bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPCO-32. HIGHLY MULTIPLEXED PROTEOGENOMIC SPATIAL PROFILING OF PEDIATRIC AND ADULT H3 K27-ALTERED DIFFUSE MIDLINE GLIOMAS
Authors: Damodharan Sudarshawn , Dey Mahua 
Published: November 2022

Abstract

BACKGROUND
H3 K27-altered diffuse midline gliomas (DMG) are highly aggressive malignancies of the central nervous system that affect both pediatric and adult populations. The immune layout and genetic changes within the tumor microenvironment associated with these high-grade malignancies are thought to play an integral role in the phenotypic differences in tumor presentation and clinical course between both populations. Comparative landscapes between pediatric and adult DMGs is not known.

METHODS
The NanoString GeoMxTM Digital Spatial Profiler platform was used to determine the immune marker and genetic layout in a cohort of both pediatric and adult H3 K27-altered DMG tissue samples. 5 samples from each population were assessed in triplicates for a total of 30 samples. Three fluorescently labeled antibodies targeting immune cells (CD45), epithelial cells (PanCK), tumor cells (H3 K27M) and a nucleic acid stain (SYTO-13) were used to identify and separate out the various components within the tumor tissues from selected regions of interest. The resultant information was then pooled into libraries that were run through the NanoString spatial profiler and Illumina sequencing system to assess proteomics and gene expressions for both cohorts of samples.

RESULTS
Our data revealed that there were immune and genetic changes that were seen within both populations across multiple regions of interest within the tumor tissues. A number of immune cell types and protein markers exhibited significant difference between the pediatric and adult tissue cohorts.

CONCLUSION
The proteogenomic spatial analysis of pediatric and adult H3 K27-altered DMG shows different immune and genetic profiles which are proposed to contribute to the clinical differences between both populations. These observed differences may play a role in future treatments for H3 K27-altered DMG and further research is needed to explore this.
EPCO-35. THE ZINC FINGER IN THE CEREBELLUM (ZIC1/4) LOCUS IS A CONTEXT DEPENDENT DRIVER GENE IN MEDULLOBLASTOMA
Authors: Lee John , Tao Ran , You Zhen , Huang Frank , Northcott Paul , Taylor Michael 
Published: November 2022

Abstract
Medulloblastoma (MB) is a malignant paediatric brain tumor comprised of 4 molecularly and clinically distinct subgroups: WNT, SHH, Group 3 and Group 4. Previous studies have reported recurrent, mutually exclusive epigenetic modifier mutations converging in these subgroups, as well as aberrant H3K27me3 depositions within these tumors. While these observations hint at aberrant epigenetic mechanisms driving MB pathobiology, detailed understanding of MB chromatin landscape remains elusive to date. As such, chromatin landscape of MB was defined by conducting H3K27Ac ChIP-Seq in 102 primary MB tumors and H3K27me3 ChIP-Seq in 63 overlapping tumors. Chromatin landscape of Medulloblastoma was subgroup specific and H3K27me3 modification recurrently repressed ZIC1 in Group 3 and 4 MB, a driver gene that is also recurrently mutated within Group 4 and SHH MB. Validation cohort comprised of 251 MB samples with matching RNA-Seq and WGS data demonstrated that the ZIC1 - ZIC4 locus (ZIC1/4) undergoes recurrent epigenetic repression of single alleles in 25% of Group 3, 50% of Group 4 but rarely in other subgroups. Strikingly, ZIC1 mutations in the Group 4 tumors always occurred in the context of repression of the wildtype allele, revealing a recurrent convergence of genetic and epigenetic mechanisms targeting both copies of ZIC1. Overexpression of ZIC1 and ZIC4 together, or ZIC1 alone to a lesser extent, lead to reduced proliferation of Group 3 MB cells in vitro and in vivo. Intriguingly, while Group 4 ZIC1 mutations exhibited loss of function phenotypes, SHH ZIC1 mutations exhibited gain of function phenotypes. Overexpression of ZIC1 in Granule Progenitor Cells (GPC), which give rise to SHH MB, resulted in increased proliferation of cells in contrast to Group 3 MB cells. Taken together, we demonstrate that multiple epigenetic and genetic mechanisms converge to govern context dependent driver roles for ZIC1 and ZIC4 underlying MB pathobiology.
EPCO-42. HYPO-TRIMETHYLATION OF HISTONE H3 LYSINE 4 AND HYPER-DI/TRIMETHYLATION OF HISTONE H3 LYSINE 27 AS THE EPIGENETIC MARKERS OF POOR PROGNOSIS FOR PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMA PATIENTS
Authors: Kim Hoon Gi , Kim Young Zoon 
Published: November 2022

Abstract

PURPOSE
This study aimed to investigate the methylation status of major histone modification sites in PCNSL samples and examine their prognostic role in PCNSL patients.

METHODS
Between 2007 and 2020, 87 patients were histopathologically diagnosed as PCNSL, and they were treated with same protocol of high-dose methotrexate-based combination chemotherapy. Clinical data for PFS and OS was obtained from medical records retrospectively. Immunohistochemical staining for FFPE samples of PCNSL from pathological archives in our institute was performed for major histone modification site such as histone H3K4, H3K9, H3K27, H3K14, and H3K36. After detection of meaningful methylation site, we examine the histone modification enzyme which induce methylation or demethylation on each site using immunohistochemical staining. The meaningful immunoreactivity was validated with qRT-PCR and western blotting using fresh tissue of PCNSL under refrigerated state in N2O container.

RESULTS
Among 87 patients, 28 patients (32.2%) experienced recurrence or progression and 11 patients (12.6%) succumbed their disease during follow-up for 12 months or more. More frequent recurrences was found in hypomethylation of H3K4me3 (p=0.004), and hypermethylation of H3K27me2 (p&lt; 0.001) and H3K27me3 (p=0.002). These factors were also statistically related with short PFS and OS in univariate and multivariate analysis. At the next step, histone modification enzyme inducing demethylation of H3K4 (LSD1/2, KDM5A-D, NO66), and methylation of H3K27 (EZH1/2) was immunohistochemically stained. Among them, the immunoreactivity of KDM5A was reversely associated with methylation status of H3K4me3 (R2=-1.243), and immunoreactivity of EZH2 was directly associated with methylation status of H3K27me2 (R2=0.988) and H3K27me3 (R2=1.139). These results was confirmed using RT-PCR and western blotting in fresh sample of PCNSL.

CONCLUSION
Our presenting study suggest that hypomethylation of H3K4me3, and hypermethylation of H3K27me2 and H3K27me3 could be associated with poor outcome of PCNSL patients. These relationship was modified by KDM5A as H3K4 demethylase and EZH2 as H3K27 methyltransferase.
EPCO-47. ITCC-P4: GENOMIC PROFILING AND ANALYSES OF PEDIATRIC PATIENT TUMOR AND PATIENT-DERIVED XENOGRAFT (PDX) MODELS FOR HIGH THROUGHPUT IN VIVO TESTING
Authors: Gopisetty Apurva , Federico Aniello , Surdez Didier , Saberi-Ansari Elnaz , Iddir Yasmine , Saint-Charles Alexandra , Waterfall Joshua , Wierzbinska Justyna , Schlicker Andreas , Mack Norman , Schwalm Benjamin , Jones David T , Gojo Johannes , Chesler Louis , Vassal Gilles , Stancato Lou , Koster Jan , Molenaar Jan J , Jaeger Natalie , Schleiermacher Gudrun , Pfister Stefan , Kool Marcel 
Published: November 2022

Abstract
Advancements in state-of-the-art molecular profiling techniques has resulted in better understanding of pediatric cancers and their drivers. Conversely, it also became apparent that pediatric cancers are much more heterogeneous than previously thought. Many new types and subtypes of pediatric cancers have been identified with distinct molecular and clinical characteristics. However, for most newly recognized entities there is no specific treatment available yet. The ITCC-P4 consortium is a collaboration between many academic centers across Europe and several pharmaceutical companies involved in preclinical testing, with the overall aim to establish a sustainable platform of &gt;400 molecularly well-characterized PDX models of high-risk pediatric cancers and to use them for in vivo testing of novel mechanism-of-action based treatments. Currently, 340 models are fully established, including 87 brain and 253 non-brain tumor models, together representing different tumor types both from primary (113) and relapsed (92)/metastatic disease (42). 252 of these models have been fully molecularly characterized, representing 18 pediatric cancer entities and 43 different subtypes. Using low coverage whole-genome and whole exome sequencing, somatic mutation calling, DNA copy number, transcriptome analysis and methylation profiling we have observed that the molecular profile of most PDX models closely mimics their original tumors. Clonal evolution of somatic variants was only observed in some PDX-tumor pairs or so between disease states. Somatic copy number variant analysis highlights specific alterations for instance MYB, MYC, MYCN, NTRK3, PTEN loss differently distributed between PDX-patient tumor pairs in high-grade gliomas. Overall, our results show that we have established &gt;250 PDX models of solid pediatric cancers, that well represents the disease spectrum and that is currently being used for in vivo testing of standard of care drugs and targeted small molecules. Treatment responses will be directly linked to molecular data to identify potential biomarkers for prioritization or deprioritization of individual, patient-specific specific drugs.
DISP-04. PATIENTS WITH PROGRESSION OF SPINE METASTASES WHO PRESENT TO CLINIC HAVE BETTER OUTCOMES COMPARED TO THOSE WHO PRESENT TO THE EMERGENCY DEPARTMENT
Authors: Strong Michael , Kathawate Varun , Goethe Peyton , Tudrick Lila , Linzey Joseph , Ward Ayobami , Zaki Mark , Joshi Rushikesh , Jackson William , Szerlip Nicholas 
Published: November 2022

Abstract
As cancer therapies have improved, survival has increased. Spine metastases are becoming more common in the course of oncologic disease. Complications arising from these metastases have a significant impact on patient quality of life and the optimal method to follow these patients and avoid deficits has not yet been adequately studied. The purpose of this study was to identify characteristics of a subgroup of oncologic patients with metastatic spinal disease. Retrospective analysis of oncological patients ( &gt; 18 years) who underwent stereotactic body radiation therapy (SBRT) to the spine at the University of Michigan, from 2010 to 2020 was performed. A total of 395 radiographic isocenters in 298 patients were identified. Of these, 112 isocenters in 83 patients and 283 isocenters in 215 patients were treated after presenting to the ED or clinic, respectively. As expected, patients presenting to the ED had more deficits compared to the clinic (severe pain (30% vs 6%); difficulty ambulating (48% vs 8%); weakness (25% vs 6%); or myelopathy (11% vs 1%). Social economic factors including marital status, insurance type, and having a primary care physician were similar between groups. Of the 112 ED isocenters, 58 required surgery plus SBRT (52%); while 54 required SBRT only (48%). Additionally, of the 283 clinic isocenters, 53 required surgery plus SBRT (19%); while 230 only required SBRT (81%). The overall survival was higher for clinic compared to ED (12.6mos vs 8.5mos), respectively. Interestingly, even when surgical intervention was taken into consideration, those presenting to the ED still had poorer outcomes compared to clinic (6.7mos vs 13.3mos), respectively. Metastatic spinal disease patients who present to the ED have poorer survival than those who present to the clinic. A better understanding of the factors that drive this phenomenon is warranted in order to improve the management and outcomes of this population.
IMMU-06. REDUCTION OF CD4+ T CELLS NEGATIVELY AFFECTS SURVIVAL IN OLD BUT NOT YOUNG MICE WITH GLIOBLASTOMA
Authors: Zhai Lijie , Bell April , Lauing Kristen , Bommi Prashant , Ladomersky Erik , Mi Xinlei , Kocherginski Masha , Chandler James , Horbinski Craig , Heimberger Amy , Lukas Rimas , Wainwright Derek 
Published: November 2022

Abstract

OBJECTIVE
Previous work indicates poorer survival outcomes for older glioblastoma (GBM) patients ≥ 65 years of age as compared to younger patients &lt; 65 years of age. The cellular mechanisms associated with this age-dependent survival difference remain elusive. Here we evaluated the overall survival of young and old immunocompetent mice with intracranial brain tumors that were depleted for specific immune cell populations.

METHODS
Young 6-8 weeks of age vs old 80+ weeks of age C57BL/6 mice were treated for up to 3 weeks with either IgG isotype control antibodies or with depleting antibodies against murine CD4, CD8, or NK1.1, beginning at 3 days prior to- and every 3 days post-intracranial injection of the mouse brain tumor cell lines, GL261 or CT-2A. Overall survival was compared between groups. Additionally, absolute peripheral blood mononuclear cell (PBMC) counts for CD3+ T cells, CD4+ T cells, and CD8+ T cells were analyzed between aneurysm control- and GBM-patients.

RESULTS
Older adult mice, but not younger mice, with either intracranial GL261 or CT-2A cell-based brain tumors have a significantly decreased overall survival when depleted for CD4+ T cells as compared to the IgG control-treated group, as well as groups depleted for CD8+ T- or NK-cells (P &lt; 0.05). Coincidently, older GBM patients have fewer CD4+ T cells as compared to younger GBM patient counterparts (P &lt; 0.05).

CONCLUSIONS
The data suggest that the levels of CD4+ T cells play more important roles in the survival of old subjects with GBM than in the younger subjects. A mechanistic understanding for this CD4+ T cell-dependent survival benefit is ongoing.
IMMU-20. MODULATION OF THE PERIPHERAL T CELL BIOLOGY IN GLIOBLASTOMA
Authors: Mohme Malte , Rünger Alessandra , Glau Laura , Ryba Alice , Fita Krystian , Saygi Ceren , Alawi Malik , Westphal Manfred , Tolosa Eva , Maire Cecile , Lamszus Katrin 
Published: November 2022

Abstract
Cancer is a systemic disease. Due to the exceedingly rare occurrence of metastasis of cerebral glioma, systemic alterations have, however, not been considered to play a major role in disease progression of glioma. T cells orchestrate the adaptive immune response in an antigen-specific, cytokine mediated manner. The aim of our study was to investigate how cerebral glioma impacts systemic T cell immunobiology. We performed gene expression profiling of peripheral blood T cells in patients with IDHwt glioblastomas as well as in a murine glioma model. In addition, we analyzed the levels of soluble immune biomarkers in patient blood and performed flow-cytometric phenotyping of human peripheral blood CD3+ T cells. We discovered a significant skewing of peripheral T cell phenotypes in IDHwt glioblastoma patients compared to healthy donors (HD), showing CD4+ TH1 expansion and reduced numbers of T follicular helper cells (TFH), TH1* and mucosa associated invariant T (MAIT) cells, while TH2 and TH17 percentages remained stable. Interestingly, peripheral memory CD4+ T cells exhibited reduced Fas and PD-1 expression, while CD8 T cells were primarily affected in the non-memory CD45RA+ compartment, displaying reduced numbers of CD8+ CD127+ CD27+ cells. Compared to healthy individuals, GBM patients had significantly increased levels of soluble CD27 while levels of soluble CD25 were reduced (p &lt; 0.05). GSEA and ORA analysis of differentially expressed genes in murine gliomas showed alterations in RNA binding and processing, as well as ribosomal activity in both cell types, indicating systemic modulation in translational- and cell cycle pathways in glioblastoma. Taken together, our results demonstrate a significant skewing of the peripheral T immunobiology in patients with IDHwt gliomas. Our data highlights the importance of considering malignant glioma as a systemic disease that fundamentally alters the immune repertoire in affected patients.
IMMU-26. HEIGHTENED LEVELS OF CIRCULATING CELL-FREE DNA CONTRIBUTE TO PERIPHERAL IMMUNOSUPPRESSION DURING GBM PROGRESSION
Authors: Ayasoufi Katayoun , Wolf Delaney , Tritz Zachariah , Gulbicki Lauren , Jin Fang , Hansen Michael , Fain Cori , Johnson Aaron 
Published: November 2022

Abstract
Glioblastoma (GBM) is an incurable and aggressive form of brain cancer that is associated with severe peripheral immunosuppression. This immunosuppression is a critical barrier to patient survival and the success of immune modulatory therapies. Using the murine GL261 model of GBM, we recapitulated major features of peripheral immunosuppression observed in patients including T cell lymphopenia. We determined that peripheral immunosuppression in GBM is multifaceted and involves release of novel non-steroidal soluble factors with large molecular weight that are found in sera of glioma-bearing mice. These high molecular weight species potently inhibits T cell proliferation in vitro despite the presence of strong T cell stimulation. Our goal was to determine the identity of the immunosuppressive species in serum of glioma-bearing mice. We performed state-of-the-art comparative high throughput mass spectrometry on fractionated and multiplexed sera isolated from control and glioma-bearing mice. This proteomics analysis demonstrated histones as a top highly abundant protein in serum of glioma-bearing mice compared to naïve controls. Cell-free DNA has been recently identified as an immune suppressive factor in circulation and can be bound to histones. We, therefore, assessed cell-free DNA levels in the serum of glioma-bearing mice. We determined that sera isolated from glioma-bearing mice harbor significantly higher concentrations of double stranded and single stranded cell-free DNA compared to healthy controls. Reducing the DNA content in serum, using DNAse treatment, partially improved the defect in T cell proliferation observed when T cells are exposed to serum isolated from glioma-bearing mice. These data indicate that heighted levels of circulating DNA in serum contributes to peripheral immunosuppression in GBM. These findings provide a tractable approach to investigate the cellular source and immunosuppressive effects of cell-free DNA in murine models of GBM and to devise strategies to reverse immunosuppression with the hope of improving outcomes in patients.
IMMU-38. MYC DRIVEN IMMUNE SUPPRESSION IN GROUP 3 MEDULLOBLASTOMA
Authors: Mitra Siddhartha , Picard Daniel , Qin Nan , Cole Allison , Cruz Joselyn Cruz , Marquardt Viktoria , Venkataraman Sujatha , Vibhakar Rajeev , Remke Marc 
Published: November 2022

Abstract

BACKGROUND
The expression of MYC in tumor cells regulates the tumor microenvironment through innate and adaptive immune effector cells and immune regulatory cytokines. MYC has also been shown to regulate the expression of the immune checkpoint gene products CD47 and programmed death-ligand 1 (PD-L1). While PD-L1 inhibits adaptive immune response, CD47 on tumor cells binds to SIRPa on macrophages and acts as a “Don’t eat me” signal. We have previously shown that blocking the CD47-SIRPa pathway significantly decreases tumor burden and increases survival in five etiologically distinct adult and pediatric brain tumor xenograft models, including Group 3 or MYC-driven MB, by activating macrophage-mediated phagocytosis.

METHODS
We performed a primary screen including 78 epigenetic inhibitors and a secondary screen including 20 histone deacetylase inhibitors (HDACi) to compare response profiles in ATRT, medulloblastoma (n = 14), and glioblastoma (n = 14). This unbiased approach revealed the preferential activity of Class I HDACi in MYC-driven medulloblastoma mediated by induction of apoptosis, reduction in MYC transcription, and release of pro-inflammatory cytokines in MYC-driven medulloblastoma, with little to no activity in non-MYC-driven medulloblastoma, AT/RT, and glioblastoma in vitro. In addition, we tested the combinatorial effect of directly targeting the MYC/MAX interaction using MYCI-975 and the CD47-SIRPa phagocytosis checkpoint pathway using in-vitro phagocytosis assays and in-vivo xenograft models. In two orthotopic mouse models of MYC-driven medulloblastoma, MYCi975 displayed anti-tumoral effects at the primary site and the metastatic compartment. Furthermore, RNA sequencing revealed NFκB pathway induction as a response to MYC treatment, followed by interferon-gamma (IFN-G) release and cell surface expression of engulfment (“eat-me”) signals (such as calreticulin) and enhanced in vitro phagocytosis and survival in tumor-bearing mice.

CONCLUSION
Together, these findings suggest a dynamic relationship between MYC amplification and innate immune suppression in MYC-medulloblastoma and support further investigation of phagocytosis modulation as a strategy to enhance cancer immunotherapy responses.
IMMU-43. CXCR3 SIGNALING ENGAGES GLIOMA INFILTRATING T CELLS AND IS REQUIRED FOR THE ANTITUMOR EFFICACY OF INNATE STIMULATING IMMUNOTHERAPY
Authors: Brown Michael , Yang Yuanfan , Mckay Zachary , Bigner Darell , Ashley David , Gromeier Matthias , Nair Smita 
Published: November 2022

Abstract

BACKGROUND
T cell dysfunction is well documented in patients with gliomas, yet mechanisms explaining T cell dysfunction in gliomas are lacking. Recent evidence links CXCR3 signaling and functional immune surveillance in both preclinical models and human data sets.

METHODS
Bulk and single cell RNA-seq data sets were used to compare CXCR3 ligand expression in gliomas to that of other solid tumor types. The role of CXCR3 signaling in mediating the recruitment and phenotype of tumor infiltrating lymphocytes (TILs) was tested using CXCR3 blockade and genetic deletion of CXCR3 in murine tumor models. The capacity of relevant innate stimulating immunotherapies to induce CXCR3 ligands in human glioma tissue was assessed using an ex vivo glioma slice culture assay, and the contribution of CXCR3 signaling to polio virotherapy (PVSRIPO) and STING agonist therapy was tested in murine models.

RESULTS
Relative to other solid tumors, gliomas express significantly lower levels of CXCR3 ligands (CXCL9, 10, and 11), which are largely expressed by tumor associated myeloid cells. Blocking CXCR3 signaling profoundly restricted TIL recruitment in murine gliomas, and resulted in decreased TIL stemness features coinciding with exacerbated exhaustion phenotypes. Polio virotherapy and STING agonism efficiently induced CXCR3 ligand production in fresh human glioma tissue in a manner dependent upon myeloid cells, and at levels similar to that induced by the same agents in melanoma and breast cancer tissue. CXCR3+ TILs expressed higher levels of memory and activation markers, proliferated more, and were required for the antitumor efficacy of both polio virotherapy and a STING agonist in mice.

CONCLUSION
This work indicates that CXCR3 signaling, a key contributor to cancer immune surveillance, is disrupted in human gliomas relative to other solid tumor types. Intratumor virotherapy and STING agonists hold potential to rectify diminished CXCR3 ligand expression in gliomas.