bluuebunny/crossref_metadata_2025 huggingface dataset:
The Intersecting Effects of Lifetime Experiences of Homelessness and Incarceration on Cognitive Aging and Dementia Risk Factors in the United States
Authors: Hanes Douglas William , Clouston Sean A P
Published: November 2024

Background and Objectives

Alzheimer’s disease and related dementias (ADRD) remain a pressing concern in the US, which also has one of the highest incarceration rates worldwide. Existing research has analyzed dementia risk and care among currently incarcerated and homeless populations; this paper fills a gap by examining later-life cognitive disparities facing formerly incarcerated and/or homeless individuals.

Research Design and Methods

Using Health and Retirement Study data (HRS; 1998–2018), we tested whether formerly homeless and/or incarcerated people had earlier onset of cognitive decline, and whether they were more likely to have modifiable risk factors for ADRD than those without such experiences. We estimated prevalence of mild cognitive impairment (MCI), dementia, and self-reported ADRD diagnosis. We also used repeated observations of cognitive functioning coupled with nested nonlinear regression to examine the onset of accelerated cognitive decline.

Results

Adjusting for demographic variables, formerly homeless and/or incarcerated participants have increased odds of having risk factors for dementia, including smoking, drinking alcohol, depression, mental illness, and discrimination from healthcare providers and police. Diagnosis of MCI and ADRD were more common among participants reporting a history of incarceration or homelessness. Nested nonlinear regression revealed that previous experiences of incarceration or homelessness—alone or together—are associated with earlier onset of accelerated cognitive decline compared to those who experienced neither.

Discussion and Implications

This study suggests that, even if they occur earlier in life, homelessness and incarceration experiences may increase risk of poorer cognitive health in late life. Future work is warranted to understand the lifelong consequences linked to this adversity.
Survey of farmers’ knowledge of yam pests and diseases and management practices in southern Ethiopia
Authors: Gogile Ashebir , Kebede Misrak , Wada Eyasu , Kidanemariam Dawit , Abraham Adane
Published: November 2024

Yam is a widely consumed food in the tropics and subtropics. Determination of pests (pathogens and insects) and diseases (developed pest invasions and symptoms) and the appropriate management practices are critical in existing crop production systems. This study aimed to document farmers’ knowledge about yam pests and diseases and their management practices in southern Ethiopia. Data were collected from 342 systematically selected farmers and 96 yam fields in 5 major yam-growing zones (Dawuro, Gofa, Gamo, Kembata-Tembaro, and Wolaita) in southern Ethiopia using a semi-structured interview guide. The results showed that 54.1% of the farmers saved their planting materials for the next growing season, while 39.2% of the farmers purchased the planting materials from the local market every year. Most farmers (63.5%) reported that the cultivation of yam has been declining annually due to pests and diseases. White yam (Dioscorea rotundata) (Poir, Dioscoreales, Dioscoreaceae) and water yam (Dioscorea alata) are severely damaged by pests and diseases, as perceived by 33.9% and 24.9% of farmers, respectively. Farmers use healthy-looking pest- and disease-free tubers (39.5%), remove infected plants (24.0%), practice crop rotations (17.3%), and use animal manure (7.0%) to manage yam pests and diseases. Farmers’ knowledge can be a starting point for seeking solutions to yam pests and disease risks. This study could play an important role in improving yam cultivation by identifying strategies to improve the recent decline in yam production to meet future food needs for a rapidly growing population.
Sentiment analysis of Chinese ancient poetry based on multidimensional knowledge attention
Authors: Liu Zhongbao , Wan Guangwen , Zuo Xi , Liu Yingbin
Published: November 2024

Poetry was a unique literary genre in ancient China as an important way to express sentiments. Chinese ancient poetry not only has simple words, strict meters, and rich semantic relationships, but also widely use rhetorical techniques such as simile and personification, as well as metaphorical means such as allusion and imagery, which makes it difficult to understand their implicit sentiments quickly and accurately. Therefore, this article attempts to make full use of the semantic features of Chinese ancient poetry text and the knowledge feature of related domains under the guidance of the research paradigm of digital intelligence integration and, based on which, proposed Sentiment Analysis Model of Chinese Ancient Poetry based on Multidimensional Knowledge Attention. This model extracts semantic features from Chinese ancient poetry text, meanwhile designs a multidimensional knowledge attention to extract knowledge features from the knowledge base of Chinese ancient poetry. The recognition of Chinese ancient poetry sentiment is performed by integrating the textual feature and knowledge feature. Comparison experiments on the open ancient poetry corpus verified the effectiveness of the proposed model, and the ablation experiment explored the importance of different knowledge to the sentiment analysis result of Chinese ancient poetry.
EPCO-04. H3F3A K27M MUTATION DRIVES A REPRESSIVE TRANSCRIPTOME VIA REDUCED SERINE 31 PHOSPHORYLATION BY MODULATING CHROMATIN ACCESSIBILITY, INDEPENDENT OF H3K27ME3 IN DIFFUSE MIDLINE GLIOMA
Authors: Bhattarai Suraj , Day Charles , Hakkim Faruck , Grigore Florina , Langfald Alyssa , Hinchcliffe Edward , Robinson James
Published: November 2024

Heterozygous H3.3 K27M mutations are central to the pathogenesis of diffuse midline gliomas (DMG), causing a global reduction in H3K27 trimethylation (H3K27me3) and subsequent epigenetic dysregulation. H3.3 contains a unique Serine 31 (S31) phosphorylation site crucial for mitotic checkpoint regulation. In DMG cells, reduced mitotic S31 phosphorylation correlates with chromosomal instability and aneuploidy. Using a mouse model, we demonstrate that both H3.3K27M and H3.3S31A mutations promote high-grade glioma development, whereas wild-type H3.3 does not. Importantly, S31A, which maintains normal K27me, suggests that S31 phosphorylation loss alone is oncogenic. The H3.3K27M mutation disrupts epigenetic regulation by inhibiting the Polycomb Repressive Complex 2 (PRC2), leading to decreased H3K27me3 and unintended gene induction. Concurrently, K27M exerts a compensatory repressive effect on the transcriptome, mediated by reduced S31 phosphorylation, independent of PRC2 activity. Using CRISPR-engineered isogenic DMG cells and analyzing the transcriptome and chromatin accessibility with RNA-seq and ATAC-seq, we found that the K27M mutation produces a balanced gene expression profile, while PRC2 loss primarily leads to gene induction. Notably, cells with S31A mutations also maintain this balanced profile, linking the PRC2-independent effect of K27M to reduced S31 phosphorylation. Conversely, cells with wild-type K27 but S31A mutation show a repressive genomic state, evidenced by an up/down gene ratio of 0.75, owing to functional PRC2. We further show that the genes uniquely dysregulated by K27M or S31A, independent of PRC2, overlap significantly, with dysregulated genes displaying altered chromatin accessibility. This suggests that the effect of K27M and S31A mutations on gene regulation is primarily due to changes in chromatin state. This complex interplay points to targeting K27M-associated pathways, particularly S31 phosphorylation, as a promising therapeutic avenue in DMG, a malignancy with fewer effective treatments and dismal prognosis.
EPCO-19. MULTIOMIC PROFILING OF EPIGENETIC HETEROGENEITY IN GLIOBLASTOMA AT SINGLE-CELL RESOLUTION USING MULTIOMIC SINGLE-CELL CUT&TAG
Authors: Hardigan Andrew , Blandford Emily , Mohan Aditya , Moelker Eliese , Fecci Peter , Patel Anoop
Published: November 2024

INTRODUCTION

Recent evidence suggests epigenetic heterogeneity may be the primary driver of cell phenotype and treatment resistance in glioblastoma (GBM). Epigenetic heterogeneity is defined by alterations of chromatin histone modifications with activating marks such as H3K27 acetylation and repressive marks such as H3K27 trimethylation. Combinations of these histone marks govern the activity of functional genomic elements such as enhancers or promoters. Single-cell (“sc-”) technologies have only recently been adapted to the study of epigenetic cell states and significant technical challenges have limited their widespread adoption, especially in complex tissues. Here, we report the development of an optimized method for performing tissue processing and simultaneous single-cell epigenetic and transcriptomic analyses in flash frozen GBM samples.

METHODS

Building on our prior work, we developed a new protocol, multiomic single-cell cleavage-under-targets and tagmentation, or “mscCUT&TAG”. We optimized nuclei isolation, cleanup and permeabilization from flash frozen GBM and reaction conditions for the scCUT&TAG portion of the assay. Critically, these changes maintained high-quality, intact nuclei in suspension while limiting well-described technical issues such as nuclei clumping and sample loss. Furthermore, we incorporated the ability to multiplex both patient samples and histone marks.

RESULTS

We applied 10X scRNA-seq, 10X Multiome (RNA+ATAC-seq), and mscCUT&TAG for five histone marks to the same GBM sample, enabling an integrated evaluation of the tumor’s transcriptome, chromatin accessibility and epigenetic regulation at single-cell resolution. mscCUT&TAG enabled the first assessment of single-cell genome segmentation in GBM. We integrated across modalities to identify specific tumor cell populations, cell-type specific coordinated changes in epigenetics and transcriptome, and define functional regulatory elements.

CONCLUSIONS

We developed a novel multiomic protocol, mscCUT&TAG, that allows for a comprehensive analysis of epigenetic heterogeneity in GBM. We anticipate this protocol will enhance our understanding of fundamental biology and potential therapeutic avenues in GBM.
EPCO-30. TRANSCRIPTOMIC ANALYSIS IDENTIFIES REGIONAL BIOLOGY AND OUTCOME HETEROGENEITY IN MEDULLOBLASTOMA AND EPENDYMOMA SUBTYPES
Authors: Arora Sonali , Nuechterlein Nicholas , Jensen Matt , Glatzer Gregory , Sahm Felix , Mack Stephen , Taylor Michael , Holland Eric
Published: November 2024

Medulloblastoma, the most common malignant pediatric brain tumor, includes four distinct subtypes: Wnt, Sonic Hedgehog (Shh), Group 3, and Group 4. In contrast, ependymomas, which account for 10% of pediatric brain tumors and 4% of adult brain tumors, are categorized into three types: supratentorial (ST), posterior fossa (PF), and spinal (SP). While molecular subgrouping has significantly advanced the classification of these diseases, the extent of heterogeneity within these subgroups remains unknown. To address this, we collected bulk RNA sequencing (RNASeq) data from 888 medulloblastoma and 370 ependymoma from various institutions in North America and Europe. Our goal was to establish a comprehensive reference landscape for both medulloblastoma and ependymoma. We also included 42 forebrain and 52 hindbrain fetal samples to contrast against the tumor samples. Our analysis revealed that each disease subtype forms distinct clusters. Previously, subtyping was primarily achieved using methylation data; however, we demonstrate that bulk RNASeq data can also accurately identify disease subtypes. By examining gene expression patterns, gene fusions, and copy number aberrations, we validated existing molecular features and discovered new ones for each subtype. Additionally, we developed an innovative pipeline to identify specific biological patterns for a given region within the landscape. This resource coupled with mapping of new patients’ bulk RNASeq data onto the reference landscape, facilitating accurate disease subtype identification for new patients. This extensive dataset, available through the online tool Oncoscape, will assist the scientific community in uncovering novel therapeutic targets and advancing research in pediatric brain tumors.
EPCO-44. SPATIAL TRANSCRIPTOMICS ENABLES STATISTICAL MODELING OF SEX DIFFERENCE IN GENE CO-EXPRESSION NETWORK AND IMMUNE LANDSCAPE OF GLIOBLASTOMA
Authors: Hao Yue , Baker Angela , Reid George , Luo Jingqin , Hilbush Brian , Otero Marcos , Streck Christopher , Fink Karen L , Snipes George J , Mickey Bruce E , Sloan Andrew E , Barnholtz-Sloan Jill S , Berens Michael E
Published: November 2024

Glioblastoma (GBM) is characterized by inter- and intra-tumor molecular heterogeneity and demonstrated cell plasticity. Sex differences have been observed in various aspects: a male:female GBM incidence ratio is 1.6:1; standard of care treatments (debulking, radiation, and temozolomide) benefit females more than males. 14 human GBM samples from two study sites were subject to spatial profiling on the Vizgen Merscope platform to examine whether distinct biological and therapeutic niches in GBM were evident, to understand how the tumor microenvironments (TME) contributed to the heterogeneity of GBM, and to interrogate sex difference in the immune landscape of GBM. Multiple sets of spatial probes were designed to capture the cell identities (cancer stem cells, astrocytes, oligodendrocytes, microglia, macrophages, etc.) and the spatially-resolved expression patterns of genes with different functions. Two of the 14 GBM samples were also profiled on another FISH-based spatial platform (Veranome). The data from the two platforms exhibited a linear correlation. We explored the gene-gene co-expression network, and calculated the interaction probabilities between genes which were then compared for sex difference. We found that female samples showed significantly lower (two-fold) CD4+/CD8A+ T-cell count ratios than male samples. We also observed sample-specific spatial niches of different GBM cell subtypes and immune cell populations. Our large-scale spatial transcriptomics study revealed intrinsic sex-based differences in immune response to tumor and illuminated microenvironmental influences on GBM.
EPCO-45. COMPLETE CHROMOSOME-SCALE DIPLOID-PHASED ASSEMBLY OF A NORMAL HUMAN ASTROCYTE CELL LINE
Authors: Ranallo-Benavidez T Rhyker , Hao Yue , Fukushima Noelle , Mbegbu Ogechukwu , Barthel Floris P
Published: November 2024

Genomic studies of the malignant brain tumor glioma invariably rely on aligning sequencing reads to a reference genome such as HG38, even though no single reference can capture the diversity of an individual patient or cell line. To begin addressing these biases in genomics research, we sought to construct a chromosome-scale diploid-phased assembly of a normal human astrocyte (NHA) cell line that is frequently used as a basis for developing isogenic glioma cell models. To achieve this, we generated 45x Pacific Biosciences HiFi data (N50: 16kb), 26x Oxford Nanopore Technologies ultra-long data (N50: 80kb), and 2 billion paired-end reads of Hi-C data. The assembler verkko2 was used to integrate these data and build a phased diploid assembly. We achieved an assembly size of 6.01 Gbp, with 17 gapless chromosomes. The two haplotypes contain 214 and 182 contigs, respectively. Our assembly includes 76 fully assembled telomeres and 20 fully assembled centromeres. The contiguity of our assembly is 130 Mbp, which vastly exceeds that of HG38 (N50: 68 Mbp) and approaches that of the recent telomere-to-telomere CHM13 assembly (N50: 155 Mbp). We ran BUSCO on each haplotype of the assembly using the metazoa database to quantify the single-copy genes that are expected to be present in every animal genome. The haplotypes of our assembly contain the complete sequence of 98.6% and 99.9% of these genes respectively. Finally, we used Merqury to perform a k-mer based evaluation of the two haplotypes and found quality values of 59.09 and 59.75 respectively. This diploid genome assembly of NHA will serve as a resource for researchers that wish to develop NHA-derived glioma models. It can be used to call indels or structural variants in a haplotype-specific manner which will further elucidate genotypes underlying glioma phenotypes. Most importantly, it sets the stage for personalized genome assembly and tackling the lack of diversity in genomic studies of glioma to date.
EPCO-47. SEX-BIASED BRD4 ACTIVITY DRIVES TUMORIGENESIS IN GLIOBLASTOMA
Authors: Powell Ruby , Beaumont Thomas , Kfoury-Beaumont Najla
Published: November 2024

Consistent sex differences in incidence and outcome have been reported in cancers including brain tumors. Glioblastoma (GBM), the most common and aggressive primary brain tumor, occurs with higher incidence and shorter survival in males compared to females. Brd4 is essential for regulating transcriptome-wide gene expression and specifying cell identity. Using an isogenic murine GBM model, we have reported correlated transcriptome-wide sex differences in gene expression, Brd4-bound enhancer usage, and Brd4 localization to oncogenic and tumor suppressor transcription factors binding sites in male and female GBM cells, respectively. Sex-biased gene expression patterns were also evident in human glioblastoma. Inhibiting Brd4 function abrogates sex differences in these transcriptional states and concomitant differences in tumorigenic phenotype. Thus, sex-biased Brd4 activity drives sex differences in GBM rendering males and females differentially sensitive to BET inhibitors. These data indicate that Brd4 can exhibit dual functions as an oncogene or tumor suppressor, dependent upon cellular sex. To better understand how to globally target Brd4, we interrogated the role played by master transcriptional Brd4 regulators in coordinating this dual phenotype in GBM. Motif-based analysis revealed that Brd4 co-localized with oncogenes such as Bach1, and Klf5 at male-biased enhancers whereas female-biased enhancers were co-occupied with tumor suppressors, such as Smad4 and p53. Knockdown of Bach1 decreased clonogenic frequency in males and females. Conversely, knockdown of Smad4 increased proliferation and clonogenicity in males, further inducing the male tumorigenic phenotype, while no change was observed in females. These results indicate that Smad4 might be necessary but not sufficient to provide females with resistance to transformation. Ongoing epitranscriptomics investigating Brd4 re-localization and enhancer usage in knockdown cells will increase our understanding of Brd4 mechanism in GBM. Targeting sex-biased Brd4 function will identify novel combinatorial sex-specific therapeutics for brain tumors and could have immediate impact on the clinical treatment of GBM patients.
EPCO-51. A MULTI-OMIC ANALYSIS OF REGIONAL HETEROGENEITY IN GLIOBLASTOMA
Authors: Ellenbogen Yosef , Landry Alexander , Liu Jeff , Wu Yiyan , Gaiti Federico , Zadeh Gelareh
Published: November 2024

Glioblastoma (GBM) is the most common malignant brain tumor in adults. A hallmark of GBM is its intratumoral heterogeneity as well as infiltration into the surrounding brain. The growing understanding of the cellular diversity and cellular state diversity within GBM necessitates a need for a more granular evaluation of the molecular landscape of this disease. This study aimed to investigate this using single cell RNA sequencing combined with single-cell ATAC sequencing and spatial transcriptomics in order to delineate cellular states and enriched pathways between malignant cells in different regions of GBM. The study cohort consisted of 15 patients with primary GBM. Tumor samples were taken at the time of surgical resection using intraoperative stereotactic navigation from three anatomically distinct locations: periphery – the cortex or white matter in the peri-tumoral region that is beyond contrast-enhancing tumor, border – the contrast-enhancing border of the tumor on T1-weighted MRI, and core - the hypointense core region on T1-weighted MRI. Samples underwent combined snRNA and ATAC sequencing (10x Multiome) as well as spatial transcriptomics (10x Visium). Single-nucleus RNA + ATAC sequencing captured a total of 37,547 neoplastic cells and 18,498 non-neoplastic cells within the tumor microenvironment. The majority of non-neoplastic cells were identified within the periphery alongside a distinct group of neoplastic cells that exhibited unique a unique distribution of malignant cellular state and differentially regulated genetic pathways compared to malignant cells within the tumor border and core. Gene regulatory analysis of the malignant cells in the periphery identified a previously undefined set of enriched transcription factors that are periphery-specific regulon drivers. Overall, this analysis sheds light on the genetic and epigenetic differences between malignant GBM cells based on their location and warrant further investigation into the biology and targetable aspects of the malignant cells that exist beyond the contrast-enhancing border of the tumor.
EPCO-60. EXPRESSION OF EARLY PROGENITOR MARKERS WITHIN NF2-ASSOCIATED SPINAL EPENDYMOMA
Authors: Burket Noah , Wang Jia , Gao Hongyu , Bell Robert , Zhang Chi , Liu Yunlong , Clapp Wade , Tailor Jignesh
Published: November 2024

Spinal ependymomas (SP-EPNs) are intramedullary spinal tumors commonly found in patients with NF2-related schwannomatosis. Recent work using bulkRNA sequencing has suggested that SP-EPNs express a molecular signature most similar to ependymal cells. However, this type of sequencing may miss rare stem cell populations within tumors. The aim of this study was to assess the spatial heterogeneity within NF2-associated SP-EPNs and explore whether a stem cell population exists within SP-EPNs. Spatial transcriptomics (ST) was performed on a SP-EPN sample previously resected from a patient with NF2-related schwannomatosis using the 10X Genomics Visium Cytassist Platform. Libraries were sequenced on the Illumina NovaSeq 6000. 28-bp reads including spatial barcode and UMI sequences and 50-bp probe reads were generated with Illumina NovaSeq 6000 at the Center for Medical Genomics at Indiana University School of Medicine. Space Ranger 2.1 was used to process the raw files after sequencing. Data analysis was performed with R package Seurat 4.9.9.9041 following preprocessing with spaceranger. Sctransform normalized the spatial transcriptome dataset. Clusters were identified using “FindClusters” and “FindNeighbors” functions. There was diffuse expression of astrocyte and ependymal cell markers throughout the SP-EPN sample with smaller areas expressing radial glia and stem cell markers, as well as overlap between these regions. Expression of vascular and connective tissue markers varied throughout the tumor. There was minimal to no expression of neural genes in the sample. ST on our SP-EPN sample revealed a tumor with marked cellular and molecular heterogeneity. Although the primarily expressed ependymal cell and astrocyte markers, there does appear to be small, stem cell-like populations. This suggests that NF2-associated SP-EPNs may have a developmental hierarchy with radial glia-like cells and more mature progenitors within the ependymal cell lineage. This proof-of-concept study offers important findings that provide justification for further investigation using single-cell sequencing.
EPCO-61. THE LANDSCAPE OF ALTERNATIVE SPLICING IN PEDIATRIC GLIOMA
Authors: Geng Baobao , Wang Lin
Published: November 2024

Recent studies have identified alternative splicing (AS) as a novel source of neoantigens for immunotherapy. Surprisingly little is known about the AS milieu in Pediatric glioma, including diffuse intrinsic pontine glioma (DIPG), pediatric high grade glioma (pHGG) and medulloblastoma. We analyzed 20 primary DIPG, 22 pHGG and 20 medulloblastoma human specimens via RNA sequencing and re-analyzed RNA-sequencing data from non-malignant human brain tissues. From these data, we reconstructed the landscape of AS in Pediatric glioma and contrasted that to observed isoforms in non-malignant brain. We identified novel splicing events in cell-surface proteins that are suitable targets for engineered T-cell therapies in DIPG, pHGG and medulloblastoma. We also identified novel splicing events derived neoantigens in DIPG, pHGG and medulloblastoma respectively, which are potential immunotherapy targets. We found DIPG specific isoforms of Platelet-derived growth factor pathway genes which are expressed exclusively by DIPG tumor cells. Our studies shed light on the effect of immunotherapy on AS and identify novel targets for emerging immunotherapies in pediatric glioma.
ANGI-13. LONG NON-CODING RNALINC03045 REGULATES GLIOBLASTOMA INVASION VIAWASF3
Authors: Deshpande Krutika , Doan Tammy , Tsung Kathleen , Liu Kristie , Han Jane , Loh Eddie , Ding Li , Yang Wentao , Neman Josh , Dou Yali , Attenello Frank
Published: November 2024

Glioblastoma (GBM) is an aggressive, heterogeneous tumor characterized by extensive infiltration of tumor cells within the surrounding brain parenchyma. Invasive tumor cells that evade surgical resection, chemoradiation and immune responses underlie GBM recurrence, necessitating the evaluation of factors that govern them. A recently completed unbiased lncRNA CRISPRi screen done by our lab identified LINC03045 as the top potential regulator of GBM invasion in Matrigel assays. Since enhanced LINC03045 expression was also found to be significantly associated with glioma tumor grade and patient survival (p<0.0001), here we characterized potential mechanisms by which it regulates GBM invasion. Mediators of lncRNA effect were identified via differential expression analysis in LINC03045 knockdown glioma cells and TCGA glioma datasets, and assessed for tumor invasion in 2D and 3D assays using knockdown and rescue experiments. Differential expression analysis of protein-coding genes associated with reduced LINC03045 expression in vitro and in GBM TCGA RNAseq data revealed high positive correlation with WASF3 (p=0.016), a regulator of JAK-STAT signaling and cytoskeletal scaffolding. siRNA-mediated WASF3 knockdown was associated with significant decrease in invasion in 2D-Matrigel assays in U87 (16.4%, p<0.001), U251(27.3%, p<0.001) and patient-derived USC02 (25.7%, p<0.001) glioma cells. Additionally, 3D invasion assays showed reduced invasion of WASF3KD U87 gliomaspheres (41.1%, p=0.011) into the surrounding matrix. Finally, WASF3 overexpression in USC02s demonstrated rescue of invasive capacity lost with LINC03045 knockdown (p<0.01). Taken together, RNA-seq analysis of downstream effectors of LINC03045, coupled with tumor invasion studies establish downstream mediator WASF3 as a novel regulator of GBM invasive potential.
BIOM-12. ALLIANCE A071401: GENOMICALLY GUIDED PHASE II TRIAL OF ABEMACICLIB IN PATIENTS WITH GRADE 2/3 MENINGIOMAS HARBORING SOMATIC NF2 OR CDK PATHWAY ALTERATIONS
Authors: Brastianos Priscilla , Dooley Katharine , Geyer Susan , Gerstner Elizabeth , Kaufmann Timothy , Iafrate A John , Martinez-Lage Maria , Milhem Mohammed , Welch Mary , Kaley Thomas , Drappatz Jan , Chan Amy , Kumthekar Priya , Matsuoka Carlos Kamiya , Strowd Roy , Cohen Adam , Jaeckle Kurt , Robell Lindsay , Magge Rajiv , Nam Joo Yeon , Blondin Nicholas , Shaikh Nawal , Rabinowitz Ian , Thomas Alissa , Cahill Daniel , Santagata Sandro , Barker Frederick , Galanis Evanthia
Published: November 2024

BACKGROUND

Patients with meningiomas that have progressed after surgery and/or radiation have limited treatments. Loss of NF2 and CDKN2A/B are common in higher-grade meningiomas and promote meningioma progression. We evaluated the efficacy of abemaciclib, a cyclin-dependent kinase (CDK) 4/6 inhibitor, as part of Alliance A071401, a genomically-driven phase II trial in recurrent or progressive meningiomas.

METHODS

Eligible patients (pts) with grade 2/3 tumors and NF2 mutations or CDK pathway alterations were treated with abemaciclib 200 mg orally twice daily. Two co-primary endpoints were used: progression-free survival at 6 months (PFS6) and response rate (RR); the trial would be declared positive if either endpoint was met. Twenty-four evaluable pts provided ≥85% power to detect a PFS6 ≥41.5% (vs. null 15%; alpha=0.02), and ≥89% power to detect RR ≥20% (vs. null 2.5%; alpha=0.021).

RESULTS

Of 83 pts screened while the abemaciclib arm was open between September 15, 2021 and October 3, 2022, 36 eligible pts received abemaciclib. The observed PFS6 rate in the first 24 evaluable pts was 54% (95% CI 33-75%), thus the study met PFS6 endpoint. Of all 35 evaluable pts, median PFS was 7.6 months (95% CI 3.6-17.1 months), estimated 6-month PFS was 55% (95% CI 40-75%) and estimated 6-month OS was 88% (95% CI 77-100%). No objective responses were observed. Of the 36 pts who started treatment, two had a grade 4 adverse event at least possibly related to treatment which included ALT elevation(1), AST elevation(1) and vomiting(1). Patients with NF2 alterations (n=24) had favorable PFS6 outcomes (58%, 95% CI 37-78%) compared to those with CDK (n=4, 25%, 95% CI 1-81%) and CDK+NF2 alterations (n=7, 29% 95% CI 4-71%), (Fisher’s Exact p=0.036).

CONCLUSIONS

Abemaciclib was well-tolerated and resulted in improved PFS6, meeting the trial’s co-primary endpoint. Abemaciclib warrants further investigation for the treatment of patients with progressive meningiomas.
BIOM-28. WHOLE EXOME TUMOR MOLECULAR PROFILING FROM CEREBROSPINAL FLUID (CSF): PRELIMINARY RESULTS OF A PILOT STUDY
Authors: Tuohy Kyle , Xiu Joanne , Nicolaides Theodore , Mansouri Alireza , Aulakh Sonikpreet , Davidson Christian , Zhang Jian , Borderias Maria Perdigones , Spetzler David , Gilbert Mark , Glantz Michael
Published: November 2024

BACKGROUND

Tissue sampling for molecular profiling has become an integral part of the diagnosis, prognosis, and management of CNS malignancies. However, many tumors are surgically inaccessible, and even biopsy of accessible lesions conveys some risk, and the possibility of sampling error. We evaluated the accuracy and potential utility of CSF liquid biopsy for identifying mutations in patients with intracranial tumors.

METHODS

CSF samples were collected from ventricular reservoirs and stored at -80 degrees Celsius until analyzed. Cell-free nucleic acids were extracted, concentrated, and quantified. Samples over 110ng quantification were normalized to 110ng and input into library prep. Library prep was done using v3.5 of Caris Assure and whole exome sequencing in an S2 FC on a Novaseq 6000. Bioinformatic analysis was performed.

RESULTS

CSF samples were obtained from 20 patients (10 gliomas, 5 CNS lymphomas, 5 metastases), 19 of whom also had tumor specimens available. Two hundred eighty-one mutations were identified: 17 (6.6%) in tumor only, 184 (72.4%) in CSF only, and 80 (31.5%) in both. Key alterations found in CSF include: IDH, TERT, ATRX in gliomas, and MYD88, PIM1, BCL2, TERT in lymphomas. Glioma CSF with IDH1 mutations did not have PTEN mutations (with one exception, in which the CSF was collected 3 years after the tissue). Targetable mutations in metastases included PIK3CA, NF1, and BRCA.

CONCLUSION

These preliminary results suggest that CSF liquid biopsy may be useful for identifying mutations in primary and metastatic brain tumors. Serial sampling is feasible, and may disclose changes in diagnostic and/or driver mutations over time, with important therapeutic and diagnostic implications. Many mutations were found in CSF alone. CSF may capture the entire molecular landscape of the tumor, overcoming the sampling error inherent in tissue biopsies. Prospective studies are underway to further elucidate the clinical applications of this technique.
BIOM-47. SINGLE NUCLEOTIDE POLYMORPHISM IN SMARCB1 MUTATION FOR SCHWANNOMATOSIS
Authors: Lakhina Yuliya , Campbell Melissa , Henshey Brett , Yonk Marybeth , Haney Hurley , Tora Muhibullah , Du Yuhong , Koshkin Sergei , Lei Kecheng , Boulis Nicholas
Published: November 2024

Schwannomatosis, a form of neurofibromatosis, involves critical roles for the SMARCB1 gene. Clinical diagnosis guidelines recommend considering pathogenic variants or suspecting schwannomatosis to exclude splicing-related intron mutations. However, some patients may initially present with non-significant mutations and lack clinical signs of schwannoma, leading to misdiagnosis, missed annual assessments, malignancy awareness, and genetic consultation opportunities during pregnancy. Here, we reported a patient with a sporadic synonymous mutation in the SMARCB1 gene (SNP c.1032 C>T (p.Gly344Gly(GGC>GGT)) in exon 8), not previously associated with schwannomatosis. This patient, a 55-year-old female with an 8-year history of schwannomatosis, presented to the neurosurgical department for recurrent tumor removal. Initially, the clinical impact of the SMARCB1 mutation was undetermined, and other genes tested were wild-type. Both schwannomas exhibited a mosaic loss of nuclear SMARCB1 protein, ranging from 10% to 60%. Protein assays confirmed low levels of SMARCB1 protein, with a significant loss in the distal thigh schwannoma. It highlights the tumorigenic potential of single nucleotide polymorphism in the SMARCB1 gene and aids clinicians in making more accurate diagnoses in patients with pathologically confirmed schwannoma. It underscores the importance of long-term follow-up, increased awareness of recurrence and malignancy, and timely surgical planning in such patients.
BIOM-49. PATIENT-CENTRIC INTEGRATED GRAPH DATABASE REVEALS CRITICAL BIOMARKERS IN THE RECURRENCE OF IDH WILD-TYPE GLIOMA
Authors: Liu Yang , Kannan Kasthuri , Huse Jason
Published: November 2024

BACKGROUND

IDH wild-type glioblastoma (GBM) represents a formidable therapeutic challenge due to its consistent recurrence and progression despite standard treatments. Understanding the molecular and cellular mechanisms driving GBM recurrence through data integration is crucial. This study employs a novel graph database strategy to uncover insights into these tumors and identify functional biomarkers through graph algorithms-based pathway enrichment analysis.

METHOD

We developed a stand-alone graph database using Neo4j for primary-recurrent paired GBMs, integrating clinical and gene expression data from the Glioma Longitudinal AnalySiS (GLASS) Consortium and internal MD Anderson cohort. Based on log2 fold-change, we used hierarchical trees for differentially expressed genes to decompose the expression profile. Nodes in the database represent patients with considerable absolute log2 values determined by hierarchical trees, while shared patients define the edges. We applied graph algorithms such as degree centrality and community detection to identify potential biomarkers and supplemented these analyses with pathway identification to refine the biomarker list. Further, we divided the data set into 80% training and 20% testing sets. We evaluated the predictive performance of these biomarkers using machine learning models, including logistic regression, random forest, SVM, and neural networks.

RESULTS

DEG analysis revealed 33 down-regulated and 418 up-regulated genes in recurrent tumors. The top enriched pathways included neuroactive ligand-receptor interaction and GPCR ligand binding. Our database approach implicated 35 out of 451 genes as significant drivers of recurrence in IDH wild-type GBM. The prediction performance of these biomarkers was comparable to features selected through

methods

such as mRMR and logistic lasso and target identification

methods

like WGCNA.

CONCLUSION

Our innovative systems biology approach reveals that ligand-receptor interactions are crucial in driving recurrence in IDH wild-type GBM. This method also yielded promising mechanistic targets for recurrence, prompting focused and therapeutically relevant functional analyses. Moreover, this methodology is not limited to our study but can be applied in other multi-omics settings, offering a robust tool for biomarker discovery and validation.
BIOM-52. THE DYNAMIC GLIOMA CSF PROTEOME: IMPACT OF LOCATION AND RESECTION FOR DISEASE MONITORING
Authors: Riviere-Cazaux Cecile , Graser Christopher , Warrington Arthur , Hoplin Matthew , Andersen Katherine , Malik Noor , Carlstrom Lucas , Ghadimi Keyvan , Himes Benjamin , Jusue-Torres Ignacio , Sarkaria Jann , Meyer Fredric , Van Gompel Jamie , Kizilbash Sani , Sener Ugur , Michor Franziska , Campian Jian , Parney Ian , Burns Terry
Published: November 2024

While serial sampling of glioma tissue is rarely performed before recurrence, cerebrospinal fluid (CSF) can be acquired serially to evaluate candidate monitoring and pharmacodynamic biomarkers in patients with gliomas. However, the impact of key variables to consider in longitudinal CSF, including anatomical location and post-surgical changes, remains unknown. To that end, pre- versus post-resection intracranial CSF samples from patients with gliomas were obtained at early (1-16 days; n=20) or delayed (86-153 days; n=11) timepoints, as well as lumbar-versus-intracranial glioma CSF samples (n=14). Using aptamer-based proteomics, we identified significant differences in the glioma CSF proteome between lumbar, subarachnoid, and ventricular CSF. Indeed, intracranial CSF in paired lumbar/intracranial samples had nearly 1600 unique aptamers, regardless of which intracranial location was compared to the paired lumbar CSF, including in enrichment style analyses that evaluated the overlap between protein states. Importantly, resection had a significant, evolving longitudinal impact on the CSF proteome, with subsets of proteins associated with early versus delayed post-resection changes, many of which were enriched for inflammatory-related pathways. Interestingly, despite increased contamination from surgical debris, enrichment for plasma-associated proteins decreased with resection (FDR: 0.000), suggesting that a portion of the baseline glioma panel could be derived from plasma-originating analytes due to blood-brain barrier disruption. Despite these challenges, our data still revealed preliminary candidate monitoring biomarkers, such as brevican, that increased with progression (example patient: fold-change of 3.58x and 2.08x through lomustine and bevacizumab, respectively), but not pseudoprogression (Fold change less than 1.5). Serial intracranial CSF samples suggested the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies, including bevacizumab and pembrolizumab. In conclusion, our available data to date suggest that the intracranial glioma CSF proteome provides an abundant and evolving source of candidate biomarkers to longitudinally discern the impact of resection and systemic treatments.
BIOM-53. LOW-PASS WHOLE GENOME SEQUENCING OF CEREBROSPINAL FLUID IDENTIFIES TUMOR AGNOSTIC TP53 ABERRATIONS IN LEPTOMENINGEAL METASTATIC DISEASE
Authors: Malani Rachna , Zhang Yingqi , Dean Charlie , Boatz Laura , Harrison Brion , Wei Mei , Akerley Wallace , Bronner Marry , Underhill Hunter
Published: November 2024

Leptomeningeal metastatic disease (LMD) is the spread of cancer cells into the cerebrospinal fluid (CSF)-filled spaces surrounding the central nervous system (CNS). Once LMD occurs, patients endure devastating neurologic symptoms and survive for only a few weeks to months. The clinical diagnosis of LMD has risen as patient survival from non-CNS metastatic disease improves. Unfortunately, detection of LMD even in symptomatic patients is <50% using the current gold standard – CSF cytology. Therefore, a strong clinical need exists for the sensitive and early detection of LMD. Here, we sought to develop a minimally invasive liquid biopsy approach to diagnose LMD using next-generation sequencing. Because copy number variations (CNVs) are common in cancer and increase after chemoradiation, we hypothesized that CNV detection in CSF may offer a means to detect LMD since patients have already undergone treatment for the underlying disease. Specifically, we sought to develop low-pass whole genome sequencing (lpWGS) of cell-free DNA in CSF to detect CNVs associated with LMD. A novel lpWGS algorithm was developed using FASTQ files trimmed to 30 million total paired reads. The genome was partitioned into one million continuous base pair segments excluding problematic areas yielding 2,445 regions across 22 autosomes. Control samples were used to model the read depth for each region to establish the euploid state. Read depth across the genome for all samples was 0.6X. CSF samples from lung cancer, breast cancer, and melanoma patients with LMD demonstrated prominent evidence of monosomies and trisomies throughout the genome. Lung cancer exhibited frequent amplifications (>4-fold). Notably, we observed 17p monosomy in CSF regardless of cancer type which indicates TP53 haploinsufficiency may support LMD progression, a conjecture supported by a codeletion of TP53 in one patient. lpWGS detects LMD in solid tumor cancers and may also identify novel mechanisms for LMD progression.
BIOM-55. SENSITIVITY OF IMMUNOHISTOCHEMISTRY WITH BRAF VE1 ANTIBODY FOR BRAF V600E IN PRIMARY CENTRAL NERVOUS SYSTEM TUMORS
Authors: Blaquier Juan , Egea Sophie , Gultekin Sakir , D’Angelo Fulvio , Iavarone Antonio , de la Fuente Macarena
Published: November 2024

BACKGROUND

BRAF gene encodes for a key protein of the RAS-RAF-MEK-ERK pathway. BRAF alterations are found in a variety of primary central nervous system (CNS) tumors ranging from 3% of glioblastomas to 60% of pleomorphic xanthoastrocytomas. BRAF V600E mutation is the most common BRAF alteration found in CNS malignancies, and it has been successfully targeted with BRAF/MEK inhibitors. Novel BRAF inhibitors, still in development, have shown promising antitumor activity. Next-generation sequencing (NGS) has become a standard test in the era of histo-molecular diagnosis, but it can be unavailable or inaccessible, and results usually take longer. Immunohistochemistry (ICH) with VE1 antibody for BRAF V600E protein has shown high discordant results with sequencing in other tumor types. We aimed to establish the concordance of BRAF VE1 and NGS sequencing in CNS tumors.

METHODS

Single-center retrospective analysis of patients with BRAF V600E mutant CNS tumors by NGS testing.

RESULTS

30 patients with BRAF V600E mutant primary CNS tumors by NGS were included, 18 were male. 15 were classified as IDH-wildtype gliomas, 4 low grade neuroepithelial gliomas, 8 pleomorphic xanthoastrocytoma, 2 pilocytic astrocytomas and 1 papillary craniopharyngioma. IHC testing with BRAF VE1 antibody was done at the initial pathological classification in 23 of the cases being positive in 15 and negative in 8 cases. In 7 cases IHC was not done but has been requested for retrospective analysis and results are pending. Sensitivity for BRAF VE1 IHC was 65%.

CONCLUSION

When compared to NGS testing, ICH with BRAF VE1 antibody for BRAF V600E in CNS tumors shows modest sensitivity, being a limited tool when results are needed promptly or NGS is inaccessible. Determining specificity of the test will be crucial to establish its reliability for patient selection. Sequencing should be obtained when possible and remains the more reliable method for detecting V600E.
BIOM-71. EXPANDING THE SPECTRUM OFTERT PROMOTER NON-CANONICAL SEQUENCE VARIANTS IN CNS TUMORS: A CASE SERIES
Authors: Cook David , Trejo-Lopez Jorge , Pitel Beth , Saha Neiladri , Koganti Tejaswi , Hardcastle Jayson , Smoley Stephanie , Isaacson Matthew , Gandham Mallika , Sivasankaran Gopinath , Dasari Surendra , Fung Kar-Ming , Powell Suzanne , Trivedi Darshan , Abdullaev Zied , Aldape Kenneth , Quezado Martha , Pratt Drew , Cimino P J , Edgar Mark , Vaubel Rachael , Raghunathan Aditya , Giannini Caterina , Jenkins Robert , Ida Cristiane
Published: November 2024

Most TERT promoter (TERTp) clinically relevant sequence variants in CNS tumors are the canonical C228T and C250T mutations. Non-canonical TERTp mutations have been reported mainly in non-CNS tumors. We describe 12 CNS tumors with non-canonical TERTp variants interpreted as clinically relevant. Using clinical targeted NGS panels (2020-2024), we detected c.-100_-79dup (n=2), c.-92_-91insGGCGGCCCCGCCCCTTCCTTTC (n=1), c.-118_-117insTCCCCGGCCCAGCCCCTTCCGGG (n=1), c.-123_-76dup (n=1), c.-110_-89dup (n=2), and c.-57A>C (n=5). Most cases had chromosomal microarray (n=11) and/or methylation array data analyzed using the NCI/Bethesda v.2 classifier (n=9). All non-canonical TERTp variants occurred at a variant allele frequency suggestive of somatic clonal origin (mean, 34%; range, 18-46), and in adults (mean age, 60 years; range, 36-88). Except for the c.-57A>C variant, all non-canonical TERTp variants occurred in tumors with histological and/or molecular diagnostic features of glioblastoma, IDH-wildtype (GBM), often epigenetically aligning to this tumor type. All five tested cases matched to superfamily glioblastoma (score ≥ 0.9), with three to class GBM_RTK_I (>0.9 in 2, 0.86 in 1) and two to GBM_RTK_II (>0.9). The size and sequence of such variants suggest that these may be functionally equivalent to canonical mutations or generate favorable TERTp activation motif conformations like previously reported activating duplications. The c.-57A>C variant is a well-established oncogenic mutation observed in other cancer types but has not been reported in CNS tumors. We describe five cases with the c.-57A>C variant: one GBM matching to methylation class GBM_MES_TYP (0.99); two oligodendroglioma, IDH-mutant and 1p/19q-codeleted, one of which had methylation data matching to class O_IDH (0.99); one diffuse glioma, IDH-mutant, which was partially 1p/19q-codeleted and matched to class O_IDH (0.99); and one anaplastic meningioma, aligning to superfamily meningioma (0.99)/MNG_MAL (0.79). Our findings show that non-canonical TERTp variants typically occur in tumor types that often harbor TERTp canonical mutations, expanding the spectrum of TERTp clinically relevant variants that are molecular biomarkers in CNS tumors.
BIOS-05. PEPTIDE-BASED VACCINES VERSUS DENDRITIC CELL-BASED VACCINE THERAPIES FOR PATIENTS WITH GLIOBLASTOMA: A NETWORK META-ANALYSIS OF CONTROLLED CLINICAL TRIALS
Authors: Suresh Vinay , Bardhan Mainak , Dey Debankur , Goel Archit , Mohammad Adeeb Ali , Panchawagh Suhrud , Podder Vivek , Odia Yazmin , Chen Zhijian
Published: November 2024

BACKGROUND

Glioblastoma (GBM) is the most prevalent primary CNS malignancy in adults, often with a bleak prognosis. Reports suggest the efficacy of dendritic cell vaccines (DCV) and peptide vaccines in extending overall survival (OS). We aimed to compare their efficacy using network meta-analysis (NMA).

METHODS

We systematically searched PubMed, Cochrane database, SCOPUS, and Clinicaltrials.gov up to February 2024 for controlled trials on DCV or peptide vaccines for GBM. NMA was conducted using the frequentist approach to obtain direct and indirect comparisons of each vaccine. Pairwise analyses were performed using the inverse variance method, comparing each vaccine’s efficacy. PEPvIII-KLH and Rindopepimut were merged into “Peptide-based vaccines” [PEP], and standard of care (SOC) and (Placebo + SOC) were merged. Primary outcome: hazard ratio (HR) of overall survival with 95% confidence intervals.

RESULTS

Analysis included 5 studies with 451 patients (vaccine arm) and 445 controls, with SOC/[Placebo + SOC] as reference. Common effects model showed DCV + SOC significantly reduced the HR to 0.3385 [0.1753; 0.6539], while the peptide-based vaccine + SOC reduced the HR to 0.8276 [0.6960; 0.9840]. In the random effects model, DCV + SOC had an HR of 0.3132 [0.0839; 1.1688], and the peptide-based vaccine + SOC had an HR of 0.3888 [0.1383; 1.0928]. Heterogeneity: tau^2 = 0.6473, tau = 0.8045, I^2 = 77.7% [39.5%; 91.8%]. In a pairwise meta-analysis comparing the DCV+SOC and SOC/[Placebo + SOC] consisting of 2 trials, the common and random effects models both estimated an HR of 0.3385 [0.1753; 0.6539, I^2 = 0.0%]. Comparing the PEP+SOC and SOC/[Placebo + SOC] based on 3 trials, the common effect model estimated an HR of 0.8276 [0.6960; 0.9840], while the random effects model estimated an HR of 0.3874 [0.1360; 1.1039, I^2 = 84.4%].

CONCLUSION

Based on current evidence, DCV vaccines perform better than peptide-based vaccines in reducing mortality in GBM patients. Further trials are required to validate their efficacies.