bluuebunny/crossref_metadata_2025 huggingface dataset:
GENE-06. INTEGRATIVE ANALYSIS OF DNA METHYLATION SUGGESTS DOWN-REGULATION OF ONCOGENIC PATHWAYS AND REDUCED SOMATIC MUTATION RATES IN SURVIVAL OUTLIERS OF GLIOBLASTOMA
Authors: Kim Sojin , Dho Yun-Sik
Published: November 2019

The study of survival outliers of glioblastoma (GBM) can provide important clues on gliomagenesis as well as on the ways to alter clinical course on this almost uniformly lethal cancer type. However, there has been little consensus on genetic and epigenetic signatures of the long-term survival outliers of GBM. In this study, we compared the two groups of survival outliers of glioblastoma with IDH wild-type, consisting of the GBM patients who lived longer than 3 years (n=17) and the patients who lived less than 1 year (n=12) in terms of genome-wide DNA methylation profile. Statistical analyses were performed to identify differentially methylated sites between the two groups. Functional implication of long-term survivors of GBM (LTS-GBM)-specific sites were investigated by comprehensive enrichment analyses with genomic and epigenomic features. We found that the genome of LTS-GBM is differentially methylated relative to short-term survivor patients depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct oncogenic aspects in gliomagenesis. In the LTS-GBM-specific sites distant from CGI, somatic mutations of GBM are enriched with higher DNA methylation, suggesting that the hypomethylation in LTS-GBM can contribute to reduce the rate of somatic mutation. On the other hand, the hypermethylation near CGIs associates with transcriptional downregulation of genes involved in cancer progression pathways. Using independent cohorts of IDH1/2- wild type GBM, we also showed that these two patterns of DNA methylation can be used as molecular markers of LTS-GBM. Our results provide extended understanding of DNA methylation, especially of DNA hypomethylation, in cancer genome and reveal clinical importance of DNA methylation pattern as prognostic markers of GBM.
GENE-11. LDSCORE REGRESSION IDENTIFIES NOVEL ASSOCIATIONS BETWEEN GLIOMA AND AUTO-IMMUNE CONDITIONS
Authors: Ostrom Quinn , Edelson Jacob , Byun Jinyoung , Han Younghun , Walsh Kyle , Amos Christopher , Bondy Melissa
Published: November 2019

BACKGROUND

Prior epidemiological studies in glioma have identified 25 germline risk variants, as well as risk associations with exposure to ionizing radiation (which increases risk) and history of allergies and aspirin use (which decrease risk). In this analysis we LDscore regression, which leverages single SNP associations and known patterns of linkage disequilibrium (LD) to estimate the genetic correlation between phenotypes, to confirm prior associations as well as attempt to identify novel phenotype associations for traits not previously assessed that may improve genetic prediction for glioma.

METHODS

Summary statistics for all glioma, GBM, and non-GBM were obtained from a prior meta-analysis conducted by Melin, et al. Summary statistics for 13 immune- and atopy-related traits were obtained from the prior case-control studies and the UK biobank. Data were filtered to include only SNPs with imputation INFO value >0.7, and minor allele frequency >0.01, excluding SNPs within the HLA region. Pairwise genetic correlation between these traits was generated using LDSC. Associations were considered significant at p< 0.05

RESULTS

Significant negative correlations were identified between glioma and ulcerative colitis (rg= -0.4039, p=4.91x10-10), celiac disease (rg= -0.2028, p=1.18x10-4), lupus (rg= -0.0956, p=0.0083), and multiple sclerosis (rg= -0.5755, p=4.46x10-9). These associations were generally consistent in both GBM and non-GBM. There was a significant correlation between both self-reported (rg= -0.102, p=0.0233) and doctor diagnosed (rg= -0.116, p=0.0305) hayfever/allergic rhinitis and GBM only.

CONCLUSIONS

This analysis demonstrates a genetic basis for previously identified protective effect of allergic rhinitis on GBM, and identifies novel associations between multiple auto-immune traits and glioma. Further studies are necessary in order to confirm these associations and identify the mechanism through which increased immune activity may lower risk of glioma.
GENE-17. ATRX LOSS IN GLIOMA RESULTS IN EPIGENETIC DYSREGULATION OF THE G2/M CHECKPOINT AND SENSITIVITY TO ATM INHIBITION
Authors: Mullan Brendan , Qin Tingting , Siada Ruby , Ravindran Ramya , Garcia Taylor , Muruganand Ashwath , Harris Micah , Danussi Carla , Brosnan-Cashman Jacqueline , Pratt Drew , Zhao Xinyi , Rehemtulla Alnawaz , Sartor Maureen , Venneti Sriram , Meeker Alan , Huse Jason , Morgan Meredith , Lowenstein Pedro , Castro Maria , Yadav Vivekanand , Koschmann Carl
Published: November 2019

Gliomas are a leading cause of cancer mortality in children and adults and new targeted therapies are desperately needed. ATRX is a chromatin remodeling protein that is recurrently mutated in H3F3A-mutant pediatric GBM and IDH-mutant grade 2/3 adult glioma. We previously showed that loss of ATRX in glioma results in tumor growth and additional tumor mutations. However, the mechanism driving these phenotypes has not been fully established. We found that in ChIP-Seq datasets of mouse neuronal precursor cells (NPCs) and experimental models of human glioma cells, ATRX binds and regulates the chromatin state of promoters and enhancers for gene sets associated with regulation of the cell cycle G2/M checkpoint. In line with this, analysis of single-cell seq (sc-seq) data from IDH-mutant gliomas (n=16) shows that ATRX-mutant tumors (IDH-A) demonstrate a population of cycling cells with dysregulated cell cycle phase gene set expression when compared to ATRX-wildtype tumors (IDH-O). In glioma models, ATRX-deficient cells exhibit a seven-fold increase in mitotic index at 16 hours after sub-lethal radiation and enhanced activation of the master cell cycle regulator ATM with radiation. Treatment of ATRX-deficient gliomas with ATM inhibitors results in a selective increase in dysfunctional cell cycling and increased radio-sensitization in ATRX-deficient glioma cells. Using an ATM-luciferase reporter in orthotopically-implanted human GBM cells, both AZD0156 and AZD1390 demonstrate in vivo pathway inhibition. Mice intra-cranially implanted with ATRX-deficient GBM cells demonstrate a doubling of median survival compared to radiated controls (p=0.0018) when treated with AZD0156 combined with radiation. This study demonstrates that ATRX-deficient glioma display epigenetic dysregulation of the G2/M checkpoint, which opens a new window for therapies targeting this unique phenotype.
GENE-38. IDH1MUT INDUCES N6-METHYLADENOSINE (m6A) RNA HYPERMETHYLATION VIA D-2-HG IN GLIOMA
Authors: Pianka Sean , Li Tie , Ji Matthew , Lai Albert
Published: November 2019

INTRODUCTION

IDH1 MUT confers slower tumor growth rates and improved prognoses for glioma patients, but the precise mechanisms underlying these clinically relevant benefits remain largely unknown. IDH1MUT gliomas produce high levels of D-2-HG, a putative oncometabolite that inhibits a range of α-ketoglutarate-dependent dioxygenases. D-2-HG-mediated inhibition of TET-family proteins involved in DNA demethylation is known to be a key driver leading to the oncogenic DNA hypermethylation phenotype (known as G-CIMP) seen in IDH1MUT gliomas. Recent evidence indicates that D-2-HG also functionally inhibits FTO and AlkBH5, two dioxygenases responsible for demethylation of RNA N6-methyladenosine (m6A) sites. This study sought to determine if D-2-HG mediates an increase in m6A content in IDH1MUT gliomas.

METHODS

Total RNA was isolated from patient tumor samples, patient-derived gliomaspheres, human embryonic kidney cell (HEK293T), normal human astrocyte (NHA), and U87 glioma model systems expressing either IDH1MUT or IDH1WT. Relative abundance of m6A modifications was determined both quantitatively and qualitatively using colorimetric ELISA-like assays and m6A-antibody dot blots, respectively.

RESULTS

Quantification of m6A abundance in IDH1MUT patient tumor samples and patient-derived gliomaspheres revealed an increase in m6A content compared to IDH1WT samples. Forced expression of IDH1MUT in HEK293T, NHA, and U87 cells increased intracellular D-2-HG content and global m6A abundance in purified RNA. Additionally, D-2-HG treatment of IDH1WT cell lines increased m6A abundance, including in IDH1WT gliomaspheres. Conversely, inhibition of D-2-HG generation in IDH1MUT cell lines decreased m6A abundance. Data will also be presented suggesting that increased m6A abundance is associated with decreased cellular proliferation.

CONCLUSIONS

These results indicate that increased intracellular D-2-HG arising in the context of IDH1MUT mediates increases in RNA m6A methylation in glioma. The association with m6A hypermethylation and reduced growth suggests that RNA methylation provides a novel therapeutic target.
GENE-44. BRD4 DELETION LEADS TO CEREBELLAR DEFICITS AND ATAXIA
Authors: Ayad Nagi
Published: November 2019

Cerebellar neuronal progenitors undergo a series of divisions before irreversibly exiting the cell cycle and differentiating into neurons. Dysfunction of this process underlies many neurological diseases including ataxia and the most common pediatric brain tumor, medulloblastoma. To better define the pathways controlling the most abundant neuronal cells in the mammalian cerebellum, cerebellar granule cell progenitors (GCPs), we performed RNA-sequencing of GCPs exiting the cell cycle. Time-series modeling of GCP cell cycle exit identified downregulation of activity of the epigenetic reader protein Brd4. Brd4 binding to the Gli1 locus is controlled by Casein Kinase 1δ (CK1 δ-dependent phosphorylation during GCP proliferation, and decreases during GCP cell cycle exit. Importantly, conditional deletion of Brd4 in vivo in the developing cerebellum induces cerebellar morphological deficits and ataxia. These studies define an essential role for Brd4 in cerebellar granule cell neurogenesis and are critical for designing clinical trials utilizing Brd4 inhibitors in neurological indications.
GENE-57. COMPARATIVE MOLECULAR LIFE HISTORY OF SPONTANEOUS CANINE AND HUMAN GLIOMA
Authors: Amin Samirkumar , Anderson Kevin , Bourdreau Beth , Martínez Emmanuel , Kocakavuk Emre , Johnson Kevin C , Barthel Floris , Varn Frederick , Kassab Cynthia , Ling Xiaoyang , Kim Hoon , Barther Mary , Yee Ngan Chew , Dickinson Peter , Packer Rebecca , Taylor Amanda , Rossmeisl John , Heimberger Amy , Levine Jonathan , Verhaak Roel
Published: November 2019

Diffuse gliomas are the commonest of malignant brain tumors with high-grade tumors carrying dismal prognosis. Preclinical models have proven themselves as poor predictors of clinical efficacy, attributed to the lack of a comparable tumor microenvironment. Comparative genomics of canine and human gliomas provide an attractive alternative modality to identify conserved drivers and underlying mutational processes of glioma as well as evaluate life history tradeoffs related to tissue context and aging that can shape type and relative timing of drivers in gliomagenesis. We performed a comparative genomics analysis between whole genome-, exome-, transcriptome- and methylation-sequencing of 77 canine gliomas, and human pediatric (n=217) and adult gliomas (n=822). We found alterations in common with those in human pediatric and adult gliomas in the Tp53 and cell cycle pathways, receptor tyrosine kinase and Idh1 R132 mutations. Canine gliomas showed similarity to human pediatric gliomas in terms of lower mutational rates (0.2–0.29 per megabase), hotspot mutations and amplifications of Pdgfrα, and robust aneuploidy constrained within the syntenic regions of Pdgfrα and Myc, but also in the known pediatric drivers, Hist1 and Acvr1 genes. A mutational signature reflecting homologous repair defect was detected in canine and pediatric but not adult gliomas, potentially resulting in the observed higher rates of genomic instability. Canine gliomas in majority classified as pediatric tumors using a commonly used human brain methylation classifier (Capper et al. 2018) and cell-of-origin analysis by deconvoluting canine transcriptome using lineage-specific gene signatures. By providing a large canine glioma genomic-sequencing dataset and comparing it with human glioma, our study provides unique insights into glioma etiology and the chronology of glioma-causing somatic alterations. Further, our results effectively position preclinical models of spontaneous canine glioma for use in understanding glioma drivers, and evaluate novel therapies targeting aneuploidy, especially for pediatric brain tumors.
GENE-58. ACTIVE TRANSCRIPTION START SITES OF MENINGIOMA SAMPLES ASSOCIATED WITH RISK OF RECURRENCE
Authors: Malta Tathiane , Sarraf Sabedot Thais , Carlotti jr Carlos , Noushmehr Houtan
Published: November 2019

Meningiomas are mostly benign brain tumors but have a substantial risk of recurrence, sometimes to more aggressive subtypes. Recently, a DNA methylation signature in meningioma was described as able to stratify patients by recurrence risk (favorable and unfavorable). It is well recognized that epigenetic deregulation at distinct genomic elements can affect changes in gene expression and contribute to cancer initiation and progression. Our goal for this study is to define genes that are actively expressed or repressed by both DNA methylation and chromatin histone modification (defined by H3K4me3). For this pilot study, we selected two favorable (grades I and II) and two unfavorable (grades II and III) meningioma primary tumor samples (N=4) and mapped H3K4me3 genome-wide and whole-genome DNA methylation, in an attempt to identify active transcription start sites at known promoters. After data alignment, preprocessing and peak calling, we identified 29,514 consensus peaks for H3K4me3. The differential binding analysis resulted in 5,752 H3K4me3 regions that distinguish favorable from unfavorable meningioma, mostly gain of peaks in the unfavorable group. We identified 1,505 peaks overlapping with known promoters, 51% associated with gain of peaks in the unfavorable group. Promoter-associated chromatin changes coincided with hypomethylation in 23 unique genes in the unfavorable group. Genes such as MET, PTEN, and the long non-coding RNA RP11-60L3.1 were identified as potential regulators of meningioma recurrence. Our preliminary results describe the identification of distinct genome-wide changes in chromatin associated with meningioma patient with high risk for recurrence. Identification of candidate genes will provide knowledge of the role of epigenomics in the development of malignant meningioma and of opportunities for targeted therapy.
GENE-63. GENOMIC CHARACTERIZATION OF HUMAN BRAIN METASTASES IDENTIFIES NOVEL DRIVERS OF LUNG ADENOCARCINOMA PROGRESSION
Authors: Nayyar Naema , Shih David , Bihun Ivanna , Dagogo-Jack Ibiayi , Gill Corey , Aquilanti Elisa , Bertalan Mia , Kaplan Alexander , D’Andrea Megan , Chukwueke Ugonma , Ippen Franziska , Alvarez-Breckenridge Christopher , Camarda Nicholas , Lastrapes Matthew , McCabe Devin , Kuter Benjamin , Kaufman Benjamin , Strickland Matthew , Carlos Martinez-Gutierrez Juan , Nagabhushan Deepika , De Sauvage Magali , White Michael , Castro Brandyn , Hoang Kaitlin , Kaneb Andrew , Batchelor Emily , Ha Paek Sun , Park Sung-Hye , Martinez-Lage Maria , Berghoff Anna , Merrill Parker , Gerstner Elizabeth , Batchelor Tracy , Frosch Matthew , Frazier Ryan , Borger Darrell , John Iafrate A , Johnson Bruce , Santagata Sandro , Preusser Matthias , Cahill Daniel , Carter Scott , Brastianos Priscilla
Published: November 2019

Although lung adenocarcinomas frequently metastasize to the brain, treatment options for lung adenocarcinoma brain metastases are limited. We discovered novel candidate drivers of progression by using case-control analyses to compare whole-exome sequencing data from a cohort of 73 lung adenocarcinoma brain metastases to a control cohort of 503 primary lung adenocarcinomas. We identified 3 genomic regions with significantly more frequent amplifications in brain metastases compared to the control cohort: MYC (12% vs 6%), YAP1 (7% vs 0.8%) and MMP13 (10% vs 0.6%). We also identified CDKN2A/B as a region deleted at a significantly greater frequency in brain metastases compared to primary lung adenocarcinomas (27% vs 13%, respectively). We confirmed frequent amplifications of MYC and YAP1/MMP13 in an independent validation cohort of 105 lung adenocarcinoma brain metastasis samples using fluorescence in situ hybridization. We further validated that MYC, YAP1 and MMP13 can drive brain metastases in a patient-derived xenograft mouse model. We found a higher incidence of metastases to the brain in mice receiving intracardiac injections of tumor cells expressing the candidate drivers compared to tumor cells expressing LacZ as a control. These results indicate that somatic alterations can drive lung adenocarcinomas to metastasize to the brain. The candidate brain metastasis drivers that we identified may serve as therapeutic targets in patients with lung adenocarcinomas who develop this devastating complication.
HOUT-02. TREATMENT PATTERNS AND OUTCOMES FOR PATIENTS WITH NEWLY-DIAGNOSED GLIOBLASTOMA MULTIFORME IN A US COMMUNITY ONCOLOGY SETTING
Authors: Fu Alex , Robert Nicholas , Pham Trang , Marshall Alexander , Annavarapu Srinivas
Published: November 2019

BACKGROUND

This study aims to describe real world characteristics and outcomes of newly-diagnosed glioblastoma multiforme (GBM) patients in relationship to O6-methylguanine DNA methyltransferase promoter (MGMT) testing and methylation status, in the US.

METHODS

Patients receiving care for GBM were identified in the US Oncology Network database from 1/1/2013 to 6/30/2018 and followed up to 9/30/2018. Structured data and chart reviews were used to assess demographic and clinical characteristics, treatment patterns, type of surgery, MGMT methylation, and clinical outcomes.

RESULTS

Of 600 patient charts planned for review, 195 have been randomly selected and reviewed thus far. Of these, 165 (84.6%) had surgical resection and 30 (15.4%) had biopsy only. Eighty-eight (45.1%) patients were tested for MGMT status and 107 (54.9%) were not. Of those tested, 33 (37.5%) were methylated, and 45 (51.1%) unmethylated. Median ages in the overall (including tested and untested), methylated and unmethylated cohorts were 63.7, 58.8, and 66.7 years, respectively. Most common first-line (1L) treatment in overall, methylated, and unmethylated cohorts was radiation concurrent with temozolomide received by 86.2%, 93.9%, and 91.1%, respectively. Median duration of 1L treatment in the overall cohort was 15.1 weeks (95% confidence interval [CI]: 11.9, 21.6) and higher in the methylated vs. unmethylated cohort (25.9 [18.1, 34.6] vs. 15.1 [9.3, 23.4] weeks, p=0.0375). Unadjusted median overall survival and progression-free survival in the overall cohort were 11.4 [9.4, 14.0] months and 5.2 [3.9, 5.8] months, and higher in the methylated vs. unmethylated cohort (20.5 [14.9, not realized] vs. 12.2 [7.1, 17.0] months, p=0.0052, and 9.4 [5.6, 14.0] vs. 5.5 [3.3, 6.8], p=0.0092, respectively).

CONCLUSIONS

Fewer than half of GBM patients were tested for MGMT methylation in the US community. Clinical outcomes, while better among patients with methylated MGMT, remain poor and current treatment options are limited.
HOUT-16. A RETROSPECTIVE ANALYSIS OF SURVIVAL OUTCOMES BASED ON CONSOLIDATION REGIMENS IN PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMA
Authors: Gelhard Savannah , Maxwell Amiee , Cohen Adam , Mendez Joe
Published: November 2019

BACKGROUND

Currently, Primary Central Nervous System Lymphoma (PCNSL) is treated with induction therapy consisting of polychemotherapy followed by consolidation therapy. Besides the incorporation of high-dose methotrexate as the backbone of induction therapy, there is no accepted standard induction or consolidation regimen for patients with PCNSL in the US. In this study, we compared three consolidation techniques by analyzing overall survival (OS) and progression free survival (PFS) in patients treated for PCNSL.

METHODS

Patients treated for newly diagnosed PCNSL at Huntsman Cancer Institute after July 1, 2012 with induction followed by consolidation therapy were retrospectively reviewed. Patients who completed one of the following regimens were included: rituximab/methotrexate/vincristine/procarbazine (R-MVP), rituximab/methotrexate/temozolomide (R-MT), or rituximab/methotrexate (R-M) for induction followed by consolidation with etoposide/cytarabine (EA), high-dose cytarabine (HIDAC), or autologous stem cell transplant (ASCT). Patients were excluded if there was evidence of systemic lymphoma on PET/CT or if the patient received radiation as consolidation therapy. Survival was calculated from the date of diagnosis and last date of known survival.

RESULTS

Twenty-three patients met eligibility criteria and received the following four treatment regimens: R-MT+EA (12), R-MT+ASCT (4), R-M+ASCT (1), and R-MVP+HIDAC (6). The median age of diagnosis was 61. Patients receiving ASCT (5) had a trend towards a more favorable OS (p=0.0675) compared to the other two consolidation therapies with no recurrence or death in those patients treated with ASCT. When comparing non-transplanted patients, R-MVP-HIDAC had a trend towards better OS and PFS compared to R-MT-EA.

CONCLUSION

This small retrospective review provides evidence that ASCT may be a superior treatment consolidation strategy in patients with PCNSL compared to EA and HIDAC, and that R-MT-EA may be less successful in practice than in published trials. These findings suggest that consolidation with ASCT should be strongly considered in all patients with PCSNL despite which induction therapy was received.
HOUT-20. TIME-DEPENDENT ANALYSIS OF SELECTIVE SEROTONIN REUPTAKE INHIBITOR TREATMENT ON OVERALL SURVIVAL OF PATIENTS WITH GLIOBLASTOMA
Authors: Otto-Meyer Sebastian , DeFaccio Rian , Dussold Corey , Ladomersky Erik , Lukas Rimas , Amidei Christina , Zhai Lijie , Lauing Kristen , Scholtens Denise , Wainwright Derek
Published: November 2019

Glioblastoma (GBM) is the most common and aggressive form of primary brain tumor in adults. We recently investigated the hypothesis that treating GBM patients with psychosocial modifiers would be associated with improved overall survival (OS). Our study retrospectively analyzed 497 patients with GBM treated at Northwestern Medicine with or without selective serotonin reuptake inhibitors (SSRI) between the years 2000 and 2018. Information from the Northwestern Medicine Enterprise Data Warehouse was analyzed for baseline covariates including sex, age at diagnosis, type of surgery, and Charlson Comorbidity Index Score. Approximately one-third of analyzed patients were prescribed SSRIs, with highly variable treatment times. Several statistical methods were used to perform adjusted analyses including: (i) an extended Cox Proportional Hazards Model with SSRI as a time-dependent variable; (ii) a Cox Model using inverse probability weights; and (iii) a Cox Proportional Hazards model with landmark analyses. The hazard ratios (95% CIs) for each statistical model analyzing the association between SSRI treatment and OS were (i) 1.26 (0.97–1.63), (ii) 1.06 (0.8–1.4), and (iii) ranged from 1.01 (0.74–1.38) to 1.26 (0.75–2.09). Our analysis found no significant association between the time of SSRI treatment and GBM patient OS. Future work will study additional considerations for psychosocial modifier treatment and their potential effect(s) on GBM patient OS including: (i) confounders due to the extent of cancer treatment; (ii) comorbidities not associated with tumor burden; (iii) absolute leukocyte counts; and (iv) length of treatment time required for enhancing immune-mediated anti-GBM mechanisms.
HOUT-22. EVALUATING CLINICAL IMPACT UTILIZING THE RANO-PRO COLLABORATIVE’S STANDARDIZED PRIORITY CONSTRUCTS
Authors: Vera Elizabeth , Gilbert Mark , Aboud Orwa , Antony Ramya , Boris Lisa , Bryla Christine , Burton Eric , Cordova Christine , Crandon Sonja , Leggiero Nicole , Penas-Prado Marta , Reyes Jennifer , Siegel Christine , Theeler Brett , Wall Kathleen , Wu Jing , Armstrong Terri
Published: November 2019

Increasing recognition of the symptom burden and functional limitations among primary brain tumor (PBT) patients has led to proposing clinical outcomes assessments as an additional measure of a treatment’s effectiveness. The RANO-PRO Collaborative recommended core symptoms for evaluation in clinical care and research for malignant glioma are weakness, walking, seizures, communication, memory, and treatment-specific symptoms. We evaluated these symptoms using the MDASI-Brain Tumor (BT) in the PBT patient sample of the NCI-NOB Natural History Study, in relation to disease progression, by descriptive statistics, and independent- and paired-samples t-tests. The sample included 434 PBT patients (59% male, median age=50 (18–83), 82% white, 43% with a prior recurrence). In the 60% with a malignant glioma, weakness, walking, seizures, difficulty remembering, and fatigue were significantly worse in the group with progression at time of imaging compared to the group with stable disease (p< 0.05). In a subset of 114 patients with progression after study entry, reported severity in all symptoms (except seizures) significantly worsened from study entry to time of progression (-1.7< mean difference< -0.1, p< 0.02, 0.3< r< 0.5). Walking, weakness, difficulty remembering, and fatigue each had a difference greater than 1-point, the minimally important difference for MDASI-BT. No one core symptom accounted for the severity change; each was reported by 17%-35% of patients as their largest change in severity. Utilizing the symptom with the largest change increased the magnitude of the worsening and its effect size (mean difference=-2.9, r=0.5). The analysis was repeated in the larger PBT sample with similar statistical findings but with smaller mean differences. RANO-PRO Collaborative core symptoms were shown to worsen at time of progression on imaging, highlighting the importance of continual symptom assessment and validating this core symptom group. Further analysis will focus on degree of change with each core symptom and validation in other datasets.
HOUT-29. THE INFLUENCE OF PSYCHIATRIC ILLNESS ON OUTCOME AND CANCER CARE RECEIVED IN PATIENTS WITH GLIOMAS
Authors: Patel Palak , Li Terry , Chou Janice , Patel Amie , Crispino Sylvia , Utate Minerva , Kurz Sylvia
Published: November 2019

BACKGROUND

Data related to the prevalence of different psychiatric disorders and their impact on survival and compliance in patients with glioma is scarce and mostly anecdotal. We aimed to study the prevalence of psychiatric disorders in glioma patients and the possible influence on compliance with cancer care and outcome.

METHODS

We performed a retrospective, observational study and compared compliance with medical care and outcome in patients who had or did not have a psychiatric illness at time of diagnosis. Kaplan-Meier method was used to compare survival between groups.

RESULTS

We identified 22 subjects (M=13, F=9) with intracranial glioma with psychiatric diagnosis and 22 matched control subjects (M=13, F=9) without psychiatric illness. Psychiatric diagnoses included depression (12%), anxiety disorder (6%), Adjustment disorder & substance use problems (2% each), bipolar disorder (1%) and panic attacks (1%). Psychiatric diagnoses were predating tumor diagnosis in 9/22 (41%) subjects and occurred around tumor diagnosis in 11/22 (50%) patients. The time of diagnosis with psychiatric illness was unknown in 2/22 (9%) of cases. Tumor diagnoses were glioblastoma in 50%, anaplastic astrocytoma in 9%, anaplastic oligodendroglioma in 13%, oligodendroglioma in 4%, and astrocytoma in 9% of cases. MedianOS was not reached for cases with psychiatric illness (not reached due to censoring) but was 4.2 years (95% CI 1.1 – 7.4) in controls (p=0.263). Subjects with psychiatric illness had an increased risk (OR 7.5, 95% CI 0.81 -68.8) of poor compliance with cancer care (medication, clinic and MRI follow-up compliance) compared to controls (p=0.046).

CONCLUSION

A variety of psychiatric conditions were observed in patients with glioma and presence of psychiatric illness may influence compliance with treatment and follow-up. Studies with larger population and longer follow-up are warranted to clarify true association between psychiatric conditions and compliance and survival.
IMMU-02. NEOANTIGENS ARISING FROM ALTERNATIVE SPLICING EVENTS MAY BE TARGETED BY TUMOR INFILTRATING LYMPHOCYTES IN GLIOBLASTOMAS
Authors: Lee Alexander , Pan Yang , Mochizuki Aaron , Galvez Mildred , Chow Frances , Nathanson David , Wang Anthony , Everson Richard , Liau Linda , Xing Yi , Prins Robert
Published: November 2019

INTRODUCTION

Alternative splicing, the cellular process that converts premature mRNA to mature mRNA and allows for single genes to produce multiple protein products, is frequently dysregulated in many cancers, including glioblastoma. However, along with non-synonymous mutations in the DNA, altered splicing mechanisms in cancers may produce novel antigens (so-called neoantigens) that distinguish cancer cells from healthy cells and can thus be targeted by the immune system.

METHODS

We developed a new computation pipeline (IRIS – Isoform peptides from RNA splicing for Immunotherapy targets Screening) that took bulk RNA-sequencing data from 23 glioblastoma patient tumor samples and predicted neoantigens that may arise from alternative splicing events. We prioritized predicted neoantigens that arose in HLA*A02:01 and HLA*A03:01 patients and selected 8 potential neoantigens to generate peptide:MHC Class 1 dextramers. We tested PBMCs and/or ex vivo expanded tumor infiltrating lymphocytes (TIL) from 6 of our glioblastoma patients against these dextramers, sorted for any neoantigen-reactive T cells, and performed single-cell RNAsequencing on the sorted population to determine the TCR sequence.

RESULTS

Among the 8 predicted neoantigens tested, 7 of the neoantigens were recognized by at least 1 patient’s T cells. 1 HLA*A03:01 epitope was recognized in 3 of the 4 HLA*A03:01 patients tested and this epitope was highly positive in an expanded TIL population, representing 1.7% of all CD3+ CD8+ cells. When we sorted for those neoantigen reactive T cells from the expanded TIL population and performed single-cell RNAsequencing, we found 325 unique T cell clonotypes, but the top 10 clonotypes represented 83.6% of all TCR clonotypes. The most frequent TCR clonotype represented 39.1% of the repertoire and suggests that clonal expansion of a select few TCR clones occurred within the tumor.

CONCLUSIONS

In total, our data indicates that neoantigens arising from alternative splicing events may represent a potential target for immunotherapy in glioblastoma.
IMMU-10. ESTABLISHING EFFECTIVE MODELS FOR IMMUNOTHERAPY IN GBM
Authors: Zamler Daniel , Yen Er-Yen , Shingu Takashi , Ren Jiangong , Kassab Cynthia , Liu Jintan , Heimberger Amy , Hu Jian , Draetta Giulio , Curran Michael
Published: November 2019

The introduction of immunotherapies has been paradigm shifting for cancers that were previously a death sentence. However, preclinical/clinical studies on glioblastoma (GBM) have generated mixed outcomes in patients, likely due to its great heterogeneity of immune microenvironment, particularly the myeloid cell populations. Primary patient studies have been limited by a difficulty in performing longitudinal studies, uncontrolled environmental conditions, and genetic variability. There is also, unfortunately, a paucity of mouse models that effectively re-capitulate the immune microenvironment of the human disease. To address these difficulties, we have established the Qk/p53/Pten (QPP) triple knockout mouse model established in our lab. The QPP model uses a cre-lox system to induce Qk deletion on a Pten−/−; p53−/− background which helps NSCs maintain their stemness outside the SVZ in Nes-CreERT2;QkiL/L PtenL/L p53L/L mice, which develops glioblastoma with survival of ~105 days. We have preliminarily assessed the QPP tumors as a faithful model to study the immune response to GBM and found them to recapitulate human GBM with respect to differential response to checkpoint blockade therapy and myeloid and T-cells histopathologically, particularly regarding upregulation of Arginase-1 (Arg1). Arg1 is the canonical marker for tumor-associated macrophages (TAMs), which is a major population of myeloid cells that greatly infiltrate in human GBM, sometimes making up more than ~30% of all GBM cells. Given TAMs’ prevalence in the tumor microenvironment and their upregulation of Arg1 in both human GBM and our QPP model, we are testing whether manipulation of Arg1 will impact TAM function and influence GBM growth. We are also evaluating arginine metabolism in TAMs effect on T cell function in GBM. Lastly, we have developed a genetically engineered mouse model to study the role of Arg1 knockout in a GBM context in-vivo. Our studies suggest that Arg1 plays an important role in GBM immune interaction.
IMMU-18. IMMUNOGENOMIC RESPONDER PHENOTYPE FROM A PHASE I TRIAL OF ANTI-LAG3 OR ANTI-CD137 ALONE AND IN COMBINATION WITH ANTI-PD-1 IN PATIENTS WITH RECURRENT GBM
Authors: Jackson Christina , Choi John , Zhang JiaJia , Piotrowski Anna , Walbert Tobias , Desai Arati , Ahluwalia Manmeet , Nabors Burt , Ye Xiaobu , Desideri Serena , Fisher Joy , Wen Patrick , Grossman Stuart , Smith Kellie , Pardoll Drew , Lim Michael
Published: November 2019

BACKGROUND

Immune checkpoint inhibitors (ICIs) are not uniformly effective in glioblastoma treatment. Immunogenomic determinants may identify patients who are most likely to benefit from these therapies. Therefore, we compared the immunogenomic phenotype of a responder to combination anti-LAG-3 and anti-PD-1 therapy to non-responders.

METHODS

We performed T cell receptor (TCR) sequencing and gene expression analysis on pre-treatment, post-chemoradiation, and post-immunotherapy tumor specimens of glioblastoma patients treated with anti-LAG3 in combination with anti-PD-1 after first recurrence (NCT02658981, ongoing). We evaluated T cell clonotypes and immunophenotype of serially collected peripheral blood mononuclear cells (PBMCs) during treatment using multi-parametric flow cytometry.

RESULTS

To date, six patients have been enrolled in the initial anti-LAG-3 and anti-PD-1 cohort. One patient demonstrated complete response, one had stable disease, and four had progressive disease by radiographic evaluation. The responder demonstrated substantially higher TCR clonality in the resected tumor at initial diagnosis compared to non-responders (mean 0.028 vs. 0.005). Shared tumor infiltrating clonotypes with pre-immunotherapy PBMCs exhibited an increase in frequency from initial resection (6.8%) to resection at recurrence (20%). The responder’s tumor at initial resection exhibited increased gene signatures of PD1low CD8+ T cells, chemokine signaling, and interferon gamma pathways. On PBMC phenotypic analysis, the responder demonstrated significantly higher percentages of CD137+ CD8+T cells (median 8.38% vs 3.24%, p=0.02) and lower percentages of Foxp3+CD137+ CD4+T cells compared to non-responders (median 18.5% vs. 38.5%, p=0.006). Interestingly, dynamic analysis of PBMCs showed that the responder demonstrated a lower percentage of PD1+ CD8+ T cells pre-immunotherapy (median 2.5% vs.12.4%, p=0.002), with persistent decrease over the course of treatment while non-responders showed no consistent pattern.

CONCLUSION

Our preliminary results demonstrate significant differences in tumor and peripheral blood immunogenomic characteristics between responder and non-responders to anti-LAG3 and anti-PD-1 therapy. These immunogenomic characteristics may help stratify patients’ response to combination ICIs.
IMMU-20. ADVANCED AGING INCREASES IMMUNOSUPPRESSIVE IDO1 LEVELS THAT ARE UNINHIBITED BY IDO1 ENZYME INHIBITOR TREATMENT IN MODELS OF GLIOBLASTOMA
Authors: Ladomersky Erik , Zhai Lijie , Lauing Kristen , Qian Jun , Otto-Meyer Sebastian , Savoor Rohan , Wainwright Derek
Published: November 2019

Immunotherapy has failed to improve the overall survival (OS) of adults with GBM in all phase III clinical trials to-date. Somewhat less appreciated is that, de novo GBM is a disease associated with a median age of diagnosis at 64 years old. Because of the strong association between advanced aging and human subjects presenting with GBM, we further investigated our previously described observation of a higher mortality rate in elderly C57BL/6 wild-type (WT) mice with intracranial GL261 as compared to young counterparts after treatment with radiotherapy (RT) and anti-PD-1 (PD1)/IDO1 enzyme inhibitor (IDO1i) (Ladomersky et al., 2018; Clinical Cancer Research). Since immunosuppressive IDO1 expression significantly increases in both the mouse and human brain during advanced aging (Ladomersky et al., 2019; Frontiers in Pharm.), we decided to study how IDO1 and aging interact during immunotherapy of GBM. We found that the pretreatment effects of an IDO1 enzyme inhibitor improve OS in young but not elderly WT mice with intracranial GL261 (n=12–15/group; p< 0.05). Strikingly, in the setting of advanced aging, IDO1-/- mice with GBM show improved OS as compared with WT mice (p< 0.01) independent of treatment with an IDO1 enzyme inhibitor. Similarly stunning, 74–80 week old IDO1-/- mice with GBM treated at 14 days post-ic. with RT and PD1/IDO1i survive significantly longer as compared to elderly WT mice administered the same treatment (n=20–22/group; p< 0.05). These results collectively suggest that, the therapeutic effects of IDO1 enzyme inhibition is less effective in the setting of old age, and provides rationale for the development of new approaches that inhibit IDO1-mediated immunosuppression independent of its association with enzyme activity for eventually improving immunotherapeutic efficacy in human subjects with malignant glioma.
IMMU-24. A COMPREHENSIVE IN SILICO APPROACH TO DISCOVERING TUMOR REJECTION ANTIGENS IN MALIGNANT BRAIN TUMORS
Authors: Yang Changlin , Dyson Kyle , Yegorov Oleg , Mitchell Duane
Published: November 2019

BACKGROUND

Proteins that can serve as effective tumor rejection antigens within brain tumors are poorly characterized. Current prediction algorithms relying on identification of mutated epitopes as neoantigens are limited in low mutational burden tumors. We have developed a multi-faceted computer algorighm for identifying tumor rejection antigens called the Open Reading Frame Antigen Network (ORAN). This pipeline provides a comprehensive solution for predicting brain tumor immunogenic targetable epitopes/transcripts.

METHODS

Human and murine RNASeq and WES data were QCed. Patients individual HLA-I and HLA-II haplotypes were predicted by highly customized Optitype and Phlat Algorithms. SNPs and Indels were called from tumors WES and read through matched RNASeq data. 19,131 transcripts expression were counted per TOIL algorithm. Tumor associate antigens(TAA) of individual patient or murine tumors were selected by setting a cutoff of Transcripts Per Million (TPM) > 1 on individual patient’s tumor, while RNA Seq data from 7000 normal tissues was used to identify tumor unique transcripts. Actual sequence of HLA and SNPed Consenses TAA(CTAA) were called. Only expressed mutations and personalized TAAs were used for antigenic epitope predictions. All neoepitopes were screened against a human reference proteomic library to guarantee that epitopes were not shared by other expressed isoforms or genes. In silico validation were preformed to cross validate predictions made by ORAN.

RESULTS

In medullobastoma (N=121 samples), ORAN gives an average of 15.6 MHC class I restricted neoepitopes,11.9 epitopes encoded by Indels and with 33.2 MHC class II restricted neoepitopes and 16.2 Indel antigens per patient. The TAAs of each patient reaches average 256 antigenic epitopes per patient. ORAN also predicts the exact HLA and neo-antigens from a validated neoantigens vaccine dataset (Gros A Nat Med 2016).

CONCLUSION

ORAN accurately identifies validated neoantigens and provides a comprehensive list of potential tumor rejection antigens within human and murine brain tumors.
IMMU-31. DRIVER GENE MUTATIONS DICTATE THE COMPOSITION OF THE IMMUNE LANDSCAPE OF GLIOBLASTOMA AND CONFER SELECTIVE RESPONSE TO IMMUNOTHERAPY
Authors: Yeo Alan , Delcuze Bethany , Strauss Laura , Boussiotis Vassiliki , Charest Al
Published: November 2019

The characterization of the immune landscape of glioblastoma multiforme (GBM) is rapidly emerging. Current immunotherapeutic efforts for GBM would benefit from a comprehensive and mechanistic understanding of the relationship between distinct driver gene mutations and the composition and function of the immune tumor microenvironment. The majority of GBM tumors overexpress EGFR and EGFRvIII and ~40% are mutated for PTEN. Using genetically engineered and accurate preclinical mouse models of GBM built on combinations of these driver genes, we demonstrate that the compositions of the immune landscape and the response to checkpoint blockade immunotherapy vary according to the genotype of the GBM. Mechanistically, we show that signaling networks downstream of EGFR and PTEN establish chemokine and cytokine profiles that parallel the levels of intra-tumoral polymorphonuclear myeloid-derived suppressor cells and regulatory T cells. Additionally, tumor-associated microglia/macrophages number, function and polarization are heavily influenced by specific driver-gene mutation combinations. Furthermore, we demonstrate that efficacy of checkpoint blockade therapy using anti PD-1 as a single agent or in combination with anti CTLA-4 is dependent on EGFR and PTEN status. Taken together, our findings demonstrate that important components of the tumor immune microenvironment are influenced by specific driver gene mutations. Our results suggest that stratifying patients based on tumor genotype or signaling events may be informative for selection of appropriate candidates for checkpoint blockade therapy and present an opportunity to pharmacologically modulate GBM signaling with targeted therapeutics to sensitize patients to immunotherapy.
IMMU-33. IMMUNE PROFILING REVEALS INHIBITORY MACROPHAGES AND A DISTINCT SPATIAL DISTRIBUTION OF IMMUNE CELLS IN DIFFERENT TYPES OF BRAIN METASTASES
Authors: Kienzler Jenny , Reynoso Jeremy , Owens Geoffrey , Orpilla Joey , Lee Alexander , Mochizuki Aaron , Yong William H , Liau Linda , Prins Robert
Published: November 2019

BACKGROUND

Current treatment modalities, including surgical resection, radiosurgery and immune checkpoint inhibitors, have improved local control rates of brain metastases, but overall prognosis is still poor. AIM: To investigate the immune microenvironment in brain metastases for better understanding of treatment failures.

METHODS

We identified 42 patients with melanoma (M), breast (B) and lung (L) brain metastases and performed multiplex immunofluorescent staining for immune markers (CD4, CD8, CD45, PD1, PD-L1) and quantitative analysis with HALO software. NanoString nCounter mRNA gene expression assay was used for identification of immune pathways. CyTOF and single cell RNA sequencing were done on 12 different brain metastases and their matched peripheral blood samples.

RESULTS

The median CD8, CD4 and PD1 density (as a total number of cells) was 0.24%, 0.13%, and 0.07% for M, 0.24%, 0.51% and 0.08% for B, and 0.87%, 1.36%, 0.67% for L. CD4 and CD8+PD1+ expression was significantly different between all groups (p=0.01), CD4+PD1+ in M vs. L (p=0.03) and PD1 in B vs. L (p=0.03). No significant difference was found in terms of CD45 positive cells (M 2.13%, B, 1.99%, L 4.95%). PD-L1 expression was significantly different between histologies; the highest expression was present in breast metastases (M: 1.51%, B: 49.98%, L: 31.90%, p=0.0002). Spatial distribution revealed a characteristic pattern with a peritumoral border infiltrate in M, and predominant intratumoral distribution in B and L (M 0.2%, B 2.6%, L 3.6%, p=0.02). CyTOF clustering demonstrated that macrophages are the most prevalent immune population overall (83.08%), with an inhibitory phenotype and gene expression pattern present in different histologies (S100A9, CCL20, IFI16, MARCO). T-cells (predominantly CD4+, 3.6%), and B-cells (1.5%) comprise the remaining immune cell populations.

CONCLUSION

Neoadjuvant targeted treatment approaches may be needed to alter predominance of inhibitory macrophages and recruit activated T lymphocytes in brain metastases.
IMMU-39. RNA LOADED LIPID-NANOPARTICLES FUNCTION AS CUSTOMIZABLE IMMUNOTHERAPEUTIC VEHICLES AGAINST MALIGNANT GLIOMAS
Authors: Grippin Adam , Wummer Brandon , Mendez-Gomez Hector , Stover Brian , Huang Jianping , Rinaldi Carlos , Mitchell Duane , Dobson Jon , Sayour Elias
Published: November 2019

BACKGROUND

While dendritic cell (DC) vaccine therapy has shown considerable promise for glioblastoma (GBM) patients (Mitchell et al. Nature, 2015), their advancement into human clinical trials has been fraught with challenges in the development, manufacturing, and marketing of successful cancer immunotherapies. To circumvent the challenges associated with cell therapy, we have developed a new platform technology consisting of tumor derived mRNA complexed into lipid-nanoparticles (RNA-NPs) for systemic delivery to DCs in vivo and induction of antigen specific T cell immunity against GBM. OBJECTIVES/

METHODS

We sought to assess if surface and charge modifications to our custom lipid-NP could facilitate its localization to lymphoid organs and the brain tumor microenvironment.

RESULTS

We demonstrate that intravenous administration of our unmodified custom RNA-NPs mediate systemic activation of DCs; these include activation of CD11c+ cells in the brains of animals with intact blood brain-barriers (BBBs). RNA-NPs mediate antigen specific T cell immunity and anti-tumor efficacy with increased tumor infiltrating lymphocytes against a NF-1/p53 mutant glioma that recapitulates features of human GBM in immunocompetent mice. Modification of surface charge could direct these RNA-NPs to lymphoid organs (e.g. spleen, lymph nodes) while modification of the lipid backbone (with cholesterol) enhances localization to innate immune cells in NF-1/p53 mutant and GL261 gliomas. We therefore assessed if this customizable lipid-NP could be leveraged for delivery of immune checkpoint inhibitors (ICIs) (i.e. PD-L1 siRNA) to the brain tumor microenvironment. Compared with scrambled siRNA-NPs in combination with ICIs, surface modified siRNA-NPs (antagonizing PD-L1) in combination with ICIs mediated significant antitumor efficacy with 37% long term survivors in an otherwise fatal brain tumor model.

CONCLUSION

We designed multifunctional RNA-NPs with a simple, scalable synthesis method that enables delivery of nucleic acids to innate immune cells in lymphoid organs and brain tumors.