bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPCO-02. GENOME-WIDE DNA METHYLATION PROFILING AND GENETIC CHARACTERIZATION OF LONG-TERM SURVIVAL IDH WILD-TYPE GLIOBLASTOMA PATIENTS
Authors: Miele Evelina , Lazzarini Elisabetta , Ciolfi Andrea , Pedace Lucia , Nardini Claudia , Patrizi Sara , Mastronuzzi Angela , Tartaglia Marco , Anghileri Elena , Calatozzolo Chiara , Lamperti Elena Antonia , Patanè Monica , Locatelli Franco , Indraccolo Stefano , Pollo Bianca 
Published: November 2022

Abstract
Glioblastoma multiforme (GBM) has a dismal outcome of approximately 12 months. Less than 5% of patients (long-term survivors-LTS) survives more than 5-years, including IDH-mutant gliomas. Nevertheless, the molecular fingerprint of LTS remains largely uncharted. DNA methylation (DNAm) is an epigenetic modification, altered in cancer and used to classify brain tumors. In this multicentric study sponsored by Alleanza Contro il Cancro (ACC) network, we aimed to molecularly characterize LTS vs standard survival GBM (CTR) by DNAm/Copy Number Variation (CNV) and mutation profiling. We analyzed 51 IDHwt GBM samples (27LTS/24CTR) by Illumina EPIC beadChip and AmpliSeq Comprehensive Cancer Panel. We ran methylation data through the brain tumor classifiers v11b4 and v12.5, performed multidimensional scaling analysis and investigated differentially methylated regions (DMR) correlating them with survival. According to v11b4, cases were classified as: 43 GBM IDHwt (22LTS/21CTR), 27 with a calibrated score &gt;0.84 (16LTS); Plexus Tumor with low scores (2LTS/3CTR); 3 LTS samples did not match. A diagnostic refinement was observed by the v12.5, with 48 cases classifying as GBM IDHwt (25LTS/23CTR) and 35 (19LTS) with optimal score. The LTS group was more heterogeneous, with 4 cases matching in the pedHGG subtypes, including 2 cases in young adults, one with high tumor mutational burden and MSH6 mutation. No specific DNAm genomic profile was observed for LTS patients but we identified 18 significant DMRs, 4 associated with survival probability. At CNV analysis, most cases showed classical alterations (Chr7 gain with or w/o EGFR amplification, 9p21 loss, Chr10 loss) while pedHGG were associated with PDGFRA amplification, 1q gain, 13q loss. NGS identified at least 1 pathogenic variant in 40 cases (22CTR/18LTS) and showed a higher prevalence of mutation negative cases among LTS. No significant difference between the 2 groups was observed in terms of prevalence of mutated genes or number of VUS per sample.
EPCO-03. PATHWAY-BASED STRATIFICATION OF GLIOBLASTOMA BY MULTI-OMICS INFORMS SUBTYPE-SPECIFIC MASTER KINASES-PHOSPHOSITE SUBSTRATES
Authors: Migliozzi Simona , Oh Young Taek , Hasanain Mohammad , Garofano Luciano , D'Angelo Fulvio , Picca Alberto , Bielle Franck , Sarkaria Jann , Ceccarelli Michele , Sanson Marc , Lasorella Anna , Iavarone Antonio 
Published: November 2022

Abstract
Tumor heterogeneity and broad therapeutic resistance are major challenges when treating patients with glioblastoma (GBM). Moreover, different from other cancer types, the absence of clinically useful classifiers for glioblastoma has hampered the translation of genomic and proteomic information to improve diagnosis and design precision therapeutics for patients. We analyzed a large dataset of human GBM to determine the multi-omics features characterizing the four GBM subtypes that we have recently identified through single-cell RNA sequencing and validated in bulk tumor analysis. Each subtype exhibits activation of unique functional traits that confer distinct therapeutic vulnerabilities. The examination of proteomics, phosphoproteomics, metabolomics, lipidomics and acetylomics data revealed that each GBM subtype has a coherent molecular structure driving the dominant function traceable in each analytical platform. Functional classes are not a specific attribute of GBM as we identified the same subtypes in breast and lung cancer. To test the translational impact of proteomic data in GBM, we developed an unbiased protein kinase signaling network approach for the selection of master kinases (MKs) aberrantly activated in each GBM subtype. We identified therapeutically actionable MKs and novel phosphorylation substrates that we experimentally validated. To provide rapid translation of the functional classifier for precision medicine in GBM, we developed a probabilistic classification tool which determines the probability that a patient’s GBM belongs to one of the four subtypes, exhibiting optimal performance when using RNA extracted from either frozen and paraffin-embedded tissues. The algorithm is publicly accessible and can be used to evaluate the association of therapeutic response with GBM subtypes and as tool for selection criteria in prospective clinical trials.
EPCO-05. DIFFERENTIAL MOLECULAR PROFILING OF IDH WILD TYPE GLIOBLASTOMA SURVIVORS REVEALS THE ASSOCIATION OF NEOANTIGEN QUALITY WITH EXCEPTIONAL LONG SURVIVAL
Authors: D'Angelo Fulvio , Garofano Luciano , Aoki Kosuke , Ceccarelli Michele , Lasorella Anna , Sanson Marc , Iavarone Antonio 
Published: November 2022

Abstract
Glioblastoma multiforme (GBM) is the most common and malignant type of primary brain tumor. Despite intensive multimodal treatment, the prognosis of GBM patients is poor with the median overall survival under 15 months. Defining the genetic profiles of rare long-term GBM survivors may provide insights into the molecular basis of GBM progression. IDH mutations have been identified as a favorable prognostic factors, and define a clinically and molecularly distinct group of GBM. Additional molecular mechanisms underlying the prolonged survival in IDHwt GBM patients remained unclear. Therefore, we explored the molecular profiles of 71 IDHwt GBM homogeneously treated patients exhibiting disproportionate survival. The cohort included 36 short-term survivors that deceased within 1 year after diagnosis (median survival of 7 months) and 35 long-term survivors exhibiting an exceptional survival above 4 years (median survival of 88 months). The differential genetic landscape of short- and long-term IDHwt GBM survivors outlined similar mutation load and few differences in the frequency of recurrent alterations, including chromosomes 19 and 20 duplication significantly overrepresented in long-term survivors. To assess the potential impact of T lymphocyte neoantigen-mediated activation towards extended GBM survival, we inferred the restricted HLA binding affinity of the somatic mutations and applied the immune fitness model to accurately predict high-quality neoantigens. Although the general neoantigen burden remained unvaried between short- and long-term survivors, we found that the immune quality of the predicted neoantigens is significantly higher in the patients with exceptional long survival. Moreover, the immune deconvolution of the tumor microenvironment from the gene expression data indicated the presence of CD8+ T lymphocytes and pro-inflammatory macrophages in samples harboring high-quality neoantigens from long-term survivors. This study identified the neoantigen quality as a main distinctive feature of exceptionally long-term survivors supporting the key role of cellular-mediated immune response to restrict tumor progression in IDHwt GBM.
EPCO-06. THE IMPACT OF MISMATCH REPAIR DEFICIENCY (MMRD) ON SURVIVAL OF TEMOZOLOMIDE (TMZ)-TREATED PATIENTS WITH MGMT METHYLATED (M-MGMT) GLIOBLASTOMA (GBM): A CELLWORKS COMPUTATIONAL BIOSIMULATION PILOT STUDY
Authors: Castro Michael , Iwamoto Fabio , Ahluwalia Manmeet , Usmani Shahabuddin , Kumar Ansu , Kapoor Shweta , Suseela Rakhi Purushothaman , Kulkarni Shruthi , Mohanty Jharana , Shyamasundar Vijayashree , Ghosh Adity , Prasad Nagendra , Patil Mamatha , Choudhury Sayantani Roy , Chauhan Jyoti , Sauban Mohammed , Joseph Vishwas , Kumari Pallavi , Mitra Upasana , Pampana Anusha , Azam Humera , G Poornachandra , Prakash Annapoorna , Basu Sayani 
Published: November 2022

Abstract

BACKGROUND
TMZ-induced G:T mismatches trigger MMR to perform futile repair of O6-methylguanine leading to apoptosis. Without MMR, the G:T mutation is genomically incorporated to produce DNA mutation signature #11. Hypermutation ensues and may compromise survival without the redemptive benefit of immunotherapy. MMR genes are infrequently mutated or deleted. More commonly, MMRD results from epigenetic silencing, transcription failure, or micro-RNA compromising translation.

METHODS
Comprehensive genomic profiling and Cellworks biosimulation was utilized to diagnose MMRD and correlated with survival in 38 TCGA patients with newly diagnosed, IDH wildtype, m-MGMT GBM treated with adjuvant TMZ. The signaling pathway consequences for MutSα and MutLα were assessed. Kaplan-Meier curves were constructed for PFS and OS.

RESULTS
Patients were characterized: MMR proficient (Grp 1) and deficient (Grp 2). Half (19/38) had compromise of 1-10 pathways impacting MMR: 3 had deletions of MLH1 or PMS2. Others included deletions of EP300, CREBBP, KMT2A-D, ARID1A, HUS, or EXO1 and amplifications of KDM4A/C or MIR21/155. Grp 1 had significantly higher MMR biosimulation scores than Grp 2. (p=0.00082). The median PFS was 10.51 and 3.58 months (p=0.0072) and median OS was 16.96 and 9.40 (p=0.0059) months in Group 1&2, respectively.

CONCLUSIONS
Up to half of GBM patients have MMRD caused by pathway dysregulation. Biosimulation of MMRD predicts early progression on TMZ, echoing the long-held observation that TMZ does not trigger apoptosis in MMRD cancers. The study also reports inferior OS for MMRD compared to the historical experience of unmethylated-MGMT patients, suggesting that TMZ-induced hypermutation may compromise survival. As lomustine does not rely on intact MMR, 2nd-line lomustine may have blunted the impact of MMR on OS. Alternatively, upfront lomustine might have produced superior disease control in MMRD patients. Computational biosimulation offers the opportunity to diagnose patients who should not receive TMZ despite m-MGMT and who could benefit from alternative adjuvant strategies.
EPCO-09. TRANSCRIPTOMIC LANDSCAPE OF LOWER GRADE GLIOMA BASED ON AGE-RELATED NON-SILENT SOMATIC MUTATIONS
Authors: Sung Kyoung Su , Lim Jaejoon 
Published: November 2022

Abstract
Glioma accounts for 80% of all malignant brain tumours and is the most common adult primary brain tumour. Age is an important factor affecting the development of cancer, as somatic mutations accumulate with age. Here, we aimed to analyse the significance of age-dependent non-silent somatic mutations in glioma prognosis. Histological tumour grade depends on age at diagnosis in patients with IDH1, TP53, ATRX, and EGFR mutations. Age of patients with wild-type IDH1 and EGFR increased with increase in tumour grade, while the age of patients with IDH1 or EGFR mutation remained constant. However, the age of patients with EGFR mutation was higher than that of patients with IDH1 mutation. The hierarchical clustering of patients was dominantly separated by IDH1 and EGFR mutations. Furthermore, patients with IDH1 mutation were dominantly separated by TP53 and ATRX double mutation and its double wild-type counterpart. The age of patients with ATRX and TP53 mutation was lower than that of patients with wild-type ATRX and TP53. Patients with the double mutation showed poorer prognosis than those with the double wild type genotype. Unlike IDH1 mutant, IDH1 wild-type showed upregulation of expression of epithelial mesenchymal transition associated genes.
EPCO-12. SEX-SPECIFIC PATTERNS CONNECTING LOCOREGIONAL MRI FEATURES AND IMMUNOHISTOCHEMISTRY OF IMAGE-LOCALIZED BIOPSIES OF GLIOBLASTOMA
Authors: Langworthy Jazlynn , Jackson Pamela , Hawkins-Daarud Andrea , Ranjbar Sara , Singleton Kyle , Boyett Deborah , Argenziano Michael , Grinband Jack , Canoll Peter , Swanson Kristin 
Published: November 2022

Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumor with a median survival of 14 months. GBMs are challenging to treat due to their heterogeneous nature. It has also been seen that these tumors have sex differences in their cellular subtypes as well as imaging. Radiomics has the potential to provide a non-invasive, spatial understanding of genetic and epigenetic diversity in these complex tumors and to aid in treatment planning. We have an ongoing study to obtain image-localized biopsies from GBM patients, allowing us to complete radiomic analysis and make connections between immunohistochemistry (IHC) and magnetic resonance imaging (MRI) features. We sought to determine if the patterns on imaging were correlated with underlying tumor biology. We focused on immunohistochemistry (IHC) markers of key features of tumor biology including SOX2 for stem-like tumor cells, CD68 for immune response and Ki67 for proliferation kinetics. Our study included 38 patients with a total of 99 biopsies (bxs): 27 males with 77 bxs and 11 females with 22 bxs. Biopsies were sectioned and stained for the SOX2, CD68, and KI67 markers. We computed 18 first-order radiomic features at each biopsy location for patients’ multimodal MRIs: T1W, T1Gd, T2W, FLAIR, apparent diffusion coefficient, diffusion weighted imaging (DWI) and susceptibility weighted imaging. We then performed correlation analysis between each radiomic feature and marker abundance for each IHC stain. Overall, we found sex-distinct patterns connecting imaging with these IHC markers. For example, amongst female patients, DWI held more prominent correlations with SOX2 than in males. Whereas there were more correlations between CD68 IHC abundance and T1Gd imaging features in males compared to females. Taken together, the overall patterns connecting locoregional imaging features to these IHC markers showed sex-distinct patterns suggesting the potential for sex to be an important biological variable when interpreting the biology underlying imaging changes.
EPCO-16. ESTIMATING THE DIFFERENTIATION POTENTIAL AND PLASTICITY OF GLIOBLASTOMA CELLS USING STATISTICAL MECHANICS
Authors: Lång Adam , Larsson Ida , Jörnsten Rebecka , Nelander Sven 
Published: November 2022

Abstract
Glioblastoma (GBM) is the most common form of adult brain tumors and patients diagnosed with GBM face a very dismal prognosis with a median survival rate of 15 months. The challenges in treating GBM are many, there is a complex cellular and molecular heterogeneity, both between patients and within individual tumors. In a single tumor, individual cancer cells adopt a variety of stem-like, progenitor-like, and more differentiated phenotypes (a.k.a. cell states). Recent advances in single-cell technology have made it possible to detect this diversity of cellular states, but yet we lack a good explanation for how the states arise and if transitions between states can be exploited to therapeutic ends. We here propose a new computational strategy to measure the differentiation potential of GBM cells, based on the Ising models from statistical mechanics. Originally used to model coupled magnets on a lattice, the Ising models can be generalized to represent the probability of a particular configuration of any system of n variables. We show that the models can be fitted to high-dimensional single cell data in a matter of seconds by solving a convex optimization problem, and that the models help explain cell differentiation in terms of minimization of an energy function of the system. In our on-going work we have fitted the model to single cell data from our previous work on state transitions in GBM (Larsson, Dalmo et al, Molecular Systems Biology 2021) and shown that the predicted differentiation potential of cell states is consistent with the cell state hierarchies derived from lineage tracing experiments. Moving forward, we are now exploring how the Ising models can be used to model state transitions in GBM and to predict the effect of targeted therapy on the cell’s differentiation potential.
EPCO-21. THE SPATIAL ORGANIZATION OF H3-K27M MUTANT DIFFUSE MIDLINE GLIOMA
Authors: Liu Ilon , Li Jiang , Samuelsson Erik , Salas Sergio Marco , Beck Alexander , Hack Olivia , Jeong Daeun , Shaw McKenzie , Englinger Bernhard , Labelle Jenna , Mire Hafsa , Madlener Sibylle , Mayr Lisa , Quezada Michael , Trissal Maria , Panditharatna Eshini , Ernst Kati , Gatesman Taylor , Halbert Matthew , Palova Hana , Pokorna Petra , Sterba Jaroslav , Slaby Ondrej , Geyeregger Rene , Diaz Aaron , Resnick Adam C , Suva Mario , Jones David , Agnihotri Sameer , Ostlin Jessica , Koschmann Carl , Haberler Christine , Czech Thomas , Slavc Irene , Cotter Jennifer , Ligon Keith , Alexandrescu Sanda , Yung W K Alfred , Arrillaga-Romany Isabel , Gojo Johannes , Monje Michelle , Nilsson Mats , Filbin Mariella 
Published: November 2022

Abstract
Histone 3 lysine27-to-methionine mutant diffuse midline gliomas (H3-K27M DMGs) are among the most lethal brain tumors. Their putative cellular hierarchy has been shown to be driven by self-renewing stem-like cells arrested in an oligodendrocyte precursor-like (OPC-like) state, of which few cells are able to differentiate towards more mature astrocyte (AC)-like and oligodendrocyte (OC)-like cells. However, the spatial organization underlying this tumor cell architecture and its microenvironmental interactions in intact H3-K27M DMG tissues remain unknown. Here, we profiled the single cell transcriptomes of 45 patient H3-K27M DMGs and derived cell population-specific marker gene combinations to characterize the single cell spatial organization of 16 tumors using targeted in situ sequencing. We thereby resolved different malignant and non-malignant cell populations including cycling, OPC-like, AC-like, OC-like, mesenchymal tumor cells, and non-malignant oligodendrocytes, astrocytes, neurons, myeloid cells, T cells, and vascular cells directly in situ. Global neighborhood analyses indicate a higher tendency of cycling OPC-like cells, vascular cells, and neurons to localize within a more restricted homogeneous compartment, whereas AC-like cells, non-malignant astrocytes and myeloid cells tend to intermingle with different cell populations in a more diffuse manner. Among malignant cells, we observed cycling OPC-like and OC-like cells to co-localize within a niche-like structure that is surrounded by more differentiated AC-like cells. We further validated this stem-like niche at the protein level using multiplexed immunofluorescence via the CODEX system. Finally, we characterized relationships between malignant and non-malignant cells, consistently identifying preferred neighborhoods of mesenchymal tumor cells with vascular and myeloid cells. Together, this study resolves the spatial architecture of H3-K27M DMG malignant and non-malignant cells at single cell resolution and identifies a local niche of the oligodendroglial lineage containing the OPC-like cancer stem-like cells, thus providing novel insights into the cancer stem-like compartment in H3-K27M DMGs and suggesting potential avenues for its perturbation.
EPCO-23. DYSFUNCTION OF LARGE H3K9ME3 DOMAINS IN ATRX DEFICIENT GLIOMAS INDUCES GENETIC REARRANGEMENTS AND LATENT DEVELOPMENTAL SIGNALING NETWORKS THROUGH SUPER-ENHANCER LANDSCAPES
Authors: Malgulwar Prit Benny , Danussi Carla , Singh Anand , Saw Ajay Kumar , Rai Kunal , Huse Jason 
Published: November 2022

Abstract
Somatic alterations in ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-linked), a member of SWI/SNF family chromatin regulator has been found to be frequently mutated in diffuse gliomas and defines molecular subtypes with aggressive behavior. Mechanistically, ATRX regulates incorporation of histone H3.3 into chromatin sites across the genome, maintains alternative lengthening of telomeres and establishes genomic distribution of polycomb responsive genes. To understand in depth role of ATRX in gliomas, we performed ChIP-seq and/or Cut-and-tag for histone marks that define active transcription, enhancers, repressors, gene bodies and CTCF on Atrx intact and deficient mNPCs (mouse Neural Progenitor Cells). Our integrated analysis reports depletion of H3K9me3 loci’s that coincidently enriched with Atrx binding sites and Lamina-Associated Domains with genes enriched for cell cycle, motility and chromosome organization. This chromatin perturbations at heterochromatin domains was further confirmed in our Hi-C analysis with switching of A-B and B-A compartments, reorganization of TADs with occasional CTCF marks and gain of novel interacting loops that showed gene expression leakage required for gliomagenesis using Capture Hi-C. Notably, we observed aberrant levels of endogenous retroviral elements (ERVs) family members, including upregulation of Line-1 elements in mNPCs and patient derived glioma stem cells (GSCs) and our analysis shows increased copy number variations in ATRX deficient gliomas as a consequence of Line-1 activation in these subsets of tumors. Finally, our integrated omics- analysis demonstrates enrichment of super-enhancers in Atrx deficient background with several putative druggable candidates for clinical benefits. As an example, we show presence of H3K27ac super-enhancer over HOXA locus and targeting pan-HOXA genes using small inhibitor peptides diminished proliferation and migration of mNPCs and GSCs with increased in cell apoptosis with alterations in downstream developmental signaling pathways. To summarize,our data establishes tangible links between Atrx deficiency and multiscale dysregulated cellular phenotype in gliomas with identifying novel targets for therapy.
EPCO-34. INTEGRATIVE DNA METHYLATION ANALYSIS OF PEDIATRIC BRAIN TUMORS REVEALS TUMOR TYPE-SPECIFIC DEVELOPMENTAL TRAJECTORIES AND EPIGENETIC SIGNATURES OF MALIGNANCY
Authors: Pekkarinen Meeri , Nordfors Kristiina , Uusi-Mäkelä Joonas , Kytölä Ville , Rauhala Minna , Urhonen Henna , Häyrynen Sergei , Afyounian Ebrahim , Yli-Harja Olli , Zhang Wei , Helen Pauli , Lohi Olli , Haapasalo Hannu , Haapasalo Joonas , Nykter Matti , Kesseli Juha , Granberg Kirsi 
Published: November 2022

Abstract
Understanding oncogenic epigenetic mechanisms in brain tumors is crucial for improved diagnosis and treatment. Recently DNA methylation has proven to be powerful for brain tumor characterization and diagnostic classification. To evaluate tumor type specific features, we compared atypical teratoid/rhabdoid tumors (AT/RTs), medulloblastomas (MBs), and choroid plexus tumors with each other by integrating DNA methylation (507 samples), gene expression (120 samples), and transcription factor (TF) -binding data. Different tumor entities were used to find unique changes affecting each of the entities and further to identify functions driven by these changes. Our results provide insight on how the aberrant DNA methylation induces oncogenesis of AT/RTs. These tumors are known for their aggressiveness and exceptionally low mutation rates. Our results suggest that in AT/RT, elevated DNA methylation masks the binding sites of TFs such as NEUROD1, ASCL1 and MYCN driving neural development. DNA methylation in AT/RTs is also associated with reduced gene expression for specific neural regulators such as NEUROG1 and NEUROD2. For MBs, DNA methylation patterns predict a more advanced differentiation state. In MB, we found masked TF binding sites for TFs such as REST and ZEB1 that normally inhibit neural differentiation. We then wanted to further characterize DNA methylation and compared these tumors to pluripotent stem cells (PSCs) and normal fetal brain samples. As a result, we were able to find two different regulatory programs in AT/RTs: One in which DNA methylation is similar to PSCs and which harbors mostly neural TF binding sites. Second program has AT/RT-specific DNA methylation, and these sites are uniquely associated with polycomb repressive complex 2 members. However, this second program also covers neural TF binding sites and is likely to have relevance in oncogenic regulation.