bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPID-28. YEARS OF LIFE LOST FOR BRAIN AND OTHER CENTRAL NERVOUS SYSTEM TUMORS IN THE UNITED STATES, 2018
Authors: Neff Corey , Price Mackenzie , Gerstl Jakob , Kruchko Carol , Barnholtz-Sloan Jill , Bernstock Joshua , Smith Timothy , Claus Elizabeth , Ostrom Quinn 
Published: November 2023

Abstract
Brain and other central nervous system tumors (BTs) contribute disproportionately to cancer morbidity and mortality relative to their incidence. To estimate the national burden due to these tumors in the United States (US), we estimated Years of Life Lost (YLL) due to premature death from BT overall and specific histopathologies. Mortality data for malignant and non-malignant BT were obtained from the National Vital Statistics System (~100% of US); survival data were obtained from the CDC’s National Program of Cancer Registries (NPCR, ~82% of the US) Survival Analytic Dataset for the years 2004-2018. YLL was calculated by adding estimated years of life left at their age of death. Mean YLL (mYLL) with corresponding 95% confidence intervals (95%CI) were reported by behavior, age at death, sex, and race/ethnicity for each data source, and by histopathology for NPCR. Total YLL due to malignant BT was 4,913,397 (mYLL=22.0) and 3,253,999 (mYLL=22.4), while non-malignant BTs contributed 208,278 YLL (mYLL=14.2). Females (mYLL=22.5), Hispanic individuals (mYLL=30.7), and children aged 0-14 years (mYLL=71.6), had the greatest mYLL due to malignant BTs. Glioblastoma had the highest total YLL (62.2% of all YLL, mYLL=19.8), while atypical teratoid/rhabdoid tumors had the greatest mYLL despite accounting for less than 1% of total YLL due to malignant BT (mYLL=74.4). Meningiomas accounted for 79% of total YLL due to non-malignant tumors, with a mYLL of 13.7. Compared to non-malignant BT, malignant BTs have the greatest mYLL, reflecting their short survival time post-diagnosis. BT are the most common type of cancer in children, leading to relatively high total (475,290 YLL) and mYLL for pediatric BT which may contribute substantially to cancer-specific mortality in this population. These estimates provide a compliment to other population-based BT statistics in demonstrating the impact of these debilitating tumors.
EPCO-01. THE GENOMIC LANDSCAPE OF BRAIN METASTASIS
Authors: Skakodub Anna , Walch Henry , Kumar Rahul , Eichholz Jordan , Cooper Claire , Khatri Ishaani , Del Balzo Luke , Miao Emily , Gui Chengcheng , Ma Jennifer , Tringale Kathryn , Gaeta Benjamin , Kelly Daniel , Moss Nelson , Yu Kenny Kwok Hei , Wilcox Jessica , Bale Tejus , Yu Yao , Yamada Yoshiya , Imber Brandon , Gomez Daniel , Schultz Nikolaus , Pike Luke 
Published: November 2023

Abstract

BACKGROUND
The prognosis for patients with brain metastasis (BM) is devastating, while the underlying biology of BM development remains poorly understood. Identification of genomic biomarkers can offer promising opportunities for prediction of BM development and guidance in personalized treatment. In this study we evaluate the genomic alterations present in a large cohort of resected BM.

METHODS
Upon retrospective review, we identified 868 patients with diagnosis of solid primary cancers who had undergone a standard of care craniotomy at Memorial Sloan Kettering Cancer Center (MSKCC). BM samples were profiled by MSK-IMPACT, a next-generation sequencing (NGS) assay designed to detect a wide range of genetic alterations in 341-505 cancer genes. Genomic alterations were filtered for driver variants using OncoKB. Disease sites included cancers of head and neck, breast, lung, lower and upper gastrointestinal tract, kidney, ovary, uterus, prostate, skin, soft tissues, and others.

RESULTS
More than half (57%; 493/868) of patients were female and the median age was 63 (range 22-93). Foreseeably, the most common histology was non-small cell lung cancer (NSCLC; 38%), followed by invasive carcinoma of the breast and melanoma (16% and 13%, respectively). The most frequently encountered alterations were inTP53 (60%), CDKN2A (25%), TERT (23%), KRAS (18%), and PTEN (12%) across all BM samples. The median fraction of genome altered was 0.41 [range: 0-0.99] and the median tumor mutational burden was 6.6 muts/Mb [range: 0-395]. Additionally, TP53 was the most frequently altered gene after stratifying by primary histology in most cancer types, except for melanoma, renal, and thyroid, which were enriched for alterations in TERT, CDKN2A, and TERT, respectively.

CONCLUSION
The landscape of genomic alterations present in BM is distinct and varies by primary histologic diagnosis. Ongoing analyses of matched primary-BM pairs and clinicogenomic correlation will identify factors predisposing patients to BM development and progression.
EPCO-20. DYNAMICS OF TUMOR GENOME SHAPING AND CLINICAL RESPONSE IN GLIOBLASTOMAS UNDER IMMUNE CHECKPOINT INHIBITORS
Authors: Choi Seung-Won , Rabadan Raul , Iwamoto Fabio , Pan Peter 
Published: November 2023

Abstract
Immune checkpoint inhibitors (ICI) have shown remarkable success in several tumor types; however, this success has not been common in glioblastomas (GBMs). Given the immune-suppressive tumor microenvironment, the timing when to apply ICI may be a determining factor for clinical success. With this hypothesis, we compiled a longitudinal cohort of GBMs treated with different ICI schemes and a control cohort (upfront ICI (n=16), recurrent ICI (n=23), and control cohort by standard of care (n=33)). We investigated the genomic correlates to clinical response. Neither ICI itself nor different timing strategies failed to show a survival benefit for GBMs. However, the upfront-ICI cohort had more long-term survivors (overall survival &gt;= 36 months) than the recurrent-ICI cohort (37.5% (n=6/16) vs. 26.1% (n=6/23)). Genomic analysis revealed that alterations in the PI3K-pathway or TP53 were associated with a poor response to ICI, while BRAF mutation was related to a favorable response. Interestingly, only TP53 alteration was associated with a worse prognosis in GBMs treated with upfront ICI. Tumor mutational burden (TMB) or the amount of neo-antigens failed to show any correlation with the response to ICI. However, ICI-treated GBMs experienced divergent evolution regarding the TMB, while GBMs treated by standard of care only exhibited unidirectional change. We also explored the immunogenomic shifts following different treatment modalities. ICI-treated GBMs showed more variable changes in both HLA alleles and neo-antigen burden (p-value=0.41 & 0.008, respectively). Among the upfront-ICI cohort, GBMs with a better response showed an increased neo-antigen burden upon recurrence (p-value=0.03), suggesting the selection of fitting clones during therapy. Collectively, we observed that that GBMs experienced distinct evolutions under different treatment schemes. The vulnerability of GBMs to ICI should be considered in the context of tumors’ capability to dynamically shape the tumor genome to fit into therapeutic pressure.
EPCO-23. EFFECTS OF H3.3G34V MUTATION ON GENOMIC H3K36 AND H3K27 METHYLATION PATTERNS IN ISOGENIC PEDIATRIC GLIOMA CELLS
Authors: Huang Tina , Piunti Andrea , Qi Jin , Bartom Elizabeth , Saratsis Amanda 
Published: November 2023

Abstract

BACKGROUND
Histone H3.3 mutation (H3F3A) occurs in 50% of cortical pediatric high-grade gliomas (pHGGs). This mutation replaces glycine 34 with arginine or valine (G34R/V), impairing SETD2 activity (H3K36-specific trimethyltransferase). Consequently, reduced H3K36me3 is observed on H3.3G34V nucleosomes relative to wild-type, contributing to genomic instability and driving a distinct gene expression signature associated with tumorigenesis. However, it is not known if this differential H3K36me3 enrichment is due to H3.3G34V mutant protein alone. Therefore, we set to elucidate the effect of H3.3G34V mutant protein in pediatric glioma on H3K36me3, H3K27me3 and H3.3 enrichment in vitro.

METHODS
Experiments were conducted using an established H3.3G34V mutant patient-derived pediatric high-grade glioma cell line (KNS42), and Histone H3.3 wild-type human astrocytes (NHAs). Lentiviral delivery of a doxycycline-inducible RNAi vector targeted against H3F3A was transduced to KNS42 cells to knock down H3.3G34V protein expression. Cell lines were then compared via ChIP-Seq, Western Blot, proliferation and viability studies.

RESULTS
We found that the doxycycline-inducible shRNA knockdown of mutant H3F3A encoding the H3.3G34V protein resulted in loss of H3.3G34V enrichment and increased H3K36me3 enrichment throughout the genome. After knockdown, H3.3G34V enrichment was preserved at loci observed to have the greatest H3.3G34V and H3K36me3 enrichment prior to knockdown. Induced expression of mutant H3.3G34V protein in vitro was insufficient to induce genomic H3K36me3 enrichment patterns observed in H3.3G34V mutant glioma cells. We also observed strong co-enrichment of H3.3G34V and wild-type H3.3 protein, as well as greater H3K27me3 enrichment, in cells expressing H3.3G34V.

CONCLUSION
Our study demonstrates the effects of H3.3G34V mutant protein on genomic H3K36me3, H3K27me3 and H3.3 enrichment patterns in isogenic cell lines.
EPCO-25. HETEROGENEITY OF INSERTION/DELETION AND SINGLE NUCLEOTIDE VARIATION IN DRIVERS OF LOWER GRADE GLIOMAS
Authors: Chen Lee , Stevers Nicholas , Costello Joseph 
Published: November 2023

Abstract
Single nucleotide variation (SNV) and copy number variation (CNV) have been extensively studied across tumor types. Their impact on tumor evolution has been a primary research focus. However, insertion/deletion (indels) have received less attention due to their high false positive and false negative rate and the absence of hotspot indel sites. We examine adult IDH wildtype/mutant gliomas, and utilize spatially mapped samples within the same tumors (84 tumors, averaging 8 to 9 samples/tumor), as well as primary/recurrent paired samples (n=37), to investigate the heterogeneity and progression of indels and SNVs. We used two indel-detecting algorithms, Pindel and Muect2, and discovered and validated several indels, which had not been previously emphasized, including in TCHH. We report on two frequently mutated driver genes, CIC and ATRX, in IDHmut-Codel and IDHmut-noncodel gliomas, respectively. CIC SNVs and indels are observed as complementary occurrences. For example, among 9 samples of the tumor recurrence of one patient, 6 showed CIC SNVs, with only two sharing the same mutation. In contrast, 8 of 9 samples exhibited CIC indels, representing 4 different types. Notably, all samples displayed either CIC SNVs or indels. In IDHmut-noncodel tumors, a similar pattern was observed with ATRX. Nonetheless, all samples displayed either ATRX SNVs or indels. This study highlights the tremendous intratumor heterogeneity and evolution in drivers of LGG, emphasizing their complex role in tumorigenesis. Prior studies may have underestimated the frequency and heterogeneity due to calling accuracy and limitations in tumor sampling. By focusing on indels and other genetic variations within gliomas, this study sheds light on their significance in understanding tumor progression, the essential nature of CIC and ATRX inactivation over whole tumors, and the potential implications for therapeutic interventions.
EPCO-27. RECONSTRUCTION OF THE SPATIAL ECOSYSTEM OF GLIOBLASTOMA REVEALS RECURRENT RELATIONSHIPS BETWEEN TUMOR CELL STATES AND TUMOR MICROENVIRONMENT
Authors: Adabbo Bruno , Migliozzi Simona , Garofano Luciano , Oh Young Taek , Gultekin Sakir H , D'Angelo Fulvio , Roberts Evan R , Bilbao Daniel C , Davila Pedro M , Williams Sion L , Currall Benjamin B , Ceccarelli Michele , Lasorella Anna , Iavarone Antonio 
Published: November 2023

Abstract
Glioblastoma multiforme (GBM) is the most aggressive form of primary brain tumor, with no curative treatment options. Multiple studies have characterized at single cell resolution the GBM as being composed of transcriptional cell states interconnected with components in the tumor immune microenvironment (TME). Our group proposed and validated the first single cell guided functional classification of GBM in four tumor-intrinsic cell states which informed clinical outcome and delivered therapeutic options. However, single cell technologies lack the spatial relationships among the cell states of GBM and between GBM cell states and TME. Spatially resolved transcriptomic technologies are emerging as powerful tools to reconstruct the spatial architecture of a tissue. We performed spatial transcriptomics of multicellular regions of interest (ROI) in 8 IDH wild-type GBM with both CosMx Spatial Molecular Imager, which analyzes 1,000 RNA probes and 64 proteins at single cell resolution, and GeoMx Digital Spatial Profiler which profiles the whole transcriptome (~18,000 genes) at ROI resolution. We integrated the two platforms to define single cell states and non-malignant cells and developed a computational deconvolution approach for CosMx spatial data which utilized GeoMx ROI resolved transcriptomic profiles as a-priori information to predict cell type abundances. Spatial deconvolution of CosMx derived single cells revealed spatial segregation of the tumor cell clones and cellular states and highlighted recurrent patterns of cell states, distinct TME cell types associated with coherent histopathological features across multiple samples. Our studies established a scalable approach to resolve the transcriptional heterogeneity of GBM and reconstruct the architecture of GBM cell states and tumor microenvironment.
EPCO-31. THE PROGNOSTIC IMPLICATIONS OF THE RELATIVE ABUNDANCE OF DECONVOLVED TUMOR AND NON-TUMORAL SUBPOPULATIONS IN MULTI-REGIONAL BIOPSIES OF HIGH GRADE GLIOMA WITH BULK RNA-SEQ
Authors: Curtin Lee , Bond Kamila , Velez Sebastian , Hawkins-Daarud Andrea , Urcuyo Javier , De Leon Gustavo , Langworthy Jazlynn , Sereduk Christopher , Singleton Kyle , Jackson Pamela , Krishna Chandan , Zimmerman Richard , Patra Devi , Bendok Bernard , Smith Kris , Nakaji Peter , Donev Kliment , Baxter Leslie , Mrugala Maciej , Hu Leland , Tran Nhan , Al-Dalahmah Osama , Canoll Peter , Swanson Kristin 
Published: November 2023

Abstract
High-grade glioma continues to have dismal survival owing in part to its intra- and inter-patient heterogeneity. Standard clinical protocol collects tumor samples with the aim of providing or confirming a diagnosis and determining the status of a few key genes (e.g. IDH1, MGMT). However, this protocol is unable to capture the diversity within tumor regions, immune expression or normal cell abundances that play key roles in the development of the disease. To overcome this, during surgery we collect image-localized multi-regional biopsies to characterize this disease heterogeneity. Data collection is ongoing, and we currently have 202 samples from 58 patients with available bulk RNA-Seq. With a single-cell reference dataset from Columbia University, we used CIBERSORTx, a deconvolution method, to predict relative abundances of 7 normal, 6 glioma, and 5 immune cell subpopulations for each sample. We used Cox proportional hazard models with first-order statistics (mean, minimum, maximum) of abundances within patients to determine whether these are prognostic, then used TCGA RNA-Seq data to validate these findings. We found that one glioma proneural subtype was significantly beneficial for patient survival relative to other glioma subtypes across all statistics (and showed significance in TCGA). Proliferative and mesenchymal glioma subtypes also showed significance for one or two of the calculated statistics. Oligodendrocyte progenitor cell abundances were consistently significantly beneficial for patient survival in our cohort, while an increased abundance of abnormal (reactive) astrocytes is associated with poor prognosis. We also ran these analyses within invasive margin and core tumor regions to determine location-specific population abundances associated with patient survival. In conclusion, understanding the in vivo diversity of cellular subpopulations within high grade glioma is important for treatment stratification and patient benefit.
EPCO-34. IMAGE-BASED PHENOTYPIC HIGH-CONTENT CRISPR-CAS9 SCREEN FOR CHARACTERIZING CANCER DRIVERS IN PEDIATRIC HIGH-GRADE GLIOMA
Authors: Amin Samir , Gujar Amit , Yi Eunhee , Kang Wonyeong , Costa Megan , Gabriel Paul , Sjogren Greg , Maher Leigh , Lee Charles , Robson Paul , Dickinson Peter , Packer Rebecca , Courtois Elise , Verhaak Roel 
Published: November 2023

Abstract
The genomic landscape of pediatric high-grade glioma is characterized by a high level of aneuploidy but few focal amplifications or homozygous deletions. Cancer aneuploidies are the principal source of tumor heterogeneity driving tumor growth and therapy resistance. Here, we deployed an image-based phenotypic high-content CRISPR-Cas9 screen to identify aneuploidy-associated pediatric glioma driver genes. Through integrated computational analyses combining whole-genome sequencing datasets from 106 pediatric gliomas and 81 canine gliomas, we identified a set of 460 genes present in regions of aneuploidy in both diseases. We designed a custom guideRNA library to systemically knockout the 460 gene set using an arrayed CRISPR-Cas9 knockout screen in two pediatric high-grade glioma cell lines. By deploying 72 of 384-well plates on automated confocal Opera Phenix High-Content Screening System and dyes staining cell membrane, nucleus, and apoptotic cells, we established 5 million live-cell images across three timepoints (day 7, 8, 9 post-transduction). Each gene was randomized to 32 randomized wells across four 384-well plates to gather robust morphological profiles. Through image-based nucleus and cell segmentation workflow, we characterized 50 million single cells across 27,648 wells over three time points. Using semi-supervised machine learning methods, we derived 1,050 cell morphological features to characterize knockout phenotypes, e.g., viability, growth, and morphology (size, shape, texture of nucleus and cells) across cells. The top ranked genes were then linked to oncogenes and tumor suppressors based on pathway and ontology analysis as well as functional in vitro and in silico validation using Pediatric Cancer Dependency Map. We find convergence of the most impactful molecular abnormalities - based on their knockout phenotypes - on candidate signaling pathways for the development of new drugs and repurposing of existing drugs for pediatric high-grade glioma.
EPCO-38. SINGLE-CELL MULTIMODAL ANALYSIS OF IDH-MUTANT GLIOMAS ASSOCIATES PROGENITOR CELL DEDIFFERENTIATION WITH TUMOR PROGRESSION
Authors: Wu Jingyi , Castro Luis Nicolas Gonzalez , Miller Tyler , Battaglia Sofia , D'Antonio Joshua , El Farran Chadi , Thompson Margaret , Buenrostro Jason , Suva Mario , Bernstein Bradley 
Published: November 2023

Abstract
Isocitrate dehydrogenase (IDH) mutant gliomas are progressive, invariably fatal brain tumors affecting young and middle-age adult patients. Previous single-cell transcriptomic characterization of IDH-mutant gliomas has uncovered heterogeneous cell states, with a hierarchy ranging from neural progenitor-like to differentiated cell states. Despite this understanding, the dynamics of these cell states as tumors undergo grade progression, and the factors that facilitate or restrict cell state transitions remain poorly understood. Here, we characterize the cell states of IDH-mutant gliomas spanning all grades using fresh patient samples and compare them with transcriptional programs of normal brain cells. We find that tumor cell states experience a marked shift as tumors undergo progression. In low-grade tumors, predominant cell states mimic slow-cycling oligodendrocyte progenitor cells (OPCs). With grade progression, cell states transition to resemble highly proliferative neural progenitor cells (NPCs). Additionally, single-cell analyses of accessible chromatin (ATAC-seq) revealed novel cellular states defined in chromatin space, which could facilitate this transition. Genetic analyses identified several molecular alterations in high-grade tumors, including loss of DNA methylation, oncogene amplification, and the deletion of genes associated with the interferon (IFN) response. Lastly, we validate the role of DNA hypomethylation in favoring immune evasion with grade progression using an IDH-mutant glioma organoid model. Overall, our findings provide evidence that tumor progression in IDH-mutant gliomas is driven by an interplay of epigenetic and genetic mechanisms that promote more mitotically active cell states as well as decreased anti-tumoral immune activation.
EPCO-44. RHABDOID TUMOR PREDISPOSITION SYNDROME DUE TO A GERMLINE SMARCB1 MUTATION IN TWO INFANT SIBLINGS
Authors: Quintero Ana , Hanson Derek , Pedro Helio , Vogel Timothy 
Published: November 2023

Abstract

INTRODUCTION
Rhabdoid tumors (RTs) are highly aggressive malignancies caused by a loss–of–function mutation in the SMARCB1 tumor suppressor gene on chromosome 22 that makes up the SW1/SNF chromatin remodeling complex involved in gene transcription. In rhabdoid tumor predisposition syndrome (RTPS), a biallelic germline SMARCB1 mutation markedly increases the risk of affected individuals developing early, aggressive, and rapidly progressing RTs, most commonly in the CNS, referred to as atypical teratoid rhabdoid tumors (AT/RT), and the kidneys, but oftentimes presents with synchronous lesions. In this case series, we present a family affected by RTPS with a recurrence of AT/RT in two infant siblings with the same germline SMARCB1 mutation.

CASE SERIES DESCRIPTION
An 8-month-old female was brought to the emergency department for 3 months of vomiting, developmental regression, and CN VI palsy. Brain imaging revealed a posterior fossa mass, acquired obstructive hydrocephalus, and spinal metastasis. Four years later, her 3-month-old sister was also brought in for evaluation for 2 months of vomiting, irritability, increasing head circumference, and vertical gaze palsy. Her brain imaging similarly showed a posterior fossa mass and acquired obstructive hydrocephalus, but no metastasis. Both siblings underwent subtotal tumor resections and ventriculoperitoneal shunt placement followed by chemotherapy. While on active treatment, they experienced rapid disease progression and ultimately succumbed to their illness. Genetic testing on the family identified the same in-frame deletion in the SNF5 homology domain of SMARCB1 and loss of heterozygosity of chromosome 22 in the two sisters; their mother was found to be a carrier.

CONCLUSION
This case series describes a family affected by RTPS, demonstrating the risk of familial recurrence in SMARCB1 germline mutations and emphasizing the need for genetic testing and counseling for these families should they wish to have additional children.