bluuebunny/crossref_metadata_2025 huggingface dataset:
BIOM-31. MOLECULAR ANALYSIS OF RESECTED BREAST CANCER BRAIN METASTASES REVEALS CEREBELLAR LOCATION AND TRIPLE NEGATIVE SUBTYPE ARE NEGATIVE PROGNOSTIC FACTORS
Authors: Huppert Laura , Salans Mia , Kuwahara Kelsey , Zhou Maggie , Boreta Lauren , Braunstein Steve , Melisko Michelle , Aghi Manish , Morshed Ramin , Vasudevan Harish
Published: November 2024

BACKGROUND

Brain metastases (BMs) are a significant cause of morbidity and mortality in metastatic breast cancer (MBC), yet prognostic and predictive biomarkers remain poorly understood.

STUDY DESIGN

90 consecutive patients with breast cancer BMs who underwent surgical resection from 2006-2022 were retrospectively identified. Review of the electronic medical record and institutional cancer registry were completed to identify baseline clinical parameters and outcomes. BM mutation analysis was performed using a CLIA-certified targeted DNA mutation sequencing assay as part of routine clinical care.

RESULTS

All patients were female, median age at first BM resection was 57.9 years (range 27.0-81.3 years), and receptor subtypes included HR+/HER2- (n=27, 30.0%), HER2+ (n=33, 36.7%), and triple negative BC (TNBC; n=30, 33.3%). At time of first BM resection, most patients had a solitary BM (n=55, 61.1%), with anatomic locations including cerebellar (n=29, 32.2%), frontal (n=26, 28.9%), and parietal (n=17, 18.9%) sites. BM DNA mutation analysis (n= 20) revealed pathogenic alterations in TP53 (n=17, 85.0%), ERBB2 amplification (n=7, 35.0%), PIK3CA (n=4, 20.0%), BRCA1 (n=3, 15.0%), and BRCA2 (n=2, 10.0%). Most patients received postoperative radiation (n=82, 90.8%) and/or systemic therapy (n=67, 82.7%). Cerebellar location was significantly associated with the risk of developing leptomeningeal disease compared to other BM resection sites (HR = 2.75, p=0.02). Among all patients, median overall survival (OS) from first BM resection was 27.8 months (range 0.1-196.6 months). HR+/HER2- (median 37 months) or HER2+ (median 36 months) MBC was associated with significantly increased OS compared to TNBC (14.4 months) (p<0.01, log-rank test).

CONCLUSIONS

Patients with breast cancer BMs exhibited a median OS of >2 years following BM resection, and patients with TNBC had a significantly worse prognosis. Targetable mutations were observed in 40% of resected BM specimens, supporting the utility of molecular analysis of resected BMs to help guide clinical management.
BIOM-32. GENOMIC DETERMINANTS OF DIFFUSELY INFILTRATIVE GLIOMATOSIS CEREBRI PATTERN
Authors: Dasgupta Pushan , Dagher Samir , Chi Xiaohan , Soomro Zaid , Wathoo Chetna , Lin Ruitao , Wintermark Max , Chen Melissa , Puduvalli Vinay K , Majd Nazanin K
Published: November 2024

Gliomatosis cerebri (GC), though no longer a distinct pathological entity in WHO 2021, is a unique and aggressive phenotype of diffuse gliomas with extensive and widespread infiltration. GC can present as primary de novo or secondary after treatment. We aimed to study the genomic determinants of GC. We identified 72 GC cases from 2013-2023 at MD Anderson Cancer Center. Cases were confirmed by detailed radiographic review. This included 57 glioblastoma (79%), 13 IDH mutant astrocytoma (18%), 1 IDH mutant oligodendroglioma (1.4%), and 1 high-grade astrocytoma with piloid features (1.4%). 53/72 (73.6%) were primary and 19/72 (26.4%) were secondary GC. We used 40 patients without the GC pattern as controls. Among glioblastoma GC cases and in comparison with controls, mutations in PTEN and EGFR were significantly associated with the GC pattern: 18/57 (32%) vs 3/38 (7.9%), p-value=0.01 and 23/57 (40%) vs 6/38 (16%), p-value=0.013, respectively. This held true in primary but not secondary GC. Out of 20 most commonly mutated genes in GC, mutations in EGFR, TERT, and MDM4 were associated with worse PFS: p-value=0.004, p-value=0.007, p-value=0.013, respectively and mutations in TERT and MDM4, but not EGFR, were associated with worse OS: p-value=0.003, p-value=0.015, respectively. Secondary GC was associated with IDH mutation compared to control non-GC cases: 8/19 (42%) vs 2/40 (5%), p-value=0.001. As expected, IDH mutation was associated with improved PFS, p-value<0.001 and OS, p-value=0.003 in GC. No genes were significantly associated with laterality of GC. We found novel associations between PTEN and EGFR mutations and the GC phenotype and IDH mutation with the occurrence of secondary GC after treatment. While MDM4 is not associated with outcomes in gliomas, we show that MDM4 mutation is associated with poor survival in GC. These findings shed light into molecular basis of GC and need to be further validated in larger studies.
BIOM-33. INVESTIGATING MIR-21 AS A NON-INVASIVE PROGNOSTIC BIOMARKER IN GLIOMA PATIENTS IN RESOURCE CONSTRAINT SETTINGS
Authors: Laghari Altaf Ali , Naeem Sana , Sufiyan Sufiyan , Amin Wajiha , Ilyas Sahar , Bajwa Mohammad Hamza , Qazi Siraj Uddin , Mughal Nouman , Enam Syed Ather
Published: November 2024

BACKGROUND

Glioma treatment remains challenging due to high recurrence rates and resistance to treatment. Diagnosis and follow-up in resource-constrained regions often leads to significant patient attrition. Serum microRNA (miRNA) expression profiles are shown to be expressed in tumor tissue and peripheral samples, offering a pathway for non-invasive, repetitive liquid biopsies. miR-21 shows promise in many populations; however, there is a dearth of data from our region.

METHODOLOGY

we collected 89 intraoperative tumor tissue samples, 42 pre- and post-operative serum samples from glioma patients, and included 10 control tissue samples along with 8 normal serum samples and analyzed for miR-21 expression through qPCR. Serum samples were collected before tumor resection and post-surgery (pre- and post-operative). Correlational analysis with molecular markers IDH, Ki-67, ATRX, p53, and survival curves through the Kaplan-Meier method were calculated in high and low miR-21 expression groups, The hazard ratio was quantitatively determined using Cox regression analysis, considering both univariate associations and multivariate correlations with clinical parameters.

RESULTS

miR-21 expression in tissue increased with higher grades of glioma (p=0.00064), of patients above 50 years (p=0.0027), and shows a positive correlation with tumor volume (r= 0.22, p=0.081). IDH-wildtype (p=2.06e-03) and high Ki-67 (p=2.50e-03) expression in tumors showed significant upregulation of miR-21 compared to IDH-mutant and low Ki-67. Patients with low miR-21 expression had significantly longer overall survival (OS) than patients with high miR-21 expression (p =0.006). Quantitative hazard analysis indicates that patients in the high expression group have a 2.77 times higher risk of mortality (95% CI: upper - 0.19, lower - 0.92), in comparison to patients in the low expression group (p= 0.008).

CONCLUSION

Our findings validate the future utility of miR-21 as a serum assay to help diagnose and assess treatment response in different grades of glioma, within our population. Keywords: Glioma, Biomarker, Molecular markers, Liquid biopsy
BIOM-35. COMPREHENSIVE IDENTIFICATION OF MRNA ISOFORMS AND THEIR DIAGNOSTIC POTENTIAL IN GLIOMAS
Authors: Goel Pallavi , Sadasivam Subhashini , Ghanekar Yashoda , Roy Vijaylaxmi , Sreegiriraju Vijay , Kumari Neha , Madiraju Surya , Ray Amit
Published: November 2024

Most genes generate multiple mRNA isoforms which may differ in their protein-coding capacity. Also, cancer and its prognosis are associated with the altered expression of specific isoforms of a variety of genes as cancer cells can manipulate regulatory mechanisms to express isoforms that provide a survival advantage and/or resistance to therapy. However, the underlying mechanisms behind their pathology are poorly understood. Fifty seven glioma samples that could be categorized unambiguously into Astrocytoma (n=17), Oligodendroglioma (n=16) and Glioblastoma (n=24) based on pathology reports and according to WHO standards were selected for this analysis. Total RNA-Sequencing (RNA-Seq) was performed on RNA isolated from these 57 samples. RNA-Seq data analysis was performed using the DRAGEN RNA application in Illumina BaseSpace and transcript counts were generated after alignment. From these counts, isoforms that were significantly differentially expressed in Astrocytoma (Astro) vs Oligodendroglioma (Oligo), and Astrocytoma vs Glioblastoma (GBM) were identified using the R package, IsoformSwitchAnalyzeR. Approximately 93,000 transcripts were screened in both comparisons of which 4388 and 44 transcript switches were identified as significant at FDR<0.05 in the Astro vs GBM and Astro vs Oligo comparisons, respectively. Applying an additional cut-off based on the difference in isoform fraction or dIF of a transcript between the two groups being compared (dIF>1.0 and dIF<-0.1), the most significant top switches were identified.. Similarly, in the Astro vs GBM comparison, the isoform switch in genes such as MDF1 and RER1 whose overexpression is known to be involved in tumorigenesis and metastasis were among the 155 top switches. Among the six top switches in the Astro vs. Oligo comparison were transcripts of the RENBP and GCNT2 genes which play an important role in the progression of melanoma, gastric and lung cancers. These results indicate that there may be isoform-specific dysregulation within gliomas, and further suggest that their biological significance and diagnostic potential can be explored.
BIOM-42. RESPONSE TO DABRAFENIB/TRAMETINIB IN A PATIENT WITH WHO-CNS GRADE 3 BRAF V600E-MUTATED PLEOMORPHIC XANTHOASTROCYTOMA
Authors: Alalami Huda , Bannykh Serguei , Vail Eric , Patil Chirag , Rudnick Jeremy , Hu Jethro
Published: November 2024

BACKGROUND

Pleomorphic xanthoastrocytoma (PXA) is a rare central nervous system tumor. Mutations in BRAF V600E are present in 60-80% of cases. While traditionally managed with surgical resection and adjuvant radiation, emerging evidence suggests targeted therapies may be effective, particularly in cases harboring the BRAF V600E mutation.

CASE SUMMARY

A 35-year-old male with no significant medical history presented in November 2023 with diplopia and headache leading to the discovery of a large left temporal/parietal tumor. A partial resection was performed. Initial histopathological diagnosis was glioblastoma (GBM); thus, the patient was treated with concurrent radiation and temozolomide for 6 weeks. Molecular pathological analysis demonstrated the presence of BRAF V600E mutation and CDKN2A/B copy number loss. Methylation-based tumor profiling was performed at the National Cancer Institute, with composite methylation profile indicating a consensus match to pleomorphic xanthoastrocytoma. Following chemoradiation, a repeat brain MRI in March 2024 showed tumor progression, prompting the initiation of dabrafenib and trametinib therapy. After 1 month of targeted treatment, a repeat brain MRI demonstrated a partial response with a decrease in tumor size and enhancement. In April 2024, he underwent a planned repeat resection. Symptomatically, the patient experienced intermittent headaches and nausea that were responsive to oral steroids with no serious adverse effects to targeted therapy.

DISCUSSION

This case highlights the therapeutic potential of double BRAF/MEK blockade with dabrafenib and trametinib in BRAF V600E-mutant anaplastic PXA. The observed partial response on imaging suggests the efficacy of targeted therapy in this molecular subtype. These findings underscore the importance of molecular profiling in guiding treatment decisions.
BIOM-44.18F-DOPA-PET THRESHOLDS FOR BOTH NEWLY DIAGNOSED AND RECURRENT ASTROCYTOMA USING PATHOLOGICAL GROUPING OF SPATIALLY CORRELATED BIOPSIES
Authors: Pafundi Deanna , Parney Ian , Burns Terry , Giannini Caterina , Raghunathan Aditya , Hunt Christopher , Dooley Katharine , Kabat Brian , Lowe Val , Kaufmann Timothy , Morris Jonathan , Zakhary Mark , Grams Michael , Seaburg Maasa , Breen William , Sarkaria Jann , Johnson Derek , Laack Nadia , Brinkmann Debra
Published: November 2024

BACKGROUND

Glioma radiotherapy planning requires accurate tumor delineation. While T1- contrast-enhanced-MRI (T1-CE-MRI) is the standard, due to blood-brain-barrier breakdown dependencies, T1-CE-MRI fails to reflect the extent of glioma. Studies using amino acid PET tracers report glioma uptake up to 3cm-4cm beyond T1-CE. In this study, amino acid tracer 18F-fluoro-dihydroxyphenylalanine (18F-DOPA) uptake was correlated with histopathological features to determine tumor thresholds.

METHODS

Using registered 18F-DOPA-PET and T1-CE-MRI images in the Stealth Neuronavigation system targeting concordant and discordant regions, 181 stereotactic biopsy samples (newly-diagnosed=74; recurrent=107) were obtained from 59 enrolled astrocytoma patients across two prospective phase II clinical trials between 2010-2019. An experienced neuropathologist reviewed each sample with hematoxylin and eosin stain and assigned an alphanumeric score: mitotic activity (0=no tumor; 1=no mitosis; 2=few/scattered mitosis; 3=frequent mitosis) and cellular density (A=<25%; B=25%-50%; C=50%-75%; D=>75%). Samples assigned 1C-1D, 2B-2D, or 3A-3D were categorized as histopathological high-score (aggressive disease), remaining samples as low-score. Relative mean (rFDOPA_mean) tumor-to-background uptake ratios were computed for 5mm uniformly expanded volumes from each Stealth biopsy coordinate using the crescent and wedge normalization methods. Relative uptake was compared overall and separately within newly-diagnosed/recurrent disease subgroups. An optimal rFDOPA_mean threshold to delineate high- from low-score was determined using the maximal Youden index of ROC curves.

RESULTS

Overall, high-score samples (n=116) had higher median (IQR) rFDOPA_mean uptake than low-score samples (n=65): high-score rFDOPA:mean=1.70(1.16-2.26), low-score rFDOPA:mean=1.16(0.83-1.49), Kruskal-Wallis p<0.001. The uptake difference between high- vs. low-score samples was observed within newly-diagnosed and recurrent subgroups, but was only significant for newly-diagnosed (p<0.001). For newly-diagnosed, an rFDOPA:mean=1.49 cutoff between high- and low-score groups shows 69% accuracy, 63% sensitivity, 80% specificity (AUC=0.782). Using the wedge normalization method, rFDOPA_mean values were 0.2 higher than crescent method values.

CONCLUSIONS

This work presents histologically verified 18F-DOPA-PET thresholds for aggressive disease in newly-diagnosed astrocytoma patients. Separate thresholds will need to be determined for recurrent glioma patients.
BIOM-48. UTILITY OF CIRCULATING TUMOR DNA (CTDNA) FROM CEREBROSPINAL FLUID (CSF) FOR PROGNOSIS OF PATIENTS WITH RECURRENT HIGH-GRADE GLIOMA
Authors: Miller Alexandra M , Nandakumar Subhiksha , Holle Bridget M , Kreitzer Christoph , Song Timothy , Tartaro Marlene , Hertz Charli Ann J , Rafailov Johnathan , Campos Carl , Brannon A Rose , Solit David B , Pasquini Luca , Meng Alicia , Reiner Anne , Young Robert , Socci Nicholas D , Arcila Maria E , Berger Michael F , Schultz Nikolaus , Mellinghoff Ingo K
Published: November 2024

High-grade gliomas (HGGs) are the most aggressive primary brain tumors, and molecular characterization is vital for their diagnosis and treatment. Due to their location, tumor sampling is often challenging. Therefore, developing minimally invasive diagnostic methods is urgently needed. Here we report that circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) can identify key genomic alterations and track clonal evolution in HGGs. Detection of CSF ctDNA correlates with leptomeningeal disease and overall survival, indicating its potential for integration into clinical decision-making. Our study includes 313 samples from 253 patients with recurrent glioma treated at MSKCC who underwent CSF collection using the MSK-IMPACT targeted sequencing assay. 37% of genomic alterations were detected using our less stringent variant calling criteria and Gaussian Mixture Model to call copy number events. CSF ctDNA positivity was determined by the presence of at least one oncogenic disease-defining alteration or any shared alteration with the tumor. We found 212 CSF ctDNA positive (68%) and 101 CSF ctDNA negative (32%) samples. CSF ctDNA positivity was the highest amongst histone mutant tumors (96%). We noticed 44% of alterations shared between the tumor and the CSF, additionally, we noted considerable tumor evolution particularly within the growth signaling pathways (e.g. PDGFRA). Our cohort demonstrated that patients with positive CSF ctDNA had a significantly shorter overall survival compared to those who were CSF ctDNA negative (4.83 months vs 14.14 months, HR 2.4, p < 0.001). Radiographic findings such as enhancing disease and contact of the tumor with the ventricular space were positively associated with CSF ctDNA positivity. Additionally, CSF ctDNA was associated with positive cytology in 12/12 cases (100%). With our improved pipeline, we hypothesize CSF ctDNA may be used as a prognostic biomarker for survival, but confirmation requires further validation in a prospective study.
BIOM-56. HEAT SHOCK PROTEINS PREDICT CLINICAL RESPONSE AND POTENTIATE LOCAL IMMUNOGENICITY AFTER LITT FOR GLIOBLASTOMA
Authors: Chandar Jay , Berke Chandler , Seetharam Deepa , Govindarajan Vasundara , Bhatia Shovan , Valdez Mynor Mendez , Desgraves Jelisah , Jaman Emade , Lu Victor , Castro Jesus , Hudson Anna , Ramsoomair Christian , Ivan Michael , Komotar Ricardo , Shah Ashish
Published: November 2024

Glioblastoma (GBM) remains one of the deadliest cancers despite advances in therapies. Laser interstitial thermal therapy (LITT) is a minimally invasive technique used to ablate intra-axial brain tumors. Non-ablative LITT-induced hyperthermia (33-43˚C) increases intra-tumoral mutational burden and neoantigen production, promoting neoantigen presentation via heat shock proteins (HSPs). HSPs are protein-folding chaperones that present novel intracellular antigens for immune recognition. We investigated HSPs as predictors of local immune response and clinical outcomes of GBM patients undergoing LITT. We conducted immune deconvolution of bulk RNA-sequencing data from The Cancer Genome Atlas to determine the correlation between 97 unique HSPs and tumor infiltration of CD8+, CD4+, B, macrophage, neutrophil, and dendritic cells. We evaluated the association between HSP expression and overall survival (OS). Pre-LITT biopsies from 9 patients (responders and non-responders) were analyzed via immunohistochemistry (IHC) to identify spatial HSP expression. Next-generation sequencing was utilized to validate findings and identify other predictive biomarkers. We identified two HSPs for further investigation: SACS and HSPA5. SACS was associated with improved survival based on TCGA data (14.9 vs. 11 months, HR:1.3, p<0.0001). HSPA5 was associated with worse outcomes (12.1 vs. 15.0 months, HR:0.73, p<0.0001). Immune deconvolution showed HSPA5 positively correlated with dendritic cell infiltration (r=0.50, p=6.1E-27) and SACS with CD8+ infiltration (r=0.31, p=6.8E-11). IHC of 9 patients demonstrated high SACS expression was associated with improved OS (p<0.05) after LITT. Multiplex IHC illustrated that immune cell infiltration was associated with therapeutic response post-LITT. Our ongoing immunohistochemical and genomic analyses aim to clarify the role of HSPs in enhancing immunogenicity in GBM. Further investigation into SACS and immune cell infiltration may reveal how hyperthermia via LITT improves response through neoantigen presentation.
BIOM-58. RE-INDUCTION OF INTRATHECAL CHEMOTHERAPY IN PRIOR RESPONDERS AND CORRELATION WITH CEREBROSPINAL FLUID CIRCULATING TUMOR CELLS
Authors: Yazzie Skye Dawn , Orosco Heather , Turpin Tiffany , Bazhenova Lyudmila , Shatsky Rebecca , Schulte Jessica , Piccioni David
Published: November 2024

INTRODUCTION

Leptomeningeal carcinomatosis (LMC) is an aggressive form of metastasis, with a historically poor median overall survival. Newer therapies and treatment strategies are improving outcomes, and more long-term responders exist. However, there are limited options for intrathecal (IT) chemotherapy, and re-induction in prior responders may be a reasonable treatment strategy. In addition, quantitative cerebrospinal fluid circulating tumor cells (CSF CTCs) are a valuable tool in LMC, for both surveillance of recurrence and evaluation of response.

METHODS

We retrospectively identified 10 patients with LMC who showed a response to IT chemotherapy and were followed with quantitative CSF CTCs on a commercially available platform. At progression, patients underwent re-induction of IT chemotherapy, on a twice a week schedule, and were evaluated for response.

RESULTS

All 10 patients were treated with re-induction IT chemotherapy. Six patients were re-challenged with topotecan, 3 with topotecan + trastuzumab, and 1 with pemetrexed + trastuzumab. Six patients had a primary diagnosis of breast cancer, three with lung cancer and one with ovarian cancer. The median KPS was 70. Eight were female. Prior to re-induction, all 10 had an increase in quantitative CSF CTCs. Only 1/10 had new symptoms, and 5/10 showed imaging changes on MRI. At the time of re-induction, 3/10 also received stereotactic radiosurgery to brain metastases and 2/10 had a change in systemic chemotherapy. 9/10 had improved CSF CTC counts on the next restaging, typically at 8 weeks. The median overall survival from re-challenge was 12.7 months.

CONCLUSION

Quantitative CSF CTCs were a more sensitive predictor of recurrence than symptoms or imaging, and were a marker of response to re-induction IT chemotherapy. Re-induction showed a durable survival benefit, and is a reasonable treatment strategy in patients who were prior responders
BIOM-67. DIFFERENTIAL DNA METHYLATION PATTERNS IN THE CSF OF PATIENTS WITH DIFFUSE GLIOMAS
Authors: Wang Daniel , Shah Mauli , Arjuna Srividya , Dono Antonio , Patel Chirag , Huse Jason , Kerrigan Brittany Parker , Nguyen Sophia , Lang Frederick , Esquenazi Yoshua , Ballester Leomar
Published: November 2024

Studies have shown that different central nervous system (CNS) tumor types exhibit unique DNA methylation profiles. DNA methylation-based machine learning classification of CNS tumor tissue has been demonstrated to be highly-accurate in differentiating between tumor types, including between diffuse glioma subtypes. While similar analyses have been performed using cell-free DNA (cfDNA) from blood, few studies have looked at the potential of DNA methylation as a biomarker for diffuse gliomas using CSF-derived cfDNA. In this study, we analyzed CSF cfDNA methylation patterns in diffuse glioma patients. DNA methylation profiling of CSF of patients with glioblastoma, IDH-wildtype (GBM) (n=37), IDH-mutant diffuse gliomas (n=12), and non-neoplastic conditions (n=5) was performed using cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq). Methylation quantification was estimated for each genomic region. Significance testing was performed between diagnostic groups to discover differentially-methylated regions (DMRs). The 300 most differentially-methylated regions (DMRs) for each comparison (IDH-wildtype vs. IDH-mutant, IDH-mutant vs. control, IDH-wildtype vs. control), for a total of 900 DMRs, were utilized as features in dimensionality reduction analysis and machine learning. Out of ~1×107 defined genomic regions, there were ~7×105 DMRs between GBM and control samples and ~1.5×106 DMRs between GBM and IDH-mutant samples, accounting for ~7% and ~15% of the genome, respectively. Uniform manifold approximation and projection (UMAP) and hierarchical clustering analysis revealed that samples were mostly clustered by diagnosis. Random forest analysis of the 900 DMRs with an 80/20 train/test split resulted in an overall accuracy of 0.815. In conclusion, CSF cfDNA methylation profiles of diffuse glioma patients exhibit differential methylation patterns between IDH-mutant and IDH-wildtype tumors, as well as between tumor and control, and could be informative biomarkers for the diagnosis of patients with diffuse gliomas.
BIOM-68. OUTCOMES IN PATIENTS WITH HIGH-GRADE MENINGIOMA (HGM): A MULTI-INSTITUTIONAL STUDY
Authors: Mohammed Nasser , Patel Chirag , Balar Ashish , Van Buskirk Samuel , McGovern Susan , Raza Shaan , DeMonte Franco , Ballester Leomar , Youssef Michael , Kamiya-Matsuoka Carlos
Published: November 2024

BACKGROUND

High-grade meningiomas (HGMs) are associated with increased risk of recurrence after primary treatment. This study aimed to evaluate factors affecting survival.

METHODS

We performed a multi-institutional retrospective chart review study of patients with HGM (defined as grade 2 or 3 meningioma) whose tumor had undergone next-generation sequencing. Statistical testing was performed in Stata/MP version 16.1 (StataCorp, College Station, TX) on the patients’ demographic, anatomic, clinical, and survival data (using Kaplan-Meier survivor function and long-rank test). Data are presented as mean±SD, median [interquartile range], or percent. Age/time reported in years.

RESULTS

There were 46 patients (45.7% female) with an age of 57.9±14.0 at initial HGM diagnosis. The most frequent HGM sites were middle cranial fossa (37.0%), frontal (28.3%), parietal (15.2%), posterior fossa (13.0%), parasagittal (10.9%), and petrous (10.9%). The most common presenting symptoms were headache (37.0%), seizure (23.9%), weakness (21.7%), vision changes (19.6%), memory issues (10.9%), and diplopia (10.9%). The most frequent gene mutations were in NF2 (58.7%), CDKN2A (13.0%), and TERT (8.7%). Median follow-up was 2.85 [1.4-7], during which time 65.2% of patients experienced recurrence. mPFS was 2.7 [0.83-6]. Kaplan-Meier analysis showed a mPFS of 5 [1.2-9] and 2.3 [0.8-3] in females and males, respectively (p=0.26). Age and Ki67 proliferative index at diagnosis did not significantly predict PFS. mOS was not reached (NR) [7-NR]. NF2 mutation status and presence of extracranial invasion did not significantly separate the PFS Kaplan-Meier curves on log-rank testing. However, the presence of NF2 mutation [mOS NR (5.2-NR) vs. NR (7-NR), p<0.0001], extracranial invasion [mOS 10 (2.4-NR) vs. NR (NR-NR), p<0.0001], and HGM recurrence [mOS NR (2.7-NR) vs. NR (7-NR), p<0.0001], were associated with shorter mOS.

CONCLUSIONS

These HGM patients experienced a high recurrence rate during the follow-up period. The presence of NF2 mutation, extracranial invasion, and recurrent HGM were associated with shorter OS.
BIOM-69. THE ONCOGENIC FLIP IN PATIENTS WITH LEPTOMENINGEAL METASTATIC DISEASE (LMD): LONGITUDINAL DETECTION IN CEREBROSPINAL FLUID TUMOR CELLS (CSF-TCS) REVEALS IMPLICATIONS FOR DIFFERENTIAL TREATMENT OF THE LMD TUMOR
Authors: Tripathy Arushi , Corkos Perry , Blouw Barbara , Moore Melissa , LaFrance Norman , Hedrick Marc , Youssef Michael , Piccioni David , Nagpal Seema , Kumthekar Priya
Published: November 2024

INTRODUCTION

Patients with LMD have poor prognosis and limited treatment options. Oncogene amplification of primary, metastatic, and CNS metastatic tumors can be heterogeneous. Therefore, patients with LMD may benefit from assessment of clinically relevant biomarkers in CSF, which may guide the choice of a targeted therapy specifically for the LMD tumor. CNSide is a CLIA-validated laboratory-developed test ordered commercially at the discretion of physicians for CSF-TC enumeration, immunocytochemical (ICC) and fluorescence in situ hybridization (FISH) analysis of oncogene amplification. We longitudinally analyze oncogenes in CSF-TCs in patients with LMD of various primary cancers.

METHODS

CSF was collected from patients with suspected or confirmed LMD; 613 tests were ordered on 218 individual patients with breast (N=105 patients), lung (N=65), gastrointestinal (N=10), and other cancers. Using CNSide, CSF-TCs were isolated and tested via ICC (ER, PD-L1, and PR), and FISH (ALK, cMET, cMyc, EGFR, FGFR1, HER2, NTRK1, NTRK3, PTEN, RET, and ROS1).

RESULTS

In patients with lung cancer, ALK was detected in 14% (17/118) of samples, CMET in 61% (78/128), HER2 in 73% (16/22), and RET in 4% (4/90). In patients with breast cancer, HER2 was detected in 39% (65/168) of samples, FGFR1 in 32% (19/60), ER in 26% (44/168) and PR in 4% (5/120). 66 patients underwent 2+ CSF draws; 24 underwent 5+. Among these, there were 13 ICC flips (7 acquired mutations) and 58 FISH probe detection flips (26 acquired mutations). 20/66 patients (30.3%) had at least one flip in their ordered biomarkers.

CONCLUSION

CNSide can be used to detect oncogene amplification on CSF-TCs of patients with LMD, and mutational status of the LMD tumor may differ from the original tumor biopsy. CSF-TC analysis may provide therapeutic insights that vary from the original tumor and could open the door to additional treatment targets for patients struck with LMD.
BIOM-70. CSF TUMOR CELL (CSF-TC) DETECTION, QUANTIFICATION AND BIOMARKER ASSESSMENT HELPS IN CLINICAL MANAGEMENT OF BREAST CANCER AND NON-SMALL CELL LUNG CANCER PATIENTS HAVING LEPTOMENINGEAL DISEASE (FORESEE STUDY, NCT05414123)
Authors: Kumthekar Priya , Youssef Michael , Yang Jonathan , Piccioni David , Beruti Sue , Gillis Laura , Gordon Kelly , Blouw Barbara , Moore Melissa , LaFrance Norman , Hedrick Marc , Nagpal Seema
Published: November 2024

Leptomeningeal metastases (LM) or the presence of cancer cells in the cerebrospinal fluid (CSF)/pia remains a challenging disease to diagnosis and treat. Current standard of care methods to diagnose or assess treatment response of LM (Clinical Evaluation, MRI and Cytology) have limited sensitivity and specificity and are poorly quantifiable. This creates challenges for physicians to manage LM or determine the best course of treatment. The FORESEE Study was a multi-center, prospective clinical trial evaluating a novel diagnostic platform, CNSide, that aimed to overcome these challenges. The FORESEE study enrolled patients with breast or non-Small Cell Lung Cancer (NSCLC) with suspicion of or confirmed LM. CNSide can detect and quantify tumor cells in the CSF from patients with breast cancer or NSCLC having a suspicious or confirmed LM. This platform also is able to identify actionable mutations in the CSF via Fluorescent In Situ Hybridization (FISH) and next-generation sequencing. The primary end point of the FORESEE study was clinical utility and the impact of CNSide on physician treatment decisions. Secondary endpoints included evaluating the clinical performance of CNSide vs. cytology in tumor cell detection (sensitivity, specificity, PPV and NPV). The study enrolled 40 patients (22 breast cancer and 18 NSCLC). Each patient underwent standard of care diagnostic evaluations at baseline and at three follow up timepoints through their treatment. CNSide aided clinical decision making in 93% (50/54) of the clinical decisions. At baseline 39 patients were assessed and confirmed a positive LM diagnosis in 15% (6/39), a negative LM diagnosis in 8% (3/39), progression in 15% (6/39), resolution in 15% (6/39) and no progression, or resolution in 36% (14/39) of the patients. CNSide informed the specific drug selected for treatment in 26% (10/39) patients at baseline and demonstrated clinical high utility. The FORESEE data is undergoing ongoing analysis; updated analysis will be presented at the meeting.
BIOM-75. MRI FLAIR SIGNAL ASSESSMENT IN NEURO-ONCOLOGY (SANO) AS A MEASURABLE TIMEPOINT FOR INTERVENTIONAL THERAPY PRIOR TO PROGRESSION IN HIGH GRADE GLIOMAS: A WINDOW OF OPPORTUNITY
Authors: Gatson Na Tosha , Chen Shuyi , Ornelas Sara , Bross Shane
Published: November 2024

BACKGROUND

There are no validated clinical or radiographic assessments for response to therapy in glioblastoma (GBM). Offering interventions at the time of progression using our current assessment tools is likely too late as second-line therapies have failed to significantly delay progression and extend survival. In 2020, our team was first in the US to publish the largest and most comprehensive retrospective review identifying the T2/FLAIR MRI signal assessment protocol as an early indicator of progressive GBM. We proposed that the time of FLAIR signal abnormality within the resection cavity (RC) anticipated GBM progression by nearly 4 months and if used as a timepoint for therapeutic intervention could reshape glioma clinical trial design.

METHODS

To support validation of SANO, a prospective assessment of 146 GBM patients between 2019-2021 yielded 71 cases meeting resection and imaging inclusion criteria. We analyzed sequential brain MRIs from initial diagnosis to first progression for development of T2 FLAIR signal intensity (SI) within the RC as previously reported (Gatson et al 2020) and included cases with ventricle associated surgery as a comparator. PFS and OS were evaluated using Kaplan-Meier curves stratified by SI.

RESULTS

Development of SI occurred in 80.3% (n=57) GBM patients on average 2.8 months before RANO-assessed progression. A faster time to progression from SI development occurred in cases with ventricle associated RC. SI-positivity again portended poorer outcomes for PFS and OS as compared to SI-negative cases. Use of the eye (globe) for FLAIR assessment, instead of the ventricles, to qualitatively discern the presence of SI in ventricle associated RC.

CONCLUSIONS

This small prospective review supports our initial findings to validate a highly sensitive brain tumor imaging biomarker, SI, and should at least supplement existing response assessment criteria to improve declaration of GBM progression. Furthermore, use of SANO might also offer an earlier window of opportunity for salvage therapy intervention and offer new avenues for glioma clinical trial design.
BIOS-06. MACHINE LEARNING MODEL INDEPENDENTLY IDENTIFIES CLINICAL FEATURES ASSOCIATED WITH WILD-TYPE GLIOBLASTOMA VERSUS MUTANT GRADE 4 ASTROCYTOMA
Authors: Abdelmoneum Farida , Stoller Jared , Muldoon Leslie , Ambady Prakash , Jr Ramon Barajas
Published: November 2024

BACKGROUND

Glioblastoma (GBM), the most common and aggressive primary brain tumor in adults, presents significant clinical challenges due to its invasive nature and high recurrence rates. Understanding the clinical demographic factors associated with IDH wild-type (IDH-wt) versus mutant grade 4 astrocytoma (IDH-Mut) is critical for prognosis and treatment strategies. This study aimed to utilize a novel machine learning method to identify key clinical and demographic factors linked to IDH status.

METHODS

The Cancer Imaging Archive dataset included 617 patients but required preprocessing and cleaning. The cleaning process ensured data completeness and consistency by removing non-relevant variables like date and time, resulting in 20 potential predictors and 317 observations. A random forest model using Gini impurity score was built to classify patient IDH status. The dataset was split into a training set (two-thirds) and a test set (one-third). A variable importance plot identified significant variables based on the mean decrease in the Gini index.

RESULTS

Our machine learning model achieved 98% accuracy on the test set, outperforming the previously published model of 80% accuracy. A variable importance plot identified age at diagnosis, gender, ethnicity, and race as key predictors of IDH status, with age being the most important. Age was the most important predictor, but race (Caucasian) and ethnicity (not Hispanic or Latino) were also significant.

CONCLUSIONS

We present a highly accurate machine learning model for differentiating glioma IDH molecular status based only on patient clinical and demographic factors; improving upon prior published models. Future work will use a generalized logistic model to explore variable interactions and predict IDH-wt versus IDH-Mut status. These steps are vital for enhancing predictive accuracy and supporting personalized treatment strategies. Furthermore, we will define associations and interactions between these variables with other biological and therapeutic variables in predicting clinical outcome.
BIOS-07. GRADUAL METABOLIC ALTERATIONS RESTRUCTURE THE SPATIAL ARCHITECTURE AND IMMUNITY IN GLIOBLASTOMA
Authors: Kueckelhaus Jan , Kada-Benotmane Jasim , Schnell Oliver , Beck Jürgen , Villa Giulia , Heiland Dieter-Henrik
Published: November 2024

The organized layered structure of the human neocortex contrasts sharply with the chaotic architecture of malignant CNS tumors. The heterogenous nature of glioblastoma (GBM) poses significant challenges to research and treatment, given that effective strategies require consistent biological patterns. Here, we leverage recent advances in spatial biology, integrating spatially resolved transcriptomics and metabolomics to identify drivers of GBM-specific architectural evolution. We performed spatial metabolomics (MALDI) and transcriptomics (Visium n=43 and MERFISH n=25) on glioblastoma patients, with computational analysis conducted using the SPATA2 R package. Our findings reveal that most spatial recurrent patterns in glioblastoma emerge in a gradient-like organization, particularly influenced by proximity to areas of necrosis and hypoxia. Samples without hypoxic regions demonstrated less spatial organization. Metabolomic and transcriptomic profiling indicated enhanced responses to hypoxia, reduced cell proliferation, and elevated expression indicative of the S phase in cell division near necrotic regions. The vicinity to hypoxic areas was associated with increased extracellular matrix remodeling and epithelial-to-mesenchymal transition, suggesting that the invasive capabilities of GBM cells originate from these hypoxic niches. By further integrating spatially resolved TCR-sequencing, we identified that hypoxic gradients drive defined T cell responses with a higher likelihood of T cell dysfunction within a distance of 235 µm (sd: 132 µm) to hypoxia. This suggests that the presence of necrosis, hypoxia, and hypoxia-associated metabolites could serve as potential predictive markers for T-cell behavior and exhaustion in glioblastoma. Our study offers an in-depth analysis of the influence of two prevalent niches in glioblastoma: necrosis and hypoxia. We reveal that the complex architecture of glioblastoma is not solely dictated by genetic randomness and stochastic occurrences but is significantly influenced by spatial proximity to key factors like necrosis and hypoxia. This insight contributes to an evolving model that seeks to unravel the intricate biology underpinning this formidable disease.
CNSC-02. ANTICANCER ABILITY OF THE BERBERINE TO PROMOTE THE APOPTOSIS EFFECT AND ATTENUATE THE ROS GENERATION CAPACITY ON DBTRG BRAIN CANCER CELLS
Authors: Shen Chiung-Chyi , Yang Meng-Yin , Yang Yi-Chin , Hung Huey-Shan
Published: November 2024

Abstract In this research, berberine (BB), and its effect on the biological performance of DBTRG brain cancer cells and normal endothelial cells (EC) was investigated. Firstly, the DBTRG cancer cell and EC cell were cultured with different concentrations of BB (0.5, 1, 5 and 10 μg/ml), and it was confirmed that BB significantly reduced the proliferation of DBTRG cancer cells. However, there is no significant toxic effect on EC cells. The results of cell cycle analysis confirmed that BB significantly induced DBTRG cancer cell undergo apoptotic effect in a dose dependent manner. The assessment of cell migration behavior showed that BB significantly inhibited cell migration in DBTRG cancer cell, but not in BAEC as well as attenuated the matrix metalloproteinase 2/9 (MMP2/9) in a dose dependent manner. Furthermore, the reactive oxygen species (ROS) generation capacity among DBTRG cancer cell, EC cell and macrophages (Raw 264.7). It was demonstrated that BB was prominently decreased the ROS generation of DBTRG instead of EC or Raw264.7 cell. Moreover, the pro-inflammatory cytokines of TNF-α, IL-1β and IL-6 were significantly inhibited by BB in a dose dependent manner of DBTRG brain cancer cell. As mentioned above, it was demonstrated that bioactive BB molecules is potential for anti-brain cancer drugs may via anti-immune response and anti-oxidative generation capacity for brain cancer therapy. BB biomolecules may target for DBTRG cell which cannot cause inevitable toxic damage to the normal EC cell. Altogether, the promising findings of BB biomolecule on DBTRG cancer cell suggest that BB may be a good candidate of anticancer drug or adjuvant for the treatment of human brain cancer. Key words: berberine, DBTRG brain cancer, anti-immune response, anti-oxidative generation
CNSC-06. NAVIGATING BRAIN CANCER: PATIENT STORIES AND MEDICAL BREAKTHROUGH
Authors: Vanukuru Kiran Deepthi
Published: November 2024

The complex interplay of genetic mutation, dys regulated signalling pathways, Epigenetic modifications and Interaction with tumor microenvironment are the major aggravating factors for Brain Tumors. Neurological complications involve Increased Intracranial pressure, Seizures, Motor and Sensory deficits, Aphasia, Hydrocephaly, Behavioral and personality changes, Cerebellar Symptoms. It is diagnosed in a sequential steps. Collecting good history from patient in primary then examining the patient all through and making some investigations to come to a final diagnosis. On asking history to a patient he complains of recurrent convulsions, Personality changes and some motor activity deficit and loss of few senses. On examination we can reveal defect in cranial nerve functions, Motor or sensory deficits, loss of reflexes and coordination. Then Investigations being the next step for diagnosis, We ask the patient to undergo for a test for Blood Biomarkers and CSF analysis in case of suspection of metastatic Brain tumors. Biopsy to obtain for Histopathological Examination. Histopathological examination is done for analysis of genetic mutations and molecular markers. The other imaging techniques like MRI, MRS, CT, PET, EEG are done. This gives a clear picture of what actually caused tumor and shows a way for treatment. Now the treatment involves both Medical and Surgical treatment. Medical treatment includes Chemotherapy along with radiation therapy where the drugs given are Temozolomide and targeted therapy included EGFR BRAF inhibitors for glioblastoma and low grade gliomas respectively. Tumor treating fields- Optune is given. Surgical treatment involves Craniotomy for removal of primary Brain tumors, Neuro Endoscopy if tumor is present in ventricles or base of Brain, Laser interstitial Thermal therapy for deap seated and recurrent brain tumors. This is all about the treatment and now the patient management is very important for further clinical help. Physical, occupational and speech therapy helps patients recover. Symptomatic approach for inoperable tumors Provide comprehensive support for patients nearing end of life, Emphasise confidence and Quality of life.
CNSC-14. GLIOBLASTOMA MULTIFORME TUMOR VOLUME AND PERSISTENCE OF CHIMERIC ANTIGEN RECEPTOR T CELLS FOLLOWING TREATMENT
Authors: Veerappan Devi , Thomas Reena
Published: November 2024

Glioblastoma Multiforme (GBM) is one of the most common and aggressive high-grade primary brain tumors that arises from the glial cells of the central nervous system and occurs most often in the frontal and temporal lobes. Despite current treatment options, long-term prognosis of GBM remains low with no significant improvement rates. Chimeric antigen receptor (CAR)-expressing T cells target the B cell marker CD19 and have shown increased efficacy in B cell lymphomas, and lymphoblastic leukemias suggesting benefits in GBM. This study aims to quantify the persistence of CAR-T cells in the context of GBM tumor volume following neurosurgical debulking procedure. A radiology software known as the mint Lesion was utilized to provide Tumor Response Assessment by Criteria (TRAC) reports that consist of volumetric measurements of the tumor lesions (target enhancing lesions, non-target enhancing lesions, and non-target non-enhancing lesions). Fluorescence-activated cell sorting (FACS) analysis takes a sample mixture of cells and sorts them into different populations based on specific biomarkers and characteristics. B7-H3 CAR-T cell persistence was increased in patients with a larger post-surgical tumor volume (3.04% Subject 001 with 2438 mm² volume and 2.38% Subject 003 with 224 mm² tumor volume). However, the number of CAR-T cells per 1 mm² was significantly reduced in patients with a larger post-surgical tumor volume (0.0012 cells/mm² Subject 001 and 0.010 cells/mm² Subject 003). This study shows that although there is an overall increased CAR-T cell persistence for a larger tumor volume, the number of CAR-T cells per 1 mm² is significantly smaller for larger tumor volumes, while illustrating that a larger post-surgical tumor bulk volume is correlated with an increased CAR-T cell persistence within 1-week post-infusion. These findings provide novel information and complement other correlative studies as part of the Phase 1 interventional clinical trial for glioblastoma patients.
CNSC-18. A SCOPING REVIEW OF HISTONE 3.3 G34R/V HIGH-GRADE GLIOMA: EPIGENETIC AND MOLECULAR PROFILES, CLINICOPATHOLOGY, AND TREATMENT AVENUES
Authors: Tang Kayen , Cesaire Melissa , McDonald Taylor , Castro Maria , Jackson Sadhana
Published: November 2024

Survival of pediatric and young adults with malignant glioma remains poor despite progress in treatment. This is especially true for histone 3.3 G34R/V (H3.3G34R/V) mutated gliomas, which often present in adolescent and young adult patients. While treatments to date delay progression, post 5-year overall survival is exceedingly rare. Historically, there has been limited research on H3G34R/V mutant tumors, which likely contributes to lack of advancements in current treatments. This scoping review fills the current knowledge gap of H3G34R/V mutated gliomas and summarizes future targets and therapeutic options. In October 2023, MEDLINE, Embase, Cochrane Library, and Web of Science Core Collection were searched. Two reviewers screened all articles by title and abstract review and three independent reviewers extracted all studies meeting inclusion criteria relevant to H3G34R/V tumors (preclinical and clinical studies). Of the 2203 articles screened, 200 were deemed eligible. The 200 articles included 68 literature reviews, 9 systematic reviews, 54 preclinical studies, and 69 clinically oriented studies. We found that the United States and ACTA neuropathologica are the top country and journal contributors, respectively, to understanding molecular diagnosis, disease pathology, and potential targeted treatment options of H3.3G34R/V tumors. This literature collectively demonstrates the involvement of numerous oncogenes and tumor suppressor genes involved in RAS/MAPK, MYCN, NOTCH, and LIF/STAT pathways such as ATRX, PDGFRA, and TP53 in influencing the neural characteristics and prognostic outcomes of the tumor. While certain therapeutic modalities, including H3K9 methyltransferase inhibitors and bevacizumab-based therapy have exhibited preclinical efficacy and some indication of positive clinical outcomes, more research on agents that permeate the blood-brain barrier to impair growth are necessary. Additionally, further research into the supportive role of the tumor microenvironment that enables disease progression is warranted. Collectively, these studies will empower intelligent prospective clinical trials using H3.3G34R/V targeted therapies which enhance disease survival.