Striking up a Conversation: Exploring Advising in Graduate Programs in Health Professions Education

INTRODUCTION

Advising is happening across the medical education continuum, within non-medical graduate education programs, and is central to the advancement of said learners. This suggests that advising should play a role in graduate health progressions education (HPE) programs.

MATERIALS AND METHODS

To explore advising curricula among HPE programs, we conducted a website review of all published HPE programs on the Foundation for Advancement of International Medical Education and Research's website.

RESULTS

We recognized the lack of information published on advisory roles in graduate HPE programs. This prompted a literature review, which revealed a similar gap.

CONCLUSIONS

Advising serves to benefit a student, advisor, and program thus carrying importance and need for discussion. This article is intended to kick-start a scholarly discussion about advising within graduate HPE programs.

Abstract 895: Tumor-wide neoantigen-specific T-cells infiltrating mutant IDH1 low-grade gliomas and persisting in peripheral blood allow for personalized TCR-based immunotherapies

BACKGROUND: The low mutational burden and immunologically “cold” microenvironment of mutant IDH1 low-grade gliomas (LGG) are considerable challenges facing immunotherapy against these tumor types. However, we hypothesize that LGG-targeting T-cells may exist at low frequency and with limited regional infiltration within the tumor. Multi-region tumor sampling coupled with high-throughput T-cell receptor (TCR) profiling across the LGG landscape detected neoantigen-specific T-cells that persisted in peripheral blood. TCR-engineered T-cells transduced with these TCRs demonstrated neoantigen-specific immunogenicity.

METHODS: Maximal-anatomical sampling of at least 10 distinct tumor regions were collected at the initial resection for three WHO Grade II diffuse astrocytoma patients for exome-based prediction of clonally and subclonally expressed neoantigens, RNAseq analysis of regional immune cell composition, and TCR beta deep sequencing. We used these predictions to generate a barcoded library of patient-specific peptide-HLA multimers loaded with predicted neoepitopes. With this library, neoantigen-specific CD8+ T-cells were captured and isolated from patient peripheral blood. Single cell TCR sequencing allowed us to identify the neoantigen-reactive TCR clonotypes which were transduced subsequently into Jurkat76 cell lines for functional validation.

RESULTS: We screened patient-derived peripheral blood drawn two years after initial resection in 3 mutant IDH1 LGG patients and detected a total of 20 TCR clonotypes recognizing neoepitopes derived from truncal, tumor-wide mutations in CNTNAP1 (n=8), TP53 (n=3), and MRPL46 (n=2) as well as subclonal mutations in PRMT5 (n=1) and ZDHHC5 (n=6). Multi-sampling RNAseq analysis indicated varying degrees of interpatient and intratumoral immune infiltration as well as distally located populations of neoantigen-reactive T-cells within the tumor, suggesting widespread migration of neoantigen-specific T-cells across the glioma landscape. We proceeded with TCR functional analysis for one patient (P375) with 5 detected TCR clonotypes recognizing neoantigens derived from mutations in PRMT5, MRPL46, and TP53. Jurkat76 cells transduced with the mutant-PRMT5-specific TCR demonstrated a neoantigen-specific immune response when co-cultured with mutant-PRMT5 pulsed-antigen presenting cells expressing HLA-A*0201 (T2 cells).

CONCLUSION: Our study demonstrates the existence and persistence of neoantigen-targeting T-cells within the blood and tumor of mutant IDH1 LGG patients. We identified a TCR clonotype that successfully recognizes and induces an immune response against mutant-PRMT5. These findings suggest a feasible methodology to develop personalized T-cell-based immunotherapies for patients with mutant IDH1 LGGs.

Citation Format: Darwin W. Kwok, Michael Y. Zhang, Cliff Wang, Nicholas Stevers, Tyler Borrman, Zheng Pan, Benjamin Yuen, Songming Peng, Diana Nguyen, Michael Martin, Chibo Hong, Stephanie Hilz, Joanna Phillips, Anny Shai, Nancy Ann Oberheim Bush, Shawn Hervey-Jumper, Michael McDermott, Stefanie Mandl, Hideho Okada, Joseph Costello. Tumor-wide neoantigen-specific T-cells infiltrating mutant IDH1 low-grade gliomas and persisting in peripheral blood allow for personalized TCR-based immunotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 895.

Graduate health professions education programs as they choose to represent themselves: A website review

Introduction: In an age of increasingly face-to-face, blended, and online Health Professions Education, students have more choices of institutions at which to study their degree. For an applicant, oftentimes, the first step is to learn more about a program through its website. Websites allow programs to convey their unique voice and to share their mission and values with others such as applicants, researchers, and academics. Additionally, as the number of health professions education (HPE) programs rapidly grows, websites can share the priorities of these programs.  Methods: In this study, we conducted a website review of 158 HPE websites to explore their geographical distributions, missions, educational concentrations, and various programmatic components. Results: We compiled this information and synthesized pertinent aspects, such as program similarities and differences, or highlighted the omission of critical data. Conclusions: Given that websites are often the first point of contact for prospective applicants, curious collaborators, and potential faculty, the digital image of HPE programs matters. We believe our findings demonstrate opportunities for growth within institutions and assist the field in identifying the priorities of HPE programs. As programs begin to shape their websites with more intentionality, they can reflect their relative divergence/convergence compared to other programs as they see fit and, therefore, attract individuals to best match this identity. Periodic reviews of the breadth of programs, such as those undergone here, are necessary to capture diversifying goals, and serves to help advance the field of HPE as a whole.

Placenta Accreta Spectrum: A 2-year Retrospective Observational Study

Aims To assess the management and outcomes of Placenta Accreta Spectrum disorders and highlight the important management recommendations from international guidelines. Methods A retrospective audit of women diagnosed with Placenta Accreta Spectrum disorder from January 2018 to December 2019. Results Nine cases (0.16%) of placenta accreta from 5695 births were identified. All women received caesarean section under general anaesthesia. Caesarean hysterectomy occurred in seven cases (78%). Mean (±SD) age of women was (34.4 ± 3.9 years) and mean parity score was (3.2 ± 1.2). Mean gestational age at birth was 35.1 ± 0.8 weeks. Bilateral iliac artery balloon occlusion occurred in eight (89%) cases. Median estimated blood loss [range] was 1700 mL [1000-7000] with only 11% of patients (1/9) experiencing more than 3L of blood loss. Intraoperative red blood cell transfusion occurred in six cases (67%). Median number of units of red cell transfusion [range] was four units [0-10]. Mean hospital length of stay was (6.7 ± 1.1 days) and there were no maternal deaths. Multidisciplinary team involvement of senior anaesthetists and obstetricians was noted in all cases. Discussion Placenta accreta spectrum is increasing in incidence in obstetric practice and is associated with significant maternal morbidity and mortality. Implementing national guidelines can improve patient outcomes.

Abstract 3621: 3D spatial sampling and integrated omics reveal sources and patterning of intratumoral heterogeneity in glioblastoma

Treatment failure in glioblastoma, the most common and lethal primary brain tumor in adults, is often attributed to intratumoral heterogeneity as it fosters tumor evolution and selection of resistant clones. Sources of intratumoral heterogeneity may include genomic alterations, such as single-nucleotide and structural variants, and epigenomic alterations, such as changes in chromatin structure and transcriptional regulation. The relative extent and functional significance of these contributors to intratumoral heterogeneity in glioblastoma have yet to be elucidated. In collaboration with neurosurgeons and neuro-imaging experts, we have established a novel approach towards characterizing intratumoral heterogeneity in three-dimensional (3D) space. For patients undergoing tumor resection, we utilize 3D surgical neuronavigation to safely acquire ~10 samples representing maximal anatomical diversity. Samples are mapped by 3D spatial coordinates and integrated with patient MRI scans for 360º visualization of sample location in context of the brain. We have now conducted whole-exome sequencing (Exome-Seq), assay for transposase-accessible chromatin (ATAC-Seq), and RNA-sequencing (RNA-Seq) for 83 spatially mapped samples obtained from 8 patients with primary IDH-WT glioblastoma. Integrative data analysis provides unprecedented insight into sources of intratumoral heterogeneity in glioblastoma and their 3D spatial patterning. We find that tumor cells show aberrant transcription factor activity, activation of fetal brain programs, and variable chromatin accessibility at CTCF-binding loop anchors indicating plasticity in higher-order chromatin structure. Chromosome conformation capture analysis by Hi-C extends these findings and reveals intratumoral differences in long-range chromatin interactions due to structural variants and enhancer hijacking. Further, we use deconvolution to identify microenvironmental contributors to epigenomic intratumoral heterogeneity including neural, glial, and immune populations. We define chromatin signatures associated with microenvironmental cell types and states, revealing their 3D spatial patterning, and validate these findings by single-cell ATAC-Seq. Our work thus establishes both tumor and microenvironmental sources of intratumoral heterogeneity in glioblastoma, revealing their chromatin programs and 3D spatial patterning. As a resource for further investigation, we have developed an interactive data sharing platform that enables visualization of brain tumor intratumoral heterogeneity in 360 degrees.

Citation Format: Radhika Mathur, Qixuan Wang, Patrick Schupp, Ana Nikolic, Takafumi Yamaguchi, Stephanie Hilz, Chibo Hong, Ivan Smirnov, Marisa LaFontaine, Joanna Phillips, Susan Chang, Yan Li, Janine Lupo, Paul Boutros, Marco Gallo, Michael Oldham, Feng Yue, Joseph Costello. 3D spatial sampling and integrated omics reveal sources and patterning of intratumoral heterogeneity in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3621.

Abstract 4170: Integrative transcriptomic and proteomic analysis reveals immunogenic and spatially-conserved HLA-binding neoantigen targets derived from tumor-specific alternative splicing events

BACKGROUND: While immunotherapy is profoundly efficacious in certain cancers, its success is limited in cancers with lower mutational burden, such as gliomas. Therefore, investigating neoantigens beyond those from somatic mutations can expand the repertoire of immunotherapy targets. Recent studies detected alternative-splicing (AS) events in various cancer types that could potentially translate into tumor-specific proteins. Our study investigates AS within glioma to identify novel MHC-I-presented neoantigen targets through an integrative transcriptomic and proteomic computational pipeline, complemented by an extensive spatiotemporal analysis of the AS candidates.

METHODS: Bulk RNA-seq of high tumor purity TCGA-GBM/LGG (n=429) were analyzed through a novel systematic pipeline, and tumor-specific splicing junctions (neojunctions) were identified in silico by cross-referencing with bulk RNA-seq of GTEx normal tissue (n=9,166). Two HLA-binding prediction algorithms were subsequently incorporated to predict peptide sequences with high likelihood for HLA-presentation. Investigation of the tumor-wide clonality and temporal stability of the candidates was performed on extensive RNA-seq data from our spatially mapped intratumoral samples and longitudinally collected tumor tissue RNA-seq. Proteomic validation was conducted through mass-spec analysis of the Clinical Proteomic Tumor Analysis Consortium (CPTAC)-GBM repository (n=99).

RESULTS: Our analysis of TCGA-GBM/LGG bulk RNA-seq identified 249 putative neojunctions that translate into 222 cancer-specific peptide sequences which confer 21,489 tumor-specific n-mers (8-11 amino acids in length). Both prediction algorithms concurrently identified 271 n-mers likely to bind and be presented by HLA*A0101, HLA*A0201, HLA*A0301, HLA*A1101, or HLA*A2402. We confirmed the expression of 15 out of 58 HLA*A0201-binding candidates in RNA-seq of two HLA*A0201+ patient-derived glioma cell lines with a subset of candidates found tumor-wide. Analysis of CPTAC-GBM mass-spec data detected 23 tumor-specific peptides with 5 containing detected n-mers highly predicted to be HLA-presented.

CONCLUSION: Tumor-specific neojunctions identified in our unique integrative pipeline present novel candidate immunotherapy targets for gliomas and offer a new avenue in neoantigen discovery across cancer types.

Citation Format: Darwin Kwok, Takahide Nejo, Aidan Du, Maggie Colton, James Woo, Joseph Costello, Hideho Okada. Integrative transcriptomic and proteomic analysis reveals immunogenic and spatially-conserved HLA-binding neoantigen targets derived from tumor-specific alternative splicing events [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4170.

COVID-19, Telemedicine and Emergency Department Referrals: Patient Presentations and Follow-up Times to a Community Mental Health Team

Introduction

The COVID-19 pandemic caused changes to how healthcare services are utilised and delivered.

Objectives

We examine the impact of COVID-19 on the pattern of emergency patient presentations referred on to the community mental health team and the impact of utilising telemedicine on time to follow-up.

Methods

We retrospectively reviewed all clinical records of patients currently attending our service. We identified presentations to the emergency department (N=119) who were subsequently referred on for mental health follow-up.

Results

Patients being referred to our team from emergency departments were significantly younger during, mean age 33.1 years (SD=12.3) compared to before the pandemic, mean age 40.0 years (SD=14.5), p=0.006 and a higher proportion were new patients during, 55.8%, compared to pre-pandemic period 33.3%, p=0.015. There was also a higher proportion of patients presenting with suicidal ideation and lower proportions of affective, psychosis and suicidal/self-injurious acts during the pandemic period compared to before, p=0.006. The ratio of female to male patients on the other hand were similar during both periods, p=0.853. There appeared to be no difference in median time to follow-up pre and during the pandemic (6.0 vs 5.5 days, p=0.995). Further analysis also found no significant impact on time to follow-up upon implementing telemedicine consultations, with median days to initial follow-up of 6 days pre-pandemic, 4.5 days during pandemic + prior to telemedicine and 6.5 days during pandemic + telemedicine, p=0.602.

Conclusions

This study provides preliminary data on the impact of COVID-19 on mental health emergency presentations and utilization of telemedicine on time to follow-up by CMHTs.

Disclosure

No significant relationships.

BIOM-14. METABOLIC BIOMARKERS OF TERT-TARGETED THERAPY FOR HUMAN GLIOBLASTOMA DETECTED BY MAGNETIC RESONANCE SPECTROSCOPY

BACKGROUND

TERT promoter mutations that result in TERT expression are observed in over 80% of GBM. Moreover, the upstream transcription factor GABPB1 was recently identified as an ideal therapeutic target for tumors with TERT promoter mutations. In that context, non-invasive reliable biomarkers that can help detect TERT expression are needed. The aim of this research was to assess the value of MRS-detectable metabolic changes as biomarkers of TERT expression and TERT-targeted therapy in GBM.

METHODS

Genetically engineered GBM cells (NHARas/TERT) treated with TERT siRNA were compared to siCtrl-treated cells, and stable TERT and GABPB1 knock down GBM cells (U251, GBM1) were compared to shCtrl. 1H-MRS and 13C-MRS metabolic data was acquired from cell extracts using a Bruker 500MHz scanner. Hyperpolarized MRS studies of live cells used a HyperSense DNP polarizer and data was acquired using a Varian 500MHz scanner. Spectra were analyzed using Mnova and Matlab software. Multivariate data analysis was performed using SIMCA software.

RESULTS

Unbiased PCA analysis of 1H-MRS metabolic data showed separation of TERT or GABPB1 knock down and control cells. VIP predictive scores revealed that lactate and GSH were the top altered metabolites with a significant drop observed in both metabolites in every model following TERT silencing. Consistent with the reduction in GSH, spectrophotometric assays showed a significant drop in NADPH and NADH. 2-13C glucose flux analysis revealed that both glycolysis and PPP-related metabolites were reduced in TERT knock down cells. Hyperpolarized [1-13C]-pyruvate flux to lactate was also reduced, confirming that the glycolytic pathway was altered following TERT knock down.

CONCLUSION

1H MRS-detectable lactate and GSH, combined with hyperpolarized 13C MRS-detectable metabolic fluxes, could serve as metabolic biomarkers of TERT-targeted therapy for human GBM with TERT promoter mutations. These biomarkers could be translated to the clinical, improve the monitoring of GBM patients and advance precision medicine.

PATH-28. RE-DEFINING CLONALITY OF THE TERT PROMOTER MUTATION WITH DEEP SEQUENCING AND MAXIMAL SAMPLING OF NEWLY DIAGNOSED AND RECURRENT GBM AND OLIGODENDROGLIOMA

TERT promoter mutation (TPM), found in over 80% of IDH-wildtype glioblastomas (GBMs) and oligodendrogliomas, leads to reactivation of telomerase and consequently tumor cell immortalization, which is potentially reversible. TERT could therefore serve as an effective target in treating tumors with TPM, if TPM is present throughout the tumor. Previous studies using a single sample or minimal sampling per tumor have shown potentially conflicting results, suggesting TPM is clonal in some cases and subclonal in others. Here we use spatially mapped tumor samples representing maximal tumor sampling to address this critical issue. Sanger sequencing was performed on 311 newly diagnosed and recurrent tumor samples from 19 IDH-wildtype GBMs and 10 oligodendrogliomas. To validate Sanger sequencing and resolve potentially ambiguous samples, deep amplicon sequencing was performed on 164 samples. To determine tumor purity and TERT expression levels, whole exome sequencing (164 samples) and RNA-Seq (129 samples) data sets were analyzed computationally. Sanger and amplicon sequencing showed that TPM was present in 305 of 311 samples (98.1%). TPM was not detected in 6 samples which had tumor purity estimates too low to be accurately determined by FACETS and lacked evidence of any driver mutation. Variant allele frequencies (VAFs) of TPM showed high positive correlation with those of clonal alterations in GBMs (r(90) = .93, p < .0001) and oligodendrogliomas (r(48) = .96, p < .0001). TPM VAFs also showed high positive correlation with tumor purity in both GBMs (r(112) = .92, p < .0001) and oligodendrogliomas (r(48) = .89, p < .0001). TPM VAF showed a moderate positive correlation with TERT expression in GBMs (r(78) = .40, p < .001) and oligodendrogliomas (r(47) = .49, p < .001). Therefore, TPM is a tumor-wide, clonal mutation in both newly diagnosed and recurrent GBMs and oligodendrogliomas. TPM VAF is moderately correlated with TERT expression.

NIMG-51. DEUTERIUM METABOLIC IMAGING OF BRAIN TUMOR IMMORTALITY USING 2H-PYRUVATE

Telomere maintenance is essential for tumor immortality and sustained tumor proliferation. Most tumors, including high-grade glioblastomas and low-grade oligodendrogliomas achieve telomere maintenance via reactivation of the expression of telomerase reverse transcriptase (TERT), which is silenced in normal somatic cells. Due to this essential role, TERT is a therapeutic target and TERT inhibitors such as 6-thio-2’-deoxyguanosine are in clinical trials. Non-invasive methods of imaging TERT, therefore, have the potential to provide a readout of tumor proliferation and response to therapy. We previously showed that TERT expression is associated with elevated levels of NADH in gliomas. Since NADH is essential for the conversion of pyruvate to lactate, measuring pyruvate flux to lactate could be useful for imaging TERT expression. In this context, deuterium magnetic resonance spectroscopy (2H-MRS) recently emerged as a novel, clinically translatable method of monitoring metabolic fluxes. The goal of this study was to assess the potential of [U-2H]pyruvate for non-invasive imaging of TERT status in gliomas. Following intravenous injection of [U-2H]pyruvate, lactate production was significantly higher in mice bearing orthotopic oligodendroglioma (SF10417, BT88) or glioblastoma (GBM1, GBM6) tumors relative to tumor-free controls. 2D chemical shift imaging showed localization of lactate production to tumor vs. contralateral normal brain. Importantly, following treatment of mice bearing orthotopic GBM6 or BT88 tumors with the TERT inhibitor 6-thio-2’-deoxyguanosine, lactate production from [U-2H]pyruvate was significantly reduced at early timepoints when alterations in tumor volume could not be detected by anatomical imaging, pointing to the ability of [U-2H]pyruvate to report on pseudoprogression. Collectively, we have, for the first time, demonstrated the utility of [U-2H]pyruvate for metabolic imaging of brain tumor burden and treatment response in vivo. Importantly, since 2H-MRS can be implemented on clinical scanners, our results provide a novel, non-invasive method of integrating information regarding a fundamental tumor hallmark, i.e. TERT, into glioma patient management.

TAMI-10. CHARACTERIZATION OF CANCER-ASSOCIATED FIBROBLASTS IN GBM AND DEFINING THEIR PRO-TUMORAL EFFECTS

Cancer-associated fibroblasts (CAFs) constitute a key component of the tumor microenvironment. While pro-tumoral CAFs have been identified in some cancers, CAFs had been presumed absent in glioblastoma given the lack of brain fibroblasts. We found that serial trypsinization of primary glioblastoma cultures yields cells that morphologically resemble fibroblasts and transcriptomically resemble CAFs as shown by bulk RNA-seq and single-cell RNA-seq. Moreover, Single-cell RNA-seq from patient GBMs showed a mesenchymal lineage for CAFs. We demonstrate that Glioblastoma CAFs are chemotactically attracted to glioblastoma stem cells (GSCs) and CAFs enriched GSCs. To identify CAF/GSC interaction mediators, we created a resource of inferred crosstalk by mapping the expression of receptors to their cognate ligands/agonists. This analysis suggested PDGF-b and TGF-b as mediators of GSC recruitment and proliferation of CAFs, and osteopontin and hepatocyte growth factor (HGF) as mediators of CAF-induced GSC enrichment, hypothesis confirmed by blocking antibodies. Glioblastoma CAFs also induce hypertrophied vessels and M2 macrophage polarization, the latter through unique CAF production of the EDA fibronectin variant which binds macrophage toll-like receptor 4 (TLR4) in a targetable manner. Glioblastoma CAFs were enriched in the subventricular zone which houses the neural stem cells that produce GSCs. Depleting CAFs in GSC-derived xenografts slowed their in vivo growth. These findings are among the first to identify glioblastoma CAFs and reveal their involvement with GSCs, making them an intriguing target.

EPCO-14. MULTIFACETED TRANSCRIPTOMIC AND PROTEOMIC ANALYSES IDENTIFIED PUTATIVE ALTERNATIVE SPLICING-DERIVED CELL SURFACE ANTIGENS IN GLIOMA

BACKGROUND

To develop effective immunotherapy for gliomas, it is crucial to expand the repertoire of targetable antigens. Recent studies have suggested that alternative splicing (AS), or its deriving tumor-specific junctions (“neojunctions”), could generate cryptic amino acid sequences that can be a source of neoantigens. In this study, we investigated neojunctions based on multifaceted transcriptomic and proteomic analyses, seeking the potential cell surface antigens that may be targeted by CAR.

METHODS

For screening, we analyzed bulk RNA-sequencing data of TCGA-GBM/LGG with high tumor purity (n = 429) and GTEx normal tissues (n = 9,166). Cohorts of spatially mapped intratumoral samples and longitudinally collected tumors were used to determine clonality and stability of the candidate neojunctions. Nanopore long-read amplicon sequencing was deployed to confirm the full-length transcript sequence. Their protein-level expression was explored by analyzing the Clinical Proteomic Tumor Analysis Consortium (CPTAC)-GBM proteomics dataset.

RESULTS

In the screening analysis comparing TCGA and GTEx datasets, we identified 218 neojunctions with adequate expression, prevalence, and tumor-specificity. Of these, 12 were predicted to be cell-surface antigens. Eight of the 12, such as BCAN, DLL3, and PTPRZ1, were also observed in multiple cases of another validation dataset. In the analysis of tumors with spatially mapped intratumoral samples, 7 of the 12 were recurrently detected in no less than 50% of the samples in multiple cases. In addition, 5 of the 12 were found to be conserved in primary and recurrent pairs of tumors in multiple cases. Full-length transcript sequencing corroborated our predictions based on short reads, and also demonstrated more complex AS patterns. Finally, CPTAC-GBM proteomics analysis identified one cryptic peptide that substantiated the corresponding transcriptome-based prediction. CONCLUSION: We identified neojunctions with the potential to generate cell-surface antigens. These multifaceted transcriptomic and proteomic analyses provide the rationale to pursue the development of immunotherapy targeting neojunction-derived antigens.

EXTH-46. MRS BASED BIOMARKERS OF IDH1 MUTANT GLIOMA RESPONSE TO THE IDH INHIBITOR BAY-1436032

Gliomas are the most prevalent type of brain tumor in the central nervous system. Mutations in the cytosolic enzyme isocitrate dehydrogenase 1 (IDH1) are a common feature of primary low-grade gliomas, catalyzing the conversion of α-ketoglutarate (αKG) to the oncometabolite 2-hydroxyglutarate (2HG), and mutant IDH1 is a therapeutic target for these tumors. Several mutant IDH inhibitors are currently in clinical trials, nonetheless, complementary non-invasive early biomarkers to assess drug delivery and potential therapeutic response are still needed. The goal of this study was therefore to determine the potential of 1H and hyperpolarized 13C magnetic resonance spectroscopy (MRS)-based biomarkers as indicators of mutant IDH1 low-grade glioma response to treatment with the clinically-relevant IDH1 inhibitor BAY-1436032 in cells and animal models. Immortalized human astrocytes engineered to express mutant IDH1 were treated with 500nM (IC50 value) of BAY-1436032 and BT257 tumors implanted in rats were treated with 150mg/kg of BAY-1436032. To assess steady-state metabolite levels, 1H MRS spectra were acquired on a 500 MHz MRS cancer for cells and a 3 T scanner for animal studies. To assess metabolic fluxes, we used hyperpolarized 13C MRS and probed the fate of hyperpolarized [1-13C]αKG. 1H MRS showed a significant decrease in 2HG as well as a significant increase in glutamate (Glu) and phosphocholine (PCh) following BAY-1436032 treatment in both cell and animal models compared to controls. Furthermore, hyperpolarized 13C MRS showed that hyperpolarized 2HG production from hyperpolarized [1-13C]αKG was decreased and hyperpolarized glutamate production from hyperpolarized [1-13C]αKG was increased in the BAY-1436032 treated groups compared to controls. These findings are consistent with our previous study, which investigated the MRS-detectable consequences of two other mutant IDH inhibitors: AG120 and AG881. Collectively, our work identifies translatable MRS-based metabolic biomarkers of mutant IDH1 inhibition.

CBIO-26. A NEW MODEL OF THE GABP-TERT REGULATORY AXIS IN MAINTAINING IMMORTALITY OF TERT PROMOTER MUTANT TUMOR CELLS

Tumor cell immortality is a fundamental hallmark of human cancers. Normally silenced during somatic cell differentiation, 90% of human tumors reactivate Telomerase Reverse Transcriptase (TERT) expression to achieve cellular immortality. TERT, the catalytic subunit of telomerase, complexes with the RNA template molecule TERC to maintain telomeres. Mutations in the TERT promoter (TERTp) are the most common non-coding mutation across all cancer types and the most frequent mutation within many cancers, such as IDH wildtype glioblastoma (GBM), Melanoma, and Bladder Cancer. TERTp mutations generate de novo E26 Transformation Specific (ETS) binding motifs that are spaced full helical turns from TERTp native ETS sites. Together the de novo and native ETS motifs specifically recruit the GABP tetrameric complex but not the GABP dimer. CRISPR-cas9 mediated insertion/deletion mutagenesis of the unique exon of GABP tetramer forming subunit, GABPB1L (B1L), reduces TERT transcriptional activity in a TERT promoter-mutation dependent manner. Here we show that GABPB1S (B1S), the GABP dimer restricted alternative isoform of GABPB1, is consistently and significantly increased following B1L reduction, a process we have determined to be driven by a conserved homeostatic mechanism whereby the GABP tetramer suppresses expression of one of its own components, GABPB1. In contrast to the native setting, in the absence of B1L the elevated B1S expression leads to dimer binding to the mutant TERTp and maintenance of TERT expression. Indeed, co-targeting B1L and B1S together, but not B1L alone, via CRISPR-cas9 knockout resulted in a near complete elimination of GABP recruitment to the TERTp and TERT expression, and lead to tumor cell death and eventual senescence in a telomere length dependent manner. Together, this data suggests a new model of the TERT-GABP axis involving the tetramer and dimer and highlights a new and potentially more potent therapeutic strategy to eliminate TERT expression and reverse tumor cell immortality.

BIOM-10. PRECLINICAL PLATFORM FOR THE IDENTIFICATION OF DEUTERIUM MAGNETIC RESONANCE SPECTROSCOPY-BASED BIOMARKERS OF BRAIN TUMOR METABOLISM

Metabolic reprogramming is a fundamental hallmark of cancer, which can be exploited for non-invasive tumor imaging. Deuterium magnetic resonance spectroscopy (2H-MRS) recently emerged as a novel, translational method of interrogating flux from 2H-labeled substrates to metabolic products. However, to date, preclinical studies have been performed in vivo, an endeavor which suffers from low-throughput and potential wastage of animal life, especially when considering studies of treatment response. Developing in vitro assays for monitoring metabolism of 2H-labeled substrates will enhance throughput, lead to the rapid evaluation of new 2H-based probes and enable identification of treatment response biomarkers, thereby allowing the best 2H-based probes to be translated for further in vivo assessment. The goal of this study was to develop a preclinical cell-based platform for quantifying metabolism of 2H-labeled probes in brain tumor models. Since the Warburg effect, which is characterized by elevated glycolytic production of lactate, is a metabolic phenotype of cancer, including brain tumors, we examined metabolism of 2H-glucose or 2H-pyruvate in patient-derived glioblastoma (GBM6) and oligodendroglioma (BT88) cells and compared to normal human astrocytes (NHACONTROL). Following incubation in media containing [6,6’-2H]glucose or [U-2H]pyruvate, 2H-MR spectra obtained from live cell suspensions showed elevated 2H-lactate production in GBM6 and BT88 cells relative to NHACONTROL. Importantly, 2H-lactate production from [6,6’-2H]glucose or from [U-2H]pyruvate was reduced in GBM6 or BT88 cells subjected to irradiation and temozolomide, which is standard of care for glioma patients, pointing to the utility of this method for detecting response to therapy. Collectively, we have, for the first time, demonstrated the ability to quantify metabolism of 2H-MRS probes in live cell suspensions and validated the utility of our assay for differentiating tumor from normal cells and assessing response to therapy. Our studies will expedite the identification of novel 2H-MRS probes for imaging brain tumors and potentially other types of cancer.

IMMU-33. NEOANTIGEN-SPECIFIC T CELLS CAN INFILTRATE IDH-MUTANT LOWER GRADE GLIOMAS AND PERSIST IN THE PERIPHERAL BLOOD

The prospect of using immunotherapy for IDH-mutant LGGs has been daunting given the immune-poor microenvironment and low mutational burden. We hypothesized that LGG-targeting T cells might still be present at low frequency and with limited regional infiltration into the tumor. To improve sensitivity, we combined high-density multi-region tumor sampling with high-throughput neoantigen-T cell screening for a patient with WHO Grade II diffuse astrocytoma who eventually progressed, at second recurrence, to anaplastic astrocytoma. We performed maximal-anatomic sampling from 10 distinct regions of the tumor at the initial resection, as well as single sampling at first recurrence, for exome-based prediction of clonal and subclonal expressed neoantigens, RNAseq-based estimation of regional immune cell composition, and T cell receptor (TCR) beta deep sequencing. Based on our predictions, we then generated a barcoded library of patient-specific peptide-HLA multimers loaded with predicted neopeptides. Using this library, neoantigen-specific CD8 T cells were captured and isolated from patient peripheral blood and subjected to single cell TCR sequencing. We screened patient-derived peripheral blood drawn two years after initial resection and identified five T cell clones recognizing three LGG neoepitopes. Two neoepitopes were derived from truncal, tumor-wide mutations, including a truncating splice-site mutation in TP53 and a missense mutation in MRPL46. Each of these neoepitopes were recognized by two distinct TCRs, consistent with TCR convergence. A third neoepitope was derived from a subclonal MRPL46 mutation. Using the TCR beta sequence as a molecular barcode, TCRs specific to the 2 clonal neoepitopes, but not the subclonal neoepitope, were detectable in the glioma and blood at initial resection, as well as in the recurrent glioma. In summary, we demonstrate the existence and persistence of neoantigen-targeting T cells within the blood and tumor of an IDH-mutant LGG patient. These findings suggest a feasible methodology to develop personalized T cell-based immunotherapies for IDH-mutant LGGs.

ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma

Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and selection of therapy-resistant clones. While genomic alterations are known contributors to ITH, emerging studies highlight functional roles for epigenomic ITH which integrates differentiation status, stochastic events, and microenvironmental inputs. Here, we have established a novel platform for integrative characterization of genomic and epigenomic ITH of glioblastoma in three-dimensional (3-D) space. In collaboration with neurosurgeons and biomedical imaging experts, we utilize 3-D surgical neuro-navigation to safely acquire ~10 tumor samples per patient representing maximal anatomical diversity. We conduct whole-exome sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-Seq) on each sample. The spatial location of each sample is mapped by its 3-D coordinates, allowing 360-degree visualization of genomic and epigenomic ITH for each patient. We demonstrate this approach on 8 patients with primary IDH-WT glioblastoma (83 spatially mapped samples), providing unprecedented insight into their spatial organization at the genomic and epigenomic levels. We link genetically defined tumor subclones to patterns of open chromatin and gene regulation, revealing underlying transcription factor binding at active promoters and enhancers. We also identify ITH in whole-genome doubling and focal oncogene amplification events in multiple patients, which we then link with epigenomic ITH. Further, to study microenvironmental inputs and their contribution to epigenomic ITH, we conduct deconvolution of RNA sequencing and ATAC-Seq data by analyzing feature co-variation. We resolve the 3-D spatial organization of immune, neural, and other nontumor cell types present in glioblastoma, characterizing their functional states and interactions with tumor cells. This work provides the most comprehensive spatial characterization of genomic and epigenomic ITH to date in glioblastoma. As a resource for further investigation, we have developed an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

Analysis of single comments left for bioRxiv preprints till September 2019

INTRODUCTION

While early commenting on studies is seen as one of the advantages of preprints, the type of such comments, and the people who post them, have not been systematically explored.

MATERIALS AND METHODS

We analysed comments posted between 21 May 2015 and 9 September 2019 for 1983 bioRxiv preprints that received only one comment on the bioRxiv website. The comment types were classified by three coders independently, with all differences resolved by consensus.

RESULTS

Our analysis showed that 69% of comments were posted by non-authors (N = 1366), and 31% by the preprints' authors themselves (N = 617). Twelve percent of non-author comments (N = 168) were full review reports traditionally found during journal review, while the rest most commonly contained praises (N = 577, 42%), suggestions (N = 399, 29%), or criticisms (N = 226, 17%). Authors' comments most commonly contained publication status updates (N = 354, 57%), additional study information (N = 158, 26%), or solicited feedback for the preprints (N = 65, 11%).

CONCLUSIONS

Our results indicate that comments posted for bioRxiv preprints may have potential benefits for both the public and the scholarly community. Further research is needed to measure the direct impact of these comments on comments made by journal peer reviewers, subsequent preprint versions or journal publications.

A Light Tolerant Neural Recording IC for Near-Infrared-Powered Free Floating Motes

A key challenge for near-infrared (NIR) powered neural recording ICs is to maintain robust operation in the presence of parasitic short circuit current from junction diodes when exposed to light. This is especially so when intentional currents are kept small to reduce power consumption. We present a neural recording IC that is tolerant up to 300 μW/mm² light exposure (above tissue limit) and consumes 0.57 μW at 38°C, making it lowest power among standalone motes while incorporating on-chip feature extraction and individual gain control.

Bridging the"Last Millimeter" Gap of Brain-Machine Interfaces via Near-Infrared Wireless Power Transfer and Data Communications

Arrays of floating neural sensors with high channel count that cover an area of square centimeters and larger would be transformative for neural engineering and brain-machine interfaces. Meeting the power and wireless data communications requirements within the size constraints for each neural sensor has been elusive due to the need to incorporate sensing, computing, communications, and power functionality in a package of approximately 100 micrometers on a side. In this work, we demonstrate a near infrared optical power and data communication link for a neural recording system that satisfies size requirements to achieve dense arrays and power requirements to prevent tissue heating. The optical link is demonstrated using an integrated optoelectronic device consisting of a tandem photovoltaic cell and microscale light emitting diode. End-to-end functionality of a wireless neural link within system constraints is demonstrated using a pre-recorded neural signal between a self-powered CMOS integrated circuit and single photon avalanche photodiode.

BIMG-02. IMAGING IMMORTALITY: TERT EXPRESSION ALTERS GLUCOSE METABOLISM IN LOW-GRADE GLIOMAS IN A MANNER THAT CAN BE LEVERAGED FOR NONINVASIVE METABOLIC IMAGING

Telomerase reverse transcriptase (TERT) is essential for tumor immortality and uncontrolled proliferation, including in low-grade oligodendrogliomas (LGOGs). Since it is silenced in somatic cells, TERT is also a therapeutic target. Non-invasive imaging of TERT can differentiate tumor from normal brain or lesions such as gliosis and allow assessment of response to therapy. The goal of this study was to identify magnetic resonance spectroscopy (MRS)-detectable metabolic alterations associated with TERT that can be leveraged for noninvasive imaging in LGOGs. We examined patient-derived BT54 neurospheres in which TERT expression was silenced by RNA interference. ¹H-MRS showed that steady-state levels of NAD(P)/H, glutathione, aspartate and AXP were elevated in BT54_TERT+ neurospheres relative to BT54_TERT-. Glucose flux through the pentose phosphate pathway (PPP) is essential for generating NADPH, which maintains glutathione homeostasis. ¹³C-MRS confirmed that [2-¹³C]-glucose flux through the PPP was elevated in BT54_TERT+ neurospheres relative to BT54_TERT-, an effect associated with higher activity of the PPP enzyme glucose-6-phosphate dehydrogenase (G6PDH). Hyperpolarized ¹³C-MRS is a method of increasing the signal to noise ratio of ¹³C-MRS such that it can monitor metabolic fluxes noninvasively in cells, animals and patients. Consistent with elevated PPP flux and G6PDH activity, hyperpolarized [U-¹³C]-glucose metabolism via the PPP to 6-phosphogluconate (6-PG) was elevated in BT54_TERT+ neurospheres relative to BT54_TERT-. Importantly, examination of an additional patient-derived LGOG model, the SF10417 model which readily forms orthotopic tumor xenografts in rats, showed that 6-PG production from hyperpolarized [U-¹³C]-glucose demarcated tumor from normal brain. Furthermore, LGOG patient biopsies had elevated NAD(P)/H, glutathione, aspartate, AXP and G6PDH activity relative to gliosis biopsies, confirming the clinical validity of our observations. Collectively, we have identified a metabolic signature of TERT expression that can be leveraged via hyperpolarized [U-¹³C]-glucose to improve diagnosis and treatment response monitoring for LGOG patients.

BIMG-08. DEUTERIUM MAGNETIC RESONANCE SPECTROSCOPY USING 2H-PYRUVATE ALLOWS NON-INVASIVE IN VIVO IMAGING OF TERT EXPRESSION IN BRAIN TUMORS

Telomere shortening constitutes a natural barrier to uncontrolled proliferation and all tumors must find a mechanism of maintaining telomere length. Most human tumors, including high-grade primary glioblastomas (GBMs) and low-grade oligodendrogliomas (LGOGs) achieve telomere maintenance via reactivation of the expression of telomerase reverse transcriptase (TERT), which is silenced in normal somatic cells. TERT expression is, therefore, a driver of tumor proliferation and, due to this essential role, TERT is also a therapeutic target. However, non-invasive methods of imaging TERT are lacking. The goal of this study was to identify magnetic resonance spectroscopy (MRS)-detectable metabolic biomarkers of TERT expression that will enable non-invasive visualization of tumor burden in LGOGs and GBMs. First, we silenced TERT expression by RNA interference in patient-derived LGOG (SF10417, BT88) and GBM (GS2) models. Our results linked TERT silencing to significant reductions in steady-state levels of NADH in all models. NADH is essential for the conversion of pyruvate to lactate, suggesting that measuring pyruvate flux to lactate could be useful for imaging TERT status. Recently, deuterium (²H)-MRS has emerged as a novel, clinically translatable method of monitoring metabolic fluxes in vivo. However, to date, studies have solely examined ²H-glucose and the use of [U-²H]pyruvate for non-invasive ²H-MRS has not been tested. Following intravenous injection of a bolus of [U-²H]pyruvate, lactate production was higher in mice bearing orthotopic LGOG (BT88 and SF10417) and GBM (GS2) tumor xenografts relative to tumor-free mice, suggesting that [U-²H]pyruvate has the potential to monitor TERT expression in vivo. In summary, our study, for the first time, shows the feasibility and utility of [U-²H]pyruvate for in vivo imaging. Importantly, since ²H-MRS can be implemented on clinical scanners, our results provide a novel, non-invasive method of integrating information regarding a fundamental cancer hallmark, i.e. TERT, into glioma patient management.

BIOM-38. PI3K/AKT/mTOR SIGNALING PATHWAY ACTIVITY IN IDH-MUTANT DIFFUSE GLIOMA

PI3K/AKT/mTOR signaling pathway activation is a common mechanism of tumor progression in diffuse lower grade glioma. Robust and accurate biomarkers are needed to stratify patients for therapies targeting this pathway. To investigate the potential of phosphoprotein quantification to provide a direct and functional pathway readout, we analyzed 90 tumors from 83 patients with IDH-mutant diffuse glioma. The cohort comprised 50 IDH-mutant astrocytomas, 40 IDH-mutant and 1p/19q-codeleted oligodendrogliomas, 7 of whom had paired samples from initial diagnosis and recurrence. We developed and validated a pipeline using multiplex immunofluorescence to quantify tumor cell-specific phospho-protein expression of 3 pathway nodes, ribosomal protein S6 (RPS6), PRAS40, and 4E-BP1. In oligodendroglioma the fraction of tumor cells expressing each of the three phosphorylated proteins increased with tumor grade (p< 0.05). Comparing tumors at initial diagnosis (n=48) and at recurrence (n=42), p-RPS6 and p-PRAS40 increased in tumor cells (p< 0.05) and there was an overall increase in intertumoral heterogeneity of signaling activity at recurrence (p< 0.04). Analysis of paired samples demonstrated increased signaling pathway activity in a subset at recurrence. Robust signaling activity, defined as a phospho-positive tumor cell fraction ≥ median for all three phosphoproteins, was identified in 71.4% of grade 3 IDH-mutant astrocytoma(5/7) and 45.4% of grade 3 IDH-mutant, 1p/19q-codeleted oligodendroglioma(5/11). In a subset of cases analyzed by targeted NGS, robust signaling pathway activity was identified in 38%(11/29) at the protein level while genetic alterations predicted to activate the pathway were present in only 17.2% (5/29). Our results demonstrate robust PI3K/AKT/mTOR signaling activity in a significant fraction of IDH-mutant diffuse glioma, an association with increasing tumor grade in oligodendroglioma, and an increase at recurrence in both oligodendroglioma and astrocytoma. Overall, our data suggest that quantitative evaluation of phosphoproteins may be a sensitive method to detect PI3K/AKT/mTOR pathway activity and may be useful for patient stratification.

TAMI-08. A TALE OF TWO TELOMERE MAINTENANCE MECHANISMS: TERT EXPRESSION AND THE ALT PATHWAY INDUCE UNIQUE MRS-DETECTABLE METABOLIC REPROGRAMMING IN LOW-GRADE GLIOMAS

Telomeres are nucleoprotein structures at chromosomal ends that shorten with cell division and constitute a natural barrier to proliferation. In order to proliferate indefinitely, all tumors require a telomere maintenance mechanism (TMM). Telomerase reverse transcriptase (TERT) expression is the TMM in most tumors, including low-grade oligodendrogliomas (LGOGs). In contrast, low-grade astrocytomas (LGAs) use the alternative lengthening of telomeres (ALT) pathway as their TMM. As molecular hallmarks of tumor proliferation, TMMs are attractive tumor biomarkers and therapeutic targets. Non-invasive imaging of TMM status will, therefore, allow assessment of tumor proliferation and treatment response. However, translational methods of imaging TMM status are lacking. Here, we show that TERT expression and the ALT pathway are associated with unique magnetic resonance spectroscopy (MRS)-detectable metabolic reprogramming in LGOGs and LGAs respectively. In genetically-engineered and patient-derived LGOG models, TERT expression is linked to elevated 1H-MRS-detectable NAD(P)/H, glutathione, aspartate and AXP. In contrast, the ALT pathway in LGAs is associated with higher α-ketoglutarate, glutamate, alanine and AXP. Importantly, elevated flux of hyperpolarized [1-13C]-alanine to pyruvate, which depends on α-ketoglutarate, is a non-invasive in vivo imaging biomarker of the ALT pathway in LGAs while elevated flux of hyperpolarized [1-13C]-alanine to lactate, which depends on NADH, is an imaging biomarker of TERT expression in LGOGs. Mechanistically, the ALT pathway in LGAs is linked to higher glutaminase (GLS), a key enzyme for α-ketoglutarate biosynthesis while TERT expression in LGOGs is associated with elevated nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme for NADH biosynthesis. Notably, TERT expression and the ALT pathway are linked to MRS-detectable metabolic reprogramming in LGOG and LGA patient biopsies, emphasizing the clinical validity of our observations. Collectively, we have identified unique metabolic signatures of TMM status that integrate critical oncogenic information with noninvasive imaging modalities that can improve diagnosis and treatment response monitoring for LGOG and LGA patients.

PATH-12. TEMOZOLOMIDE-INDUCED HYPERMUTATION IS ASSOCIATED WITH HIGH-GRADE TRANSFORMATION, DISTANT RECURRENCE AND REDUCED SURVIVAL IN INITIALLY LOW GRADE IDH-MUTANT GLIOMAS

Temozolomide, a commonly used alkylating agent, can induce somatic hypermutation in gliomas. The prevalence and implications of this phenomenon are not well characterized. Using targeted and whole exome sequencing from a cohort of 82 patients with recurrent IDH-mut LGG, we evaluated the clinical implications of hypermutation. Hypermutation was identified at transformation in 57% of recurrent gliomas exposed to TMZ and occurred for both IDH-mutant astrocytomas (52%) and oligodendrogliomas (64%). Among astrocytomas, receipt of radiotherapy prior to transformation was associated with decreased risk of hypermutation (11% vs 70%, p=0.0052), but this trend was not observed for oligodendrogliomas (78% vs 54%, p=NS). Among hypermutated tumors, 94% were transformed to higher WHO grades. Hypermutation was associated with transformation to higher WHO grade (OR 12.0 95% CI 2.5-115.5, p=0.002) and shorter survival after transformation (HR 2.1, 95% CI 1.1-4.0, p=0.018) compared with non-hypermutated transformed tumors. It remained prognostic (controlling for grade, molecular subtype, age, and prior radiotherapy. Patients with transformation to glioblastoma had poor survival regardless of hypermutation (p=0.78). Multivariate models were validated using an external, independent dataset (Harrel’s C=0.72). Strikingly, hypermutated tumors were also associated with development of discontiguous disease after transformation (3-year CI 41% vs 8% p=0.005), including ependymal and leptomeningeal distributions and four cases of spinal dissemination that were not observed in non-hypermutated tumors. These data have significant implications for management of IDH-mut LGG at recurrence.

EPCO-36. GENOMIC INSTABILITY AND TRANSCRIPTOMIC SIGNATURES UNDERLYING EPIGENETIC MENINGIOMA SUBGROUPS REVEALS MECHANISMS OF IMMUNE INFILTRATION AND THERAPEUTIC VULNERABILITIES

BACKGROUND

Meningioma treatments are limited due to incomplete understanding of meningioma biology. To address this, we performed multiplatform molecular profiling on 565 meningiomas with comprehensive clinical data to define genomic drivers and identify therapeutic vulnerabilities.

METHODS

DNA methylation profiling was performed on meningiomas from UCSF (n=200, discovery) and Hong Kong University (n=365, validation). Median follow-up was 5.6 years, and there were 388/142/35 WHO grade I/II/III meningiomas. Copy number variants (CNVs) were calculated for all meningiomas, and RNA sequencing was performed on UCSF meningiomas. Cell type deconvolution, metagenomics, CRISPR, and pharmacology were used for mechanistic and functional validation.

RESULTS

Unsupervised hierarchical clustering of differentially methylated DNA probes revealed that meningiomas were comprised of 3 epigenetic subgroups associated with good, intermediate, and poor outcomes, with representation from all WHO grades in each subgroup. Meningiomas from the subgroup with the best outcomes (52% WHO grade I) were distinguished by recurrent gain of Chr5. Meningiomas from the subgroup with intermediate outcomes (31% WHO grade II) were distinguished by genomic stability, enrichment of innate immune genes, and immune infiltration in the setting of endogenous retroviral gene re-expression, a mechanism of immune recruitment. The most aggressive subgroup of meningiomas (57% WHO grade III) was distinguished by genomic instability, including recurrent loss of Chr22q harboring NF2, and decreased immune infiltration. Consistently, NF2 suppression in primary meningioma cells derived from immunogenic meningiomas decreased expression of innate immune genes critical for immune recruitment, suggesting a novel immunostimulatory function of NF2. The most aggressive subgroup of meningiomas were further distinguished by activation of the mitogenic FOXM1 transcriptional program, and recurrent loss of Chr9p harboring CDKN2A/B, which rendered primary meningioma cells from this subgroup susceptible to CDK4/6 inhibitors.

CONCLUSIONS

Meningiomas are comprised of 3 epigenetic subgroups defined by genetic mechanisms driving immune infiltration in the tumor microenvironment and meningioma cell proliferation.

BIOM-19. METABOLIC ALTERATION INDUCED BY SELECTIVE KNOCK DOWN OF GABPB1L IN U251 CELLS

BACKGROUND

TERT promoter mutations that result in TERT expression are observed in over 80% of GBM and upstream inhibition of TERT expression by targeting GABPB1L is currently under investigation. In that context, non-invasive reliable biomarkers that can help detect TERT expression are needed. The aim of this research was to assess the value of magnetic resonance spectroscopy (MRS)-detectable metabolic changes as biomarkers of TERT expression in GBM.

METHODS

GABPB1L knock down clones (GABPB1LKD) were established by introducing Crispr Cas9 plasmid vector targeting GABPB1L into U251 cells. Two representative clones with different knock down efficiency were chosen and compared to control cells. Tumor forming capacity was evaluated by colony formation assay and magnetic resonance imaging of orthotopically implanted tumors in mice. Cells were extracted using the dual phase extraction method and 1H-MRS data of cell extracts acquired using a Bruker 500 scanner. The data was analyzed using Mnova software. Multivariate analysis was performed using the SIMCA software.

RESULTS

TERT expression was significantly reduced in GABPB1LKD compared to control cells depending on the GABPB1L knock down efficiency. Colony forming capacity was impaired in GABPB1LKD compared to control cells. In vivo MRI data showed significantly smaller tumor volumes in GABPB1LKD compared to control. Unbiased PCA analysis of 1H-MRS data showed separation of GABPB1LKD and control extracts and VIP scores derived from the OPLS-DA analysis, demonstrated that the common metabolites leading to separation of GABPB1LKD and control cells were aspartate, glutathione, glycerophosphocholine, glutamine, NAD(P)+, AXP. This data was confirmed by univariate analysis that revealed that aspartate, glutathione, glutamine, NAD(P)+, AXP level was significantly reduced in GABPB1LKD.

CONCLUSIONS

GABPB1L knock down cells that show reduced TERT expression demonstrate MRS-detectable metabolic changes. These could be translated into clinical applications, improve the monitoring of GBM patients and advance precision medicine.

EPCO-31. EPIGENOMIC INTRATUMORAL HETEROGENEITY OF GLIOBLASTOMA IN THREE-DIMENSIONAL SPACE

Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and generation of therapy-resistant clones. While ITH in glioblastoma has been well-characterized at the genomic and transcriptomic levels, the extent of ITH at the epigenomic level and its biological and clinical significance are not well understood. In collaboration with neurosurgeons, neuropathologists, and biomedical imaging experts, we have established a novel topographical approach towards characterizing epigenomic ITH in three-dimensional (3-D) space. We utilize pre-operative MRI scans to define tumor volume and then utilize 3-D surgical neuro-navigation to intra-operatively acquire 10+ samples representing maximal anatomical diversity. The precise spatial location of each sample is mapped by 3-D coordinates, enabling tumors to be visualized in 360-degrees and providing unprecedented insight into their spatial organization and patterning. For each sample, we conduct assay for transposase-accessible chromatin using sequencing (ATAC-Seq), which provides information on the genomic locations of open chromatin, DNA-binding proteins, and individual nucleosomes at nucleotide resolution. We additionally conduct whole-exome sequencing and RNA sequencing for each spatially mapped sample. Integrative analysis of these datasets reveals distinct patterns of chromatin accessibility within glioblastoma tumors, as well as their associations with genetically defined clonal expansions. Our analysis further reveals how differences in chromatin accessibility within tumors reflect underlying transcription factor activity at gene regulatory elements, including both promoters and enhancers, and drive expression of particular gene expression sets, including neuronal and immune programs. Collectively, this work provides the most comprehensive characterization of epigenomic ITH to date, establishing its importance for driving tumor evolution and therapy resistance in glioblastoma. As a resource for further investigation, we have provided our datasets on an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

Temozolomide-induced hypermutation is associated with high-grade transformation, distant recurrence, and reduced survival after transformation in initially low-grade IDH-mutant diffuse gliomas

2506

Background: Temozolomide, a commonly used alkylating agent to treat gliomas, can induce somatic hypermutation. The prevalence and clinical implications of this phenomenon are not well characterized. Methods: We used targeted and whole exome sequencing from a cohort of 82 patients with recurrent IDH-mutant low grade gliomas undergoing re-operation to evaluate the prevalence as well as the clinical implications of hypermutation. Results: Hypermutation was identified at transformation in 57% of recurrent gliomas exposed to Temozolomide, 94% of which were transformed to higher WHO grades. All patients who developed hypermutation were exposed to Temozolomide. Hypermutation was associated with transformation to higher WHO grade (OR 12.0 95% CI 2.5 – 115.5, p = 0.002) and shorter survival after transformation (HR 2.1, 95% CI 1.1-4.0, p = 0.018) compared with non-hypermutated transformed tumors, controlling for grade, molecular subtype, age, and prior radiotherapy. Patients with transformation to glioblastoma had poor survival regardless of hypermutation (p = 0.78). Hypermutated tumors were associated with development of discontiguous disease at a significantly higher frequency (p = 0.003), including four cases with spinal dissemination. Conclusions: TMZ-induced hypermutation is associated with high grade transformation, unique patterns of dissemination and shortened survival after transformation. Next generation sequencing should be considered in this patient population. These data have important implications for the management of newly diagnosed and recurrent IDH-mutant low grade gliomas.

IMMU-11. SPATIOTEMPORAL IMMUNOGENOMIC ANALYSIS OF THE T-CELL REPERTOIRE IN IDH-MUTANT LOWER GRADE GLIOMAS

The design and evaluation of immunotherapies in IDH-mutant lower grade gliomas (LGG) is hindered by a poor understanding of the LGG T-cell repertoire. We present data on the temporal evolution, intratumoral spatial distribution, and prognostic value of the T-cell repertoire in IDH-mutant LGGs. We performed immunogenomic profiling using T-cell receptor beta-chain sequencing of 163 glioma and peripheral blood samples from 33 immunotherapy-naive glioma patients (22 astrocytomas, 11 oligodendrogliomas). T-cell repertoire evolution was analyzed in a subset of 26 patients (69 samples) with matched primary (WHO grade II) and recurrent (WHO grade II-IV) glioma samples. T-cell repertoire diversity was defined as the number of unique T-cell clonotypes by V-gene, J-gene, and CDR3 nucleotide sequences. Malignant transformed (Grade III or IV) recurrent gliomas demonstrated increased T-cell repertoire diversity compared to their patient-matched primary tumors (p=0.0023), but grade II recurrences did not show the same increased diversity (p=0.26). This increase in T-cell repertoire diversity was greater in patients who underwent transformation in the context of TMZ-associated hypermutation compared to spontaneously transformed counterparts (p=0.035). In grade II primary astrocytomas (n=17), T-cell repertoire diversity above the median (186 unique T-cell clonotypes per sample) was associated with worse transformation-free (HR=4.2, p=0.045) and overall survival (HR=6.4, p=0.025). Next, we evaluated intratumoral immune heterogeneity in 7 patients by sampling from up to 10 distinct and maximally-separated intratumoral sites per LGG (64 samples). Eighty-two to 96% of unique clonotypes within a given tumor were present only within a single sampled site. Despite this heterogeneity, six LGG patients harbored T-cell clonotypes present tumor-wide across all sampled sites within a given tumor. Ten of 24 (42%) tumor-wide T-cell clonotypes were enriched in the glioma compared to matched peripheral blood, suggesting glioma-specificity. Taken together, T-cell receptor profiling in LGGs may have utility both as a prognostic biomarker and to identify glioma-specific T-cells.

PATH-48. THE DNA METHYLATION LANDSCAPE OF CORE AND PERIPHERAL DIFFUSE GLIOMA REGIONS SHOWS LITTLE SPATIAL SUBTYPE HETEROGENEITY AFTER CONSIDERING TUMOR PURITY

While diffuse gliomas are notorious for their histopathological, genetic and transcriptional spatial heterogeneity, little is known about their epigenetic spatial heterogeneity. The result of spatial (epi)genetic analysis is strongly influenced by the proportion of cancer cells in a sample, so called tumor purity. However, a gold standard for assessment of tumor purity is lacking. We set out to analyze tumor purity using different measurement modalities and explore tumor purity-corrected DNA methylation spatial heterogeneity in glioma. DNA methylation(-derived), quantitative histological and radiological measurements of tumor purity, as well as DNA methylation profiles, were analyzed in 133 image-guided multi-sector stereotactic biopsy samples of 16 patients with newly diagnosed glioma. These biopsies were acquired in regions with and without abnormalities on MRI. Data was validated in two independent populations of respectively 102 multi-region samples in 24 glioma patients and 64 single-region samples from patients without glioma. DNA methylation profiles from The Cancer Genome Atlas and the patients without glioma was used to predict DNA methylation and transcriptional subtype. Consensus measurement of tumor purity estimates (CPE) ranged from 0 to 91% and was most correlated with the DNA methylation measurement of tumor purity. Neuropathological qualitative assessment of tumor presence generally corresponded well with CPE, but occasionally samples reported as ‘histologically normal’ demonstrated tumor purities up to 53%. After filtering specimens with tumor purity less than 50%, DNA methylation subtype showed little spatial heterogeneity, this in contrast to transcriptional subtype. Samples from core and peripheral regions showed similar DNA methylation profiles. Non-purity related intratumoral heterogeneity for promotor methylation of epigenetically regulated genes was minimal, but higher in IDH-wildtype than in IDH-mutant gliomas. In conclusion, after considering DNA methylation-based measurement of tumor purity DNA methylation in diffuse gliomas shows little spatial heterogeneity; incorporating such tumor purity information can further increase the reliability of methylation-profiling-based tumor classification.

GENE-35. MGMT PROMOTER METHYLATION IN NEWLY DIAGNOSED LGG AS A POTENTIAL BIOMARKER FOR TMZ-ASSOCIATED HYPERMUTATION AT RECURRENCE

Low-grade gliomas (LGGs), which include grade II astrocytoma and grade II oligodendroglioma, inevitably recur despite aggressive treatment with surgery, and sometimes, with radiation and the chemotherapeutic agent temozolomide (TMZ). The clinical benefit of TMZ in LGG is unclear, and a subset of TMZ-treated LGGs recur with hypermutation in association with malignant progression to high-grade tumors. It is currently unknown why some TMZ-treated LGGs recur with hypermutation while others do not. O6-methylguanine-DNA methyltransferase (MGMT) is a DNA repair protein that reverses mutagenic lesions induced by TMZ. The amount of MGMT protein in a cell is regulated at the epigenetic level by promoter methylation. Here, we hypothesize that epigenetic silencing of MGMT by promoter methylation facilitates TMZ-induced mutagenesis and contributes to the development of hypermutation. We demonstrate in a cohort of 37 TMZ-treated patients with an initial diagnosis of IDH-mutant LGG that methylation level of the MGMT promoter in initial untreated tumors is significantly associated with hypermutation at recurrence. We also confirm our previous finding that methylation level of the MGMT promoter in recurrent hypermutated tumors is higher than in recurrent tumors that are not hypermutated. These results provide a plausible mechanistic basis for observed differences in propensity of TMZ-treated LGG patients to develop hypermutation at recurrence. Furthermore, they establish the potential of MGMT promoter methylation level to inform treatment decisions in the clinic for patients with newly diagnosed LGG.

GENE-47. A 3D ATLAS TO EVALUATE THE SPATIAL PATTERNING OF GENETIC ALTERATIONS AND TUMOR CELL STATES IN GLIOMA

BACKGROUND

Previous studies of solid tumors have been restricted in their ability to map how heterogeneous cell populations evolved within the tumor in three-dimensional (3D) space due to insufficient sampling, typically one sample per tumor, and a lack of knowledge of where within the tumor the sample was obtained. Knowledge of the extensivity of heterogeneity and how it is spatially distributed is crucial for assessing whether a therapeutic target is truly tumor-wide, and for exploring how mutations relate to heterogeneity in the local microenvironment.

METHODS

We developed a novel platform to integrate and visualize in 3D multi-omics data generated from each of 8–10 spatially mapped samples per tumor. Together, the 171 samples collected using this approach from 16 adult diffuse glioma at diagnosis and recurrence form a novel resource – the 3D Glioma Atlas.

RESULTS

By maximally sampling the tumor geography without excluding samples based on low cancer cell fraction (CCF), we identify a subpopulation of glioblastoma with pervasively lower CCF likely excluded by other atlases, such as the TCGA, that used stringent CCF cutoffs. Exome sequencing of 3D-mapped samples from lower-grade tumors revealed that clonal expansions are typically spatially segregated, implying minimal tumor-wide intermixing of genetically heterogenous cells. Heterogeneity is less spatially segregated for faster-growing high-grade tumors, suggesting that cell populations expand in these tumors differently. Recurrent low-grade tumors have greater intratumoral mutational heterogeneity than newly diagnosed tumors, though this did not translate into greater dissimilarity in gene expression profiles for recurrent tumors, suggesting minimal functional impact of this additional mutational diversity on gene expression.

CONCLUSIONS

The delineation of spatial patterns of heterogeneity that our work provides enables more informed interpretation of biopsies and greater insight into the factors shaping intratumoral variation of gene expression patterns. Ongoing work is exploring the spatial patterning of amplification events and the tumor microenvironment.

CSIG-24. GABP LINKS AMPK SIGNALING TO TERT REGULATION IN A TERT PROMOTER MUTATION DEPENDENT MANNER

Over 90% of human tumors achieve immortality by reactivating telomerase reverse transcriptase (TERT), the catalytic subunit of telomerase. Two mutually exclusive, heterozygous mutations that activate the TERT promoter (TERTp) occur in a wide range of cancers including ~80% of glioblastomas (GBM). The mutations and TERTp activation enable cells to avoid replicative senescence and continue to divide beyond the normal limits on cellular lifespan, thus becoming immortal. Our lab has demonstrated that each mutation creates a novel E26-transformation specific binding site that allows the tetrameric form of the GA-binding protein GABP to bind and aberrantly activate the mutant TERTp. We further showed that reducing a tetramer-forming subunit of GABP, the GABPB1L transactivating subunit, reverses cellular immortality in vitro and reduces tumor growth in vivo. Beyond GABP, little is known about pathways that contribute to immortality via activation of the mutant TERTp. The heterotrimeric 5’ AMP-activated protein kinase (AMPK) complex is activated in human GBM compared to normal brain, and was previously implicated in regulating GABP expression. Here, we have determined that AMPK inhibition decreases transcription of both subunits of the tetrameric GABP complex (GABPA and GABPB1L) in GBM cells, and is sufficient to reduce TERT expression and telomerase activity in a TERT promoter mutation dependent manner. Together, these data suggest a novel and targetable connection between the AMPK signaling axis, telomerase activity and potentially tumor cell immortality.

TMOD-27. A NEURAL CREST CELL SUBPOPULATION UNDERLIES INTRATUMOR HETEROGENEITY IN MENINGIOMA

BACKGROUND

Meningiomas are the most common primary intracranial tumor, and high grade meningiomas are resistant to most cancer therapies. Intratumor heterogeneity is a recognized source of resistance to treatment in numerous malignancies. Thus, we hypothesized that investigating molecular heterogeneity in meningiomas would elucidate biologic drivers and shed light on tumor evolution and mechanisms of resistance.

METHODS

We collected 86 spatially distinct samples at the time of resection from 13 meningiomas. Seven meningiomas were WHO grade I (46 samples), three were grade II (22 samples), and three were grade III (18 samples). Seven meningiomas were sampled at the time of salvage surgery (48 samples), and 6 were sampled at the time of initial diagnosis (38 samples). We performed multiplatform molecular profiling of these samples to identify drivers of intratumor heterogeneity, and validated our results using meningioma cells co-cultured with human cerebral organoids and RNA sequencing of paired primary and recurrent meningiomas.

RESULTS

Using bulk RNA sequencing, DNA methylation profiling and phylogenetic analysis of spatially distinct samples, we discovered significant transcriptomic, epigenomic and genomic heterogeneity in meningioma. In particular, we identified chromosomal structural alterations and differences in immune and neuronal signaling that underlie clonal evolution in high grade tumors. Using MRI-stratified bulk RNA sequencing, single nuclear RNA sequencing, RNA sequencing of paired primary and recurrent meningiomas, and live cell microscopy and single cell RNA sequencing of meningioma cells in co-culture with human cerebral organoids, we revealed a rare meningioma cell subpopulation with strong transcriptional concordance to the neural crest, a multipotent embryonic tissue that forms the meninges in development.

CONCLUSIONS

These data suggest that misactivation of a developmental cell population underlies intratumor heterogeneity in meningioma and that expression of neural crest and immediate early genes are an important step in meningeal oncogenesis.

GENE-43. TARGETING GABPb1L INHIBITS IN VIVO GROWTH OF TERT PROMOTER MUTANT GLIOBLASTOMA

Understanding cancer cell immortality in primary glioblastoma (GBM) is essential for the development of more informed treatments. Multiple cancer types, including >80% of GBMs, undergo immortalization by reactivating Telomerase Reverse Transcriptase (TERT) through acquired mutations in the TERT promoter. TERT, the catalytically active and rate-limiting subunit of telomerase, functions to maintain telomeres, which cap and protect the ends of chromosomes. Our past work has demonstrated that the transcription factor GABP - and specifically its tetramer-forming isoform GABPb1L - binds and activates the mutant TERT promoter. The generation of CRISPR-induced indels in GABPb1L results in a gradual loss of cell viability in TERT promoter mutant but not TERT promoter wild type tumor cells in vitro, but the extent to which GABPb1L function is compromised in this setting is unclear. Thus, the potential for use of GABPb1L as an effective therapeutic target for TERT promoter mutant GBM requires further investigation. Here, we use CRISPR-based strategies to demonstrate that full knockout of GABPb1L is rapidly lethal in TERT promoter mutant cells in vitro, in association with a decrease in both TERT mRNA and telomerase activity. Heterozygous deletion of GABPb1L in the context of TERT promoter mutations leads to slowed growth of orthotopic xenograft tumors in mice, and prolonged survival. Additionally, inducible RNAi-mediated inhibition of GABPb1L in growing tumors is also capable of decreasing tumor burden and increasing survival, further strongly suggesting that targeting GABPb1L in patient tumors could be a viable treatment strategy. Finally, reduced GABPb1L synergizes with temozolomide (TMZ) therapy such that TMZ treatment in the context of low GABPb1L and low TERT leads to a complete ablation of orthotopic GBM xenografts. These results highlight the potential to improve disease outcomes by targeting TERT through inhibition of GABPb1L, particularly in conjunction with TMZ treatment.