bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPCO-07. NON-GENOMIC DETERMINANTS OF TUMOR CELL PHENOTYPES IN ADULT GLIOBLASTOMA
Authors: Zador Zsolt , Mikolajewicz Nicholas , Han Hong , Chokshi Chirayu , Venugopal Chitra , Maich Will , Jason Moffat , Singh Sheila 
Published: November 2022

Abstract
Non-genomic determinates of oncogenic cellular phenotypes is an emerging concept that expanded our model of tumor hallmarks. We hypothesized that oncogenic programs in adult glioblastoma (GBM) such as angiogenesis, proliferation, DNA repair, epithelial to mesenchymal transition and quiescent states are achieved independently of mutational background or clonal linage. We therefore explored the assortations of large-scale chromosomal rearrangements and canonical driver mutations with oncogenic programs in single cell RNA sequencing (scRNA-seq) of over 3000 tumor cells in 4 adult GBM using open data. We find recurring patterns where tumor cells from diverse mutational background and clonal linage converge upon oncogenic tumor phenotypes. We validate this observation in 9 tumors comprising over 16,000 cells and in xenograft animal models of GBM pre- and post temozolamide treatment. We finally explore the epigenetic associations of oncogenic phenotypes via computational label transfer from scRNA-seq to chromatic accessibility data from single cell ATAC sequencing (scATAC-seq). We find open genomic regions associated with canonical regulators, such as the highly oncogenic mesenchymal phenotype driven by TWIST1. Our results suggest a paradigm shift towards non-genetic determinants of oncogenic phenotypes in GBM complementing the conventional concept of cancer clonal evolution.
EPCO-10. SYSTEMS BIOLOGY-BASED THERAPEUTIC PREDICTIONS WITH GBMSYGNAL AND CLINICAL CORRELATES IN THE REAL-WORLD LONGITUDINAL OUTCOMES REGISTRY XCELSIOR
Authors: Stuhlmiller Timothy , Turkarslan Serdar , Friedland Julie , Shapiro Mark , Kesari Santosh , Patel Anoop , Baliga Nitin 
Published: November 2022

Abstract
Glioblastoma is an aggressive disease with multiple disrupted signaling networks in the same tumor, demanding the development of personalized combination regimens. Using SYstems Genetics Network AnaLysis we analyzed TCGA multiomics datasets for 422 glioblastoma patients to generate a predictive disease network model (gbmSYGNAL). This model seeks to uncover how subsets of mutations causally modulate regulators (transcription factors, miRNAs, etc.) that mechanistically regulate gene modules (“regulons”) associated with disease progression. Using the real-world registry XCELSIOR (NCT03793088), we identified 55 anti-cancer therapies utilized in glioblastoma treatment (N = 354 patients) and associated them with positive or negative regulon activity within individual patients across the TCGA cohort. A median of 12 regulons were targeted by each drug. Interestingly, nilotinib targeted only 5 regulons but they were found to be active in 38% of patients and regulons overactive in &gt;35% of patients were targeted by repurposed anti-cancer drugs including celecoxib, hydroxychloroquine, and tocilizumab. Standard-of-care treatments lomustine and bevacizumab were predicted to be active in only 28% and 23% of patients, respectively. Using gbmSYGNAL, we then prioritized drugs for 12 additional patients from the XCELSIOR registry. Median overactive regulons per patient was 110 (range 55-254) represented by a median 28 molecular targets (range 17-37). Surprisingly, regulons targeted by metformin were predicted to be overactive in all patients. Certain regulons displayed a binary pattern (high “on” activity or completely “off” per patient) including those targeted by pemetrexed, pembrolizumab, and valproic acid while others showed a gradient of activity across patients including selinexor, panobinostat, palbociclib, and alpelisib. Systems biology analysis of commercially available NGS data combined with the XCELSIOR direct patient engagement platform yielded therapeutically actionable insights for glioblastoma patients in real time. Correlation with clinical outcomes is ongoing for ~50 additional patients and will be presented at the meeting.
EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY
Authors: Johnson Kevin , Anderson Kevin , Nehar-Belaid Djamel , Varn Frederick , Gujar Amit , Courtois Elise , Robson Paul , Moon Hyo-Eun , Golebiewska Anna , Paek Sun Ha , Niclou Simone , Verhaak Roel 
Published: November 2022

Abstract
Glioma cellular heterogeneity and plasticity represent fundamental obstacles to effective therapies. Understanding the determinants that govern glioma cell diversity and adaptability is critical to overcoming treatment resistance. Recent single cell DNA methylation studies have demonstrated that dynamic epigenetic alterations facilitate glioma cell state shifts and stress response. However, information regarding other modes of epigenetic gene regulation, such as chromatin accessibility, and how therapy shapes cellular heterogeneity remains limited. To determine the critical regulators of glioma cell state plasticity under treatment, we profiled 36 tumors (n = 23 adult patients) with joint single nucleus RNA and ATACseq including 13 longitudinal initial – recurrent pairs that yielded a total of 79,945 cells (37,883 malignant cells). We identified chromatin peaks that were uniquely open in glioma cells (n = 14,462 peaks, FDR &lt; 0.05) compared with tumor microenvironmental cells including neuronal, perivascular, glial, and immune populations. Among malignant cells, differentiated-like cells exhibited more recurrent regions of accessibility than stem-like cells. These populations could be further delineated by differential peak enrichment of transcription factor binding sites in the stem-like (TCF12, ASCL1), differentiated-like (SMARCC1, JUN), and proliferating stem-like (E2F4) malignant cells nominating these transcription factors as master regulators. We confirmed that these cell state-specific open chromatin peaks overlapped enhancer regions via single nucleus multiomics and bulk H3K27ac profiling in 3 patient-derived cell lines. We further demonstrated that there are cell state-specific chromatin changes at recurrence with a trend toward a more open chromatin state that was associated with coordinated transcriptional changes. Finally, we incorporated matched longitudinal whole genome sequencing data to evaluate mutational profiles and differentiate between predominantly epigenetically driven changes and epigenomic co-evolution with the genome. Together, these findings define the key epigenetic switches that shape glioma cell states and facilitate plasticity during tumor progression.
EPCO-19. ADAPTIVE RESPONSES TO GENOME-WIDE DNA DAMAGE RESULT IN TOPOLOGIC GENOME REORGANIZATION IN GLIOBLASTOMA
Authors: Modrek Aram , Do Catherine , Zhang Zeyan , Deng Yingwen , Karp Jerome , Ezhilarasan Ravesanker , Valor Belen , Cova Giulia , Jafari Matiar , Snuderl Matija , Tsirigos Aristotelis , Skok Jane , Sulman Erik 
Published: November 2022

Abstract
In glioblastoma, treatment with radiation and chemotherapy leads to DNA-damage and most DNA breaks are faithfully repaired, but the impact on the epigenome is largely unknown. Using newly developed tools to enable these studies, we hypothesize that genome-wide DNA damage leads to local alterations in DNA-methylation, genome organization, and results in persistent gene-expression alterations near sites of repaired damage. We use patient-derived human glioblastoma stem-like cells (GSCs) as a model. DNA breaks are induced using (i) irradiation or (ii) a novel “multi-cut” CRISPR-Cas9 DNA break system followed by multi-omic profiling. With radiation, we find significant and wide-spread alterations in DNA-methylation after treating multiple glioblastoma cultures. However, it is challenging to study local alterations around sites of radiation induced damage because breaks are introduced at different sites in each cell, resulting in stochastic DNA methylation alterations. To circumvent this issue, we developed a multi-cut CRISPR-Cas9 DNA break system that targets 142 or 483 pre-defined loci. Induction of pre-mapped genome-wide cuts reproduces a similar level of toxicity as standard doses of radiation. To assess repair efficiency and confirm induction of breaks, we performed targeted sequencing of the 142 or 483 sites to allow for high coverage sequencing. To understand how DNA damage may lead to regional epigenetic and 3D chromatin organization changes, we performed HiC, Methylation-seq, ChIP-seq of the chromatin organizing factor CTCF and enhancer marker H3K27ac, as well as RNA-seq, before and after cut induction. Our findings show significant mega-base scale alterations in chromatin contacts centered around cut sites, enrichment of DNA methylation alterations at regulatory elements and altered gene-expression. The findings here provide a mechanistic view of the interplay between genome-wide DNA damage, DNA methylation and genome re-organization, and have wide ranging implications for the effect of DNA damage on the epigenome in glioblastoma.
EPCO-20. EXPLORATION OF DNA METHYLATION PATTERNS IN GLIOBLASTOMA REPROGRAMMED MICROGLIAL CELLS
Authors: Richart Lorraine , Cialini Camille , Heurtaux Tony , Müller Tanja , Hau Ann-Christin , Mittelbronn Michel 
Published: November 2022

Abstract
Glioblastoma (GBM) is the most frequent and malignant adult-type diffuse glioma (WHO grade IV) with a median patient survival of less than 15 months despite multimodal treatment. The poor prognosis of GBM, among others, is associated with a tumor-supporting microenvironment characterized by a rather anti-inflammatory state, where the tumor cells have been shown to hijack microglial gene expression profiles. These so-called tumor-associated microglia cells (TAMs) repress normal immune functions, such as phagocytosis and pro-inflammatory cytokine secretion through transcriptional reprogramming, further underlying morphological changes. It is currently starting to emerge that the exceptional cellular plasticity required to orchestrate such microglial reactivity could originate from pre-imposed epigenetic modifications. We thus hypothesize that TAM reprogramming in GBM is controlled by epigenetic mechanisms, and therefore aim to understand if modifications in DNA methylation patterns can lead to pro-tumor transcriptomic and phenotypical changes.Reactive microglia are classically described as either ‘pro-inflammatory’ M1 or ‘anti-inflammatory’ M2 phenotypes, inducable by Lipopolysaccharide (LPS) and Interferon-gamma (IFNɣ) or Interleukin-4 (IL-4), respectively. In a GBM context, microglial cells have been mostly classified as M2, but exhibit heterogeneous features among the M1 to M2 activation spectrum. In this study, we exposed human and murine microglial cell lines to LPS, IFNɣ, IL-4, and GBM-conditioned medium (GBM-CM), followed by morphological assessment, transcript expression and secretome characterization. The onset of activation was followed in time series every 12h to interrogate epigenetic and transcriptomic changes together with protein expression and secretion. After exposure to GBM-CM, microglial cells exhibited a bipolar and more elongated phenotype. We observed significant variations in cytokine production together with a decrease in phagocytosis in LPS-treated microglia, whereas the secretome in GBM-CM was only slightly altered. We furthermore observed differentially methylated regions (DMRs) using the novel Infinium® Mouse Methylation BeadChip, suggesting a role of DNA methylation in microglial reprogramming.
EPCO-22. SINGLE CELL ANALYSIS TO UNDERSTAND SEX DIFFERENCES IN GBM OUTCOME
Authors: Llaci Lorida , Rubin Joshua , Mitra Rob 
Published: November 2022

Abstract
Males have a higher incidence and mortality in certain cancers compared to females. The same is true in glioblastoma (GBM) regardless of age, suggesting that cell-intrinsic factors rather than extrinsic factors such as circulating sex hormones are causing these sex differences. Our lab has demonstrated cell-intrinsic sex differences with respect to growth, clonogenicity, and in vivo tumorigenesis using an isogenic murine astrocyte cell culture model of GBM (Nf1 -/-; DNp53). Male astrocytes are more likely to adapt and grow when exposed to irradiation-induced stress compared to female astrocytes, which are more likely to undergo growth arrest after the same exposures. These sex differences in response to treatment can be explained by the different chromatin and transcriptional profiles established from the moment of fertilization that can result in different levels of transcriptional heterogeneity, a well-established cause for resistance to induced stress in GBM. However, so far sex has not been considered when exploring transcriptional heterogeneity. As such, we used 10x Genomics technology to extract single nuclei RNA (snRNA) and ATAC (snATAC) sequencing from the same nuclei and identified different levels of transcriptional heterogeneity in male and female astrocytes cells from our model. We also identified different chromatin profiles of crucial genes, such as Sox2, an important TF for the reprogramming of differentiated GBM into stem-like cells, which can then form tumors in vivo. We expect for the male astrocytes to be more effective in escaping growth arrest and adapting to irradiation-induced stress because of these different transcriptional and chromatin profiles. Our work will identify epigenetic mechanisms by which male cells are more able to adapt to treatment-induced stress compared to female cells and will further advance our understanding of sex differences in treatment-response in GBM and cancer overall, while giving avenues for the development of novel treatments.
EPCO-25. MULTI-OMIC ANALYSIS OF THE GLIOBLASTOMA EPIGENOME AND TRANSCRIPTOME INFORMS OF MIGRATORY INTERNEURON-LIKE DEVELOPMENTAL REGULATORS
Authors: Ramos Susana Isabel , Mussa Zarmeen , Giotti Bruno , Tsankov Alexander , Tsankova Nadejda 
Published: November 2022

Abstract
Recent studies have demonstrated that, despite their nomenclature, gliomas recapitulate an interneuron progenitor-like state that drives tumor progression. During human neurodevelopment, interneurons arise from the subcortical ganglionic eminences and migrate tangentially into the neocortex, settling in the cortical plate where they integrate local neurocircuitry. Analogously, malignant glioblastoma (GBM) cells migrate from the tumor core into the surrounding healthy tissue. This innate infiltrative property renders these malignant cells elusive to surgical resection, leading to tumor recurrence. To understand the regulatory networks that drive tumor infiltration from a neurodevelopmental perspective, we generated a single-nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) dataset of 41,000 nuclei from the core and infiltrative edge of surgically resected GBM specimens (n = 4). Concurrently, we sequenced 46,000 nuclei from non-pathological, postmortem samples of second- and third-trimester neocortices (n = 17). We integrated these datasets with paired single-nucleus RNA sequencing (snRNA-seq) data and identified candidate regulatory TFs that exhibit high correlation between motif enrichment and TF expression. Using single-trajectory inference and pseudo-time analyses, we identified TCF12 as a potential driver of interneuron lineage fate in developing cortical progenitors. Given its implication in projection neuron migration, we were intrigued to find that TCF12 activity is highest in GBM cells with a migratory interneuron signature, hinting at its putative role in tumor infiltration. To understand the significance of these findings, we will interrogate other genes in the TCF12 regulatory network with the ultimate goal of identifying therapeutic targets that inhibit GBM infiltration.
EPCO-27. REVEALING TUMOR HETEROGENEITY AND IMMUNE MICROENVIRONMENT IN NF-1 GLIOMA BY SINGLE-CELL GENE EXPRESSION PROFILING
Authors: D'Angelo Fulvio , Garofano Luciano , Oh Young Taek , Najac Ryan , Ceccarelli Michele , Eoli Marica , Sanson Marc , Lasorella Anna , Iavarone Antonio 
Published: November 2022

Abstract
Germline mutations in the NF1 tumor suppressor gene cause neurofibromatosis type 1 (NF-1), the most common human genetic cancer predisposition syndrome. NF1 patients are prone to develop peripheral and central nervous system tumors, with glioma occurring in 15-20% of patients. The molecular profiles of glioma from patients with NF-1 have been previously explored by large scale DNA and RNA bulk analyses, providing the first comprehensive genetic landscape of NF-1 glioma. However, the intra-tumoral architecture and the microenvironment organization remained largely concealed within the global bulk profile. Here, to characterize the complexity of molecular states of both malignant and non-malignant cells, we profiled NF-1 glioma gene expression at individual cell resolution. We performed single-nuclei RNA sequencing (Nucseq) on frozen NF-1 glioma specimens, including high-grade and low-grade tumors. The functional classification of the transcriptional programs activated in the individual tumor cells identified three main molecular states that partially overlapped with the cellular subtypes of sporadic glioblastoma. Tumor cells of low-grade NF-1 glioma exhibited marked enrichment of neuronal functions, suggesting that the gliomagenesis process in the context of NF1 inactivation might be supported by specialized neuronal activities. Conversely, the proliferative state characterized high-grade NF-1 glioma, indicating that cell cycle-associated pathways are drivers of tumor progression. The single-cell deconvolution of immune microenvironment in NF-1 low grade glioma revealed infiltration of CD8+ T lymphocytes and the active crosstalk of these cells with pro-inflammatory macrophages and mature dendritic cells, supporting a possible anti-tumor cell-mediated response. The identification of divergent tumor cell states as well as the characterization of the immune infiltrates provide new insights for accurate stratification of NF-1 glioma patients and to inform personalized therapeutics.
EPCO-29. KLF5 IS REQUIRED FOR THE SEX-DIFFERENCES ACROSS MULTIPLE TUMORIGENIC PHENOTYPES IN PEDIATRIC GLIOBLASTOMA (GBM)
Authors: Abou-Antoun Tamara , Rubin Joshua , Mitra Rob , Kfoury Najla , Chen Xuhua , Warrington Nicole , Reiss India 
Published: November 2022

Abstract
High-grade glioblastoma (GBM) is a highly heterogeneous, malignant cancer with no cure to date. A sex-biased incidence and therapeutic response is reported (1) for GBM with a male to female incidence ratio of 1.6:1 and female patients having a 4-6 month survival advantage (2) compared to male patients. In our current work, we sought to determine the molecular basis for the sex-bias in incidence and therapeutic response using an isogenic murine model of GBM with dual loss of neurofibromin 1 (NF1) and P53 (DNP53) in astrocytes. Our model yielded GBM from the murine astrocytes in a sex-biased manner, with male GBM cells exhibiting a highly significant proliferative, migratory, in-vivo tumorigenicity, stem-cell enrichment rate and therapeutic resistance compared to female GBM cells. Using transposon calling cards, we mapped Brd4 enhancer usage across the genome in male, compared to female GBM cells and identified key transcription factors that differentially enriched at male-biased, compared to female-biased Brd4 bound enhancers. Interestingly, female-biased Brd4-bound enhancers were enriched for transcription factors with tumor suppressor roles including P53 and SMAD4, whereas male-biased Brd4-bound enhancers were enriched for transcription factors with oncogenic roles, including Oct4, MYC and KLF5. Genetic or chemical silencing of KLF5 reduced the tumorigenic potential in male GBM with rates of cellular proliferation, survival, migration and stem-cell frequency significantly reduced to levels that resemble female GBM. Using transposon calling cards, we mapped KLF5 genomic localization in male and female GBM cells and identified significant peaks that affiliated with differentially expressed genes between the sexes. Interestingly, genes induced by KLF5 in the male cells were affiliated with poor survival in patients with various cancers, whereas those induced by KLF5 in the female cells were affiliated with favorable prognosis. This signifies the need to explore molecular mechanisms by which KLF5 drives these sex differences in GBM.
EPCO-30. IDENTIFICATION OF PRECANCEROUS CELLS LEADING TO INTRATUMORAL HETEROGENEITY IN GLIOBLASTOMA
Authors: Kim Hyun Jung , Cha Do Hyeon , Kim Keon Woo , Kim Myeong Heui , Park Jung Won , Kim Ja Hye , Yoon Seon Jin , Kang Seok-Gu , Lee Jeong Ho 
Published: November 2022

Abstract
Glioblastoma (GBM) is the most common and aggressive primary brain cancer in adults. Although multiple oncogenic mutations have been identified in neural stem cells of the subventricular zone (SVZ) in humans, the dynamic process of how tumor initiation begins with a mutation-harboring stem cells remains elusive. To better understand how GBM evolves, we analyzed longitudinal transcriptomic changes of mutation-harboring stem cells using a spontaneous, somatic GBM animal model with EGFRvIII, TP53, PTEN mutations. Using single-cell RNA sequencing, we have identified precancerous cell populations originating from oligodendrocyte precursor cells, with increased proliferation and decreased capacity to differentiate into oligodendrocytes. The precancerous cell populations undergo malignant transformation to become heterogeneous cancer cells characterized by immune evasion, mesenchymal transition, and cell cycle. We further identified the precancerous populations in the SVZ of human GBM patients with chromosomal aberrations. Our findings suggest that GBM evolution is closely related to oligodendrocyte precursor cell specification, and the time-dependent transcriptomic changes in precancerous cells is a novel therapeutic target for tumor evolution.