bluuebunny/crossref_metadata_2025_split huggingface dataset:
DDDR-23. IN SILICO DRUG DISCOVERY REVEALS SUBTYPE-SPECIFIC COMBINATION THERAPIES WITH CASEIN KINASE 2 INHIBITOR CX-4945 IN GLIOBLASTOMA
Authors: Ayad Nagi , Suter Robert , Jermakowicz Anna , Kaeppeli Simon 
Published: November 2022

Abstract
The treatment for glioblastoma (GBM) is maximal safe resection, temozolomide chemotherapy, and radiation therapy. However, with a median survival of only 15 months, new therapies are needed. GBM tumors are highly heterogeneous and three tumor subtypes, namely classical, proneural, and mesenchymal, have been identified. On a single cell level, differences are even more granular. Casein kinase 2 (CK2), which regulates invasion and important pathways including Wnt, Shh, and Notch in GBM, may be a promising target in distinct subpopulations. The CK2 inhibitor CX-4945 (silmitasertib) is in clinical trials for several cancers, including medulloblastoma. We employed single-cell RNA sequencing and analyzed bulk RNA sequencing data of PDX tumors (Brain Tumor PDX national resource at the Mayo Clinic). We found that on the tumor level, CX-4945 may preferentially target mesenchymal subtypes, which are the most invasive. On a single-cell level, CX-4945 was predicted to target cells with Astrocyte-like and Mesenchymal-like transcriptional states, which we show to become enriched upon treatment with the pan-aurora kinase inhibitor alisertib. Thus, CX-4945 in combination with a treatment targeting tumor subtypes and cell populations that evade CK2 inhibition may achieve beneficial clinical results. We identified several promising small molecules that could complement CX-4945 treatment based on the predicted reversal of the transcriptional disease gene expression signatures, which are specific for each subtype. Among these drugs are multiple anti-cancer agents that have shown favorable tolerability and brain penetrance in patients and may be effective in combination therapies. In a next step, we will evaluate the predicted combinations with CX-4945 in vitro and in vivo, with a particular focus on how they influence invasion and migration.
DDDR-27. A PATIENT-DERIVED DRUG SCREENING PLATFORM PREDICTS RESPONSE TO TEMOZOLOMIDE AND IDENTIFIES POTENTIAL NEW TREATMENTS FOR GLIOBLASTOMA
Authors: Ntafoulis Ioannis , Kleijn Anne , Posthoorn-Verheul Cassandra , Koolen Stijn L W , Kers Trisha , den Hollander Chelsea W J , Ju Jie , Li Yunlei , Stubbs Andrew P , Dirven Clemens M F , Leenstra Sieger , Lamfers Martine L M 
Published: November 2022

Abstract

BACKGROUND
Major obstacles that have impeded the development of effective new therapies for GBM include inter- and intratumoral heterogeneity, the blood-brain-barrier and use of sub-optimal cell line-based preclinical models. Taking these hurdles into account, we have set up a patient-derived GBM drug-screening platform. We optimized protocols to improve cell culture success rate and retrospectively assessed the predictive power of our assay for patient response to TMZ. A large panel of GBM cells was screened for sensitivity to available oncological agents. Drugs of interest were selected based on favorable physicochemical properties for BBB crossing and potent activity in (a subset of) GBM cultures. Finally, we determined the success rate of performing a small-scale screen with 20 selected agents within 4 weeks of receiving tumor tissue.

RESULTS
By combining both CUSA and tissue piece-derived dissociation protocols, culture success increased to 95%, ensuring representation of the near-complete spectrum of GBM subtypes. Single-cell sequencing studies confirmed heterogeneity in our low-passage cell cultures. In vitro screening of TMZ on a large cohort (n = 55) identified 3 response categories (responders/intermediates/non-responders) for which Cox regression analysis revealed significantly different overall survival curves of corresponding patients. Screening of 107 FDA-approved anticancer agents on 45 GBM cultures underscored the tremendous intertumoral heterogeneity in drug sensitivities. We identified 20 potent agents each effective at clinically-achievable concentrations in (a subset of) GBM cultures and having favorable BBB penetration properties (CNS-MPO score). Screening of these agents on a per patient basis within 4 weeks of receiving tissue was successful in 18 out of 24 (75%) tested tumors. In the remaining cases the tumor cells grew very slowly and longer culture times were required.

CONCLUSION
Our drug screening platform offers a tool to predict TMZ response and assess sensitivity to candidate treatments, either for GBM subsets or on a per patient basis.
DDDR-29. THE HYDROGEL-CXCL9-MRNA (HCM) VACCINE RESULTS IN SIGNIFICANT ANTI-TUMOR EFFICACY THROUGH RECRUITMENT OF NATURAL KILLER (NK) CELLS
Authors: Dastmalchi Farhad , Thomas Nagheme , Ebrahim Ghaidaa , Frain Matt , Moore Ginger , Mendez-Gomez Hector , Sayour Elias , Tomdio Macaulay , Subramaniam Vignesh , Angelini Thomas , Mitchell Duane , Rahman Maryam 
Published: November 2022

Abstract
INTRODUCTION: Immunotherapy for GBM has resulted in limited benefits to overall survival due to the targeting of limited antigens and the hostile TME. Our group has developed a patented vaccine platform that combines an mRNA-nanoparticle with CXCL9 loaded polyethylene glycol (PEG) hydrogel. The HCM vaccine is given SQ and recruits a diverse immune cell population to deliver a large payload of mRNA. The objective of these studies was to evaluate the efficacy and mechanisms of action of the HCM vaccine. METHODS: C57BL/6 mice underwent intracranial implantation of KR158 glioma cells. The HCM vaccine was formulated with total tumor mRNA, DOTAP, CXCL9 and PEG hydrogel created in collaboration with the College of Engineering. Survival studies were analyzed with the Mantel-Cox test. Flow cytometry and ELISA data was analyzed using ANOVA. Graphpad was used for statistical analysis. RESULTS: KR158-glioma intracranial tumor bearing mice were treated with SQ injection of the HCM vaccine (total tumor mRNA, DOTAP, CXCL9, PEG hydrogel). KR158 tumor bearing animals are resistant to treatment with radiation, temozolomide and other immunotherapy platforms in our laboratory. Treatment animals lived significantly longer compared to control animals (35 days versus 22 days, p &lt; 0.0001). In a separate experiment, the fat pad was collected after vaccination and flow cytometry revealed recruitment of dendritic cells (DCs), CD4 and CD8 T cells and NK cells. Large numbers of antigen specific CD8 T cells were found in the spleen and within the TME after vaccination. When NK cells were blocked (NK 1.1 blocking antibody), the survival benefit from the vaccine was completely abrogated. NK cells were found to increase antigen presentation and available IFN-gamma within the PEG hydrogel scaffold. CONCLUSION: The HCM vaccine demonstrates efficacy in resistant murine glioma models and the efficacy is dependent on recruitment of NK cells at the site of vaccination.
DDDR-33. TARGETING TGFΒ PATHWAY DEPENDENCIES IN GROUP 3 MEDULLOBLASTOMA
Authors: Qadeer Zulekha , Westelman Samantha , Johnson Mackenzie , Grele Shane , Hendrikse Liam , Taylor Michael , Weiss William 
Published: November 2022

Abstract
Medulloblastoma (MB) is one of the most prevalent malignant brain tumors in children, with tremendous cognitive and neuroendocrine disability among survivors. Group 3 (G3) MBs have poor overall survival at &lt; 50%, few recurrent mutations, higher frequency of metastasis, and no targeted therapies. Amplification of MYC (c-myc) and activation of TGFβ signaling are frequent in G3 MB. We hypothesize that the TGFβ pathway and MYC contribute to the intrinsic resistance of G3 MB through deregulation of key genes and pathways. We previously established humanized models for SHH MB by introducing MYCN or PTCH1 deletions into neuroepithelial stem (NES) cells derived from normal human induced pluripotent stem cells (hIPSCs). In this study, we transduced NES cells with TGFb effectors activated in G3 MB (ACVR2A, TGFbR1, TGFb1, TGFb3, and SMAD5) alone and/or in combination with MYC, prioritizing combinations observed in patients. Excitingly, both MYC and TGFβ effectors drove tumor formation in vivo with the combination of TGFβ effectors with MYC leading to more aggressive tumors. We thus describe six new humanized isogenic models for both non-MYC and MYC driven G3 MB. We next found that NES cells expressing MYC with either TGFβR1 or TGFβ1 showed resistance to clinical TGFβR1 inhibitors, compared to cells driven by either TGFβR1 or TGFβ1 alone. To decipher mechanisms of resistance, we integrated CUT & RUN to probe for MYC genomic localization and relevant histone PTMs with RNA-seq analysis of MYC and TGFβ pathway driven NES cells. We discovered a subset of genes upregulated in MYC and TGFb-driven lines that are targets of the histone demethylase KDM2B. We postulate that epigenetic remodeling via MYC and recruitment of other MYC-interacting cofactors culminates in transcriptional changes that lead to aggressive disease. Overall, our studies provide insights on identifying new therapeutic avenues for patients with MYC and TGFβ driven G3 MB.
DDDR-36. VAL-083 IN PATIENTS WITH RECURRENT GLIOBLASTOMA TREATED UNDER EXPANDED ACCESS PROGRAM
Authors: Kamiya-Matsuoka Carlos , Majd Nazanin , Harrison Rebecca , Knight Stephanie , Langlands John , Brown Dennis , Puduvalli Vinay 
Published: November 2022

Abstract
Current standard-of-care for glioblastoma (GBM) includes surgery followed by radiation with concurrent and adjuvant temozolomide. There are limited treatment options available upon progression or recurrence of disease. Options often involve participation in clinical trials with promising new therapies. However, patients may not meet the strictly defined entry criteria to participate in these clinical trials. Under an Expanded Access (EA) program, we have treated 14 recurrent GBM patients with VAL-083, they were not eligible to participate in other clinical trials. The median time from last progression to start of VAL-083 was 1.0 month (95%CI:0.09-2.67). All patients had received chemoradiation with temozolomide. Five (5/14;36%) patients had ≥ 2 recurrences, 8/14 (57%) had multifocal disease, and the median KPS was 80 (95%CI:70-90). All patients had unmethylated MGMT promoter, 13/14 (93%) were IDH-WT, 9/14 (64%) had a TERT promoter mutation, 6/14 (43%) had a PTEN mutation, and 4/14 (28%) had an EGFR mutation. All patients received treatment with VAL-083 at 30 mg/m2 x 3 days every 21 days. Five patients with cerebral edema refractory to steroids received bevacizumab (BEV;10 mg/kg) concurrently with VAL-083, and 8 patients received dexamethasone (Dex; &gt;4 mg/day) with VAL-083. This is the first report of the use of VAL-083 in combination with BEV (VAL-03/BEV).The main adverse event was thrombocytopenia consistent with prior experience. Four (4/14; 28%) patients had a dose reduction, 3 of which were due to thrombocytopenia. No patients had a dose reduction while receiving VAL-083/BEV. Two patients who progressed on VAL-083, were later treated with CCNU, and myelosuppression was not observed.Median progression-free survival (mPFS) and median overall survival (mOS) from last progression were 5.7 months (95%CI:1.3-7.9) and 8.3 months (95%CI:3.0-14.3), respectively. Additional treatment, safety and outcome data will be presented at the meeting.Clinicaltrials.gov Identifier: NCT03138629. EA treatment plans were approved by MD Anderson Cancer Center IRB.
EPID-22. MATERNAL USE OF TOBACCO, ALCOHOL, AND ILLICIT DRUGS DURING PREGNANCY AND ASSOCIATION WITH CHILDHOOD CANCER SUBTYPES
Authors: Wimberly Courtney , Gulrajani Natalie , Towry Lisa , Landi Daniel , Walsh Kyle 
Published: November 2022

Abstract

OBJECTIVE
To investigate the association between maternal prenatal substance use/abuse and diagnosis of childhood cancer subtypes, including childhood brain tumors. To minimize recall bias, we employed a case-only study design in which all respondents had a child diagnosed with cancer. STUDY DESIGN: We deployed a cross-sectional, case-only survey of parents of children diagnosed with cancer regarding prenatal smoking, drinking, and illicit drug use behaviors (scored on 1-7 Likert scale), demographic, gestational, and perinatal factors. Multivariable logistic regression assessed associations of gestational smoking, alcohol, and illicit drug use with childhood cancer subtypes, adjusting for child sex, race/ethnicity, birthweight, and household income.

RESULTS
3145 families completed the survey, including 232 with astrocytoma (grades I-IV, including DIPG) and 210 with an embryonal CNS tumor (medulloblastoma, AT/RT, PNET). A minority reported ever smoking tobacco products during pregnancy (Likert score ≥ 2; 14%), ever consuming illicit drugs during pregnancy (Likert score ≥ 2; 4%), or drinking more than a moderate amount of alcohol during pregnancy (Likert score ≥ 5; 2%). Prenatal smoking was associated with lower odds of rhabdomyosarcoma (OR=0.48, P=0.023) and moderately elevated odds of non-Hodgkin lymphoma (OR = 1.52, P=0.098) and AML (OR = 1.52, P = 0.083). Moderate to heavy alcohol consumption was unassociated with cancer subtypes. Prenatal illicit drug use was associated with increased odds of retinoblastoma (OR = 5.03, 95% CI = 1.73-14.7, P = 0.003) and CNS embryonal tumors (OR = 2.56, 95% CI = 1.32-4.99, P = 0.006), with similar effects across subgroups of medulloblastoma, AT/RT, and supratentorial PNETs.

CONCLUSIONS
Associations between self-reported use of alcohol, tobacco, and illicit drugs during pregnancy and risk of childhood cancer is often biased by differential misreporting among parents of affected children. Consistent with prior reports, we observe elevated odds of hematologic malignancies in association with gestational tobacco smoke exposure and novel association between maternal illicit drug use during pregnancy and elevated odds of retinoblastoma and CNS embryonal tumors.
EPID-23. TRAUMATIC BRAIN INJURY AND SUBSEQUENT BRAIN TUMOR DEVELOPMENT: A SYSTEMATIC REVIEW OF THE LITERATURE
Authors: Shah Darsh , Sanan Akshat , Morell Alexis , Eichberg Daniel , Shah Ashish , Luther Evan , Elarjani Turki , Higgins Dominique , Patel Nitesh , Jagid Jonathan , Ivan Michael , Komotar Ricardo 
Published: November 2022

Abstract
Background The role of prior head trauma in stimulating brain tumor development has been previously described in the literature but continues to be debated. The goal of this study was to conduct a systematic review interrogating the contemporary literature to delineate any possible relationship between traumatic brain injury and brain tumor development. Methods A systematic review exploring development of post-TBI brain tumor was conducted by searching electronic databases. Abstracts from articles were read and selected for full-text review according to criteria previously established in the scientific literature. Relevant full-text articles were divided into case reports and single-arm studies and epidemiological studies. Results Of 1070 resultant articles, 18 case reports and single-arm studies (level of evidence of IV and V) with 45 patients were included. The most common cause of TBI was traffic accidents. The average period between TBI and subsequent tumor diagnosis was 12.8 years. Meningiomas represented the largest share of tumors, followed by gliomas. Most post-TBI brain tumors developed in the frontal and temporal lobes. Fifteen epidemiological studies were also interrogated from a variety of countries (level of evidence of III). Case–control studies were more common than cohort studies. There were 9 of 15 studies proposed a possible relationship between history of head trauma and development of brain tumor. Conclusion The relationship between head trauma and neoplastic growth continues to be heavily debated. There are certainly case reports and epidemiological studies in the literature that suggest a correlational relationship between the two. However, there is no concrete evidence of a causal relationship between TBI and brain tumors. More research is needed to definitively delineate the extent of any such relationship.
EPCO-14. ISOSCELES: AN INTEGRATIVE FRAMEWORK FOR THE PREDICTION OF TREATMENT RESISTANT GLIOBLASTOMA CELLS
Authors: Suter Robert , Jermakowicz Anna , Stathias Vasileios , Ruiz Luz , D'Antuono Matthew , Kaeppeli Simon , Baker Grace , Veeramachaneni Rithvik , Walters Winston , Cepero Maria , Williams Sion , Ivan Michael , Komotar Ricardo , De La Fuente Macarena , Sarkaria Jann , Schürer Stephan , Ayad Nagi 
Published: November 2022

Abstract
Glioblastoma (GBM) remains the most common and lethal adult primary brain cancer. Two of the most significant issues preventing the development of effective GBM treatments are inter- and intra-tumor heterogeneity. To address these issues, we developed a novel platform termed ISOSCELES (Inferred cell Sensitivity Operating on the integration of Single-Cell Expression and L1000 Expression Signatures). ISOSCELES integrates single-cell gene expression data in individual GBM tumors with perturbation-response data derived from the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) L1000 dataset to predict sensitive and resistant tumor cell populations. Importantly, we analyzed the predictive power of ISOSCELES in an in vivo xenograft model and demonstrated that ISOSCELES reveals the GBM cell identities primed for lineage expansion during treatment with the aurora kinase inhibitor alisertib. These studies suggest that ISOSCELES can be used to identify sensitive and resistant cell populations to targeted therapies in GBM, which can inform treatment decisions in ongoing and future clinical trials.
EPCO-15. LINKING HISTOLOGICAL GLIOBLASTOMA PHENOTYPES TO TRANSCRIPTIONAL SUBTYPES AND PROGNOSIS USING DEEP LEARNING
Authors: Roetzer-Pejrimovsky Thomas , Kiesel Barbara , Nenning Karl-Heinz , Klughammer Johanna , Rajchl Martin , Bock Christoph , Hainfellner Johannes , Baumann Bernhard , Langs Georg , Woehrer Adelheid 
Published: November 2022

Abstract
Deep learning is increasingly utilized in medical image analysis and shows promise to substantially inform treatment decisions in clinical practice. While it finds broad applications in radiology or genomics, there are still relatively few applications of deep learning to the analysis of histological images. A disease in which a better understanding of underlying phenotype-genotype correlations seems crucial is glioblastoma, the most common malignant brain tumor in adults that features a dismal prognosis and limited therapeutic options. Using a large cohort of 276 glioblastoma patients with available histological, immunohistochemical, clinical and molecular data, we trained an Xception convolutional neural network to predict patient survival and transcriptional subtypes on histological images alone. We used 5-fold cross validation to evaluate the performance of the trained network. We achieve a high accuracy for predicting overall survival on univariable (p &lt; 0.001) and multivariable (p = 0.01) analysis. Moreover, we observe a high accuracy for predicting the predominant transcriptional subtype with an AUC of 0.84, 0.81, and 0.71 for classical, mesenchymal and proneural subtypes, respectively (all p &lt; 0.001). Finally, we plot heatmaps of the predicted transcriptional subtype and risk scores to directly link them to the histological phenotypes and the tumor microenvironment. Reassuringly, we find an association of the mesenchymal subtype with the perinecrotic niche and of the proneural subtype with the infiltrating edge. In conclusion, we introduce an easily adaptable convolutional neural network model for working with histological data, which can accurately predict outcomes and transcriptional subtypes in glioblastoma.
EPCO-17. UNMASKING CLONAL EVOLUTION OF DIFFUSE INTRINSIC GLIOMA USING MULTI-MODAL GENOMIC DATA
Authors: Patel Palak , Ryall Scott , Turinsky Andrei , Siddaway Robert , Pajovic Sanja , Buczkowicz Pawel , Brudno Michael , Ramani Arun , Hawkins Cynthia 
Published: November 2022

Abstract
Diffuse intrinsic pontine glioma (DIPG) is an infiltrative incurable tumor affecting children. DIPG tumors often harbor a recurrent H3K27M mutation which leads to a global loss of H3K27me2/3 and overall DNA hypomethylation, suggesting an important role of the epigenome, and consequent transcriptome in DIPG pathogenesis. To thoroughly characterize the clonal evolution of DIPG, we collected 33 samples from 7 DIPG patients using a multi-region sampling strategy and generated whole-exome and transcriptome sequencing, and DNA methylation profiling data. Using our novel bioinformatics approach, 28 distinct tumor sub-clones were identified and characterized in our cohort of DIPG patients whilst simultaneously interrogating the tumor’s ability to migrate and disseminate. When present, initiating tumor clone (Clone 1) exclusively contained H3K27M with significant DNA methylation changes whereas the divergent clones that arise later in DIPG evolutionary trees were typically driven by the copy number aberrations. Further characterization of DIPG sub-clones identified unique gene expression profiles (i.e. cell migration and angiogenesis programs) that support and enable DIPG dissemination. In this study, we uncovered how DIPG evolves at the genetic, epigenetic, and transcriptional levels in parallel and in doing so, reveal novel evolutionary phenotypes at the sub-clonal level related to the tumor’s behavior. We are further validating these results in single-cell RNA sequencing experiments and gaining further insights into the underlying molecular mechanisms responsible for invasive and aggressive DIPG phenotypes.
EPCO-28. DOT1L AND PRC2 REGULATE A SHARED EPIGENETIC MECHANISM IN GLIOBLASTOMA AND MIXED LINEAGE LEUKEMIA
Authors: Assaf Samir , Bozek Danielle , Luchman H Artee , Weiss Samuel 
Published: November 2022

Abstract
Glioblastoma (GBM) is the most aggressive adult brain tumor, with a median survival of 15 months despite current treatments. We recently established that the epigenetic regulator Disruptor of Telomeric Silencing-1-Like (DOT1L) was essential for the growth of brain tumor stem cells (BTSCs), which are thought to underlie GBM tumor initiation and treatment resistance. Given the previously recognized importance of DOT1L histone methylation for the regulation of the similarly rare and aggressive childhood cancer, Mixed Lineage Leukemia (MLL), we interrogated for common mechanisms in both BTSCs and MLL cells, that overlap due to the epigenetic role of DOT1L. To gain a more detailed perspective of the importance of the DOT1L epigenetic mark in BTSCs, we performed a chemogenomic screen using the DOT1L inhibitor, EPZ-5676. Results from this screen revealed genes from transcriptional and epigenetic complexes required for a therapeutic response to DOT1L inhibition in BTSCs. Gene targeting approaches and growth assays further identified the Polycomb Repressive Complex 2 (PRC2) as a common determining factor for the growth response of both BTSCs and MLL cells following DOT1L inhibition. Furthermore, analysis of the chromatin accessibility changes regulated by DOT1L and PRC2 histone methylation identified both shared and unique epigenetic characteristics of GBM and MLL. The extent to which these shared mechanisms underpin the pathogenic process in these distinct diseases is being further investigated by assessing the divergence in transcriptional responses that emerge from this common epigenetic phenomenon. The findings from this study will provide insight into the importance of shared epigenetic mechanisms that underlie the tumorigenesis of unique cancers affecting the brain and blood.