bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular motion in supramolecular ionic crystal of Swiss cheese structure
Authors: Kanamaru Kazuya , Takahashi Kiyonori , Huang Rui-Kang , Xue Chen , Wu Jia-bing , Noro Shin-ichiro , Nakamura Takayoshi
Published: November 2024

In most molecular crystals, crystal structure collapses when solvent molecules are removed. We report the crystal of (isobutylammonium+)(dibenzo[18]crown-6)[Ni(dmit)2]−•0.4CH3CN with Swiss cheese–like structure, in which 60% of the CH3CN sites are voids. The motion of isobutylammonium+ adjacent to the void sites maintains the single crystallinity, which occupy an apparently larger volume than in the static state. This study opens up the possibility of developing novel relaxor dielectrics based on molecular motion in the crystal of partially occupied voids.
Classical allusions and narrative guidance in Robert Louis Stevenson’s Kidnapped
Authors: Gregory Justina
Published: November 2024

Kidnapped is the most Scottish novel Robert Louis Stevenson ever wrote. Set in the aftermath of the Battle of Culloden, it integrates historical with fictional events and features detailed Highland topography, along with a gallery of Scottish character types. Yet despite its regional ambiance Kidnapped is imbued with classical references that broaden its focus, illuminating issues of class and education within the story and of genre and narrative structure without. At the close of the novel David Balfour’s grasp of a Latin tag proves crucial to establishing, if not his identity as heir to a Scottish estate, at least his position as an educated gentleman. This status contrasts with his earlier identity as ‘the lad with the silver button’. A cluster of motifs connects the novel to the epic genre, while the observance of narrative principles set forth in Horace’s Ars Poetica adds an authentic eighteenth-century touch.
Transcatheter tricuspid valve implantation with LuX-Valve utilizing a novel patient-specific virtual and physical simulator: a case report
Authors: Delamarre Enzo , Nejjari Mohammed , Dreyfus Julien , Lesage Frédéric , Ben Ali Walid
Published: November 2024

Background

The rise of transcatheter tricuspid valve implantation (TTVI) therapies represents a major advancement for high-risk patients with severe tricuspid valve regurgitation, offering a safer, minimally invasive alternative to open-heart surgery. However, the low volume of procedures and training highlights an urgent need for skills development and pre-procedural preparation, which simulation can address by enhancing learning and expanding treatment availability.

Case summary

An 87-year-old woman with permanent atrial fibrillation and symptomatic severe functional tricuspid regurgitation underwent a transcatheter tricuspid valve replacement with the LuX-Valve system. We developed a novel patient-specific virtual reality simulator, combining virtual and physical simulations, to enhance training and education for TTVI. This system utilizes high-resolution computed tomography images, machine learning algorithms, and a video game engine to recreate realistic procedural environments. We performed a safe intervention following the simulation session, achieving successful clinical outcomes in the patient.

Discussion

The developed platform is the first to propose a patient-specific hybrid simulation for TTVI engaging both interventional and imaging cardiologists. The simulator's potential to improve clinical and safety outcomes warrants further evaluation through specifically designed comparative studies.
Thermal analysis of smartening a central heating unit for a small-scale network; characteristic, comparisons and impacts
Authors: Shayesteh Ali Akbar , Fazeli Atila
Published: November 2024

Central heating units (CHUs) significantly influence energy consumption and air quality in developing countries. Key challenges in infrastructure enhancement include the prevalent use of outdated heating technologies and the high costs involved in upgrading them. In Tehran, Iran, advancements have been made by incorporating intelligent heating systems into the local domestic engine rooms, through the use of control subsystems based on thermodynamic modeling. These subsystems, which include temperature, air control, and central processing networks, have improved the system's energy efficiency and environmental impact. A notable feature of this project is the integration of advanced thermal management in thermostats and the development of specialized algorithms to optimize combustion. Results from numerical studies indicate that these intelligent CHU systems can cut CO emissions by as much as 78% and reduce fuel consumption by up to 30%. Thus, investing in the enhancement of adaptable Combined Heat and Power (CHP) units within communities is a viable, eco-friendly strategy that promises greater reliability, reduced fuel use, and better environmental outcomes.
The Limits of the Law: Work in the Light of Capitalist Reproduction
Authors: Tzanakopoulou Maria
Published: November 2024

The article explores alternatives to capitalist work from the point of view of reproduction of capitalist relations. The latter occurs in a cyclical manner as capitalist structures—the economic, juridico-political and ideological levels—co-constitute and reproduce one another. Given the difficulty inherent in breaking the cycle of reproduction, a reflection on alternatives to capitalist work requires that work is reconceptualised, to the extent possible, beyond current structures: as transformations at any one individual level cannot produce radical change, alternatives to capitalist work require a holistic reimagining of the social totality, transcending, for example, mere legal or mere political reform. The force that can disrupt the cycle of capitalist reproduction and open space for such holistic reimagination is class struggle. The latter becomes embedded in the process of redefining work in so far as it is the force that can precipitate structural and unforeseeable change. It also acts a reminder that the substantive redefinition of work is a collective process, and cannot be the task of any single individual situated externally to that struggle.
Pregnant women and healthcare workers’
perceptions on tuberculosis and screening: a cross-sectional study in Indonesia
Authors: Rahari Dzerlina Syanaiscara , Nurdiati Detty Siti , Thobari Jarir At , Suyanto Suyanto , Liabsuetrakul Tippawan
Published: November 2024

Background

There is a scarcity of studies regarding the obstacles in tuberculosis (TB) screening in pregnant women. This study aimed to assess the perceptions of TB as a disease and TB screening among pregnant women and healthcare workers, describe pregnant women's perceptions on specific TB screening methods and explore associations between the perceptions of TB with the intention to have TB screening by pregnant women.

Methods

A cross-sectional study was conducted at six primary healthcare centres in Yogyakarta Municipality, Indonesia among 240 pregnant women and 126 healthcare workers interviewed with a structured questionnaire about their perceptions. Perceptions were analysed as percentages and associated factors were tested by multivariable logistic regression.

Results

Most pregnant women and healthcare workers supported TB screening in pregnant women based on their perceptions of the susceptibility to or severity of TB and the benefits and risks of TB screening. Women who perceived the high susceptibility of TB disease and the benefits of TB screening were significantly more likely to have high intentions to accept TB screening in the future.

Conclusions

Pregnant women's perceptions of TB and TB screening influenced their intention to be screened; however, appropriate testing methods for universal TB screening in pregnant women in areas with a high prevalence of TB require further studies.
“Extremely Stupid Guidelines”: On The Development of Historical Questions Around Guru Tegh Bahadur’s Martyrdom
Authors: Judge Rajbir Singh
Published: November 2024

In 1675, Mughal authorities beheaded Guru Tegh Bahadur, the ninth Sikh Guru and, today, the martyrdom has become a highly contested historical question within scholarly circles. This article investigates the emergence of the event as a historical question and how the emphasis of historical fact-finding refashioned scholarly approaches to the Sikh tradition in the colonial and postcolonial periods. I end by exploring how the famous Sikh intellectual and politician, Sirdar Kapur Singh (1909-1986), drew upon the Sikh tradition to challenge the very premises of such historiographical framing in his landmark essay, “Who Killed Guru Tegh Bahadur?” and the limits to his challenge. I ask: What do we make of Kapur Singh’s frustration and disgust at the history writing that came to dominate the Sikh tradition? I show how Kapur Singh does not transcend the epistemological constraints of history through a better or more accurate rendition of the past. Instead, he disrupts the historiographical operation in his frustration with history writing and what he calls its “extremely stupid guidelines.”
webTWAS 2.0: update platform for identifying complex disease susceptibility genes through transcriptome-wide association study
Authors: Cao Chen , Shao Mengting , Wang Jianhua , Li Zhenghui , Chen Haoran , You Tianyi , Li Mulin Jun , Ding Yijie , Zou Quan
Published: November 2024

Transcriptome-wide association study (TWAS) has successfully identified numerous complex disease susceptibility genes in the post-genome-wide association study (GWAS) era. Over the past 3 years, the focus of TWAS algorithms has shifted from merely identifying associations to understanding how single nucleotide polymorphisms (SNPs) regulate gene expression, with a growing emphasis on incorporating fine-mapping techniques. Additionally, the rapid increase in GWAS summary statistics, driven largely by the UK Biobank and other consortia, has made it essential to update our webTWAS resource. To address these challenges and meet the growing needs of researchers, we developed webTWAS 2.0, an updated platform for identifying susceptibility genes for human complex diseases using TWAS. Additionally, webTWAS 2.0 provides an online TWAS analysis tool that simplifies conducting TWAS analyses. The updated resource includes 7247 GWAS summary statistics covering 1588 complex human diseases from 192 publications. It also incorporates multiple TWAS methods, such as sTF-TWAS, 3′aTWAS and GIFT, along with an updated interactive visualization tool that allows users to easily explore significant associations across different methods. Other upgrades include a personalized online analysis tool for user-submitted GWAS data and a refined search function that makes it easier to identify relevant associations and meet diverse user needs more efficiently. webTWAS 2.0 is freely accessible at http://www.webtwas.net.
SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study
Authors: Liu Zhuo , Shen Shaoqin , Li Chunjin , Zhang Chenhao , Chen Xiang , Fu Yanhong , Yu Tong , Zhou Rong , Liu Dongxu , Yang Qing-Yong , Song Xiaoming
Published: November 2024

The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements in sequencing technologies. However, existing databases are limited by incomplete species representation, a lack of comprehensive comparative genomic tools and the absence of systematic pan-genomic analyses. To address these gaps, we developed the Solanaceae Information Resource (SoIR, https://soir.bio2db.com), a comprehensive genomics database for the Solanaceae family. SoIR integrates genomic data from 81 species and transcriptomic data from 41 species, encompassing a total of 3 908 408 gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases. The resource also includes 3 437 115 CRISPR guide sequences, 212 395 transcription factors and 19 086 genes associated with methylation modification. In addition to species-specific analyses, SoIR provides extensive bioinformatics tools for investigating gene family evolution, phylogenetic relationships and karyotype reconstruction across 25 fully sequenced genomes. With advanced tools such as Blast, Synteny and Sequence Alignment, the platform provides users with interactive and intuitive visualizations for conducting cross-species comparative genomics. As the first comprehensive pan-genomic resource for the entire Solanaceae family, SoIR facilitates in-depth cross-species analysis, supporting global research initiatives in plant evolution, functional genomics and crop improvement.
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis
Authors: Yang Tingting , Wang Dingyue , Luo Lingxiao , Yin Xiaochang , Song Zhihan , Yang Minqi , Zhou Yue
Published: November 2024

PWWP-DOMAIN INTERACTOR OF POLYCOMBS (PWO) family proteins play a vital role in regulating plant development. However, the molecular mechanisms of how PWOs regulate chromatin structure is elusive. Our data show that the PWO1 binding sites are enriched with positive modifications but exclusive with H3K27me3. Moreover, PWO1 binds to the H3K27me3-enriched compartment domain (H3K27me3-CD) boundary regions, and functions to maintain the boundary strength. Meanwhile, we found that PWOs and Polycomb repressive complex 2 (PRC2) function parallelly in maintaining H3K27me3-CDs’ structure. Loss of either PWOs or PRC2 leads to H3K27me3-CD strength reduction, B to A compartment switching as well as the H3K27me3-CD relocating away from the nuclear periphery. Additionally, PWOs and lamin-like proteins collaborate to regulate multiple chromatin structures to repress gene transcription within H3K27me3-CDs. We conclude that PWOs maintain H3K27me3-CDs’ repressive state and regulate their spatial position in the nucleus.
EPCO-01. FROM HIERARCHY TO GEOGRAPHY: MULTI-CLONES DRIVE THE CELLULAR DIVERSITY AND EVOLUTION OF HUMAN MEDULLOBLASTOMA
Authors: Liu Hailong , Li Jiankang , Jiang Tao
Published: November 2024

We’ve curated a comprehensive multi-omics database of medulloblastoma (MB) serving as a resource to understand spatiotemporal organization and guide therapeutic strategies. Herein, our analysis encompasses single-nucleus transcriptome (n = 51), chromatin accessibility (n = 46), and spatial transcriptomic profiles (n = 31) from human MB samples and patient-derived xenograft lines spanning four subgroups, augmented by bulk RNA (n = 322), whole-genome short-sequencing (n = 279), and bisulfite sequencing (n = 300) from matched samples. We delineate the malignant cellular hierarchy, identifying MB cancer stem-like cells (MB-CSCs), cycling cells, and more differentiated populations. Gene signatures of different cell subpopulations strongly correlate to clinical outcomes, while spatial character of patient-derived materials emphasizes the geographically heterogeneous nature of MB. Examination of somatic copy number variants (CNVs) and transcriptional signatures at single-nucleus resolution reveals geographically defined subclones harboring distinct CNVs, suggesting a competitive agglomeration of co-existing multi-clones for MB. Alongside the trajectorial transition, we observe distinct chromosomal alterations in apical MB-CSCs compared to more differentiated cells, indicative of extensive subclone-primed spatiotemporal evolution. Further analysis of reagent-gene interactions of subclonal lineages contributes to predicting the druggable candidates for treatment optimization. Integration of spatial architecture data highlights the recapitulation of subclone-determined niches through colocation with identified malignant lineages and their own inflammatory or fibrotic adaptions. Taken together, this comprehensive database, comprising five or six kinds of datatypes on the same MB cases, facilitates combinatorial analyses across different genomic modalities, offering genetic and geographic insights into therapeutic advancements.
EPCO-03. METABOLIC INSIGHT INTO GLIOMA HETEROGENEITY: MAPPING WHOLE EXOME SEQUENCING TOIN VIVO IMAGING WITH STEREOTACTIC LOCALIZATION AND DEEP LEARNING
Authors: Servati Mahsa , Cohen-Gadol Aaron A , Parker Jason G
Published: November 2024

Intra-tumoral heterogeneity (ITH) complicates the diagnosis and treatment of glioma, partly due to the diverse metabolic profiles driven by genomic alterations. While multiparametric imaging captures spatial and functional variations enabling ITH characterization, it falls short in assessing the metabolic activities underpinning phenotypic differences. This gap stems from the challenge of integrating easily accessible, co-located pathology and genomic data with metabolic insights. This study presents a multi-faceted approach combining stereotactic biopsy with clinical open-craniotomy for sample collection, voxel-wise analysis of MR images, regression-based GAM, and whole-exome sequencing. The aim is to demonstrate the potential of machine learning algorithms to predict variations in cellular and molecular tumor characteristics. This retrospective study enrolled ten treatment-naïve patients with radiologically confirmed glioma who underwent multiparametric MR scans (T1W, T1W-CE, T2W, T2W-FLAIR, DWI) prior to surgery. During craniotomy, at least one stereotactic biopsy was collected from each patient, with the screenshots of sample locations saved for spatial registration to pre-surgical MR data. Whole-exome sequencing was performed on flash-frozen tumor samples, prioritizing five glioma-related genes: IDH1, TP53, EGFR, PIK3CA, and NF1. Regression was implemented with a GAM using a univariate shape function for each predictor. Standard ROC analyses were used to evaluate detection, with AUC calculated for each gene target and MR contrast combination. Mean AUC for five gene targets and 31 MR contrast combinations was 0.75±0.11, with individual AUCs as high as 0.96 for IDH1 and TP53 with T2W-FLAIR and ADC, and 0.99 for EGFR with T2W and ADC. An average AUC of 0.85 across the five mutations was achieved using the combination of T1W, T2W-FLAIR, and ADC. These results suggest the possibility of predicting exome-wide mutation events from non-invasive, in vivo imaging by combining stereotactic localization of glioma samples with a semi-parametric deep learning method. This approach holds potential for refining targeted therapy by better addressing the genomic heterogeneity of glioma tumors.
EPCO-05. GENOMIC AND CLINICAL INSIGHTS FROM A LARGE-SCALE STUDY OF 172 RETINOBLASTOMAS
Authors: Abedalthagafi Malak , Maktabi Azza , Mesfer Saleh , Zauli Giorgio , Edward Deepak , Liu Yang , Hoehndorf Robert
Published: November 2024

Retinoblastoma, a pediatric ocular cancer, is the only central nervous system tumor visible without specialized tools, readily detectable with the naked eye. This rare childhood cancer is mainly driven by mutations in RB1 or MYCN amplification, posing significant challenges in pediatric oncology. We conducted whole exome sequencing on 172 retinoblastoma tumors along with matched blood DNA from 171 patients, which included 119 unilateral, 49 bilateral, and three trilateral cases. Our analysis identified pathogenic variants in RB1 in 76 patients and MYCN duplication in 79 cases, highlighting their crucial roles in the disease. Additionally, we found mutations in RPTOR and TSC2, components of the mTOR signaling pathway, in two patients. Notably, our copy number alteration analysis revealed recurrent arm-level changes, including gains on 1q (23.3%), 2p (20.9%), and especially 6p (41.3%), along with other changes such as 5p gain (8.1%), 17q gain (8.1%), and 16q loss (5.8%). Our findings link these genetic alterations to specific clinical features; for instance, 6p gains were associated with Rubeosis, subretinal seeds, and tumor LC beyond, while 17q gains were linked to Rubeosis. Furthermore, gene collapsing techniques identified MATR3 and CYP4F2 as additional novel retinoblastoma-related genes, and module identification analysis pinpointed retinoblastoma-associated modules including HLA-DRB1-CBL, LPAR2, RB1, and TRIM28. Our study, the largest cohort of its kind, underscores the importance of next-generation sequencing from understudied populations in uncovering the complex genetic landscape of retinoblastoma, emphasizing the potential of precision medicine to enhance therapeutic strategies and improve outcomes for retinoblastoma patients.
EPCO-09. DICER1-MUTANT PRIMARY INTRACRANIAL SARCOMA: ASSESSING THE ONCOGENIC ROLE OF MIRNA DYSREGULATION
Authors: Dasgupta Pushan , Gubbiotti Maria , Buchold Gregory , Wathoo Chetna , Joseph Jeena , Soomro Zaid , Zahid Anza , Ghia Amol , Ballester Leomar Y , Hirata Kirk , Macaulay Robert , Zhang Xinhai , Meredith David , Calin George , Puduvalli Vinay K
Published: November 2024

Cross-cancer profiling has shown that mutations in human DICER1 are recurrent in diverse cancers including intracranial sarcoma. Due to the rarity of these tumors, treatment options for these patients remain poorly defined. DICER1 encodes an endoribonuclease that processes the hairpin precursor microRNAs (miRNAs) into functionally mature miRNAs. In particular, hotspot mutations in the RNase IIIb domain of DICER1 are predicted to confer an oncogenic role although the precise mechanism is unknown. In a case of a 28-year-old male who presented with multicentric right frontal dural and parenchymal enhancing masses and underwent partial resection, pathology showed a DICER1-mutant primary intracranial sarcoma with a hotspot E1813G mutation in the RNase IIIb domain. Additionally, due to a family history of an unknown fatal brain tumor in his mother, the patient had additional molecular testing which revealed a germline BRCA2 mutation. After surgery, the patient received intensity-modulated radiation therapy followed by 6 cycles of ICE (ifosfamide, carboplatin, etoposide) chemotherapy with significant radiographic response and clinical improvement. He remains progression-free on radiological surveillance for 13 months since diagnosis. The treatment was well tolerated with clinically manageable myelosuppression (including grade 3 thrombocytopenia). This is the first reported case of an adult DICER1-mutant primary intracranial sarcoma patient with a germline BRCA2 mutation although the interaction between these oncogenic mechanisms is unclear. Based on the role of DICER1 in miRNA processing and to test the hypothesize that DICER1 mutations drive primary intracranial sarcoma through dysregulation of miRNA function, we have established a multi-institutional collaboration that is collecting and profiling DICER 1 mutant primary intracranial sarcoma cases from across the United States preliminary results of which will be presented. Identification of a miRNA-driven oncogenic mechanism in these tumors may yield novel targeted approaches beyond intensive chemotherapy for these patients.
EPCO-17. CARM1 METHYLATES GLIOBLASTOMA TUMOR SUPPRESSOR QUAKING TO REGULATE ITS TRANSCRIPTIONAL COACTIVATOR FUNCTION
Authors: Lu Kaylene , Wright Tanner , Shin Seula , Bedford Mark , Hu Jian
Published: November 2024

Glioblastoma (GBM) represents the most prevalent and deadly primary brain tumor in adults, and it remains highly refractory to current therapeutic interventions. Significant intratumor heterogeneity drives rapid invasion, immune escape, and therapeutic resistance. Therapeutic paradigms based on deconvoluting key molecular mechanisms driving gliomagenesis are urgently needed. Quaking (Qki, encoded by Qk) is frequently altered in GBM patients; Qk mutations or deletions occur in 35% percent of cases, and the Qki protein is absent in 50-60% of cases. Our lab has characterized Qki as important tumor suppressor in GBM, where deletion of Qk enables pre-malignant neural stem cells to expand outside their niche and develop into tumors that recapitulate human GBM. We discovered that Qki functions as a transcriptional coactivator of lipid metabolism genes, whereby Qki loss disrupts lipid homeostasis and compromises the integrity of various membrane structures. Several downstream processes governed by Qki have been delineated; however, upstream regulators of Qki have yet to be identified. Recurrent cancer mutations to specific Qki arginine sites implicate the dysregulation of arginine methylation, a common post-translational modification catalyzed by protein arginine methyltransferases (PRMTs). Leveraging in vitro methylation assays, we demonstrate that Qki is selectively methylated by the PRMT coactivator-associated arginine methyltransferase 1 (CARM1), specifically in the Quaking regulatory domain where cancer mutations are reported. We observe that Qki interacts with known CARM1 substrates, functioning in the transcriptional complex assembled by CARM1. Through mutagenesis studies, we identified arginine 242 (R242) and arginine 256 (R256) as specific CARM1-mediated methylation sites on Qki. Importantly, mutations to these sites compromise Qki’s activity as a transcriptional coactivator. Moreover, brain-specific deletion of CARM1 in vivo results in neurological phenotypes reminiscent of Qki deletion. Altogether, we provide evidence that CARM1 represents a novel tumor suppressor in GBM that functions through the arginine methylation of Qki.
EPCO-22. DEEP PHENOTYPING IDENTIFIES TRUNCATING MUTATIONS IN THE NF2 LINKER DOMAIN ASSOCIATED WITH DISEASE SEVERITY IN NEUROFIBROMATOSIS TYPE II
Authors: Asuzu David , Celano Emma , Mullaney Dustin , Mandal Debjani , Elkahloun Abdel , Johnson Kory , Chittiboina Prashant
Published: November 2024

INTRODUCTION

Neurofibromatosis type 2 (NF2) is an autosomal dominant tumor syndrome with protean presentation and variable penetrance. Our objective was to perform deep phenotypic and genetic analysis of a diverse NF2 population to identify predictors of worse clinical outcome.

METHODS

We evaluated 167 patients with NF2 and followed them for a mean duration of 4.5 years. Detailed clinical and radiographic characteristics were collected on each patient, and Karnofsky performance scale (KPS) scores and within-study mortality were monitored. CLIA certified genotyping was supplemented with a custom sequencing panel targeting NF2 and other schwannomatosis-related genes. Outcome predictors were assessed using multivariable linear or logistic regression.

RESULTS

Germline mutations (nonsense 36%, splice-site 16%, and large deletions 16%) were grouped by predicted protein effect (truncating 41%, non-truncating 27%, and mosaic 33%) and mapped to the NF2chromosomal locus. Patients with truncating NF2 mutations had lower mean age of diagnosis (19.9 versus 25.7, P = 0.01) and faster tumor growth rates (2.4% versus 1.1% for all tumors, P = 0.01). Patients whose truncating mutations occurred within the NF2 linker domain (exons 8, 11 and 12) had more total tumors (adjusted coefficient 15.0, 95% CI 0.8 – 29.0, P = 0.04), and specifically more schwannomas (adjusted coefficient 7.0, 95% CI 0.2 – 13.9, P = 0.04). Presence of a-helical domain mutations predicted higher within-study mortality (adjusted OR 4.3, 95% CI 1.1 – 16.2, P = 0.03).

CONCLUSIONS

The NF2 linker domain functions a hinge, facilitating binding between the tail domain and the LATS binding site within the FERM domain. In our study, truncating mutations in the NF2 linker domain were associated with higher tumor burden and over four-fold within-study mortality. The linker domain may constitute a novel therapeutic target in patients with NF2.
EPCO-23. LONGITUDINAL TRACKING AND LONG-READ CHROMATIN FIBER SEQUENCING OF HUMAN ASTROCYTES WITH TELOMERE DYSFUNCTION REVEALED ALTERED CHROMATIN ACCESSIBILITY AND INCREASED STRUCTURAL VARIATION
Authors: Hao Yue , Ranallo-Benavidez T Rhyker , Fukushima Noelle , Kyriakidou Maria , Berens Michael E , Barthel Floris P
Published: November 2024

Glioma is an aggressive cancer of the central nervous system that is genetically characterized by aneuploidy and frequent structural variation (SV). We sought to investigate the role of telomere dysfunction (TD) in shaping the SV landscape in glioma. Normal human astrocytes (NHA) were engineered to express viral E6E7 oncoproteins which are known to spontaneously trigger TD by suppressing p53/pRb. We hypothesized that NHA-E6E7 cells gradually accumulate SVs and aneuploidy over time because of progressive TD. We therefore longitudinally tracked bulk and single-cell clones of NHA-E6E7 cells for a period of over 6 months since viral infection. Overall, NHA-E6E7 cells demonstrate a growth benefit over primary NHA cells. We obtained Illumina short-read sequencing for NHA-E6E7 cells at multiple time points. Three time points were additionally selected for both Oxford Nanopore and PacBio HiFi long-read sequencing using the single-molecule chromatin fiber sequencing (fiber-seq) protocol. Copy number variation (CNV) analysis of short-read data showed deletion events in chromosome 13 as early as population doubling level (PDL) 48. K-mer based CNV analysis using the long-read data confirmed this finding and also detected deletion events in chromosome 7 at PDL 50. From the long-read data, we found an elevated number of SVs in NHA-E6E7 cells compared to the primary NHA cells. In particular, we detected telomere junctions and found that telomere-associated SVs were more prevalent in NHA-E6E7 cells compared to primary cells. Next, chromatin accessibility and regulatory elements were predicted from fiber-seq data with exogenous N6-methyladenosine (m6A) stencils. We observed large-scale chromatin actuation changes in various regulatory elements across the genome that intensified in later passages of NHA-E6E7 cells. For example, we found a decrease in the accessibility in FBXO7 which is a gene that maintains chromosome stability. Our preliminary results indicated that TD is an important mediator of structural variation in glioma.
EPCO-36. INTEGRATIVE DEEP-LEARNING AND PHARMACOGENOMIC PROFILING OF MALIGNANT GLIOMAS USING PATIENT-DERIVED TUMOR CELLS
Authors: Choi Seung-Won , Swamy Vinay , Hyun Seung Yoon , Her Nam-Gu , Kong Doo-Sik , Choi Jung Won , Seol Ho Jun , Lee Jung-Il , Nam Do-Hyun , Rabadan Raul
Published: November 2024

Malignant glioma stands as a formidable cancer with limited therapeutic options due to many factors including pronounced genetic heterogeneity, the blood-brain barrier, among others. Precision medicine, tailoring treatment based on a patient’s unique molecular profiles, is a fitting approach for addressing intra- and inter-tumor heterogeneity. Previously, we have shown the advantage of using patient-derived tumor cells (PDCs) to evaluate drug efficacy across various cancer types. Unlike cancer cell lines, which significantly differ from primary tumors, PDCs capture the molecular features of primary tumors, showing predictive clinical responses in a retrospective study. Building on these encouraging results, we have expanded PDC-based drug screening to specifically target malignant gliomas. We have established an initial cohort of over 500 malignant glioma PDCs (~ 370 patients) and screened more than 100 drugs. We have complemented our cohort with molecular profiles, including genomic and transcriptomic data to infer the potential pharmacogenomic associations of malignant gliomas. We constructed a multi-modal deep-learning model that seamlessly integrates molecular features and drug structure to predict the drug sensitivity. By employing an explainable machine learning method, we retrospectively analyzed the model to investigate the potential molecular biomarkers and their contribution to drug sensitivity. Collectively, our study demonstrates the efficacy of using patient-derived tumor cells (PDCs) combined with deep-learning models to predict drug sensitivity in malignant gliomas. This integrative approach can potentially refine personalized treatment strategies and improve clinical outcomes for glioma patients.
EPCO-37. LONGITUDINAL TUMOR-WIDE SAMPLING OF GLIOBLASTOMA REVEALS EARLY EVOLUTIONARY DIVERGENCE OF RECURRENCE AND CLUES TOWARDS IDENTIFYING THE BIOLOGICAL TUMOR CENTER
Authors: Lerman Benjamin , Hong Chibo , Schupp Patrick , Chen Lee , Zamler Daniel , Smirnov Ivan , Phillips Joanna , Shai Anny , Lupo Janine , Oldham Michael , Costello Joseph
Published: November 2024

Therapy resistance in glioblastoma is in part attributed to intratumoral heterogeneity and treatment-resistant cell populations. Understanding heterogeneity requires more complete tumor sampling at diagnosis and at recurrence. We used a whole-tumor sampling approach to obtain 43 spatially mapped biopsies from 3 glioblastomas at diagnosis and recurrence, Pyclone and ClonEvol imputed clonal evolution from exome data, and weighted gene co-expression network analysis inferred gene expression programs from RNA sequencing. Across the cohort, tumor-wide clonal alterations representing evolutionarily early expansions included canonical changes (i.e. Chr7 gain, EGFR amplification) and a diverse set of copy number variations (Chr19/20 gain), driver mutations (i.e. PTEN, KDR), and fusions (LIMCH1::UCHL1, KANK::DOCK8). In 2/3 patients, the founding clone was the only subclone common to primary and recurrence samples and 37% of cancer drivers across the cohort appeared after evolutionary divergence of the primary and recurrent tumors. We identified thirty-two transcriptional programs, six of which were differentially expressed between timepoints. Programs enriched for mitochondrial activity, endothelium/pericytes and classical glioblastoma subtype signature were more highly expressed in primary samples. Programs enriched for mesenchymal-like state, oligodendrocytes and inhibitory interneurons were more highly expressed in recurrence samples. At diagnosis, 11/16 samples showed higher expression of the classical subtype program compared to mesenchymal-like, but at recurrence the mesenchymal program dominated in 18/18 samples. Expression of the programs correlated more strongly with position relative to the contrast-enhancing rather than T2 tumor centroid (p<0.001). These findings reveal novel diversity and complexity in the genetic roots of individual glioblastoma. Recurrences arose from subclones diverging early in evolution of the primary tumor and contained clonal drivers not detected in the primary. Expression data revealed transition from an intratumorally heterogeneous mixture of classical and mesenchymal signatures to tumor-wide mesenchymal at recurrence and suggests that the contrast enhancing centroid may serve as the biological center of the tumor.
EPCO-54. MULTIOMIC ANALYSIS OF SPINAL EPENDYMOMAS REVEALS MECHANISMS OF TUMOR AGGRESSIVENESS WITH MYCN AMPLIFICATION
Authors: Rampalli Ihika , Laws Maxwell , Mullaney Dustin , Mandal Debjani , Sisay Bayu , Elkahloun Abdel , Peñas-Prado Marta , Armstrong Terri , Gilbert Mark , Chittiboina Prashant
Published: November 2024

Grade-3 spinal ependymomas, particularly those harboring MYCN amplification, have dismal prognoses despite optimal treatment regimens. MYCN functions as a transcription factor (TF) to drive the expression of key tumor driver genes. Our aim is to identify mechanisms underlying tumor aggressiveness and treatment resistance in MYCN-amplified ependymomas. MYCN amplification in spinal ependymomas was identified with custom next generation sequencing panels and bulk methylation analysis. We then conducted paired single-nucleus RNA (snRNA-seq) and chromatin accessibility (snATAC-seq) sequencing of grade-2 (n=2, 1 patient) and grade-3 spinal ependymomas (n=6, 6 patients, 4 MYCN-amplified). Comparator snRNA-seq datasets (grade-2/grade-3; 8/2) were included from a publicly available dataset (GSE163686; all non-MYCN-amplified). Canonical cell classes were identified with a combination of cluster- and cell-based strategies. Downstream analysis was conducted using R 4.3 (Seurat, Signac, clusterProfiler, CellChat), and Python 3.11 (scanpy) packages. We identified ependymoma tumor cells distinct from canonical immune cell classes with gene expression analysis and confirmed a distinct copy-number-variation pattern in these cells with chromosome 1 and 2p gain, and chromosome 6p and 22q loss. MYCN-amplified tumor cells (compared to non-MYCN-amplified grade2/3 tumor cells) showed increased differential accessibility at genes including VEGFA. Increased MYCN TF activity was confirmed with gene overexpression of downstream targets including NOTCH3, CREB5, PLK1, and VEGFA. Other genes that were highly accessible and overexpressed in MYCN-amplified tumor cells were related to oxidative stress, differentiation, and anti-apoptotic pathways. MYCN-amplified tumor cells modified the tumor microenvironment with increased VISTA signaling between MYCN-amplified tumor cells and tumor-associated macrophages, creating an immunosuppressive environment. We confirmed these effects by observing a higher proportion of M2-like macrophages in MYCN-amplified tumors (29.6% vs 18.2%). In conclusion, MYCN amplification in spinal ependymomas upregulates tumor cell proliferation, angiogenesis, and M2-like macrophage recruitment/programming.
BIOM-29. UNMASKING COPPER DEPENDENCE IN GLIOMA: 19-GENE SIGNATURE FOR PATIENT STRATIFICATION AND TARGETED THERAPY
Authors: Rose Jue Toni , Pham Vu Viet Hoang , Shai-Hee Tyler , Cazzoli Riccardo , Descallar Joseph , Nagabushan Sumanth , Koh Eng-Siew , Vittorio Orazio
Published: November 2024

Adult-type diffuse gliomas exhibit poor prognosis with limited treatment options. Although copper-targeted therapies have been previously explored in these tumors, they have yet to show significant benefits. To understand the role of copper in glioma biology we performed an in silico data analysis on the TCGA glioma cohorts to identify copper-homeostasis related genes (CHRG) with prognostic significance. This was done to enable patient stratification into appropriate treatment arms for future clinical trials involving copper targeted therapies. Furthermore, in vitro experimentation was performed to validate the functional outcomes observed from the in silico results. 19 CHRGs were identified to have prognostic association from the TCGA glioma cohorts. This gene signature regulates a broad range of cellular processes, including metal homeostasis, metabolism, extracellular matrix organization, and immune cell function. The CHRG signature enabled the development of a predictive model that allowed stratification of patients between high and low risk groups. In vitro spheroid growth assays in both U87 cell lines with or without IDH mutation elicited sustained growth inhibition after 6 days post treatment. Furthermore, copper chelation therapy modified the energy potential of these glioma cells in vitro leading to growth inhibition. This study established a predictive model using 19 CHRGs that enable patient stratification between high and low risk glioma patients. Furthermore, our in vitro experiments show the suitability of targeting intracellular copper to inhibit tumor growth. Further research is needed to understand the underlying mechanisms and explore optimal treatment combinations for improved outcomes. We aim to extend this approach to pediatric gliomas for improved risk assessment and personalized medicine.
BIOM-43. SOMATICTP53, PIK3R1, NF1 ORTERT MUTATIONS ARE ASSOCIATED WITH INFERIOR CLINICAL OUTCOME IN H3K27M-ALTERED DIFFUSE MIDLINE GLIOMA: AN INTERNATIONAL, MULTI-INSTITUTIONAL STUDY
Authors: Nguyen Thien , Lerman Benjamin , Stoller Schuyler , Müller Timothy , Comfort Lion , Leal-Ekman Steven , Lyons Samantha , Holman Lynette , Junior Calixito Hope Lucas , Banerjee Anu , Reddy Alyssa , Gupta Nalin , Whipple Nicholas , Gerber Nicolas , Stuecklin Ana , Areza Esha , Marion Rizo , Knowles Truman , Solomon David , Franson Andrea , Koschmann Carl , Partap Sonia , Monje Michelle , Prolo Laura , Cheshier Samuel , Antony Reuben , Bhatia Aashim , Foster Jessica , LaRiviere Michael , Maule Laura , Carrion Andrea Webster , Kline Cassie , Bruningk Sarah , Nazarian Javad , Waszak Sebastian , Mueller Sabine
Published: November 2024

BACKGROUND

H3K27-altered diffuse midline gliomas (DMGs) have poor prognosis with no standard of care therapy beyond radiation (RT). While RT prolongs survival, not all patients respond. Molecular biomarkers can be a strategy to predict RT response and thus patient outcomes.

METHODS

We performed a retrospective analysis of patients with biopsy-proven H3K27M-altered DMG between 2013-2023 from six US medical centers and the DMG Center in Zurich. Patients with tumor genomic sequencing and completion of RT were eligible. Genomic alterations were evaluated for somatic mutations, fusions, and chromosomal instability. Cox proportional hazard models were used to evaluate associations between genomic alterations and survival. Multivariate analysis included all significant variables at P <0.1 in initial analysis, including age at diagnosis, tumor location, TP53 and PIK3R1 alterations.

RESULTS

297 patients (135 female; median age 8.3 years; range 0.2-71.4 years) were included. Median progression-free survival (PFS) and overall survival (OS) was 7.6 months (95%CI: 6.9-8.6) and 14.0 months (95%CI: 12.9-15.7). In univariate analysis, TP53 or PIK3R1 status correlated with shorter OS (TP53-mutant 12.5 vs. TP53-wildtype 17.5 months; HR=1.5; 95%CI: (1.1-2.0), P= 0.005); (PIK3R1-mutant 12.6 vs. 14.5 months; HR=1.9, 95%CI: (1.1-3.4), P = 0.03). Multivariate analysis corroborated TP53-mutant status with poorer OS (HR=1.5; 95%CI: (1.2-2.0), P= 0.003). Subgroup univariate analysis of pontine DMG patients showed poorer OS with TP53, NF1, or TERT mutations (TP53-mutant 11.9 vs. 15.2 months; HR= 1.6; 95%CI: (1.1-2.3), P= 0.02); (NF1-mutant 8.4 vs. 13.6 months; HR= 2.3; 95%CI: (1.1-5.0), P=0.03); (TERT 8.5 vs. 13.6 months; HR= 2.5; 95%CI: (1.1-5.7), P= 0.03). Subsequent multivariate analysis corroborated the association of TERT mutations with poorer OS in pontine DMG (HR=2.5; 95%CI:1.05, 5.9, P= 0.03).

CONCLUSIONS

This is the largest cohort of H3K27M-altered DMG patients with volumetric imaging analysis ongoing. Taken together, our data suggests these genetic alterations can risk-stratify patients for RT and future investigations of radiosensitizers targeting these alterations may improve survival.
BIOM-60. UNDERSTANDING THE INTERSECTION OF RACE, SEX, AND GENOMIC PROFILES IN MENINGIOMA PATHOPHYSIOLOGY
Authors: Dincer Alper , Ghanekar Shaila , Tabor Joanna , Kim Miri , Moliterno Jennifer
Published: November 2024

BACKGROUND

While meningioma incidence and outcomes vary by sex and race, the potential underlying molecular differences possibly contributing to these disparities are less understood. Herein, we explore the clinical and genomic characteristics of meningiomas across groups characterized by age and sex.

METHODS

We analyzed adult patients with primary meningiomas resected from 2012 to 2023. Patients underwent whole exome sequencing, and demographic data were categorized into four groups based on self-reported race and sex, which included White females, White Males, Black females, and Black males. The primary analyses involved comparisons of tumor characteristics, socioeconomic status (median zip code income, % with high school diploma, health insurance status, distance from hospital), genomics, and recurrence rates.

RESULTS

The study included 509 primary meningiomas. White females exhibited low-risk genomic profiles characterized by driver mutations in KLF4 (+/- TRAF7) (p=0.010) and POLR2A (p=0.045), with no associated CNVs (p=0.410). This benign molecular profile correlated with lower WHO grades (p=0.013) and a lower incidence of recurrence (p=0.0003). Black females had meningiomas enriched with Hedgehog pathway mutations (p=0.0035) and a predilection for the anterior skull base (p=0.034), leading to an increased risk of recurrence (p=0.026). White males showed an aggressive genomic profile, including chromosome 1p loss (p=0.025) and 10q loss (p=0.067), associated with a high risk of recurrence (p=0.0002). Black males had meningiomas with chromosome 14q loss (p=0.0002), the highest incidence of high-grade meningiomas (p=0.048), and a 4.5-fold increased risk of recurrence (OR 4.5 [1.6-11.8]; p=0.006). Black males also experienced the worst progression-free survival (HR 5.5 [2.5-12.4]; p<0.0001), independent of WHO grade, extent of resection, and socioeconomic status.

CONCLUSIONS

Each demographic has a distinct molecular profile that correlates with clinical behavior in a race and sex-specific manner. Black males are disproportionately affected by biologically aggressive meningiomas, leading to higher tumor grade and recurrence rates.
BIOM-61. CSF CTDNA ANALYSIS OF PATIENTS WITH DIFFUSE GLIOMAS REVEALS DIAGNOSTIC MOLECULAR ALTERATIONS
Authors: Arjuna Srividya , Wang Daniel H , Balar Ashish , Shah Mauli , Dono Antonio , Sanchez-Espitia Alexander , Duose Dzifa , Nguyen Sophia , Patel Chirag B , Prabhu Sujit S , Lang Frederick F , Esquenazi Yoshua , Ballester Leomar Y
Published: November 2024

There is a critical need for better strategies to diagnose and monitor patients with diffuse gliomas. Liquid biopsies are less invasive than tissue biopsies and are amenable to serial collection at multiple timepoints. However, analysis of circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF) in patients with diffuse gliomas remains underutilized in clinical practice due to technical challenges and a scarcity of studies demonstrating clinical utility. We evaluated ctDNA in 49 CSF samples from patients with various types of diffuse gliomas with a next generation sequencing (NGS) panel interrogating 613 cancer-related genes. Cell-free DNA concentration obtained from CSF (0.4-5mL) ranged from 0.009 to 60ng/µL. Input DNA concentration ranged from 0.12-30ng. Mutations were detected in 29/49 (59.2%) samples including 22/49 (44.9%) with single nucleotide changes, 14/49 (28.6%) with copy number changes, and 1 fusion (2.0%). The majority of samples without mutations detected (n=20) had suboptimal DNA input (<30ng): 17/20 (85%). We identified diagnostic alterations in CSF including mutations in IDH1 (3/5 IDH-mutant gliomas), TERTp and EGFR amplification (7/34 glioblastomas), H3-3A (4/6 pediatric high-grade gliomas). Some of these mutations, in combination with other clinical parameters, allowed us to identify specific CNS tumor types based on the 2021 WHO classification of CNS tumors, resulting in the reclassification of 2 patients. Matched tumor tissue sequencing results were available for 23/49 (46.9%) patients and the results showed good concordance with CSF ctDNA analysis. In summary, our results suggest that the NGS analysis of CSF-ctDNA can provide clinically relevant information in patients with diffuse gliomas.