glioblastoma patients (23 male, 13 female, mean age=61.9). Tissue samples from areas of suspected tumor invasion and normal tissue were collected at autopsy, stained for SOX2, digitized at 40X resolution, and automatically segmented for SOX2 positive staining cell percent (SOX2+%) at MR resolution using a color deconvolution algorithm. Contrast enhanced T1 scans from acquisitions close to death were annotated manually for tumor presence and aligned to the T2-weighted FLAIR image. Tissue data was then aligned to MR images using a custom in-house software that relies on manually defined control points to generate a nonlinear transform that warps tissue into MR space while correcting for tissue shrinkage. Mean SOX2+% was computed for each patient outside of contrast enhancement and compared across age and sex as demographic factors.

RESULTS

Males were found to have a higher SOX2+% than females outside contrast enhancement (t=2.09, p=0.045), while no association with age was observed (r=0.146, p=0.397).

CONCLUSIONS

Sex differences were observed for non-enhancing SOX2 positivity, which may relate to the more aggressive tumors identified in male patients in some studies. Further research into the mechanisms behind sex differences in tumor growth patterns and molecular characteristics impacting the infiltration of tumor beyond the MR defined region is needed.
BIOM-07. SURVIVAL-ASSOCIATED GENETIC VARIATIONS IN TAIWANESE GLIOBLASTOMA MULTIFORME PATIENTS - A RETROSPECTIVE NGS STUDY
Authors: Huang Yu-FEN
Published: November 2024

This retrospective study, conducted at Taichung Veterans General Hospital in Taiwan, employed Next-Generation Sequencing (NGS) technology to analyze genetic variations associated with survival in patients with glioblastoma multiforme (GBM). The study encompassed 30 newly diagnosed GBM patients, divided into two groups based on survival duration: long-term (over two years) and short-term (under two years). The findings are outlined below: Key Mutations: Significant mutations included CHEK2, IDH1, and TP53, along with variations in the TERT promoter and TP53 RNA splicing sites. Correlation Between Mutations and Survival: Contrary to Western data, TP53 mutations were more prevalent in the long-term survival group, suggesting that regional genetic differences may influence GBM prognosis. Therapeutic Effectiveness: The application of bevacizumab was significantly associated with improved survival rates, indicating its potential efficacy in treatment. The study highlights the critical role of personalized medicine in the treatment of GBM in Taiwan and points to the necessity of further research into the genetic characteristics and treatment responses of GBM patients in Taiwan and potentially other non-Western regions. These insights underline the importance of continuing to explore effective personalized treatment strategies and enhancing our understanding of genetic determinants in diverse populations. Moreover, the prevalence of certain mutations in Taiwanese patients, which differ from those commonly observed in Western populations, prompts a reevaluation of global treatment frameworks and suggests the potential for region-specific therapeutic protocols. The implication of these findings extends beyond immediate clinical applications, providing a foundation for future clinical trials and research into genetic markers that could dictate treatment choices. In conclusion, this study not only underscores the importance of individualized treatment plans based on genetic profiling but also highlights the variations in genetic mutations across different populations, which could have profound implications for the management of GBM worldwide. Further investigation into these disparities and their implications on treatment efficacy is essential for advancing GBM treatment and improving patient outcomes globally.
BIOM-08. LEVERAGING CSF PROTEOMICS TO OPTIMIZE CNS LYMPHOMA MANAGEMENT
Authors: Mansouri Alireza , Wilding Hannah , Aastha Aastha , Mikolajewicz Nicholas , de Filho Leonardo Macedo , Glantz Michael , Kislinger Thomas
Published: November 2024

INTRODUCTION

Despite exquisite responses to initial therapy for CNS lymphoma (CNSL), relapse is common and overall responses are disappointing compared to other non-CNS diffuse large B-cell lymphomas. Incorporation of multi-agent intraventricular chemotherapy (MAIVC) alongside systemic therapy is novel. Identification of minimally-invasive biomarkers of response to MAIVC are necessary but lacking. The objectives of this study were to 1) identify baseline cerebrospinal fluid (CSF)-based proteomic predictive biomarkers of MAIVC treatment response and 2) identify tumor burden markers for longitudinal monitoring of MAIVC treatment response in CNSL.

METHODS

A cohort of patients with primary or secondary CNSL that were treated with MAIVC at Penn State Health (2015-2021) was included. Each MAIVC cycle was administered via Ommaya reservoir and included a 2-drug combination comprised of methotrexate, rituximab, cytarabine, etoposide, topotecan, gemcitabine, or thiotepa. Patient-matched CSF was sampled at pre- and post-therapeutic endpoints and profiled using shotgun proteomics. Patients were grouped by treatment response status. Early responders were defined as patients that achieved malignant cell-free CSF within 6 MAIVC cycles, whereas never responders were those patients that i) did not achieve malignant cell-free CSF by endpoint or ii) required salvage surgery or radiation during MAIVC.

RESULTS

59 patients were included (21 primary; 38 secondary CNSL) with a median age of 66 years (range 25-90) and median number of MAIVC cycles of 8 (range 2-23). A proteomic-based classifier, comprised of SGCE, LCP1 and AGRN, discriminated between early and never responders with an AUROC of 0.95. Comparison of CSF at baseline (<3 cycles MAIVC) vs. post-treatment (>12 cycles MAIVC) identified H3F3A, YWHAE, LCP1, CA1 and GAPDH as tumor burden biomarkers.

CONCLUSION

Here we developed a proteomic signature capable of predicting CNSL patient response to MAIVC, with potential to improve clinical decision making. Furthermore, the biomarkers associated with tumor burden represent important indicators of treatment response. Ongoing efforts are underway to evaluate these candidates as actionable therapeutic targets.
BIOM-11. PROGNOSTIC VALUE OF H3K27ME3 AND EZH2 IN ASTROCYTOMA, IDH-MUTANT
Authors: Onishi Shumpei , Yamasaki Fumiyuki , Amatya Vishwa Jeet , Yonezawa Ushio , Taguchi Akira , Ozono Iori , Khairunnisa Novita Ikbar , Go Yukari , Takeshima Yukio , Horie Nobutaka
Published: November 2024

BACKGROUND

H3K27 trimethylation (H3K27me3), catalyzed by EZH2, regulates gene expression through epigenetic mechanisms. H3K27me3 is used as a surrogate marker in pathology for diffuse midline glioma, ependymoma. However, the clinical value of H3K27me3 and EZH2 in astrocytoma, IDH-mutant has not been reported. The aim of this study was to evaluate the clinical significance of H3K27me3 and EZH2 in astrocytoma, IDH-mutant.

METHODS

A total of 30 patients with astrocytoma, IDH-mutant treated at our institute were included. The patients were divided into 2 groups according to the expression of immunohistochemistry (IHC) for H3K27me3. The following factors were analyzed; age, WHO grade, IHC for EZH2, CDKN2A status, ki67-index and extent of resection. The CDKN2A status was diagnosed by IHC for MTAP and was confirmed by NGS-based CGP test in some cases. Kaplan–Meier analysis and Cox regression analysis were performed to analyze overall survival (OS) and progression-free survival (PFS).

RESULTS

According to WHO classification 2021, astrocytomas were classified as follows: WHO grade2: 20 cases, grade 3: 2 cases, grade 4: 8 cases. Seventeen patients were identified as H3K27me3 positive, while fourteen patients were classified as H3K27me3 negative. The proportion of WHO grade 3 or 4 and ki-67 index were significantly higher in the H3K27me3 positive group (p=0.0011, 0.0036, respectively). OS and PFS were significantly longer in H3K27me3 positive group (p=0.0379, 0.0025). Furthermore, in the analysis of WHO grade 2/3, double-positive expression of H3K27me3 and EZH2 showed significantly shorter PFS and OS than the other group (p=0.0114 and 0.0068, respectively). In Cox regression analysis, H3K27me3 showed the highest likelihood ratio for OS (p=0.01061).

CONCLUSIONS

In Astrocytoma, IDH-mutant, the H3K27me3 positive group showed poor prognosis than H3K27me3 negative group. In addition, patients with double-positive expression of H3K27me3 and EZH2 demonstrated more unfavorable prognosis. H3K27me3 and EZH2 could be prognostic markers for astrocytoma, IDH-mutant.
BIOM-18. MAPPING TUMOR HABITATS IN IDH-WILD TYPE GLIOBLASTOMA: INTEGRATING MR IMAGING, PATHOLOGIC, AND RNA DATA FROM IVY GLIOBLASTOMA ATLAS PROJECT
Authors: Park Ji Eun , Lee Ho-Su , Lee Dongjun , Yoon Shinkyo , Song Sang Woo , Kim Young-Hoon , Hong Chang Ki , Kim Jeong Hoon , Kim Ho Sung
Published: November 2024

BACKGROUND

To identify biologic correlates and spatially validate intratumoral subregions (tumor habitat) using diffusion-weighted and dynamic susceptibility contrast-imaging on a comprehensive pathology map of the isocitrate dehydrogenase (IDH)-wild type whole glioblastoma sample using the Ivy Glioblastoma Atlas Project (Ivy GAP).

METHODS

Complete data of 20 patients with 168 slides of IDH-wild type glioblastoma were obtained from the IvyGAP (http://glioblastoma.alleninstitute.org/). On MRI, tumor habitats were defined using voxel-wise clustering of apparent diffusion coefficient (ADC) and cerebral blood volume (CBV) maps for contrast-enhancing lesion (CEL) and peritumoral non-enhancing lesion (NEL). On pathology slides, normalized areas of leading edge (LE), infiltrating tumor (IT), cellular tumor (CT), hypervascular lesion (CThypervascular), and perinecrotic lesion (CTperinecrotic) were obtained. Gross specimen pictures were co-registered on MRI images for co-localization and correlation between MRI tumor habitats. Pathologic areas were calculated using Pearson’s correlation coefficient. RNA sequencing of 67 RNA-seq samples was assessed using 4 Neftel subtypes and further correlated with pathology.

RESULTS

Six tumor habitats were correlated: hypervascular, hypovascular cellular, and hypovascular hypocellular habitats for CEL and NEL. CT was strongly correlated with hypovascular cellular habitat in CEL (C2, r = 0.238, p =.005). IT was strongly correlated with hypovascular cellular habitat in NEL (C5, r = 0.294, p =.017). CThypervascular was correlated with hypervascular habitat in NEL (r = 0.195, p =.023). CTperinecrotic was correlated with imaging necrosis (r = 0.199, p =.005). Astrocyte-like subtypes were positively correlated with IT (r = 0.256, p <.001), while mesenchymal-like subtypes were positively correlated with CTperinecrotic area (r = 0.246, p <.001).

CONCLUSION

Pathologically matched tumor subregions were cellular tumor with hypovascular cellular habitat in CEL and infiltrative tumor with hypovascular cellular habitat in NEL. Identification of the most aggressive tumor portion, and infiltrative tumor portion using non-invasive imaging can be achieved using MRI tumor habitats.
BIOM-19. METHYLATION PROFILING OF PLASMA CELL-FREE DNA IN PEDIATRIC BRAIN TUMOR PATIENTS
Authors: An Shejuan , McCortney Kathleen , Walshon Jordain , Leonard Kaethe , DeCuypere Michael , Horbinski Craig
Published: November 2024

BACKGROUND

Circulating tumor DNA (ctDNA) assays are being evaluated to inform clinical decisions in cancer care in adult patients, but the study in pediatric brain tumor patients is rare partly due to very low levels of ctDNA in blood. Currently, treatment decisions require invasive diagnostic surgical biopsies that carry risks and morbidity. The aim of this study is to utilize methylomes from plasma ctDNA for non-invasive diagnosis in pediatric brain tumor patients.

METHODS

Using cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq), which with low input DNA requirement, we measured methylation profiles of plasma samples from 77 pediatric brain tumor patients and 16 patients with non-neoplastic diseases like epilepsy. Binomial GLMnet classifiers of tumor or tumor subtype were built, in 2000 iterations of 60% training sets. Performance was evaluated in 40% test sets. RESULTS. These 77 pediatric brain tumor patients were a mixture of the most common pediatric brain tumors, include circumscribed astrocytic gliomas (N=23), glioneuronal tumors (N=16), embryonal tumor (N=9), ependymal tumor (N=7), pediatric type diffuse high grade glioma (N= 5), glioma NOS (N=4), mesenchymal tumor (N=4) and other pediatric brain tumors (N=9). The methylation profile differentiated brain tumors from non-neoplastic diseases with 82.9% accuracy (precision = 92.6%, sensitivity = 86.2%, specificity = 66.7 %). For subtype analysis, the methylation profile detected circumscribed astrocytic glioma from non-neoplastic diseases with 85.7% accuracy (precision = 87.5%, sensitivity = 87.5 %, specificity = 83.3 %), and glioneuronal tumors from non- neoplastic diseases with 83.3% accuracy (all precision, sensitivity, and specificity = 83.3 %).

CONCLUSIONS

The results suggest that methylation profiling of plasma cell-free DNA has the potential to discriminate between pediatric brain tumor patients and patients with non- neoplastic diseases. Larger population cohorts to train even more accurate classifiers will be needed.
BIOM-20. EVALUATING THE POTENTIAL OF PSMA TARGETING IN CNS TUMORS: INSIGHTS FROM LARGE-SCALE TRANSCRIPTOME PROFILING
Authors: Kraya Adam , Rathi Komal , Jin Run , Kesherwani Varun , Resnick Adam , Nabavizadeh Ali
Published: November 2024

PURPOSE

Prostate-specific membrane antigen (PSMA) is a well-established target in prostate cancer therapy that has shown potential as a theranostic target across non-central nervous system (CNS) and CNS tumor types. We aimed to investigate the pan-tissue expression pattern of the PSMA-encoding gene FOLH1 to assess whether transcriptome profiling can inform tumor theranostics.

EXPERIMENTAL DESIGN

We assessed FOLH1 expression from the Open Pediatric Cancer Project (OpenPedCan, n = 2132 specimens), The Cancer Genome Atlas (TCGA, n = 10411 specimens), and the Genotype Tissue Expression Project (GTEx, n = 17382 specimens) in relation to published reports of PSMA radionuclide uptake.

RESULTS

When comparing FOLH1 expression across tumor versus normal tissues, we found that non-CNS tumors exhibiting elevated expression of at least two-fold (FDR < 0.05) were reported to have successful PSMA radionuclide uptake in contrast to tumors with less than a two-fold elevation or with lower expression of FOLH1 relative to normal. Notably, CNS tumors universally exhibited lower expression of FOLH1 relative to normal brain tissue, but we observed considerable variation in the expression of blood-tumor barrier (BTB) components associated with reports of BTB integrity and uptake of PSMA radiotracers.

CONCLUSIONS

Large-scale transcriptomics data may help guide the application of PSMA-based radionuclide therapies in non-CNS tumors, but care should be taken to account for BTB effects in CNS tumors when assessing the potential for radionuclide success. Our analysis demonstrated that FOLH1 showed a lack of tumor-specific expression for both adult and pediatric CNS tumors when compared to normal brain tissue, suggesting that PSMA is not a desirable target in this disease type. This study highlights the utility of utilizing large-scale molecular data to guide the selection of theranostic targets.
BIOM-25. MOLECULAR PROFILING PREDICTS EARLY AND LATE PROGRESSION IN GLIOBLASTOMA
Authors: Nikolopoulos Marina , Wu Megan , Bahcheli Alexander , Kellett Sorcha , Myrehaug Sten , Sahgal Arjun , Spears Melanie , Pai Shraddha , Bayani Jane , Das Sunit
Published: November 2024

Patients with glioblastoma experience a wide variation in response to standard treatment, with nearly 30% experiencing tumour progression during treatment, and nearly 6% surviving more than 5 years. To date, there are few non-invasive clinical biomarkers to predict response to first – line treatment. Chemical exchange saturation transfer (CEST) MRI may have the potential to fill this gap. CEST MRI is sensitive to treatment-induced changes and changes in tumor metabolism. Our team has obtained CEST data for patients before, during and after the end of standard chemoradiation treatment, and found that CEST provides markers of early response and can identify early, standard and late progressors before treatment initiation. In this study, we aimed to establish molecular profiles of early, standard and late progressors with IDH wild-type glioblastoma. Patients (n=180) with primary, IDH wild-type glioblastoma were imaged with CEST-MRI at multiple time points throughout standard chemoradiation treatment. DNA and RNA were co-extracted from matched normal and tumour pairs and processed for whole genome sequencing, enzymatic methyl-seq and gene expression analysis using Nanostring. Clinical variables such as age, extent of resection, sex, ECOG status and MGMT promoter methylated were also collected. A survival analysis was conducted using the Kaplan-Meier method with log-rank tests. Univariate and multi-variate hazard ratios for clinical variables were calculated by fitting Cox Proportional Hazards Models. Early progressors reported a median progression-free survival (PFS) of 142 days compared to 832 days in late progressors (p<0.0001). Early progressors also harbored distinct and statistically significant differences in gene expression and genomic alterations, namely in DNA damage repair, glucose transport and arginine metabolism pathways. A gene signature was prognostic of PFS and overall survival. Collectively, this data has the potential to serve as a radiogenomic biomarker to assess treatment response before or within early phases of treatment and allow for individual tailoring of the treatment plan.
BIOM-27. VOXEL-WISE SURVIVAL ANALYSIS IN GLIOBLASTOMA: TUMOR PROBABILITY MAPS REVEAL CRITICAL REGIONS NEAR WHITE MATTER TRACTS
Authors: Nath Biprojit , Winiarz Aleksandra , Bobholz Samuel A , Lowman Allison K , Duenweg Savannah R , Kyereme Fitzgerald , Aaronson Daniel , Connelly Jennifer Connelly , Mrachek E Kelly , Krucoff Max , Banerjee Anjishnu , LaViolette Peter S
Published: November 2024

BACKGROUND

Glioblastoma is the most aggressive primary brain tumor, characterized by rapid growth and poor prognosis. Understanding spatial determinants of survival in GBM is crucial for improving prognostic accuracy and treatment strategies. Our study employs voxel-wise survival analysis (VSA) of tumor probability maps (TPMs) derived from MRI to identify high-risk brain regions. TPMs are generated through radio-pathomic mapping and can predict non-enhancing tumor regions not captured by traditional imaging. We aim to determine if high tumor probability regions are near previously identified critical white matter (WM) tracts and assess their impact on survival outcomes.

METHODS

We analyzed data from 374 GBM patients from the UCSF-PDGM-v2 dataset. Using a pretrained radio-pathomic model, TPMs were predicted based on T1, T1C, ADC, and FLAIR MRI sequences. All TPMs were rigidly registered to MNI space using ANTs. A Cox proportional hazards model was applied voxel-wise to assess the association between tumor probability and overall survival (OS). A p-value map was generated, thresholded, and cluster corrected (p < 0.05) for further analysis.

RESULTS

The VSA revealed that high tumor probability regions were significantly associated with poorer OS in GBM. Gray matter (GM) regions near WM tracts with high tumor probability showed markedly reduced survival. GM regions adjacent to the left IFOF (p < 0.05, HR = 1.19, 845 vs. 961 days for high/low TPM), Corpus Callosum Forceps Minor (p = 0.0001, HR = 1, 740 vs. 902 days), Body of the Corpus Callosum (p = 0.005, HR = 0.97, 748 vs. 798 days for high/low TPM) and other WM tracts, such as the left thalamic radiation superior and left reticulospinal tracts had similar trends.

CONCLUSIONS

Our study demonstrates that regions with high tumor probability, particularly those in the GM near critical WM tracts, are strongly associated with worse overall survival in GBM patients.
BIOM-36. DETECTION OF CIRCULATING TUMOR DNA (CTDNA) IN CEREBROSPINAL FLUID (CSF) IN PATIENTS WITH GLIOBLASTOMA TREATED IN PHASE I CLINICAL TRIAL
Authors: Porte Marie , Beshiri Kristi , Ouali Kaissa , Postel-Vinay Sophie , Massard Christophe , Loriot Yohann , Champiat Stéphane , Hollebecque Antoine , Smolenschi Cristina , Sakkal Madona , Gazzah Anas , Bahleda Rastilav , Michot Jean-Marie , Hueso Thomas , Jeanson Aurore , Rouleau Etienne , Lacroix Ludovic , Baldini Capucine
Published: November 2024

BACKGROUND

As circulating tumor DNA (ctDNA) has been shown to be a source of tumor-specific biomarkers, liquid biopsy has emerged as a novel noninvasive tool in diagnosis, disease monitoring and treatment selection in several solid tumors. However, its use in brain tumors remains challenging because ctDNA is commonly not detected in blood. Thus, CSF (cerebrospinal fluid) has emerged as a potential source of ctDNA in the context of brain tumors.

PATIENTS AND METHODS

We prospectively evaluated the detection of ctDNA in CSF (CSF-ctDNA) +/- blood of patients with pre-treated MTAP-deleted glioblastoma, currently treated in a phase I clinical trial evaluating PRMT5 inhibitors. We did CSF samples at C2D15 and at progression, after patient’s oral and written consent. CSF was collected by lumbar puncture and analyzed with a panel of 35 genes including IDH1-2, TERT promoter and EGFR. Blood was collected, synchronously with CSF, by peripheral veinous punction and analyzed with the Foundation One Liquid CDx panel.

RESULTS

Between January and April 2024, five patients were included. All of them undergone initial surgical resection and received at least one previous systemic treatment associated with radiotherapy. At least one somatic mutation was identified in each patient, including EGFR amplification in 2/5 patients (40%). CSF was not available at baseline. One patient provided CSF only at progression. Four patients provided CSF at C2D15 on treatment, and among them, one patient was also collected at progression. At data cut-off, one patient was still on treatment. We identified a detectable level of CSF-ctDNA in only one patient with occipital tumor localization, with detection of EGFR amplification known at diagnosis. Synchronous blood analysis showed only clonal hematopoiesis variants.

CONCLUSION

We showed in this small cohort of patients that detection of CSF-ctDNA is technically feasible. The type of panel used might be optimized for this population especially to monitor patients as a potential surrogate biomarker for treatment response.
BIOM-38. OPPOSING EFFECTS OF LINKED CX3CR1 GERMLINE VARIANTS ON INCIDENCE, SURVIVAL, AND IMMUNE ACTIVATION IN GLIOMA
Authors: Basit Khan A , McDonald Malcolm , Curry Rachel , Lee Sungho , Yang Yuhui , Latha Khatri , Deneen Benjamin , Harmanci Akdes , Rao Ganesh
Published: November 2024

Linkage-disequilibrium connects CX3CR1 V249I and T280M single-nucleotide polymorphisms; V249I occurs as a single-variant (SV) and T280M exclusively as a double-variant (DV) concurrent with V249I. The effect of these combined haplotypes remains unexplored in glioma. We identified CX3CR1 haplotypes in internal LGG and TCGA GBM cohorts and analyzed median overall survival (mOS). The proportion of each haplotype in glioma and normal patients was assessed via meta-analysis. Bulk RNAseq analysis was conducted in TCGA and internal GBM cohorts and scRNAseq in internal IDH mutant gliomas. In LGG, SV improved mOS (n=14, 21.03yrs) by twofold compared to WT (n=45, 9.41yrs) and DV (n=31, 10.49yrs; p=0.037). In TCGA GBM, SV (n=69, 15.65mo) improved mOS over DV (n=106, mOS 11.74mo; p=0.044). In combined meta-analysis, SV patients had increased risk for glioma development (OR 1.11, 1.03-1.19 p = 0.006) and the WT genotype was protective (OR 0.95, p=0.048). Collagen genes associated with increased immunosuppression (COL6A3: log2FC=2.33, p-adj=0.004; COL6A2: log2FC=1.55, p-adj=.059) were reduced in SV. MME, an endopeptidase associated with radiation resistance, was downregulated in SV (log2FC=3.29, p-adj=2.53e-6). MN1, associated with improved glioma survival, was upregulated in SV (log2FC=-1.76, p-adj=0.001). CCL18, an immunosuppressive chemokine associated with M2 macrophage polarization was reduced in SV (log2FC=2.36, p-adj=0.014). Thus, concomitant with its improved survival, SV is biologically distinct from DV and WT. Using scRNAseq, myeloid-derived cells (microglia/macrophages; 7758 cells) were re-clustered, identifying fourteen clusters. Cells clustered by CX3CR1 status, with 58.2% of SV cells in cluster five and 84.9% of DV cells in clusters six or seven. Cluster five over-expressed IL1B (average-log2FC 3.16), a tumor-suppressive M1 macrophage marker. Clusters six and seven were characterized by IFIT genes (IFIT3 average-log2FC 2.72 and 2.16 respectively), which corresponds to glioma associated microglia from recent scRNAseq microglial atlases. We demonstrate that CX3CR1 SV has improved survival and reduced immunosuppression over wildtype and this is lost with in the linked CX3CR1 DV genotype.
BIOM-39. GENOMIC AND CLINICAL ASSOCIATIONS WITH RADIATION NECROSIS IN PATIENTS WITH DIFFUSE INFILTRATING GLIOMAS
Authors: Kienhöfer Michael , Lin Heather , Campbell Erick , Wathoo Chetna , Bhat Surya , Perni Subha , Puduvalli Vinay , Majd Nazanin K
Published: November 2024

BACKGROUND

Radiation necrosis (RN) is a complication of radiotherapy (RT) that can significantly affect quality of life and outcomes in patients with gliomas. Clinical and molecular factors predisposing patients to RN are not clearly established. We hypothesize that clinicogenomic data can be leveraged to identify patients at high risk for RN.

METHODS

We identified patients from 2014-2024 with diffuse gliomas and RN diagnosed based on Advanced-Brain-Tumor-Imaging which includes conventional MRI, 3 perfusion parameters, spectroscopy and/or pathology at MD Anderson. Inclusion criteria included diagnosis of RN 12-weeks after RT and concordance of 4 ABTI parameters. For each case, we identified 2 controls who were gender-,diagnosis-, and age-matched using a nearest neighborhood algorithm. We evaluated the correlation between 15 most mutated genes in baseline tissue and occurance of RN. A logistic regression model was employed to assess the multivariable relationship between patient characteristics, gene mutations, and RN.

RESULTS

We identified 62 patients with RN; 50 glioblastoma (80.6%), 8 diffuse astrocytoma (12.9%) and 4 oligodendroglioma (6.5%). Time from RT to RN diagnosis was 254 days (IQR 154-483). 18(29%) of RN cases and 29(24.4%) of controls had received more than one course of RT. Patients treated with bevacizumab before RT had significantly lower odds of developing RN compared to those who did not receive bevacizumab (OR 0.103 [0.011 – 0.960], p=0.0459). BRAF mutations were more frequent in the RN cohort (8.1% vs. 2.4%) and patients with BRAF mutation were more likely to have RN than those without BRAF mutation (OR 6.842 [1.2, 39.01], p=0.0304). Age, gender, diagnosis, IDH, MGMT or 1p19q status were not associated with RN.

CONCLUSION

We found that bevacizumab administration was associated with a significant reduction in RN development. We also found a novel association between presence of BRAF mutations and increased risk of RN in glioma patients, which warrants further investigation.
BIOM-40. BLOOD AND NASAL BIOMARKERS OF BRAIN MICROENVIRONMENT BLOOD–BRAIN BARRIER PERMEABILITY: CLINICAL AND APPLIED CONCEPTS
Authors: Garo Virginia , Turco Erica Lo , Quaranta Chiara , Galati Rosario , Gallucci Gianmarco , Ferrazzo Teresa , Bonapace Giuseppe , Donato Giuseppe , Ferrazzo Francesca , Policicchio Domenico , Mauro Giuseppe , Malara Natalia , Lavano Angelo , La torre Domenico
Published: November 2024

The limiting step to treating glioblastoma (GBM) patients is the close blood-brain barrier (BBB) which protects the brain making it an inaccessible compartment. Although multiple studies have highlighted the presence of circulating tumour cells (CTCs) in glioblastoma multiforme (GBM) patients their relationship with brain microenvironment and BBB permeability was not explored in depth. We studied the development of GBM by transferring tumour cells into the mouse brain and also in a subcutaneous location to verify how the different microenvironment affected the release of circulating tumour and endothelial cells. Glioblastoma U3T3MG IDHwt secondary cell line was transfected to track circulating tumour cells released. Moreover, both U3T3 cells and short-time-expanded CTCs1 from GBM patients were used for intracranial xenografts and patient-derived xenografts (PDX). The in vivo models demonstrated the correspondence between BBB permeability with the release of CTCs and the increment of endothelial progenitor cells in GBM HIFpos >20% compared to subcutaneous xenografts releasing CTCs in GBM HIFpos< 20%. These data were confirmed in HIFpos tissue biopsy of GBM-IDHwt patients with CTCs >30 cells/ml. Both in PDXs and in the GBM patient demonstrated that the release of CTCs was intermittent, related to BBB opening induced by HIF-dependent cytokines release (IL8, TNFa)2. In parallel, the analysis of structural Glial fibrillary acidic protein (GFAP)3, on nasal secretion and interstitial fluid, collected in surgical treated GBM patients, demonstrated that the recognition of the two GFAP isoforms (p150 and p50 kDa) were the result of inflammatory microenvironment enriched for proteases induced by IL8, TNFa. Overall data indicate at least two different ways of monitoring the BBB and the brain microenvironment, one distal (blood) and one proximal (nasal secretion) useful to perform precision treatments in patients with GBM.

REFERENCES

1) Malara, N. et al. Mol Cancer 23, 32 (2024). doi.org/10.1186/s12943-024-01951-x2) Coluccio ML. et al Cancers (2020) doi: 10.3390/cancers12061362.3) Malara, N. et al Front. Oncol.(2021) doi.org/10.3389/fonc.2021.737730
BIOM-46. REAL-WORLD EXPERIENCE WITH CIRCULATING TUMOR DNA IN CEREBROSPINAL FLUID IN PATIENTS WITH CENTRAL NERVOUS SYSTEM TUMORS
Authors: Hickman Richard , Miller Alexandra M , Holle Bridget M , Jee Justin , Liu Si-Yang , Ross Dara , Yu Helena , Riely Gregory J , Ombres Christina , Gerwitz Alexandra , Reiner Anne S , Nandakumar Subhiksha , Price Adam , Kaley Thomas J , Graham Maya S , Vanderbilt Chad , Rana Satshil , Hill Katherine , Chabot Kiana , Campos Carl , Nafa Khedoudja , Shukla Neerav , Karajannis Matthias , Li Bob , Berger Michael , Ladanyi Marc , Pentsova Elena , Boire Adrienne , Brannon A Rose , Bale Tejus , Mellinghoff Ingo K , Arcila Maria E
Published: November 2024

Next generation sequencing (NGS) of circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) offers a minimally invasive approach to identify somatic alterations for individuals with central nervous system (CNS) cancers. Here, we review our ‘real world’ experience using a clinically validated, FDA-authorized platform, MSK-IMPACTTM, to comprehensively profile ctDNA from CSF samples with and without clinically documented CNS involvement by cancer (1007 samples, 711 patients). The patient cohort included patients with over 90 distinct tumor types of primary CNS and metastatic origin, with lung cancer (n = 188), breast cancer (n = 150), and glioma (n = 148) representing the most common broad categories. We identified genetic alterations (ctDNA-positive) in 489/922 (53.0%) CSF samples from patients with clinically documented CNS cancer. Over half of these ctDNA-positive samples (248, 50.7%) possessed a biomarker that was predictive of response to an FDA-approved drug (OncoKB level 1). Furthermore, the distribution of clinically actionable somatic alterations was consistent with tumor-type specific alterations across the AACR GENIE cohort. Of patients without clinical documentation of CNS cancer, none of these 85 CSF samples were ctDNA-positive (specificity = 100%). Successive CSF sequencing over time identified clonal evolution and the emergence of resistance mechanisms to therapies. ctDNA positivity corresponded with shortened overall survival after CSF collection (HR: 3.23, 95% CI: 2.58-4.05, P < 0.001). NGS of CSF cfDNA can detect clinically actionable somatic alterations in a large subset of CNS cancer patients and allows tracking of tumor evolution. Detection of somatic alterations in CSF may be a useful prognostic biomarker for survival in cancer patients.
BIOM-50. SERIAL INTRACRANIAL CEREBROSPINAL CELL-FREE DNA FOR DISEASE MONITORING IN PATIENTS WITH GLIOMAS
Authors: Riviere-Cazaux Cecile , Dong Xiaoxi , Wei Mo , Kumar Rahul , Carlstrom Lucas , Nesvick Cody , Andersen Katherine , Hoplin Matthew , Jusue-Torres Ignacio , Malik Noor , Sener Ugur , Ruff Michael , Uhm Joon , Campian Jian , Eckel-Passow Jeanette , Kaufmann Timothy , Routman David , Kizilbash Sani , Jia Shidong , Du Pan , Warrington Arthur , Burns Terry
Published: November 2024

Improved response assessment methods are needed for patients with gliomas. Intracranial cerebrospinal fluid (CSF) is longitudinally accessible and provides an abundance source of candidate biomarkers, such as cell-free DNA (cfDNA), for disease monitoring. To evaluate the clinical feasibility of molecular profiling from longitudinal intracranial CSF, CSF was acquired from patients with CSF access devices, including Ommaya reservoirs and ventriculoperitoneal shunts. cfDNA was extracted and analyzed via PredicineCARE (Next Generation sequencing) or PredicineSCORE (low pass whole genome sequencing). Five patients (2 females, 3 males; median age: 40 years, range 32-64 years) underwent longitudinal intracranial CSF collection via Ommaya reservoirs (n=4) or VP shunt (n=1). In total, forty-eight CSF samples were obtained (median volume: 4.00 mL; 0.5-5 mL), with 39 samples (81.3%) yielding sufficient cfDNA for variant profiling. Our initial findings suggest that tumor fraction increased by 6.28x, 2.87x, and 8.31x with radiographic progression in three patients. Tumor fraction decreased by 0.08x and 0.04x in two patients with paired immediate pre-versus-post chemoradiation samples. Despite ongoing pseudoprogression in one patient, tumor fraction decreased to unmeasurable levels from a post-resection baseline of 0.26. Patient-specific tumor-associated variant allelic frequencies (VAFs), including TP53, PTEN, TERT, and CDKN2A/B, decreased within individual patients after resection and chemoradiation. In two patients with isocitrate dehydrogenase (IDH) mutant gliomas, decreasing IDH1 VAF after resection and chemoradiation correlated with decreased CSF D-2-hydroxyglutarate (D-2-HG) levels (0.64x and 0.62x, respectively, for the first patient, and 0.01x and 0.07x for the other patient). Both CSF IDH1 VAF and CSF D-2-HG increased a patient who had radiographic progression (2.56x and 9.21x, respectively). Moreover, CNB decreased below the limit of quantification during treatment and increased above the limit at progression. In conclusion, longitudinal CSF cfDNA can feasibly be obtained via CSF access devices in patients with gliomas during their disease course toward evaluating candidate monitoring biomarkers.
BIOM-51. MOLECULAR SUBTYPES, CLINICAL CHARACTERISTICS, AND THERAPEUTIC IMPLICATIONS FOR CNS TUMORS WITHBCOR/BCORL1 FUSION/INTERNAL TANDEM DUPLICATION
Authors: Gojo Johannes , Federico Aniello , Geisemeyer Neal , Schmitt-Hoffner Felix , Mauermann Monika , Sill Martin , Bruckner Katharina , Korshunov Andrey , Stichel Damian , Capper David , Tauziede-Espariat Arnault , Varlet Pascale , Aldape Kenneth , Abdullaev Zied , Donson Andrew M , Pahnke Jens , Schüller Ulrich , Galbraith Kristyn , Snuderl Matija , Alexandrescu Sanda , Filbin Mariella , Gramatzki Dorothee , Urbanic-Purkart Tadeja , Ziad Fouzia , Toledano Helen , Kerl Kornelius , Hasselblatt Martin , Papusha Ludmila , Brandner Sebastian , Łastowska Maria , Miele Evelina , Lugt Jasper v d , Bunt Jens , Kramm Christof , André Nicolas , Appay Romain , Bouchoucha Yassine , Hansford Jordan , Zapotocky Michal , Kranendonk Mariette E , Nobusawa Sumihito , Solomon David , Haberler Christine , Jones Barbara , Sturm Dominik , Sahm Felix , Jäger Natalie , Pfister Stefan M , Hoff Katja v , Kool Marcel
Published: November 2024

Central nervous system (CNS) tumors with either BCOR internal tandem duplication (BCOR ITD) or gene fusions involving BCOR/BCORL1 (BCOR FUS) are recognized as tumor types with characteristic molecular and clinical features but lacking clear therapeutic guidance. In an extensive international effort, we compiled a retrospective cohort of 229 (148 BCOR ITD, 81 BCOR FUS) unique cases via molecular profiling of CNS tumors. By analyzing DNA methylation patterns of 220 tumors we confirmed distinct epigenetic profiles of BCOR ITD versus BCOR FUS. The majority (91 percent) of BCOR FUS primary tumors was localized in the supratentorial region whereas BCOR ITD were localized across all anatomical CNS compartments. Median patient age at diagnosis was 20 years for BCOR FUS and 4 years for BCOR ITD. Metastatic disease was rare in BCOR FUS patients but more common in BCOR ITD tumors where 10 percent presented with metastatic disease and one third showed CNS or (rarely) extra-CNS metastasis in the course of disease. This was also reflected in clinical outcome as 5-year overall survival (OS) was 89 percent in BCOR FUS but 61 percent in BCOR ITD. In contrast, 5-year progression-free survival (PFS) was comparable reaching 27 percent in BCOR FUS and 30 percent in BCOR ITD. Integrating treatment details we found a trend towards benefit of gross-total resection on OS (BCOR FUS, n=18, p<0.08; BCOR ITD, n=67, p<0.12) but not for PFS (BCOR FUS, n=16, p<0.33; BCOR ITD, n=64, p<0.59). Radiotherapy was associated with improved PFS (BCOR FUS, n=18, p<0.01; BCOR ITD, n=70, p<0.001) and OS (BCOR FUS, n=20, p<0.01; BCOR ITD, n=73, p<0.001). Further in-depth analyses of clinical outcome parameters (primary metastatic disease, radiotherapy approach, chemotherapy type, patient age) are currently ongoing. In summary, we provide first robust annotation of CNS BCOR tumor types, clinical outcomes and therapy.
BIOM-57. PERITUMORAL EDEMA AS A PREDICTOR OF PD-1 EXPRESSION IN BRAIN METASTASES
Authors: Elengickal Anthony , Wallace Gerald , Bansal Juhi , Reddy Ambur , Raval Girindra
Published: November 2024

Brain metastases represent a significant problem in oncology with associated high morbidity and mortality. They have been associated with increased peritumoral edema which can worsen neurological symptoms and patient outcomes. Peritumoral cerebral edema may be an important metric of interest as some MRI studies have suggested an association between molecular factors and peritumoral edema. We hypothesized that an association exists between PD-1 expression in brain mets from NSCLC and the radiographic peritumoral edema to enhancing tumor ratio (ETR). A retrospective analysis of tumor characteristics was conducted to identify patients with brain metastases from non-small cell lung cancer. Patients were stratified into three groups based on their tumor PD-1 expression levels: 0%, 1-49%, and 50% or higher. Tumor and edema volumes were measured in these patients using MRIs at the time of diagnosis and converted into edema to tumor ratios. Radiographic analysis has been completed for 19 patients with 9 having no PD-1 expression, 5 having low PD-1 expression, and 5 having high PD-1 expression. The no expression group had an average ETR of 3.02 while the low expression group had an average of 15.85 and the high expression group had an average of 9.12. These initial results show increased peritumoral edema in tumors with PD-1 expression when compared to tumors with no PD-1 expression, with a non-significant trend in favor of increased edema to tumor ratio (p = 0.055). The current project is ongoing with plans to expand patient cohorts to affirm or rule out significant ETR association by MRI.
BIOM-66. GENOME-WIDE DNA METHYLATION PATTERNS IN PERIPHERAL BLOOD OF PATIENTS WITH GLIOBLASTOMA ENROLLED ON THE PHASE II VERTU TRIAL
Authors: Vaios Eugene , Wimberly Courtney , Sim Hao-Wen , Barnes Liz , Koh Eng-Siew , Yip Sonia , Hall Merryn , Ashley David , Sulman Erik , Reitman Zachary , Walsh Kyle , Khasraw Mustafa
Published: November 2024

BACKGROUND

For patients with glioblastoma, the identification of a non-invasive biomarker for longitudinal molecular profiling could improve risk stratification, clinical trial design, and surveillance. In a secondary analysis of the phase II randomized VERTU trial (ACTRN12615000407594) of adult patients with newly diagnosed MGMT-unmethylated glioblastoma, we assessed the feasibility of characterizing peripheral blood genome-wide DNA methylation patterns.

METHODS

DNA was extracted from whole blood and serum samples at baseline and end-of-treatment (EOT) from patients enrolled on VERTU, which evaluated the PARP inhibitor veliparib combined with radiotherapy and temozolomide. Infinium FFPE QC qPCR and DNA Restoration Kits were used to restore and concentrate fragmented serum DNA. Genomic DNA was plated, bisulfite converted, and profiled for methylation patterns at >935,000 CpG sites using the Infinium MethylationEPIC microarray V2.0. Quality control, pre-processing, leukocyte deconvolution, and calling of MGMT status were completed in R Studio.

RESULTS

Peripheral blood methylation data were generated and passed quality control for 104/104 baseline and 24/34 EOT samples available for analysis. The median concentration of genomic DNA at baseline and EOT was 104.50 ng/μl (range:1.97-550) and 0.98 ng/μl (range:0.11-19.8). The deconvoluted median leukocyte proportions differed significantly between baseline and EOT for neutrophils (0.64vs0.90,p<0.01), CD4 memory (0.09vs0.00,p<0.01), CD4 naive (0.03vs0.01,p=0.02), CD8 memory (0.04vs0.00,p<0.01), monocyte (0.07vs0.03,p<0.01), natural killer (0.05vs0.00,p<0.01), and T regulatory (0.000vs0.001,p=0.01) cells. There were no differences in baseline leukocyte proportions between patients with (n=6) and without (n=98) biopsy-proven pseudoprogression. 2/104 samples were determined to be MGMT-methylated based on peripheral blood methylation analysis. Unsupervised hierarchical clustering based on the 1,000 most differentially methylated CpG sites generated two patient clusters (n=64, n=40).

CONCLUSIONS

To our knowledge, this is the first study to demonstrate the feasibility of analyzing peripheral blood methylation patterns from patients with glioblastoma receiving chemoradiation on a randomized clinical trial. Efforts are underway to correlate these blood methylation patterns with previously published tumor tissue methylation patterns and clinical outcomes.