IDH-mutant Gliomas Research Articles

Mutant IDH inhibitors induce lineage differentiation in IDH-mutant oligodendroglioma

A subset of patients with IDH-mutant glioma respond to inhibitors of mutant IDH (IDHi), yet the molecular underpinnings of such responses are not understood. Here, we profiled by single-cell or single-nucleus RNA-sequencing three IDH-mutant oligodendrogliomas from patients who derived clinical benefit from IDHi. Importantly, the tissues were sampled on-drug, four weeks from treatment initiation. We further integrate our findings with analysis of single-cell and bulk transcriptomes from independent cohorts and experimental models. We find that IDHi treatment induces a robust differentiation toward the astrocytic lineage, accompanied by a depletion of stem-like cells and a reduction of cell proliferation. Furthermore, mutations in NOTCH1 are associated with decreased astrocytic differentiation and may limit theresponse to IDHi. Our study highlights the differentiating potential of IDHi on the cellular hierarchies that drive oligodendrogliomas and suggests a genetic modifier that may improve patient stratification.

1238 Next Generation Sequencing of Gliomas to Identify Predictors of Time to Postoperative Epilepsy

INTRODUCTION: Seizures during the course of disease for patients with diffuse gliomas is common. As genetic characterization of gliomas has improved, how a tumors mutational profile influences the timing of postoperative seizures, and if postoperative seizures relate to survival and tumor progression, is poorly understood. METHODS: A retrospective review of consecutive adults from 2017 to 2020 who underwent resection of gliomas with next generation sequencing of tumors at a single institution was performed. Cox proportional hazards regression was performed to identify factors associated with time to postoperative seizures. Seizures within 72 hours of surgery were excluded. RESULTS: 363 patients with newly diagnosed or recurrent tumor tissue genotyped via next generation sequencing were included. Median follow-up time was 37.4 months, median time to seizure after surgery was 39.2 months (95% CI 34.6 – 60.8), and IDH-mutant tumors comprised 38.3% of the cohort. Patients with IDH-mutant tumors were more likely to have non-immediate postoperative seizures (p = 0.031) and more persistent postoperative seizures (p = 0.004) compared to IDH-wildtype tumors. PDGFRA mutation was associated with shorter time to seizure in IDH-mutant gliomas (p = 0.033), with no such genetic factors in IDH-wildtype tumors. Among IDH-mutant and wildtype tumors, patients with shorter seizure freedom had significantly shorter overall and progression-free survival. CONCLUSIONS: PDGFRA mutation is associated with earlier seizures after resection of IDH-mutant diffuse gliomas. Earlier first non-immediate postoperative seizure after resection is associated with worse overall and progression-free survival.

Determining the Underlying Mechanisms of Glioma Progression and Recurrence

INTRODUCTION: Gliomas are the most common malignant brain tumour. Despite standard-of-care therapy, these tumours inevitably recur. Recurrent tumours are often treatment-resistant and associated with a poor prognosis, and there is an urgent need for novel treatments. METHODS: The epigenome-wide methylome, transcriptome, and proteome was analyzed in a total of 271 samples from 176 patients with gliomas, including 166 primary (pre-treatment) and 105 recurrent (post-treatment) tumours. Included is a unique cohort of 81 patients with paired tumour samples collected at both pre- and post- treatment. RESULTS: Epigenomics accounted for the majority of observed variance between samples and was driven by IDH status. Paired analyses identified epigenetic stability in IDH wildtype tumours at recurrence, compared to a loss of methylation at recurrence in IDH mutant tumours. Loss of methylation in IDH mutant gliomas at recurrence was driven by astrocytomas undergoing malignant transformation. Integrated, multi-platform analyses of paired samples undergoing malignant transformation identified novel genetic markers and pathways of transformation. Finally, a novel subgroup of IDH wildtype GBM with improved survival and a distinct proteomics signature was discovered. Multi-platform analyses characterized this novel subgroup as exhibiting hypermethylation, increased DNA mismatch repair and cell cycle regulation, and an altered tumour microenvironment. CONCLUSIONS: In conclusion, this study identifies targetable molecular factors that promote malignant transformation in IDH mutant gliomas and classifies a novel subgroup of IDH wildtype GBM with improved prognosis.

1242 Metabologenomic Characterization Uncovers Heterogeneity Amongst IDH Mutant Gliomas

INTRODUCTION: Mutations in isocitrate dehydrogenase (IDH) enzymes are recognised to drive the molecular footprint of diffuse gliomas through the accumulation of oncometabolite R-2-hydroxyglutarate which drives the widespread restructuring of the DNA methylome; however, beyond R-2-hydroxyglutarate, a comprehensive metabologenomic characterization of IDH-mutant gliomas has yet to be performed. METHODS: Glioma samples from a cohort of 154 patients underwent multiplatform molecular analysis, including metabolomic studies, genome-wide DNA methylation profiling and bulk RNA sequencing. A integrative analysis was performed, including hierarchical clustering and principal component analysis of identified metabolites, differentially methylated probes, copy number alteration and bulk mRNA data. Survival analysis as well as multivariable hazard ratios for clinical variables were calculated by fitting Cox Proportional Hazards Models. RESULTS: We discovered a group of IDH-mutant gliomas whose metabolic profile highly resembled IDH wildtype tumors. Notably, these IDH-mutant gliomas with dysregulated metabolism were distinguished from their IDH-mutant counterparts by significantly shorter overall survival (median OS 118.9 months vs 173.6 months, p=0.048). The IDH-mutant tumors with dysregulated metabolism harbored distinct epigenetic alterations that converged to drive proliferative and stem-like transcriptional profiles. The prognostic relevance of dysregulated metabolism complements, but was not wholly explained by canonically recognized prognostic classifications in IDH-mutant gliomas including 1p/19q codeletion, glioma CpG Island Hypermethylator (GCIMP) status and CDKN2A homozygous deletion. CONCLUSIONS: Utilizing a cross-platform analysis we have uncovered a novel subtyping of IDH-mutant gliomas with dysregulated cellular metabolism with similar survival to IDH-wildtype tumors. The metabolic profile provides unique information on glioma phenotypes, which may facilitate a more comprehensive understanding of glioma biology, and provide a window to target novel dependencies.

Demographic bias in misdiagnosis by computational pathology models.

Despite increasing numbers of regulatory approvals, deep learning-based computational pathology systems often overlook the impact of demographic factors on performance, potentially leading to biases. This concern is all the more important as computational pathology has leveraged large public datasets that underrepresent certain demographic groups. Using publicly available data from The Cancer Genome Atlas and the EBRAINS brain tumor atlas, as well as internal patient data, we show that whole-slide image classification models display marked performance disparities across different demographic groups when used to subtype breast and lung carcinomas and to predict IDH1 mutations in gliomas. For example, when using common modeling approaches, we observed performance gaps (in area under the receiver operating characteristic curve) between white and Black patients of 3.0% for breast cancer subtyping, 10.9% for lung cancer subtyping and 16.0% for IDH1 mutation prediction in gliomas. We found that richer feature representations obtained from self-supervised vision foundation models reduce performance variations between groups. These representations provide improvements upon weaker models even when those weaker models are combined with state-of-the-art bias mitigation strategies and modeling choices. Nevertheless, self-supervised vision foundation models do not fully eliminate these discrepancies, highlighting the continuing need for bias mitigation efforts in computational pathology. Finally, we demonstrate that our results extend to other demographic factors beyond patient race. Given these findings, we encourage regulatory and policy agencies to integrate demographic-stratified evaluation into their assessment guidelines.

Relaxation Along a Fictitious Field, continuous wave T1rho, adiabatic T1rho and adiabatic T2rho imaging of human gliomas at 3T: A feasibility study.

In pre-clinical models of brain gliomas, Relaxation Along a Fictitious Field in second rotating frame (TRAFF2), continues wave T1rho (T1ρcw), adiabatic T1rho (T1ρadiab), and adiabatic T2rho (T2ρadiab) relaxation time mappings have demonstrated potential to non-invasively characterize brain gliomas. Our aim was to evaluate the feasibility and potential of 4 different spin lock methods at 3T to characterize primary brain glioma. 22 patients (26-72 years) with suspected primary glioma. T1ρcw was performed using pulse peak amplitude of 500Hz and pulse train durations of 40 and 80 ms while the corresponding values for T1ρadiab, T2ρadiab, TRAFF2 were 500/500/500Hz and 48 and 96, 64 and 112, 45 and 90 ms, respectively. The parametric maps were calculated using a monoexponential model. Molecular profiles were evaluated from tissue specimens obtained during the resection. The lesion regions-of-interest were segmented from high intensity FLAIR using automatic segmentation with manual refinement. Statistical descriptors from the voxel intensity values inside each lesion and radiomic features (Pyrad MRC package) were calculated. From extracted radiomics, mRMRe R package version 2.1.0 was used to select 3 features in each modality for statistical comparisons. Of the 22 patients, 10 were found to have IDH-mutant gliomas and of those 5 patients had 1p/19q codeletion group comparisons. Following correction for effects of age and gender, at least one statistical descriptor was able to differentiate between IDH and 1p/19q codeletion status for all the parametric maps. In the radiomic analysis, corner-edge detector features with Harris-Stephens filtered signal showed significant group differences in IDH and 1p/19q codeletion groups. Spin lock imaging at 3T of human glioma was feasible and various qualitative parameters derived from the parametric maps were found to have potential to differentiate IDH and 1p19q codeletion status. Future larger prospective clinical trials are warranted to evaluate these methods further.

Impaired creative cognition after surgery for an IDH-mutated glioma: A proof-of-concept study

Assessment of high cognitive functions, such as creativity, is often overlooked in medical practice. However, it is crucial to understand the impact of brain tumors, specifically low-grade gliomas, on creative cognition, as these tumors predominantly affect brain regions associated with cognitive creativity. In this study, we investigated creative cognition using the Alternative Uses Task (AUT) and the Combination of Associates Task (CAT) in a cohort of 29 patients who underwent brain surgery for a low-grade glioma, along with 27 control participants. While the group of patients did not exhibit deficits in clinical neuropsychological assessments, our results revealed significant impairment in generating original and creative ideas compared to the control group. Furthermore, when analyzing the specific brain regions affected by the tumors, patients with lesions overlapping the left rostro-lateral prefrontal cortex, a critical region for creativity, displayed more pronounced impairments in the CAT compared to patients with lesions outside this region. These findings provide proof of concept that patients can experience impaired creative cognition following surgery for low-grade glioma, highlighting the importance of assessing higher-order cognitive functions, including creativity, in neurosurgical patients. Moreover, beyond its clinical relevance, our study contributes to advancing our understanding of the neuroscience of creativity.

Hypoxia drives shared and distinct transcriptomic changes in two invasive glioma stem cell lines

Glioblastoma (GBM) is the most common primary malignant cancer of the central nervous system. Insufficient oxygenation (hypoxia) has been linked to GBM invasion and aggression, leading to poor patient outcomes. Hypoxia induces gene expression for cellular adaptations. However, GBM is characterized by high intertumoral (molecular subtypes) and intratumoral heterogeneity (cell states), and it is not well understood to what extent hypoxia triggers patient-specific gene responses and cellular diversity in GBM. Here, we surveyed eight patient-derived GBM stem cell lines for invasion phenotypes in 3D culture, which identified two GBM lines showing increased invasiveness in response to hypoxia. RNA-seq analysis of the two patient GBM lines revealed a set of shared hypoxia response genes concerning glucose metabolism, angiogenesis, and autophagy, but also a large set of patient-specific hypoxia-induced genes featuring cell migration and anti-inflammation, highlighting intertumoral diversity of hypoxia responses in GBM. We further applied the Shared GBM Hypoxia gene signature to single cell RNA-seq datasets of glioma patients, which showed that hypoxic cells displayed a shift towards mesenchymal-like (MES) and astrocyte-like (AC) states. Interestingly, in response to hypoxia, tumor cells in IDH-mutant gliomas displayed a strong shift to the AC state, whereas tumor cells in IDH-wildtype gliomas mainly shifted to the MES state. This distinct hypoxia response of IDH-mutant gliomas may contribute to its more favorable prognosis. Our transcriptomic studies provide a basis for future approaches to better understand the diversity of hypoxic niches in gliomas.

Ultra-high b-value DWI accurately identifies isocitrate dehydrogenase genotypes and tumor subtypes of adult-type diffuse gliomas.

To distinguish isocitrate dehydrogenase (IDH) genotypes and tumor subtypes of adult-type diffuse gliomas based on the fifth edition of the World Health Organization classification of central nervous system tumors (WHO CNS5) in 2021 using standard, high, and ultra-high b-value diffusion-weighted imaging (DWI). This prospective study enrolled 70 patients with adult-type diffuse gliomas who underwent multiple b-value DWI. Apparent diffusion coefficient (ADC) values including ADCb500/b1000, ADCb500/b2000, ADCb500/b3000, ADCb500/b4000, ADCb500/b6000, ADCb500/b8000, and ADCb500/b10000 in tumor parenchyma (TP) and contralateral normal-appearing white matter (NAWM) were calculated. The ADC ratios of TP/NAWM were assessed for correlations with IDH genotypes, tumor subtypes, and Ki-67 status; diagnostic performances were compared. All ADCs were significantly higher in IDHmutant gliomas than in IDH wild-type gliomas (p < 0.01 for all); ADCb500/b8000 had the highest area under the curve (AUC) of 0.866. All ADCs were significantly lower in glioblastoma than in astrocytoma (p < 0.01 for all). ADCs other than ADCb500/b1000 were significantly lower in glioblastoma than in oligodendroglioma (p < 0.05 for all). ADCb500/b8000 and ADCb500/b10000 were significantly higher in oligodendroglioma than in astrocytoma (p = 0.034 and 0.023). The highest AUCs were 0.818 for ADCb500/b6000 when distinguishing glioblastoma from astrocytoma, 0.979 for ADCb500/b8000 and ADCb500/b10000 when distinguishing glioblastoma from oligodendroglioma, and 0.773 for ADCb500/b10000 when distinguishing astrocytoma from oligodendroglioma. Additionally, all ADCs were negatively correlated with Ki-67 status (p < 0.05 for all). Ultra-high b-value DWI can reliably separate IDH genotypes and tumor subtypes of adult-type diffuse gliomas using WHO CNS5 criteria. Ultra-high b-value diffusion-weighted imaging can accurately distinguish isocitrate dehydrogenase genotypes and tumor subtypes of adult-type diffuse gliomas, which may facilitate personalized treatment and prognostic assessment for patients with glioma. • Ultra-high b-value diffusion-weighted imaging can accurately distinguish subtle differences in water diffusion among biological tissues. • Ultra-high b-value diffusion-weighted imaging can reliably separate isocitrate dehydrogenase genotypes and tumor subtypes of adult-type diffuse gliomas. • Compared with standard b-value diffusion-weighted imaging, high and ultra-high b-value diffusion-weighted imaging demonstrate better diagnostic performances.

Abstract 7445: Association between C-reactive protein and cognitive impairment in IDH-mutant gliomas

Abstract Cognitive impairment is common in primary brain tumor (PBT) patients, as a result of the disease and secondary damage from directed and systemic therapy. Recently, the risk in patients with IDH-mutant gliomas and role of interconnectivity of the tumor with neurons and the tumor microenvironment has heightened interest in exploration of biomarkers of impairment to inform care. Here, we investigate Montreal Cognitive Assessment (MoCA) scores and peripheral blood levels of C-reactive protein (CRP) in a cross-sectional cohort of 47 adult IDH-mutant PBT patients enrolled in a natural history study (NHS, NCT02851706: PI T. Armstrong). MoCA raw scores (range 0-30) were dichotomized (≤ 25 = cognitive dysfunction). Baseline CRP was quantified in banked serum samples in duplicate using (V-Plex/Vascular Injury Panel-2, Meso Scale Discovery [MSD], Rockville, MD) in a QuickPlex SQ 120 instrument (MSD). Lab personnel were blinded to diagnosis and clinical status. To reduce skewness in CRP raw values, we used log transformation. Descriptive statistics, Pearson’s correlation, and logistic regression were conducted using IBM SPSS and SAS Statistics software. The sample was predominately male (62%), white (70%), with high-grade gliomas (III/IV) (68%) and an average age at diagnosis of 36 years (SD: 9; median: 34; range: 20-53). The mean MoCA score was 25 (SD: 5; median: 26; range: 11-30). Dichotomizing MoCA scores showed that less than half (43%) of participants exhibited moderate-severe (≤ 25) cognitive impairment. MoCA binary group was negatively correlated with levels of CRP (r=-0.42, p&amp;lt;.003). The log mean concentration of CRP was higher in participants with cognitive impairment (7.99, SD=0.47 vs 7.57, SD=0.45, p&amp;lt;.003) than those without impairment. Finally, when controlling for age and sex, CRP remained predictive of cognitive impairment (OR 8.18, 95% CI 1.70,39.23). Higher levels of CRP were associated with lower MoCA scores in a cross-sectional sample of patients with IDH-mutant gliomas, suggesting an association between the severity of inflammation and cognitive impairment in IDH-mutant glioma patients. Further analysis in large, more diverse longitudinal cohorts will be needed to validate these findings in this population and compare to those with IDH-WT tumors and develop predictive models to inform biomarker development. Citation Format: McKenzie C. Kauss, Michelle L. Wright, Dhaivat Raval, Emory Hsieh, Kaitlynn Slattery, Terri S. Armstrong, Tito R. Mendoza, Vivian A. Guedes. Association between C-reactive protein and cognitive impairment in IDH-mutant gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7445.

D-2-HG Inhibits IDH1mut Glioma Growth via FTO Inhibition and Resultant m6A Hypermethylation.

IDH1mut gliomas produce high levels of D-2-HG, an oncometabolite capable of inhibiting α-ketoglutarate-dependent dioxygenases critical to a range of cellular functions involved in gliomagenesis. IDH1mut gliomas also exhibit slower growth rates and improved treatment sensitivity compared to their IDH1wt counterparts. This study explores the mechanism driving apparent reduced growth in IDH1mut gliomas. Specifically, we investigated the relationship between IDH1mut and the RNA m6A demethylases FTO and ALKBH5, and their potential for therapeutic targeting. We investigated the role of D-2-HG and m6A in tumor proliferation/viability using glioma patient tumor samples, patient-derived gliomaspheres, and U87 cells, as well as with mouse intracranial IDH1wt gliomasphere xenografts. MeRIP-Seq RNA sequencing was used to identify m6A enriched transcripts in IDH1mut glioma. We show that IDH1mut production of D-2-HG is capable of reducing glioma cell growth via inhibition of the m6A epitranscriptomic regulator, FTO, with resultant m6A hypermethylation of a set of mRNA transcripts. Based on unbiased MeRIP-Seq epitranscriptomic profiling, we identify ATF5 as a hypermethylated, downregulated transcript that potentially contributes to increased apoptosis. We further demonstrate how targeting this pathway genetically and pharmacologically reduces the proliferative potential of malignant IDH1wt gliomas, both in vitro and in vivo. Our work provides evidence that selective inhibition of the m6A epitranscriptomic regulator FTO attenuates growth in IDH1wt glioma, recapitulating the clinically favorable growth phenotype seen in the IDH1mut subtype.

Abstract 6304: Seizure self-report and monitoring: Agreement between patient and clinician report and implications for care in patients with IDH-mutant and IDH-wild type gliomas

Abstract Primary brain tumor (PBT) patients commonly experience seizures, which can be measured and monitored by a variety of tools. Here, we explore the concordance between 2 tools and their use in reporting seizures over time among PBT patients enrolled in a natural history study (NCT02851706, PI: T. Armstrong). Patients complete the M.D. Anderson Symptom Inventory - Brain Tumor (MDASI-BT), which measures symptom severity (including seizure) within the last 24 hours from 0-10; and, as part of the same visit, pairs of clinicians and patients complete the Seizure Control Composite Index (RANO-SCCI), which includes the questions ‘Have you ever had a seizure’ (RANO-SCCIQ1) and ‘Have you had a seizure since your last clinic visit’ (RANO-SCCIQ2). Responses to each measure are reported in aggregate and by IDH status. Participants included 89 patients with gliomas who were primarily white (84%) males (62%) with a median age of 48 years (range: 27-78) and KPS ≥ 90 (85%). Based on patient reports, 65% endorsed ever having a seizure (RANO-SCCIQ1), 17% had a recent seizure (RANO-SCCIQ2), and 12% had a seizure within the last 24 hours (MDASI-BT). For the RANO-SCCIQ1 data, patients and clinicians generally agreed except for 6 pairs (7%) where clinicians indicated a seizure but patients did not. Of the 59 who reported recent seizures (RANO-SCCIQ2), two pairs (3%) disagreed, with patients indicating a recent seizure but clinicians not endorsing a seizure had occurred. Good overall agreement (86%) was observed between the RANO-SCCIQ2 and MDASI-BT for both clinician and patient responses, with 3 and 2 paired disagreements respectively, in which seizures were indicated in the last 24 hours but not recorded as a recent seizure on the (RANO-SCCIQ2). Comparing clinician report of seizures in those with IDH-mutated (n=39) to IDH-wildtype (n=15) tumors, 85% (33/39) versus 47% (7/15) reported ever having a seizure and 7 of 33 (21%) with IDH-mutant and 1 of 7 (14%) with IDH-wild type (IDH-WT) tumors respectively reported a seizure since the last visit. Disparities in recognition of seizures between patient and clinician highlights a need for patient education to increase awareness of events and recognition of ongoing risk. Although those with IDH-mutated tumors are at higher risk of having seizures, nearly half of those with IDH-WT reported ever having seizures, underscoring the need for all patients to be educated on recognizing and assessing seizure symptoms. Citation Format: Hope Miller, Ewa Grajkowska, Alvina Acquaye-Mallory, Anna Choi, Jennifer Reyes, Mark R. Gilbert, Edward K. Avila, Terri S. Armstrong, Elizabeth Vera. Seizure self-report and monitoring: Agreement between patient and clinician report and implications for care in patients with IDH-mutant and IDH-wild type gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6304.

Abstract 7448: Serum IL-10 is associated with neurologic symptoms and interference in primary brain tumor patients

Abstract Background: Primary brain tumors (PBT) are associated with neurocognitive symptoms as a direct result of the tumor or its treatment. IDH-mutant gliomas are associated with longer survival, but with higher incidence of seizures and neurocognitive symptoms.​ Correlations between cytokines and neuroinflammation have been reported in other structural brain lesions but have not been evaluated in PBT. Here, we investigate elevated peripheral blood levels of proteins (cytokine levels) in a cross-sectional cohort (n=47) of adult, IDH-mutant PBT patients enrolled in a natural history study (NCT02851706, PI: T. Armstrong) versus healthy subjects (n=32) and the correlations between cytokine levels and patient-reported outcomes (PROs). Methods: Patient-reported symptoms and activity-related interference were collected via the MD Anderson Symptom Inventory-Brain Tumor at study entry. Serum samples were stored at -80°C for batch processing and used for biomarker analysis. Ten cytokines (interleukin-1β [IL-1β], IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, interferon-γ [IFN-γ], and tumor necrosis factor-α [TNF-α]) were quantified in duplicate using an immunoassay (V-Plex/Proinflammatory, Meso Scale Discovery [MSD], Rockville, MD). Lab personnel were blinded to diagnosis and patient clinical status. Mean concentration (pg/mL) levels or ‘present or not detectable’ values were used. Descriptive statistics, Mann-Whitney tests, and Spearman correlations were conducted at p &amp;lt;0.05. Results: The patient sample was mostly male (62%), White (70%), employed (64%), had no prior recurrence (62%), high grade (3-4) tumors (70%), and an average age at diagnosis of 36 years (SD: 9; median: 34; range: 20-53). The healthy subject sample was mostly female (53%) and White (72%), with an average age of 46 years (SD: 19; median: 50; range: 19-78). Five cytokines (IFN-γ, IL-6, IL-8, IL-10, and TNF-α) were detectable in patients and healthy subjects with levels of IL-6, IL-10, and TNF-α higher in patients than healthy subjects. Serum levels of IL-10 (mean rank=50.7 vs 24.3, p&amp;lt;0.001) and TNF-α (mean rank=50.6 vs 24.2, p&amp;lt;0.001) were higher in PBT patients when compared to healthy subjects. Only IL-10, but not other cytokines, positively correlated with severity of patient-reported symptoms [pain (r=0.290, p=0.048), numbness/tingling (r=0.302, p=0.039)], and activity-related interference, including work (r=0.323, p=0.027), and walking (r=0.402, p=0.005). Conclusions: Higher IL-10 levels and detection differences in other cytokines, may indicate a reduction in immune-mediating processes and heightening inflammation in patients. Future analysis will include replication of this work in a larger cohort across PBT types to evaluate risk, explore mechanisms, and associations with treatment types. Citation Format: Kaitlynn A. Slattery, Michelle L. Wright, Dhaivat Raval, Emory Hsieh, McKenzie C. Kauss, Terri S. Armstrong, Tito R. Mendoza, Vivian A. Guedes. Serum IL-10 is associated with neurologic symptoms and interference in primary brain tumor patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7448.

DNA damage response in brain tumors: A Society for Neuro-Oncology consensus review on mechanisms and translational efforts in neuro-oncology.

DNA damage response (DDR) mechanisms are critical to maintenance of overall genomic stability, and their dysfunction can contribute to oncogenesis. Significant advances in our understanding of DDR pathways have raised the possibility of developing therapies that exploit these processes. In this expert-driven consensus review, we examine mechanisms of response to DNA damage, progress in development of DDR inhibitors in IDH-wild-type glioblastoma and IDH-mutant gliomas, and other important considerations such as biomarker development, preclinical models, combination therapies, mechanisms of resistance and clinical trial design considerations.

Abstract 2279: Evaluating the metabolic status of gioma microenvironment at single-cell resolution

Abstract Gliomas are brain tumors with low therapeutic response, markedly heterogeneous, and very proliferative. Mutations in the isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) genes are present in most lower-grade gliomas and less frequent in high-grade gliomas. The reprogramming of energy metabolism marks cancer to support rapid tumor growth and tumor survival. The remodeling of the epigenome in gliomas with and without IDH1/2 mutations is associated with changes in the energy metabolism, which has implications for the evolution of the tumor and for patient outcomes. Comprehending the metabolic reprogramming of different subtypes of gliomas is crucial to understanding tumor development and for the identification of better treatment targets. In this research, we explored the cell-to-cell metabolic variability using public single-cell RNA-seq (scRNA-seq) data of IDH wild-type (IDHwt) and IDH-mutant (IDHmut) gliomas. We analyzed 13,000+ single cells from four datasets [IDHwt (n=7,930), IDHmut codel (n=3,304), IDHmut non-codel (n=6,333), and IDHwt/K27M mutant (n=4,084)]. Data was processed using Seurat. CopyKat was used to distinguish malignant from non-malignant cells. Known marker genes were used to identify normal cell populations (macrophages, T cells, oligodendrocytes). Finally, ssGSEA was used to create a score of activity of 70 important metabolic pathways extracted from KEGG, for each individual cell. Our exploratory analysis revealed a metabolic heterogeneity among malignant cells even within the same patient. Steroid biosynthesis and valine/leucine/isoleucine biosynthesis are the top contributors to metabolic heterogeneity. Oxidative phosphorylation (OXPHOS), fatty acid metabolism (FA), and tricarboxylic acid cycle (TCA) are among the highest metabolic activities. Comparing the distinct glioma subtypes, IDHmut codel showed the lowest OXPHOS, TCA, and glycolysis/gluconeogenesis (GLYCO) activities, suggesting a potential link between low metabolic activity and better prognosis. Comparing astrocytomas IDHmut and IDHwt we observed lower TCA, GLYCO, and FA activities in mutant tumors. Overall, malignant cells showed higher metabolic activity than non-malignant cells of the same tumor. The metabolic microenvironment of IDHmut differed the most compared to the other subtypes. Immune and normal cells could also be distinguished by their metabolic features. We observed subpopulations of T cells and macrophages presenting distinct metabolic activity which may reflect distinct immune activation stages. Collectively, we covered the heterogeneity in energy metabolism of gliomas with potential prognostic value. Understanding the metabolic status of cells in the tumor microenvironment could shed light on intratumoral heterogeneity and aid in identifying therapeutic vulnerabilities. Citation Format: Felipe Pimenta Carcanholo, Livia Maria Fonseca, Renan Lima Simões, Sergio Akira Uyemura, Tathiane Maistro Malta. Evaluating the metabolic status of gioma microenvironment at single-cell resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2279.

Abstract 7564: DNA methylation profiling identifies two distinct groups of oligosarcoma, IDH-mutant with distinct genetic alterations and clinical outcomes

Abstract DNA methylation has been extensively adopted for the classification of brain tumors and is endorsed by current neuropathology guidelines. Recently, oligosarcoma, IDH-mutant has been characterized as a distinct group of IDH mutant gliomas by DNA methylation classification. However, emerging studies revealed the variety in this group. Here, we employed DNA methylation-based t-SNE analysis to characterize oligosarcomas identified by the dkfz brain tumor classifier (v12.5). Thereby, we uncovered that oligosarcomas were segregated into two distinct groups, namely, subgroup A and subgroup B, which were further validated by genetic alterations and clinical outcomes. Next-generation Sequencing revealed subtype A tumors enriched with chr 1p/19q co-deletion, chr 6q loss, CDKN2A/B homogeneous deletion, TERT promoter mutation, and NF1 mutation, while subtype B tumors showed chr7 gaining and TP53 mutation. RNA sequencing and gene set enrichment analysis (GSEA) revealed that neuronal-tumor interaction and muscular progression pathways were more enriched in subtype A tumors. In contrast, subtype B tumors showed enrichment for angiogenesis and mTOR pathways. Additionally, inter-chromosomal fusion genes were more frequently found in subtype A tumors. Clinically, patients with subgroup A oligosarcomas manifested poorer survival and distinct imaging features in magnetic resonance imaging (MRI) compared to those with subgroup B. Collectively, we provided more cases of oligosarcoma, IDH-mutant, confirming the existence of this newly identified group, and revealed the subgroups harboring different genetic alterations and suffering different prognoses, providing new evidence for the molecular pathology in diffuse glioma. Citation Format: Kenan Zhang, Lingyu Liu, Xing Liu, Tao Jiang. DNA methylation profiling identifies two distinct groups of oligosarcoma, IDH-mutant with distinct genetic alterations and clinical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7564.

Abstract 4333: Identification of glucose-6-phosphate dehydrogenase dependency in IDH1 mutant glioma cells using functional genomics

Abstract Astrocytoma and oligodendroglioma are most commonly initiated by missense mutations at the arginine 132 codon of isocitrate dehydrogenase 1 (IDH1). Biochemically the mutant IDH1 protein acquires neomorphic activity: reductive NADPH-dependent catalysis of α-ketoglutarate (αKG) to (R)-2-hydroxyglutarate [(R)-2-HG]. (R)-2-HG interferes with the function of αKG-dependent epigenetic modifiers, resulting in extensive epigenetic remodeling that impairs cellular differentiation and promotes gliomagenesis. Strategies for selectively targeting IDH1-mutant cells offer promise for improved treatment over the standard modalities of surgery, chemotherapy and radiotherapy. Whole-genome CRISPR/Cas9 knockout screens were conducted to identify gene dependencies in isogenic IDH1-mutant and wild-type (WT) U-87 MG cells. Cells were transduced with the Brunello single guide RNA (sgRNA) library, grown for 21 days, then sgRNA distributions were assessed by amplicon sequencing. Gene dependencies were identified using CRISPRcleanR and BAGELR pipelines. We discovered that glucose-6-phosphate dehydrogenase (G6PD), a pentose phosphate pathway (PPP) enzyme, was needed for viability of IDH1-mutant cells, but was dispensable for U-87 MG WT cells. The PPP is the main producer of cytosolic NADPH that is required for de novo lipogenesis, maintenance of antioxidants and production of (R)-2-HG by mutant IDH1. Previous reports demonstrated that IDH1-mutant cells increase PPP flux to support these processes. We have validated this dependency using G6PDi-1, a cell-active inhibitor of G6PD. Growth inhibition (IC50) assays demonstrated that IDH1-mutant U-87 MG cells were threefold more sensitive to G6PDi-1 with IC50 of 23 μM and enhanced cell death (increased propidium iodide uptake), compared with WT U-87 MG cells with IC50 of 67 μM. G6PD knockout was then conducted to further validate this dependency. Nucleofection of IDH1 WT U-87 MG cells with G6PD multi guide RNA-Cas9 ribonucleoproteins resulted in highly efficient knockout of G6PD at day 5 (99-100%), which was maintained at day 21 (96-98%). In contrast, efficient G6PD knockout in IDH1-mutant U-87 MG cells at day 5 (98-100%) was lost following 21 days culture (0-5%), indicating death of almost all edited cells within the culture. Finally, Kaplan-Meier analysis of IDH1-mutant patients in the TCGA lower grade glioma dataset demonstrated that higher G6PD expression correlated with worse median overall survival (7.3 versus 9.5 years; log-rank p=0.01), but was not prognostic in the IDH1 WT TCGA glioblastoma multiforme dataset. These findings demonstrate that a cell line model of IDH1-mutant glioma is highly dependent on G6PD for survival. This observation builds on the recognized importance of the PPP in the metabolic biology of IDH1-mutant malignancy by establishing G6PD as a targetable dependency in this disease. Citation Format: Kim M. Paras, Pooja Patel, Paul Choi, William R. Wilson, Tet-Woo Lee, Stephen M. Jamieson, Dean C. Singleton. Identification of glucose-6-phosphate dehydrogenase dependency in IDH1 mutant glioma cells using functional genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4333.

Region-specific DNA hydroxymethylation along the malignant progression of IDH-mutant gliomas.

The majority of low-grade isocitrate dehydrogenase-mutant (IDHmt) gliomas undergo malignant progression (MP), but their underlying mechanism remains unclear. IDHmt gliomas exhibit global DNA methylation, and our previous report suggested that MP could be partly attributed to passive demethylation caused by accelerated cell cycles. However, during MP, there is also active demethylation mediated by ten-eleven translocation, such as DNA hydroxymethylation. Hydroxymethylation is reported to potentially contribute to gene expression regulation, but its role in MP remains under investigation. Therefore, we conducted a comprehensive analysis of hydroxymethylation during MP of IDHmt astrocytoma. Five primary/malignantly progressed IDHmt astrocytoma pairs were analyzed with oxidative bisulfite and the Infinium EPIC methylation array, detecting 5-hydroxymethyl cytosine at over 850,000 locations for region-specific hydroxymethylation assessment. Notably, we observed significant sharing of hydroxymethylated genomic regions during MP across the samples. Hydroxymethylated CpGs were enriched in open sea and intergenic regions (p < 0.001), and genes undergoing hydroxymethylation were significantly associated with cancer-related signaling pathways. RNA sequencing data integration identified 91 genes with significant positive/negative hydroxymethylation-expression correlations. Functional analysis suggested that positively correlated genes are involved in cell-cycle promotion, while negatively correlated ones are associated with antineoplastic functions. Analyses of The Cancer Genome Atlas clinical data on glioma were in line with these findings. Motif-enrichment analysis suggested the potential involvement of the transcription factor KLF4 in hydroxymethylation-based gene regulation. Our findings shed light on the significance of region-specific DNA hydroxymethylation in glioma MP and suggest its potential role in cancer-related gene expression and IDHmt glioma malignancy.

Global health status and fatigue score in isocitrate dehydrogenase-mutant diffuse glioma grades 2 and 3: A longitudinal population-based study from surgery to 12-month follow-up.

At the group level, health-related quality of life (HRQoL) in patients with IDH-mutant diffuse glioma grades 2 and 3 seems to remain stable over time. However, clinical experience indicates that there are patients with unfavorable outcomes on key HRQoL subdomains. The aim of this longitudinal population-based study, following patients over a period of 12 months from surgery, was to describe individual-level data on global health status and fatigue score and explore possible predictors of deterioration. All patients undergoing surgery for presumed glioma grades 2 or 3 at the Sahlgrenska University Hospital during 2017-2022, were screened for the study. Patients were invited to complete the European Organization of Research and Treatment of Cancer core questionnaires and brain module at baseline, 3 and 12 months postoperatively. Data is reported with respect to minimal clinical important difference (MCID). We included 51 patients with IDH-mutant diffuse glioma grades 2 or 3. There was no difference in group-level data of either global health status or fatigue score from baseline to the 12-month follow-up (P-value > .05). Unfavorable individual changes (beyond MCID) in global health status and fatigue score were observed in 12 and in 17 patients, respectively (23.5% and 33.3%). A lower proportion of proton radiotherapy was found in patients with unfavorable changes in fatigue (10/15, 66.7%) compared to all other patients undergoing radiotherapy (22/23, 95.7%, P-value .03). Deterioration beyond MCID was seen in approximately one-third of patients. Changes in global health status could not be predicted, but changes in fatigue may be influenced by tumor-targeted and symptomatic treatment.

The diagnostic efficiency of integration of 2HG MRS and IVIM versus individual parameters for predicting IDH mutation status in gliomas in clinical scenarios: A retrospective study.

Currently, there remains a scarcity of established preoperative tests to accurately predict the isocitrate dehydrogenase (IDH) mutation status in clinical scenarios, with limited research has explored the potential synergistic diagnostic performance among metabolite, perfusion, and diffusion parameters. To address this issue, we aimed to develop an imaging protocol that integrated 2-hydroxyglutarate (2HG) magnetic resonance spectroscopy (MRS) and intravoxel incoherent motion (IVIM) by comprehensively assessing metabolic, cellular, and angiogenic changes caused by IDH mutations, and explored the diagnostic efficiency of this imaging protocol for predicting IDH mutation status in clinical scenarios. Patients who met the inclusion criteria were categorized into two groups: IDH-wild type (IDH-WT) group and IDH-mutant (IDH-MT) group. Subsequently, we quantified the 2HG concentration, the relative apparent diffusion coefficient (rADC), the relative true diffusion coefficient value (rD), the relative pseudo-diffusion coefficient (rD*) and the relative perfusion fraction value (rf). Intergroup differences were estimated using t-test and Mann-Whitney U test. Finally, we performed receiver operating characteristic (ROC) curve and DeLong's test to evaluate and compare the diagnostic performance of individual parameters and their combinations. 64 patients (female, 21; male, 43; age, 47.0 ± 13.7years) were enrolled. Compared with IDH-WT gliomas, IDH-MT gliomas had higher 2HG concentration, rADC and rD (P < 0.001), and lower rD* (P = 0.013). The ROC curve demonstrated that 2HG + rD + rD* exhibited the highest areas under curve (AUC) value (0.967, 95%CI 0.889-0.996) for discriminating IDH mutation status. Compared with each individual parameter, the predictive efficiency of 2HG + rADC + rD* and 2HG + rD + rD* shows a statistically significant enhancement (DeLong's test: P < 0.05). The integration of 2HG MRS and IVIM significantly improves the diagnostic efficiency for predicting IDH mutation status in clinical scenarios.