bluuebunny/crossref_metadata_2025 huggingface dataset:
DDDR-14. DEVELOPMENT OF A NOVEL CYP17A1-TARGETED INHIBITOR FOR GLIOBLASTOMA
Authors: Chen Hsien-Chung , Hsu Tsung-I
Published: November 2023

Glioblastoma (GBM) is a highly aggressive and invasive brain tumor, resistant to current standard treatments, including temozolomide (TMZ) and radiotherapy. Despite these interventions, GBM's intrinsic drug resistance often renders it incurable, thus highlighting the dire need for novel therapeutic strategies. In this study, we used ultra-high pressure liquid chromatography-mass spectrometry to examine the levels of neurosteroids in tumor specimens from primary and recurrent GBM patients. This led to the discovery of differential expression patterns, most notably in androgen, including dehydroepiandrosterone and testosterone. Our results indicated androgen over-production weakens the GBM's sensitivity to TMZ by inducing post-translational modification of Sp1 protein, which aids in DNA repair. Interestingly, Sp1 activity is further enhanced by histone deacetylase (HDAC) 6, which in turn diminishes the DNA damage caused by TMZ. In addition, proteomic analysis revealed an overexpression of cytochrome (CYP) 17A1, particularly in recurrent GBM, which led us to hypothesize that a drug inhibiting both CYP17A1 and HDAC6 could potentially serve as a viable treatment for TMZ-resistant GBM. To validate this, the drug was tested in vitro on U87MG-R cells and patient-derived Pt#3 TMZ-resistant cells, demonstrating the therapeutic efficacy based on cell viability assays. In vivo testing in the TMZ-resistant GBM orthotopic mouse model also showed promising anti-tumor activity, with treated mice demonstrating increased survival times compared to controls. In conclusion, our findings suggest that this drug targeting both CYP17A1 and HDAC6 presents a potential breakthrough in GBM-targeted therapy, addressing the pervasive issue of TMZ resistance.
DDDR-15. RESISTANCE TO TARGETED ANTI-MITOTICS IN GLIOBLASTOMA IS DRIVEN BY STAT3 ACTIVATION AND THERAPY INDUCED SENESCENCE
Authors: Kenchappa Rajappa , Zarco Natanael , Dovas Athanassios , Argenziano Michael , Haddock Ashley , Canoll Peter , Rosenfeld Steven
Published: November 2023

Tumor cells require the mitotic spindle to drive chromosome separation in metaphase, which has made the spindle a compelling target for development of anti-mitotics. However, most of these spindle inhibitors target microtubules and can thereby be highly neurotoxic. This has motivated development of targeted anti-mitotics that inhibit non-microtubule components of the spindle, including kinesins and mitotic kinases. These drugs are not neurotoxic and prolong survival in tumor patients, but resistance limits their efficacy. We reported (Kenchappa et al., Cell Reports, 2022) that resistance to one of these—ispinesib, a highly specific inhibitor of the mitotic kinesin Kif11—requires two functions of STAT3: activation of transcription in the nucleus and of oxidative phosphorylation in the mitochondria. Inhibiting both functions reverses ispinesib resistance. Furthermore, combining ispinesib with a CNS-permeant STAT3 inhibitor significantly prolongs survival over ispinesib alone in both immunocompetent and PDX GBM models. We now report that resistance to two other targeted anti-mitotics—alisertib (Aurora Kinase inhibitor) and volasertib (Polo Like Kinase inhibitor)—works similarly and can likewise be reversed with STAT3 inhibitors. For all three of these anti-mitotics, resistance goes hand-in-hand with development of therapy-induced senescence (TIS) in approximately half of GBM cells. TIS cells secrete a variety of soluble factors, referred to as the senescence associated secretory phenotype (SASP), which stimulate stemness, angiogenesis, and immunosuppression. We propose that: 1) TIS cells require STAT3 for survival, and that they in turn maintain a drug resistant state by suppressing mitosis in the remaining, non senescent cells through components of the SASP; and 2) by killing TIS cells, STAT3 inhibitors restore anti-mitotic sensitivity in the remaining, non-senescent tumor cells. We propose that this STAT3/TIS model of resistance may also apply to how resistance develops to other GBM therapies, and may guide similar translational approaches to enhancing therapeutic efficacy.
DDDR-20. FOSL1 INDUCES TMZ-CHEMORESISTANCE IN GLIOBLASTOMA VIA REGULATION OF IL-6-STAT3TYR705PATHWAY-MEDIATED STEMNESS
Authors: Sim Jeongmin , Park JeongMan , Kim Yu Jin , Kim Dongkil , Cho Kyunggi , Moon Ju Hyung , Sung Kyoung Su , Lim Jaejoon
Published: November 2023

Glioblastoma (GBM) is the most lethal brain tumors with intensive resistance to drug. Although glioblastoma has been tried to treat with diverse strategies, drug resistance is still concerning. Finding new therapeutic targets to improve conventional drug sensitivity has remained a major challenge. Here, a novel therapeutic target, FOSL1, to conventional drug resistant patients was established, in which FOSL1 knockdown restores the temozolomide (TMZ) sensitivity via regulation of IL-6-induced stemness characteristic in glioblastoma cells. We show that FOSL1, contributing to poor prognosis of GBM patients, is closely linked chemo-resistant molecular signatures. In glioblastoma cells, FOSL1 knockdown is affect to apoptosis, G0/G1 arrest, tumor migration and expression of stemness hallmark. These alterations were induced by FOSL1-mediated IL-6-pSTAT3Tyr705 activation via MGMT independent manner. Finally, we show that vemurafenib, targeting FOSL1 expression, can be potential therapeutics for TMZ resistant glioblastoma. Taken together, our results demonstrate that FOSL1 facilitates TMZ chemoresistance via regulating IL-6-pSTAT3Tyr705-mediated stemness in GBM cells. FOSL1 can represent a novel therapeutic target to overcome GBM chemoresistance.
DDDR-27. CLASS I HDAC INHIBITOR AGAINST TM-MEDIATED NETWORK CONNECTIVITY IN GLIOBLASTOMA
Authors: Weil Sophie , Azorín Daniel Domínguez , Hoffmann Dirk , Horschitz Sandra , Jabali Ammar , Jung Erik , Koch Philipp , Wick Wolfgang , Winkler Frank
Published: November 2023

Tumor microtubes (TMs) are long thin cellular protrusions extended by one glioblastoma cell to connect to another and integrate into a communicating network that contributes to glioblastoma’s high therapy resistance. Understanding the biological functions of tumor cell connectivity and overcoming network resistance has emerged as a new therapeutic opportunity. The combinatorial treatment of an anti-TM compound with a cytotoxic treatment has come to focus after it was shown that non-connected glioblastoma cells are more vulnerable to cytotoxic therapy. Besides the development of therapies against specific proteins in TM function, other drugs have also been repurposed and tested for their anti-TM activity and potential additional benefits with radiotherapy. Among these, we tested histone deacetylase (HDAC) inhibitors regarding their potential to overcome TM mediated connectivity and thereby open vulnerabilities in glioblastoma. To investigate the drugs, we applied our drug testing pipeline in vitro and in vivo. Here, we observed fewer TMs in an in vitro monolayer of glioblastoma monoculture after treatment with a class I HDAC inhibitor as opposed to two other compounds from the HDAC inhibitor group. In a 3D co-culture model with human neuronal organoids, treatment with the most promising class I HDAC inhibitor showed a dose-dependent inhibitory effect on cell proliferation and TMs. We then continued to examine the HDAC inhibitor’s effect in our in vivo two photon microscopy model with radiotherapy as cytotoxic co-treatment. After the implantation and establishment of xenograft glioblastoma under a chronic cranial window in mice, treatment with the HDAC inhibitor was started and a course of radiotherapy was added. After six weeks after treatment start, tumors of the co-treated animals were smaller than in animals that were only irradiated. Further studies will involve the examination of the underlying biological mechanism of the anti-TM effects and continued long-term treatment to further improve overall anti-tumor effectivity.
DDDR-32. EVALUATING THE THERAPEUTIC EFFECTS OF SMALL MOLECULE INHIBITORS OF CDK4/6 AND FAK IN PRECLINICAL MENINGIOMA MODELS
Authors: Ijad Nazanin , Waller Katie , Nayyar Naema , Yamazawa Erika , Summers Elizabeth , Migliarese Christian , Galanis Evanthia , Sarkaria Jann , Vaubel Rachael , Wakimoto Hiroaki , Brastianos Priscilla
Published: November 2023

BACKGROUND

New therapies are needed for meningioma since treatment options are limited once patients have exhausted surgery and radiation. FAK, CDK4/6 and RAF/MEK represent potential targets because of synthetic lethality with NF2, loss of CDKN2A, and activation of MAPK signaling pathway in meningioma, respectively. The objective of this study was to evaluate the efficacy of targeting FAK, CDK4/6 and RAF/MEK as monotherapies and combination therapies in traditional and patient-derived cell lines and xenografts.

METHODS

In vitro, cell viability and proliferation assays were used to test abemaciclib (CDK4/6 inhibitor), defactinib (FAK inhibitor) and VS-6766 (RAF/MEK inhibitor) as monotherapy and in combination. To better recapitulate the meningioma microenvironment, targeted agents were evaluated with Matrigel, an artificial extracellular matrix. The efficacy of VS-4718 (in vivo formulation of defactinib) and abemaciclib were evaluated in a subcutaneous IOMM-lee meningioma model (having CDKN2A loss) in nude mice. Furthermore, we are establishing cell cultures and patient-derived cell and xenograft (PDX) models using freshly-resected tissue from patients with recurrent or high-grade (WHO grade 2-3) meningiomas.

RESULTS

In vitro evaluation identified the combination of defactinib with abemaciclib resulted in a synergistic decrease in cell viability relative to each monotherapy alone, while the combination of defactinib+VS-6766 was not beneficial. The presence of Matrigel enhanced the sensitivity of all three agents. In vivo, we observed improved survival in mice treated with abemaciclib vs control (45 days vs 26 days; p=0.03), as well as combination of VS-4718 + abemaciclib vs control (44 days vs 26 days; p=0.04, Gehan-Breslow-Wilcoxon test). We did not observe survival extension with VS-4718 monotherapy. Lastly, we successfully established an orthotopic meningioma PDX using a WHO Grade 3 tumor for evaluation of novel therapies in meningioma.

CONCLUSION

Abemaciclib showed promising efficacy in preclinical meningioma xenografts with CDKN2A loss. Studies to evaluate these therapies in other orthotopic models are underway.
EOLP-02. EFFECT OF HEALTH DISPARITIES ON END OF LIFE CARE IN GLIOBLASTOMA, IDH WILDTYPE (GBM) PATIENTS
Authors: Helfer Cassandra , Ludmir Ethan , Farinholt Paige , Rao Ganesh , Patel Akash , Jalali Ali , Mandel Jacob
Published: November 2023

GBM is the most common malignant brain tumor in adults. Given the highly aggressive course and rapid neurologic decline, end of life care is critical. Proactive referral to hospice care is associated with improved quality of life and is recommended under current oncology guidelines. Utilization of these services is limited, with hospice referral rates ranging from 60-75%. The role of healthcare disparities upon quality of end of life care remains unclear. The goal of this study was to investigate the influence of healthcare disparities upon hospice service utilization by comparing patients at Ben Taub (BT), a Houston public safety net hospital, to Baylor St. Luke’s (BSL), a private academic institution. 50 patients (16 BT, 34 BSL) diagnosed with GBM, IDH wildtype, since 2016 were analyzed via retrospective chart review. Patient demographics and insurance status varied, with BT patients more likely to be Hispanic or African American (BT 94%, BSL 29%) and to be uninsured or insured via the county financial aid program (BT 88%, BSL 6%). Hospice referral rates were overall consistent with prior studies (BT 75%, BSL 68%). BT patients were referred to hospice later (BT 3.8, BSL 5.5 weeks mean survival after referral, p=0.118) and were more likely to be referred while in an inpatient setting (BT 75%, BSL 36%, p=0.07). Additionally, BT patients were more likely to be admitted to the hospital in the month prior to death (BT 44%, BSL 33%, p=0.537) and to die in an inpatient setting (BT 19%, BSL 3%, p=0.096). These findings call attention to the impact of healthcare disparities upon utilization of end of life services. Further research is needed to investigate factors contributing to these discrepancies and implement tools to improve quality of life in all patients with late-stage GBM regardless of race, socioeconomic, or insurance status.
EOLP-04. EXTRA-NEURAL DISSEMINATION OF MYC-ACTIVATED INFANT MEDULLOBLASTOMA DESPITE MULTIMODAL THERAPY
Authors: Horbaczewski Alysia , Jacobsen Chad , Kelly Amy , Pearsal Katherine , Ladra Matthew , Kilburn Lindsay , Gass David
Published: November 2023

Extra neural metastases of infant medulloblastoma portend poor prognosis. Previous reports were in patients receiving treatment with radiation alone or patients with ventriculoperitoneal shunt (VPS). Recently with multimodal therapy, reports of extra-neural medulloblastoma are rarely reported. We report two patients with stage M3 MYC-Activated Infant Medulloblastoma who received aggressive therapy yet developed extra-neural relapses. The first case was a 2-year-old male who underwent gross total resection, which was complicated by hydrocephalus requiring VPS placement. He completed treatment as per ACNS0334 and achieved a near-complete response. Next, he received four cycles of five drug anti-angiogenic therapy followed by 2 cycles of expanded access therapy with I-3F8 antibody. He progressed both in brain and spinal cord, then received palliative craniospinal irradiation with boost. Two months following radiation, he died of disease with significant pancytopenia and hypoechoic nodules throughout the liver, suggestive of disseminated disease. Our second patient is a five-year-old girl, who was diagnosed at age two. She achieved a CR after treatment as per ACNS0334. She then enrolled on a clinical trial with Difluoromethylornithine (DFMO) for three months. On initial disease evaluation, she had progression in brain and spine. She underwent palliative radiation with craniospinal irradiation and boost with concurrent Indoximod on phase 2 clinical trial. Following radiation, she received compassionate use indoximod and temadar for 24 months and remained in CR. Three months after stopping therapy, she progressed to left orbit, pelvis and ribs. She is currently receiving palliative care. MYC-activated medulloblastoma has a very poor outcome and requires multimodal including radiation to achieve remission. Despite aggressive therapy, disease is highly evasive and can spread extracranially to multiple areas including bones, bone marrow, liver, and abdomen. Novel therapies and more exhaustive surveillance regiments need to be developed to limit extracranial dissemination and achieve more durable remissions.
EPID-02. HISTORY OF ALLERGY OR ATOPY DECREASES RISK OF BRAIN METASTASIS IN LUNG CANCER AND MELANOMA
Authors: Neff Corey , Price Mackenzie , Liu Zhen , Cioffi Gino , Barnholtz-Sloan Jill , Walsh Kyle , Fecci Peter , Ostrom Quinn
Published: November 2023

Both allergy/atopy and autoimmune disease (AD) are associated with decreased prevalence of glioma. We leveraged cancer registry data combined with Medicare claims to investigate the effect of prior atopy/AD on incidence, and overall survival, of brain metastasis (BrM) in lung cancer (LC) and melanoma. Surveillance, Epidemiology and End. RESULTS: data linked to Medicare claims were obtained, containing cases of melanoma and LC diagnosed from 2008-2017. Patients < 65 years of age, enrolled in Medicare Advantage, with prior/subsequent cancer diagnosis, or missing variables were excluded. History of allergy/atopy/ or AD (≥6 months prior to primary cancer diagnosis) and BrM status were identified by ICD-9/ICD-10 codes and SEER variables. Treatment pattern was determined using ICD-9/ICD-10 and HCPCS/CPT codes. Time to BrM and overall survival among individuals diagnosed with BrM were estimated via Cox proportional hazards regression adjusted for age, sex, race/ethnicity, stage at diagnosis, treatment, and Charlson comorbidity score. Of the 154,203 and 66,593 cases of LC and melanoma, 18.6% and 2.5% developed BrM at any point, respectively. Among LC with BrM, 27% and 16% had atopy and/or AD (compared to 33% and 20% in LC without BrM), while there were 26% and 16% of cases with atopy and/or AD among melanoma with BrM (compared to 33% and 18% in melanoma without BrM). History of atopy was associated with decreased hazard of BrM in melanoma and LC (HR=0.73, p-value< 0.001 and HR=0.90, p=0.024, respectively). Among those with a BrM, both history of atopy and AD were associated with improved survival in LC (HR=0.90, p< 0.001 and HR=0.95, p< 0.001) but not melanoma. History of AD is associated with a moderate survival benefit in LC with BrM, while history of allergy/atopy decreased incidence of BrM in LC and melanoma. Further research is necessary to identify potential causes of this association.
EPID-19. THE INFLUENCE OF FACILITY TYPE ON INTRACRANIAL MENINGIOMA TREATMENT AND OUTCOMES: PREDICTING OVERALL SURVIVAL USING THE NATIONAL CANCER DATABASE
Authors: Brown Nolan , Chakravarti Sachiv , Gendreau Julian
Published: November 2023

There is a growing body of evidence demonstrating improved outcomes for patients with CNS neoplasms treated at academic centers (ACs) versus non-academic centers (non-ACs). This represents a potential healthcare disparity within neurosurgery. Herein, we investigate the relationship between facility type and surgical outcomes in meningioma patients. METHODS: The National Cancer Database was queried for adult patients diagnosed with intracranial meningioma requiring intervention between 2004 and 2019. Patients were stratified by facility type and the Mann-Whitney U and Fisher exact tests were used for bivariate analysis of continuous and categorical variables. Multivariable logistic and linear regression were used to assess whether demographic variables predicted treatment at non-ACs. Furthermore, multivariate cox proportion hazard and log-rank tests were used to determine whether facility type was related to overall survival (OS). RESULTS: In total, 314,651 patients diagnosed with meningioma were included; 122,112 (38.8%) patients were treated at an AC and 192,539 patients (61.2%) were treated at a non-AC. On bivariate analysis, patients treated at an AC were more likely to be white (30.7% vs 24.7%, p< 0.001), have an income higher than $63,000 (31.8% vs 29% p< 0.001) and have a larger tumor (43.3±113.6 vs 39.3±106.8, p< 0.001). On multivariate Cox models, the risk of death for patients treated at ACs was 16.7% lower than that of non-AC patients (HR = 0.883, 95% CI 0.858–0.908, p < 0.001). When controlling for demographic and clinical variables, patients treated at ACs were more likely to undergo surgical intervention (OR = 1.059, 95% CI 1.033-1.087, p < 0.001) but less likely to receive radiotherapy (OR = 0.921, 95% CI 0.897-0.947, p < 0.001). CONCLUSIONS: Our results indicate that AC facility type is associated with disparate survival outcomes in treatment of intracranial meningiomas. Namely, patients treated at non-ACs appear to suffer a survival disadvantage.
EPID-22. AN INTEGRATED, MULTI-DATABASE ANALYSIS OF THE SAFETY OF BENIGN MENINGIOMA RESECTION IN OCTOGENARIANS
Authors: Zhu Ping , Ma Jun , Chen Clark
Published: November 2023

OBJECT

Given that multiple co-morbidities are present in up to 80% of octogenarians, resection of benign tumors, such as meningiomas, is a challenging proposition, especially in the context of frailty naturally associated with aging. Here, we characterized the patterns of clinical practice, morbidity, and mortality associated with benign meningioma resection for octogenarian using the Surveillance, Epidemiology and End

RESULTS

(SEER), SEER-Medicare (SEER-M), National Cancer Database (NCDB), and National Readmission Database (NRD).

METHODS

Logistic regression, propensity-score matching (PSM)-method (covariates balanced using PSM: socio-demographics, facility features, and comorbidities), and accelerated failure time (AFT) models.

RESULTS

In SEER, the adjusted odds ratios of recommendation for surgery were 0.59 (95%CI=0.53-0.66, p< 0.001) and 0.17 (95%CI=0.15-0.21, p< 0.001) for benign meningioma patients age 60-79 and > 80, relative to patients age 40-59. Expectedly, the hazard of death increased with advancing aging strata in patients who underwent meningioma resection. However, in independent analyses of NCDB and SEER-M, likelihood of death after benign meningioma resection was not significantly elevated in patients age > 80 relative to age- and PSM-matched patient cohorts. In the NRD, age > 80 was associated with increased odds of 90-day medical readmission after meningioma resection (OR: 1.63, 95%CI=1.33-1.99) but not 90-day neurologic readmission (OR: 1.02, 95%CI:0.76-1.37) relative to age 40-59.

CONCLUSION

We found no increased risk for patients age > 80 who were selected for and underwent resection in terms of mortality and 90-day neurologic readmission risk. However, the octogenarians have a higher risk of 90-day medical readmission. These findings suggest that neurosurgeons, in general, exert sound judgment in the selection of elderly patients for benign meningioma resections.
EPID-28. YEARS OF LIFE LOST FOR BRAIN AND OTHER CENTRAL NERVOUS SYSTEM TUMORS IN THE UNITED STATES, 2018
Authors: Neff Corey , Price Mackenzie , Gerstl Jakob , Kruchko Carol , Barnholtz-Sloan Jill , Bernstock Joshua , Smith Timothy , Claus Elizabeth , Ostrom Quinn
Published: November 2023

Brain and other central nervous system tumors (BTs) contribute disproportionately to cancer morbidity and mortality relative to their incidence. To estimate the national burden due to these tumors in the United States (US), we estimated Years of Life Lost (YLL) due to premature death from BT overall and specific histopathologies. Mortality data for malignant and non-malignant BT were obtained from the National Vital Statistics System (~100% of US); survival data were obtained from the CDC’s National Program of Cancer Registries (NPCR, ~82% of the US) Survival Analytic Dataset for the years 2004-2018. YLL was calculated by adding estimated years of life left at their age of death. Mean YLL (mYLL) with corresponding 95% confidence intervals (95%CI) were reported by behavior, age at death, sex, and race/ethnicity for each data source, and by histopathology for NPCR. Total YLL due to malignant BT was 4,913,397 (mYLL=22.0) and 3,253,999 (mYLL=22.4), while non-malignant BTs contributed 208,278 YLL (mYLL=14.2). Females (mYLL=22.5), Hispanic individuals (mYLL=30.7), and children aged 0-14 years (mYLL=71.6), had the greatest mYLL due to malignant BTs. Glioblastoma had the highest total YLL (62.2% of all YLL, mYLL=19.8), while atypical teratoid/rhabdoid tumors had the greatest mYLL despite accounting for less than 1% of total YLL due to malignant BT (mYLL=74.4). Meningiomas accounted for 79% of total YLL due to non-malignant tumors, with a mYLL of 13.7. Compared to non-malignant BT, malignant BTs have the greatest mYLL, reflecting their short survival time post-diagnosis. BT are the most common type of cancer in children, leading to relatively high total (475,290 YLL) and mYLL for pediatric BT which may contribute substantially to cancer-specific mortality in this population. These estimates provide a compliment to other population-based BT statistics in demonstrating the impact of these debilitating tumors.
EPCO-01. THE GENOMIC LANDSCAPE OF BRAIN METASTASIS
Authors: Skakodub Anna , Walch Henry , Kumar Rahul , Eichholz Jordan , Cooper Claire , Khatri Ishaani , Del Balzo Luke , Miao Emily , Gui Chengcheng , Ma Jennifer , Tringale Kathryn , Gaeta Benjamin , Kelly Daniel , Moss Nelson , Yu Kenny Kwok Hei , Wilcox Jessica , Bale Tejus , Yu Yao , Yamada Yoshiya , Imber Brandon , Gomez Daniel , Schultz Nikolaus , Pike Luke
Published: November 2023

BACKGROUND

The prognosis for patients with brain metastasis (BM) is devastating, while the underlying biology of BM development remains poorly understood. Identification of genomic biomarkers can offer promising opportunities for prediction of BM development and guidance in personalized treatment. In this study we evaluate the genomic alterations present in a large cohort of resected BM.

METHODS

Upon retrospective review, we identified 868 patients with diagnosis of solid primary cancers who had undergone a standard of care craniotomy at Memorial Sloan Kettering Cancer Center (MSKCC). BM samples were profiled by MSK-IMPACT, a next-generation sequencing (NGS) assay designed to detect a wide range of genetic alterations in 341-505 cancer genes. Genomic alterations were filtered for driver variants using OncoKB. Disease sites included cancers of head and neck, breast, lung, lower and upper gastrointestinal tract, kidney, ovary, uterus, prostate, skin, soft tissues, and others.

RESULTS

More than half (57%; 493/868) of patients were female and the median age was 63 (range 22-93). Foreseeably, the most common histology was non-small cell lung cancer (NSCLC; 38%), followed by invasive carcinoma of the breast and melanoma (16% and 13%, respectively). The most frequently encountered alterations were inTP53 (60%), CDKN2A (25%), TERT (23%), KRAS (18%), and PTEN (12%) across all BM samples. The median fraction of genome altered was 0.41 [range: 0-0.99] and the median tumor mutational burden was 6.6 muts/Mb [range: 0-395]. Additionally, TP53 was the most frequently altered gene after stratifying by primary histology in most cancer types, except for melanoma, renal, and thyroid, which were enriched for alterations in TERT, CDKN2A, and TERT, respectively.

CONCLUSION

The landscape of genomic alterations present in BM is distinct and varies by primary histologic diagnosis. Ongoing analyses of matched primary-BM pairs and clinicogenomic correlation will identify factors predisposing patients to BM development and progression.
EPCO-20. DYNAMICS OF TUMOR GENOME SHAPING AND CLINICAL RESPONSE IN GLIOBLASTOMAS UNDER IMMUNE CHECKPOINT INHIBITORS
Authors: Choi Seung-Won , Rabadan Raul , Iwamoto Fabio , Pan Peter
Published: November 2023

Immune checkpoint inhibitors (ICI) have shown remarkable success in several tumor types; however, this success has not been common in glioblastomas (GBMs). Given the immune-suppressive tumor microenvironment, the timing when to apply ICI may be a determining factor for clinical success. With this hypothesis, we compiled a longitudinal cohort of GBMs treated with different ICI schemes and a control cohort (upfront ICI (n=16), recurrent ICI (n=23), and control cohort by standard of care (n=33)). We investigated the genomic correlates to clinical response. Neither ICI itself nor different timing strategies failed to show a survival benefit for GBMs. However, the upfront-ICI cohort had more long-term survivors (overall survival >= 36 months) than the recurrent-ICI cohort (37.5% (n=6/16) vs. 26.1% (n=6/23)). Genomic analysis revealed that alterations in the PI3K-pathway or TP53 were associated with a poor response to ICI, while BRAF mutation was related to a favorable response. Interestingly, only TP53 alteration was associated with a worse prognosis in GBMs treated with upfront ICI. Tumor mutational burden (TMB) or the amount of neo-antigens failed to show any correlation with the response to ICI. However, ICI-treated GBMs experienced divergent evolution regarding the TMB, while GBMs treated by standard of care only exhibited unidirectional change. We also explored the immunogenomic shifts following different treatment modalities. ICI-treated GBMs showed more variable changes in both HLA alleles and neo-antigen burden (p-value=0.41 & 0.008, respectively). Among the upfront-ICI cohort, GBMs with a better response showed an increased neo-antigen burden upon recurrence (p-value=0.03), suggesting the selection of fitting clones during therapy. Collectively, we observed that that GBMs experienced distinct evolutions under different treatment schemes. The vulnerability of GBMs to ICI should be considered in the context of tumors’ capability to dynamically shape the tumor genome to fit into therapeutic pressure.
EPCO-23. EFFECTS OF H3.3G34V MUTATION ON GENOMIC H3K36 AND H3K27 METHYLATION PATTERNS IN ISOGENIC PEDIATRIC GLIOMA CELLS
Authors: Huang Tina , Piunti Andrea , Qi Jin , Bartom Elizabeth , Saratsis Amanda
Published: November 2023

BACKGROUND

Histone H3.3 mutation (H3F3A) occurs in 50% of cortical pediatric high-grade gliomas (pHGGs). This mutation replaces glycine 34 with arginine or valine (G34R/V), impairing SETD2 activity (H3K36-specific trimethyltransferase). Consequently, reduced H3K36me3 is observed on H3.3G34V nucleosomes relative to wild-type, contributing to genomic instability and driving a distinct gene expression signature associated with tumorigenesis. However, it is not known if this differential H3K36me3 enrichment is due to H3.3G34V mutant protein alone. Therefore, we set to elucidate the effect of H3.3G34V mutant protein in pediatric glioma on H3K36me3, H3K27me3 and H3.3 enrichment in vitro.

METHODS

Experiments were conducted using an established H3.3G34V mutant patient-derived pediatric high-grade glioma cell line (KNS42), and Histone H3.3 wild-type human astrocytes (NHAs). Lentiviral delivery of a doxycycline-inducible RNAi vector targeted against H3F3A was transduced to KNS42 cells to knock down H3.3G34V protein expression. Cell lines were then compared via ChIP-Seq, Western Blot, proliferation and viability studies.

RESULTS

We found that the doxycycline-inducible shRNA knockdown of mutant H3F3A encoding the H3.3G34V protein resulted in loss of H3.3G34V enrichment and increased H3K36me3 enrichment throughout the genome. After knockdown, H3.3G34V enrichment was preserved at loci observed to have the greatest H3.3G34V and H3K36me3 enrichment prior to knockdown. Induced expression of mutant H3.3G34V protein in vitro was insufficient to induce genomic H3K36me3 enrichment patterns observed in H3.3G34V mutant glioma cells. We also observed strong co-enrichment of H3.3G34V and wild-type H3.3 protein, as well as greater H3K27me3 enrichment, in cells expressing H3.3G34V.

CONCLUSION

Our study demonstrates the effects of H3.3G34V mutant protein on genomic H3K36me3, H3K27me3 and H3.3 enrichment patterns in isogenic cell lines.
EPCO-25. HETEROGENEITY OF INSERTION/DELETION AND SINGLE NUCLEOTIDE VARIATION IN DRIVERS OF LOWER GRADE GLIOMAS
Authors: Chen Lee , Stevers Nicholas , Costello Joseph
Published: November 2023

Single nucleotide variation (SNV) and copy number variation (CNV) have been extensively studied across tumor types. Their impact on tumor evolution has been a primary research focus. However, insertion/deletion (indels) have received less attention due to their high false positive and false negative rate and the absence of hotspot indel sites. We examine adult IDH wildtype/mutant gliomas, and utilize spatially mapped samples within the same tumors (84 tumors, averaging 8 to 9 samples/tumor), as well as primary/recurrent paired samples (n=37), to investigate the heterogeneity and progression of indels and SNVs. We used two indel-detecting algorithms, Pindel and Muect2, and discovered and validated several indels, which had not been previously emphasized, including in TCHH. We report on two frequently mutated driver genes, CIC and ATRX, in IDHmut-Codel and IDHmut-noncodel gliomas, respectively. CIC SNVs and indels are observed as complementary occurrences. For example, among 9 samples of the tumor recurrence of one patient, 6 showed CIC SNVs, with only two sharing the same mutation. In contrast, 8 of 9 samples exhibited CIC indels, representing 4 different types. Notably, all samples displayed either CIC SNVs or indels. In IDHmut-noncodel tumors, a similar pattern was observed with ATRX. Nonetheless, all samples displayed either ATRX SNVs or indels. This study highlights the tremendous intratumor heterogeneity and evolution in drivers of LGG, emphasizing their complex role in tumorigenesis. Prior studies may have underestimated the frequency and heterogeneity due to calling accuracy and limitations in tumor sampling. By focusing on indels and other genetic variations within gliomas, this study sheds light on their significance in understanding tumor progression, the essential nature of CIC and ATRX inactivation over whole tumors, and the potential implications for therapeutic interventions.
EPCO-27. RECONSTRUCTION OF THE SPATIAL ECOSYSTEM OF GLIOBLASTOMA REVEALS RECURRENT RELATIONSHIPS BETWEEN TUMOR CELL STATES AND TUMOR MICROENVIRONMENT
Authors: Adabbo Bruno , Migliozzi Simona , Garofano Luciano , Oh Young Taek , Gultekin Sakir H , D'Angelo Fulvio , Roberts Evan R , Bilbao Daniel C , Davila Pedro M , Williams Sion L , Currall Benjamin B , Ceccarelli Michele , Lasorella Anna , Iavarone Antonio
Published: November 2023

Glioblastoma multiforme (GBM) is the most aggressive form of primary brain tumor, with no curative treatment options. Multiple studies have characterized at single cell resolution the GBM as being composed of transcriptional cell states interconnected with components in the tumor immune microenvironment (TME). Our group proposed and validated the first single cell guided functional classification of GBM in four tumor-intrinsic cell states which informed clinical outcome and delivered therapeutic options. However, single cell technologies lack the spatial relationships among the cell states of GBM and between GBM cell states and TME. Spatially resolved transcriptomic technologies are emerging as powerful tools to reconstruct the spatial architecture of a tissue. We performed spatial transcriptomics of multicellular regions of interest (ROI) in 8 IDH wild-type GBM with both CosMx Spatial Molecular Imager, which analyzes 1,000 RNA probes and 64 proteins at single cell resolution, and GeoMx Digital Spatial Profiler which profiles the whole transcriptome (~18,000 genes) at ROI resolution. We integrated the two platforms to define single cell states and non-malignant cells and developed a computational deconvolution approach for CosMx spatial data which utilized GeoMx ROI resolved transcriptomic profiles as a-priori information to predict cell type abundances. Spatial deconvolution of CosMx derived single cells revealed spatial segregation of the tumor cell clones and cellular states and highlighted recurrent patterns of cell states, distinct TME cell types associated with coherent histopathological features across multiple samples. Our studies established a scalable approach to resolve the transcriptional heterogeneity of GBM and reconstruct the architecture of GBM cell states and tumor microenvironment.
EPCO-31. THE PROGNOSTIC IMPLICATIONS OF THE RELATIVE ABUNDANCE OF DECONVOLVED TUMOR AND NON-TUMORAL SUBPOPULATIONS IN MULTI-REGIONAL BIOPSIES OF HIGH GRADE GLIOMA WITH BULK RNA-SEQ
Authors: Curtin Lee , Bond Kamila , Velez Sebastian , Hawkins-Daarud Andrea , Urcuyo Javier , De Leon Gustavo , Langworthy Jazlynn , Sereduk Christopher , Singleton Kyle , Jackson Pamela , Krishna Chandan , Zimmerman Richard , Patra Devi , Bendok Bernard , Smith Kris , Nakaji Peter , Donev Kliment , Baxter Leslie , Mrugala Maciej , Hu Leland , Tran Nhan , Al-Dalahmah Osama , Canoll Peter , Swanson Kristin
Published: November 2023

High-grade glioma continues to have dismal survival owing in part to its intra- and inter-patient heterogeneity. Standard clinical protocol collects tumor samples with the aim of providing or confirming a diagnosis and determining the status of a few key genes (e.g. IDH1, MGMT). However, this protocol is unable to capture the diversity within tumor regions, immune expression or normal cell abundances that play key roles in the development of the disease. To overcome this, during surgery we collect image-localized multi-regional biopsies to characterize this disease heterogeneity. Data collection is ongoing, and we currently have 202 samples from 58 patients with available bulk RNA-Seq. With a single-cell reference dataset from Columbia University, we used CIBERSORTx, a deconvolution method, to predict relative abundances of 7 normal, 6 glioma, and 5 immune cell subpopulations for each sample. We used Cox proportional hazard models with first-order statistics (mean, minimum, maximum) of abundances within patients to determine whether these are prognostic, then used TCGA RNA-Seq data to validate these findings. We found that one glioma proneural subtype was significantly beneficial for patient survival relative to other glioma subtypes across all statistics (and showed significance in TCGA). Proliferative and mesenchymal glioma subtypes also showed significance for one or two of the calculated statistics. Oligodendrocyte progenitor cell abundances were consistently significantly beneficial for patient survival in our cohort, while an increased abundance of abnormal (reactive) astrocytes is associated with poor prognosis. We also ran these analyses within invasive margin and core tumor regions to determine location-specific population abundances associated with patient survival. In conclusion, understanding the in vivo diversity of cellular subpopulations within high grade glioma is important for treatment stratification and patient benefit.
EPCO-34. IMAGE-BASED PHENOTYPIC HIGH-CONTENT CRISPR-CAS9 SCREEN FOR CHARACTERIZING CANCER DRIVERS IN PEDIATRIC HIGH-GRADE GLIOMA
Authors: Amin Samir , Gujar Amit , Yi Eunhee , Kang Wonyeong , Costa Megan , Gabriel Paul , Sjogren Greg , Maher Leigh , Lee Charles , Robson Paul , Dickinson Peter , Packer Rebecca , Courtois Elise , Verhaak Roel
Published: November 2023

The genomic landscape of pediatric high-grade glioma is characterized by a high level of aneuploidy but few focal amplifications or homozygous deletions. Cancer aneuploidies are the principal source of tumor heterogeneity driving tumor growth and therapy resistance. Here, we deployed an image-based phenotypic high-content CRISPR-Cas9 screen to identify aneuploidy-associated pediatric glioma driver genes. Through integrated computational analyses combining whole-genome sequencing datasets from 106 pediatric gliomas and 81 canine gliomas, we identified a set of 460 genes present in regions of aneuploidy in both diseases. We designed a custom guideRNA library to systemically knockout the 460 gene set using an arrayed CRISPR-Cas9 knockout screen in two pediatric high-grade glioma cell lines. By deploying 72 of 384-well plates on automated confocal Opera Phenix High-Content Screening System and dyes staining cell membrane, nucleus, and apoptotic cells, we established 5 million live-cell images across three timepoints (day 7, 8, 9 post-transduction). Each gene was randomized to 32 randomized wells across four 384-well plates to gather robust morphological profiles. Through image-based nucleus and cell segmentation workflow, we characterized 50 million single cells across 27,648 wells over three time points. Using semi-supervised machine learning methods, we derived 1,050 cell morphological features to characterize knockout phenotypes, e.g., viability, growth, and morphology (size, shape, texture of nucleus and cells) across cells. The top ranked genes were then linked to oncogenes and tumor suppressors based on pathway and ontology analysis as well as functional in vitro and in silico validation using Pediatric Cancer Dependency Map. We find convergence of the most impactful molecular abnormalities - based on their knockout phenotypes - on candidate signaling pathways for the development of new drugs and repurposing of existing drugs for pediatric high-grade glioma.
EPCO-38. SINGLE-CELL MULTIMODAL ANALYSIS OF IDH-MUTANT GLIOMAS ASSOCIATES PROGENITOR CELL DEDIFFERENTIATION WITH TUMOR PROGRESSION
Authors: Wu Jingyi , Castro Luis Nicolas Gonzalez , Miller Tyler , Battaglia Sofia , D'Antonio Joshua , El Farran Chadi , Thompson Margaret , Buenrostro Jason , Suva Mario , Bernstein Bradley
Published: November 2023

Isocitrate dehydrogenase (IDH) mutant gliomas are progressive, invariably fatal brain tumors affecting young and middle-age adult patients. Previous single-cell transcriptomic characterization of IDH-mutant gliomas has uncovered heterogeneous cell states, with a hierarchy ranging from neural progenitor-like to differentiated cell states. Despite this understanding, the dynamics of these cell states as tumors undergo grade progression, and the factors that facilitate or restrict cell state transitions remain poorly understood. Here, we characterize the cell states of IDH-mutant gliomas spanning all grades using fresh patient samples and compare them with transcriptional programs of normal brain cells. We find that tumor cell states experience a marked shift as tumors undergo progression. In low-grade tumors, predominant cell states mimic slow-cycling oligodendrocyte progenitor cells (OPCs). With grade progression, cell states transition to resemble highly proliferative neural progenitor cells (NPCs). Additionally, single-cell analyses of accessible chromatin (ATAC-seq) revealed novel cellular states defined in chromatin space, which could facilitate this transition. Genetic analyses identified several molecular alterations in high-grade tumors, including loss of DNA methylation, oncogene amplification, and the deletion of genes associated with the interferon (IFN) response. Lastly, we validate the role of DNA hypomethylation in favoring immune evasion with grade progression using an IDH-mutant glioma organoid model. Overall, our findings provide evidence that tumor progression in IDH-mutant gliomas is driven by an interplay of epigenetic and genetic mechanisms that promote more mitotically active cell states as well as decreased anti-tumoral immune activation.
EPCO-44. RHABDOID TUMOR PREDISPOSITION SYNDROME DUE TO A GERMLINE SMARCB1 MUTATION IN TWO INFANT SIBLINGS
Authors: Quintero Ana , Hanson Derek , Pedro Helio , Vogel Timothy
Published: November 2023

INTRODUCTION

Rhabdoid tumors (RTs) are highly aggressive malignancies caused by a loss–of–function mutation in the SMARCB1 tumor suppressor gene on chromosome 22 that makes up the SW1/SNF chromatin remodeling complex involved in gene transcription. In rhabdoid tumor predisposition syndrome (RTPS), a biallelic germline SMARCB1 mutation markedly increases the risk of affected individuals developing early, aggressive, and rapidly progressing RTs, most commonly in the CNS, referred to as atypical teratoid rhabdoid tumors (AT/RT), and the kidneys, but oftentimes presents with synchronous lesions. In this case series, we present a family affected by RTPS with a recurrence of AT/RT in two infant siblings with the same germline SMARCB1 mutation.

CASE SERIES DESCRIPTION

An 8-month-old female was brought to the emergency department for 3 months of vomiting, developmental regression, and CN VI palsy. Brain imaging revealed a posterior fossa mass, acquired obstructive hydrocephalus, and spinal metastasis. Four years later, her 3-month-old sister was also brought in for evaluation for 2 months of vomiting, irritability, increasing head circumference, and vertical gaze palsy. Her brain imaging similarly showed a posterior fossa mass and acquired obstructive hydrocephalus, but no metastasis. Both siblings underwent subtotal tumor resections and ventriculoperitoneal shunt placement followed by chemotherapy. While on active treatment, they experienced rapid disease progression and ultimately succumbed to their illness. Genetic testing on the family identified the same in-frame deletion in the SNF5 homology domain of SMARCB1 and loss of heterozygosity of chromosome 22 in the two sisters; their mother was found to be a carrier.

CONCLUSION

This case series describes a family affected by RTPS, demonstrating the risk of familial recurrence in SMARCB1 germline mutations and emphasizing the need for genetic testing and counseling for these families should they wish to have additional children.
EPCO-47. HETEROZYGOUS CDKN2A LOSS IS ASSOCIATED WITH HIGHER RECURRENCE AND LOWER SURVIVAL IN HIGH-, BUT NOT LOW-GRADE MENINGIOMAS
Authors: Tabor Joanna , Chavez Miguel Millares , O'Brien Joseph , Morales-Valero Saul , Pappajohn Alexandros , McGuone Declan , Erson-Omay Zeynep , Yasuno Katsuhito , Gunel Murat , Moliterno Jennifer
Published: November 2023

INTRODUCTION

Homozygous loss of CDKN2A/B is known to be associated with more aggressive meningiomas and is now considered in the updated criteria for WHO grading. The relevance of heterozygous loss (hetloss) of CDKN2A/B is less clear and the potential association of hetloss CDKN2A with aggressive meningioma phenotype remains underexplored.

OBJECTIVE

We sought to understand the clinical associations of hetloss CDKN2A meningiomas.

METHODS

Clinical and whole exome sequencing (WES) data for patients who underwent resection of sporadic meningiomas were reviewed and analyzed.

RESULTS

Of the 564 meningiomas included, 16 tumors harbored a heterozygous mutation of CDKN2A; 6 of these were low-grade (WHO grade I) and 10 were high-grade (grade II or III). CDKN2A hetloss meningiomas were more likely to be high-grade (p=0.03) and to be diagnosed at older ages (p=0.04) than wild type (WT). Compared to high-grade hetloss meningiomas, low-grade ones were more likely to have elevated proliferative index (p=0.04) and were more common along the skull base (p=0.04). Low-grade meningiomas with hetloss CDKN2A compared to WT ones were more likely to be symptomatic (p=0.023); there was no difference in the tumor make-up or progression free survival (PFS) (p=0.4). High-grade hetloss CDKN2A meningiomas, however, had higher mitotic count (p=0.014), increased chromosomal instability (p=0.004), and higher recurrence rates (p< 0.001), as well as shorter PFS (p< 0.001) and decreased overall survival (OS) (p=0.002), compared to high-grade WT meningiomas. These findings remained significant amongst high-grade hetloss CDKN2A meningiomas even when controlling for underlying NF2 mutation.

CONCLUSION

Heterozygous loss of CDKN2A is associated with more aggressive histological and genomic characteristics in high-grade meningiomas. Additionally, high-grade meningiomas with hetloss CDKN2A differ from those without the mutation with higher recurrence rates and shorter PFS and lower OS, irrespective of underlying somatic NF2 mutation. These findings may have clinical implications for management.
EPCO-51. FUNCTIONAL ANALYSIS OF REGULATORY MUTATIONS IN PEDIATRIC BRAIN TUMORS
Authors: Narta Kiran , Verhey Theodore , Manoharan Varsha Thoppey , Morrissy Sorana
Published: November 2023

Pediatric brain tumors are the primary cause of cancer related mortality in children and are characterized by low mutations burden. The known somatic drivers reside in the coding regions of the genome. The role of non-coding mutations in brain tumors is important yet underexplored. In this study we investigate the impact of regulatory region mutations in pediatric brain tumors. We studied 1.3 million open chromatin regions (OCRs) genome-wide from 9 studies including developing/adult brain, and cancer. Within these OCRs we identified recurring mutations in whole genome sequences from 1003 pediatric brain tumors from CBTN and PCAWG cohorts. A total of 567 OCRs with significantly recurring mutations were found, showing enrichment in brain-specific enhancers and in repressed polycomb regions in stem cells. The mutations in these OCRs resulted in motif disruption or creation of 217 transcription factor binding sites. Differential expression analysis of mutated vs nonmutated samples identified perturbations of gene or protein expression in 67 (RNA) and 16 (protein) OCR-gene pairs. Furthermore, 17 mutated OCRs were found to correlate with alterations in gene expression programs, indicating a potential regulatory role affecting multiple downstream genes. We further performed network analysis to explore clusters of OCR associated genes that share biological networks and pathways, and identified 24 clusters. Among these, OCR mutation-associated genes in 6 clusters showed a survival impact in patients. These 6 clusters mapped to pathways including mRNA decay and degradation, longevity regulating pathway, autophagy, p53 pathway, HIF2-alpha transcription factor network, pathways in cancer among others. In summary, we report functionally important regulatory elements in the genome that impact the biological processes in pediatric brain tumors.